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TalkOrigins Archive Panda's Thumb Antievolution.org Start Here article Introduction to the TalkDesign.org Site Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most Open article Evolution of the bacterial flagellum A detailed and testable scenario for the evolutionary origin of the bacterial flagellum. Open article A Philosophical Premise of 'Naturalism'? Science makes no assumption of naturalism beyond what intelligent design advocates already accept Open drupal_article Introduction to the TalkDesign.org Site Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. 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Routes pdf How Intelligent Design Advocates Turn the Sordid Lessons from Soviet and Nazi History Upside Down PDF article by Wesley R. Elsberry and Mark Perakh. Open article Moonshine: Why the Peppered Moth Remains an Icon of Evolution Matt Young takes up the criticisms that \"intelligent design\" advocates make about peppered moths and the studies showing that natural selection acted on their populations. The peppered moth example is still an excellent example of natural s Open article Evolution of the bacterial flagellum A detailed and testable scenario for the evolutionary origin of the bacterial flagellum. Open article Background A detailed and testable scenario for the evolutionary origin of the bacterial flagellum. Open article - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Open article Bottaro's Letter to WNYE Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life . Open article A Philosophical Premise of 'Naturalism'? Science makes no assumption of naturalism beyond what intelligent design advocates already accept Open article Honesty in \"Darwin on Trial\" The Truth, the Whole Truth, and Nothing but the Truth? Why Phillip Johnson's Darwin on Trial and the \"Intelligent Design\" movement are neither science�nor Christian by Brian Spitzer DRAFT Open article A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. Open article Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . Open article Quixotic References [1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID move Open article \"The Quixotic Message\", or \"No Free Hunch\" Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates. Open article Irreducible Complexity Demystified new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity Open article The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few p Open drupal_article - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Open drupal_article Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . Open drupal_article Irreducible Complexity Demystified new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity Open drupal_article Grist for the EF mill Original: Grist for the EF mill , by Matt Brauer, posted on March 25, 2004 06:36 AM. Open drupal_article Icon of Obfuscation: Jonathan Wells' book Icons of Evolution and why most of what it teaches about evolution is wrong Nick Matzke reviews Jonathan Wells's book, Icons of Evolution . Icons of Evolution purports to document that \"students and the public are being systematically misinformed about the evidence for evolution.\" But it is Icons itself that is rea Open drupal_article Meyer's Hopeless Monster Alan Gishlick, Nick Matzke, and Wesley R. Elsberry critique the paper published by \"intelligent design\" advocate Stephen C. Meyer in Proceedings of the Biological Society of Washington in August, 2004. They conclude that Meyer's review pape Open drupal_article Introduction Reed Cartwright provides an introduction to the series of chapter reviews of Jonathan Wells's book. Open drupal_article Review of Chapter One Burt Humburg examines Chapter 1, and finds that Jonathan Wells has a severe case of Humtpy-Dumptyism. Wells just can't seem to bring himself to use words in a consistent manner. Open drupal_article Review of Chapter Three PZ Myers reviews Chapter 3, which takes up developmental biology. Consistently, Jonathan Wells has to serve up a mishmash of the biology in order to dismiss it. Open drupal_article Review of Chapter Nine Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Open drupal_article Review of Chapter Ten Ian Musgrave critiques Chapter 10 of PIGDID in this essay, titled \"IC is not nice\". Open drupal_article Review of Chapter Fifteen Burt Humburg points out the irony of Jonathan Wells, Unification Church sanctioned theologian, setting himself up as a defender of traditional Christianity in this review of Chapter 15. Open drupal_article Critique Concerning Legal Issues Tim Sandefur takes on statements by Wells concerning legal issues surrounding the lawsuit over the Understanding Evolution website. Open drupal_article Review of Chapter Sixteen Mark Perakh reviews Chapter 16, wherein Jonathan Wells engages in a massive fit of projection to try to smear evolutionary biologists with the heritage of Trofim D. Lysenko. Open drupal_article Ohio Richard B. Hoppe takes Wells to task over Wells's misleading version of events in Ohio. Open drupal_article PT Reviews \"The Politically Incorrect Guide to Darwinism and Intelligent Design\" A number of the contributors to the Panda's Thumb weblog review chapters from \"intelligent design\" advocate Jonathan Wells's 2006 book, The Politically Incorrect Guide to Darwinism and Intelligent Design . The book proved to be a farrago of Open drupal_article The Truth, the Whole Truth, and Nothing but the Truth? Brian Spitzer's review of Phillip Johnson's Darwin on Trial tells why it and the \"Intelligent Design\" movement are neither science—nor Christian. Open drupal_article The Design Revolution? How William Dembski Is Dodging Questions About Intelligent Design Mark Perakh's essay on the tactics used by William Dembski in responding to, or not responding to, criticism and critics. Open drupal_article How Intelligent Design Advocates Turn the Sordid Lessons from Soviet and Nazi History Upside Down Wesley R. Elsberry and Mark Perakh examine the invidious comparisons made by \"intelligent design\" advocates where they liken evolutionary biologists to Soviet and Nazi leaders. In particular, the bizarre misuse by ID advocates of the exampl Open drupal_article Theory Is As Theory Does Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright examine the claims of the Michael Behe and David Snoke paper published in Protein Science in 2004. While the goal of the Behe and Snoke paper is to generate impressive-looking improbabi Open drupal_article You Missed a Spot, Dr. Dembski William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design . The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to t Open drupal_article Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch Richard Wein's review of No Free Lunch argues that Dembski's case is nothing more than a god-of-the-gaps argument dressed up in misleading pseudoscientific mumbo jumbo. Open drupal_article Response? What Response? Richard Wein replies to William Dembski's reply to Wein's Not a Free Lunch But a Box of Chocolates. Open drupal_article A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. Open article ID-Commentaries A collection of commentaries on ID-texts, written by Morgan Grey. Open article ID-Commentaries A collection of commentaries on ID-texts, written by Morgan Grey. Open article ID-Commentary: \"Explaining Specified Complexity\" A commentary of William Dembski's Open article ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" A commentary on William Dembski's Open article ID-Commentary: \"Another Way to Detect Design?\" A commentary of William Dembski's Open article ID-Commentary: \"Disbelieving Darwin -- And Feeling No Shame!\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Fri Oct 12, 2001 9:54 am Message: 21889 Subject: ID-Commentary: \"Disbelieving Darwin...\" This is my fo Open article ID-Commentary: \"Who's Got the Magic?\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sun Oct 21, 2001 5:44 pm Message: 22008 Subject: ID-Commentary: \"Who's Got the Magic?\" Group, This is Open article Dembski's Agency Triad From: \"Wesley R. Elsberry\" < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 1998/11/26 Message-ID: <199811261107.DAA21334@CX33978-A.DT1.SDCA.HOME.COM>#1/1 Subject: Dembski's Agency Triad [Quote] The actualization of one am Open article Re: No free lunch theorems From: Wesley R. Elsberry < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 7 Jun 2001 19:10:29 -0400 Message-ID: <200106080021.RAA13020@CX33978-A.DT1.SDCA.HOME.COM> Subject: Re: No free lunch theorems In article <42YT6.1424 Open article Re: Re[2]: [DebunkCreation] Any books on evolution? From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Sep 8, 2001 12:10 pm Message: 21340 Subject : Re: Re[2]: [DebunkCreation] Any books on evolution? Open article Re: Re[2]: [DebunkCreation] Any books on evolution? From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Mon Sep 10, 2001 9:58 am Message: 21397 Subject: Re: Re[2]: [DebunkCreation] Any books on evolution? - Open article Dembski `retracts' comments about Dennett From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Oct 20, 2001 8:04 pm Message: 21990 Subject: Dembski `retracts' comments about Dennett As readers Open article Who's Got the Magic? 042: Who's Got the Magic? by William Dembski Metaviews 042. 2000.04.25. Approximately 2286 words. In the posting below, William Dembski from the Michael Polanyi Center at Baylor University offers a critical review of Robert Pennock's book \" Open article Explaining Specified Complexity Meta 139: Dembski on \"Explaining Specified Complexity\" grassie@VOICENET.COM William Grassie Meta 139. 1999/09/13. Approximately 1883 words. Below is a column entitled \"Explaining Specified Complexity\" by William Dembski at Baylor University Open article Dembski & the TSP From: Wesley R. Elsberry < welsberr@orca.tamu.edu > Newsgroups: talk.origins,comp.ai.genetic Date: 1997/02/28 Message-ID: <5F5BLK$LC1@NEWS.TAMU.EDU>#1/1 Subject: Dembski & the TSP William Dembski gave a talk last Saturday at the \"Naturalism Open article Other On-line Articles Other On-line Articles These are some of the on-line articles I refer to in my ID-commentaries: Metaviews: Who's Got the Magic? (ARCHIVEID=2595) Disbelieving Darwin -- And Feeling No Shame! (ARCHIVEID=2581) Explaining Specified Complexity ( Open article Who's the Real Fraud? Short Description of page Open", "text_length": 12380, "text_sha256": "3f1d318cb989b12a7e36e5492c58f98cf93966a80aad9694c604e88a613a8c07" }, { "route": "/faqs/", "title": "Browse TalkDesign FAQs", "description": "Generated FAQ and article browser for core TalkDesign explanatory pages.", "content_kind": "faq_index", "text": "faq_index Browse TalkDesign FAQs Generated FAQ and article browser for core TalkDesign explanatory pages. Home Translation status Generated Surface 16 routes listed This page is generated from the modernization route inventory, not hand-maintained legacy navigation. Routes article Evolution of the bacterial flagellum A detailed and testable scenario for the evolutionary origin of the bacterial flagellum. Open article Background A detailed and testable scenario for the evolutionary origin of the bacterial flagellum. Open article A Philosophical Premise of 'Naturalism'? Science makes no assumption of naturalism beyond what intelligent design advocates already accept Open article - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Open article Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . Open article Evolving Immunity Evolving Immunity A Response to Chapter 6 of Darwin's Black Box By Matt Inlay Draft 1.2 - email author for comments and feedback created 5/31/02, la Open article Honesty in \"Darwin on Trial\" The Truth, the Whole Truth, and Nothing but the Truth? Why Phillip Johnson's Darwin on Trial and the \"Intelligent Design\" movement are neither science�nor Christian by Brian Spitzer DRAFT Open article Moonshine: Why the Peppered Moth Remains an Icon of Evolution Matt Young takes up the criticisms that \"intelligent design\" advocates make about peppered moths and the studies showing that natural selection acted on their populations. The peppered moth example is still an excellent example of natural s Open article A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. Open article Bottaro's Letter to WNYE Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life . Open article Incompatible Magisteria INCOMPATIBLE MAGISTERIA By Mark Perakh INTRODUCTION If I were asked to give a brief definition of science, I would have a hard time to come up with Open article Wesley at CSICOP ID advocacy at the 4th annual World of Skeptics Conference On June 21st, 2002, \"Intelligent Design\" advocates squared off against representatives of evolution at the 4th annual World of Sk Open article Quixotic References [1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID move Open article \"The Quixotic Message\", or \"No Free Hunch\" Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates. Open article Irreducible Complexity Demystified new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity Open article The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few p Open", "text_length": 3635, "text_sha256": "3d010cb3adc698905623afd931dbd0a968787cc29375618fec2d18d9e87b574f" }, { "route": "/cs/", "title": "Drupal-Era TalkDesign Archive", "description": "Generated browser for clean static routes captured from the Drupal-era TalkDesign section.", "content_kind": "drupal_index", "text": "drupal_index Drupal-Era TalkDesign Archive Generated browser for clean static routes captured from the Drupal-era TalkDesign section. Home Translation status Generated Surface 34 routes listed This page is generated from the modernization route inventory, not hand-maintained legacy navigation. Routes drupal_article Welcome to TalkDesign.org! This web site, a sub-site of TalkOrigins.org, is a response to the \"Intelligent Design\" movement of creationism. It is dedicated to: Open drupal_article Introduction to the TalkDesign.org Site Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most Open drupal_article Change at TalkDesign TalkDesign is moving away from static, hand-written HTML pages to a spiffy content management system, Civicspace. The theme, for the moment, is the \"interlaced\" theme. We hope that with the change in system, more of the TalkDesign crew will Open drupal_article Bottaro's Letter to WNYE Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life . Open drupal_article - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Open drupal_article Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . Open drupal_article Background to \"Evolution in (Brownian) space: a model for the origin of the bacterial flagellum\" Nick Matzke provides a brief article covering some of the background information needed to understand arguments made about bacterial flagella and Michael Behe's claims of 'irreducible complexity' for that organelle. Open drupal_article Grist for the EF mill Original: Grist for the EF mill , by Matt Brauer, posted on March 25, 2004 06:36 AM. Open drupal_article Irreducible Complexity Demystified new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity Open drupal_article Icon of Obfuscation: Jonathan Wells' book Icons of Evolution and why most of what it teaches about evolution is wrong Nick Matzke reviews Jonathan Wells's book, Icons of Evolution . Icons of Evolution purports to document that \"students and the public are being systematically misinformed about the evidence for evolution.\" But it is Icons itself that is rea Open drupal_article Meyer's Hopeless Monster Alan Gishlick, Nick Matzke, and Wesley R. Elsberry critique the paper published by \"intelligent design\" advocate Stephen C. Meyer in Proceedings of the Biological Society of Washington in August, 2004. They conclude that Meyer's review pape Open drupal_article Moonshine: Why the Peppered Moth Remains an Icon of Evolution Matt Young takes up the criticisms that \"intelligent design\" advocates make about peppered moths and the studies showing that natural selection acted on their populations. The peppered moth example is still an excellent example of natural s Open drupal_article Introduction Reed Cartwright provides an introduction to the series of chapter reviews of Jonathan Wells's book. Open drupal_article Review of Chapter One Burt Humburg examines Chapter 1, and finds that Jonathan Wells has a severe case of Humtpy-Dumptyism. Wells just can't seem to bring himself to use words in a consistent manner. Open drupal_article Review of Chapter Three PZ Myers reviews Chapter 3, which takes up developmental biology. Consistently, Jonathan Wells has to serve up a mishmash of the biology in order to dismiss it. Open drupal_article Review of Chapter Nine Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Open drupal_article Review of Chapter Ten Ian Musgrave critiques Chapter 10 of PIGDID in this essay, titled \"IC is not nice\". Open drupal_article Review of Chapter Fifteen Burt Humburg points out the irony of Jonathan Wells, Unification Church sanctioned theologian, setting himself up as a defender of traditional Christianity in this review of Chapter 15. Open drupal_article Critique Concerning Legal Issues Tim Sandefur takes on statements by Wells concerning legal issues surrounding the lawsuit over the Understanding Evolution website. Open drupal_article Review of Chapter Sixteen Mark Perakh reviews Chapter 16, wherein Jonathan Wells engages in a massive fit of projection to try to smear evolutionary biologists with the heritage of Trofim D. Lysenko. Open drupal_article Ohio Richard B. Hoppe takes Wells to task over Wells's misleading version of events in Ohio. Open drupal_article PT Reviews \"The Politically Incorrect Guide to Darwinism and Intelligent Design\" A number of the contributors to the Panda's Thumb weblog review chapters from \"intelligent design\" advocate Jonathan Wells's 2006 book, The Politically Incorrect Guide to Darwinism and Intelligent Design . The book proved to be a farrago of Open drupal_article Quixotic References [1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID move Open drupal_article \"The Quixotic Message\", or \"No Free Hunch\" Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates. Open drupal_article The Truth, the Whole Truth, and Nothing but the Truth? Brian Spitzer's review of Phillip Johnson's Darwin on Trial tells why it and the \"Intelligent Design\" movement are neither science—nor Christian. Open drupal_article The Design Revolution? How William Dembski Is Dodging Questions About Intelligent Design Mark Perakh's essay on the tactics used by William Dembski in responding to, or not responding to, criticism and critics. Open drupal_article How Intelligent Design Advocates Turn the Sordid Lessons from Soviet and Nazi History Upside Down Wesley R. Elsberry and Mark Perakh examine the invidious comparisons made by \"intelligent design\" advocates where they liken evolutionary biologists to Soviet and Nazi leaders. In particular, the bizarre misuse by ID advocates of the exampl Open drupal_article TalkDesign Volunteers Mark Perakh, PhD Dr.Sci, Professor of Physics Emeritus California State University Fullerton perakh@bigfoot.com www.nctimes.net/~mark, www.talkreason.org Wesley R. Elsberry, Ph.D. Wildlife and Fisheries Sciences, Texas A&M University http:/ Open drupal_article The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few p Open drupal_article Theory Is As Theory Does Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright examine the claims of the Michael Behe and David Snoke paper published in Protein Science in 2004. While the goal of the Behe and Snoke paper is to generate impressive-looking improbabi Open drupal_article Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch Richard Wein's review of No Free Lunch argues that Dembski's case is nothing more than a god-of-the-gaps argument dressed up in misleading pseudoscientific mumbo jumbo. Open drupal_article Response? What Response? Richard Wein replies to William Dembski's reply to Wein's Not a Free Lunch But a Box of Chocolates. Open drupal_article A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. Open drupal_article You Missed a Spot, Dr. Dembski William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design . The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to t Open", "text_length": 8453, "text_sha256": "60a2d38d69a4870c60df57a38804966639a256711f8fac38544ba2f687756ee1" }, { "route": "/search/", "title": "Search TalkDesign", "description": "Static search over the current TalkDesign modernization candidate.", "content_kind": "search", "text": "Search Search the TalkDesign candidate. This static search surface indexes the current modernized seed pages and generated navigation routes. Index 77 documents The index is generated at build time from English candidate pages. Search terms Enter two or more characters.", "text_length": 270, "text_sha256": "d9e0be86eb72bc08f58f78a262c83ff99a476e7b3ce5b7a7283f80644184c4eb" }, { "route": "/introfaq.html", "title": "Introduction to the TalkDesign.org Site", "description": "Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most", "content_kind": "article", "text": "Legacy route: /introfaq.html Content source: /cs/td_faq/ Introduction to the TalkDesign.org Site Q. What is the purpose of Talkdesign.org? A. Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most up-to-date of these articles, as well as a collection of articles written specifically for this site. It also provides other material relevant to ID, including links to the web sites of ID advocates. Q. Who runs Talkdesign.org? A. Talkdesign.org is run by several volunteers , of a variety of religious and philosophical persuasions, who are all critics of ID and supporters of mainstream evolutionary biology. Talkdesign.org is hosted by the TalkOrigins Archive , a longstanding web site devoted to the the wider creation/evolution controversy. The TalkOrigins Archive Foundation, a Texas 501(c)(3) tax-exempt non-profit organization, provides the support for the TalkOrigins Archive, TalkDesign, the Panda's Thumb, and Antievolution.org. Q. What is Intelligent Design? A. The beliefs of ID advocates vary greatly. But the core beliefs which they all appear to share are the following: (a) The action of an intelligent (presumably conscious) being was involved in the evolution of living organisms. (b) There already exists empirical evidence of this action, sufficient to justify a scientific inference that such action occurred. The term \"Intelligent Design\" usually refers to these beliefs together with the arguments which are made in support of them. It is important to note that people who hold belief (a) but not belief (b) do not generally consider themselves to be advocates of ID, and this web site has no quarrel with such people. It is the claim that there is empirical evidence of design in biology which has provoked a controversy, and which we consider to be false. We argue that this claim is based on pseudoscience, and enjoys the support it does only because it appeals to the religious and/or ideological beliefs of its adherents. Q. What is the Intelligent Design movement? A. The ID movement has grown out of a creationist tradition which argues against evolutionary theory from a religious (usually Christian) standpoint. Although ID advocates often claim that they are only arguing for the existence of a \"designer\", who may or may not be God, all the leading advocates do believe that the designer is God, and frequently accompany their allegedly scientific arguments with discussion of religious issues, especially when addressing religious audiences. In front of other audiences, they downplay the religious aspects of their agenda. Lawyer and creationist Phillip Johnson is usually credited with having founded the Intelligent Design movement, with the avowed intention of overthrowing \"materialist science\", and replacing it with \"theistic science\". This agenda is now being actively pursued by a well-funded body, the Center for Science and Culture (CSC), part of the Discovery Institute, a right-wing think tank funded by conservative Christians . (Until recently, the CSC was known as the Center for the Renewal of Science and Culture; the name change is most likely an attempt to render their ideological adgenda less overt.) The CSC now plays the leading role in the promotion of ID, and its fellows include most of the leading ID advocates: William Dembski, Michael Behe, Jonathan Wells, Stephen Meyer, etc. The goal of their Wedge Strategy is for ID to become \"the dominant perspective in science\" and to \"permeate our religious, cultural, moral and political life\". Realizing that their \"scientific\" arguments have little chance of acceptance within the mainstream scientific community, ID advocates address their arguments primarily to the general public, politicians, philosophers, and other non-scientists. The allegedly scientific material which they produce is full of misleading rhetoric, equivocal terminology, and misrepresentations of the facts. They also produce much material which does not even aspire to be scientific, and which can frankly be best described as propaganda. Q. Do scientists support Intelligent Design? A. ID advocates are very keen to give the impression that they have the support of scientists. It is true that a number of scientists support ID, as indeed there are scientists who support Young Earth Creationism and many other pseudosciences. But they are a tiny number in relation to the total number of scientists, the vast majority of whom support evolutionary theory. In 2001, the Discovery Institute took out advertisements in national newspapers to announce that 100 scientists had signed a statement saying that they were \"skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life.\" The signatories did not say that they supported ID, though some of them certainly do. Compare this with a letter sent to Congress in support of the current teaching of evolution in schools, signed by the presidents of 80 scientific organizations . To put things into perspective, the National Center for Science Education (NCSE), a group which supports the teaching of evolution in public schools, released Project Steve , a spoof on anti-evolutionist lists such as the one by the Discovery Institute mentioned above. Signatories to the list agreed to a statement supporting evolution and rejecting ID, but there’s one catch: all of the signatories are named \"Steve\" or a version thereof. Given that Steves make up approximately 1% of the population, the 300+ signatories (at the time of this writing) indicate that for every scientist agreeing with the Discovery Institute, perhaps as many as a few hundred disagree. Q. Is opposition to Intelligent Design based on naturalism? A. Intelligent Design is rejected by the vast majority of scientists, particularly those in the relevant fields. The proportion of scientists who accept ID is insignificant. To explain away this overwhelming rejection of their arguments by those who are experts in the subject, ID advocates employ an ad hominem argument. They accuse the vast mass of scientists of being too biased by a commitment to \"materialism\" or \"naturalism\" to be able to judge the arguments fairly. This is despite the fact that many of these scientists are themselves theists. It is true that many (though not all) mainstream scientists and philosophers of science argue that science must be committed to a principle of \"methodological naturalism\", which states that only \"natural\" explanations can be allowed in science. Unfortunately, the meaning of the term \"natural\" is unclear. It is often assumed that this would rule out any explanations involving divine action, but it may be that a hypothesis involving divine action could be considered \"natural\" if it was empirically testable. These are murky philosophical waters, and it seems that most scientists simply adopt the principle of methodological naturalism as rule of thumb, based on the more general principle that extraordinary claims require extraordinary evidence. More importantly, good scientific theories contain virtues like testability, parsimony, and explanatory power. ID tends to be lacking these virtues and many others; the \"naturalism\" claim is often a cover for the fact that ID has a difficult time meeting basic scientific criteria. In any case, ID advocates assure us that their arguments do not imply a divine designer. The designer could have been an extraterrestrial alien. Methodological naturalism certainly does not rule out such a designer. Confusion over this issue has been caused by the ambiguity of the word \"natural\", which can mean either \"not artificial\" or \"not supernatural\" (in addition to other possible meanings). ID advocates frequently conflate these definitions for rhetorical purposes. This issue is explored in greater detail in Mark Issak’s essay, A Philosophical Premise of ‘Naturalism’? Q. Is Intelligent Design a form of creationism? A. The answer to this question depends partly on what one means by \"creationism\". At one end of the spectrum, creationism can be simply the belief that the Universe was created by God, a belief which is probably shared by all monotheists. At the other end, it can be Young Earth Creationism, the belief that the Genesis account of creation is literally true and that the scientific evidence supports this belief. A reasonable intermediate definition is the belief that individual species or \"kinds\" of animals were divinely created. The core ID belief does not strictly entail divine involvement in the origin of species, but all the leading ID advocates believe in such involvement. Many (perhaps most) also deny common descent, the continuity of descent from parent to offspring from the earliest organisms down to the present day. Much of the CSC's material attacks common descent. Deniers of common descent include Phillip Johnson and Jonathan Wells. Dembski is ambivalent on the subject, attempting to cast doubt on common descent without actually denying it. At least one fellow of the CSC, Paul Nelson, is a Young Earth Creationist. Part of the strategy of ID is to create a \"big tent\", in which all opponents of evolutionary theory can join forces, from the most extreme Young Earth Creationists to those, such as Michael Behe, who accept virtually all of evolutionary theory except the proposition that evolution was fully natural. In order to maintain the unity of this big tent, those towards the latter end of the spectrum are careful to avoid criticizing even the most egregious arguments of the Young Earth Creationists. Furthermore, many of the ID arguments and tactics are very similar to those of Young Earth or Old Earth Creationists. Irrelevant appeals to information theory and thermodynamics; bogus probability calculations based on purely random combinations of proteins; gaps in the fossil record; use of out-of-context quotations; all of these and others are staples of the creationist menu. A major distinguishing feature of ID is the attempt to shift the focus of the debate away from the details of Earth history and towards more abstract concepts such as \"design\" or \"teleology\", terms which are rarely used in a non-question-begging manner. Unlike Young Earth Creationism, which is very easy to falsify, ID is difficult or impossible to test according to standard scientific practice. This gives the ID movement a tactical advantage by allowing its adherents to argue from a position that holds no testable affirmative beliefs, yet allows them to attack almost any aspect of evolutionary theory they think might be vulnerable. Note that this does not make ID a better theory than creationism; many argue that this renders ID even less scientific. It is also clear that much of the motivation for creating an ID movement distinct (to some degree) from the existing creationist movement was to evade the legal restriction (in the U.S.A.) on teaching creationism in public schools. The U.S. Supreme Court has ruled that \"scientific\" creationism is a religious position, and therefore violates the First Amendment's constitutional separation of Church and State. One of the more telling commonalities between the creationist and ID movements is the primary focus on getting their views taught in public schools despite the lack of endorsement from the scientific community. Whether these many connections between ID and creationism justify considering ID to be a form of creationism is ultimately a matter of individual judgment. Many have concluded that they do, and one will sometimes see ID referred to as IDC, or Intelligent Design Creationism. While sometimes frank about the religious and political aspirations of ID, advocates at other times will try to create the impression that ID is a purely scientific issue. Use of the term Intelligent Design Creationism helps to draw attention to the true nature of the movement. Q. Is Intelligent Design a pseudoscience? A. We argue that Intelligent Design is a pseudoscience, like Young Earth Creationism, astrology, Atlantis, and the many other belief systems parading as science which fill the mass media. By pseudoscience, we mean a belief system which is claimed to be based on science, but which is actually based on arguments that are not only flawed, but are so egregiously bad that they do not stand up to any serious open-minded examination. Advocates of pseudoscience are motivated by a dogmatic commitment to their position which renders their minds closed to contrary arguments. Common (though not universal) additional symptoms of pseudoscience include the following: arguments are directed towards an audience of non-scientists; grandiose claims are made, often in fields where the claimant has little expertise ( viz Dembski's claims to new laws of information and thermodynamics); the overwhelming mass of scientists are claimed to be too biased to judge the arguments fairly; arguments are couched in superfluous technical jargon; arguments use poorly defined new technical terms (or old terms given new meanings); technical arguments are outnumbered by rhetoric; excessive use is made of quotations, often from popular books and often out of context. Q. What are the \"scientific\" arguments used to support Intelligent Design? A. The arguments for Intelligent Design are primarily arguments from ignorance, also known as god-of-the-gaps arguments. ID advocates also claim to have positive evidence of ID, in the form of \"specified complexity\" and \"irreducible complexity\", but these arguments turn out to be disguised arguments from ignorance. In addition, ID advocates sometimes make an argument from analogy. A lot of their effort is also devoted to attacking specific aspects of evolutionary theory, rather than giving support to their own ID hypothesis. Q. What is the argument from ignorance, or god-of-the-gaps argument? A. ID advocates point out that the evolution of certain biological structures has not been fully explained by biologists. This is true, and will continue to be true for the foreseeable future, since our knowledge of such structures is highly limited at present. From this, they conclude that those biological structures cannot have an evolutionary explanation, and so must have been designed by an intelligent agent. Although this line of argument can sometimes be seen clearly in their work, more often they disguise the argument with a lot of superfluous and misleading terminology, such as \"irreducible complexity\", \"specified complexity\" and \"information\". Q. What is the argument from analogy? A. The argument from analogy typically runs as follows. Biological systems have some quality in common with man-made machines, e.g. they consist of multiple coordinated parts. Whenever we have directly observed the origin of such a machine, an intelligent being was responsible for designing it. Therefore an intelligent being must have designed biological systems. Here is an example of such an argument: \"In order to reach a conclusion based on an analogy, it is only necessary that the induction flow out of the shared properties: The irreducibly complex Rube Goldberg machine required an intelligent designer to produce it; therefore the irreducibly complex blood-clotting system required a designer also.\" (Michael Behe, \"Darwin's Black Box\", p. 218) Arguments from analogy, a type of inductive argument, are notoriously unreliable. The onus is on the advocate of the argument to make a compelling case for the significance of the shared properties and the insignificance of the divergent properties (or disanalogies). In fact, biological systems are very different from man-made machines in all sorts of ways. The most fundamental difference is that biological organisms, unlike man-made machines, have reproduced themselves over millions of generations with random variation and natural selection. This process is known to result in adaptation, and some degree of adaptation by natural evolution is accepted even by ID advocates. To make an argument from analogy in the face of such a fundamental disanalogy is unreasonable. If we ignore significant disanalogies, as ID advocates do, then it is easy to arrive at absurd conclusions. For example, since it was humans who were responsible for designing the machines of which we have directly observed the origin, should we not infer that biological \"machines\" were designed by humans? Before the first balloon flight of the Montgolfier brothers, we might have inferred that, because all wingless creatures were then unable to fly, human beings would not be able to fly. (At some time in the past scientists might have had good reasons to think that human flight would be impossible, but those reasons would have been based on their current knowledge of physics, not on an absurd argument from analogy.) Q. What is \"irreducible complexity\"? A. The term \"irreducibility complexity\" was introduced by biochemist Michael Behe. ID advocates claim that an irreducibly complex biochemical system cannot (with any reasonable degree of probability) have evolved by natural evolution. Irreducible complexity was originally defined in such a way that it could be detected simply by observing the current state of a system, without any consideration of how it might have evolved (rather like the second sense of specified complexity above): if the removal of any part of a biochemical system would render that system non-functional, then it was considered to be irreducibly complex. Acknowledged problems with this definition have forced Behe and Dembski to propose new definitions, which increasingly require the observer to consider the possibility of evolutionary predecessors in determining whether a system is irreducibly complex. This makes it increasingly difficult to judge whether a system is irreducibly complex or not. However, even if a system is judged irreducibly complex by any of the available definitions, this does not rule out the possibility of an evolutionary origin. The arguments of Behe and Dembski are based on the assumption that a system retains the same function as it evolves. But biological systems often become adapted to new functions as they evolve. Behe divided possible evolutionary pathways into two categories: \"direct\" pathways, which do not involve a change of function, and \"indirect\" pathways\" which do. He then gave an argument against the viability of \"direct\" evolutionary pathways to an irreducibly complex system. He also claimed that the probability of evolution by an indirect pathway was too low for this to be an acceptable explanation. However, this claim was based on nothing more than his own intuition and an argument from ignorance: biologists have not yet provided a detailed account of any such pathway. In fact, biologists have now proposed evolutionary explanations for several of the systems introduced as examples by Behe, such as the immune system , but these will probably not be detailed enough to satisfy Behe or Dembski, who demand a precise account of every step of the pathway. Nevertheless, as these explanations gradually become more detailed, ID advocates increasingly choose to concentrate on just one of Behe's examples, the bacterial flagellum, which is perhaps the least well explained at present. Detailed critiques of Behe's arguments can be found here . See also Irreducible Complexity Demystified . Q. What is \"specified complexity\"? A. ID advocates claim that \"specified complexity\" is a reliable marker of intelligent design. However, they use the term in two quite different senses, which they tend to conflate. The term \"specified complexity\" was coined by biologist Leslie Orgel, as a way of characterizing what it is that distinguishes living organisms from non-living objects. The term was later adopted and used in a similar way by physicist Paul Davies. For t", "text_length": 20000, "text_sha256": "db841aad192f391679717c506afd2ede5c1ba7f863fde072a1620263d846f119" }, { "route": "/aboutus.html", "title": "About Us", "description": "About Us The members of Talkdesign.org are diverse group of individuals spread out across the United States and Europe. We are a blend of students, professors, and working professionals wh", "content_kind": "article", "text": "Legacy route: /aboutus.html About Us The members of Talkdesign.org are diverse group of individuals spread out across the United States and Europe. We are a blend of students, professors, and working professionals who collectively possess a wide range of knowledge and experience in the evolution/creation controversy. We feel that the controversy is not a scientific one, but rather political, and we set out to create a website where those interested in the Intelligent Design movement could read well-thought, in-depth, and scientifically accurate articles representing the viewpoints of both the layperson as well as the scientific mainstream. Our casual peer-review system was created to ensure that readers could trust the accuracy of the content of the material. We hope that this website will serve as a valuable resource to ID critics, and provide a forum for aspiring authors. The members of Talkdesign.org include, but are not limited to: Wesley Elsberry Nick Tamzek Burt Humburg \"dunk\" Richard Wein Ian Musgrave Gordon Elliot Jack Krebs Brian Poindexter \"theyeti\" Liz Craig Mark Perakh Jason Parent Randy Bennett", "text_length": 1124, "text_sha256": "fb386742b35466835ca8fbbb5248ccc4ae002f8536f23061b95bca55d8eda16c" }, { "route": "/volunteers.html", "title": "TalkDesign Volunteers", "description": "Mark Perakh, PhD Dr.Sci, Professor of Physics Emeritus California State University Fullerton perakh@bigfoot.com www.nctimes.net/~mark, www.talkreason.org Wesley R. Elsberry, Ph.D. Wildlife and Fisheries Sciences, Texas A&M University http:/", "content_kind": "article", "text": "Legacy route: /volunteers.html Content source: /cs/td_volunteers/ TalkDesign Volunteers Mark Perakh, PhD Dr.Sci, Professor of Physics Emeritus California State University Fullerton perakh@bigfoot.com www.nctimes.net/~mark, www.talkreason.org Wesley R. Elsberry, Ph.D. Wildlife and Fisheries Sciences, Texas A&M University http://www.antievolution.org/ John S Wilkins, Ph.D. - jointly between History and Philosophy of Science, and Botany University of Melbourne Topic: Species concepts Jack Krebs Vice-President Kansas Citizens for Science www.sunflower.com/~jkrebs Liz Craig President, Kansas Citizens For Science www.kcfs.org Freelance writer lizard6849@yahoo.com Randy Bennett Associate Professor, Biology Juniata College Evolutionary Developmental Biology http://faculty.juniata.edu/bennett/ James H. Swan, PhD Professor Public Health Sciences Wichita State University jim.swan@wichita.edu Board Member, Kansas Citizens for Science Burt Humburg Resident in General Surgery University of Minnesota Minneapolis, MN Matt Young Department of Physics Colorado School of Mines www.mines.edu/~mmyoung", "text_length": 1097, "text_sha256": "2037161a0b3e1514a9d192740cd75c9c790664a5abde181bfe481e9064cda25b" }, { "route": "/submissions.html", "title": "Request for Submissions", "description": "Request for Submissions As mentioned in the homepage, Talkdesign.org is a website dedicated to: Assessing the claims of the Intelligent Design movem", "content_kind": "article", "text": "Legacy route: /submissions.html Request for Submissions As mentioned in the homepage, Talkdesign.org is a website dedicated to: Assessing the claims of the Intelligent Design movement from the perspective of mainstream science Addressing the wider political, cultural, philosophical, moral, religious, and educational issues that have inspired the ID movement Providing an archive of materials that critically examine the scientific claims of the ID movement. Talkdesign.org is always looking for new articles and new perspectives on ID to publish. If you would like to contribute an article to our website, please send submissions to name@emailaddress. Because Talkdesign.org is dedicated to publishing accurate information, all original submissions are subject to review by the editors. Articles already published on other websites are welcome, and will not be edited. Talkdesign.org does not restrict authors from publishing their articles elsewhere after they have been published by Talkdesign.org. Those interested in contributing an article or FAQ, but do not have a specific topic in mind can go here for suggestions.", "text_length": 1124, "text_sha256": "621dc2955f4413389cba53b85c7e79504646f0c2b238b48d3caf04d499bb8392" }, { "route": "/Acknowledgements.html", "title": "Acknowledgements", "description": "Acknowledgements Talkdesign.org is brought to you by: Wesley Elsberry Nick Tamzek Burt Humburg \"dunk\" Richard Wein Ian Musgrave Gordon Elliot Jack Krebs Brian Poindexter \"theyeti\" Liz Crai", "content_kind": "article", "text": "Legacy route: /Acknowledgements.html Acknowledgements Talkdesign.org is brought to you by: Wesley Elsberry Nick Tamzek Burt Humburg \"dunk\" Richard Wein Ian Musgrave Gordon Elliot Jack Krebs Brian Poindexter \"theyeti\" Liz Craig Mark Perakh Jason Parent", "text_length": 251, "text_sha256": "467abb99d24bee4f4c1167b8f76aac96c333d2ee1dad7c917e46b44bc565fbf9" }, { "route": "/faq2002.html", "title": "Introduction to the Talkdesign.org Web Site", "description": "Introduction to the Talkdesign.org Web Site DRAFT , 13 June, 2002 Q. What is the purpose of Talkdesign.org? A. Talkdesign.org was created to provide", "content_kind": "article", "text": "Legacy route: /faq2002.html Introduction to the Talkdesign.org Web Site DRAFT , 13 June, 2002 Q. What is the purpose of Talkdesign.org? A. Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most up-to-date of these articles, as well as a collection of articles written specifically for this site. It also provides other material relevant to ID, including links to the web sites of ID advocates. Q. Who runs Talkdesign.org? A. Talkdesign.org is run by several volunteers , of a variety of religious and philosophical persuasions, who are all critics of ID and supporters of mainstream evolutionary biology. Talkdesign.org is hosted by the Talk.Origins Archive , a longstanding web site devoted to the the wider creation/evolution controversy. Neither Talkdesign.org nor the Talk.Origins Archive receives any outside financial support. Q. What is Intelligent Design? A. The beliefs of ID advocates vary. But the core beliefs which they all appear to share are the following: (a) The action of an intelligent (presumably conscious) being was involved in the evolution of living organisms. (b) There already exists empirical evidence of this action, sufficient to justify a scientific inference that such action occurred. The term \"Intelligent Design\" usually refers to these beliefs together with the arguments which are made in support of them. It is important to note that people who hold belief (a) but not belief (b) do not generally consider themselves to be advocates of ID, and this web site has no quarrel with such people. It is the claim that there is empirical evidence of design in biology which has provoked a controversy, and which we consider to be false. We argue that this claim is based on pseudoscience, and enjoys the support it does only because it appeals to the religious beliefs of its adherents. Q. What is the Intelligent Design movement? A. The ID movement has grown out of a creationist tradition which argues against evolutionary theory from a religious (usually Christian) standpoint. Although ID advocates often claim that they are only arguing for the existence of a \"designer\", who may or may not be God, all the leading advocates do believe that the designer is God, and frequently accompany their allegedly scientific arguments with discussion of religious issues, especially when addressing religious audiences. In front of other audiences, they downplay the religious aspects of their agenda. Lawyer and creationist Phillip Johnson is usually credited with having founded the Intelligent Design movement, with the avowed intention of overthrowing \"materialist science\", and replacing it with \"theistic science\". This agenda is now being actively pursued by a well-funded body, the Center for the Renewal of Science and Culture (CRSC), part of the Discovery Institute, a right-wing think tank funded by conservative Christians. The CRSC now plays the leading role in the promotion of ID, and its fellows include most of the leading ID advocates: William Dembski, Michael Behe, Jonathan Wells, Stephen Meyer, etc. The goal of their Wedge Strategy is for ID to become \"the dominant perspective in science\" and to \"permeate our religious, cultural, moral and political life\". Realizing that their \"scientific\" arguments have little chance of acceptance within the mainstream scientific community, ID advocates address their arguments primarily to the general public, politicians, philosophers, and other non-scientists. The allegedly scientific material which they produce is full of misleading rhetoric, equivocal terminology and misrepresentations of the facts. They also produce much material which does not even aspire to be scientific, and which can frankly be best described as propaganda. Q. Do scientists support Intelligent Design? A. ID advocates are very keen to give the impression that they have the support of scientists. It is true that a number of scientists support ID, as indeed there are scientists who support Young Earth Creationism and many other pseudosciences. But they are a tiny number in relation to the total number of scientists, the vast majority of whom support evolutionary theory. In 2001, the Discovery Institute took out advertisments in national newspapers to announce that 100 scientists had signed a statement saying that they were \"skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life.\" The signatories did not say that they supported ID, though some of them certainly do. Compare this with a letter sent to congress in support of the current teaching of evolution in schools, signed by the presidents of 80 scientific organizations . Q. Is opposition to Intelligent Design based on naturalism? A. Intelligent Design is rejected by the vast majority of scientists, particularly those in the relevant fields. The proportion of scientists who accept ID is a tiny fraction of one per cent. To explain away this overwhelming rejection of their arguments by those who are experts in the subject, ID advocates employ an ad hominem argument. They accuse the vast mass of scientists of being too biased by a commitment to \"materialism\" or \"naturalism\" to be able to judge the arguments fairly. This is despite the fact that many of these scientists are themselves theists. It is true that many (though not all) mainstream scientists and philosophers of science argue that science must be committed to a principle of \"methodological naturalism\", which states that only \"natural\" explanations can be allowed in science. Unfortunately, the meaning of the term \"natural\" is unclear. It is often assumed that this would rule out any explanations involving divine action, but it may be that a hypothesis involving divine action could be considered \"natural\" if it was empirically testable. These are murky philosophical waters, and it seems that most scientists simply adopt the principle of methodological naturalism as rule of thumb, based on the more general principle that extraordinary claims require extraordinary evidence. In any case, ID advocates assure us that their arguments do not imply a divine designer. The designer could have been an extraterrestrial alien. Methodological naturalism certainly does not rule out such a designer. Confusion over this issue has been caused by the ambiguity of the word \"natural\", which can mean either \"not artificial\" or \"not supernatural\" (in addition to other possible meanings). Although some casual critics of ID have appealed to methodological naturalism to reject ID out of hand, serious critics have considered the arguments on their merits. None of the articles at Talkdesign.org makes any appeal to methodological naturalism. We show the ID arguments to be fallacious, and reject them on that basis. Q. Is Intelligent Design a form of creationism? A. The answer to this question depends partly on what one means by \"creationism\". At one end of the spectrum, creationism can be simply the belief that the Universe was created by God, a belief which is probably shared by all monotheists. At the other end, it can be Young Earth Creationism, the belief that the Genesis account of creation is literally true and that the scientific evidence supports this belief. A reasonable intermediate definition is the belief that individual species or \"kinds\" of animals were divinely created. The core ID belief does not strictly entail divine involvement in the origin of species, but all the leading ID advocates believe in such involvement. Many (perhaps most) also deny common descent, the continuity of descent from parent to offspring from the earliest organisms down to the present day. Some of the CRSC's material attacks common descent. Deniers of common descent include Phillip Johnson and Jonathan Wells. Dembski is ambivalent on the subject, attempting to cast doubt on common descent without actually denying it. At least one fellow of the CRSC, Paul Nelson, is a Young Earth Creationist. Part of the strategy of ID is to create a large tent, in which all opponents of evolutionary theory can join forces, from the most extreme Young Earth Creationist to those, such as Michael Behe, who accept virtually all of evolutionary theory except the proposition that evolution was fully natural. In order to maintain the unity of this large tent, those towards the latter end of the spectrum are careful to avoid criticizing even the most egregious arguments of the Young Earth Creationists. Furthermore, many of the ID arguments and tactics are very similar to those of Young Earth or Old Earth Creationists. Irrelevant appeals to information theory and thermodynamics; bogus probability calculations based on purely random combinations of proteins; gaps in the fossil record; use of out-of-context quotations; all of these and others are staples of the creationist menu. It is also clear that much of the motivation for creating an ID movement distinct (to some degree) from the existing creationist movement was to evade the legal restriction (in the U.S.A.) on teaching creationism in public schools. The U.S. Supreme Court has ruled that \"scientific\" creationism is a religious position, and therefore violates the First Amendment's constitutional separation of Church and State. Whether these many connections between ID and creationism justify considering ID to be a form of creationism is ultimately a matter of individual judgment. Many have concluded that they do, and one will sometimes see ID referred to as IDC, or Intelligent Design Creationism. While sometimes frank about the religious and political aspirations of ID, advocates at other times will try to create the impression that ID is a purely scientific issue. Use of the term Intelligent Design Creationism helps to draw attention to the true nature of the movement. Q. Is Intelligent Design a pseudoscience? A. We argue that Intelligent Design is a pseudoscience, like Young Earth Creationism, astrology, Atlantis, and the many other belief systems parading as science which fill the mass media. By pseudoscience, we mean a belief system which is claimed to be based on science, but which is actually based on arguments that are not only flawed, but are so egregiously bad that they do not stand up to any serious open-minded examination. Advocates of pseudoscience are motivated by a dogmatic commitment to their position which renders their minds closed to contrary arguments. Common (though not universal) additional symptoms of pseudoscience include the following: arguments are directed towards an audience of non-scientists; grandiose claims are made, often in fields where the claimant has little expertise ( viz Dembski's claims to new laws of information and thermodynamics); the overwhelming mass of scientists are claimed to be too biased to judge the arguments fairly; arguments are couched in superfluous technical jargon; arguments use poorly defined new technical terms (or old terms given new meanings); technical arguments are outnumbered by rhetoric; excessive use is made of quotations, often from popular books and often out of context. Q. What are the \"scientific\" arguments used to support Intelligent Design? A. The arguments for Intelligent Design are primarily arguments from ignorance, also known as god-of-the-gaps arguments. ID advocates also claim to have positive evidence of ID, in the form of \"specified complexity\" and \"irreducible complexity\", but these arguments turn out to be disguised arguments from ignorance. In addition, ID advocates sometimes make an argument from analogy. A lot of their effort is also devoted to attacking specific aspects of evolutionary theory, rather than giving support to their own ID hypothesis. Q. What is the argument from ignorance, or god-of-the-gaps argument? A. ID advocates point out that the evolution of certain biological structures has not been fully explained by biologists. This is true, and always will be, since science never has all the answers. From this, they conclude that those biological structures cannot have an evolutionary explanation, and so must have been designed by an intelligent agent. Although this line of argument can sometimes be seen fairly clear in their work, more often they disguise the argument with a lot of superfluous and misleading terminology, such as \"irreducible complexity\", \"specified complexity\" and \"information\". Q. What is the argument from analogy? A. The argument from analogy typically runs as follows. Biological systems have some quality in common with man-made machines, e.g. they consist of multiple co-ordinated parts. Whenever we have directly observed the origin of such a machine, an intelligent being was responsible for designing it. Therefore an intelligent being must have designed biological systems. Here is an example of such an argument: \"In order to reach a conclusion based on an analogy, it is only necessary that the induction flow out of the shared properties: The irreducibly complex Rube Goldberg machine required an intelligent designer to produce it; therefore the irreducibly complex blood-clotting system required a designer also.\" (Michael Behe, \"Dawin's Black Box\", p. 218) Arguments from analogy, a type of inductive argument, are notoriously unreliable. The onus is on the advocate of the argument to make a compelling case for the significance of the shared properties and the insignifance of the divergent properties (or disanalogies). In fact, biological systems are very different from man-made machines in all sorts of ways. The most fundamental difference is that biological organisms, unlike man-made machines, have reproduced themselves over millions of generations with random variation and natural selection. This process is known to result in adaptation, and some degree of adaptation by natural evolution is accepted even by ID advocates. To make an argument from analogy in the face of such a fundamental disanalogy is unreasonable. If we ignore significant disanalogies, as ID advocates do, then it is easy to arrive at absurd conclusions. For example, since it was humans who were responsible for designing the machines of which we have directly observed the origin, should we not infer that biological \"machines\" were designed by humans? Before the first balloon flight of the Montgolfier brothers, we might have inferred that, because all wingless creatures were then unable to fly, human beings would not be able to fly. (At some time in the past scientists might have had good reasons to think that human flight would be impossible, but those reasons would have been based on their current knowledge of physics, not on an absurd argument from analogy.) Q. What is \"irreducible complexity\"? A. The term \"irreducibility complexity\" was introduced by biochemist Michael Behe. ID advocates claim that an irreducibly complex biochemical system cannot (with any reasonable degree of probability) have evolved by natural evolution. Apparently, the claim does not extend to larger-scale irreducibly complex systems. Irreducible complexity was originally defined in such a way that it could be detected simply by observing the current state of a system, without any consideration of how it might have evolved (rather like the second sense of specified complexity above): if the removal of any part of a biochemical system would render that system non-functional, then it was considered to be irreducibly complex. Acknowledged problems with this definition have forced Behe and Dembski to propose new definitions, which increasingly require the observer to consider the possibility of evolutionary predecessors in determining whether a system is irreducibly complex. This makes it increasingly difficult to judge whether a system is irreducibly complex or not. However, even if a system is judged irreducibly complex by any of the available definitions, this does not rule out the possibility of an evolutionary origin. The arguments of Behe and Dembski are based on the assumption that a system retains the same function as it evolves. But biological systems often become adapted to new functions as they evolve. Behe divided possible evolutionary pathways into two categories: \"direct\" pathways, which do not involve a change of function, and \"indirect\" pathways\" which do. He then gave an argument against the viability of \"direct\" evolutionary pathways to an irreducibly complex system. He also claimed that the probability of evolution by an indirect pathway was too low for this to be an acceptable explanation. However, this claim was based on nothing more than his own intuition and an argument from ignorance: biologists have not yet provided a detailed account of any such pathway. In fact, biologists have now proposed evolutionary explanations for several of the systems introduced as examples by Behe, but these will probably not be detailed enough to satisfy Behe or Dembski, who demand a precise account of every step of the pathway. Nevertheless, as these explanations gradually become more detailed, ID advocates increasingly choose to concentrate on just one of Behe's examples, the bacterial flagellum, which is perhaps the least well explained at present. Detailed critiques of Behe's arguments can be found here . Q. What is \"specified complexity\"? A. ID advocates claim that \"specified complexity\" is a reliable marker of intelligent design. However, they use the term in two quite different senses, which they tend to conflate. The term \"specified complexity\" was coined by biologist Leslie Orgel, as a way of characterizing what it is that distinguishes living organisms from non-living objects. The term was later adopted and used in a similar way by physicist Paul Davies. For these writers, an object is complex if it cannot be compressed to a shorter description. For example, a sequence of 100 identical digits, \"1111111111...\", can be compressed to the description \"100 1s\", and is therefore not complex at all. On the other hand, a sequence of 100 random binary digits is complex because it cannot be compressed in this way. This corresponds to a widely-used concept in information theory, known as \"algorithmic information\" or \"Kolmogorov complexity\". Since random sequences are highly complex in this sense, it is clear that complexity alone is not enough to characterize life. So Orgel and Davies add the criterion of \"specification\" or \"specificity\". Specificity can broadly be thought of here as indicating the presence of some special property. Davies gives the example of a DNA sequence, which is \"specified\" because it is a member of that special set of sequences which code for a living organism. Orgel summarizes as follows: In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [Leslie Orgel, \"The Origins of Life\", Chapman & Hall, 1973.] The term \"specified complexity\" has now been recycled by Intelligent Design advocate William Dembski, a mathematician and philosopher. He, however, uses the word \"complexity\" in a very different sense. For Dembski, \"complexity\" is merely a rescaled measure of improbability. If an object has only a small probability of occurring, he labels it \"complex\", regardless of whether it is simple or complex in the usual sense of the words. If the origin of an object can be shown to have sufficiently small probability under a particular hypothesis, Dembski tells us to reject ", "text_length": 20000, "text_sha256": "a803b444c19ebb3a141f21292fa39ce24c3793c7307d641bcbdd8ccf9cb090a1" }, { "route": "/faqs/flagellum.html", "title": "Evolution of the bacterial flagellum", "description": "A detailed and testable scenario for the evolutionary origin of the bacterial flagellum.", "content_kind": "article", "text": "Legacy route: /faqs/flagellum.html Evolution of the bacterial flagellum Evolution in (Brownian) space: a model for the origin of the bacterial flagellum Copyright 2003 by N. J. Matzke Version 1.0 (last updated November 10, 2003) ( Update section added September 2006.) E-mail address: matzke@ATncseweb. (please remove obvious anti-spam modification) Abstract: The bacterial flagellum is a complex molecular system with multiple components required for functional motility.� Such systems are sometimes proposed as puzzles for evolutionary theory on the assumption that selection would have no function to act on until all components are in place.� Previous work (Thornhill and Ussery, 2000, A classification of possible routes of Darwinian evolution. J Theor Biol. 203 (2), 111-116) has outlined the general pathways by which Darwinian mechanisms can produce multi-component systems. However, published attempts to explain flagellar origins suffer from vagueness and are inconsistent with recent discoveries and the constraints imposed by Brownian motion.� A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria.� Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility.� The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility.� The selectability of each stage is documented using analogies with present-day systems.� Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F 1 F 0 -ATP synthetase. (2) Much of the flagellum�s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization.� (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events.� (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components.� Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum.� Contents: Update (September 2006) Introduction 1.1. A complex contrivance 1.2. An evolutionary puzzle Figure 1: Composite electron micrograph of the flagellum basal body and hook 1.3. Theory: the evolution of systems with multiple required components 1.4. Constructing and testing evolutionary models Background 2.1. Modern flagella Figure 2: Schematic diagram of a typical bacterial flagellum Table 1: Structural components of the E. coli flagellum Table 2: Components of the E. coli regulation/assembly and chemotaxis systems 2.2. Previous attempts to explain flagellar origins 2.2.1. Short discussions Table 3: Some microbial motility systems 2.2.2. Cavalier-Smith (1987) 2.2.3. Rizzotti (2000) Figure 3: Rizzotti's (2000) scenario for the origin of a proto-flagellum from an F 1 F 0 ATP synthetase The Model 3.1. Phylogenetic context and assumed starting organism 3.2. Starting point: protein export system 3.2.1. Type III secretion systems Figure 4: Systems with components homologous to flagellar components Figure 5: Various secretion systems of prokaryotes 3.2.2. Are nonflagellar type III secretion systems derived from flagella? 3.2.3. An ancestral type III secretion system is plausible Table 4: Convergent functions of well-characterized prokaryote secretion systems 3.2.4. The origin of a primitive type III export system 3.2.5. The relationship between type III export and the F 1 F 0 -ATP synthetase Table 5: Similarities between proteins of the F 1 F 0 -ATP synthetase and the flagellar type III export apparatus that may suggest homology 3.3. Type III secretion system 3.4. Origin of a type III pilus 3.4.1. Filament-first hypothesis 3.4.2. Cap-first hypothesis 3.4.3. Modified filament-first hypothesis 3.4.4. Improvements on the type III pilus 3.5. The evolution of flagella 3.5.1. The selective advantage of undirected motility Figure 6: Relative diffusion advantage of motility as a function of cell size and absolute swimming velocity 3.5.2. Primitive flagella 3.5.3. Loss of outer membrane secretin 3.5.4. Refinements 3.5.5. Chemotaxis and switching 3.5.6. Hook and additional axial components 3.5.7. Modern variations Conclusions Figure 7: Summary of the evolutionary model for the origin of the flagellum, showing the six major stages and key intermediates 4.1. Evaluating the model Table 6: Functions and analogs at each stage of the presented model 4.2. The evolution of other microbial motility systems 4.3. The construction of evolutionary models Acknowledgements References Update, September 2006 This essay has now been cited in the literature (Pallen et al . 2006, �Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases.� Protein Science , 15(4), 935-941 - DOI ) and linked from a peer-reviewed article I have just coauthored (Pallen and Matzke 2006, �From The Origin of Species to the origin of bacterial flagella.� Nature Reviews Microbiology , 4(10), 784-790. Advanced Online Publication on September 5, 2006 - DOI ). Therefore, in order to avoid confusion, I will not update the text of this article at this address. I have, however, made some minor formatting changes, and updated the Reader Background page . While �Evolution in (Brownian) Space� was admittedly a first attempt, and I was a dedicated enthusiast rather than a professional, I think the model has stood up rather well over the last two and a half years. Writing in 2006, I would still agree with about 90% of the 2003 model. To summarize the major updates I would make: First, the hypothesis of homology between the Type 3 Secretion System export apparatus and the F 1 F 0 -ATPase (and its archaeal and eukaryotic equivalents) has been dramatically strengthened by the findings of two papers, Lane et al . 2006 (�Molecular basis of the interaction between the flagellar export proteins FliI and FliH from Helicobacter pylori .� Journal of Biological Chemistry, 281(1), 508-17 - DOI ), and the aforementioned Pallen et al . 2006 . As I predicted in 2003, sequence studies have now confirmed homology between FliH/YscL and F 0 -b (and its equivalents in other ATPases). They also strongly indicate that F 1 -delta is homologous to the C-terminal domain of FliH; I did not predict this, but it does further confirm my more general prediction of �a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F 1 F 0 -ATP synthetase.� However, I would retract some of my more speculative suggestions for ATPase homology to FliJ, FliO, and FliP (FliJ and FliO are apparently not even universally required in flagella). I am still hopeful regarding the suggestions for FliQ and FliR. Secondly, in the 2003 essay I for the most part assumed that the nonflagellar Type 3 Secretion System (NF-T3SS) was derived from the flagellum, rather than being an outgroup with a sister group relationship. I took this position partially to show that even under this assumption the evidence for evolution was strong, and partially because the evidence seemed to lean slightly in that direction. The parsimony argument of Pallen et al . 2005 and various minor points now have me leaning somewhat towards the view that the flagellar and nonflagellar systems are sister groups, and the NF-T3SS is therefore an outgroup. However, as we note in Pallen and Matzke 2006 the scientific community is split on this question. There are several avenues of investigation that might clarify matters, which I will explore in the future. Thirdly, the question of which proteins are actually universally �essential� for flagellum function, and which proteins have homology to other flagellar proteins or nonflagellar proteins, has been systematically reviewed in Table 1 of Pallen and Matzke (2006). I have reposted the table in my blog post on Panda's Thumb . It is important to note that this table is much more conservative than the Matzke 2003 homology suggestions, which ranged from well-established to loose speculation. The homologies in the 2006 table are all well-confirmed by standard BLAST techniques, except for five proteins where homology is based on structural or other similarities. Even for these five, two of the flagllar proteins have other known homologies based on sequence (FliC to FlgL and FliH to YscL), two are not universally essential (FliH and FliJ), and three of the homologies have been repeatedly put forward in the literature (FliC to EspA, FliK to YscP, and FliH/YscL to F 0 -b+F 1 -delta and equivalents). In the entire list, only one required protein has a new proposed homology that could be considered speculative (FliG, to MgtE). Many of the homologous and/or inessential proteins found in Table 1 of Pallen and Matzke 2006 were cited in the 2003 paper, but the 2006 table is an authoritative update and supercedes what is said here. The important overall point, as discussed in my blog post , is that of the 42 proteins in Table 1 of Pallen and Matzke, only two proteins, FliE and FlgD, are both essential and have no identified homologous proteins. This is substantially more impressive than the situation in 2003, and means that the evidence for the evolutionary origin of the flagellum by standard gene duplication and cooption processes is even stronger than in 2003. Important specific updates include: a homolog of FlgA has been confirmed (along the lines that I suggested in 2003); FliG has no homolog in NF-T3SS or the Exb/Tol systems, rather it may be homologous to the magnesium transporter MgtE; and the flagellar filament protein FliC (and its sister FlgL) is probably homologous to EspA and other pilus proteins found in NF-T3SS. I still suspect that all of the axial proteins (including FliE and FlgD) are homologous to each other and therefore to pilus proteins in NF-T3SS, but only the confirmed homologies are reported in Pallen and Matzke 2006. Finally, if I were doing a revision, I would update the terminology along the lines suggested in Desvaux et al . 2006 (�Type III secretion: what's in a name?� Trends in Microbiology 14(4), 157-160, April 2006 - DOI ). As they point out, the terminological distinction between \"flagellum\" and \"type 3 secretion system\" is dubious and artificial, and it is more true to acknowledge that flagella have a type III secretion system. Therefore, there are two known groups of type III secretion systems, flagellar and nonflagellar, abbreviated F-T3SS and NF-T3SS. There is much more to be said about recent research and its implications for flagellum evolution. For the near future I intend to post my thoughts on this in the new flagellum evolution section of the Panda's Thumb blog. 1. Introduction 1.1. A complex contrivance The bacterial flagellum is one of the most striking organelles found in biology.� In Escherichia coli the flagellum is about 10 μm long, but the helical filament is only 20 nm wide and the basal body about 45 nm wide.� The flagellum is made up of approximately 20 major protein parts with another 20-30 proteins with roles in construction and taxis (Berg, 2003; Macnab, 2003).� Many but not all of these proteins are required for assembly and function, with modest variation between species.� Over several decades, thousands of papers have gradually elucidated the structure, construction, and detailed workings of the flagellum.� The conclusions have often been surprising.� Berg and Anderson (1973) made the first convincing case that the flagellar filament was powered by a rotary motor. This hypothesis was dramatically confirmed when flagellar filaments were attached to coverslips and the rotation of cells was directly observed (Silverman and Simon, 1974).� The energy source for the motor is proton motive force rather than ATP (Manson et al. , 1977).�� The flagellar filament is assembled from the inside out, with flagellin monomers added at the distal tip after export through a hollow channel inside the flagellar filament (Emerson et al. , 1970).� The flagella of E. coli rotate bidirectionally at about 100 Hz, propelling the rod-shaped cell (dimensions 1x2 μm) 10-30 μm/sec.� The flagella of other species, powered by sodium ions rather than hydrogen ions, can rotate at over 1500 Hz and move cells at speeds of several hundred μm/sec.� The efficiency of energy conversion from ion gradient to rotation may approach 100% (DeRosier, 1998).� The bacterial flagellum is now one of the best understood molecular complexes, although numerous detailed questions remain concerning the function of various protein components and the exact mechanism of torque generation.� However, the origins of this remarkable system have hardly been examined.� This article will propose a detailed model for the evolutionary origin of the bacterial flagellum, along with an assessment of the available evidence and proposal of further tests.� That the time is ripe for a serious consideration of this question is discussed below. 1.2. An evolutionary puzzle Biologists find it almost inescapable to compare the bacterial flagellum to human designs: DeRosier remarks, �More so than other structures, the bacterial flagellum resembles a human machine� (DeRosier, 1998).� The impression is heightened by electron micrograph images ( Figure 1 ) reminiscent of a engine turbine (e.g., Whitesides, 2001), and the scientific literature on the flagellum is filled with analogies to human-designed motors.� There is no shortage of authorities willing to express mystification on the question of the evolutionary origin of flagella.� In a 1978 review, Macnab concluded, As a final comment, one can only marvel at the intricacy, in a simple bacterium, of the total motor and sensory system which has been the subject of this review and remark that our concept of evolution by selective advantage must surely be an oversimplification. What advantage could derive, for example, from a �preflagellum� (meaning a subset of its components), and yet what is the probability of �simultaneous� development of the organelle at a level where it becomes advantageous?� (Macnab, 1978).� The basic puzzle is that the flagellum is made up of dozens of protein components, and deletion experiments show that the flagellum will not assemble and/or function if any one of these components is removed (with some exceptions).� How, then, could this system emerge in a gradual evolutionary fashion, if function is only achieved when all of the required parts are available?� Figure 1 : Composite electron micrograph of the flagellum basal body and hook, produced by rotational averaging (Francis et al. , 1994).� The motor proteins and export apparatus (included in Figure 2 ) do not survive the extraction procedure and so are not shown. Image courtesy of David DeRosier, reproduced with permission. 1.3. Theory: the evolution of systems with multiple required components The standard answer to this question was put forward by Darwin.� Mivart (1871) argued that the �incipient stages of useful structures� could not have evolved gradually by variation and natural selection, because the intermediate stages of complex systems would have been nonfunctional.� Darwin replied in the 6 th edition of Origin of Species (Darwin, 1872) by emphasizing the importance of change of function in evolution.� Although Darwin�s most famous discussion of the evolution of a complex system, the eye, was an example of massive improvement of function from a rudimentary ancestor (Salvini-Plawen and Mayr, 1977; Nilsson and Pelger, 1994), Darwin gave equal weight to examples of functional shift in evolution.� These included the complex reproductive devices of orchids and barnacles, groups with which he was particularly familiar (Darwin, 1851, 1854, 1862).� Intricate multi-component systems such as these could not have originated by gradual improvement of a single function, but if systems and components underwent functional shift, then selection could have preserved intermediates for a function different from the final one. The equal importance of improvement of function and change of function for understanding the evolutionary origin of novel complex systems has been similarly emphasized by later workers (Maynard Smith, 1975; Mayr, 1976).� Recent studies give cooption of structures a key role in the origin of feathers (Prum and Brush, 2002), and novel organs (Pellmyr and Krenn, 2002); Mayr (1976) gives many other examples.� Computer simulations also show the importance of cooption for the origin of complex systems with multiple required parts (Lenski et al. , 2003). Do these common insights from classical, organismal evolutionary biology help us to understand the solution to the puzzle Macnab put forward regarding the origin of flagellum? Cooption at the molecular level is in fact as well-documented at it is at the macroscopic level (Ganfornina and Sanchez, 1999; Thornhill and Ussery, 2000; True and Carroll, 2002).� It has been implicated in origin of ancient multi-component molecular systems such as the Krebs cycle (Melendez-Hevia et al. , 1996) as well as the rapid origin of multi-component catabolic pathways for abiotic toxins that humans have recently introduced into the environment, such as pentachlorophenol (Anandarajah et al. , 2000; Copley, 2000), atrazine (de Souza et al. , 1998; Sadowsky et al. , 1998; Seffernick and Wackett, 2001), and 2,4-dinitrotoluene (Johnson et al. , 2002); many other cases of catabolic pathway evolution exist (Mortlock, 1992).� All of these systems absolutely require multiple protein species for proper function.� Even for some molecular systems equaling the flagellum in complexity, reasonably detailed reconstructions of evolutionary origins exist. Generally these are available for systems which originated relatively recently in geological history, which are well-studied due to medical importance, and where phylogeny is relatively well resolved; examples include the vertebrate blood-clotting cascade (Doolittle and Feng, 1987; Hanumanthaiah et al. , 2002; Jiang and Doolittle, 2003) and the vertebrate immune system (Muller et al. , 1999; Pasquier and Litman, 2000). Thornhill and Ussery (2000) summarized the general pathways by which systems with multiple required components may evolve. They delineate three gradual routes to such systems: parallel direct evolution (coevolution of components), elimination of functional redundancy (�scaffolding,� the loss of once necessary but now unnecessary components) and adoption from a different function (�cooption,� functional shift of components); a fourth route, serial direct evolution (change along a single axis), could not produce multiple-components-required systems.� However, Thornhill and Ussery�s analysis did not distinguish between the various levels of biological organization at which these pathways might operate.� The above-cited literature on the evolution of complex molecular systems indicates that complex systems usually originate by a key shift in function of an ancestral system, followed by an intensive period of improvement of the originally crudely functioning design. At the level of the system, cooption is usually the key event in the origin of the modern system with the function of interest.� However, a great deal of the complexity in terms of numbers of parts is added to the system after origination.� These accessory parts get added by duplication and cooption of novel genes (for reviews of gene duplication in evolution, see Long, 2001; Chothia et al. , 2003; Hooper and Berg, 2003) and/or duplication", "text_length": 20000, "text_sha256": "232fd456053131a6f684555c8ddd90c3156908cad3ddc9f663446333b97667d1" }, { "route": "/faqs/flagellum_background.html", "title": "Background", "description": "A detailed and testable scenario for the evolutionary origin of the bacterial flagellum.", "content_kind": "article", "text": "Legacy route: /faqs/flagellum_background.html Background to \"Evolution in (Brownian) space: a model for the origin of the bacterial flagellum\" Copyright 2003 by N. J. Matzke Version 1.1 (last updated September 2006) Please send comments to: matzke@ATncseweb.org (remove obvious anti-spam modification) Introduction The article \" Evolution in (Brownian) space: a model for the origin of the bacterial flagellum \" is an attempt to put forward a reasonably detailed model for the evolutionary origin of the bacterial flagellum. The flagellum is a complex structure that some bacteria use for swimming, and it has featured prominently in the arguments of the \"Intelligent Design\" movement. The article is long and somewhat technical, and may not be readily accessible to many readers. This page attempts to give readers some background, and recommend some introductory material that will (hopefully) make the full article much more digestible. Suggestions for further improvements along these lines are welcome. Background For some time, advocates of \"Intelligent Design\" (ID) have been promoting Mike Behe's \"irreducible complexity\" argument. Behe argues that biological systems with multiple required components could not have evolved gradually, because intermediates lacking components would be nonfunctional. The argument has been answered in general terms numerous times (see http://www.talkorigins.org/faqs/behe.html for a survey), and detailed treatments of the evolution of specific \"irreducibly complex\" biochemical systems are now available in the case of blood clotting (see Ken Miller's article on the Evolution of Vertebrate Blood Clotting ) and the immune system (see Matt Inlay's very detailed article Evolving Immunity ). However, the ID movement's favorite example of irreducible complexity, the bacterial flagellum, has not received similar treatment. The bacterial flagellum was only discussed briefly in Behe's Darwin's Black Box , but perhaps because of the counterarguments and literature available on the evolution of other systems, the bacterial flagellum soon became the favorite example of irreducible complexity, and has ascended to near-iconic status for the ID movement. Part of the problem with discerning the evolutionary origin of the bacterial flagellum is that the flagellum is billions of years older than Behe's other example IC systems. With blood-clotting and the immune system, homologs of many of the proteins have been well-known for decades. As the phylogeny of multicellular animals is reasonably well understood, the identification of ancestral systems is not too difficult. In bacteria, on the other hand, phylogeny is confused, and for a long time not many homologs of flagellar proteins were known. Only recently have enough homologs of flagellar proteins been identified to make it possible to piece together a reasonable scenario. The question of the origin of the bacterial flagellum has intrigued me for some time, and it always struck me as a topic that \"someone\" should examine in more detail. It seemed clear that more could be said on the topic than \"flagella don't fossilize.\" For awhile I followed debates on the topic, and slowly accumulated relevant literature. With the publication of thorough, up-to-date reviews of flagellum function and assembly by Berg (2003) and Macnab (2003) , I realized that I probably had enough information to give it a try, and made it my extracurricular summer project. It took rather longer than I planned to synthesize the data into an article, but a version is finally done and I think that several of the findings advance our understanding of flagellar origins significantly. Like any scientific model, this one will have some inadequacies. Some of them are due to our basic lack of knowledge: the functions of many flagellar proteins are uncharacterized, the molecular mechanisms of motor function and protein export are vague, and large-scale bacterial phylogeny is unresolved. There may also be some errors attributable to the inexpert nature of the author; formally I have nothing more than an undergraduate background in biochemistry, although I daresay that I've read enough of the relevant literature to at least avoid major errors, and even to correct a few errors in the peer-reviewed literature. As no one has ever really given the topic of flagellar origins the serious treatment it deserves, there is currently no such thing as an expert. If the article is deemed sufficiently provocative, some of this material may eventually find its way into a journal; however, the article is a bit long and unconventional compared to most journal articles, so releasing it first on the web seemed appropriate. Comments, corrections, suggestions for improvement, and suggestions about more formal publication venues are welcome and should be directed to my email (above). Alternatively, you may post comments at the EvoWiki page for Comments on \"Evolution in (Brownian) space\" . Introductory resources As not every reader will be very familiar with the relevant molecular systems and proteins, I have included some background links that should help bring readers up to speed. To have any hope of following the article, readers should read and understand the below material first. Berg's popular article is particularly recommended as a starting point. Flagellum A good short introduction to the three unrelated kinds of \"flagella\" can be found at Wikipedia: flagellum A detailed popular article on the bacterial flagellum by Howard Berg Chapter 15 of Alberts et al. (1994), Molecular Biology of the Cell , 3rd edn. Section 34.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry F 1 F 0 ATP synthetase (also known as ATP synthase or ATPase) Hongyun Wang's webpage on his ATP synthase research Chapter 14 of Alberts et al. (1994), Molecular Biology of the Cell , 3rd edn. Section 18.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry Life in the viscous microscopic world of bacteria Life at Low Reynolds Number by Purcell (1976) Intelligent Design arguments about the flagellum The article is an attempt at a \"straight\" science piece, with no attempt made to address the various tenditious arguments and equivocating definitions of ID proponents. For articles discussing ID arguments about the flagellum specifically, see the articles below by Miller and Musgrave. At some point I may attempt to write an article comparing ID proponents' wild misconceptions about evolutionary models of flagellar origins (e.g., Bill Dembski's use of cake-baking as an analogy for the evolutionary origin of the flagellum) to an actual serious evolutionary model of flagellar origins. For the moment, however, I encourage readers to look up some of the ID proponents' articles on the topic, and to compare them to the proposed model. Relevant links are given below. Behe on the flagellum in Darwin's Black Box (1996) Molecular Machines and Irreducible Complexity at the Access Research Network Dembski on the flagellum: Chapter 5, No Free Lunch (2002) Bracht, The Bacterial Flagellum: A Response to Ursula Goodenough (2002) Mike Gene, Evolving the Bacterial Flagellum Through Mutation and Cooption (2001-2) Rebuttals to ID flagellum arguments Miller, Kenneth (2003) \" Answering the biochemical argument from design .\" In: Manson, N. (Ed.), God and design: the teleological argument and modern science , Routledge, London, pp. 292-307. Miller, Kenneth (2004) The Flagellum Unspun: The Collapse of Irreducible Complexity .\" In: Dembski, W., and Ruse, M. (Eds.), Debating Design: from Darwin to DNA , Cambridge University Press, New York, pp. 81�97. See also Ken Miller's website . Dembski responded to Miller in an online essay Still Spinning Just Fine on his Design Inference website Musgrave, Ian (2004). \"Evolution of the Bacterial Flagellum.\" In: Young, M., and Edis, T. (Eds.), Why Intelligent Design Fails: A Scientific Critique of the Neocreationism , Rutgers University Press, Piscataway, N.J., pp. 72-84. Matzke, Nicholas J. (2004). \"Behe's Blunder: Irreducible Complexity and Change of Function.\" Bay Area Skeptics Information Sheet , pp. 7-9. April-June 2004. Cavalier-Smith T. (2006). \" Rooting the tree of life by transition analyses .\" Biology Direct , 1(1). Epub ahead of print, July 11, 2006. [ PubMed ] [ Journal ] [ DOI ] [ Google Scholar ] Pallen MJ, Matzke NJ. (2006). � From The Origin of Species to the origin of bacterial flagella .� Nature Reviews Microbiology , 4(10), 784-790. October 2006. (Published online ahead of print on September 5, 2006.) [ PubMed ] [ Journal ] [ DOI ] [ Google Scholar ] Nick Matzke's post on the Panda's Thumb blog, \" Flagellum evolution in Nature Reviews Microbiology \" summarizes a key point in the article for readers and contains further discussion in the comments. See also the PT flagellum evolution section .", "text_length": 8839, "text_sha256": "658ea7c8cc82668b38264ee233156274b877c9577f140f7327154ffde751dfdf" }, { "route": "/faqs/naturalism.html", "title": "A Philosophical Premise of 'Naturalism'?", "description": "Science makes no assumption of naturalism beyond what intelligent design advocates already accept", "content_kind": "article", "text": "Legacy route: /faqs/naturalism.html A Philosophical Premise of 'Naturalism'? by Mark Isaak Copyright © 2002 [posted: Sept. 24, 2002] The main objection some prominent intelligent design (ID) creationists have against evolution is that it is unjustifiably based on the philosophical underpinning of naturalism. \"The Neo-Darwinian conclusion about the process of evolution is based on a premise of metaphysical naturalism: that there are no causes except matter in mindless motion.\" (ARN, 1996) And \"The metaphysical assumptions of scientific materialism are not themselves established by scientific investigation, but rather are held a priori as unchallengeable and usually unexamined components of the 'scientific' worldview.\" (Johnson, 1989) This leads to the claim that evolution excludes God (Johnson, 1999), and that it is only fair to teach an alternative (intelligent design) that allows supernatural influence. This essay, however, will show that the above claims are false. Although science does make some assumptions that might be considered naturalistic in a sense, the assumptions that science is based on are not as restrictive as creationists claim. Furthermore, the proponents of intelligent design make exactly the same assumptions in their own work. Finally, we will see that the complaint about naturalism is applied unfairly to discredit only those parts of science that naturalism's critics oppose on ideological grounds. Naturalism We first must clarify (or try to do so) what is meant by \"naturalism.\" Naturalism is the philosophy that states that explanations for all phenomena must be in terms of natural causes. Some usages of \"materialism\" are similar, and the two terms are sometimes used interchangeably. The main point that naturalism's critics object to is exclusion of the supernatural. Some people distinguish between philosophical naturalism, which states that natural causes are all there are, and methodological naturalism, which says merely that natural causes are all that is available for science to work with. In either case, the definition invites the question of what \"nature\" means. A complete definition would have to explain how to distinguish whether something is natural or supernatural. I have never seen that problem addressed satisfactorily, and I will not attempt to do so here. I will use the terms \"nature\" and \"supernatural\" in their usual informal senses. \"Supernatural\" refers to certain inexplicable or inscrutable phenomena that are traditionally given that label, and nature refers to everything else in the universe. Naturalism gets associated with science because natural explanations have such a good track record for explaining observed phenomena. To date, natural explanations have been determined for very, very many previously unknown areas, and supernatural explanations have been determined for none. When exploring another unknown area, the possibility of a natural explanation is the way to bet. Researchers bet that way routinely, and as a result the human race has benefitted with incredible advances in medicine, agriculture, electronics, materials science, and more. Supernatural explanations, on the other hand, have led nowhere. Indeed, many supernatural explanations are rejected not because they are supernatural but because they cannot or do not lead anywhere. It is possible to come up with any number of possible explanations for anything -- lost socks could be caused by extradimensional vortices which our observations prevent from forming; hiccups could be caused by evil spirits inside us trying to escape; stock market fluctuations could be caused by the secret manipulations of powerful extraterrestrials. Scientists reject such claims on the grounds of parsimony. All of those claims are possible, but they require adding complicated entities which there is no adequate evidence for. To make matters worse, the nature of those entities effectively prevents investigation of them, and the impossibility of investigation prevents us from learning anything new about them. We cannot conclude that any of those explanations are wrong. But from a scientific standpoint, they are worse than wrong; they are useless. The naturalism that anti-evolutionists most object to is philosophical naturalism, which insists on natural explanations even outside science -- i.e., that \"nature is all there is.\" Many scientists, however, do not accept philosophical naturalism either. Some are staunch believers in God or other supernaturalism, including major contributors to evolutionary theory, such as Alfred Russel Wallace, Theodosius Dobzhansky, and Ronald Fisher, and active researchers and defenders of evolution today, such as Kenneth R. Miller and Francisco J. Ayala (see also Slack, 1997). In the United States, by one poll, roughly 40% of scientists believe in an active personal God, and there are surely many more who believe in a God fitting a definition less restrictive than the one used in the poll (Larson & Witham, 1999). These scientists would hardly work to support a philosophical position that they are steadfastly opposed to. Right away, then, we see that the main complaint about naturalism is trivially untrue. Critics of naturalism (I will call them ID advocates for short, although some other creationists make the same criticisms) still deny such obvious facts, though. One method of denial is to claim that the God that their opponents believe in doesn't count. For example: \"Naturalistic evolution is consistent with the existence of 'God' only if by that term we mean no more than a first cause which retires from further activity after establishing the laws of nature and setting the natural mechanism in motion.\" (Johnson, 1990) To those of us who know a few evolutionary biologists personally, such assertions are beyond ludicrous. There are likely some people who believe as Johnson describes, but there are many others for whom God is a personal, ever-present force in their life. Several denominations of Christianity and other religions, including Catholics, Methodists, Presbyterians, and Jews, see no conflict between God and evolution. (NCSE, 2000) This could hardly be the case if a naturalism inherent in evolution was inimical to theistic religion. The other common method of denial is to focus attention on the handful of scientists who do support philosophical naturalism, such as William Provine and Richard Dawkins. These scientists, however, do not speak for all of science. Indeed, no scientists do. Part of science's strength is its diversity. Since scientists of many diverse religions are studying evolution, any religious bias one scientist tries to insert into it will soon be rejected by another. Moreover, philosophers of science, who have no stake in actual theories, also scrutinize science for unwarranted assumptions. With these watchdogs, we can be confident that the theory in the end will be virtually free of religious bias. Likewise for various philosophical, political, and cultural views. Some scientists will disagree with some of the things I say below about the supernatural. But the fact remains that there are many scientists who accept supernatural views in their religion -- some who even see their religion as motivating and inspiring their science -- and who are completely accepted in the field of science. Once one understands the basic requirements of science (more on this below), this should not be surprising. Focusing only on the most materialist scientists and disregarding the rest is a propaganda ploy, not an argument. Most scientists would admit that there will always be phenomena that have not been explained. The more we learn, the more areas of ignorance we uncover. The wise person, when looking at these unknown areas, will say simply, \"I don't know.\" The ID advocates, on the other hand, see the unknowns as openings for the supernatural, perhaps even evidence for it. This is the god of the gaps. Many people, including religious scientists, reject the god of the gaps for purely theological reasons, reasons that have nothing to do with naturalism. For example, they see such a position as opposing a belief in a God that is active in all creation; and, as new discoveries fill the gaps in which God is placed, they see the god-of-the-gaps as undermining a reason to believe in God. (Miller, 1998; Lamoureaux, 1999) Far from denying the supernatural, they are denying that human ignorance is a basis for worship. Spirituality expresses itself differently to different people. Some people see their God denied by the theory of evolution. Others see God in the operation of nature, inseparable from the theory of evolution; they see a need for blatantly supernatural evidence of God as effectively denying God. Others have a variety of entirely different views. This range of views exists among scientists as well as the population at large. One may fail to understand all these views, but to pretend they don't exist is the height of insensitivity. A single spiritual view will not apply to everyone, and trying to impose one will benefit nobody but the arms dealers. A related claim is that adherence to naturalism rules out, a priori , the possibility of detecting design (SEAO, n.d.). This claim also is easily seen to be utterly false, and not just because scientists needn't adhere to naturalism. Even when assuming naturalism, detecting design is obviously possible. One example comes from Carl Sagan, who suggests that design can be inferred from a sequence of bits counting out the first few prime numbers. In fact, this is a favorite example of one of intelligent design's main advocates (Dembski, 1998a). Carl Sagan certainly didn't assume exceptions to naturalism when he proposed that indication of design. (It is worth noting that actual SETI researchers look for an entirely different kind of evidence. They aren't looking for any pattern in the signal except a narrow bandwidth, which they consider a likely indicator based on what people would do. (SETI Institute, n.d.)) Evidence could conceivably be found that points to design of biological organisms, too; for example, records from an ancient ET civilization describing their bioengineering on Earth. Detecting design is a routine part of science already; there is no reason to change existing scientific practices to make it possible. What Science is Based On Many people, including some scientists, misunderstand the foundations of science, believing that science assumes naturalism in some form. As noted above, though, science is based on nature, not on naturalism. To explain this more fully, we must say something about what science is and what it is based on. There is disagreement among philosophers over the exact definition of science, but for our purposes, we needn't go into such depth. We will cover only the basic philosophical assumptions that science makes and qualities of science that are generally agreed upon. Some basic philosophical assumptions are necessary, because conclusions can't be made until you have something to make them with. Whether they realize it or not, virtually everybody makes just a few very basic philosophical assumptions; most people would call them common sense. First, we assume that our memories are not altogether faulty; in other words, that the past is (or was) real. Second, we make an assumption about the future, namely that patterns and principles that have held true in the past will probably continue. These two assumptions together may be considered the single assumption of continuity of phenomena. Most people also assume that there is an external reality, and that our senses give at least a partially accurate indication of it. The assumption of a continuity of phenomena is used by everybody. Consider eating, for example. You need to make assumptions about the past and its applicability to the future in order to find food, even if finding food means nothing more than remembering what cupboard it is in. You need the assumptions again to decide, say, that drain cleaner hasn't suddenly become edible today. You need the assumption to decide that this thing that looks and tastes like an apple is, in fact, and apple and not an old shoe. In short, the assumption is so basic that we need it for survival. Those basic assumptions--a memorable past, a predictable future, and an observable external reality--are the only assumptions made by science (and even the assumption of external reality is rejected by some philosophical idealists). Science makes no other assumptions. With perception and memory, we can see that there are certain regularities in the world, and with induction, we can put them to use. In short, we can learn. Science assumes only that there is a past, present, and future that we can know something about. Once we have that, the real world provides the rest. It is worth repeating that those assumption are not limited to science. Everybody makes them. Even if they deny them with their words, they live their lives according to them. Most people make additional assumptions, but they make those basic ones, too. Some people think that science makes additional assumptions, but it really doesn't. It has been suggested, for example, that science assumes that the laws of nature have been constant throughout time (e.g., Morris, 1994). However, that is not an assumption but a conclusion. Uniformity of natural laws is something that scientists actively test. To date, their tests show that there has been little if any change in the last six billion years, but there is some evidence (still relatively weak) that the fine structure constant has changed slightly before that (Webb et al, 1999). The assumption of naturalism is another assumption that science gets falsely accused of. Science does not make this assumption. Science does not assume that gods are necessary, but it does not assume they are absent, either. Science does not assume that miracles occurred, but neither does it assume a priori that they never have. (Miracles and science are discussed more below). Science is in the business of testing assumptions, not adding new ones. Individual scientists may believe one way or the other, but their beliefs are not a basis for science. All science is based on observations of nature, which leads some scientists to say that science must assume methodological naturalism (e.g. Singham, 2002). But a little investigation shows that even this is an overstatement. The observations that science is based on are natural, but that is simply because the things we call supernatural are not observable, at least not directly. Supernatural forces can, in theory, have effects that are observable. Science allows for this possibility. In fact, several scientific studies have been done to investigate phenomena that most people would consider supernatural, including the power of prayer (Benor, 1990; Byrd, 1988; Harris et al, 1999; Cha et al, 2001), divination (Randi, 1982; Enright, 1999), prophecy (Witztum et al., 1994; McKay et al., 1999; Perakh, 2000), life after death (Schwartz et al., 2001), ESP (Wiseman et al., 1996), and more. Some organizations actively encourage scientific investigation of the supernatural (JREF, 2002). Science can hardly be called naturalistic when it actively delves into the supernatural. If a supernatural phenomenon is found to give repeatable, verifiable results, science will study it. For example, if fairies appear where they can be repeatedly observed, measured, and tested, then they will be valid objects of scientific study. Under such circumstances, though, most people would start calling the phenomenon \"natural.\" The fairies that come to be part of normal shared experience will get labelled \"natural\" even if we don't yet understand how they fly, make the little sparkling lights, and turn some of the researchers into frogs. As I mentioned earlier, delimiting the supernatural is not easy. But what about individual miracles? What about so-called supernatural events that can't be studied? Suppose, for example, an apparition of a dead relative appears and speaks to one person on one occasion, and nothing like it ever happens again. Science has a place for such phenomena as well: that place is outside science. But they are outside science because the observations cannot be verified, not because they are supernatural. Unverifiable natural events are also outside of science. When President Harrison signed the statehood proclamations admitting North Dakota and South Dakota to the United States, he purposely did not let anyone see which he signed first. The question of which state was admitted earlier is, in practice, outside of science, because no verifiable observations can be made to answer it. (However, simply being a one-time event does not place something outside of science. The observations must be repeatable, not necessarily the event being studied. Most events have observable consequences that persist long after the event. The origin of the moon, for example, can be studied scientifically because different mechanisms for its origin imply different modern-day properties such as the chemical composition of moon rocks.) To the extent that a reputed supernatural event leaves lasting evidence, the event can be studied scientifically. And again, we find science actively engages in studying such events. However, where verifiable evidence is lacking, science does not apply. Scientists and philosophers can disagree over other defining features of science, but at least one requirement is clear. For something to qualify as science, the observations must be independently verifiable by others. Perhaps the greatest strength of science is that all its findings are subject to testing, and verifiability of the raw data is foundational to such testing. The effect of this requirement is to remove from scientific consideration subjective impressions and unevidenced phenomena. This does not imply that subjective and unevidenced phenomena aren't important, merely that they cannot be used as the basis for scientific research. Science has never claimed to be all-encompassing. The few people who say otherwise are usually people who want the good reputation of science to apply to their own ideas outside science. Intelligent design proponents fit in this group (Dembski, 1998b). What these people want is more akin to scientism than to science. They want the reputation of science without having earned it. The status of Intelligent Design as science has nothing whatsoever to do with its being natural or supernatural. As we have seen, simply being supernatural doesn't disqualify something from scientific study. Intelligent Design is rejected from science simply because there is no verifiable evidence to support it. Most of Intelligent Design theory is purely subjective, saying little more than \"it sure looks designed to me.\" Only two lines of argument have even a pretense of being scientific. The first, irreducible complexity, is a God-of-the-gaps argument. Certain biological systems, it is claimed, could not have evolved, leaving design as the alternative (Behe, 1996). This argument fails first because a lack of evolution does not imply design, and second because the arguments fail to allow for several biological processes that make the evolution of irreducible complexity not only possible but expected (Muller, 1939). The second supposedly scientific argument for design is specified complexity (Dembski, 1998c). But specified complexity is also a god-of-the-gaps argument. In fact, Dembski's \"explanatory filter\" for detecting design is really just the god-of-the-gaps expressed as a formal flow-chart; plus, it relies on irreducible complexity for its conclusions. The ID advocates deny that their arguments are god-of-the-gaps, and Dembski's arguments in particular are dressed with lots of rhetoric and confusing and inconsistent terminology to make them look more substantive, ", "text_length": 20000, "text_sha256": "3c00113b0fe2a282496cf8d956a0c77ae11f9cedfcdaaaf12abf8fac25bcba9b" }, { "route": "/faqs/demskiscompass.html", "title": "- DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection.", "description": "Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life .", "content_kind": "article", "text": "Legacy route: /faqs/demskiscompass.html Content source: /cs/dembskis_compass/ - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Andrea Bottaro University of Rochester School of Medicine and Dentistry [Posted: 10 August 2003] Leading Intelligent Design Creationism (IDC) proponent Dr. William Dembski has quoted my recent critique of the video \"Unlocking the Mystery of Life\" 1 in \"The Myths of Darwinism\", the Introduction to his latest edited book \"Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing\" 2 . Unflatteringly, alas, the quote is meant to illustrate a purportedly common misinformation strategy (the \"Myth of Victory Past\") used by \"Darwinists\" to surreptitiously dispatch significant objections. According to Dembski, when a valid criticism to evolutionary theory is leveled, first it is \"dismissed without an adequate response\", and later defined as a \"discredited criticism that was refuted a long time ago\", without an adequate refutation in fact ever being offered. I am fingered by Dembski as an example of how this supposed \"Darwinist\" conspiracy works Here, I wish to specifically address Dembski's charge that I \"misdirected\" readers of my \"Unlocking\" critique, and argue that, in fact, it is Dembski's own compass that must be malfunctioning 3 . 1. Setting off... in the wrong direction After describing the \"Myth of Victory Past\" for his readers, Dembski writes: \"It will help to see how this Darwinist technique of \"passing the buck\" actually plays out in practice. ... Here is what Bottaro says about irreducible complexity: \"The crucial argument ... widely discussed in the video, is the concept of \"irreducibly complex\" systems, and the purported impossibility of conventional evolutionary mechanisms to generate them. Although it was quickly rejected by biologists on theoretical and empirical grounds [ref.#6], \"irreducible complexity\" has remained the main staple of [Intelligent Design] Creationism. Ironically, this argument was just recently delivered a fatal blow in the prestigious science journal Nature, where a computer simulation based entirely on evolutionary principles (undirected random mutation and selection) was shown to be able to generate \"irreducibly complex\" outputs [ref.#7].\" \"This sounds quite impressive and damning until one follows the paper trail. Indeed, what are references #6 and #7 to which Bottaro refers? Reference #6 is to Kenneth Miller's book \"Finding Darwin's God\". Unfortunately, you won't find the promised refutation of irreducible complexity's challenge to Darwinism there. \" 2 Dembski continues with a brief account of some of Miller's counter-arguments in \"Finding Darwin's God\", and references his own book \"No Free Lunch\" as the site of refutation of those arguments. Solemnly, Dembski concludes: \"Reference #6 is therefore an exercise in misdirection.\" 2 Well, actually, it isn't. In fact, quite ironically, Dembski has barely set foot on the \"paper trail\" and he's already lost. His confident statement notwithstanding, my original reference #6 is not to Miller's \"Finding Darwin's God\". It's unclear how Dembski even reached that conclusion, since my reference, in its entirety, reads: \"6. see for instance several articles by Dr. Ken Miller, Brown University: http://www.millerandlevine.com/km/evol/ Accessed 6/30/03\" 1 [emphasis added] As anyone can verify at the click of a mouse, that link leads to Dr. Miller's web site, where more links to a number of articles are found. Here, \"Finding Darwin's God\" is represented by a single excerpt from its concluding chapter, very general in tone and void of any mention of either Behe or irreducible complexity. Oddly enough, Dembski even goes as far as directly quoting Miller from what he says is my own reference, but for the life of me I cannot find that quote on Miller's web page, or any of its side-links. On the other hand, Miller's site does contain several pertinent works, including his original review of \"Darwin's Black Box\" and a few more articles on irreducible complexity and IDC, written both before and after Dembski's \"No Free Lunch\". Dembski ignores the articles I referenced, discusses an arbitrarily chosen quote from \"Finding Darwin's God\" (that I didn't reference), and tells his readers to trust that he already neatly disposed of all these objections in his own book 4 . Without excessively dwelling on this rather straightforward issue, if Dembski wishes to publicly accuse me of \"misdirection\" in my use of references, at the very least he should discuss, and direct his own readers to the references I actually give, rather than others of his own choosing. 2. A detour OK, fine, wrong reference. Perhaps Dembski might still contend that even my real reference does not contain \"the promised refutation of irreducible complexity's challenge to Darwinism\" 2 . Except, that'd be wrong as well. As Dembski's own quote of my writing plainly shows, I never \"promised\" that readers would find some sort of definitive \"refutation of irreducible complexity's challenge to Darwinism\" in my reference #6, as he implies. What I did in fact was to simply refer readers to a source where they could find examples of the theoretical and empirical arguments based on which biologists rejected Behe's irreducible complexity 5 . Of course, it shouldn't surprise anybody that Dembski finds those arguments insufficient - or he wouldn't be today at the top of yet another list of \"Darwinism doubters\". Similarly, however, Dembski himself should perhaps consider the real possibility that biologists, such as myself, still find these same objections quite convincing, and his supposed refutations of them inadequate 6 . For someone like Dembski, who has been engaged in essentially the same argument for almost a decade in the absence of any significant rate of \"conversion\" of his opponents, this shouldn't represent a major revelation. Truthfully, I can't actually tell what point Dembski is ultimately trying to make here. He certainly can't be arguing that biologists did not quickly reject irreducible complexity on several theoretical and empirical grounds, or that some of those grounds are not described in reference #6 (either mine, or his imaginary one). And if this is the case, and my reference accurately reflects what was \"promised\" in the text, then Dembski's claim to the contrary is manifestly unsupported. 3. Walking in circles Next, Dembski goes on to deal with my reference #7. The Lenski paper 7 , he informs us, \"... describes a computer simulation and thus contains no actual biology. ... The validity of this study therefore depends on whether the simulation maps faithfully onto biological reality. Unfortunately, it does not, and the study therefore doesn't prove a thing about real-life biological evolution.\" 2 There are two separate issues here. The first relates again to my alleged \"myth-making\". Clearly, I was not referring here to some old paper which failed to really address the issue in question and/or had since been refuted (the forms of \"Myth of Victory Past\" previously described by Dembski). On the contrary, I was referring to a very recently published paper, which (to my knowledge) had not been formally addressed, let alone refuted, by Dembski or any other prominent ID advocate. Unless in Dembski's eyes I am guilty of misdirection because I did not anticipate a forthcoming refutation, and didn't proactively alert my readers to it, it's hard to understand his objection to this part of my critique and supporting references. Secondly, and more importantly, Dembski's purported refutation of Lenski still has to come. Dembski's entire justification for the dismissal of the Nature paper boils down to his claim that its computer simulation does not \"map faithfully onto biological reality\". Why it doesn't, however, Dembski forgets to tell us, either in Myths or (as far as I know) anywhere else 8 . Until Dembski does so, of course, he can hardly accuse me of misdirection. At most, he can charge me with incompetence, for not seeing the obvious faults he finds in the paper, but then I'd still be in such company as the paper's own authors (as well as Nature's reviewers and editors). If the alternative is to take Dembski's rain check for a future substantial and convincing refutation 9 , I'll gladly stick with the other \"incompetents\" for the time being. 4. Conclusion - Dr. Dembski's compass In \"Myths of Darwinism\", Dr. Dembski levels against me the rather serious accusation that I misled my readers, making me a participant in the pervasive misinformation ploy he alleges \"Darwinists\" routinely engage in. But, Dembski assures, if his readers follow his steps on the \"paper trail\", they can find their way back and safely arrive to their truthful destination. Alas, at the end of the road, it is Dembski himself who appears quite off course, having lost his way, along with a chance for restraint and careful scholarship, while looking for signs of deceit in those 2 fateful references. When the facts are examined, one finds that: quite embarrassingly, in his efforts to prove my \"misdirection\" Dembski seems to have taken the wrong turn himself (intentionally or as a result of plain shoddiness, I can't say), all the way to a reference which is not the one I clearly pointed to; contrary to Dembski's claim, the first of my references leads my readers exactly to the information I said it would; the second reference, Lenski's paper, still seems to represent the fatal blow to \"irreducible complexity\" I said it is, and will remain so as long as Dembski and fellow IDC advocates fail to provide any meaningful rebuttal of its conclusions. In my critique of \"Unlocking the Mystery of Life\", I commented on the tendency of that unfortunate \"documentary\" to create straw-man versions of scientific knowledge to oppose to ID philosophy. Regrettably, in his Introduction to \"Uncommon Dissent\", Dembski appears to have chosen the very same approach to reach his rhetorical goal: he needed a good example of his purported \"Darwinian Myth\", and he simply made one up. Notes 1. \"Unlocking the Mystery of Life - More Omissions Than Facts\", in \"Bottaro's Letter to WNYE\", at the National Center for Science Education web site: http://www.ncseweb.org/resources/articles/2018_bottaro39s_letter_to_wnye_7_8_2003.asp . Accessed 7/29/03. Reproduced here on Talkdesign.org: http://www.talkdesign.org/faqs/bottaroslettertoWNYE.html 2. http://www.designinference.com/documents/2003.07.UncDiss_Intro_Contrib.pdf , pages 12-16. Accessed 7/29/03 3. My primary concern here is to uphold my professional standards, as well as the contents of my \"Unlocking\" critique, against Dembski's misguided accusation. However, substantial criticisms can in fact be raised to Dembski's other claims regarding Miller's and Lenski's work. At the risk of being accused of another round of myth-making, I would refer the reader to the comments by Nic Tamzek and others (see http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3f25217b7174ffff;act=ST;f=2;t=72 , and links therein. Accessed 7/29/03). 4. Paradoxically, Dembski seems here to engage in diversion tactics himself: first, my reference of Miller's site turns into a reference to \"Finding Darwin's God\", then Miller's numerous and complex arguments in that book get distilled into just his 4 counterexamples of \"evolved\" irreducible complexity. Finally, Dembski simply declares he has definitively shown those to be faulty in \"No Free Lunch\" - case closed. In fact, whether he successfully did it or not (arguable, but that's beside the point here), that can hardly be considered a wholesale refutation of \"Finding Darwin's God\", let alone of the many arguments against irreducible complexity raised by biologists I was referring to in my text. 5. For irreducible fans of the controversy, there are luckily many other freely available critiques of irreducible complexity on the web, in addition to Miller's. Among the best are several at www.talkorigins.org and www.talkreason.org (links found here: http://www.talkorigins.org/faqs/behe.html and http://www.talkreason.org/index.cfm?category=0 . I particularly recommend Pete Dunkelberg's recent overview \"IC Demystified\": http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html , and, closer to my own field of expertise, Matt Inlay's discussion of immune system evolution: http://www.talkdesign.org/faqs/Evolving_Immunity.html ). An often entertaining series of exchanges between several ID advocates, including Dembski, and my U of R colleague H. Allen Orr can be found at the Boston Review web site ( http://bostonreview.net/BR21.6/orr.nclk ; http://bostonreview.net/BR22.1/BR22.1.nclk ; http://bostonreview.net/BR27.3/orr.nclk ; http://bostonreview.net/BR27.5/exchange.nclk ). Al sites accessed 7/29/03 6. I suspect this very inability to accept even the possibility of honest disagreement, out of absolute self-assuredness and/or lack of internal critical feed-back, is in fact the origin of some of IDC's recurrent and often bizarre conspiracy theories about \"darwinian censorship\" and the likes, such as Dembski's \"myth\" discussed here. 7. Lenski RE, Ofria C, Pennock RT, Adami C. \"The evolutionary origin of complex features.\" Nature. May 8 2003; 423 (6936):139-44 8. To be fair, Dembski goes on to offer a cursory explanation. The authors, he says, begged the issue of irreducible complexity \"by requiring of their simulation that complex features exhibiting complex functions can always be decomposed into simpler features exhibiting simpler functions... There is no evidence that real-life irreducibly complex biochemical machines can be decomposed this way.\" 2 As pointed out by Tamzek, however, this can't really be Dembski's reason for rejecting Lenski's conclusions, since Dembski himself has previously conceded this very same point: \"That an irreducibly complex system may have subsystems that have functions of their own (functions distinct from that of the original system) is therefore allowed in the definition.\" (from \"Still Spinning Just Fine: A Response to Ken Miller\", http://www.designinference.com/documents/2003.02.Miller_Response.htm . This is actually just one of several Dembski's statements on the same subject, quoted in the previously linked Antievolution.org thread by Tamzek). 9. Cynics could say they almost see a strategy emerging: \"When a valid criticism ... is first proposed, it is dismissed without an adequate response, either on some technicality or with some irrelevancy or by simply being ignored. ... Thereafter, the criticism becomes known as \"that discredited criticism that was refuted a long time ago\".\" 2 But of course, according to Dembski only \"Darwinists\" do that, so I am looking forward to his forthcoming refutation of Lenski's paper.", "text_length": 14961, "text_sha256": "e442f4009126101abbb8308ba674d9c9d1b8c40b048587500577ef49952722b2" }, { "route": "/faqs/Evolving_Immunity.html", "title": "Evolving Immunity", "description": "Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box .", "content_kind": "article", "text": "Legacy route: /faqs/Evolving_Immunity.html Content source: /cs/evolving_immunity/ Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . < A Response to Chapter 6 of Darwin's Black Box by Matt Inlay Version 1.4 [Contributed June 6, 2002; Last Modified July 17, 2002] email author for comments and feedback Introduction Immune systems are generally characterized by their ability to distinguish between self and non-self cells, tissues, or molecules, and to eliminate the non-self (for review see Janeway 2001 ). The mammalian immune system is an incredibly complex and intricate system that can recognize non-self and provide protection from a wide variety of pathogens. While there is a high degree of interconnectivity between its components, the immune system can be loosely divided into two subsystems, the innate and the adaptive immune systems. In general, innate immunity is a non-specific, inducible response to pathogens. It is immediate in action, yet short-lived. On the other hand, the adaptive immune system is much more specific, but takes longer to activate. It also features immunological memory, and can augment itself to respond more quickly and with greater specificity to future infections of similar pathogens. Both systems work together to provide protection against a diverse and rapidly-evolving array of pathogens. While much is known about the evolution of the immune system, the details of its origin remain to be elucidated. The innate immune system is the more ancient of the two systems, with roots deep in the deuterostome branch of the bilaterians, roughly one billion years ago. Conversely, the adaptive immune system appeared more recently and quite suddenly, around 450 million years ago with the emergence of the gnathostomes, more commonly called the jawed vertebrates. Because of its high degree of complexity and interconnectivity, the mammalian immune system has been labeled as \"irreducibly complex\", and its evolution and origin through \"Darwinian\" mechanisms challenged [i] . Michael Behe, in his book Darwin's Black Box ( Behe 1996 ), defines irreducible complexity (IC) as: \"[A] single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.\" (page 39). Unfortunately, each of the terms \"system\", \"well-matched\", \"interacting\", \"parts\", and \"function\" can have multiple meanings, depending on the context, so nonarbitrarily labeling a system as IC is not an easy task. For instance, \"system\" in Behe's definition differs significantly from the same word in the context of \"immune system\". His use of \"system\" refers specifically to biochemical systems. What is the difference? The components, or parts of a biochemical system are molecular in nature, like proteins or complexes of molecules. \"System\" as is used in immune system refers not just to molecules, but to the cells and tissues involved in conferring immunity. The immune system as a whole contains numerous biochemical systems within it. It is important to note this distinction because Behe only addresses biochemical systems as IC. Systems, whether biochemical or not, are often defined according to their function. However, the term \"function\" is also nebulous. The \"function\" of the immune system is rather broad, encompassing any action involved in either immune recognition or response. Even the skin is considered to be part of the immune system. The \"function\" of a biochemical system is much more specific. Here, function refers to a specific biochemical function, such as the formation of a blood-clot, the spinning of a flagellum to produce locomotion, or the synthesis of a biomolecule from a precursor. This type of function usually consists of a series of biochemical reactions. This is important because Behe is trying to make a specific argument about the origin and evolution of IC biochemical systems. Immediately after defining IC, Behe states: \"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.\" Behe is trying to suggest that because of the nature of IC, biochemical systems that possess this quality could not have evolved through random mutation and natural selection, or \"blind-watchmaking\". Essentially, Behe is using IC to disprove evolution. As an alternative, Behe suggests that the only way that IC biochemical systems could have originated is through intelligent intervention. He offers as evidence the fact that all IC systems whose origins are known were designed by intelligent agents, us. There are many problems with Behe's argument. Basically, Behe is saying that because we do not know how an IC system could have evolved, it didn't evolve. This type of argumentation is referred to as an argument from ignorance . The problem with arguments from ignorance is that they make a conclusion based on a lack of knowledge. There is still much we do not know about evolution. What seems like a conundrum right now may be easily resolved in the future. Biology, and science in general, is filled with mysteries and unknowns. The whole point of science is to seek answers to those questions. Secondly, he tries to use arguments against evolution as evidence for intelligent design. Negative arguments against one theory do not necessarily provide evidence for a particular alternative. It would be like trying to show how safe a Honda Civic is by providing evidence that a Toyota Corolla is unsafe. No matter how unsafe the Corolla is, it says nothing about the Civic. Negative argumentation is scientifically useless without an alternative that can be positively tested. These fallacies do not rule out the possibility that Behe has raised an interesting and useful challenge to our current understanding of evolution. However, a closer look reveals he hasn't. In chapter 6 of Darwin's Black Box , entitled \"A Dangerous World\", Behe outlines three IC biochemical systems in the immune system; clonal selection, V(D)J recombination, and the complement cascade. However, in his analysis of each of these systems, Behe makes critical mistakes. For the process of clonal selection, Behe targets the antibody molecules, which have the ability to rearrange their genes, and to switch from a membrane-bound form to a secreted form. Behe assumes that an antibody molecule missing one of these features would be useless. However, there are many examples of proteins that do not undergo rearrangement, but are able to switch forms. Additionally, there is a gene closely related to antibodies which can also undergo rearrangement, but does not switch forms. Behe neglects to mention either of these intermediate-like molecules. Instead, he scrutinizes the process of antibody gene rearrangement as the second IC system. He describes the numerous features of this system and claims there is no pathway through which it could have evolved. However, he assumes that the only selectable function for the genes involved in rearrangement is rearrangement. There are well-studied systems that bear remarkable similarity to V(D)J recombination that have nothing to do with immunity. He fails to recognize the existence of these other systems, nor realizes that most of the components of recombination are already present there. Finally, in his description of the third IC system, Behe mistakenly assigns a single function to the complement pathway. He fails to realize that the complement system has several different functions, and several mechanisms of activation. This would allow for a gradual, stepwise accumulation of parts and functions. In fact, many other groups of organisms possess a complement system that lacks his primary function. According to Behe's definition of irreducible complexity, those systems shouldn't exist. In each case, Behe claims that a lack of articles in the scientific literature provides evidence that these systems could not have evolved. However, there are hundreds to thousands of articles published on these systems. Much was known about the evolution of each of these systems at the time Darwin's Black Box was published. Additionally, much has been learned since then. This article will attempt to summarize the existing knowledge about the origins of these systems, and propose a possible pathway for their evolution through a Darwinian mechanism. It is not necessary to \"prove\" that these systems evolved. Because the essence of his argument is \"how could this have evolved?\", this article merely seeks to provide an answer to that question. One issue that will not be discussed is whether or not these systems are actually irreducibly complex. The term is not very useful to the discussion of origins because of the ambiguities surrounding its definition. In fact, IC as a term has failed to make much of an impression on the scientific community, as a search on the publication database PubMed, fails to turn up any references to \"irreducible complexity\" [ii] . IC system I: Clonal selection The first system Behe describes in chapter 6 is the process of clonal selection, which is how the adaptive immune system detects non-self molecules and initiates a response. This system focuses on a protein called immunoglobulin (Ig), and the complex it is part of, called the B cell receptor complex (BCR). Immunoglobulins, also called antibodies, are Y-shaped proteins that can recognize and bind foreign molecules (Figure 1a,b). They are produced by lymphocytes called B cells, and are initially expressed on the cell surface. In its membrane-bound form, an immunoglobulin molecule binds to two additional proteins, Ig a and Ig b , to form the BCR (Figure 1c). The target of an immunoglobulin is referred to as its antigen (Ag). Antigen can be essentially any molecule, though there is a preference for proteins. Because of the way in which immunoglobulins are produced, the specific antigen that each Ig recognizes is different in each B cell. This occurs through a process of gene rearrangement called V(D)J recombination, which will be explained later. When an unactivated, or naïve, B cell's Ig recognizes its particular antigen, it sends a signal back into the interior of the cell to initiate activation. This signal is transmitted via a series of modifications through a series of \"messenger\" proteins, which ultimately trigger the transcription of a panel of genes involved in B cell activation. In order to become fully activated, further interaction with a second class of lymphocyte, called T cells, is required. Once the B cell is activated it proliferates and differentiates into a plasma cell, and the function of the immunoglobulin changes from recognition to response. The immunoglobulin switches from a membrane-bound form (mIg) to a secreted form (sIg), where it can diffuse throughout the tissues of the host organism and there bind its cognate antigen. The only difference between the two forms is at the very tip of the bottom of the Y shape, which corresponds to the very tail end of the gene. The switch from mIg to sIg production results from a switch between two alternative RNA splicing patterns, such that the terminal coding exon directs either the translation of a membrane-bound or soluble C-terminal domain, respectively (Figure 2). The process of amplifying a particular B cell (or subset of B cells) from amongst billions based on its antigen specificity is called clonal selection (Figure 3). This process allows the immune system to choose from which B cell (or subset of B cells) it will mount an immune response. Additional discussion of the clonal selection system in the context of irreducible complexity can be found in the web article: The Evolution of Improved Fitness (http://www.talkorigins.org/faqs/fitness/) Behe summarizes this first system as a group of 3 components (page 125): membrane-bound form of the antibody messenger secreted form of the antibody Behe has this to say about the evolution of the clonal selection system: \"A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there's no way to tell if it's doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps.\" (Page 125) Switch forms or rearrange? So the question is, could the clonal selection system have evolved? Certainly. One thing to realize is that the immunoglobulins are not the only molecules that can undergo gene rearrangement to produce a diverse set of antigen-receptors. T cell receptors (TCRs) are antigen-receptors quite similar to immunoglobulins. However, TCRs exist only in a membrane-bound form, yet are able to carry out their particular function without the need to leave the cell surface. Their receptors are used only for the detection of foreign antigens, and do not directly mediate an effector response. So even if immunoglobulins would be unable to effectively carry out their job if they were restricted to the membrane-bound form, they could have evolved from a TCR-like gene, which does not require secretion. If that occurred, then the ability to rearrange and the ability to switch forms could evolve in separate steps, with each step offering a selectable advantage. It remains unclear whether a TCR-like gene appeared first or an Ig-like gene. However, it is also possible that the ability to rearrange came after the evolution of the alternative splicing pattern, resulting in the ability to switch. This would require that antigen receptors with a single specificity be effective mediators of immunity. Could this have occurred? Absolutely. There are several families of innate receptors that do not rearrange, called pattern recognition receptors (PRRs) ( Medzhitov and Janeway 1997 ). Bacteria possess many unique and essential surface molecules that are distinct from metazoan surface molecules. For example, organisms ranging from insects to humans bear numerous receptors capable of recognizing the bacterial cell wall component lipopolysaccharide (LPS) ( Fenton and Golenbock 1998 ). Examples include the macrophage scavenger receptor, CD14, and the b 2 -integrins. Binding to these receptors induces a variety of responses, from the release of inflammatory agents to the phagocytosis of the LPS-carrying particle. Some of these receptors are membrane-bound and some are secreted. Interestingly, there are some that can exist in both forms, such as CD14. So here we have examples of receptors that do not rearrange, can be membrane-bound, secreted, or both, and can mount an effective immune response. Recently, a gene was discovered in the silkmoth Hyalophora cecropia whose expression is upregulated upon exposure to LPS ( Sun, Lindstrom et al. 1990 ). The gene product, a protein called hemolin, is secreted into the hemolymph (the invertebrate \"blood\") and can bind to the most toxic region of LPS ( Daffre and Faye 1997 ). This protein is also constitutively expressed in a membrane-bound form on the surface of hemocytes (the invertebrate white blood cell equivalents). Interestingly, the structure of this protein was found to contain 4 Ig domains, and is a member of the Ig superfamily ( Lindstrom-Dinnetz, Sun et al. 1995 ). Ig domains are a type of 3D protein structure first identified in immunoglobulins, consisting of 7 or 8 b -pleated sheets. Additionally, the crystal structure was recently solved and revealed a shape loosely similar to an immunoglobulin arm ( Su, Gastinel et al. 1998 ). However, sequence analysis shows that hemolin most likely does not represent a precursor to immunoglobulins as the type of Ig-domain it possesses (the I-set) is one not found in vertebrates. Hemolin does show similarities both structurally and functionally to cell-adhesion molecules, and also contains some cell-adhesion activity. This dual function, both for immune response and cell-adhesion, suggests that immune molecules arose from cell-adhesion molecule precursors. Hemolin is a clear example of an inducible immune molecule that can exist in both membrane-bound and secreted forms. Immunoglobulin signal transduction When an antibody recognizes an antigen, it sends a signal back into the cell, which \"primes\" the cell for activation. But what is the nature of this signal? How exactly does the binding of antigen, which occurs on the exterior of the cell, induce a signaling cascade on the interior? The answer lies in the branched nature of the immunoglobulin. As previously stated, immunoglobulins are loosely shaped like a Y, with two arms sticking out into the extracellular space, and the bottom embedded into the membrane. Associated with each Ig molecule are the two accessory proteins Ig a and Ig b . These accessory molecules have long cytoplasmic tails, and contain motifs specialized for attracting the type of kinases required to initiate the cascade. These motifs are called ITAMs ( I mmunoreceptor T yrosine-based A ctivation M otifs). These motifs serve as targets for protein tyrosine kinases, which phosphorylate certain tyrosine residues on the ITAMs. Because most antigens have multiple epitopes (i.e. multiple binding sites for antibodies), and because the immunoglobulins have multiple arms, the recognition of an antigen results in a clustering of immunoglobulins in the area of the membrane where the antigen comes in contact with the B cell (Figure 4). This process is often called crosslinking, and is the key to activating the cell. Visually, it resembles a \"hands across America\", where each arm of the Ig is linked to an arm of another Ig, and so on and so on. As more and more Igs cluster around the antigen, a family of kinases, called the src family kinases, which are loosely associated with the cytoplasmic tails of Ig a and Ig b , begin to phosphorylate the ITAMs. Because the src kinases bind to phosphorylated tyrosines, this sets up a positive feedback loop, and more and more src kinases are recruited to the site. The phosphorylated tyrosines also bind another kinase called syk. The newly bound syk kinase begins to phosphorylate and activate other syk molecules, which in turn phosphorylate and activate the next molecule in the signaling cascade, thereby propagating and amplifying the signal. The downstream components of this cascade are also expressed in other cell types, and are considered more general signal transducers. In this way, a general transduction pathway can be co-opted by more specific signal molecules. This leads to the activation of transcription factors (TFs), which then enter the nucleus and initiate the transcription of genes involved in cell proliferation and differentiation. In this particular situation, the B cell becomes \"primed\" for activation by T cells. Most of the \"messengers\", or components of the BCR signaling pathway are homologous to many other signaling pathways present in other tissues and in other organisms. For instance, one of the final components in the pathway is the activation of the transcription factor NF- ", "text_length": 20000, "text_sha256": "1d75c361edaf5bb848b62cd40907d9e3e52d87cc113abf90565f1d7a514dc832" }, { "route": "/faqs/Evolving_Immunity1.2.html", "title": "Evolving Immunity", "description": "Evolving Immunity A Response to Chapter 6 of Darwin's Black Box By Matt Inlay Draft 1.2 - email author for comments and feedback created 5/31/02, la", "content_kind": "article", "text": "Legacy route: /faqs/Evolving_Immunity1.2.html Evolving Immunity A Response to Chapter 6 of Darwin's Black Box By Matt Inlay Draft 1.2 - email author for comments and feedback created 5/31/02, last modified 6/03/02 Introduction Immune systems are generally characterized by their ability to distinguish between self and non-self cells, tissues, or molecules, and to eliminate the non-self ( Janeway 2001 ). The mammalian immune system is an incredibly complex and intricate system that can recognize non-self and provide protection from a wide variety of pathogens. While there is a high degree of interconnectivity between its components, the immune system can be loosely divided into two subsystems, the innate and the adaptive immune systems. In general, innate immunity is a non-specific, inducible response to pathogens. It is immediate in action, yet short-lived. On the other hand, the adaptive immune system is much more specific, but takes longer to activate. It also features immunological memory, and can augment itself to respond more quickly and with greater specificity to future infections of similar pathogens. Both systems work together to provide protection against a diverse and rapidly-evolving array of pathogens. While much is known about the evolution of the immune system, the details of its origin remain to be elucidated. The innate immune system is the more ancient of the two systems, with roots deep in the deuterostome branch of the bilaterians, roughly one billion years ago. Conversely, the adaptive immune system appeared more recently and quite suddenly, around 450 million years ago with the emergence of the gnathostomes, more commonly called the jawed vertebrates. Because of its high degree of complexity and interconnectivity, the mammalian immune system has been labeled as \"irreducibly complex\", and its evolution and origin through \"Darwinian\" mechanisms challenged [i] . Michael Behe, in his book Darwin's Black Box ( Behe 1996 ), defines irreducible complexity (IC) as: \"[A] single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.\" (page 39). Unfortunately, each of the terms \"system\", \"well-matched\", \"interacting\", \"parts\", and \"function\" can have multiple meanings, depending on the context, so nonarbitrarily labeling a system as IC is not an easy task. For instance, \"system\" in Behe's definition differs significantly from the same word in the context of \"immune system\". His use of \"system\" refers specifically to biochemical systems. What is the difference? The components, or parts of a biochemical system are molecular in nature, like proteins or complexes of molecules. \"System\" as is used in immune system refers not just to molecules, but to the cells and tissues involved in conferring immunity. The immune system as a whole contains numerous biochemical systems within it. It is important to note this distinction because Behe only addresses biochemical systems as IC. Systems, whether biochemical or not, are often defined according to their function. However, the term \"function\" is also nebulous. The \"function\" of the immune system is rather broad, encompassing any action involved in either immune recognition or response. Even the skin is considered to be part of the immune system. The \"function\" of a biochemical system is much more specific. Here, function refers to a specific biochemical function, such as the formation of a blood-clot, the spinning of a flagella to produce locomotion, or the synthesis of a biomolecule from a precursor. This type of function usually consists of a series of biochemical reactions. This is important because Behe is trying to make a specific argument about the origin and evolution of IC biochemical systems. Immediately after defining IC, Behe states: \"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.\" Behe is trying to suggest that because of the nature of IC, biochemical systems that possess this quality could not have evolved through random mutation and natural selection, or \"blind-watchmaking\". Essentially, Behe is using IC to disprove evolution. As an alternative, Behe suggests that the only way that IC biochemical systems could have originated is through intelligent intervention. He offers as evidence the fact that all IC systems whose origins are known were designed by intelligent agents, us. There are many problems with Behe's argument. Basically, Behe is saying that because we do not know how an IC system could have evolved, it didn't evolve. This type of argumentation is referred to as an argument from ignorance . The problem with arguments from ignorance is that they make a conclusion based on a lack of knowledge. There is still much we do not know about evolution. What seems like a conundrum right now may be easily resolved in the future. Biology, and science in general, is filled with mysteries and unknowns. The whole point of science is to seek answers to those questions. Secondly, he tries to use arguments against evolution as evidence for intelligent design. Negative arguments against one theory do not necessarily provide evidence for a particular alternative. It would be like trying to show how safe a Honda Civic is by providing evidence that a Toyota Corolla is unsafe. No matter how unsafe the Corolla is, it says nothing about the Civic. Negative argumentation is scientifically useless without an alternative that can be positively tested. These fallacies do not rule out the possibility that Behe has raised an interesting and useful challenge to our current understanding of evolution. However, a closer look reveals he hasn't. In chapter 6 of Darwin's Black Box , entitled \"A Dangerous World\", Behe outlines three IC biochemical systems in the immune system; clonal selection, V(D)J recombination, and the complement cascade. However, in his analysis of each of these systems, Behe makes critical mistakes. For the process of clonal selection, Behe targets the antibody molecules, which have the ability to rearrange their genes, and to switch from a membrane-bound form to a secreted form. Behe assumes that an antibody molecule missing one of these features would be useless. However, there are many examples of proteins that do not undergo rearrangement, but are able to switch forms. Additionally, there is a gene closely related to antibodies which can also undergo rearrangement, but does not switch forms. Behe neglects to mention either of these intermediate-like molecules. Instead, he scrutinizes the process of antibody gene rearrangement as the second IC system. He describes the numerous features of this system and claims there is no pathway through which it could have evolved. However, he assumes that the only selectable function for the genes involved in rearrangement is rearrangement. There are well-studied systems that bear remarkable similarity to V(D)J recombination that have nothing to do with immunity. He fails to recognize the existence of these other systems, nor realizes that most of the components of recombination are already present there. Finally, in his description of the third IC system, Behe mistakenly assigns a single function to the complement pathway. He fails to realize that the complement system has several different functions, and several mechanisms of activation. This would allow for a gradual, stepwise accumulation of parts and functions. In fact, many other groups of organisms possess a complement system that lacks his primary function. According to Behe's definition of irreducible complexity, those systems shouldn't exist. In each case, Behe claims that a lack of articles in the scientific literature provides evidence that these systems could not have evolved. However, there are hundreds to thousands of articles published on these systems. Much was known about the evolution of each of these systems at the time Darwin's Black Box was published. Additionally, much has been learned since then. This article will attempt to summarize the existing knowledge about the origins of these systems, and propose a possible pathway for their evolution through a Darwinian mechanism. It is not necessary to \"prove\" that these systems evolved. Because the essence of his argument is \"how could this have evolved?\", this article merely seeks to provide an answer to that question. One issue that will not be discussed is whether or not these systems are actually irreducibly complex. The term is not very useful to the discussion of origins because of the ambiguities surrounding its definition. In fact, IC as a term has failed to make much of an impression on the scientific community, as a search on the publication database PubMed, fails to turn up any references to \"irreducible complexity\" [ii] . IC system I: Clonal selection The first system Behe describes in chapter 6 is the process of clonal selection, which is how the adaptive immune system detects non-self molecules and initiates a response. This system focuses on a protein called immunoglobulin (Ig), and the complex it is part of, called the B cell receptor complex (BCR). Immunoglobulins, also called antibodies, are Y-shaped proteins that can recognize and bind foreign molecules (Figure 1a,b). They are produced by lymphocytes called B cells, and are initially expressed on the cell surface. In its membrane-bound form, an immunoglobulin molecule binds to two additional proteins, Ig a and Ig b , to form the BCR (Figure 1c). The target of an immunoglobulin is referred to as its antigen (Ag). Antigen can be essentially any molecule, though there is a preference for proteins. Because of the way in which immunoglobulins are produced, the specific antigen that each Ig recognizes is different in each B cell. This occurs through a process of gene rearrangement called V(D)J recombination, which will be explained later. When an unactivated, or na�ve, B cell's Ig recognizes its particular antigen, it sends a signal back into the interior of the cell to initiate activation. This signal is transmitted via a series of modifications through a series of \"messenger\" proteins, which ultimately trigger the transcription of a panel of genes involved in B cell activation. In order to become fully activated, further interaction with a second class of lymphocyte, called T cells, is required. Once the B cell is activated it proliferates and differentiates into a plasma cell, and the function of the immunoglobulin changes from recognition to response. The immunoglobulin switches from a membrane-bound form (mIg) to a secreted form (sIg), where it can diffuse throughout the tissues of the host organism and there bind its cognate antigen. The only difference between the two forms is at the very tip of the bottom of the Y shape, which corresponds to the very tail end of the gene. The switch from mIg to sIg production results from a switch between two alternative RNA splicing patterns, such that the terminal coding exon directs either the translation of a membrane-bound or soluble C-terminal domain, respectively (Figure 2). The process of amplifying a particular B cell (or subset of B cells) from amongst billions based on its antigen specificity is called clonal selection (Figure 3). This process allows the immune system to choose from which B cell (or subset of B cells) it will mount an immune response. Additional discussion of the clonal selection system in the context of irreducible complexity can be found in the web article: The Evolution of Improved Fitness (http://www.talkorigins.org/faqs/fitness/) Behe summarizes this first system as a group of 3 components (page 125): membrane-bound form of the antibody messenger secreted form of the antibody Behe has this to say about the evolution of the clonal selection system: \"A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there's no way to tell if it's doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps.\" (Page 125) Switch forms or rearrange? So the question is, could the clonal selection system have evolved? Certainly. One thing to realize is that the immunoglobulins are not the only molecules that can undergo gene rearrangement to produce a diverse set of antigen-receptors. T cell receptors (TCRs) are antigen-receptors quite similar to immunoglobulins. However, TCRs exist only in a membrane-bound form, yet are able to carry out their particular function without the need to leave the cell surface. Their receptors are used only for the detection of foreign antigens, and do not directly mediate an effector response. So even if immunoglobulins would be unable to effectively carry out their job if they were restricted to the membrane-bound form, they could have evolved from a TCR-like gene, which does not require secretion. If that occurred, then the ability to rearrange and the ability to switch forms could evolve in separate steps, with each step offering a selectable advantage. It remains unclear whether a TCR-like gene appeared first or an Ig-like gene. However, it is also possible that the ability to rearrange came after the evolution of the alternative splicing pattern, resulting in the ability to switch. This would require that antigen receptors with a single specificity be effective mediators of immunity. Could this have occurred? Absolutely. There are several families of innate receptors that do not rearrange, called pattern recognition receptors (PRRs) ( Medzhitov and Janeway 1997 ). Bacteria possess many unique and essential surface molecules that are distinct from metazoan surface molecules. For example, organisms ranging from insects to humans bear numerous receptors capable of recognizing the bacterial cell wall component lipopolysaccharide (LPS) ( Fenton and Golenbock 1998 ). Examples include the macrophage scavenger receptor, CD14, and the b 2 -integrins. Binding to these receptors induces a variety of responses, from the release of inflammatory agents to the phagocytosis of the LPS-carrying particle. Some of these receptors are membrane-bound and some are secreted. Interestingly, there are some that can exist in both forms, such as CD14. So here we have examples of receptors that do not rearrange, can be membrane-bound, secreted, or both, and can mount an effective immune response. Recently, a gene was discovered in the silkmoth Hyalophora cecropia whose expression is upregulated upon exposure to LPS ( Sun, Lindstrom et al. 1990 ). The gene product, a protein called hemolin, is secreted into the hemolymph (the invertebrate \"blood\") and can bind to the most toxic region of LPS ( Daffre and Faye 1997 ). This protein is also constitutively expressed in a membrane-bound form on the surface of hemocytes (the invertebrate white blood cell equivalents). Interestingly, the structure of this protein was found to contain 4 Ig domains, and is a member of the Ig superfamily ( Lindstrom-Dinnetz, Sun et al. 1995 ). Ig domains are a type of 3D protein structure first identified in immunoglobulins, consisting of 7 or 8 b -pleated sheets. Additionally, the crystal structure was recently solved and revealed a shape loosely similar to an immunoglobulin arm ( Su, Gastinel et al. 1998 ). However, sequence analysis shows that hemolin most likely does not represent a precursor to immunoglobulins as the type of Ig-domain it possesses (the I-set) is one not found in vertebrates. Hemolin does show similarities both structurally and functionally to cell-adhesion molecules, and also contains some cell-adhesion activity. This dual function, both for immune response and cell-adhesion, suggests that immune molecules arose from cell-adhesion molecule precursors. Hemolin is a clear example of an inducible immune molecule that can exist in both membrane-bound and secreted forms. Immunoglobulin signal transduction When an antibody recognizes an antigen, it sends a signal back into the cell, which \"primes\" the cell for activation. But what is the nature of this signal? How exactly does the binding of antigen, which occurs on the exterior of the cell, induce a signaling cascade on the interior? The answer lies in the branched nature of the immunoglobulin. As previously stated, immunoglobulins are loosely shaped like a Y, with two arms sticking out into the extracellular space, and the bottom embedded into the membrane. Associated with each Ig molecule are the two accessory proteins Ig a and Ig b . These accessory molecules have long cytoplasmic tails, and contain motifs specialized for attracting the type of kinases required to initiate the cascade. These motifs are called ITAMs ( I mmunoreceptor T yrosine-based A ctivation M otifs). These motifs serve as targets for protein tyrosine kinases, which phosphorylate certain tyrosine residues on the ITAMs. Because most antigens have multiple epitopes (i.e. multiple binding sites for antibodies), and because the immunoglobulins have multiple arms, the recognition of an antigen results in a clustering of immunoglobulins in the area of the membrane where the antigen comes in contact with the B cell (Figure 4). This process is often called crosslinking, and is the key to activating the cell. Visually, it resembles a \"hands across America\", where each arm of the Ig is linked to an arm of another Ig, and so on and so on. As more and more Igs cluster around the antigen, a family of kinases, called the src family kinases, which are loosely associated with the cytoplasmic tails of Ig a and Ig b , begin to phosphorylate the ITAMs. Because the src kinases bind to phosphorylated tyrosines, this sets up a positive feedback loop, and more and more src kinases are recruited to the site. The phosphorylated tyrosines also bind another kinase called syk. The newly bound syk kinase begins to phosphorylate and activate other syk molecules, which in turn phosphorylate and activate the next molecule in the signaling cascade, thereby propagating and amplifying the signal. The downstream components of this cascade are also expressed in other cell types, and are considered more general signal transducers. In this way, a general transduction pathway can be co-opted by more specific signal molecules. This leads to the activation of transcription factors (TFs), which then enter the nucleus and initiate the transcription of genes involved in cell proliferation and differentiation. In this particular situation, the B cell becomes \"primed\" for activation by T cells. Most of the \"messengers\", or components of the BCR signaling pathway are homologous to many other signaling pathways present in other tissues and in other organisms. For instance, one of the final components in the pathway is the activation of the transcription factor NF- k B. This transcription factor is used in multiple tissues in a wide variety of organisms to transcribe numerous immune-related genes. The DNA sequence recognized by", "text_length": 20000, "text_sha256": "ae991a2e2b719212d52cdad49bf42e59ff99ccf242ddee4c245c62613411f0f0" }, { "route": "/faqs/johnson.html", "title": "Honesty in \"Darwin on Trial\"", "description": "The Truth, the Whole Truth, and Nothing but the Truth? Why Phillip Johnson's Darwin on Trial and the \"Intelligent Design\" movement are neither science�nor Christian by Brian Spitzer DRAFT", "content_kind": "article", "text": "Legacy route: /faqs/johnson.html Honesty in \"Darwin on Trial\" The Truth, the Whole Truth, and Nothing but the Truth? Why Phillip Johnson's Darwin on Trial and the \"Intelligent Design\" movement are neither science�nor Christian by Brian Spitzer DRAFT, Version 1.1 email author for comments and feedback [Contributed July 15, 2002; Last Modified: July 18, 2002] Introduction Darwin on Trial Lawyer games Just the facts, ma'am How science isn't done Did they really say that? Colin Patterson Steven Jay Gould Nature on the British Museum of Natural History Tricks of the trade Distortions and inventions The tautology argument The missing links which aren't, and other examples The log in your own eye Selective use of evidence The moving target Johnson's response Conclusions Additional examples Bait-and-switch Selective use of evidence Ad hominems and innuendo Misrepresentations of science Quote mining Begging the question \"Straw man\" arguments Conspiracy theory Introduction Lawyers are not the best-respected professionals in our society. Being a lawyer gives one a certain prestige because law requires expertise, like medicine or science, but we tend to put lawyers in the same shady box as salesmen and politicians. We don't trust them. And�perhaps�there are good reasons not to. Courtroom lawyers are called upon to represent the guilty as often as the innocent, and they are duty-bound to build the best case that they can. It follows logically that a courtroom lawyer will spend half of his or her time trying to convince a jury of the truth; the other 50% of the time, they are trying to persuade the jury to believe something which isn't the truth. This is not only permissible in the courtroom, it's necessary for our justice system to work. It's ironic that a system of justice requires what could be called 'injustice' from its participants, but that's what the law demands: lawyers playing parts which they may not even believe. Our law dictates that even the guilty should be represented in court, and most of us would agree that this curious tangle of competing fictions turns out to make our justice system more just. Because of this, it is entirely acceptable for a lawyer to play his or her false part in court, just as it is acceptable for an actor to play someone fictional on the stage. But when people assume false identities offstage, we call them impostors. I would argue that when a lawyer plays lawyer games outside the courtroom, it is just as morally wrong. Of course, you can't have a debate without having debating tactics. It's entirely fair, inside the courtroom or out, to showcase the facts that are most favorable to you. In the same way, it's perfectly fair to write a radio ad pointing out that your brand of widgets is cheaper and more reliable than your competitor's�if those favorable facts are actually true. But we're all aware of sleazy sales pitches where the tactics are used to obscure or distract attention from the relevant facts. I am not claiming that the line between these two is crystal-clear. But I am claiming that those who try to sway public opinion�especially if they are laying claim to the moral mantle of Christianity�are ethically bound to stick to the fair methods and leave the lawyer games in court. Back to top 1. Darwin on Trial Darwin on Trial , the book by Phillip Johnson which founded the neocreationist movement of \"intelligent design\", was written in 1991. I first encountered it in 1996. At the time I knew nothing at all about creationism. A friend-like me, a serious Christian as well as a scientist�suggested that I take a look at it, and I was curious enough to do so. There are certainly things about the book which I applauded, at the time. I've always been irritated by pop-science works which try to make statements about God (or the lack thereof) as though these statements are supported by scientific fact, and I was glad to see someone taking on Richard Dawkins. But even without much training (I had only a B.A. in biology), while reading through Johnson's book I began to notice some puzzling things. At first, they were quite small: a claim in one place which contradicted a different claim in another. A strange lapse of logic-perhaps excusable on account of the author's inexpertise? Statements which didn't fit with what I knew firsthand about science and scientists. I was naive. I assumed that a Christian writing to other Christians would provide a scrupulously fair and accurate account of the facts [1] . But the deeper I got into Darwin on Trial , the less naive I became. And the clearer it became that the driving force behind Johnson's book was neither fairness nor accuracy. A few years passed with this troubling thought at the back of my mind. I entered graduate school and started doing real science myself. And, the more I learned, the less I trusted Darwin on Trial . I finally challenged myself to put my mistrust to the test. Perhaps Johnson was merely confused about some things. What I should do, I told myself, is look at the sources he actually used in writing Darwin on Trial , and see what they say. Perhaps part of what Johnson says is accurate; perhaps his sources misled him in places. So I went to the campus library and started checking his claims. I was a lot less naive when I finished that task. I found that almost every scientific source cited by Johnson had been misused or distorted, in ways ranging from simple misinterpretations and innuendos to the construction of what appears to be outright fiction. The more closely I examined Darwin on Trial , the more inaccuracies I found, until it became almost impossible to catalogue all of the misleading statements in Johnson's work. This book-upon which the \"intelligent design\" movement is trying to hang a program of social reform and public education-is perhaps the ugliest and most deceptive book I have ever seen. It may seem irrelevant to critique a book over a decade since it was published. But Darwin on Trial was the work which founded the \"intelligent design\" movement, and Phillip Johnson is still regarded as the \"godfather\" of that entire school of thought. Later \"intelligent design\" creationists have adopted many of his exact arguments, as well as many of the questionable tactics and strategies used in Darwin on Trial . Perhaps most importantly, nobody in the \"intelligent design\" movement has, to my knowledge, ever criticized or disavowed any of the claims in Darwin on Trial . As I will show, this book is so full of questionable tactics that it would be hard for any informed reader not to notice any of the inaccuracy. All of the stars of the \"intelligent design\" movement, by their silent approval of these tactics, stand under a cloud of suspicion at the very least. Many Christians have welcomed the \"intelligent design\" creationists in the belief that they are fighting for God and truth. But, as the televangelism scandals of the 1980's should remind us, there are some more unsavory reasons for seeking celebrity in the Christian community: money, fame, applause, or power, especially political power. In short, there are a wealth of reasons why Christians need to be careful about trusting the stars of the \"intelligent design\" movement. And even well-intentioned debaters, if they let their desire to win the argument outstrip their respect for the facts, will turn out a product which is grossly misleading. Integrity is important. If�as I will show in this essay�the claims of \"intelligent design\" are more a product of debating tactics and tricks than they are a fair and honest presentation, Christians need to seriously consider whether they can support this movement in good faith. Back to top 2. Lawyer games To understand a lawyer's book, talk to another lawyer. Darwin on Trial has been reviewed by, among other people, a practicing lawyer by the name of Thomas C. Sager. In his review, Sager makes some very interesting points about the legal profession which he and Johnson share. He puts it succinctly: \"The job of a lawyer is not to find the truth, (that is the job of the judge or jury) but to defend (or prosecute) the client.... The standard is to vigorously argue on behalf of one's client, rather than to pursue an abstract 'truth' or even 'justice'.\" Sager goes on to note: \"In supporting the client, the lawyer may use any ethical means available. It is perfectly ethical for a lawyer to make ad hominem attacks on the opposing witnesses, to present incomplete information to a jury, to bring in irrelevant data, and of course to use a wide panoply of rhetorical skills and tricks. Science, obviously, has different goals. But the lawyer's orientation should be kept in mind when analyzing Johnson's book, because he is a lawyer, he has titled his subject a trial, he pursues it as a trial, and his job is to prosecute Darwinism. Lots of things are 'fair', from his point of view.\" [2] Johnson might protest that none of these tactics� ad hominem arguments, half-truths, and rhetorical sleight-of-hand-are technically lies . I am not interested in quibbling over fine shades of meaning in such definitions; in my view, deliberately misleading people does not become more acceptable because it goes under a different name. To a certain extent, it does not even matter whether these inaccuracies are deliberate or not. If Johnson is being intentionally misleading, that is an ethical and intellectual crime. If he is merely letting a desire to attack evolutionists override his concern for careful and accurate research, that indifference to fairness is also a crime, though a lesser one. In either case, Darwin on Trial cannot safely be trusted at face value as a guide to the facts. Back to top 3. Just the facts, ma'am Phillip Johnson, perhaps even by his own admission, is not terribly interested in facts. Indeed, the heart of the argument against evolution which is presented in Darwin on Trial �and echoed throughout the \"intelligent design\" movement up until the present day�is that science isn't actually about facts. According to Darwin on Trial , it's about \"ideology.\" The accusation is that evolutionary scientists are all hopelessly biased, wedded to an atheistic ideology, and that the only reason they support evolutionary theory is that they need some way to explain the marvels of biology without bringing up God. This is a clever strategy, because a number of well-known and outspoken scientists are in fact atheists, and the Christian community in America has long had a vein of simmering resentment against a few individuals, like Richard Dawkins, who have preached atheist ideology while calling it science. Johnson taps into this vein skillfully, claiming that \"Darwinism\" is not only the view that natural forces created biology as we see it today, but also the insistence that God is a mere fable, uninvolved in evolution or�for that matter�anything else. The problem is that this argument isn't true. The truth is that biologists are overwhelmingly convinced that the theory of evolution really does explain the natural world accurately. That's why they support it, not some \"ideology.\" Johnson and the other \"intelligent design\" creationists are aware that a large number of evolutionists maintain a deep faith in God. However, if the \"intelligent design\" creationists acknowledged them, they would have to admit that there are other reasons besides ideology to agree with the theory of evolution. Their strategy has been to deny that these people exist. A Gallup poll conducted in 1982 [3] found that only about 10% of Americans think that \"Man evolved over millions of years from less developed forms. God had no part in this process.\" 90% of us, then, reject \"Darwinism\" as Johnson defines it, and the \"intelligent design\" creationists are fond of quoting this statistic. What they avoid mentioning is the other half of the poll, in which Gallup went not to the average American but to the average American scientist. About 40% of scientists declared their belief in both evolution and in an actively intervening God very much in control of the process. Either 40% of the scientists in America are fighting tooth and nail in defense of an ideology which they actually reject , or-based on the very poll which Johnson likes to cite-Johnson's argument about ideology is bunk. There is plenty of other evidence suggesting that Johnson should know this argument to be just that: bunk. Upon reading through the sources cited in Darwin on Trial , I found that the distinction between science and atheism was drawn quite clearly on a number of occasions It is made repeatedly by theologian Langdon Gilkey ( Creationism on Trial , pp.34-35, 97, 175-176) [4] and scientist Douglas Futuyma ( Science on Trial , p.217) [5] , both of whom are cited by Johnson. While Darwin on Trial points out that evolutionists like Dawkins, Julian Huxley, and Steven Jay Gould claim or imply that God is dead, it neglects to mention that all these figures have been criticized harshly and publicly by evolutionary biologists for muddying the line between scientific conclusions and metaphysical preferences. Johnson has a ready excuse: he claims that any time scientists say that they are not atheists, it is only to fool the public�or, as he puts it in one of his nastier moments, \"for fear of jeopardizing the funding for scientific research\" (p.127). However, Darwin on Trial gives no evidence to back up this accusation. That's because no such evidence exists. If Johnson wants to convince us that his accusations of atheism are not just conspiracy theory, he has had plenty of opportunity to do so. Several reviews of his book have criticized him for pretending that the personal views of a few inflammatory scientists are the consensus view of the scientific community, but Johnson has made no attempt to correct his claims or provide evidence for them. To my knowledge, neither have any of the other leaders of \"intelligent design\" creationism. There can be no denying it: stereotypes are rhetorically handy. But they aren't honest. The attempts by a few scientists to clothe their personal philosophies in the authority of science are certainly deplorable, and I believe that Christians are right to deplore them. But is the correct response to meet one mistruth with another? The way science works�methodological naturalism, to call it by its highbrow name [6] �is to try to explain the world in terms of ideas which can be empirically tested. The tests can be experimental, or one may posit an hypothesis and then look for those empirical signs which would follow logically if that hypothesis were true. Johnson's strategy is to claim that this is the same as atheism (see, for example, pp.116-117 of Darwin on Trial ). This argument does not stand up for long under scrutiny. We may not call it by such an elaborate name, but when a plumber tries to find out why your sink is clogged, or when police try to solve a crime, or when an engineer tries to design a bridge�in fact, whenever anyone tries to figure out pretty much anything about the physical world we live in�they are using methodological naturalism. You yourself use it every day. So do the \"intelligent design\" creationists. Scientists aren't precommitted to atheism. They're precommitted to a scientific method that can actually work. The only alternative to methodological naturalism�that is, to trying to understand the world in terms of ideas which can be empirically tested�is to try to understand the world in terms of ideas which can't be tested at all. See if you can unclog your sink that way. Johnson should, by now, be painfully aware that this argument does not hold up. He has been challenged clearly and publicly (for instance, by Robert Pennock) [7] to present a working alternative to methodological naturalism. Despite the fact that he has had over a decade to work out a method for what he calls \"theistic science\", Johnson has had nothing to say. Writes Pennock: \"This is not surprising, for he has consistently refused to say anything positive about how a theistic science is supposed to work.\" If Johnson really feels that scientists have other options�if we really do have a choice other than methodological naturalism in science�he should give us a hint about what those options are. Until the intelligent design creationists explain to scientists what other methods they could be using, I find it very hard to blame the scientists for considering methodological naturalism to be a limited but indispensable tool. Back to top 4. How science isn't done Darwin on Trial misrepresents science just as it misrepresents scientists. Johnson seems to suggest that any event which has not been directly observed may be dismissed as \"pure philosophy\", but inferential evidence-as he should know from law-can prove a point as well as direct observation. Essentially all modern science, including particle physics, astrophysics, geology, microbiology, and chemistry, relies on inferential evidence. He claims that scientists disagree over \"every detail\" of evolutionary theory, but Douglas Futuyma, on p.171 of Science on Trial (again, a book cited in Darwin on Trial ) explains accurately and clearly what is and is not in dispute in the scientific community. On p.30 of Darwin on Trial , Johnson dismisses evolutionary mechanisms such as developmental constraints and pleiotropy�despite the fact that they are proven, genuine mechanisms that are not only compatible with Darwinian theory but are practically logical outgrowths of it. Darwin on Trial claims on pp.72-73 that, because developmental processes are different in different classes of tetrapods, the resulting traits cannot be homologues of one another; but this is only true if evolution adheres strictly to the principle of recapitulation [8] , a principle which was rejected decades ago by modern science. It suggests on p.80 that Archaeopteryx is just a mosaic along the lines of the platypus (it isn't); suggests on p.94 that the isolation of present-day taxa is at odds with the theory of evolution (this is incorrect); and on pp.95-96 claims that neutral theory is incompatible with Darwinian theory (a conclusion soundly rejected in at least one paper actually cited on the subject in Darwin on Trial ) [9] . After examining the sources which Johnson himself used in writing Darwin on Trial , I find it very difficult to understand how a writer with a serious concern for fairness could have reached the conclusions which are stated in Darwin on Trial . Serious misunderstandings of science pervade Darwin on Trial . For example, Johnson suggests that all scientists stick to the Darwinist party line out of self-interest�apparently unaware that scientific careers are made not by conformity but by coming up with radical new ideas. Any working scientist could have told him that. He does not understand basic scientific terminology (such as the word \"tentative\", for example, an error which he has not corrected even after being informed of it), or how the \"self-correcting\" nature of the scientific enterprise works. Many of these misunderstandings are so basic that Johnson seems to have done little or no research on the topic. In short, rather than do the work involved in understanding how science actually works, Johnson apparently made up a picture of modern biology which he finds useful for rhetorical purposes. Is this really the sort of work on which a true intellectual movement can be founded? Is this the sort of ethics with which the Christian community wants to ally itself? Back to top 5. Did they really say that? a. Colin Patterson Most damning of all is the way in which Darwin on Trial represents the views of other individuals. In several cases, Johnson cites the published opinions of scientists on various matters; it is therefore possible to set his book side-by-side with the original statements and see if they match up. Time and time again, they do not. Even on a generous reading of t", "text_length": 20000, "text_sha256": "7e40fc25785154863fded7a7a3a5113612164c10a0b2baaf1b20b1791819678e" }, { "route": "/faqs/present_arguments.html", "title": "A Presentation Without Arguments", "description": "Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002.", "content_kind": "article", "text": "Legacy route: /faqs/present_arguments.html Content source: /cs/without_arguments/ A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. How William Dembski defeats skepticism, or does he? By Mark Perakh [Contributed June 29, 2002, Last Modified July 3, 2002] Starting on June 20, 2002 and through June 23, the 4 th World Conference of Skeptics took place in Burbank, CA. Its main organizer in the USA was CSICOP, which stands for Committee for the Scientific Investigation of Claims of the Paranormal. Although the forum in question was designed as a meeting of skeptics, whose participants are all squarely on the side of genuine science and opponents of all incarnations of creationism regardless of the disguises the latter employs (such as Intelligent Design, Irreducible Complexity, etc) one not quite common feature of that meeting's program was that its organizers invited two prominent proponents of modern modifications of creationism, William Dembski and Paul Nelson, to give talks and to defend their views in an open dispute with two opponents of the anti-evolution movement, Wesley Elsberry and Kenneth Miller. I cannot remember a single conference of creationists wherein the opponents of creationism were scheduled to give talks in an open discussion. The proponents of creationism sometimes accuse their detractors of being doctrinaire adherents of anti-religious bias whose motivation is not pursuing the truth but assaulting the religious faith. Although this may be not the most important point, still it seems worth mentioning that both Elsberry and Miller have asserted that they are not atheists. Professor of biology Miller is a faithful Catholic, and Elsberry, while vigorously defending the theory of evolution, has also said that he is a \"theistic evolutionist.\" Hence, both Dembski and Nelson were given a chance to argue in favor of their position using arguments of substance, based on facts rather than on ideology, in a dispute with opponents who had no reason to assault Dembski's and Nelson's religious beliefs In this brief essay I will discuss only the presentation by Dembski. The text of Dembski's presentation [1] is notable by the almost complete absence of any arguments relevant to the gist of the dispute between ID advocates, like he himself, and the opponents of that theory. Indeed, the only instance of Dembski's touching on the substance of the dispute seems to be a paragraph on page 4 in [1] where Dembski mentions his term of Specified Complexity and unequivocally defines it as a synonym for \"specified improbability.\" Of course, there is nothing new in that statement. Dembski's interpretation of complexity as \"disguised improbability\" was expressed by him in various forms in many of his articles and books (for example, in [2,3]). This interpretation has been criticized more than once as being contrary to logic and to the accepted mathematical notion of complexity (see the partial list of references at the end of this essay). Dembski's statement illustrates once again his disdainful dismissal of all and every criticism directed at his work. Dembski does not bother to offer any reply to the critique of his interpretation of complexity and steadfastly adheres to his concept which is viewed by many critics as deficient. Continuing in the same vein, Dembski repeats his thesis, suggested by him many times before, that what he calls \"specified complexity\" is a necessary indicator of design. The fallacy of that statement was demonstrated more than once (for example in [4,5]). Indeed, consider an example discussed several times before. Imagine a pile of pebbles found on a river shore. Usually each of them has an irregular shape, its color varying over its surface, and often its density also varying over its volume. There are no two pebbles which are identical in shape, color and density distribution. I guess even Dembski would not argue that the irregular shape, color and density distribution of a particular pebble resulted from intelligent design, regardless of how complex these shapes and distributions may happen to be. Each pebble formed by chance. Now, what if among the pebbles we find one which has a perfectly spherical shape, with an ideally uniform distribution of color and density? Not too many people would deny that this piece in all likelihood is a product of design. However, it is much simpler than any other pebble, if, of course, complexity is defined in a logically consistent manner rather than in Dembski's idiosyncratic way. A logically consistent definition of complexity is given, for example, in the algorithmic theory of randomness-probability-complexity (and is often referred to as Kolmogorov complexity). Kolmogorov complexity of a perfectly spherical piece of stone is much lower than it is for any other pebble having irregular shape and non-uniform distribution of density and color. Indeed, to describe the perfectly spherical piece one needs a very simple program (or algorithm), actually limited to just one number for the sphere's diameter, one number for density and a brief indication of color. For a piece of irregular shape, the program necessarily must be much longer, as it requires many numbers to reproduce the complex shape and the distributions of density and of color. This is a very simple example of the fallacy of Dembski's thesis according to which design is indicated by \"specified complexity.\" Actually, in this example (as well as in an endless number of other situations) it is simplicity which seems to point to design while complexity seems to indicate the chance as the antecedent cause of the item's characteristics. That is about all Dembski chose to discuss in his presentation with regard to the substance of the dispute. Instead, Dembski dabbles in prophecy. His argument in favor of ID mainly boils down to the references to polls which show that the majority of Americans believe in some form of creationism. This may be true. However, Dembski himself gives an example of astrology which is no less popular in America than ID, but this by no means makes astrology plausible. Dembski is not arguing in his presentation that ID will win the minds because it is true. It will win, predicts Dembski, because the American public is predisposed to believe in ID. The same may be true though for astrology and other fads and fallacies he himself listed as being widespread despite their contradicting scientific data. One more argument by Dembski is that young people are inclined to take the side of innovators, and, since ID-ists are the new guys in town, the sympathy of the younger generation will be with them, thus ensuring their victory. Maybe so. What does it have to do with the merits of ID \"theory?\" If scientific theories were accepted or rejected by a popular vote, or just by the vote of young people, quantum mechanics, the general theory of relativity and a whole bunch of other great achievements of the human mind would never have had a chance to take their legitimate place in the progress of humankind. On page 4 Dembski argues that his ID theory is \"not a crank theory (at least not one that is obviously so).\" The sole argument Dembski offers in favor of that statement is that Paul Davies \"thinks that it's onto something important,\" thus disagreeing with those who, like Wesley Elsberry, \"think it merely codifies the argument from ignorance.\" This seems to be a rather weak argument, even by Dembski's standards. The reference to Davies can be interpreted in various ways and is far from endorsing ID as a real scientific theory. Moreover, so what if Davies or any other writer has indeed said something which can somehow be interpreted charitably regarding Dembski's ideas? The position whose strength can be sustained only by such ambiguous references is weak indeed and can be suspected of being crank science with a high degree of likelihood. If all Dembski can say in support of his views is that somebody thinks it has \"something to it,\" it raises a suspicion that he has no factual evidence favoring his suppositions. To show that certain ideas or theories indeed belong in real rather than crank science, one has to subject those ideas to merciless tests, wherein evidence supporting these ideas can be reproduced and independently verified. Dembski and his colleagues in the ID \"movement\" not only did not ever produce such evidence which could be independently verified, but in fact offered no evidence at all despite having a substantial financial support and a substantial fighting force at their Discovery Institute of Seattle. Instead of supporting his theory by factual evidence and arguments of substance, all Dembski was able to do was to resort to a dubious reference which proves nothing and is largely irrelevant. That is the tenor of Dembski's entire presentation. In a similar manner, Dembski plays with other quotations allegedly supporting his thesis, like a quotation from Mencken on page 2, juxtaposed with a quotation from Gould, which, Dembski implies, contradict each other. These two quotations may or may not contradict each other (and actually they were relating to different situations and therefore their juxtaposition was meaningless). It is, however, always possible to mine a host of quotations on every subject and pretend that they prove something even if they are not relevant to each other in any way. Such play with mutually irrelevant quotations confirms the suspicion that Dembski has no real arguments which would be necessary in a talk to an audience not consisting of such ID adherents who would happily swallow anything seemingly confirming their already held preconceptions. One the main points stressed by Dembski in his presentation is the assertion that Intelligent Design, unlike such fringe pseudo-science as astrology and the like, has by now become firmly \"mainstream\" in science. In this, Dembski depicts the desired as if it is real. So far, the overwhelming majority of mainstream scientists ignore ID as can be seen by searching through the scientific literature. Practically no scientific magazine has published articles by scientists wherein a discussion of ID and related matters could be found. No references to ID can be found in the mainstream peer-reviewed scientific publications. The ID advocates either publish their productions as popular or semi-popular books and collections by non-scientific publishers or in their own periodicals mostly connected to their Discovery Institute. The only exception seems to be Dembski's monograph [2] published by the Cambridge University Press. Even this book, reportedly, was Dembski's doctoral dissertation in philosophy rather than in science. Regardless of how many times Dembski will repeat his mantra about \"mainstreaming\" ID, the scientific community has not and will not accept the claims by ID-ists unless and until he and his colleagues present real data supporting their contentions. So far no such data have been presented. The overall level of Dembski's acerbic assault on skeptics can be exemplified by his comment that the letters COP in the abbreviation CSICOP are \"not accidental.\" Is this so? In the absence of real arguments, they may be sometimes replaced with attempts at being witty by using irrelevant puns. Dembski wants the readers to believe that the organization of skeptics is like police trying to muzzle its opponents. Somehow he does not notice the absurdity of such an accusation given the fact that he and his cohort Nelson are freely presenting their views at the meeting organized by the same CSICOP which allegedly is out to prevent the IDists from presenting their views. Maybe in his actual talk Demski said something beyond the irrelevant discussion of the prospects for ID versus evolution to win the minds of masses? It does not seem to be the case. According to the reports by the attendees of the conference, in his actual talk Dembski did not say anything beyond the immaterial quasi-arguments of his posted piece [1]. (This can also be verified by viewing the video tape of the session in question, available from CSICOP). Let me list some of the items that were discussed by Dembski's critics (a partial list of critical reviews of Dembki's literary production includes, but not limited to [4,5,6,7,8,9,10,11,12,13,14,15,16,17]). To some of his critics Dembski never replied in any form. To some others he responded (for example in his latest book [3]) with superficial and largely irrelevant arguments, but he never really replied to the substance of a number of points listed below, which constitute essential elements of his theory. Dembski asserted that complexity is tantamount to low probability. This assertion was rebuffed more than by one of the listed critics. Dembski never replied to that critique. Dembski asserted that his Explanatory Filter never produces \"false positives.\" This assertion was rebuffed by several of the listed (as well as by some not listed) critics. Dembski never replied to them. (It can be argued though that in his latest book [3] Dembski by implication concedes that false positives can be produced by his Explanatory Filter after all but he still does not admit this explicitly). Dembski announced a supposedly new important law – the so-called Law of Conservation of Information. More than one critic argued that the law in question does not exist. Dembski never replied to those critics. Dembski widely used a concept of what he called Specified Complexity. More than one critic argued that the concept in question is meaningless in the sense it has been used by Dembski. The latter never replied to this critique. The same can be said about Dembski's concept of Complex Specified Information (CSI). Dembski insists that design can be reliably inferred if low probability of an event is combined with its specification. More than one among the listed critics argued that the specification as defined by Dembski has no reasonable interpretation. Dembski never responded to that critique. There are other items claimed by Dembski, subjected to critique to which Dembski never responded while he continues to promote the same criticized concepts and assertions. In his presentation, Dembski condescendingly suggested a program of action for skeptics if the latter wish to defend their position against ID. In his uncompromising self-confidence Dembski seems not to realize that if he suggests a new, allegedly revolutionary theory, the burden of proof is on him and on his colleagues in the ID camp. It is ID-ists who need to provide evidence, any evidence, in support of their position. It is precisely the absence of evidence for the ID theory that makes skeptics (read: mainstream scientists) to reject ID as an unsubstantiated attempt to overturn the facts established by science. If Dembski or any of his colleagues showed any reasonable evidence supporting their views, then, beyond doubts, scientists would be much more receptive in regard to their theory. So far this has not happened. Therefore, rather than suggesting what skeptics should do to defend their views from the assault by ID, Dembski should better think of how to search for any believable proof of his own so far arbitrary and dubious assertions. By inviting Dembski and Nelson to give talks at the 4 th World Skeptics Conference, its organizers offered Dembski a chance to reply to his critics on the matters of substance and to defend his position in front of a diversified audience, mostly not very friendly to his views. By taking the floor at the conference in question, Dembski put himself in an unenviable position of denying a simple fact obvious to all – he was complaining about skeptics suppressing his views while speaking to the same skeptics who provided to him the forum. Acknowledgements I would like to thank Brian Spitzer, Pete Dunkelberg, and Wesley Elsberry for constructive remarks regarding the initial version of this article. References [1] William A. Dembski, [online], Skepticism's Prospects for Unseating Intelligent Design , http://www.iscid.org/papers/Dembski_SkepticismsProspects_062102.pdf , accessed on June 22, 2002. [2] William A. Dembski, The Design Inference , (Cambridge University Press, 1998). [3] William A. Dembski, No Free Lunch – Why Specified Complexity Cannot Be Purchased without Intelligence , (Rowman and Littlefield, Lanham, Maryland, 2002). [4] Mark Perakh, A Consistent Inconsistency, [online], www.talkreason.org/articles/dembski.cfm , accessed on June 22, 2002 [5] Mark Perakh, A Free Lunch in a Mousetrap, [online], www.talkreason.org/articles/dem_nfl.cfm , accessed on June 22, 2002 [6] Richard Wein, [online], http://website.lineone.net/~rwein/skeptic/whatswrong.htm , accessed on November 22, 2001 [7] Richard Wein, Not a Free Lunch But a Box of Chocolate, [online]. www.talkreason.org/articles/choc_nfl.cfm , accessed on June 22, 2002. [8] Matt Young, [online], www.pcts.org/journal/young2002a.html , accessed on March 10, 2002. [9] Victor J. Stenger, [online], http://spot.colorado.edu/~vstenger/Found/04MessageW.pdf , accessed on January 17, 2002. [10] Robert T. Pennock, Tower of Babel (Cambridge, MA: The MIT Press, 2000). [11] Taner Edis, [online], www.csicop.org/si/2001-03/intelligent-design.html , accessed on January 17, 2002. [12] Eli Chiprout, [online], http://members.aol.com/echiprt/dembski.htm . Accessed on July 25, 2001 [13] Wesley R. Elsberry, [online], www.infidels.org/library/modern/science/creationism/dembski.htm , accessed on November 22, 2001 [14] Wesley R. Elsberry, [online], www.talkreason.org/articles/inference.cfm , accessed on June 22, 2002. [15] Thomas D. Schneider, [online], www.lecb.ncifcif.gov/~toms/paper/ev/dembski/claimtest.html , accessed on November 22, 2001. [16] Branden Fitelson, Christopher Stephens and Elliott Sober, Philosophy of Science , 66, (1999): 472. [17] John S. Wilkins and Wesley R. Elsberry, The Advantages of Theft over Toil: The Design Inference and Arguing From Ignorance, Biology and Philosophy, v.16, 711 (2001).", "text_length": 18145, "text_sha256": "068a1a1ecba4fc6cf56bb98e0c5d235a68542353dec6a6da9d11a1c924c5b8e4" }, { "route": "/faqs/bottaroslettertoWNYE.html", "title": "Bottaro's Letter to WNYE", "description": "Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life .", "content_kind": "article", "text": "Legacy route: /faqs/bottaroslettertoWNYE.html Content source: /cs/bottaro_wnye_uml_letter/ Bottaro's Letter to WNYE Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life . by Andrea Bottaro The following letter was originally sent to the WNYE PBS station in anticipation of their programmed broadcast of the Intelligent Design \"documentary\" \"Unlocking the Mystery of Life\". Eventually, WNYE aired the program with a disclaimer regarding its contents (see the NCSE site for the text of WNYE's disclaimer and other comments about \"Unlocking\"). Mr. Laing Kandel General Manager WNYE New York Dr. Joe Klein Chancellor Dept. of Education New York Dear Mr. Kandel and Dr. Klein: It was recently announced by the Discovery Institute in Seattle, WA, that the New York Department of Education's WNYE television station is planning to broadcast the documentary video \"Unlocking the Mystery of Life\" (hereafter, UML) on July 6, 2003. While I realize that the purpose of WNYE is to provide its viewers with the broadest and most diverse information from different sources and points of view, there are a few background issues about this video that I believe you and WNYE viewers should be made aware of. UML presents itself as a well-crafted, purely scientific documentary, while it is factually misleading in many respects, and its main purpose is propaganda for a pseudo-scientific movement known as Intelligent Design Creationism. UML has its (strategically concealed) origins close to religious fundamentalist and Creationist circles, and displays a pattern of poor scholarship, including misrepresentation/omission of key scientific evidence. Ultimately, these result in a misleading picture of the facts and of current scientific knowledge, as well as of the ultimate goals of the documentary itself. (More details about these problems are found in the attachment to this letter.) While as a scientist I fully subscribe to the free dissemination of opinions from any source, I think you owe WNYE viewers that such background information is made available to them, so that they may properly judge the documentary's message. Addition of a disclaimer to the broadcast, explaining that the documentary presents a one-sided view of a fringe, pseudo-scientific idea rejected by the overwhelming majority of scientists, and that its main purpose is religious/philosophical in nature, would probably be sufficient to alert your viewers of the true significance of \"Unlocking the Mystery of Life\". Thank you very much for your consideration. Please feel free to contact me if you have further questions or require additional information. Sincerely Andrea Bottaro University of Rochester Medical Center Rochester, NY, 6/30/03 UNLOCKING THE MYSTERY OF LIFE - MORE OMISSIONS THAN FACTS The source: \"Unlocking the Mystery of Life\" is the first and only production of an entity called \"IllustraMedia\". In fact, \"IllustraMedia\" is one and the same with \"Discovery Media Productions\" 1 . Discovery Media is a production company whose previous videos are devoted to evangelical topics, such as \"Heaven and Hell\" and \"The End Times\" 2 . While there is nothing wrong with an evangelical video company producing a science documentary, the fact that to do so it was felt necessary to create a \"shell\" production outfit highlights the aura of ambiguity that pervades the entire enterprise (more examples to follow). Furthermore, the purpose of the video as a propagandistic and religious, rather than scientific/educational tool is underscored by how UML is being publicized within fundamentalist circles. For instance, Mission Frontiers, the Bulletin of the evangelical U.S. Center for World Missions, hails it as \"the most impressive evangelistic tool ever made\" 3 . The contents: As a documentary, UML is a skillful and sophisticated production, showing some well-made computer animations of cellular processes at the molecular level. In discussing such mechanisms, the video claims that the scientific evidence points to insurmountable difficulties for standard evolutionary theory, and supports instead the hypothesis that a superior intelligence directly intervened to create and/or diversify life (hence the name \"Intelligent Design\", or ID, Creationism 4 ). The video discusses such purported evidence and devotes much of its time to the historical origins and philosophical underpinnings of the ID movement. The fundamental question is whether ULM conforms to basic scientific standards of adherence to evidence and facts. In this, it fails at several levels. First of all, throughout the documentary mainstream scientific views, supported by the overwhelming majority of scientists, are not even independently presented. Instead, oversimplified, sometime downright scornful presentations of mainstream scientific theories and hypotheses are provided by supporters of ID (as a counterexample, the recent PBS \"Evolution\" series, though clearly favoring a scientific view, featured the opinions of several prominent representatives of Creationism). In UML, therefore, the viewers are treated to descriptions of scientific evidence and theories that have little connection with what is in fact going on in the science world. For reasons of space, I'll just mention a few examples. The most glaring omission deals with UML's discussion of Origins of Life (OoL) science. The only non ID-based views on OoL discussed in the video are those proposed, in the late '60s, by one of the current ID proponents, Dr. Dean Kenyon. According to UML, those models have been later shown by Kenyon and colleagues to be insufficient to explain key aspects of early molecular and cellular evolution. In fact, most of Kenyon's original views have long been superseded by more thorough, and better empirically supported, scientific hypotheses - indeed, it was those hypotheses and evidence that led to the demise of Kenyon's ideas in scientific circles long before ID Creationism appeared on the scene. Alas, what is arguably the current (and has been for more than a decade now) favored hypothesis about OoL, the so-called \"RNA World\" model, 5 finds no mention whatsoever in UML. This is not surprising, perhaps, since the objections raised in UML by ID proponents to Kenyon's original theory would not stand against this new model. Thus, the viewer is given the false impression that the current scientific choice is between ID Creationism and its outright miraculous Origin of Life, or Dr. Kenyon's outdated 1960's theory. Of course, our understanding of OoL is still very limited, and highly speculative. Nevertheless, it is far more advanced and scientifically solid than the UML parody would want its audience to believe. Other mistakes in UML include an equally superficial, almost mockingly simplified discussion of cooption, a crucial evolutionary mechanism for which in fact significance evidence exists in the biological world. UML's \"experts\" even commit a basic error regarding the role of nucleic acids in the cell, which are presented as uniquely involved in genetic information storage and transfer, while it is now well known that they are directly active in crucial molecular processes functionally comparable to those carried out by protein enzymes - a key piece of evidence in favor of the \"RNA World\" hypothesis mentioned above (and the possible reason why it also went unmentioned). The crucial argument underlying the whole ID philosophy, widely discussed in the video, is the concept of \"irreducibly complex\" systems, and the purported impossibility of conventional evolutionary mechanisms to generate them. Although it was quickly rejected by biologists on theoretical and empirical grounds, 6 \"irreducible complexity\" has remained the main staple of ID Creationism. Ironically, this argument was just recently delivered a fatal blow in the prestigious science journal Nature, where a computer simulation based entirely on evolutionary principles (undirected random mutation and selection) was shown to be able to generate \"irreducibly complex\" outputs 7 . While of course the video cannot be faulted for not predicting the results of future scientific research, this episode serves as a good example of the shaky grounds on which ID reasoning is built. Indeed, not only does scientific evidence continue to accumulate contradicting the ID arguments, but even more damningly, in over 10 years from the onset of the \"movement\", no single scientific result supporting ID has been published in the scientific literature , despite its supporters continuing claims of the existence of such results. Indeed, even the ID advocates' own journal, the electronically published Progress in Complexity, Information and Design, has failed to publish any experimental result supporting ID 8 . In short, despite the appeals by ID advocates to \"let the evidence speak for itself\", there is in fact no positive scientific evidence in support of ID, and on the contrary the theoretical arguments of its advocates are constantly being proven erroneous in the professional literature. To avoid facing this lack of evidence, UML resorts instead to systematic distortions of mainstream science theories and omissions of key ideas and pieces of evidence. The people: The experts interviewed for UML, and ID advocates in general, are fond to present themselves as \"scientists\", often accompanied by the qualifier \"a small but growing number of\". In fact, most ID advocates are not scientists by any meaningful definition of the term, and their numbers (for which \"small\" is an overstatement) are anything but growing. Of the experts who appear in UML, 4 can in fact qualify as bona fide scientists: Michael Behe, Scott Minnich, Dean Kenyon, and Jed Macosko. The first two hold tenured positions in Biochemistry and Microbiology, respectively, at mainstream universities, but despite their own research experience and active labs, as discussed above they have failed to produce any evidence in support of the ideas they so eloquently argue for. Dean Kenyon was scientifically active until the mid-'70s, after which he has not published further in the scientific literature (however, he has since co-authored the notorious Creationist school textbook \"Of Pandas and People\" 9 ). 16 Jed Macosko, whose image is accompanied in UML by the qualifier \"Molecular Biologist, UC Berkeley\", although a Berkeley graduate and former postdoctoral trainee, in fact is not, or has ever been, on the Berkeley faculty, as that title could suggest. Indeed, Dr. Macosko is apparently not even affiliated with UC Berkeley anymore; if he was at the time of interview, he certainly was there as a junior postdoc trainee, hardly an \"expert\" in the field by any standards. Currently, Dr. Macosko is listed on some ID web sites as teaching chemistry at the religious La Sierra University in Riverside, CA 10 , although he does not appear on the faculty list there either 11 . Such \"generous\" use of credentials is not unique in the documentary. One of the leading proponents of ID, William Dembski, is labeled as a \"mathematician - Baylor University\" in UML, although he is affiliated with Baylor's Institute for Faith and Learning, which focuses on theology and philosophy 12 . Indeed, almost the entirety of Dr. Dembski's vast published opus, with the exception of a mathematics paper in 1990, is about various aspects of theology, apologetics and philosophy 13 (Dr. Dembski holds PhDs in Mathematics and Philosophy, and a M.Div. in Theology). Finally, Jonathan Wells, presented as \"biologist\" in UML, does hold a PhD in Developmental Biology from UC Berkeley. By his own words, however, he entered the program not based on any genuine interest in science and biology, but following the direction of the Rev. Sun Myung Moon, with the expressed goal to \"devote his life to destroying Darwinism\" 14 . Not surprisingly, there is no record of Dr. Wells performing any meaningful research work after his training at Berkeley, and he has since entirely dedicated himself to anti-evolutionist propaganda (including the book \"Icons of Evolution\", some editions of which even contained stickers for students to deface biology textbooks 15 ). Thus, the definitions of professional background and academic affiliation used throughout UML are at the very least ambiguous, and clearly result in an inflation of the apparent academic clout and relevant expertise of the participants. In summary, \"Unlocking the Mystery of Life\" is a depiction of a fringe, at best semi-scientific philosophical movement very close, ideologically and organizationally, to religious Creationism. The documentary misrepresents itself, its goals, the existing scientific evidence and its own experts in several significant ways. While it is your prerogative to air the programs that you believe best suit your audience's needs and interests, it is equally important that your viewers be provided with information that may help them put this product's contents and purpose in the appropriate context. This is necessary not only in the spirit of openness and full disclosure, but also to avoid that your broadcast of the documentary appear as an implicit endorsement of this new form of \"stealth\" Creationism by one of the largest Departments of Education in the country. Notes 1. Verifiable by a \"WHOIS\" search for the domain name \"illustramedia.com\": http://www.networksolutions.com/cgi-bin/whois/whois?STRING=illustramedia.com&SearchType=do Accessed 6/30/03 2. http://www.discoverymedia.org/dm_products_page.htm Accessed 6/29/03 3. http://www.missionfrontiers.org/2002/06/PDFs/Unlocking_Mystery.pdf Accessed 6/28/03 4. For an in-depth discussion of ID Creationism, see \"Intelligent Design Creationism and its Critics\", Robert T. Pennock, ed, MIT Press, 2001, ISBN 0-262-16204-0; review in http://www-unix.oit.umass.edu/~cheathwo/Phil100/nytimes.html Accessed 6/30/03 5. http://www.lawrenceroberge.com/RNAWORLD.htm Accessed 6/30/03 http://www.americanscientist.org/template/AssetDetail/assetid/21438?fulltext=true Accessed 6/30/03 6. see for instance several articles by Dr. Ken Miller, Brown University: http://www.millerandlevine.com/km/evol/ Accessed 6/30/03 7. Lenski RE, Ofria C, Pennock RT, Adami C. \"The evolutionary origin of complex features.\" Nature. May 8 2003; 423 (6936):139-44 8. http://www.iscid.org/pcid.php Accessed 6/29/03 9. http://63.74.14.138/page/001/PROD/BOFPA1 , reviewed at the National Association of Biology Teachers web site http://www.nabt.org/sub/evolution/panda1.asp Both accessed 6/30/03. 10. http://www.iscid.org/jed-macosko.php ; http://www.lasierra.edu/ Both accessed 6/30/03 11. http://www.lasierra.edu/resources/phonelists/phonename_m-s.html Accessed 6/30/03 12. http://www3.baylor.edu/IFL/ Accessed 6/28/03 13. http://www.designinference.com/documents/05.02.CV.htm Accessed 6/30/03 14. http://www.tparents.org/library/unification/talks/wells/DARWIN.htm Accessed 6/30/03 15. Links to reviews of Icons of Evolution can be found at the National Center of Science Education's web site http://www.ncseweb.org/resources/articles/9855_reviews_of_icons_of_evolution_10_31_2002.asp Accessed 6/30/03 16. Note added July 8, 2003: After this letter first appeared on the NCSE web site, Dr. Kenyon kindly and quickly informed me that he has in fact one scientific publication later than the mid-'70s: \"A Comparison of Proteinoid and Aldocyanoin Microsystems as Models of the Primordial Protocell\", in Molecular Evolution and Protobiology [K. Matsuno, K. Dose, K. Harada, and D. L. Rohlfing, eds.], pp. 163-188, Plenum Press, 1984. My original statement was based on a search of the main scientific literature databases available: Pubmed, BasicBIOSIS, CSA Biological Sciences, and the Institute for Scientific Information's \"Web of Science\" Science Citation Index. The book article in question does not seem to appear in any of these databases, nor has it apparently ever been referenced by any other later publication also in the database. Nevertheless, for the record, the existence of Dr. Kenyon's 1984 paper should be noted. Addendum, 8/5/03: Dr. Dembski has recently charged that my critique of \"Unlocking the Mystery of Life\" misleads readers. He's wrong: Dembski's Compass .", "text_length": 16298, "text_sha256": "4624139b419fbace4ebfc296785bf8a9b9209e493f2e88dd9507f752ab84aa91" }, { "route": "/faqs/magisteria.html", "title": "Incompatible Magisteria", "description": "INCOMPATIBLE MAGISTERIA By Mark Perakh INTRODUCTION If I were asked to give a brief definition of science, I would have a hard time to come up with", "content_kind": "article", "text": "Legacy route: /faqs/magisteria.html Incompatible Magisteria By Mark Perakh INTRODUCTION If I were asked to give a brief definition of science, I would have a hard time to come up with a definition which, on the one hand, would encompass everything that belongs in science, and on the other hand, leaves out everything which is not science. In the paper [1] a descriptive definition of science is offered as “ a human endeavor consciously aimed at acquiring knowledge about the world in a systematic and logically consistent manner, based on factual evidence obtained by observation and experimentation .” O course, as stated in the same article [1] this definition does not pretend to encapsulate in one sentence such a multifaceted and complex human activity as science. It leaves out many important features of science, such, for example, as the question of the quality of evidence or of the proper rules for the interpretation of evidence, and many others. It is just a first-approximation definition made painted with a wide brush. If I were asked to give a definition of religion (which I have never tried) I would have an even harder time finding a brief sentence which would encompass everything that belongs in religion and leave out everything that is not (because there are so many religions and they often are so vastly differing from each other). Be that as it may be, I think that religions, like science, also try to comprehend the world, but using very different means. Philosophy, which is neither science nor religion, hangs in the no-man’s land between them, sometimes leaning toward science and sometimes toward religion. In this article I will omit discussions of philosophy and its place between science and religion (which is briefly discussed in [1]). And of course I will not go anywhere close to theology. I also do not intend to delve into nuances, thus leaving out the many well known variations in the principles and practices of various religions, concentrating instead on the most crucial overall difference between religions in general and science. Therefore some of my statements may sound too categorical, but I believe that, while they ignore many subtle points and can therefore invoke indignation or denials on the part of adherents of this or that faith, they do nevertheless reflect certain real features common to all religions. I will try to suggest tentative answers to two questions: (1) What is the most substantial difference between the ways science and religion approach the task of explaining the world? (2) Why do so many people fervently adhere to a religious dogma even when it obviously contradicts the scientific data supported by experience and reason? “CONTRA EVIDENTIA CREDO” VERSUS “CREDO QUIA EVIDENTIA” The two Latin expressions in this section’s title seem to grasp in a succinct form the principal difference between the attitudes of religion and science to the search for truth. (The first three Latin words translate as “I believe despite the evidence,” and the last three words as “I believe because of the evidence.”) The first maxim reflects the attitude of religions, and the second – of science. Of course, as in the case of science, these are just intentionally simplified generalizing statements painted with a wide brush and ignoring many facets of such a complicated phenomenon as religion, in particular the attempts at rationalizing its foundations. In the same intentionally simplified way, it seems possible to succinctly state the following: Religions are based on faith. Science is based on evidence. Reason seems to favor science. Emotions often favor religion. I can easily imagine the indignation by many a believer at the above assertions. He is confident that his faith is based on evidence and logic. I’ll return to the discussion of the supposed rational foundations of faith a little later, wherein I’ll try to offer a justification for the above general formulation of the basic difference between the approaches of religions and of science to the comprehension of the reality. I could have stopped at that point because there is little of essence that can be added to the above succinct rendition of the principal difference between religion and science. However, many additional questions are vexing in their own right, calling for an elaboration of the above maxims. If reason favors science, why are religions so widespread and so stubbornly persistent even when faced not only with the lack of evidence in favor of their veracity, but also with overwhelming evidence against their tenets? Indeed, another version of the first maxim in the title is “credo quia absurdum,” which has been pronounced by prominent defenders of religious faith [2] and which means “I believe because it is absurd.” Even if adherents of some religions other than Catholicism may deny that they share the above maxim, I believe it applies to a certain extent to all religions, even if not always in such an extreme form. The quoted maxim implies the antinomy between “knowledge” and “faith.” It seems to imply furthermore, that we “know,” for example, from scientific evidence that the earth is billions of years old. However, according to the above maxim, a believer may adhere to the notion that the earth is only about 6,000 years old, not because he “knows” that but because he “believes” in that, however absurd the latter notion may be in view of the contrary evidence; moreover, the very absurdity of the notion in question is claimed by the quoted maxim as the reason to believe in it. Precisely because it is absurd from the rational viewpoint, its acceptance requires belief . Of course, the believers are often confident that their faith has also strong rational foundations, and religious apologists of all varieties work hard to supply alleged proofs of such rational foundations. Christian apologists [3,4] point out the alleged historical evidence supporting the story told in the gospels, for example, quoting ancient writers like Josephus Flavius or Suetonius. Jewish apologists [5, 6, 7, 8] refer to the allegedly uninterrupted tradition forwarded through generations from the entire nation of Israelites witnessing Moses’s receiving the Torah directly from Jehova; or they point out the alleged fulfillment of the prediction made in the Torah in regard to the history of the Jewish people. Islamic apologists [9] developed the so-called Kalam argument allegedly proving the existence of God (in its Islamic version). In our time, Islamic apologists maintain huge websites [10] wherein a variety of allegedly rational arguments are offered for the veracity of the Islamic faith. Various specious rationalizations have also been developed by Hindus, Druses, Bahais, Buddhists, Sintoists, Taoists, etc., (although some of them are much more limited in scope and sophistication). Another form of exegesis which has been practiced mainly by Christian and Jewish writers is devoted to the alleged reconciliation between the biblical story and science by interpreting the former in various metaphorical and non-literal ways [11, 12, 13, 14, 15 ]. However, the existence of various forms of exegesis does not eliminate the prevalent feature of religions – their reliance on faith rather than on evidence. So, why do billions of people adhere to religious faiths even when they contradict facts established by science via a process of a rational investigation based on evidence? Whereas the answer to that question may require an excursion into human psychology, for which I have no taste whatsoever, there seem to be relatively simple ways to survey certain facts relevant to the difference between the scientific and the religious approaches to understanding the world we live in. There are various estimates [16] of how many religions exist on our planet. It is obvious though that their number is in thousands. There are certain similarities between some of those religions, but the differences between various religious systems, often to the extent of complete incompatibility, are much more pronounced. Even those religions which have stemmed from the same root, as, for example, Judaism, Christianity, and Islam have developed many more differences than preserved similarities, not only in secondary details, but also in the basic concepts inherent in their foundations. Within each of them there are numerous variations, both in details and in fundamentals. The Baptists have a conceptual framework vastly different from that of, say, the Catholics, and the Mormons from the Pentecostals. The Shiah Moslems do not accept at all many of the firm beliefs of the Sunni Moslems. Druses, Sikhs, Zoroastrians, Buddhists, and a myriad of other sects, sub-sects, and systems of beliefs, vastly differing from each other, each have their own fervent adherents unshakably confident in the veracity of only their faith and denying the plausibility of all other faiths. Of course, if the matter stopped at that and members of different faiths simply adhered to whatever is a commonly accepted belief within their communities, a reasonable attitude to that divergence of beliefs would be to benignly accept this as simply a fact of life. Unfortunately, the peaceful coexistence of various faiths seems to be more of an exception than a rule. Remember the horrifying history of crusades [17]. Overwhelmed with a whipped up religious fervor, the crusaders, on their way to the Holy Land, mercilessly killed uncounted thousands of Jews in Europe. In Northern Ireland, the Protestants kill the Catholics and the Catholics kill the Protestants, both speaking the same language, coming from the same ethnic stock and largely sharing the same history. In Kashmir Hindus kill Moslems and Moslems kill Hindus at every opportunity. Both are of the same ethnic origin, share their early history, and often speak the same languages. Of course there are many factors besides religions which spawn hatred and murders, and it may be equally possible to point to the positive role played by religions in certain historical periods and in certain countries. However, in the above cases it is religious faith that converts those uncounted thousands into murderers. Let us now note the following facts. It is common knowledge that conversion from a religion a person was raised in to some other faith is relatively rare. How many Lindh’s [18] are there in the US and Europe? A very small percentage of the population. How many Moslems have converted to Christianity? A tiny percentage of the Moslem population. However, even these numbers are much larger than a conversion of, say, Moslems or Christians to Judasim, Bahai, or the Sikh faith. Are Judaism, Bahai and Sikh faiths “worse” than other religions? It seems obvious that the conversion caused by a person’s sincere realization of the truthfulness of a religion other than the one he grew up with is a rare phenomenon indeed. A much more potent incentive for conversion seems to be pressure from the social environment. This leads us to the conclusion that adherence to a certain religious faith is caused mainly (albeit not necessarily only ) by indoctrination at an early age. Such indoctrination (or instruction, if one prefers a milder term) creates powerful emotional ties, inextricably connected to the person’s subconscious traces of the impressions gained in the early childhood. Therefore, a person born in Salt Lake City quite probably will grow up and remain a Mormon, a child born in Tel-Aviv, most likely, will be a part of the Jewish community for the rest of her life, and a boy born and raised in Islamabad hardly can be expected to be anything other than a Moslem, and, with a considerable probability, a very fervent one. As was mentioned earlier in this article, religious apologists routinely offer allegedly rational arguments in favor of their beliefs. Even if we will not discuss numerous holes in those allegedly rational arguments, the natural question seems to be: if these arguments are indeed convincing, why are they accepted only within the communities of co-religionists? Why Christians do not seem to be impressed by the Islamic apologetics, and Hindus, by the Christian one? The two indisputable facts – the very existence of thousands of religions with their often incompatible tenets, and the rare occurrences of conversion from a faith one grew up with – make the apologetics of any variety quite doubtful, and with it equally doubtful the supposed rational foundations of faiths. Now, what about science? Isn’t the “knowledge” and hence acceptance of the facts and theories of science also indoctrinated through education and media? Yes, it is. There are, however, fundamental differences between the indoctrination in a religious faith and indoctrination in science. Look, say, at physics, or chemistry, or mathematics, or engineering. Are there many or even a few differing physics, each fervently adhered to in specific countries or parts of the world? No, there is only one “physics,” the same in the USA, Russia, Northern Ireland, Pakistan and Japan. Are there dissenters among the physicists? No, if the basic concepts of that science are in question. Yes, if specific theories or data are under discussion. Does in science the concept of a heretic exist? No. Although heated disputes among scientists happen regularly, they do not usually lead to killing one’s opponent. Differing views are tolerated, and after sometimes prolonged discussions, a consensus is usually reached, accepted in Tokyo as well as in Moscow or Pasadena, CA. What are the criteria usually applied in religious disputes? Appeals to authority. In a religious dispute within a community of co-religionists a proper quotation from the “holy books” of the faith decides the controversy. The authority of a “holy book” is above any other considerations and arguments. What are the criteria applied in scientific disputes? Appeals to facts and reason. In religious indoctrination, assertions are made from authority and one is invited (or, better, pushed) to accept them on faith. As to the allegedly rational reasons to believe, they play a subordinate role in the religious indoctrination, and are designed mainly to bolster the faith of the doubting believers rather than to indoctrinate the young. In scientific indoctrination, statements directed at the uninitiated are also made from authority, but one is invited to accept them for reason and to look for their verification. In a religious indoctrination, doubts in regard to the principal dogmas of the faith are discouraged. In some religions (like the Russian Orthodox faith) even discussion of small details of the rites are not permitted. Even in those religions wherein various interpretations of the sacred texts are common (like in Judaism, where the Talmud is an immense compendium of often conflicting teachings by various early Rabbinic authorities) the main tenets (such as the divine origin of the Torah which is considered the depository of everything that can be known about the world) are out of discussion’s limits. Indeed, here is what one of the most revered Rabbinic authorities, the 12 th century rabbi Moses ben Maimon (Maimonides) wrote in his famous codex Mishneh Torah (Laws Regarding Idolatry, chapter 2, law 3): “Not only one is forbidden to follow idolatry even in his mind, but we are forewarned not to entertain any thought whatsoever which is capable of shattering a person’s faith in one of the main principles of Torah… Thus our Sages said on this matter: ‘ means heresy, means fornication.” ( The Babylonian Talmud, Berakhot 12b). Of course this partial quote does not reflect Maimonides’s views in all of their complexity and thus may create an unjustified impression of his dogmatic and complete rejection of all and every dissent in the matters of faith. However, even this relatively tolerant and wise religious thinker was obviously not willing to compromise in the “main principles” of his faith. Since the question of what constitutes “main principles” can be answered in many ways, including quite restrictive ones, the boundaries of the matter allowed for discussion and dissent can be (and actually often were) set right at one’s elbow. Faith does not presume the existence of an escape route from the faith’s tenets. An apostate is despised and hated. In a scientific indoctrination doubts are expected and an escape route is always available, while the possibility of change or even of a complete rejection of the existent concepts is always accepted, provided new evidence is discovered. There are mavericks and iconoclasts in science, but no apostates. The worst an iconoclast may expect from other scientists is an ironic condescension, but more often just a cautious reservation until the dissenting ideas have been tested by normal means of scientific exploration. An apostate will never earn respect from his former co-religionists, and normally would be expelled from his former community, and in the extreme cases may be even killed. An iconoclast may become a highly respected authority if his unusual ideas find confirmation in the normal process of scientific inquiry. Science freely admits that knowledge is incomplete and imperfect. However, the established concepts of science more often than not have at least some truth in them, even if it is not perfect, and this truth is the same in New York, Kyoto, Jerusalem, and Canberra. Religions all insist that they possess the ultimate and perfect truth, which, strangely, is very different depending on where it is proclaimed to be such, in a mosque, church, synagogue or any of the multitude of various temples and shrines. ARE THE MAGISTERIA INDEED NONOVERLAPPING? The late biologist Stephen Jay Gould, known equally as a staunch defender of the evolution theory and as an iconoclast in its interpretation, published in 1997 an article [19] (reprinted in 2001 [20] ) titled “Nonoverlapping Magisteria.” The term magisterium, used by the Catholic Church to denote the teaching authority of the Church, stems from the Latin word “magister” meaning “teacher.” Brilliantly written, as most of Gould’s essays were, this article had gained a considerable popularity. Gould’s main idea is that the two “magisteria,” that of religion and that of science, have both legitimate areas of reign and have no reason to overlap and even less to engage in a war. Regarding the conflict between religion and science Gould wrote, “No such conflict should exist because each subject has a legitimate magisterium, or domain of teaching authority – and these magisteria do not overlap…” It is easy to see that Gould’s position has nothing in common with the attempts to reconcile the biblical story with scientific data which are practiced by scores of religious authors (see, for example [10, 11,12,13,14,15]). The goal of the listed writers is to interpret non-literally the biblical story in order to show that its contradictions with science are illusory and disappear if only the Bible (mainly the book of Genesis) is properly understood in some allegorical way. Gould’s thesis is principally different. He is not in the business of reconciling the story told in Genesis with the data from astronomy, physics, and biology. However, although Gould himself claimed to be an agnostic, his position, as expressed in the quoted article, seems to be close to that succinctly expressed by a quotation often attributed to Galileo, “Science tells us how the heavens go, and the Bible tells us how to go to the Heavens.” As befits a brilliant but contradictory man who combined one of the best defenses for the evolution theory with a rather strong attack on some of its commonly accepted parts, Gould wrote, just a few paragraphs later, “… in fact, the two magisteria bump right up against each other, interdigitating in wondrously complex ways along their joint border. Many of our deeper question", "text_length": 20000, "text_sha256": "468bca42b70a24d42d99347eda076d99cc532c0e656b35307e2851bf84388137" }, { "route": "/faqs/CSICOP.html", "title": "Wesley at CSICOP", "description": "ID advocacy at the 4th annual World of Skeptics Conference On June 21st, 2002, \"Intelligent Design\" advocates squared off against representatives of evolution at the 4th annual World of Sk", "content_kind": "article", "text": "Legacy route: /faqs/CSICOP.html Wesley at CSICOP ID advocacy at the 4th annual World of Skeptics Conference On June 21st, 2002, \"Intelligent Design\" advocates squared off against representatives of evolution at the 4th annual World of Skeptics Conference in Burbank, CA. The event was organized by the Committee for the Scientific Investigation of Claims of the Paranormal (CSICOP). The two ID advocates were William Dembski and Paul Nelson of the Discovery Institute, a Seattle-based think tank that promotes the teaching of intelligent design. Representing evolution were Ken Miller and Wesley Elsberry. Here, Wesley shares his comments on the day's events. Massimo Pigliucci moderated this session from 9AM to noon on Friday, June 21st. The evolution team, Ken Miller and myself, won the coin toss. We decided to present first and third, with me taking the first position. Massimo gave an overview of the history of intelligent design, starting with Plato and bringing the audience up through Paley to the modern ID movement. There were a couple of minor problems in his otherwise excellent talk. Knowing that Paul Nelson's abstract made the claim that ID advocates were useful in keeping \"their mainstream rivals honest\", I made a note of these. It was then my turn at the podium. My initial nervousness was not helped by problems with the microphone. However, once I got started, things fell into place. I pointed out that scientists made a habit of correcting each other, and thus noted that Massimo had an incorrect date for Paley's publication of \"Natural Theology\" and that the figures he showed of the \"flagellum\" were actually of the eukaryote cilium. This gave a positive example of ID's \"mainstream rivals\" keeping each other honest. I then proceeded with my set talk. It seemed to go over well with the audience. I have a preliminary version online here , which I will update with more of the quoted material and links to sources as I get time. Paul Nelson then gave his talk. He didn't follow his abstract. Instead, he talked about naturalism and how adherence to naturalism prevented one from finding \"intelligent design\" in biology even if ID were true. Kind of a \"Give ID a chance\" talk. Ken Miller went next. Ken proceeded to work over Behe's \"irreducible complexity\" and Dembski's \"specified complexity\" with biological examples. For Behe and Dembski's use of the E. coli flagellum, Ken pointed out that parts of the flagellum had functional significance, as demonstrated by Type 3 Secretory Systems, and at least four other functional subsets of flagellum anatomy. Ken again showed that the blood-clotting example used by Behe could withstand the removal of a part, as cetaceans lack Factor XII (Hagemann factor) and are still able to clot blood. My favorite part, though, had to be Ken's use of my web calculator to apply Dembski's formula from NFL p.301 to the Krebs citric acid cycle. Ken found by Dembski's calculation that the Krebs cycle has a probability of less than 10 -440 . Ken then showed that biologists have published an evolutionary pathway for the origin of the Krebs cycle. This provides us with a false positive for Dembski's EF/DI. Dembski presented last. His talk was on \"Prospects for skeptics unseating 'intelligent design' in the next 25 years\". Mark Todd, who was in the audience, said that the audience was in a good mood after Ken's talk, but that within seconds Dembski had managed to almost completely alienate the audience. Dembski brought up polls to demonstrate that ID was a popular stance, and that skeptics would have a tough time displacing ID in the public. Dembski did note that this could be considered an argumentum ad populum. Dembski's talk was remarkably content-free. He brought up little of his work on \"specified complexity\". The panel then went into point-counterpoint mode. Paul Nelson led off with a question for Ken Miller, claiming that the paper Ken depended upon for an evolutionary pathway to the Krebs cycle indicated that their work was incomplete, and that there was a \"missing enzyme\". Why didn't Ken make note of this inconvenient fact? I was watching Ken navigate through folders on his Mac laptop as Paul set up his question. Ken asked to come back to the question in another five minutes in order to get some information from his computer. Paul asked another question of Ken concerning negation of logical propositions and \"empirical content\". I bought a little time with a discussion of Nelson's approach to this, such that he had extracted one clause of a logical conjunction for separate examination, and asked him how he justified that. Ken then took up that question, while still prepping for the other one. (Amazingly, none of the panel members - not a one of us - caught the very basic blunder in Paul's setup. As Jan Willem Nienhuys pointed out to me the next day, Nelson had failed to apply de Morgan's law when he distributed the negation over the statement. I spoke to Paul about this later, and he said he'll revisit that to see if he still has an argument left there.) Ken finally got a PDF of the paper in question up, hooked up to display on-screen for the audience, and found the passage that Paul was referring to. The paper did not have the phrase, \"missing enzyme\", but it did say that they assumed the development of an enzyme to alter succinyl CoA. Ken then estimated the size of such an enzyme as about 300 amino acids, and pointed out that Bill Dembski's calculations would show that the probability of such a small protein would be about 10 -40 , well above Dembski's \"universal probability bound\", and thus readily attributable to the action of natural selection. Ken said that for the evolvability of this protein, his authority was none other than Bill Dembski. Another interesting exchange was when I asked Paul Nelson about what science could exclude. Paul had stated in his talk that empirical evidence made a difference to propositions, and that the evidence presented in the \"Skeptical Inquirer\" meant that there obviously were no UFOs in the sense of alien visitations. I asked for Paul's reason why in science classes we should avoid mentioning another conjecture shown to be false by the evidence, that of the age of the earth being less than 10,000 years old. Paul said that there was no reason for science to avoid stating that. While I was satisfied with getting that from Paul, both Paul and Bill then got into a discussion of why I would bring up a question that was irrelevant to \"intelligent design\" and expressing disappointment that the content of their arguments was not being addressed. I responded that a similar question had been posed to Dembski at the AMNH debate in April, and I wanted to see if Nelson was any more responsive than Dembski was. Paul reiterated that he didn't see the relevance of the question. At that point, Massimo stepped in and directed Paul to answer the question of whether Paul personally agreed with the YEC stance on the age of the earth. Paul hemmed and hawed, and Bill objected on the grounds of irrelevance. At this point, there were audible calls from the audience for Paul to answer the question. Paul eventually said that it was well known that he adhered to the YEC view of the age of the earth. Ken said to Paul, \"See, that wasn't so hard.\" Paul said that the only reason to bring it up was to score a rhetorical point, at which point an audience member called out, \"It goes to your credibility.\" Both Paul and Bill denied that. There were various other questions asked. I've bought a copy of the video, so I may add more detail later. Ratings: Ken Miller was the star of the session. If you get a chance to hear Ken talk, make sure to go. Paul Nelson and Massimo Pigliucci gave well-polished presentations. I fear my delivery was marred by my initial nervousness and my relative inexperience, this being my third outing of this sort in the past 5 years. Dembski, though, really failed to connect with the audience at any point.", "text_length": 7995, "text_sha256": "29b5ade653d6e4f45bee58a96263716688af65dea27fd0b6abc7b487619ed114" }, { "route": "/faqs/hunch/IDnotes.html", "title": "Quixotic References", "description": "[1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID move", "content_kind": "article", "text": "Legacy route: /faqs/hunch/IDnotes.html Content source: /cs/qrefs/ Quixotic References [Return to The Quixotic Message ] [1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID movement. Very strange it is then that IDist press releases and newspaper articles keep mentioning the same handful of names over and over again, year after year, particularly Dembksi, Wells, and Behe, as if these guys just happen to be a sample of the thousands who are joining in the movement. (Just for clarity, Behe is the only one out of those three who can fairly be called a scientist.) For numerous examples of IDist/creationist proclamations of imminent success, see The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism by Glenn Morton: \"In recent reading of Dembski and other ID proponents I saw them make a claim which has been made for over 40 years. This claim is one that the young-earthers have been making. The claim is that the theo ry of evolution (or major supporting concepts for it) is increasingly being abandoned by scientists, or is about to fall. This claim has many forms and has been made for over 162 years.\" [2] IDists are very keen to protect their image by claiming that they're not creationists, and that they're not even anti-evolutionists. But then their latest tactic for getting ID into public schools is to \"teach the evidence against evolution\". Consider the crowing that they've done about a poll in Ohio: Darwin Would Love This Debate : \"Which option (\"A\" or \"B\") represents your view? \"A. Biology teachers should teach only Darwin's theory of evolution and the scientific evidence that supports it.\" \"B. Biology teachers should teach Darwin's theory of evolution, but also the scientific evidence against it.\" \"Only 15 percent of adults nationally, according to a 2001 Zogby poll, agree with \"A,\" while 71 percent agree with \"B.\" (Not sure: 14 percent.) \" This is a perfect example of a loaded question, because it makes people think that there actually is evidence against evolution, and if this is true, then how can it be objectionable to teach it? IDists also say that what they want is for \"origins science\", as they call it, to be taught \"objectively\". When they say \"objective\" what they really mean is giving equal weight to ID arguments, as if a truly objective and knowledgeable person would find them legitimate. George Orwell would be proud. In a sense though, they're right about one thing: referring to ID as \"the evidence against evolution\" is somewhat appropriate, since it really is nothing more than a collection of criticisms, albeit bad ones. [3] There is very little consistency in IDist beliefs, even among the prominent leaders of the movement. Michael Behe, for example, accepts an ancient Earth and common descent, but does not believe that natural processes can account for all of evolution. In contrast, Philip Johnson staunchly denies common descent. Paul Nelson, in further contrast, is a young Earth creationist. Obviously, at least two of these people are seriously wrong about one or more major aspects of their beliefs, yet the ID movement does everything it can to downplay these differences. Amazingly, they claim that drawing conclusions about these scientific issues, which are precisely what they've been arguing about all along, is not even relevant! To the best of my knowledge, Behe is the only prominent IDist who unequivocally accepts evolution (although he heaps praise upon those who argue against it). Most of the others can be safely classified as creationists, or they're much too circumspect for anyone to know just what they believe. But don't call them creationists -- they'll go bonkers and accuse you of misrepresentation. In fact, the ID movement gets a lot of rhetorical mileage out of claiming that they're being stereotyped by \"Dogmatic Darwinists\" who are trying to persecute and discredit them by linking them to creationism. But not only is it true that most of them are creationists, it's also true that the ID movement uses essentially the same tactics and has the exact same overriding goals as those of the old-school movement: Religious apologetics and \"cultural renewal\". [4] This is a major part of the \"Wedge strategy\" formulated by Philip Johnson. The idea is to advocate a scientific theory (or more correctly, an objection to an existing theory) by avoiding the details at all costs, thereby allowing numerous mutually exclusive viewpoints to exist under the same \"Big Tent\". The details, according to Johnson, can be worked out later, after the Evil Empire has been defeated. Won't that be fun to watch. The Wedge strategy is purely political. A real scientific movement would vigorously debate the differences held among its members, as do evolutionary biologists. The irony is that it's hard to know just what if anything the IDists are objecting to, because they refuse to go into specifics. This has the added benefit of making them extremely slippery in debate. See this interview with Johnson for more: \"So the question is: \"How to win?\" That's when I began to develop what you now see full-fledged in the \"wedge\" strategy: \"Stick with the most important thing\"-the mechanism and the building up of information. Get the Bible and the Book of Genesis out of the debate because you do not want to raise the so-called Bible-science dichotomy. Phrase the argument in such a way that you can get it heard in the secular academy and in a way that tends to unify the religious dissenters. That means concentrating on, \"Do you need a Creator to do the creating, or can nature do it on its own?\" and refusing to get sidetracked onto other issues, which people are always trying to do. They'll ask, \"What do you think of Noah's flood?\" or something like that. Never bite on such questions because they'll lead you into a trackless wasteland and you'll never get out of it.\" [5] Creationists and neo-creationists absolutely love the argument from authority, presumably because it fits in well with their authoritarian world-view. The irony is that scientific authority is almost universally against them when it comes to evolution. The Discovery Institute has made a big deal about its 100 scientists, even though the statement that they signed does not mention ID, and it's language is largely noncontroversial: Discovery Institute pdf Doubting Darwinism Through Creative License. (NCSE) Compare their list to a poll of Ohio scientists , or a letter opposing ID sent by 80 scientific organizations . The predictable IDist retort is to claim that the scientific community is too biased to judge things fairly, which makes one wonder why they seek scientific authority in the first place. [6] See Becoming a Disciplined Science: Prospects, Pitfalls, and Reality Check for ID by Bill Dembski. This was a keynote speech of his at the 2002 RADIP conference in which he proposes ways for ID to be become a \"disciplined science\". His proposals for \"scientific research\" are nothing more than suggestions on how the ID movement can sharpen its polemical skills: \"Building a design curriculum is educational in the broadest sense. It includes not just textbooks, but everything from research monographs for professors and graduate students to coloring books for preschoolers. [...] \"Do the same names associated with intelligent design keep coming up in print or are we constantly adding new names? Are we fun to be around? Do we have a colorful assortment of characters? Other things being equal, would you rather party with a design theorist or a Darwinist? \"These, then, are my recommendations for turning intelligent design into a disciplined science.\" To answer his question, I would much rather party with a design \"theorist\". Anyone who can do what they do with a straight face has got to be good at telling jokes. :-) [7] Time and time again we're told that evolutionary theory is somehow sorely lacking, but when asked how well ID \"theory\" can stack up to it in terms of explaining the natural world, we're told that ID doesn't have to, because, well, just because. This makes it not only a \"different kind of theory\" than evolution, it makes it different from any scientific theory, past or present. See this ISCID Brainstrorms thread containing posts by Bill Dembski; many other examples could be given: \"You've charged me with moving the goalposts and adjusting the definition of irreducible complexity because I require of evolutionary biologists to \"connect the dots\" in a causally convincing way. The dots here are functional precursors that could conceivably have evolved into the final system of interest. [...] \"As for your example, I'm not going to take the bait. You're asking me to play a game: \"Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.\" ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots.\" [8] Here's an excerpt from The Truth, the Whole Truth, and Nothing but the Truth? by Brian Spitzer, which is a critical review of Philip Johnson's Darwin on Trial : \"It is useless to try to explain science to someone who isn't interested in what the facts have to say. And it's useless to try to learn anything from such people. If they are clever, as Johnson is, they can find a way to claim that almost any fact supports their position. If evolutionists agree on something, it's a dogmatic orthodoxy; if they disagree, they're squabbling about every detail of evolutionary theory. ...\" This tactic is frequently encountered on debate fora as well, though it's probably unintentional most of the time. An ID advocate will pull out a \"maverick\" scientist who takes a different view on things, and then claim that this is somehow evidence of evolutionary theory's deficiency. But why are all of these scientists against ID? Dogmatic orthodoxy, of course... [9] The ID movement's claim that Darwinists are driven by religious and/or ideological motivations is so glaringly hypocritical, it serves as its own parody. The leaders of the movement are very careful to do what they can to downplay their own biases, at least for public mass consumption (they tend to be a bit less coy in front of religious audiences). Here are the two specific examples alluded to: Evolving Banners at the Discovery Institute . (NCSE) The Center's Name Change (C(R)SC) [10] Lest anyone thinks this is an exaggeration, simply check out Bill Dembksi's forward to Discovery Institute Fellow Benjamin Wiker's book, Moral Darwinism: How We Became Hedonists . This article is a masterpiece of hypocrisy, even by Dembski's standards. (And the title of Wiker's book should tell you a thing or two as well.): \"Understanding this movement [Darwinism] is absolutely key to understanding the current culture war. Believers in God often scratch their heads about western culture's continual moral decline. What was unacceptable just a few years ago is today's alternative lifestyle and tomorrow's preferred lifestyle. Abortion, euthanasia, divorce, sexual preference, and drug abuse are just a few of the moral issues that have undergone massive changes in public perception. [...] \"Epicurus's most prominent disciple is without question Charles Darwin. Darwinism is not only the most recent incarnation of Epicurean philosophy but also the most potent formulation of that philosophy to date. Darwinism's significance consists in the purported scientific justification it brings to the Epicurean philosophy. But the science itself is weak and ad hoc. As Wiker shows, Darwinism is essentially a moral and metaphysical crusade that fuels our contemporary moral debates. Furthermore, Wiker argues that the motivation behind Darwinism today is its alternative moral and metaphysical vision rather than the promotion of science. \"Wiker's project has nothing to do with scapegoating Epicurus, Darwin, or anyone else for that matter.\" Sure Dr. Dembski, sure . Blaming the all of the world's problems, real or perceived, on just one scientific theory isn't scapegoating. Nah ... [11] To be fair, disparaging the contradictory philosophies that Darwinian evolution has supposedly spawned has been a long-standing staple of the old-school creationists, and it is far easier to find examples of this coming from them than it is to find it from the neo-creationists. But ID's big tent has welcomed the old-schoolers with open flaps, so the IDists have little right to complain if people have a hard time telling who's who. Furthermore, the type of IDists commonly found in online debate fora, who, unlike the national movement, do not all share a common metaphysical viewpoint, will tend to contradict each other far more often. Thus a far left anarchist type will blame Darwin for contributing to capitalism, while the more common far right types will try to blame Darwin for Communism. Nevertheless, the consequentialist fallacy -- that Darwinism causes \"bad things\" and thus can't be true -- is high on the ID movement's list of propaganda techniques. It's extremely easy to cull such examples from \"regular\" creationists or online debaters, but just to be sporting, I've only provided references from leading members of the ID movement: On Liberalism: Nihilism and the End of Law by Philip Johnson. \"The primary answer is that modernist thinking assumes the validity of Darwinian evolution, which explains the origin of humans and other living systems by an entirely mechanistic process that excludes in principle any role for a Creator. In the word of the neo-Darwinist authority George Gaylord Simpson, the meaning of \"evolution\" is that \"man is the result of a purposeless and natural process that did not have him in mind.\" For modernist intellectuals, belief in evolution in precisely this sense is equated with having a scientific outlook, which is to say, with being a modernist. The price for denying \"science\" is to be excluded from modernist discourse altogether. [...] Greenawalt defends a limited role for religious convictions in a jurisprudential culture whose ruling paradigm, called \"liberalism,\" is roughly identical to what I have been calling modernism. Or Benjamin Wiker's article, Playing Games with Good & Evil: The failure of Darwinism to explain morality : \"Allow me (since we are going to be playing games for rather high stakes) to lay my own cards on the table. I find this sort of talk absurd. Darwinian game theory is not new but simply a rehash of liberal political theory disguised as cutting-edge science. Give it a few vigorous scratches and we find Thomas Hobbes, the very father of modern political liberalism, back to haunt us from the 17th century. Hobbes was also the father of modern materialism, and his political liberalism was rooted in his mechanistic account of nature and human nature.\" On Racism : Not Just in Kansas Anymore by our friend Philip Johnson: \"In short, Congress contemplated that biology classes should explore matters that Darwinists would prefer to ignore, such as criticisms of classic textbook examples like the faked drawings of embryonic similarities, and even the possible role of Darwinian concepts in encouraging the scientific racism embodied in eugenics programs.\" More Johnson: Domesticating Darwin . \"This explanatory project carried some extremely racist implications, however. Because he was determined to establish human continuity with animals, Darwin frequently wrote of 'savages and lower races' as intermediate between animals and civilized people. Thus Degler observes that it was as much Darwin himself as any of the so-called \"social Darwinists\" who set the evolutionary approach to human behavior on a politically unacceptable course. 'Thanks to Darwin's acceptance of the idea of hierarchy among human societies,' he tells us, 'the spread and endurance of a racist form of social Darwinism owes more to Charles Darwin than to Herbert Spencer.' \"Nor is a scientific grounding for racism the only unsavory heritage of nineteenth-century Darwinism. Degler also cites Darwin's theories about the intellectual inferiority of women, and describes how Darwin's cousin, Francis Galton, employed Darwinian logic in favor of an ambitious eugenics program to improve the breed.\" (Note also the charge of sexism.) And then there is this truly deplorable letter by John Calvert (of the Kansas \"ID Network\") to the local paper in response to one written by KCFS (Kansas Citizens for Science) about teaching ID in public schools: What were we fighting against in Bastogne? We were fighting against a Nazi regime that used the philosophy of Naturalism to justify a eugenics program of terrifying proportions. Naturalism is the belief that all phenomena result only from the laws of chemistry and physics and that teleological or design explanations are not valid. Naturalism is not science. It is a belief system. (You can read a reply to Calvert's letter here .) On Capitalism (and other rightist thought): As reported by CBN news : [Philip] Johnson explained, \"Andrew Carnegie, John D. Rockefeller, they loved Darwinism because it said they were right to amass all the money in the world, you know. And if other people didn't have as much money, it was because they were inferiors.\" Richard Weikart, Discovery Institute Fellow, in The Roots of Hitler's Evil . \"Second, since Hitler believed that nothing exists beyond nature, he tried to find his purpose in life in obeying the iron laws of nature. Darwinian biology was especially significant in this regard, as he tried to apply its lessons to politics and society. Darwinism especially forms of it often disparagingly called Social Darwinism today taught him that life is a constant struggle for existence leading to biological progress. Hitler embraced eugenics and racial extermination of allegedly inferior races as means to improve the human species and foster progress.\" H-Ideas archived post by Weikart: \"It is, of course, true that many distorted Darwin's views, but Darwin's own work reflected laissez-faire economic views and propagated racial inequality (he claimed \"savages\" were inferior mentally and morally).\" In fairness, from what little is available from him online, Weikart tends to dispel some common myths about Darwin's link to Social Darwinism, and has himself pointed out that people from completely opposite political viewpoints have tried to find support in Darwinism (much like the Bible, I suppose). Yet he puts more blame on Darwin than traditional scholars, such Robert Bannister, whose 1979 treatise on the subject Weikart calls \"revisionist\" . The next book he has planned, apparently with Discovery Institute backing, is to be titled, From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Devaluing Human Life in Germany . Given the typical style of books published by the DI Fellows, it will be interesting to see how Weikart presents this one. Regardless of its content, you can bet the DI will use it as an ad hominem against evolutionary theory. Ironically, Weikart's published dissertation is titled Socialist Darwinism: Evolution in German Socialist Thought from Marx to Bernstein , which brings us to... Socialism (and other leftist thought): The most infamous of ID writings is known as the Wedge Document , which is the de facto manifesto of the ID movement, having been unintentionally leaked from the Discovery Institute: \"Finally, materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promi", "text_length": 20000, "text_sha256": "ffede92d3874a8c174a3f9ec69f83328695c3ff221699b73125543a05fbf1344" }, { "route": "/faqs/hunch/hunch.html", "title": "\"The Quixotic Message\", or \"No Free Hunch\"", "description": "Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates.", "content_kind": "article", "text": "Legacy route: /faqs/hunch/hunch.html Content source: /cs/quixotic_message/ \"The Quixotic Message\", or \"No Free Hunch\" Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates. by theyeti * [contributed January 22nd, 2003] [Author's note: This collection of contradictions and absurdities was originally composed and posted to the antievolution.org discussion board. It was later decided to put it up on the web so that it can be exposed to a larger audience. This collection is meant to be lighthearted and funny, though it does highlight some serious issues in the ID debate. If this presents a problem for you, then go read something else. Furthermore, at the urging of several readers, I decided to make a references page to document these inconsistencies. It can be reached by clicking on any one of the numbered references below. If you feel that this would detract from the humor, then feel free to skip it. But as Dave Barry would say, I'm not making this up ...] IDists... On Intelligent Design... ID is whatever we say it is, and we don't agree. Greater and greater numbers of scientists are joining the ID movement, which is why we keep referring to the same three year after year. [ 1 ] ID is not creationism, and can be perfectly compatible with evolution. This is why we're asking schools to teach the \"evidence against evolution\".[ 2 ] We're not creationists, except for those of us who are, but the rest of us won't confirm that we're not. But if you call us creationists, we'll complain to no end. [ 3 ] The correct stance on issues like an ancient Earth, the common ancestry of organisms, and natural selection can be worked out later, after we've convinced the public that they should be rejecting at least one of these. [ 4 ] ID is a widely accepted theory in the scientific community. Just last year, over 100 scientists signed a statement which does not support ID, but does say that they are \"skeptical\" of Darwinism. The opinions of tens of thousands of other scientists don't count, because they're all biased. [ 5 ] ID is a program for research into the science of design, nothing more. Part of our research plans are to produce coloring books for preschoolers, and to make ourselves more likeable at parties. [ 6 ] ID is a scientific theory for detecting purpose and teleology in nature. But don't ask us what that purpose is, because that's a religious question that's separate from ID. The Designer could be anything from God to a space alien. But the Raelians, who believe it was a space alien, are being illogical. On Darwinism... Darwinism can't explain the evolution of life in every single detail, therefore it's wrong. But don't ask IDists to explain these things, because that's not the kind of theory ID is. [ 7 ] Mainstream scientists dare not disagree with the monolithic block that is Darwinian orthodoxy. However, here are a number of mainstream scientists who disagree with each other on some issues, which means that they can't agree on anything. [ 8 ] Darwinists are driven by religious and ideological motivations. But since we've removed the picture of God and the phrase \"Cultural Renewal\" from our website, everyone knows this isn't true of us. [ 9 ] Absolutely everything wrong in society is caused by dogmatic Darwinian atheistic materialists. Including stereotyping, demonizing, and scapegoating. [ 10 ] Darwinists are responsible for both socialism and laissez-faire capitalism. Both racism and liberalism. Both feminism and sexism. Both animal research and the animal rights movement. And Commie-Nazism. [ 11 ] On philosophy... Philosophers cannot agree on exactly where the line between science and non-science lies. Therefore, anything can be considered science if we say so. If a living system looks well designed, it's evidence for ID. If it looks poorly designed, that's just because we have no way of knowing what constitutes good and bad design. Afterall, we can't tell that it's bad design because we have no way of knowing what the Designer really intends. But we do know that ID will revolutionize culture, society, and law, according to what the Designer intends. [ 14 ] Methodological naturalism is an unfair rule that keeps us from considering supernatural explanations. But this would mean that detectives couldn't consider an intelligent agent in a person's death, because as we all know, murderers are supernatural. [ 15 ] A good scientific theory like ID should be vague and ambiguous, and refuse to propose any specific details about mechanism or history. Some unspecified being \"designed\" something, somewhere, at some point in time, somehow, is a perfectly good explanation. The argument from design is not a theological argument, because we aren't necessarily talking about God. But any rebuttal of the design argument is theological, because it requires us to say \"God wouldn't do it this way\", and this is not legitimate. [ 16 ] On the Evidence... Since the peppered moth case has been proven problematic, natural selection is disproven. The other 1,582 studies of natural selection in the wild, as well as the numerous laboratory studies, don't count. [ 17 ] And peppered moths don't rest on tree trunks. The actual datasets of moths found in natural positions in the wild, off but also on trunks, are irrelevant because researchers have captured thousands of moths over the years in their moth traps, and not once has a moth in a trap been found on a tree trunk. [ 18 ] Since moths don't rest on tree trunks but instead higher up in the branches, this means that birds can't get to them, because there is a magic barrier preventing birds from visiting tree branches. As demonstrated above, moths don't rest on tree trunks, which means that the photographs showing the contrasting conspicuousness of moths on tree trunks found in textbooks are FRAUDS, FRAUDS, FRAUDS. All the other staged animal photos in textbooks are however unobjectionable. The fact that more inclusive groupings, such as phyla, appeared before more specific groupings, such as genera, is evidence against evolution. Likewise, the fact that Europeans first appeared before Tony Blair is evidence against shared human ancestry. [ 19 ] Evolution can't produce novel information, because any change to an enzyme that increases substrate specificity reduces the reactivity of the enzyme with other compounds, which is a loss of information. Similarly, any change which increases the enzyme's generality is a loss of information because the enzyme has lost some specificity. [ 20 ] Life could not come about by natural means because it has Specified Complexity. Specified Complexity means something that cannot come about by natural means, therefore life must exhibit Specified Complexity. [ 21 ] It was very nice of our loving Designer to design an immune system to protect us from the deadly diseases He designed. The fundamental unity of living things means that there is only one Designer. The extraordinary variation among living things, including their tendency to kill each other, just means that our singular Designer is very creative and whimsical. [ 22 ] Lateral gene transfer, which is a powerful mechanism of evolution, is evidence against evolution. The fact that the laws of the universe are perfect for life is evidence for a Designer. The fact that the laws of the universe can't produce life is evidence for a Designer. [ 23 ] Irreducibly Complex structures require multiple parts. Therefore they can't evolve. If someone demonstrates how a structure that requires multiple parts could have evolved, that just means that it wasn't Irreducibly Complex. IC structures must be molecular systems. Except mousetraps. \"Indirect\" pathways are wildly unlikely and as hard to find as leprechauns, and are therefore only a \"bare\" possibility but not a realistic one and can be safely disregarded, despite the detailed attention paid to them by every major biologist from Darwin to Dawkins. [ 26 ] The ID hypothesis, on the other hand, bears no resemblance to leprechauns. [*] \"theyeti\" is a pseudonym of Steven Reuland. Comments, suggestions, additions, or threats of eternal damnation can be sent to reulansn@musc.edu.", "text_length": 8259, "text_sha256": "a47db70a992c085e29006f6295e921f2c3db1bea9b8ce041fe6f8c345efd106f" }, { "route": "/faqs/icdmyst/ICDmyst.html", "title": "Irreducible Complexity Demystified", "description": "new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity", "content_kind": "article", "text": "Legacy route: /faqs/icdmyst/ICDmyst.html Content source: /cs/ic_demystified/ Irreducible Complexity Demystified Pete Dunkelberg's essay will prove helpful to educators, boards of education, legislators and members of the press who may be wondering about \"Irreducible Complexity\". by Pete Dunkelberg [Posted: 26 April 2003] \"Evolution is cleverer than you are.\" -biologists' proverb Introduction The Argument That Irreducible Complexity Cannot Evolve How Might Irreducible Complexity Evolve? Irreducible Complexity in Nature Venus' Flytrap How to Eat Pentachlorophenol Hemoglobin for the Active Life The Blood Clotting System: is it IC? Swimming Systems The Eukaryote Cilium The Archaeal Flagellum The Bacterial Flagellum IC Cores How Does Irreducible Complexity Get Its Charm? IC, ID, and Creationism Conclusions References Introduction new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity (also denoted IC) has gained prominence as the evidence for the intelligent design (ID) movement, which argues that life is so complicated that it must be the work of an intelligent designer (aka God) rather than the result of evolution. As you may have heard, the ID movement wants this taught in public schools as a new scientific theory. This essay will, I hope, prove helpful to any school teachers, boards of education, legislators and members of the press who may be wondering about it. The argument from IC to ID is simply: IC things cannot evolve If it can't have evolved it must have been designed This article just looks at the first part, the argument that irreducibly complex systems cannot be produced by evolution, either because they just can't evolve, or because their evolution is so improbable that the possibility can be ignored. Let's take a look at the definition of IC, and then see if we can figure out its relation to evolution, and why scientists are so unimpressed. Here is the definition, from page 39 (page numbers refer to Darwin's Black Box unless otherwise noted): \"By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.\" [emphasis in original] IC is now a single defined term. The new definition, not the ordinary meaning of the words, is now our guide. IC refers to an organism doing something (the function) in such a way that the system (that portion of the organism that directly performs the function) has no more parts than are strictly necessary. How do we decide when the term IC applies? Organisms don't come with parts, functions and systems labeled, nor are 'part', 'system' and 'function' technical terms in biology. They are terms of convenience. We might say, for instance, that the function of a leg is to walk, and call legs walking systems. But what are the parts? If we divide a leg into three major parts, removal of any part results in loss of the function. Thus legs are IC. On the other hand, if we count each bone as a part then several parts, even a whole toe, may be removed and we still have a walking system. We will see later that Behe's treatment of cilia and flagella follows this pattern. What about the boundary of the system? This too is up to us. Take the digestive system for example. We may be interested only in the action of acids and enzymes in the stomach, or we may include saliva and chewing, or the lower intestine where some extraction of water and nutrients continues. As a mental exercise, try before reading on to formulate an argument to prove that IC systems cannot evolve. IC is supposed to be the biochemical challenge to evolution, and thus the case when the parts are molecules, usually proteins, is the important case. So of course there may be multiple copies of a part. Losing a part means losing all copies of it, or at least so many that the function is effectively lost. The Argument That Irreducible Complexity Cannot Evolve Behe's argument that IC cannot evolve is central to ID, so it deserves our attention. His method is to divide evolution into what he calls 'direct', which he defines in a special way, and 'indirect' (everything else). He finds that direct evolution of IC is logically impossible, and indirect evolution of IC is too improbable. The argument against 'direct' evolution of IC is contained in this long sentence right after the definition: \"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.\" The last part of the sentence, \"...because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.\" is why we should agree to the rest of the sentence. There are some problems: The first part of the sentence refers to slight changes. Removing a whole part is a major change; this is a major 'disconnect' between the parts of Behe's argument. It is not true that a precursor missing a part must be nonfunctional. It need only lack the function we specified. Even a single protein does something. The actual precursor may have had more parts, not fewer. If the individual parts evolve, the precursor may have had the same number of parts, not yet codependent. We will learn more about this possibility shortly. How can one construct a valid argument that IC cannot be produced directly? ID proponents have not found a way. Yet it's easy (and left as an exercise for the reader) once you realize that a valid argument from definitions requires carefully defining the terms so that the argument becomes a tautology. This may be accomplished by redefining 'direct' or 'IC', or (best, I think) by defining Behe's expression 'be produced' which he uses in place of 'evolve'. A precursor to IC lacking a part can have any functions except the specified one, which brings us to 'indirect' evolution. Consider a cow's tail. So far as I know, the main thing a cow uses its tail for is to swat flies. Did tails originally evolve for this function? Hardly. There were tails before there were flies. Long ago, tails helped early chordates to swim. Going back still farther, some very early animals started to have two distinct ends; one end for food intake (with sense organs for locating food) and the other end for excretions. As a consequence, this back end, and muscular extensions of it, could also be used to help the animal move. This illustrates yet another important facet of evolution: not only single mutations, but even large organs may begin more or less accidentally. It also illustrates that biological functions evolve. Indeed organisms and ecosystems evolve. It may not even make sense to expect a precursor to have had the same function. The long term evolution of most features of life has not been what Behe, or indeed most people, would call direct. And even short term evolution can be indirect in Behe's terms. So it is surprising to read, on page 40, Behe's argument against indirect evolution of IC systems. Here is the crux of it: \"Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously.\" (page 40) He simply asserts that evolution of irreducible complexity by an indirect route is so improbable as to be virtually out of the question, except in simple cases. He makes no special connection between indirect evolution and IC. He offers no evidence. He just asserts that it is too improbable. Actually, a more complex system probably has a long evolutionary history. Since evolution does not aim at anything in advance, the longer the history, the more circuitous it may be. And his very limited meaning of 'direct' renders much indirect that is not circuitous at all. Yet he insists: \"An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.\" (page 39) Here's another exercise: before reading on, try to think of ways that IC systems, including biochemical ones, might evolve after all. How Might Irreducible Complexity Evolve? How might an IC system evolve? One possibility is that in the past, the function may have been done with more parts than are strictly necessary. Then an 'extra' part may be lost, leaving an IC system. Or the parts may become co-adapted to perform even better, but become unable to perform the specified function at all without each other. This brings up another point: the parts themselves evolve. Behe's parts are usually whole proteins or even larger. A protein is made up of hundreds of smaller parts called amino acids, of which twenty different kinds may be used. Evolution usually changes these one by one. Another important fact is that DNA evolves. What difference does this make, compared to saying that proteins evolve? If you think about it, each protein that your body makes is made at just the right time, in just the right place and in just the right amount. These details are also coded in your DNA (with timing and quantity susceptible to outside influences) and so are subject to mutation and evolution. For our purposes we can refer to this as deployment of parts. When a protein is deployed out of its usual context, it may be co-opted for a different function. A fourth noteworthy possibility is that brand new parts are created. This typically comes from gene duplication, which is well known in biology. At first the duplicate genes make the same protein, but these genes may evolve to make slightly different proteins that depend on each other. We can summarize these four possibilities this way: Previously using more parts than necessary for the function. The parts themselves evolve. Deployment of parts (gene regulation) evolves. New parts are created (gene duplication) and may then evolve. The first of these only comes up if we are looking for IC. The others are the major forms of molecular evolution observed by biologists, phrased in terms of parts. They can lead to new protein functions, sometimes slowly and sometimes, especially when parts are redeployed, abruptly. Gene duplication and changes in protein deployment may introduce a new protein 'part' into a system. Then the parts may coevolve to do something better, but in a codependent manner so that all are required, without further change in the number of parts. But what happens in nature? Irreducible Complexity in Nature Can evolution lead to IC or not? It is time to look at living examples and let nature decide. Behe's most famous example is a mousetrap. But since a mousetrap is not alive, it doesn't tell us much about whether or how living IC systems might evolve. How about a flytrap instead? Venus' Flytrap The Venus' flytrap, Dionaea muscipula , is a small flowering plant which grows naturally in acidic wetlands in North and South Carolina. It has a ferocious looking tooth-edged trap for unwary creatures . It traps and digests insects to make up for the lack of nitrogen in the soils of its habitat. Here's how the trap works. When an insect brushes against the trigger hairs in the center, the lobes snap most of the way shut with surprising speed. If a small insect is caught, it may escape between the teeth, and then the trap reopens without fully closing. If a good sized bug is caught it is digested over the next few days as the trap closes the rest of the way. Then the trap reopens. A trap can only be fully closed about 4 times, so it must be used sparingly. Do we have an IC system here? We must specify a function and all the parts needed to carry it out (and no extra parts). The function of interest is trapping insects for food in a manner that brings the plant more benefit than the cost of the trap. The parts are the two lobes, the hinge between the lobes (the midrib of the leaf, which anchors the lobes), the trigger hairs, and spines projecting from the edges of the lobes that make a set of bars as the trap closes. The system is just all these parts, and the trap needs all its parts in order to work. Hence it is an IC system. How might this trap have evolved? I say 'might' have because Venus' flytraps haven't left any fossils that I know of, except a few grains of pollen. Are there any related plants that might provide a clue? Let's look at the well known sundews ( Drosera ). Sundews trap insects using flypaper traps, slowly closing around insects that get stuck. Darwin, whose book Insectivorous Plants ( 2 ) is now available online , made careful observations of these remarkable plants, especially the round leaf sundew D. rotundifolia . As Darwin notes, If a small organic or inorganic object be placed on the glands in the centre of a leaf, these transmit a motor impulse to the marginal tentacles. The nearer ones are first affected and slowly bend towards the centre, and then those farther off, until at last all become closely inflected over the object. This takes place in from one hour to four or five or more hours. [...] Not only the tentacles, but the blade of the leaf often, but by no means always, becomes much incurved, when any strongly exciting substance or fluid is placed on the disc. Drops of milk and of a solution of nitrate of ammonia or soda are particularly apt to produce this effect. The blade is thus converted into a little cup. The manner in which it bends varies greatly. ( 2 , pp 9, 12) Here is D. rotundifolia with a fly; Makoto Honda ( 3 ) shows the action with a faster species, D. intermedia . Recent genetic research confirms that Venus's flytrap and the waterwheel plant Aldrovanda are related and are in the sundew family Droseraceae, and that snap-traps very likely evolved from flypaper traps ( 4 ) as Darwin thought: CONCLUDING REMARKS ON THE DROSERACEAE. The six known genera composing this family have now been described in relation to our present subject, as far as my means have permitted. They all capture insects. This is effected by Drosophyllum, Roridula, and Byblis, solely by the viscid fluid secreted from their glands; by Drosera, through the same means, together with the movements of the tentacles; by Dionaea and Aldrovanda, through the closing of the blades of the leaf. In these two last genera rapid movement makes up for the loss of viscid secretion. [...] The parent form of Dionaea and Aldrovanda seems to have been closely allied to Drosera, and to have had rounded leaves, supported on distinct footstalks, and furnished with tentacles all round the circumference, with other tentacles and sessile glands on the upper surface. ( 2 , pp 355-6, 360). How did the Venus' flytrap avoid the argument that IC can't evolve? In two ways. First, rather than gaining a part, it lost a part - the glue that the sundews use. Even more interestingly, the trap was able to evolve because the parts evolved. The trap started out as a Drosera -like leaf, and the parts of the leaf were progressively changed. This makes a striking contrast with the mousetrap which Behe has repeatedly presented to illustrate why IC cannot evolve. As a manufactured item the mousetrap neatly illustrates his definition, but with its static parts it cannot model evolution. With evolving parts, nature can create a snap-trap after all. The mechanical and manufacturing analogies so influential in Behe's thinking miss the flexibility of living things. How to Eat Pentachlorophenol Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur naturally, that has been used as a wood preservative since the 1930's. It is now recognized as a dangerous pollutant that we need to dispose of. But how? Evolution to the rescue! A few soil bacteria have already worked out a way to break it down and even eat it. And conveniently for us, they do it in an irreducibly complex way. The best known of these bacteria is called Sphingomonas chlorophenolica (also called Sphingobium chlorophenolicum ). The PCP molecule is a six carbon ring with five chlorine atoms and one hydroxyl (OH) group attached. The chlorines and the ring structure are both problems for bacteria. S. chlorophenolica uses three enzymes in succession to break it down, as follows: the first one replaces one chlorine with OH. The resulting compound is toxic, but not quite as bad as PCP itself. The second enzyme is able to act on this compound to replace two chlorines, one after the other, with hydrogen atoms. The resulting compound, while still bad, is much easier to deal with, and the third enzyme is able to break the ring open. At this point, what is left of PCP is well on its way to being food for the bacterium. All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts. In fact the first and third enzymes were used for this. As a result the cell is triggered to produce them in the presence of chlorophenols. The second enzyme (called PcpC) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role. Thanks to this unusual situation PcpC is available when it is needed to help eat PCP. The inefficient regulation of PcpC is evidently the key to the whole process. So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium. It also happens that both PcpC and the first enzyme in the process are now slightly optimized for dealing with PCP; they handle it better than the corresponding enzymes in strains of S. chlorophenolica that use PcpC only in its normal role, but not nearly as well as would be expected for an old, well adapted system. These factors, combined with the fact that PCP is not known to occur naturally, make a strong circumstantial case that this system has evolved very recently. The chemistry and probable evolution of this system are explained in much greater detail in Shelly Copley's article \"Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach\" in Trends in Biochemical Sciences ( 5 ). Hemoglobin for the Active Life Hemoglobin is a wonderful protein that picks up oxygen in our lungs and delivers it to the rest of our cells. Oxygen binds to hemoglobin very quickly in our lungs and stays bound. Then in our tissues oxygen is released very quickly. How does this happen? What we call a hemoglobin molecule is a complex of four hemoglobin chains, or subunits. There are two each of two different chains called alpha and beta hemoglobin. The complex binds reversibly to oxygen, one O 2 molecule per each subunit. It tends not to bind to the first oxygen until the oxygen concentration is fairly high, which is the usual situation in our lungs. Then the complex changes shape so that the next O 2 binds more readily, the third still faster, and the fourth faster yet. Then it holds the oxygen until the surrounding oxygen concentration is quite low, which happens in our tissues. When finally one oxygen is released, the next is released faster and so on. This mechanism for oxygen transport is much more efficient than can be achieved with alpha or beta hemoglobin alone, and allows for our active life style. It takes all four parts to do this; take away part of the complex and it doesn't work ( 6 ). So we have another IC system. Behe discusses hemoglobin briefly (pp 206-207), mai", "text_length": 20000, "text_sha256": "b6044c5e1264138688338b7e1553a08b6b395031fb223c24f65c11caa49fd8f1" }, { "route": "/faqs/theftovertoil/theftovertoil.html", "title": "The advantages of theft over toil: the design inference and arguing from ignorance", "description": "John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few p", "content_kind": "article", "text": "Legacy route: /faqs/theftovertoil/theftovertoil.html Content source: /cs/theft_over_toil/ The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few papers in the peer-reviewed literature that is explicitly about \"intelligent design\". John S. Wilkins 1 , Wesley R. Elsberry 2 Unedited version. Published as: Wilkins, John S, and Wesley R Elsberry. 2001. The advantages of theft over toil: the design inference and arguing from ignorance. Biology and Philosophy 16 (November):711-724. Abstract Intelligent design theorist William Dembski has proposed an \"explanatory filter\" for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design. Keywords Intelligent design, Bayesian inference, natural selection, Darwin, Dembski Sam Spade enters his office to find \"Fingers\" Finagle, a reformed safecracker, standing in front of his open safe holding the priceless artifact the Cretan Sparrow that Spade was looking after for a client. \"Fingers\" insists he did not crack the safe, but merely spun the combination dial a few times idly, and it opened by itself. Spade knows from the promotional literature that came with the safe when he bought it at the Chump end-of-season sale that is has over 10 billion (1010) possible combinations, and that only one of these will open it. Moreover, he knows that the dial must be turned in alternating directions, not - as \"Fingers\" claims he did - in the same direction repeatedly. What does Spade know about this situation? Is the safe open by design, or by accident? William Dembski (1998) thinks he can answer this question definitively. Dembski has proposed an \"explanatory filter\" (EF) which, he claims, enables us to reliably distinguish events that are due to regularities, those that are due to chance, and those that are due to design. Such a filter is needed, he believes, to determine the reason for cases like Spade's safe, the discrimination of signals by the Search for Extra-Terrestrial Intelligence project (SETI) that are due to intelligent senders from those that are caused by ordinary phenomena like quasars, and most critically, whether all or some aspects of the biological world are due to accident or design. In other words, Dembski's filter is a reworking of Paley's design inference (DI) in the forensic manner of identifying the \"guilty parties\". We will argue that Dembski's filter fails to achieve what it is claimed to do, and that were it to be adopted as a scientific heuristic, it would inhibit the course of science from even addressing phenomena that are not currently explicable. Further, the filter is a counsel of epistemic despair, grounded not on the inherent intractability of some classes of phenomena, but on the transient lacunae in current knowledge. Finally, we will argue that design is not the \"default\" explanation when all other explanations have been exhausted, but is another form of causal regularity that may be adduced to explain the probability of an effect being high, and which depends on a set of background theories and knowledge claims about designers. Spade's immediate intuition is that \"Fingers\" has indeed burgled the safe, but Spade is no philosopher and he knows it. He has, however, read The Design Inference by the detective theoretician, Dembski, and so he applies the filter to the case in hand (literally, since he has \"Fingers\" by the collar as he works through the filter on the whiteboard). The EF is represented as a decision chart (p37): HP events are explained as causal regularities. If it is very likely that an event would turn out as it did, then it is explained as a regularity. IP events are events which occur frequently enough to fall within some deviation of a normal distribution, and which are sufficiently explained by being between those extremes. The rolling of a \"snake eyes\" in a dice game is an IP event, as is the once-in-a-million lottery win. SP events come in two flavours: specified and unspecified. Unspecified events of small probability do not call for explication. An array of stones thrown will have some pattern, but there is no need to explain exactly that pattern, unless the specifiable likelihood of a pattern is so small that its attainment calls for some account. If an array of stones spells out a pattern that welcomes travellers to Wales by British Rail, then that requires explanation; to wit, that the stones were placed there by an employee of British Rail, by design. The minuscule probability that a contextually significant message in English would occur by chance is ruled out by the specified complexity of that sentence. This Dembski calls the Law of Small Probabilities - specified events of small probability do not occur by chance. 3 Spade, though not given to deep reflection, nevertheless studied statistics at the Institute of Forensic Studies, and so he wishes to be thorough. He traverses the filter step-by-step. E: the safe door is open. HP? No, the door regularly remains locked without intervention, and \"Fingers\" did not know the combination. IP? No, there is no significant chance that random spinning of the dial would happen on the combination. Even had \"Fingers\" chanced to spin the dial the right directions - an IP event - the chance is one in ten billion (10-10) that he would have happened on the combination. The chance is effectively zero, using the Law of Small Probabilities. SP? Yes, the event has a very small probability. sp/SP? Yes, the prior probabilities are exactly specified in addition to being very small. Conclusion: \"Fingers\" opened the safe by design, not by accident. \"Fingers\" is duly charged and arraigned for burglary. He engages the renowned deep thinking lawyer, Abby Macleal, and she defends him with skill. Before we get to the courtroom scene, however, let us go back in time, over a century, to the musings of a young naturalist. This naturalist - call him Charles - is on a voyage of discovery. He has read his Paley; indeed, he might almost have written out Paley's Evidences with perfect correctness by memory. Although he has not heard of Dembski's filter, he knows the logic: whatever cannot be accounted for by natural law or chance must be the result of design. Young Charles encounters some pattern of the distribution and form of a class of organisms - let us suppose they are tortoises - on an isolated archipelago and the nearest large continent. Each island has a unique tortoise most similar to the autochthon of the neighboring island and the island closest to the continent is most similar to that species. On the basis of the biological theories then current, he knows that there is no known process that can account for this pattern. It is so marked that one can draw a tree diagram from the continental form to the islands, and it will match a diagram showing the similarity of each form to the others. What should Charles rationally infer from this? Let us assume for comparative purposes that Charles is in possession of the filter; he will therefore reason like this: E: Species are distributed such that morphological distance closely matches geographic distance. HP? No, there is no regularity that makes this distribution highly probable. IP? No, the likelihood of such a distribution is extremely low. SP? Yes, it is a very small probability (made even smaller as more variables are taken into account). sp/SP? Yes, the problem is (more or less) specified. Conclusion: The tortoises have the biogeographic distribution and formal distribution they do by design. By Dembski's framework, Rational Charles should have ascribed the tortoises' situation to intelligent agency, and his subsequent research should have been directed to identifying that agency, perhaps by building balsa rafts to test the likelihood that continental sailors might have taken varieties now extinct on the continent and placed them each to an island according to some plan. An even more parsimonious explanation, and one more agreeable to the Rev. Paley's natural theology, might be that a single agent had created them in situ, along a plan of locating similar species adjacent to each other, which has the added virtue of explaining a large number of similar distributions known throughout the world, as Alfred, a later young voyager, was to note. Unfortunately for the progress of rational science, Actual Charles is not rational in this manner. He infers that some unknown process accounts for this distribution as a regularity, instead of inferring design. He irrationally conjectures that all the variants are modified descendants of the continental species, and that the morphological and geographical trees are evidence of a family tree of species evolution; and thus the theory of common descent is born. Charles is, rightly, castigated by his friends for irrationality and lack of scientific rigor. His leap to an unknown process is unwarranted, as is his subsequent search for a mechanism to account for it. Were his ideas to be accepted, perhaps out of fashion or irreligion, science would be put back for more than a century until Dembski came along to put it right. Lest this seem to be a parody of Dembski's views, consider his treatment of the evolution versus creation debate and the origins of life. Dembski (wrongly) conflates the two, treating the origins of life as a test case for the validity of evolutionary theory (it isn't - even if the major groups of living organisms had separate origins, or were created by an agent, their subsequent history could and would have an explanation in terms of \"undesigned\" evolution). Creationists - the actual ones that do reject evolutionary theories in the way that Rational Charles should have in the 1830s - challenge what Dembski putatively does not, that species share common ancestors with their closest relatives and that natural selection accounts for adaptation. As an adjunct to their arguments, they also, along with Dembski, give credence to the \"calculations\" of the probability that prebiotic processes would spontaneously form the building blocks of life (the LIFE event), especially of genetic molecules, that various authors have given. Dembski discusses Stuart Kauffman's (and others') blocking of the design inference (Kauffman 1993, 1995) with the following argument: Premise 1: LIFE has occurred. Premise 2: LIFE is specified. Premise 3: If LIFE is due to chance then LIFE has small probability. Premise 4: Specified events of small probability do not occur by chance (the Law of Small Probabilities). Premise 5: LIFE is not due to a regularity. Premise 6: LIFE is due to regularity, chance, or design (the filter). Conclusion: LIFE is due to design. Of Dawkins' arguments (Dawkins 1986: 139, 145-146) that there is a lot of \"planetary years\" available because there are a very large number of planets in the universe in which LIFE might have occurred and a lot of time available on each, Dembski says \"... because Dawkins never assigns an exact probability to LIFE, he never settles whether LIFE is a high probability event and thus could legitimately be attributed to a regularity\" (p58, italics added). Therefore, he says, we may infer that Dawkins accepts Premise 5! But what Dawkins actually says is that the improbability of life occurring had better not exceed the probability that it arose by chance on any one of the available number of planets on which it might have done. This sets a minimum bound to the probability of life, and Dawkins says that on (then) current knowledge, he doesn't know how probable life is. For all he knows, life is indeed due to a regularity. Kauffman's work on the dynamics of autocatalytic polymer sets supports the notion that the upper bound to the probability of life occurring is very high indeed, and life is to be \"expected\" in appropriate conditions. Dembski's comment? This is a \"commitment\". The implication is that it is a mere belief or act of faith on Kauffman's part. In fact, it is considerably more than that, and the real problem for origins of life researchers is not to find a possible scenario, but to decide which of a growing number of them holds the most promise, or which combination. But Dembski's filter makes it unnecessary to even try. 4 So, let us return now to the courtroom drama in time to hear Abby Macleal rebut prosecutor Pearl E. Mason's case. Abby calls retired Chump engineer Lachlan (Locky) Smith to the stand, and elicits from him the information that the Chump safe Spade owns has an inherent design flaw. If the tumbler is spun five times or more, centrifugal force will cause the lock to spontaneously open. Spade suddenly realizes why he got it so cheap. \"Fingers\" is acquitted, and initiates civil action for mental anguish and loss of reputation. Clearly, the background information has changed the probability assignments. At the time Spade found \"Fingers\" at the open safe, he was in possession of one set of background information, Bi. The probability of the event E requiring explanation led to a design inference. After Smith's testimony, a different set of background information, Bj, comes into play, and so the filter now delivers a \"regularity\" assignment to E. Suppose, though, that Smith had delivered yet another background set, Bk, by testifying that the model in question only actually used two of the five cylinders in the lock. Given that there are 100 possible numbers that might match the successful open state for each cylinder, the probability of a random opening is now 10-4, which is a much higher probability, given the number of Chumps of that model in use in the Naked City (particularly after Chump's massive sell-off of that model to clear the faulty stock). Now the same filter delivers us a chance explanation given Bk. The point is that Dembski's filter is supposed to regulate rational explanation, especially in science, and yet it is highly sensitive to the current state of knowledge. One single difference of information can change the inference from design to regularity to chance. This goes to the claim that Dembski's explanatory filter reliably finds design. Reliability, Dembski tells us, is the property that once an event is found to have the property of \"design\", no further knowledge will cause the event to be considered to have the property of \"regularity\" or \"chance\". What the filter lacks that real-world design inferences already have is a \"Don't know\" decision. If we can say of a problem that it is currently intractable or there is insufficient information to give a regularity or chance explanation now, then the Filter tells us we must ascribe it to design if it is specifiable. But it can be specifiable without the knowledge required to rule out regularity or chance explanations. This is clearly a god of the gaps stance, and it can have only one purpose: to block further investigation into these problems. Supposing we do insert a \"don't-know\" branch: where should it go? There is an ambiguity in Dembski's treatment of his argumentative framework. The Explanatory Filter is written about as if it describes a process of analysis, but Dembski's further argumentation is cast in terms of a first-order logical calculus. In a process, we would come to a \"don't-know\" conclusion after some evaluation of alternatives, but in a logical framework, there is no temporal dependency. We will here ignore the demands of process and concentrate on the logic. As Dembski's filter eliminates hypotheses from high probability to low probability, clearly an inability to assign a probability in the first place makes the decision the first branch point. So if, on Bi, the probability of E is undecidable, that needs to be worked out first: Undecidable probabilities lead us to a blocking of the inference at all. No further inferences can be drawn, and no design is required to explain any event for which there is no assignment. However, even if E is decidable on Bi, that in no way licences the expectation that on Bj or Bk those probabilities will remain fixed. For example, when Dawkins wrote in 1986, the state of knowledge about prebiotic chemical reactions was sparse; the range of possible RNA codes and molecular alternatives was not properly understood. As knowledge has grown, our estimate of the probability that some ribonucleotides, or perhaps ribonucleoproteins, or even polyaminoacids, might enter into protobiotic autocatalytic cycles has become much higher. Some even think that in a geologically short time after the cooling of the earth's surface, with the right conditions (themselves now expected to be of reasonably high probabilities on earth) life is almost certain to arise. Perhaps, then, we need another branching at each decision, leading to \"Don't-know-yet\". As Dembski's probabilities are Bayesian assignments made on the basis of a set of prior knowledge and default hypotheses, this seems to be a perfectly reasonable move. However, it has one glaring problem - it blocks any inferences of design, and that is too much. There are well attested cases of design in the world: we humans do things by design all the time. So an explanatory filter had better not exclude design altogether. How can it be included here? When is a design inference legitimate? The problem with a simple conclusion that something is designed, is its lack of informativeness. If you tell me that skirnobs are designed but nothing else about them, then how much do I actually know about skirnobs? Of a single skirnob, what can I say? Unless I already know a fair bit about the aims and intentions of skirnob designers, nothing is added to my knowledge of skirnobs by saying that it is designed. I do not know if a skirnob is a good skirnob, fulfilling the design criteria for skirnobs, or not. I do not know how typical that skirnob is of skirnobs in general, or what any of the properties of skirnobs are. I may as well say that skirnobs are \"gzorply muffnordled\" 5 , for all it tells me. But if I know the nature of the designer, or of the class of things the designer is a member of, then I know something about skirnobs, and I can make some inductive generalizations to the properties of other skirnobs. The way we find out such things about designers is to observe and interact, and if we can, converse, with them. In this way we can build up a model of the capacities and dispositions of designers. Experience tells me that a modernist architect will use certain materials to certain effect. Lacking any information about modernist architects leaves me none the wiser knowing that an architect is modernist (in contrast to other architects). Once we have such knowledge of designers, though, what we can say about them is that they generate regularities of outcomes. We know, for example, what the function of the Antikythera Device, a clockwork bronze assembly found in an ancient Greek shipwreck, was because we know the kinds of organisms that made it, we know the scientific, religious and navigational interests they had, we know about gears, and we know what they knew about the apparent motions of the heavens. Hence we can infer that the Antikythera Device is an astrolabe, used for open sea navigation by the stars, or a calendrical calculator, or both (de Solla Price 1974). But suppose it was found by interstellar visitors long after humans went extinc", "text_length": 20000, "text_sha256": "6c482496c7d38a25736d159da6e181cd7f1a64e5fb905661fa4117083836cd29" }, { "route": "/cs/welcome/", "title": "Welcome to TalkDesign.org!", "description": "This web site, a sub-site of TalkOrigins.org, is a response to the \"Intelligent Design\" movement of creationism. It is dedicated to:", "content_kind": "drupal_article", "text": "Legacy route: /cs/welcome/ Welcome to TalkDesign.org! This web site, a sub-site of TalkOrigins.org, is a response to the \"Intelligent Design\" movement of creationism. It is dedicated to: Assessing the claims of the Intelligent Design movement from the perspective of mainstream science Addressing the wider political, cultural, philosophical, moral, religious, and educational issues that have inspired the ID movement Providing an archive of materials that critically examine the scientific claims of the ID movement. We feel that the \"Intelligent Design\" arguments require this kind of focused attention due to their widespread use in antievolutionary activity.", "text_length": 663, "text_sha256": "8e09950095777cd044547176192301defa66c5f20a65ae23e5866104a51b4b5a" }, { "route": "/cs/td_faq/", "title": "Introduction to the TalkDesign.org Site", "description": "Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most", "content_kind": "drupal_article", "text": "Legacy route: /cs/td_faq/ Introduction to the TalkDesign.org Site Q. What is the purpose of Talkdesign.org? A. Talkdesign.org was created to provide a one-stop location for responses to the arguments of the Intelligent Design (ID) movement. Many articles critical of ID are scattered around the Web. Talkdesign.org provides links to the best and most up-to-date of these articles, as well as a collection of articles written specifically for this site. It also provides other material relevant to ID, including links to the web sites of ID advocates. Q. Who runs Talkdesign.org? A. Talkdesign.org is run by several volunteers , of a variety of religious and philosophical persuasions, who are all critics of ID and supporters of mainstream evolutionary biology. Talkdesign.org is hosted by the TalkOrigins Archive , a longstanding web site devoted to the the wider creation/evolution controversy. The TalkOrigins Archive Foundation, a Texas 501(c)(3) tax-exempt non-profit organization, provides the support for the TalkOrigins Archive, TalkDesign, the Panda's Thumb, and Antievolution.org. Q. What is Intelligent Design? A. The beliefs of ID advocates vary greatly. But the core beliefs which they all appear to share are the following: (a) The action of an intelligent (presumably conscious) being was involved in the evolution of living organisms. (b) There already exists empirical evidence of this action, sufficient to justify a scientific inference that such action occurred. The term \"Intelligent Design\" usually refers to these beliefs together with the arguments which are made in support of them. It is important to note that people who hold belief (a) but not belief (b) do not generally consider themselves to be advocates of ID, and this web site has no quarrel with such people. It is the claim that there is empirical evidence of design in biology which has provoked a controversy, and which we consider to be false. We argue that this claim is based on pseudoscience, and enjoys the support it does only because it appeals to the religious and/or ideological beliefs of its adherents. Q. What is the Intelligent Design movement? A. The ID movement has grown out of a creationist tradition which argues against evolutionary theory from a religious (usually Christian) standpoint. Although ID advocates often claim that they are only arguing for the existence of a \"designer\", who may or may not be God, all the leading advocates do believe that the designer is God, and frequently accompany their allegedly scientific arguments with discussion of religious issues, especially when addressing religious audiences. In front of other audiences, they downplay the religious aspects of their agenda. Lawyer and creationist Phillip Johnson is usually credited with having founded the Intelligent Design movement, with the avowed intention of overthrowing \"materialist science\", and replacing it with \"theistic science\". This agenda is now being actively pursued by a well-funded body, the Center for Science and Culture (CSC), part of the Discovery Institute, a right-wing think tank funded by conservative Christians . (Until recently, the CSC was known as the Center for the Renewal of Science and Culture; the name change is most likely an attempt to render their ideological adgenda less overt.) The CSC now plays the leading role in the promotion of ID, and its fellows include most of the leading ID advocates: William Dembski, Michael Behe, Jonathan Wells, Stephen Meyer, etc. The goal of their Wedge Strategy is for ID to become \"the dominant perspective in science\" and to \"permeate our religious, cultural, moral and political life\". Realizing that their \"scientific\" arguments have little chance of acceptance within the mainstream scientific community, ID advocates address their arguments primarily to the general public, politicians, philosophers, and other non-scientists. The allegedly scientific material which they produce is full of misleading rhetoric, equivocal terminology, and misrepresentations of the facts. They also produce much material which does not even aspire to be scientific, and which can frankly be best described as propaganda. Q. Do scientists support Intelligent Design? A. ID advocates are very keen to give the impression that they have the support of scientists. It is true that a number of scientists support ID, as indeed there are scientists who support Young Earth Creationism and many other pseudosciences. But they are a tiny number in relation to the total number of scientists, the vast majority of whom support evolutionary theory. In 2001, the Discovery Institute took out advertisements in national newspapers to announce that 100 scientists had signed a statement saying that they were \"skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life.\" The signatories did not say that they supported ID, though some of them certainly do. Compare this with a letter sent to Congress in support of the current teaching of evolution in schools, signed by the presidents of 80 scientific organizations . To put things into perspective, the National Center for Science Education (NCSE), a group which supports the teaching of evolution in public schools, released Project Steve , a spoof on anti-evolutionist lists such as the one by the Discovery Institute mentioned above. Signatories to the list agreed to a statement supporting evolution and rejecting ID, but there’s one catch: all of the signatories are named \"Steve\" or a version thereof. Given that Steves make up approximately 1% of the population, the 300+ signatories (at the time of this writing) indicate that for every scientist agreeing with the Discovery Institute, perhaps as many as a few hundred disagree. Q. Is opposition to Intelligent Design based on naturalism? A. Intelligent Design is rejected by the vast majority of scientists, particularly those in the relevant fields. The proportion of scientists who accept ID is insignificant. To explain away this overwhelming rejection of their arguments by those who are experts in the subject, ID advocates employ an ad hominem argument. They accuse the vast mass of scientists of being too biased by a commitment to \"materialism\" or \"naturalism\" to be able to judge the arguments fairly. This is despite the fact that many of these scientists are themselves theists. It is true that many (though not all) mainstream scientists and philosophers of science argue that science must be committed to a principle of \"methodological naturalism\", which states that only \"natural\" explanations can be allowed in science. Unfortunately, the meaning of the term \"natural\" is unclear. It is often assumed that this would rule out any explanations involving divine action, but it may be that a hypothesis involving divine action could be considered \"natural\" if it was empirically testable. These are murky philosophical waters, and it seems that most scientists simply adopt the principle of methodological naturalism as rule of thumb, based on the more general principle that extraordinary claims require extraordinary evidence. More importantly, good scientific theories contain virtues like testability, parsimony, and explanatory power. ID tends to be lacking these virtues and many others; the \"naturalism\" claim is often a cover for the fact that ID has a difficult time meeting basic scientific criteria. In any case, ID advocates assure us that their arguments do not imply a divine designer. The designer could have been an extraterrestrial alien. Methodological naturalism certainly does not rule out such a designer. Confusion over this issue has been caused by the ambiguity of the word \"natural\", which can mean either \"not artificial\" or \"not supernatural\" (in addition to other possible meanings). ID advocates frequently conflate these definitions for rhetorical purposes. This issue is explored in greater detail in Mark Issak’s essay, A Philosophical Premise of ‘Naturalism’? Q. Is Intelligent Design a form of creationism? A. The answer to this question depends partly on what one means by \"creationism\". At one end of the spectrum, creationism can be simply the belief that the Universe was created by God, a belief which is probably shared by all monotheists. At the other end, it can be Young Earth Creationism, the belief that the Genesis account of creation is literally true and that the scientific evidence supports this belief. A reasonable intermediate definition is the belief that individual species or \"kinds\" of animals were divinely created. The core ID belief does not strictly entail divine involvement in the origin of species, but all the leading ID advocates believe in such involvement. Many (perhaps most) also deny common descent, the continuity of descent from parent to offspring from the earliest organisms down to the present day. Much of the CSC's material attacks common descent. Deniers of common descent include Phillip Johnson and Jonathan Wells. Dembski is ambivalent on the subject, attempting to cast doubt on common descent without actually denying it. At least one fellow of the CSC, Paul Nelson, is a Young Earth Creationist. Part of the strategy of ID is to create a \"big tent\", in which all opponents of evolutionary theory can join forces, from the most extreme Young Earth Creationists to those, such as Michael Behe, who accept virtually all of evolutionary theory except the proposition that evolution was fully natural. In order to maintain the unity of this big tent, those towards the latter end of the spectrum are careful to avoid criticizing even the most egregious arguments of the Young Earth Creationists. Furthermore, many of the ID arguments and tactics are very similar to those of Young Earth or Old Earth Creationists. Irrelevant appeals to information theory and thermodynamics; bogus probability calculations based on purely random combinations of proteins; gaps in the fossil record; use of out-of-context quotations; all of these and others are staples of the creationist menu. A major distinguishing feature of ID is the attempt to shift the focus of the debate away from the details of Earth history and towards more abstract concepts such as \"design\" or \"teleology\", terms which are rarely used in a non-question-begging manner. Unlike Young Earth Creationism, which is very easy to falsify, ID is difficult or impossible to test according to standard scientific practice. This gives the ID movement a tactical advantage by allowing its adherents to argue from a position that holds no testable affirmative beliefs, yet allows them to attack almost any aspect of evolutionary theory they think might be vulnerable. Note that this does not make ID a better theory than creationism; many argue that this renders ID even less scientific. It is also clear that much of the motivation for creating an ID movement distinct (to some degree) from the existing creationist movement was to evade the legal restriction (in the U.S.A.) on teaching creationism in public schools. The U.S. Supreme Court has ruled that \"scientific\" creationism is a religious position, and therefore violates the First Amendment's constitutional separation of Church and State. One of the more telling commonalities between the creationist and ID movements is the primary focus on getting their views taught in public schools despite the lack of endorsement from the scientific community. Whether these many connections between ID and creationism justify considering ID to be a form of creationism is ultimately a matter of individual judgment. Many have concluded that they do, and one will sometimes see ID referred to as IDC, or Intelligent Design Creationism. While sometimes frank about the religious and political aspirations of ID, advocates at other times will try to create the impression that ID is a purely scientific issue. Use of the term Intelligent Design Creationism helps to draw attention to the true nature of the movement. Q. Is Intelligent Design a pseudoscience? A. We argue that Intelligent Design is a pseudoscience, like Young Earth Creationism, astrology, Atlantis, and the many other belief systems parading as science which fill the mass media. By pseudoscience, we mean a belief system which is claimed to be based on science, but which is actually based on arguments that are not only flawed, but are so egregiously bad that they do not stand up to any serious open-minded examination. Advocates of pseudoscience are motivated by a dogmatic commitment to their position which renders their minds closed to contrary arguments. Common (though not universal) additional symptoms of pseudoscience include the following: arguments are directed towards an audience of non-scientists; grandiose claims are made, often in fields where the claimant has little expertise ( viz Dembski's claims to new laws of information and thermodynamics); the overwhelming mass of scientists are claimed to be too biased to judge the arguments fairly; arguments are couched in superfluous technical jargon; arguments use poorly defined new technical terms (or old terms given new meanings); technical arguments are outnumbered by rhetoric; excessive use is made of quotations, often from popular books and often out of context. Q. What are the \"scientific\" arguments used to support Intelligent Design? A. The arguments for Intelligent Design are primarily arguments from ignorance, also known as god-of-the-gaps arguments. ID advocates also claim to have positive evidence of ID, in the form of \"specified complexity\" and \"irreducible complexity\", but these arguments turn out to be disguised arguments from ignorance. In addition, ID advocates sometimes make an argument from analogy. A lot of their effort is also devoted to attacking specific aspects of evolutionary theory, rather than giving support to their own ID hypothesis. Q. What is the argument from ignorance, or god-of-the-gaps argument? A. ID advocates point out that the evolution of certain biological structures has not been fully explained by biologists. This is true, and will continue to be true for the foreseeable future, since our knowledge of such structures is highly limited at present. From this, they conclude that those biological structures cannot have an evolutionary explanation, and so must have been designed by an intelligent agent. Although this line of argument can sometimes be seen clearly in their work, more often they disguise the argument with a lot of superfluous and misleading terminology, such as \"irreducible complexity\", \"specified complexity\" and \"information\". Q. What is the argument from analogy? A. The argument from analogy typically runs as follows. Biological systems have some quality in common with man-made machines, e.g. they consist of multiple coordinated parts. Whenever we have directly observed the origin of such a machine, an intelligent being was responsible for designing it. Therefore an intelligent being must have designed biological systems. Here is an example of such an argument: \"In order to reach a conclusion based on an analogy, it is only necessary that the induction flow out of the shared properties: The irreducibly complex Rube Goldberg machine required an intelligent designer to produce it; therefore the irreducibly complex blood-clotting system required a designer also.\" (Michael Behe, \"Darwin's Black Box\", p. 218) Arguments from analogy, a type of inductive argument, are notoriously unreliable. The onus is on the advocate of the argument to make a compelling case for the significance of the shared properties and the insignificance of the divergent properties (or disanalogies). In fact, biological systems are very different from man-made machines in all sorts of ways. The most fundamental difference is that biological organisms, unlike man-made machines, have reproduced themselves over millions of generations with random variation and natural selection. This process is known to result in adaptation, and some degree of adaptation by natural evolution is accepted even by ID advocates. To make an argument from analogy in the face of such a fundamental disanalogy is unreasonable. If we ignore significant disanalogies, as ID advocates do, then it is easy to arrive at absurd conclusions. For example, since it was humans who were responsible for designing the machines of which we have directly observed the origin, should we not infer that biological \"machines\" were designed by humans? Before the first balloon flight of the Montgolfier brothers, we might have inferred that, because all wingless creatures were then unable to fly, human beings would not be able to fly. (At some time in the past scientists might have had good reasons to think that human flight would be impossible, but those reasons would have been based on their current knowledge of physics, not on an absurd argument from analogy.) Q. What is \"irreducible complexity\"? A. The term \"irreducibility complexity\" was introduced by biochemist Michael Behe. ID advocates claim that an irreducibly complex biochemical system cannot (with any reasonable degree of probability) have evolved by natural evolution. Irreducible complexity was originally defined in such a way that it could be detected simply by observing the current state of a system, without any consideration of how it might have evolved (rather like the second sense of specified complexity above): if the removal of any part of a biochemical system would render that system non-functional, then it was considered to be irreducibly complex. Acknowledged problems with this definition have forced Behe and Dembski to propose new definitions, which increasingly require the observer to consider the possibility of evolutionary predecessors in determining whether a system is irreducibly complex. This makes it increasingly difficult to judge whether a system is irreducibly complex or not. However, even if a system is judged irreducibly complex by any of the available definitions, this does not rule out the possibility of an evolutionary origin. The arguments of Behe and Dembski are based on the assumption that a system retains the same function as it evolves. But biological systems often become adapted to new functions as they evolve. Behe divided possible evolutionary pathways into two categories: \"direct\" pathways, which do not involve a change of function, and \"indirect\" pathways\" which do. He then gave an argument against the viability of \"direct\" evolutionary pathways to an irreducibly complex system. He also claimed that the probability of evolution by an indirect pathway was too low for this to be an acceptable explanation. However, this claim was based on nothing more than his own intuition and an argument from ignorance: biologists have not yet provided a detailed account of any such pathway. In fact, biologists have now proposed evolutionary explanations for several of the systems introduced as examples by Behe, such as the immune system , but these will probably not be detailed enough to satisfy Behe or Dembski, who demand a precise account of every step of the pathway. Nevertheless, as these explanations gradually become more detailed, ID advocates increasingly choose to concentrate on just one of Behe's examples, the bacterial flagellum, which is perhaps the least well explained at present. Detailed critiques of Behe's arguments can be found here . See also Irreducible Complexity Demystified . Q. What is \"specified complexity\"? A. ID advocates claim that \"specified complexity\" is a reliable marker of intelligent design. However, they use the term in two quite different senses, which they tend to conflate. The term \"specified complexity\" was coined by biologist Leslie Orgel, as a way of characterizing what it is that distinguishes living organisms from non-living objects. The term was later adopted and used in a similar way by physicist Paul Davies. For these writers, an object is comp", "text_length": 20000, "text_sha256": "e5495d35e986ad347b738fb5e9ee1777ceaf38e5c8665ce0c1a61f8e052867bb" }, { "route": "/cs/change_at_td/", "title": "Change at TalkDesign", "description": "TalkDesign is moving away from static, hand-written HTML pages to a spiffy content management system, Civicspace. The theme, for the moment, is the \"interlaced\" theme. We hope that with the change in system, more of the TalkDesign crew will", "content_kind": "drupal_article", "text": "Legacy route: /cs/change_at_td/ Change at TalkDesign TalkDesign is moving away from static, hand-written HTML pages to a spiffy content management system, Civicspace. The theme, for the moment, is the \"interlaced\" theme. We hope that with the change in system, more of the TalkDesign crew will participate in expanding the content here on the system. While much of this will be articles from the Panda's Thumb weblog, the advantage here will be the ability to organize that content topically. You can see that already in the \"Articles\" navigation on the sidebar, with our various articles now conveniently tagged for various categories for content and personalities in the \"intelligent design\" movement. Civicspace also provides for grassroots organization. If you want to help promote good science education, please take the time to enter your contact information. Consider registering as a user here as well.", "text_length": 910, "text_sha256": "721422ea217422d31f82de6d177f72bd79c81980e3fbf1c94dd1ec9c5ce8c281" }, { "route": "/cs/bottaro_wnye_uml_letter/", "title": "Bottaro's Letter to WNYE", "description": "Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life .", "content_kind": "drupal_article", "text": "Legacy route: /cs/bottaro_wnye_uml_letter/ Bottaro's Letter to WNYE Andrea Bottaro wrote a letter to TV station WNYE about their scheduling of the \"intelligent design\" propaganda film, Unlocking the Mystery of Life . by Andrea Bottaro The following letter was originally sent to the WNYE PBS station in anticipation of their programmed broadcast of the Intelligent Design \"documentary\" \"Unlocking the Mystery of Life\". Eventually, WNYE aired the program with a disclaimer regarding its contents (see the NCSE site for the text of WNYE's disclaimer and other comments about \"Unlocking\"). Mr. Laing Kandel General Manager WNYE New York Dr. Joe Klein Chancellor Dept. of Education New York Dear Mr. Kandel and Dr. Klein: It was recently announced by the Discovery Institute in Seattle, WA, that the New York Department of Education's WNYE television station is planning to broadcast the documentary video \"Unlocking the Mystery of Life\" (hereafter, UML) on July 6, 2003. While I realize that the purpose of WNYE is to provide its viewers with the broadest and most diverse information from different sources and points of view, there are a few background issues about this video that I believe you and WNYE viewers should be made aware of. UML presents itself as a well-crafted, purely scientific documentary, while it is factually misleading in many respects, and its main purpose is propaganda for a pseudo-scientific movement known as Intelligent Design Creationism. UML has its (strategically concealed) origins close to religious fundamentalist and Creationist circles, and displays a pattern of poor scholarship, including misrepresentation/omission of key scientific evidence. Ultimately, these result in a misleading picture of the facts and of current scientific knowledge, as well as of the ultimate goals of the documentary itself. (More details about these problems are found in the attachment to this letter.) While as a scientist I fully subscribe to the free dissemination of opinions from any source, I think you owe WNYE viewers that such background information is made available to them, so that they may properly judge the documentary's message. Addition of a disclaimer to the broadcast, explaining that the documentary presents a one-sided view of a fringe, pseudo-scientific idea rejected by the overwhelming majority of scientists, and that its main purpose is religious/philosophical in nature, would probably be sufficient to alert your viewers of the true significance of \"Unlocking the Mystery of Life\". Thank you very much for your consideration. Please feel free to contact me if you have further questions or require additional information. Sincerely Andrea Bottaro University of Rochester Medical Center Rochester, NY, 6/30/03 UNLOCKING THE MYSTERY OF LIFE - MORE OMISSIONS THAN FACTS The source: \"Unlocking the Mystery of Life\" is the first and only production of an entity called \"IllustraMedia\". In fact, \"IllustraMedia\" is one and the same with \"Discovery Media Productions\" 1 . Discovery Media is a production company whose previous videos are devoted to evangelical topics, such as \"Heaven and Hell\" and \"The End Times\" 2 . While there is nothing wrong with an evangelical video company producing a science documentary, the fact that to do so it was felt necessary to create a \"shell\" production outfit highlights the aura of ambiguity that pervades the entire enterprise (more examples to follow). Furthermore, the purpose of the video as a propagandistic and religious, rather than scientific/educational tool is underscored by how UML is being publicized within fundamentalist circles. For instance, Mission Frontiers, the Bulletin of the evangelical U.S. Center for World Missions, hails it as \"the most impressive evangelistic tool ever made\" 3 . The contents: As a documentary, UML is a skillful and sophisticated production, showing some well-made computer animations of cellular processes at the molecular level. In discussing such mechanisms, the video claims that the scientific evidence points to insurmountable difficulties for standard evolutionary theory, and supports instead the hypothesis that a superior intelligence directly intervened to create and/or diversify life (hence the name \"Intelligent Design\", or ID, Creationism 4 ). The video discusses such purported evidence and devotes much of its time to the historical origins and philosophical underpinnings of the ID movement. The fundamental question is whether ULM conforms to basic scientific standards of adherence to evidence and facts. In this, it fails at several levels. First of all, throughout the documentary mainstream scientific views, supported by the overwhelming majority of scientists, are not even independently presented. Instead, oversimplified, sometime downright scornful presentations of mainstream scientific theories and hypotheses are provided by supporters of ID (as a counterexample, the recent PBS \"Evolution\" series, though clearly favoring a scientific view, featured the opinions of several prominent representatives of Creationism). In UML, therefore, the viewers are treated to descriptions of scientific evidence and theories that have little connection with what is in fact going on in the science world. For reasons of space, I'll just mention a few examples. The most glaring omission deals with UML's discussion of Origins of Life (OoL) science. The only non ID-based views on OoL discussed in the video are those proposed, in the late '60s, by one of the current ID proponents, Dr. Dean Kenyon. According to UML, those models have been later shown by Kenyon and colleagues to be insufficient to explain key aspects of early molecular and cellular evolution. In fact, most of Kenyon's original views have long been superseded by more thorough, and better empirically supported, scientific hypotheses - indeed, it was those hypotheses and evidence that led to the demise of Kenyon's ideas in scientific circles long before ID Creationism appeared on the scene. Alas, what is arguably the current (and has been for more than a decade now) favored hypothesis about OoL, the so-called \"RNA World\" model, 5 finds no mention whatsoever in UML. This is not surprising, perhaps, since the objections raised in UML by ID proponents to Kenyon's original theory would not stand against this new model. Thus, the viewer is given the false impression that the current scientific choice is between ID Creationism and its outright miraculous Origin of Life, or Dr. Kenyon's outdated 1960's theory. Of course, our understanding of OoL is still very limited, and highly speculative. Nevertheless, it is far more advanced and scientifically solid than the UML parody would want its audience to believe. Other mistakes in UML include an equally superficial, almost mockingly simplified discussion of cooption, a crucial evolutionary mechanism for which in fact significance evidence exists in the biological world. UML's \"experts\" even commit a basic error regarding the role of nucleic acids in the cell, which are presented as uniquely involved in genetic information storage and transfer, while it is now well known that they are directly active in crucial molecular processes functionally comparable to those carried out by protein enzymes - a key piece of evidence in favor of the \"RNA World\" hypothesis mentioned above (and the possible reason why it also went unmentioned). The crucial argument underlying the whole ID philosophy, widely discussed in the video, is the concept of \"irreducibly complex\" systems, and the purported impossibility of conventional evolutionary mechanisms to generate them. Although it was quickly rejected by biologists on theoretical and empirical grounds, 6 \"irreducible complexity\" has remained the main staple of ID Creationism. Ironically, this argument was just recently delivered a fatal blow in the prestigious science journal Nature, where a computer simulation based entirely on evolutionary principles (undirected random mutation and selection) was shown to be able to generate \"irreducibly complex\" outputs 7 . While of course the video cannot be faulted for not predicting the results of future scientific research, this episode serves as a good example of the shaky grounds on which ID reasoning is built. Indeed, not only does scientific evidence continue to accumulate contradicting the ID arguments, but even more damningly, in over 10 years from the onset of the \"movement\", no single scientific result supporting ID has been published in the scientific literature , despite its supporters continuing claims of the existence of such results. Indeed, even the ID advocates' own journal, the electronically published Progress in Complexity, Information and Design, has failed to publish any experimental result supporting ID 8 . In short, despite the appeals by ID advocates to \"let the evidence speak for itself\", there is in fact no positive scientific evidence in support of ID, and on the contrary the theoretical arguments of its advocates are constantly being proven erroneous in the professional literature. To avoid facing this lack of evidence, UML resorts instead to systematic distortions of mainstream science theories and omissions of key ideas and pieces of evidence. The people: The experts interviewed for UML, and ID advocates in general, are fond to present themselves as \"scientists\", often accompanied by the qualifier \"a small but growing number of\". In fact, most ID advocates are not scientists by any meaningful definition of the term, and their numbers (for which \"small\" is an overstatement) are anything but growing. Of the experts who appear in UML, 4 can in fact qualify as bona fide scientists: Michael Behe, Scott Minnich, Dean Kenyon, and Jed Macosko. The first two hold tenured positions in Biochemistry and Microbiology, respectively, at mainstream universities, but despite their own research experience and active labs, as discussed above they have failed to produce any evidence in support of the ideas they so eloquently argue for. Dean Kenyon was scientifically active until the mid-'70s, after which he has not published further in the scientific literature (however, he has since co-authored the notorious Creationist school textbook \"Of Pandas and People\" 9 ). 16 Jed Macosko, whose image is accompanied in UML by the qualifier \"Molecular Biologist, UC Berkeley\", although a Berkeley graduate and former postdoctoral trainee, in fact is not, or has ever been, on the Berkeley faculty, as that title could suggest. Indeed, Dr. Macosko is apparently not even affiliated with UC Berkeley anymore; if he was at the time of interview, he certainly was there as a junior postdoc trainee, hardly an \"expert\" in the field by any standards. Currently, Dr. Macosko is listed on some ID web sites as teaching chemistry at the religious La Sierra University in Riverside, CA 10 , although he does not appear on the faculty list there either 11 . Such \"generous\" use of credentials is not unique in the documentary. One of the leading proponents of ID, William Dembski, is labeled as a \"mathematician - Baylor University\" in UML, although he is affiliated with Baylor's Institute for Faith and Learning, which focuses on theology and philosophy 12 . Indeed, almost the entirety of Dr. Dembski's vast published opus, with the exception of a mathematics paper in 1990, is about various aspects of theology, apologetics and philosophy 13 (Dr. Dembski holds PhDs in Mathematics and Philosophy, and a M.Div. in Theology). Finally, Jonathan Wells, presented as \"biologist\" in UML, does hold a PhD in Developmental Biology from UC Berkeley. By his own words, however, he entered the program not based on any genuine interest in science and biology, but following the direction of the Rev. Sun Myung Moon, with the expressed goal to \"devote his life to destroying Darwinism\" 14 . Not surprisingly, there is no record of Dr. Wells performing any meaningful research work after his training at Berkeley, and he has since entirely dedicated himself to anti-evolutionist propaganda (including the book \"Icons of Evolution\", some editions of which even contained stickers for students to deface biology textbooks 15 ). Thus, the definitions of professional background and academic affiliation used throughout UML are at the very least ambiguous, and clearly result in an inflation of the apparent academic clout and relevant expertise of the participants. In summary, \"Unlocking the Mystery of Life\" is a depiction of a fringe, at best semi-scientific philosophical movement very close, ideologically and organizationally, to religious Creationism. The documentary misrepresents itself, its goals, the existing scientific evidence and its own experts in several significant ways. While it is your prerogative to air the programs that you believe best suit your audience's needs and interests, it is equally important that your viewers be provided with information that may help them put this product's contents and purpose in the appropriate context. This is necessary not only in the spirit of openness and full disclosure, but also to avoid that your broadcast of the documentary appear as an implicit endorsement of this new form of \"stealth\" Creationism by one of the largest Departments of Education in the country. Notes 1. Verifiable by a \"WHOIS\" search for the domain name \"illustramedia.com\": http://www.networksolutions.com/cgi-bin/whois/whois?STRING=illustramedia.com&SearchType=do Accessed 6/30/03 2. http://www.discoverymedia.org/dm_products_page.htm Accessed 6/29/03 3. http://www.missionfrontiers.org/2002/06/PDFs/Unlocking_Mystery.pdf Accessed 6/28/03 4. For an in-depth discussion of ID Creationism, see \"Intelligent Design Creationism and its Critics\", Robert T. Pennock, ed, MIT Press, 2001, ISBN 0-262-16204-0; review in http://www-unix.oit.umass.edu/~cheathwo/Phil100/nytimes.html Accessed 6/30/03 5. http://www.lawrenceroberge.com/RNAWORLD.htm Accessed 6/30/03 http://www.americanscientist.org/template/AssetDetail/assetid/21438?fulltext=true Accessed 6/30/03 6. see for instance several articles by Dr. Ken Miller, Brown University: http://www.millerandlevine.com/km/evol/ Accessed 6/30/03 7. Lenski RE, Ofria C, Pennock RT, Adami C. \"The evolutionary origin of complex features.\" Nature. May 8 2003; 423 (6936):139-44 8. http://www.iscid.org/pcid.php Accessed 6/29/03 9. http://63.74.14.138/page/001/PROD/BOFPA1 , reviewed at the National Association of Biology Teachers web site http://www.nabt.org/sub/evolution/panda1.asp Both accessed 6/30/03. 10. http://www.iscid.org/jed-macosko.php ; http://www.lasierra.edu/ Both accessed 6/30/03 11. http://www.lasierra.edu/resources/phonelists/phonename_m-s.html Accessed 6/30/03 12. http://www3.baylor.edu/IFL/ Accessed 6/28/03 13. http://www.designinference.com/documents/05.02.CV.htm Accessed 6/30/03 14. http://www.tparents.org/library/unification/talks/wells/DARWIN.htm Accessed 6/30/03 15. Links to reviews of Icons of Evolution can be found at the National Center of Science Education's web site http://www.ncseweb.org/resources/articles/9855_reviews_of_icons_of_evolution_10_31_2002.asp Accessed 6/30/03 16. Note added July 8, 2003: After this letter first appeared on the NCSE web site, Dr. Kenyon kindly and quickly informed me that he has in fact one scientific publication later than the mid-'70s: \"A Comparison of Proteinoid and Aldocyanoin Microsystems as Models of the Primordial Protocell\", in Molecular Evolution and Protobiology [K. Matsuno, K. Dose, K. Harada, and D. L. Rohlfing, eds.], pp. 163-188, Plenum Press, 1984. My original statement was based on a search of the main scientific literature databases available: Pubmed, BasicBIOSIS, CSA Biological Sciences, and the Institute for Scientific Information's \"Web of Science\" Science Citation Index. The book article in question does not seem to appear in any of these databases, nor has it apparently ever been referenced by any other later publication also in the database. Nevertheless, for the record, the existence of Dr. Kenyon's 1984 paper should be noted. Addendum, 8/5/03: Dr. Dembski has recently charged that my critique of \"Unlocking the Mystery of Life\" misleads readers. He's wrong: Dembski's Compass .", "text_length": 16250, "text_sha256": "d9cb057c359bd556ceb0917aa5d6eb4eef58ba9fc961d624a75ed76f017e728a" }, { "route": "/cs/dembskis_compass/", "title": "- DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection.", "description": "Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life .", "content_kind": "drupal_article", "text": "Legacy route: /cs/dembskis_compass/ - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by \"intelligent design\" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Andrea Bottaro University of Rochester School of Medicine and Dentistry [Posted: 10 August 2003] Leading Intelligent Design Creationism (IDC) proponent Dr. William Dembski has quoted my recent critique of the video \"Unlocking the Mystery of Life\" 1 in \"The Myths of Darwinism\", the Introduction to his latest edited book \"Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing\" 2 . Unflatteringly, alas, the quote is meant to illustrate a purportedly common misinformation strategy (the \"Myth of Victory Past\") used by \"Darwinists\" to surreptitiously dispatch significant objections. According to Dembski, when a valid criticism to evolutionary theory is leveled, first it is \"dismissed without an adequate response\", and later defined as a \"discredited criticism that was refuted a long time ago\", without an adequate refutation in fact ever being offered. I am fingered by Dembski as an example of how this supposed \"Darwinist\" conspiracy works Here, I wish to specifically address Dembski's charge that I \"misdirected\" readers of my \"Unlocking\" critique, and argue that, in fact, it is Dembski's own compass that must be malfunctioning 3 . 1. Setting off... in the wrong direction After describing the \"Myth of Victory Past\" for his readers, Dembski writes: \"It will help to see how this Darwinist technique of \"passing the buck\" actually plays out in practice. ... Here is what Bottaro says about irreducible complexity: \"The crucial argument ... widely discussed in the video, is the concept of \"irreducibly complex\" systems, and the purported impossibility of conventional evolutionary mechanisms to generate them. Although it was quickly rejected by biologists on theoretical and empirical grounds [ref.#6], \"irreducible complexity\" has remained the main staple of [Intelligent Design] Creationism. Ironically, this argument was just recently delivered a fatal blow in the prestigious science journal Nature, where a computer simulation based entirely on evolutionary principles (undirected random mutation and selection) was shown to be able to generate \"irreducibly complex\" outputs [ref.#7].\" \"This sounds quite impressive and damning until one follows the paper trail. Indeed, what are references #6 and #7 to which Bottaro refers? Reference #6 is to Kenneth Miller's book \"Finding Darwin's God\". Unfortunately, you won't find the promised refutation of irreducible complexity's challenge to Darwinism there. \" 2 Dembski continues with a brief account of some of Miller's counter-arguments in \"Finding Darwin's God\", and references his own book \"No Free Lunch\" as the site of refutation of those arguments. Solemnly, Dembski concludes: \"Reference #6 is therefore an exercise in misdirection.\" 2 Well, actually, it isn't. In fact, quite ironically, Dembski has barely set foot on the \"paper trail\" and he's already lost. His confident statement notwithstanding, my original reference #6 is not to Miller's \"Finding Darwin's God\". It's unclear how Dembski even reached that conclusion, since my reference, in its entirety, reads: \"6. see for instance several articles by Dr. Ken Miller, Brown University: http://www.millerandlevine.com/km/evol/ Accessed 6/30/03\" 1 [emphasis added] As anyone can verify at the click of a mouse, that link leads to Dr. Miller's web site, where more links to a number of articles are found. Here, \"Finding Darwin's God\" is represented by a single excerpt from its concluding chapter, very general in tone and void of any mention of either Behe or irreducible complexity. Oddly enough, Dembski even goes as far as directly quoting Miller from what he says is my own reference, but for the life of me I cannot find that quote on Miller's web page, or any of its side-links. On the other hand, Miller's site does contain several pertinent works, including his original review of \"Darwin's Black Box\" and a few more articles on irreducible complexity and IDC, written both before and after Dembski's \"No Free Lunch\". Dembski ignores the articles I referenced, discusses an arbitrarily chosen quote from \"Finding Darwin's God\" (that I didn't reference), and tells his readers to trust that he already neatly disposed of all these objections in his own book 4 . Without excessively dwelling on this rather straightforward issue, if Dembski wishes to publicly accuse me of \"misdirection\" in my use of references, at the very least he should discuss, and direct his own readers to the references I actually give, rather than others of his own choosing. 2. A detour OK, fine, wrong reference. Perhaps Dembski might still contend that even my real reference does not contain \"the promised refutation of irreducible complexity's challenge to Darwinism\" 2 . Except, that'd be wrong as well. As Dembski's own quote of my writing plainly shows, I never \"promised\" that readers would find some sort of definitive \"refutation of irreducible complexity's challenge to Darwinism\" in my reference #6, as he implies. What I did in fact was to simply refer readers to a source where they could find examples of the theoretical and empirical arguments based on which biologists rejected Behe's irreducible complexity 5 . Of course, it shouldn't surprise anybody that Dembski finds those arguments insufficient - or he wouldn't be today at the top of yet another list of \"Darwinism doubters\". Similarly, however, Dembski himself should perhaps consider the real possibility that biologists, such as myself, still find these same objections quite convincing, and his supposed refutations of them inadequate 6 . For someone like Dembski, who has been engaged in essentially the same argument for almost a decade in the absence of any significant rate of \"conversion\" of his opponents, this shouldn't represent a major revelation. Truthfully, I can't actually tell what point Dembski is ultimately trying to make here. He certainly can't be arguing that biologists did not quickly reject irreducible complexity on several theoretical and empirical grounds, or that some of those grounds are not described in reference #6 (either mine, or his imaginary one). And if this is the case, and my reference accurately reflects what was \"promised\" in the text, then Dembski's claim to the contrary is manifestly unsupported. 3. Walking in circles Next, Dembski goes on to deal with my reference #7. The Lenski paper 7 , he informs us, \"... describes a computer simulation and thus contains no actual biology. ... The validity of this study therefore depends on whether the simulation maps faithfully onto biological reality. Unfortunately, it does not, and the study therefore doesn't prove a thing about real-life biological evolution.\" 2 There are two separate issues here. The first relates again to my alleged \"myth-making\". Clearly, I was not referring here to some old paper which failed to really address the issue in question and/or had since been refuted (the forms of \"Myth of Victory Past\" previously described by Dembski). On the contrary, I was referring to a very recently published paper, which (to my knowledge) had not been formally addressed, let alone refuted, by Dembski or any other prominent ID advocate. Unless in Dembski's eyes I am guilty of misdirection because I did not anticipate a forthcoming refutation, and didn't proactively alert my readers to it, it's hard to understand his objection to this part of my critique and supporting references. Secondly, and more importantly, Dembski's purported refutation of Lenski still has to come. Dembski's entire justification for the dismissal of the Nature paper boils down to his claim that its computer simulation does not \"map faithfully onto biological reality\". Why it doesn't, however, Dembski forgets to tell us, either in Myths or (as far as I know) anywhere else 8 . Until Dembski does so, of course, he can hardly accuse me of misdirection. At most, he can charge me with incompetence, for not seeing the obvious faults he finds in the paper, but then I'd still be in such company as the paper's own authors (as well as Nature's reviewers and editors). If the alternative is to take Dembski's rain check for a future substantial and convincing refutation 9 , I'll gladly stick with the other \"incompetents\" for the time being. 4. Conclusion - Dr. Dembski's compass In \"Myths of Darwinism\", Dr. Dembski levels against me the rather serious accusation that I misled my readers, making me a participant in the pervasive misinformation ploy he alleges \"Darwinists\" routinely engage in. But, Dembski assures, if his readers follow his steps on the \"paper trail\", they can find their way back and safely arrive to their truthful destination. Alas, at the end of the road, it is Dembski himself who appears quite off course, having lost his way, along with a chance for restraint and careful scholarship, while looking for signs of deceit in those 2 fateful references. When the facts are examined, one finds that: quite embarrassingly, in his efforts to prove my \"misdirection\" Dembski seems to have taken the wrong turn himself (intentionally or as a result of plain shoddiness, I can't say), all the way to a reference which is not the one I clearly pointed to; contrary to Dembski's claim, the first of my references leads my readers exactly to the information I said it would; the second reference, Lenski's paper, still seems to represent the fatal blow to \"irreducible complexity\" I said it is, and will remain so as long as Dembski and fellow IDC advocates fail to provide any meaningful rebuttal of its conclusions. In my critique of \"Unlocking the Mystery of Life\", I commented on the tendency of that unfortunate \"documentary\" to create straw-man versions of scientific knowledge to oppose to ID philosophy. Regrettably, in his Introduction to \"Uncommon Dissent\", Dembski appears to have chosen the very same approach to reach his rhetorical goal: he needed a good example of his purported \"Darwinian Myth\", and he simply made one up. Notes 1. \"Unlocking the Mystery of Life - More Omissions Than Facts\", in \"Bottaro's Letter to WNYE\", at the National Center for Science Education web site: http://www.ncseweb.org/resources/articles/2018_bottaro39s_letter_to_wnye_7_8_2003.asp . Accessed 7/29/03. Reproduced here on Talkdesign.org: http://www.talkdesign.org/faqs/bottaroslettertoWNYE.html 2. http://www.designinference.com/documents/2003.07.UncDiss_Intro_Contrib.pdf , pages 12-16. Accessed 7/29/03 3. My primary concern here is to uphold my professional standards, as well as the contents of my \"Unlocking\" critique, against Dembski's misguided accusation. However, substantial criticisms can in fact be raised to Dembski's other claims regarding Miller's and Lenski's work. At the risk of being accused of another round of myth-making, I would refer the reader to the comments by Nic Tamzek and others (see http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3f25217b7174ffff;act=ST;f=2;t=72 , and links therein. Accessed 7/29/03). 4. Paradoxically, Dembski seems here to engage in diversion tactics himself: first, my reference of Miller's site turns into a reference to \"Finding Darwin's God\", then Miller's numerous and complex arguments in that book get distilled into just his 4 counterexamples of \"evolved\" irreducible complexity. Finally, Dembski simply declares he has definitively shown those to be faulty in \"No Free Lunch\" - case closed. In fact, whether he successfully did it or not (arguable, but that's beside the point here), that can hardly be considered a wholesale refutation of \"Finding Darwin's God\", let alone of the many arguments against irreducible complexity raised by biologists I was referring to in my text. 5. For irreducible fans of the controversy, there are luckily many other freely available critiques of irreducible complexity on the web, in addition to Miller's. Among the best are several at www.talkorigins.org and www.talkreason.org (links found here: http://www.talkorigins.org/faqs/behe.html and http://www.talkreason.org/index.cfm?category=0 . I particularly recommend Pete Dunkelberg's recent overview \"IC Demystified\": http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html , and, closer to my own field of expertise, Matt Inlay's discussion of immune system evolution: http://www.talkdesign.org/faqs/Evolving_Immunity.html ). An often entertaining series of exchanges between several ID advocates, including Dembski, and my U of R colleague H. Allen Orr can be found at the Boston Review web site ( http://bostonreview.net/BR21.6/orr.nclk ; http://bostonreview.net/BR22.1/BR22.1.nclk ; http://bostonreview.net/BR27.3/orr.nclk ; http://bostonreview.net/BR27.5/exchange.nclk ). Al sites accessed 7/29/03 6. I suspect this very inability to accept even the possibility of honest disagreement, out of absolute self-assuredness and/or lack of internal critical feed-back, is in fact the origin of some of IDC's recurrent and often bizarre conspiracy theories about \"darwinian censorship\" and the likes, such as Dembski's \"myth\" discussed here. 7. Lenski RE, Ofria C, Pennock RT, Adami C. \"The evolutionary origin of complex features.\" Nature. May 8 2003; 423 (6936):139-44 8. To be fair, Dembski goes on to offer a cursory explanation. The authors, he says, begged the issue of irreducible complexity \"by requiring of their simulation that complex features exhibiting complex functions can always be decomposed into simpler features exhibiting simpler functions... There is no evidence that real-life irreducibly complex biochemical machines can be decomposed this way.\" 2 As pointed out by Tamzek, however, this can't really be Dembski's reason for rejecting Lenski's conclusions, since Dembski himself has previously conceded this very same point: \"That an irreducibly complex system may have subsystems that have functions of their own (functions distinct from that of the original system) is therefore allowed in the definition.\" (from \"Still Spinning Just Fine: A Response to Ken Miller\", http://www.designinference.com/documents/2003.02.Miller_Response.htm . This is actually just one of several Dembski's statements on the same subject, quoted in the previously linked Antievolution.org thread by Tamzek). 9. Cynics could say they almost see a strategy emerging: \"When a valid criticism ... is first proposed, it is dismissed without an adequate response, either on some technicality or with some irrelevancy or by simply being ignored. ... Thereafter, the criticism becomes known as \"that discredited criticism that was refuted a long time ago\".\" 2 But of course, according to Dembski only \"Darwinists\" do that, so I am looking forward to his forthcoming refutation of Lenski's paper.", "text_length": 14919, "text_sha256": "ab0a5d71e7633bff504493b9f431c13baa5268c6b325ffe2447a30e251b89ccd" }, { "route": "/cs/evolving_immunity/", "title": "Evolving Immunity", "description": "Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box .", "content_kind": "drupal_article", "text": "Legacy route: /cs/evolving_immunity/ Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . < A Response to Chapter 6 of Darwin's Black Box by Matt Inlay Version 1.4 [Contributed June 6, 2002; Last Modified July 17, 2002] email author for comments and feedback Introduction Immune systems are generally characterized by their ability to distinguish between self and non-self cells, tissues, or molecules, and to eliminate the non-self (for review see Janeway 2001 ). The mammalian immune system is an incredibly complex and intricate system that can recognize non-self and provide protection from a wide variety of pathogens. While there is a high degree of interconnectivity between its components, the immune system can be loosely divided into two subsystems, the innate and the adaptive immune systems. In general, innate immunity is a non-specific, inducible response to pathogens. It is immediate in action, yet short-lived. On the other hand, the adaptive immune system is much more specific, but takes longer to activate. It also features immunological memory, and can augment itself to respond more quickly and with greater specificity to future infections of similar pathogens. Both systems work together to provide protection against a diverse and rapidly-evolving array of pathogens. While much is known about the evolution of the immune system, the details of its origin remain to be elucidated. The innate immune system is the more ancient of the two systems, with roots deep in the deuterostome branch of the bilaterians, roughly one billion years ago. Conversely, the adaptive immune system appeared more recently and quite suddenly, around 450 million years ago with the emergence of the gnathostomes, more commonly called the jawed vertebrates. Because of its high degree of complexity and interconnectivity, the mammalian immune system has been labeled as \"irreducibly complex\", and its evolution and origin through \"Darwinian\" mechanisms challenged [i] . Michael Behe, in his book Darwin's Black Box ( Behe 1996 ), defines irreducible complexity (IC) as: \"[A] single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.\" (page 39). Unfortunately, each of the terms \"system\", \"well-matched\", \"interacting\", \"parts\", and \"function\" can have multiple meanings, depending on the context, so nonarbitrarily labeling a system as IC is not an easy task. For instance, \"system\" in Behe's definition differs significantly from the same word in the context of \"immune system\". His use of \"system\" refers specifically to biochemical systems. What is the difference? The components, or parts of a biochemical system are molecular in nature, like proteins or complexes of molecules. \"System\" as is used in immune system refers not just to molecules, but to the cells and tissues involved in conferring immunity. The immune system as a whole contains numerous biochemical systems within it. It is important to note this distinction because Behe only addresses biochemical systems as IC. Systems, whether biochemical or not, are often defined according to their function. However, the term \"function\" is also nebulous. The \"function\" of the immune system is rather broad, encompassing any action involved in either immune recognition or response. Even the skin is considered to be part of the immune system. The \"function\" of a biochemical system is much more specific. Here, function refers to a specific biochemical function, such as the formation of a blood-clot, the spinning of a flagellum to produce locomotion, or the synthesis of a biomolecule from a precursor. This type of function usually consists of a series of biochemical reactions. This is important because Behe is trying to make a specific argument about the origin and evolution of IC biochemical systems. Immediately after defining IC, Behe states: \"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.\" Behe is trying to suggest that because of the nature of IC, biochemical systems that possess this quality could not have evolved through random mutation and natural selection, or \"blind-watchmaking\". Essentially, Behe is using IC to disprove evolution. As an alternative, Behe suggests that the only way that IC biochemical systems could have originated is through intelligent intervention. He offers as evidence the fact that all IC systems whose origins are known were designed by intelligent agents, us. There are many problems with Behe's argument. Basically, Behe is saying that because we do not know how an IC system could have evolved, it didn't evolve. This type of argumentation is referred to as an argument from ignorance . The problem with arguments from ignorance is that they make a conclusion based on a lack of knowledge. There is still much we do not know about evolution. What seems like a conundrum right now may be easily resolved in the future. Biology, and science in general, is filled with mysteries and unknowns. The whole point of science is to seek answers to those questions. Secondly, he tries to use arguments against evolution as evidence for intelligent design. Negative arguments against one theory do not necessarily provide evidence for a particular alternative. It would be like trying to show how safe a Honda Civic is by providing evidence that a Toyota Corolla is unsafe. No matter how unsafe the Corolla is, it says nothing about the Civic. Negative argumentation is scientifically useless without an alternative that can be positively tested. These fallacies do not rule out the possibility that Behe has raised an interesting and useful challenge to our current understanding of evolution. However, a closer look reveals he hasn't. In chapter 6 of Darwin's Black Box , entitled \"A Dangerous World\", Behe outlines three IC biochemical systems in the immune system; clonal selection, V(D)J recombination, and the complement cascade. However, in his analysis of each of these systems, Behe makes critical mistakes. For the process of clonal selection, Behe targets the antibody molecules, which have the ability to rearrange their genes, and to switch from a membrane-bound form to a secreted form. Behe assumes that an antibody molecule missing one of these features would be useless. However, there are many examples of proteins that do not undergo rearrangement, but are able to switch forms. Additionally, there is a gene closely related to antibodies which can also undergo rearrangement, but does not switch forms. Behe neglects to mention either of these intermediate-like molecules. Instead, he scrutinizes the process of antibody gene rearrangement as the second IC system. He describes the numerous features of this system and claims there is no pathway through which it could have evolved. However, he assumes that the only selectable function for the genes involved in rearrangement is rearrangement. There are well-studied systems that bear remarkable similarity to V(D)J recombination that have nothing to do with immunity. He fails to recognize the existence of these other systems, nor realizes that most of the components of recombination are already present there. Finally, in his description of the third IC system, Behe mistakenly assigns a single function to the complement pathway. He fails to realize that the complement system has several different functions, and several mechanisms of activation. This would allow for a gradual, stepwise accumulation of parts and functions. In fact, many other groups of organisms possess a complement system that lacks his primary function. According to Behe's definition of irreducible complexity, those systems shouldn't exist. In each case, Behe claims that a lack of articles in the scientific literature provides evidence that these systems could not have evolved. However, there are hundreds to thousands of articles published on these systems. Much was known about the evolution of each of these systems at the time Darwin's Black Box was published. Additionally, much has been learned since then. This article will attempt to summarize the existing knowledge about the origins of these systems, and propose a possible pathway for their evolution through a Darwinian mechanism. It is not necessary to \"prove\" that these systems evolved. Because the essence of his argument is \"how could this have evolved?\", this article merely seeks to provide an answer to that question. One issue that will not be discussed is whether or not these systems are actually irreducibly complex. The term is not very useful to the discussion of origins because of the ambiguities surrounding its definition. In fact, IC as a term has failed to make much of an impression on the scientific community, as a search on the publication database PubMed, fails to turn up any references to \"irreducible complexity\" [ii] . IC system I: Clonal selection The first system Behe describes in chapter 6 is the process of clonal selection, which is how the adaptive immune system detects non-self molecules and initiates a response. This system focuses on a protein called immunoglobulin (Ig), and the complex it is part of, called the B cell receptor complex (BCR). Immunoglobulins, also called antibodies, are Y-shaped proteins that can recognize and bind foreign molecules (Figure 1a,b). They are produced by lymphocytes called B cells, and are initially expressed on the cell surface. In its membrane-bound form, an immunoglobulin molecule binds to two additional proteins, Ig a and Ig b , to form the BCR (Figure 1c). The target of an immunoglobulin is referred to as its antigen (Ag). Antigen can be essentially any molecule, though there is a preference for proteins. Because of the way in which immunoglobulins are produced, the specific antigen that each Ig recognizes is different in each B cell. This occurs through a process of gene rearrangement called V(D)J recombination, which will be explained later. When an unactivated, or naïve, B cell's Ig recognizes its particular antigen, it sends a signal back into the interior of the cell to initiate activation. This signal is transmitted via a series of modifications through a series of \"messenger\" proteins, which ultimately trigger the transcription of a panel of genes involved in B cell activation. In order to become fully activated, further interaction with a second class of lymphocyte, called T cells, is required. Once the B cell is activated it proliferates and differentiates into a plasma cell, and the function of the immunoglobulin changes from recognition to response. The immunoglobulin switches from a membrane-bound form (mIg) to a secreted form (sIg), where it can diffuse throughout the tissues of the host organism and there bind its cognate antigen. The only difference between the two forms is at the very tip of the bottom of the Y shape, which corresponds to the very tail end of the gene. The switch from mIg to sIg production results from a switch between two alternative RNA splicing patterns, such that the terminal coding exon directs either the translation of a membrane-bound or soluble C-terminal domain, respectively (Figure 2). The process of amplifying a particular B cell (or subset of B cells) from amongst billions based on its antigen specificity is called clonal selection (Figure 3). This process allows the immune system to choose from which B cell (or subset of B cells) it will mount an immune response. Additional discussion of the clonal selection system in the context of irreducible complexity can be found in the web article: The Evolution of Improved Fitness (http://www.talkorigins.org/faqs/fitness/) Behe summarizes this first system as a group of 3 components (page 125): membrane-bound form of the antibody messenger secreted form of the antibody Behe has this to say about the evolution of the clonal selection system: \"A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there's no way to tell if it's doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps.\" (Page 125) Switch forms or rearrange? So the question is, could the clonal selection system have evolved? Certainly. One thing to realize is that the immunoglobulins are not the only molecules that can undergo gene rearrangement to produce a diverse set of antigen-receptors. T cell receptors (TCRs) are antigen-receptors quite similar to immunoglobulins. However, TCRs exist only in a membrane-bound form, yet are able to carry out their particular function without the need to leave the cell surface. Their receptors are used only for the detection of foreign antigens, and do not directly mediate an effector response. So even if immunoglobulins would be unable to effectively carry out their job if they were restricted to the membrane-bound form, they could have evolved from a TCR-like gene, which does not require secretion. If that occurred, then the ability to rearrange and the ability to switch forms could evolve in separate steps, with each step offering a selectable advantage. It remains unclear whether a TCR-like gene appeared first or an Ig-like gene. However, it is also possible that the ability to rearrange came after the evolution of the alternative splicing pattern, resulting in the ability to switch. This would require that antigen receptors with a single specificity be effective mediators of immunity. Could this have occurred? Absolutely. There are several families of innate receptors that do not rearrange, called pattern recognition receptors (PRRs) ( Medzhitov and Janeway 1997 ). Bacteria possess many unique and essential surface molecules that are distinct from metazoan surface molecules. For example, organisms ranging from insects to humans bear numerous receptors capable of recognizing the bacterial cell wall component lipopolysaccharide (LPS) ( Fenton and Golenbock 1998 ). Examples include the macrophage scavenger receptor, CD14, and the b 2 -integrins. Binding to these receptors induces a variety of responses, from the release of inflammatory agents to the phagocytosis of the LPS-carrying particle. Some of these receptors are membrane-bound and some are secreted. Interestingly, there are some that can exist in both forms, such as CD14. So here we have examples of receptors that do not rearrange, can be membrane-bound, secreted, or both, and can mount an effective immune response. Recently, a gene was discovered in the silkmoth Hyalophora cecropia whose expression is upregulated upon exposure to LPS ( Sun, Lindstrom et al. 1990 ). The gene product, a protein called hemolin, is secreted into the hemolymph (the invertebrate \"blood\") and can bind to the most toxic region of LPS ( Daffre and Faye 1997 ). This protein is also constitutively expressed in a membrane-bound form on the surface of hemocytes (the invertebrate white blood cell equivalents). Interestingly, the structure of this protein was found to contain 4 Ig domains, and is a member of the Ig superfamily ( Lindstrom-Dinnetz, Sun et al. 1995 ). Ig domains are a type of 3D protein structure first identified in immunoglobulins, consisting of 7 or 8 b -pleated sheets. Additionally, the crystal structure was recently solved and revealed a shape loosely similar to an immunoglobulin arm ( Su, Gastinel et al. 1998 ). However, sequence analysis shows that hemolin most likely does not represent a precursor to immunoglobulins as the type of Ig-domain it possesses (the I-set) is one not found in vertebrates. Hemolin does show similarities both structurally and functionally to cell-adhesion molecules, and also contains some cell-adhesion activity. This dual function, both for immune response and cell-adhesion, suggests that immune molecules arose from cell-adhesion molecule precursors. Hemolin is a clear example of an inducible immune molecule that can exist in both membrane-bound and secreted forms. Immunoglobulin signal transduction When an antibody recognizes an antigen, it sends a signal back into the cell, which \"primes\" the cell for activation. But what is the nature of this signal? How exactly does the binding of antigen, which occurs on the exterior of the cell, induce a signaling cascade on the interior? The answer lies in the branched nature of the immunoglobulin. As previously stated, immunoglobulins are loosely shaped like a Y, with two arms sticking out into the extracellular space, and the bottom embedded into the membrane. Associated with each Ig molecule are the two accessory proteins Ig a and Ig b . These accessory molecules have long cytoplasmic tails, and contain motifs specialized for attracting the type of kinases required to initiate the cascade. These motifs are called ITAMs ( I mmunoreceptor T yrosine-based A ctivation M otifs). These motifs serve as targets for protein tyrosine kinases, which phosphorylate certain tyrosine residues on the ITAMs. Because most antigens have multiple epitopes (i.e. multiple binding sites for antibodies), and because the immunoglobulins have multiple arms, the recognition of an antigen results in a clustering of immunoglobulins in the area of the membrane where the antigen comes in contact with the B cell (Figure 4). This process is often called crosslinking, and is the key to activating the cell. Visually, it resembles a \"hands across America\", where each arm of the Ig is linked to an arm of another Ig, and so on and so on. As more and more Igs cluster around the antigen, a family of kinases, called the src family kinases, which are loosely associated with the cytoplasmic tails of Ig a and Ig b , begin to phosphorylate the ITAMs. Because the src kinases bind to phosphorylated tyrosines, this sets up a positive feedback loop, and more and more src kinases are recruited to the site. The phosphorylated tyrosines also bind another kinase called syk. The newly bound syk kinase begins to phosphorylate and activate other syk molecules, which in turn phosphorylate and activate the next molecule in the signaling cascade, thereby propagating and amplifying the signal. The downstream components of this cascade are also expressed in other cell types, and are considered more general signal transducers. In this way, a general transduction pathway can be co-opted by more specific signal molecules. This leads to the activation of transcription factors (TFs), which then enter the nucleus and initiate the transcription of genes involved in cell proliferation and differentiation. In this particular situation, the B cell becomes \"primed\" for activation by T cells. Most of the \"messengers\", or components of the BCR signaling pathway are homologous to many other signaling pathways present in other tissues and in other organisms. For instance, one of the final components in the pathway is the activation of the transcription factor NF- k B. This transcription factor is used in mul", "text_length": 20000, "text_sha256": "c5fab9bdaf77819b2ffe36720c609685d7e5f34c604a3cfc3aa0e2f2cd6c9f42" }, { "route": "/cs/flagellum_background/", "title": "Background to \"Evolution in (Brownian) space: a model for the origin of the bacterial flagellum\"", "description": "Nick Matzke provides a brief article covering some of the background information needed to understand arguments made about bacterial flagella and Michael Behe's claims of 'irreducible complexity' for that organelle.", "content_kind": "drupal_article", "text": "Legacy route: /cs/flagellum_background/ Background to \"Evolution in (Brownian) space: a model for the origin of the bacterial flagellum\" Nick Matzke provides a brief article covering some of the background information needed to understand arguments made about bacterial flagella and Michael Behe's claims of 'irreducible complexity' for that organelle. Copyright 2003 by N. J. Matzke Version 1.0 (last updated November 10, 2003) Please send comments to: matzke@ATncseweb.org (remove obvious anti-spam modification) Introduction The article \" Evolution in (Brownian) space: a model for the origin of the bacterial flagellum \" is an attempt to put forward a reasonably detailed model for the evolutionary origin of the bacterial flagellum. The flagellum is a complex structure that some bacteria use for swimming, and it has featured prominently in the arguments of the \"Intelligent Design\" movement. The article is long and somewhat technical, and may not be readily accessible to many readers. This page attempts to give readers some background, and recommend some introductory material that will (hopefully) make the full article much more digestible. Suggestions for further improvements along these lines are welcome. Background For some time, advocates of \"Intelligent Design\" (ID) have been promoting Mike Behe's \"irreducible complexity\" argument. Behe argues that biological systems with multiple required components could not have evolved gradually, because intermediates lacking components would be nonfunctional. The argument has been answered in general terms numerous times (see http://www.talkorigins.org/faqs/behe.html for a survey), and detailed treatments of the evolution of specific \"irreducibly complex\" biochemical systems are now available in the case of blood clotting (see Ken Miller's article on the Evolution of Vertebrate Blood Clotting ) and the immune system (see Matt Inlay's very detailed article Evolving Immunity ). However, the ID movement's favorite example of irreducible complexity, the bacterial flagellum, has not received similar treatment. The bacterial flagellum was only discussed briefly in Behe's Darwin's Black Box , but perhaps because of the counterarguments and literature available on the evolution of other systems, the bacterial flagellum soon became the favorite example of irreducible complexity, and has ascended to near-iconic status for the ID movement. Part of the problem with discerning the evolutionary origin of the bacterial flagellum is that the flagellum is billions of years older than Behe's other example IC systems. With blood-clotting and the immune system, homologs of many of the proteins have been well-known for decades. As the phylogeny of multicellular animals is reasonably well understood, the identification of ancestral systems is not too difficult. In bacteria, on the other hand, phylogeny is confused, and for a long time not many homologs of flagellar proteins were known. Only recently have enough homologs of flagellar proteins been identified to make it possible to piece together a reasonable scenario. The question of the origin of the bacterial flagellum has intrigued me for some time, and it always struck me as a topic that \"someone\" should examine in more detail. It seemed clear that more could be said on the topic than \"flagella don't fossilize.\" For awhile I followed debates on the topic, and slowly accumulated relevant literature. With the publication of thorough, up-to-date reviews of flagellum function and assembly by Berg (2003) and Macnab (2003) , I realized that I probably had enough information to give it a try, and made it my extracurricular summer project. It took rather longer than I planned to synthesize the data into an article, but a version is finally done and I think that several of the findings advance our understanding of flagellar origins significantly. Like any scientific model, this one will have some inadequacies. Some of them are due to our basic lack of knowledge: the functions of many flagellar proteins are uncharacterized, the molecular mechanisms of motor function and protein export are vague, and large-scale bacterial phylogeny is unresolved. There may also be some errors attributable to the inexpert nature of the author; formally I have nothing more than an undergraduate background in biochemistry, although I daresay that I've read enough of the relevant literature to at least avoid major errors, and even to correct a few errors in the peer-reviewed literature. As no one has ever really given the topic of flagellar origins the serious treatment it deserves, there is currently no such thing as an expert. If the article is deemed sufficiently provocative, some of this material may eventually find its way into a journal; however, the article is a bit long and unconventional compared to most journal articles, so releasing it first on the web seemed appropriate. Comments, corrections, suggestions for improvement, and suggestions about more formal publication venues are welcome and should be directed to my email (above). Alternatively, you may post comments at the EvoWiki page for Comments on \"Evolution in (Brownian) space\" . Introductory resources As not every reader will be very familiar with the relevant molecular systems and proteins, I have included some background links that should help bring readers up to speed. To have any hope of following the article, readers should read and understand the below material first. Berg's popular article is particularly recommended as a starting point. Flagellum A good short introduction to the three unrelated kinds of \"flagella\" can be found at Wikipedia: flagellum A detailed popular article on the bacterial flagellum by Howard Berg Chapter 15 of Alberts et al. (1994), Molecular Biology of the Cell , 3rd edn. Section 34.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry F 1 F 0 ATP synthetase (also known as ATP synthase or ATPase) Hongyun Wang's webpage on his ATP synthase research Chapter 14 of Alberts et al. (1994), Molecular Biology of the Cell , 3rd edn. Section 18.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry Life in the viscous microscopic world of bacteria Life at Low Reynolds Number by Purcell (1976) Intelligent Design arguments about the flagellum The article is an attempt at a \"straight\" science piece, with no attempt made to address the various tenditious arguments and equivocating definitions of ID proponents. For articles discussing ID arguments about the flagellum specifically, see the articles below by Miller and Musgrave. At some point I may attempt to write an article comparing ID proponents' wild misconceptions about evolutionary models of flagellar origins (e.g., Bill Dembski's use of cake-baking as an analogy for the evolutionary origin of the flagellum) to an actual serious evolutionary model of flagellar origins. For the moment, however, I encourage readers to look up some of the ID proponents' articles on the topic, and to compare them to the proposed model. Relevant links are given below. Behe on the flagellum in Darwin's Black Box (1996) Molecular Machines and Irreducible Complexity at the Access Research Network Dembski on the flagellum: Chapter 5, No Free Lunch (2002) Bracht, The Bacterial Flagellum: A Response to Ursula Goodenough (2002) Mike Gene, Evolving the Bacterial Flagellum Through Mutation and Cooption (2001-2) Rebuttals to ID flagellum arguments Answering the biochemical argument from design , by Kenneth Miller (2003), in: Manson, N. (Ed.), God and design: the teleological argument and modern science , Routledge, London, pp. 292-307. The Flagellum Unspun , by Kenneth Miller (2004), in: Dembski, W., and Ruse, M. (Eds.), Debating Design: from Darwin to DNA , Cambridge University Press, New York. See also Ken Miller's website . Dembski responded to Miller in an online essay Still Spinning Just Fine on his Design Inference website Musgrave, Ian (2004). \"Evolution of the Bacterial Flagellum\", in: Young, M., and Edis, T. (Eds.), Why Intelligent Design Fails: A Scientific Critique of the Neocreationism, forthcoming from Rutgers University Press, Piscataway, N.J.", "text_length": 8152, "text_sha256": "67d9337fa5c08b6a04310413f455e9bcf66c4496c28be57316aaa41058be9faf" }, { "route": "/cs/grist_for_the_ef_mill/", "title": "Grist for the EF mill", "description": "Original: Grist for the EF mill , by Matt Brauer, posted on March 25, 2004 06:36 AM.", "content_kind": "drupal_article", "text": "Legacy route: /cs/grist_for_the_ef_mill/ Grist for the EF mill Original: Grist for the EF mill , by Matt Brauer, posted on March 25, 2004 06:36 AM. Dembski's \"Explanatory Filter\" (EF) claims to be a reliable technique for detecting design. To date, the EF is the only method presented by the \"science\" of ID. How well does it do? Nobody knows. It has been applied precisely once, by Dembski in his book No Free Lunch . And that application was a dismal failure. Before going into the reasons that the EF is a psuedo-algorithm, I'd like to present an example of what Dawkins calls a \"designoid,\" that is, something that appears designed but isn't. A \"false positive\" for the EF, if you will. Objects almost identical to these were dredged from a shallow bay at the bottom of which some think is the remnants of an ancient city. The objects are made of a concrete-like carbonate, and have a single bore-hole down the center. They are about 4 cm in length. The natural questions to ask are: 1. Are the objects designed? 2. How would you apply the EF to determine if they are designed? 3. Are they \"specified\" (whatever that means)? 4. What objective method could one use to determine if they are specified? 5. what other information do you need to apply the EF to these objects? Do you need to know anything of the actual history of their formation? These objects are just the latest in a long line of designoids which would seem to be natural candidates for the EF (other examples include the visibility of solar eclipses, geological formations on Mars and Arctic stone circles.) So far in all cases these questions have been met with stony silence. But then again, Dembski may be doing something right: if there's no way to apply your method, you are guaranteed to have no false positives. (Thanks to Paul Heinrich of the Louisiana Geological Survey. Links to his pages will be posted later, after the design implications of these objects have been pondered awhile.)", "text_length": 1965, "text_sha256": "5a15ffeaee35b3950187c46fd4604e7964b2cd936cff6778716f426ebf660368" }, { "route": "/cs/ic_demystified/", "title": "Irreducible Complexity Demystified", "description": "new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity", "content_kind": "drupal_article", "text": "Legacy route: /cs/ic_demystified/ Irreducible Complexity Demystified Pete Dunkelberg's essay will prove helpful to educators, boards of education, legislators and members of the press who may be wondering about \"Irreducible Complexity\". by Pete Dunkelberg [Posted: 26 April 2003] \"Evolution is cleverer than you are.\" -biologists' proverb Introduction The Argument That Irreducible Complexity Cannot Evolve How Might Irreducible Complexity Evolve? Irreducible Complexity in Nature Venus' Flytrap How to Eat Pentachlorophenol Hemoglobin for the Active Life The Blood Clotting System: is it IC? Swimming Systems The Eukaryote Cilium The Archaeal Flagellum The Bacterial Flagellum IC Cores How Does Irreducible Complexity Get Its Charm? IC, ID, and Creationism Conclusions References Introduction new term, irreducibly complex , (IC) has been introduced into public discussions of evolution. The term was defined by Michael Behe in 1996 in his book Darwin's Black Box: The Biochemical Challenge to Evolution ( 1 ). Irreducible complexity (also denoted IC) has gained prominence as the evidence for the intelligent design (ID) movement, which argues that life is so complicated that it must be the work of an intelligent designer (aka God) rather than the result of evolution. As you may have heard, the ID movement wants this taught in public schools as a new scientific theory. This essay will, I hope, prove helpful to any school teachers, boards of education, legislators and members of the press who may be wondering about it. The argument from IC to ID is simply: IC things cannot evolve If it can't have evolved it must have been designed This article just looks at the first part, the argument that irreducibly complex systems cannot be produced by evolution, either because they just can't evolve, or because their evolution is so improbable that the possibility can be ignored. Let's take a look at the definition of IC, and then see if we can figure out its relation to evolution, and why scientists are so unimpressed. Here is the definition, from page 39 (page numbers refer to Darwin's Black Box unless otherwise noted): \"By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.\" [emphasis in original] IC is now a single defined term. The new definition, not the ordinary meaning of the words, is now our guide. IC refers to an organism doing something (the function) in such a way that the system (that portion of the organism that directly performs the function) has no more parts than are strictly necessary. How do we decide when the term IC applies? Organisms don't come with parts, functions and systems labeled, nor are 'part', 'system' and 'function' technical terms in biology. They are terms of convenience. We might say, for instance, that the function of a leg is to walk, and call legs walking systems. But what are the parts? If we divide a leg into three major parts, removal of any part results in loss of the function. Thus legs are IC. On the other hand, if we count each bone as a part then several parts, even a whole toe, may be removed and we still have a walking system. We will see later that Behe's treatment of cilia and flagella follows this pattern. What about the boundary of the system? This too is up to us. Take the digestive system for example. We may be interested only in the action of acids and enzymes in the stomach, or we may include saliva and chewing, or the lower intestine where some extraction of water and nutrients continues. As a mental exercise, try before reading on to formulate an argument to prove that IC systems cannot evolve. IC is supposed to be the biochemical challenge to evolution, and thus the case when the parts are molecules, usually proteins, is the important case. So of course there may be multiple copies of a part. Losing a part means losing all copies of it, or at least so many that the function is effectively lost. The Argument That Irreducible Complexity Cannot Evolve Behe's argument that IC cannot evolve is central to ID, so it deserves our attention. His method is to divide evolution into what he calls 'direct', which he defines in a special way, and 'indirect' (everything else). He finds that direct evolution of IC is logically impossible, and indirect evolution of IC is too improbable. The argument against 'direct' evolution of IC is contained in this long sentence right after the definition: \"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.\" The last part of the sentence, \"...because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.\" is why we should agree to the rest of the sentence. There are some problems: The first part of the sentence refers to slight changes. Removing a whole part is a major change; this is a major 'disconnect' between the parts of Behe's argument. It is not true that a precursor missing a part must be nonfunctional. It need only lack the function we specified. Even a single protein does something. The actual precursor may have had more parts, not fewer. If the individual parts evolve, the precursor may have had the same number of parts, not yet codependent. We will learn more about this possibility shortly. How can one construct a valid argument that IC cannot be produced directly? ID proponents have not found a way. Yet it's easy (and left as an exercise for the reader) once you realize that a valid argument from definitions requires carefully defining the terms so that the argument becomes a tautology. This may be accomplished by redefining 'direct' or 'IC', or (best, I think) by defining Behe's expression 'be produced' which he uses in place of 'evolve'. A precursor to IC lacking a part can have any functions except the specified one, which brings us to 'indirect' evolution. Consider a cow's tail. So far as I know, the main thing a cow uses its tail for is to swat flies. Did tails originally evolve for this function? Hardly. There were tails before there were flies. Long ago, tails helped early chordates to swim. Going back still farther, some very early animals started to have two distinct ends; one end for food intake (with sense organs for locating food) and the other end for excretions. As a consequence, this back end, and muscular extensions of it, could also be used to help the animal move. This illustrates yet another important facet of evolution: not only single mutations, but even large organs may begin more or less accidentally. It also illustrates that biological functions evolve. Indeed organisms and ecosystems evolve. It may not even make sense to expect a precursor to have had the same function. The long term evolution of most features of life has not been what Behe, or indeed most people, would call direct. And even short term evolution can be indirect in Behe's terms. So it is surprising to read, on page 40, Behe's argument against indirect evolution of IC systems. Here is the crux of it: \"Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously.\" (page 40) He simply asserts that evolution of irreducible complexity by an indirect route is so improbable as to be virtually out of the question, except in simple cases. He makes no special connection between indirect evolution and IC. He offers no evidence. He just asserts that it is too improbable. Actually, a more complex system probably has a long evolutionary history. Since evolution does not aim at anything in advance, the longer the history, the more circuitous it may be. And his very limited meaning of 'direct' renders much indirect that is not circuitous at all. Yet he insists: \"An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.\" (page 39) Here's another exercise: before reading on, try to think of ways that IC systems, including biochemical ones, might evolve after all. How Might Irreducible Complexity Evolve? How might an IC system evolve? One possibility is that in the past, the function may have been done with more parts than are strictly necessary. Then an 'extra' part may be lost, leaving an IC system. Or the parts may become co-adapted to perform even better, but become unable to perform the specified function at all without each other. This brings up another point: the parts themselves evolve. Behe's parts are usually whole proteins or even larger. A protein is made up of hundreds of smaller parts called amino acids, of which twenty different kinds may be used. Evolution usually changes these one by one. Another important fact is that DNA evolves. What difference does this make, compared to saying that proteins evolve? If you think about it, each protein that your body makes is made at just the right time, in just the right place and in just the right amount. These details are also coded in your DNA (with timing and quantity susceptible to outside influences) and so are subject to mutation and evolution. For our purposes we can refer to this as deployment of parts. When a protein is deployed out of its usual context, it may be co-opted for a different function. A fourth noteworthy possibility is that brand new parts are created. This typically comes from gene duplication, which is well known in biology. At first the duplicate genes make the same protein, but these genes may evolve to make slightly different proteins that depend on each other. We can summarize these four possibilities this way: Previously using more parts than necessary for the function. The parts themselves evolve. Deployment of parts (gene regulation) evolves. New parts are created (gene duplication) and may then evolve. The first of these only comes up if we are looking for IC. The others are the major forms of molecular evolution observed by biologists, phrased in terms of parts. They can lead to new protein functions, sometimes slowly and sometimes, especially when parts are redeployed, abruptly. Gene duplication and changes in protein deployment may introduce a new protein 'part' into a system. Then the parts may coevolve to do something better, but in a codependent manner so that all are required, without further change in the number of parts. But what happens in nature? Irreducible Complexity in Nature Can evolution lead to IC or not? It is time to look at living examples and let nature decide. Behe's most famous example is a mousetrap. But since a mousetrap is not alive, it doesn't tell us much about whether or how living IC systems might evolve. How about a flytrap instead? Venus' Flytrap The Venus' flytrap, Dionaea muscipula , is a small flowering plant which grows naturally in acidic wetlands in North and South Carolina. It has a ferocious looking tooth-edged trap for unwary creatures . It traps and digests insects to make up for the lack of nitrogen in the soils of its habitat. Here's how the trap works. When an insect brushes against the trigger hairs in the center, the lobes snap most of the way shut with surprising speed. If a small insect is caught, it may escape between the teeth, and then the trap reopens without fully closing. If a good sized bug is caught it is digested over the next few days as the trap closes the rest of the way. Then the trap reopens. A trap can only be fully closed about 4 times, so it must be used sparingly. Do we have an IC system here? We must specify a function and all the parts needed to carry it out (and no extra parts). The function of interest is trapping insects for food in a manner that brings the plant more benefit than the cost of the trap. The parts are the two lobes, the hinge between the lobes (the midrib of the leaf, which anchors the lobes), the trigger hairs, and spines projecting from the edges of the lobes that make a set of bars as the trap closes. The system is just all these parts, and the trap needs all its parts in order to work. Hence it is an IC system. How might this trap have evolved? I say 'might' have because Venus' flytraps haven't left any fossils that I know of, except a few grains of pollen. Are there any related plants that might provide a clue? Let's look at the well known sundews ( Drosera ). Sundews trap insects using flypaper traps, slowly closing around insects that get stuck. Darwin, whose book Insectivorous Plants ( 2 ) is now available online , made careful observations of these remarkable plants, especially the round leaf sundew D. rotundifolia . As Darwin notes, If a small organic or inorganic object be placed on the glands in the centre of a leaf, these transmit a motor impulse to the marginal tentacles. The nearer ones are first affected and slowly bend towards the centre, and then those farther off, until at last all become closely inflected over the object. This takes place in from one hour to four or five or more hours. [...] Not only the tentacles, but the blade of the leaf often, but by no means always, becomes much incurved, when any strongly exciting substance or fluid is placed on the disc. Drops of milk and of a solution of nitrate of ammonia or soda are particularly apt to produce this effect. The blade is thus converted into a little cup. The manner in which it bends varies greatly. ( 2 , pp 9, 12) Here is D. rotundifolia with a fly; Makoto Honda ( 3 ) shows the action with a faster species, D. intermedia . Recent genetic research confirms that Venus's flytrap and the waterwheel plant Aldrovanda are related and are in the sundew family Droseraceae, and that snap-traps very likely evolved from flypaper traps ( 4 ) as Darwin thought: CONCLUDING REMARKS ON THE DROSERACEAE. The six known genera composing this family have now been described in relation to our present subject, as far as my means have permitted. They all capture insects. This is effected by Drosophyllum, Roridula, and Byblis, solely by the viscid fluid secreted from their glands; by Drosera, through the same means, together with the movements of the tentacles; by Dionaea and Aldrovanda, through the closing of the blades of the leaf. In these two last genera rapid movement makes up for the loss of viscid secretion. [...] The parent form of Dionaea and Aldrovanda seems to have been closely allied to Drosera, and to have had rounded leaves, supported on distinct footstalks, and furnished with tentacles all round the circumference, with other tentacles and sessile glands on the upper surface. ( 2 , pp 355-6, 360). How did the Venus' flytrap avoid the argument that IC can't evolve? In two ways. First, rather than gaining a part, it lost a part - the glue that the sundews use. Even more interestingly, the trap was able to evolve because the parts evolved. The trap started out as a Drosera -like leaf, and the parts of the leaf were progressively changed. This makes a striking contrast with the mousetrap which Behe has repeatedly presented to illustrate why IC cannot evolve. As a manufactured item the mousetrap neatly illustrates his definition, but with its static parts it cannot model evolution. With evolving parts, nature can create a snap-trap after all. The mechanical and manufacturing analogies so influential in Behe's thinking miss the flexibility of living things. How to Eat Pentachlorophenol Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur naturally, that has been used as a wood preservative since the 1930's. It is now recognized as a dangerous pollutant that we need to dispose of. But how? Evolution to the rescue! A few soil bacteria have already worked out a way to break it down and even eat it. And conveniently for us, they do it in an irreducibly complex way. The best known of these bacteria is called Sphingomonas chlorophenolica (also called Sphingobium chlorophenolicum ). The PCP molecule is a six carbon ring with five chlorine atoms and one hydroxyl (OH) group attached. The chlorines and the ring structure are both problems for bacteria. S. chlorophenolica uses three enzymes in succession to break it down, as follows: the first one replaces one chlorine with OH. The resulting compound is toxic, but not quite as bad as PCP itself. The second enzyme is able to act on this compound to replace two chlorines, one after the other, with hydrogen atoms. The resulting compound, while still bad, is much easier to deal with, and the third enzyme is able to break the ring open. At this point, what is left of PCP is well on its way to being food for the bacterium. All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts. In fact the first and third enzymes were used for this. As a result the cell is triggered to produce them in the presence of chlorophenols. The second enzyme (called PcpC) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role. Thanks to this unusual situation PcpC is available when it is needed to help eat PCP. The inefficient regulation of PcpC is evidently the key to the whole process. So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium. It also happens that both PcpC and the first enzyme in the process are now slightly optimized for dealing with PCP; they handle it better than the corresponding enzymes in strains of S. chlorophenolica that use PcpC only in its normal role, but not nearly as well as would be expected for an old, well adapted system. These factors, combined with the fact that PCP is not known to occur naturally, make a strong circumstantial case that this system has evolved very recently. The chemistry and probable evolution of this system are explained in much greater detail in Shelly Copley's article \"Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach\" in Trends in Biochemical Sciences ( 5 ). Hemoglobin for the Active Life Hemoglobin is a wonderful protein that picks up oxygen in our lungs and delivers it to the rest of our cells. Oxygen binds to hemoglobin very quickly in our lungs and stays bound. Then in our tissues oxygen is released very quickly. How does this happen? What we call a hemoglobin molecule is a complex of four hemoglobin chains, or subunits. There are two each of two different chains called alpha and beta hemoglobin. The complex binds reversibly to oxygen, one O 2 molecule per each subunit. It tends not to bind to the first oxygen until the oxygen concentration is fairly high, which is the usual situation in our lungs. Then the complex changes shape so that the next O 2 binds more readily, the third still faster, and the fourth faster yet. Then it holds the oxygen until the surrounding oxygen concentration is quite low, which happens in our tissues. When finally one oxygen is released, the next is released faster and so on. This mechanism for oxygen transport is much more efficient than can be achieved with alpha or beta hemoglobin alone, and allows for our active life style. It takes all four parts to do this; take away part of the complex and it doesn't work ( 6 ). So we have another IC system. Behe discusses hemoglobin briefly (pp 206-207), mainly commenting that it makes a poor case fo", "text_length": 20000, "text_sha256": "fc1022e3a44da9b79e25e504a92d51405dbc8aa9d4585f29232278548f555fdc" }, { "route": "/cs/icon_of_obfuscation/", "title": "Icon of Obfuscation: Jonathan Wells' book Icons of Evolution and why most of what it teaches about evolution is wrong", "description": "Nick Matzke reviews Jonathan Wells's book, Icons of Evolution . Icons of Evolution purports to document that \"students and the public are being systematically misinformed about the evidence for evolution.\" But it is Icons itself that is rea", "content_kind": "drupal_article", "text": "Legacy route: /cs/icon_of_obfuscation/ Icon of Obfuscation: Jonathan Wells' book Icons of Evolution and why most of what it teaches about evolution is wrong Nick Matzke reviews Jonathan Wells's book, Icons of Evolution . Icons of Evolution purports to document that \"students and the public are being systematically misinformed about the evidence for evolution.\" But it is Icons itself that is really misinforming the public. Read the full article (off-site) .", "text_length": 460, "text_sha256": "7af4b39d30eee38ec18f03988c66f9f54fb0ec4c6d75fd00aa1028c54214d34b" }, { "route": "/cs/meyers_hopeless_monster/", "title": "Meyer's Hopeless Monster", "description": "Alan Gishlick, Nick Matzke, and Wesley R. Elsberry critique the paper published by \"intelligent design\" advocate Stephen C. Meyer in Proceedings of the Biological Society of Washington in August, 2004. They conclude that Meyer's review pape", "content_kind": "drupal_article", "text": "Legacy route: /cs/meyers_hopeless_monster/ Meyer's Hopeless Monster Alan Gishlick, Nick Matzke, and Wesley R. Elsberry critique the paper published by \"intelligent design\" advocate Stephen C. Meyer in Proceedings of the Biological Society of Washington in August, 2004. They conclude that Meyer's review paper presents an incomplete, misleading, and false impression of the biological evidence, and that his conclusion that \"intelligent design\" is supported because evolutionary alternatives are eliminated is illegitimate. Posted by Wesley R. Elsberry on August 24, 2004 05:56 PM Review of Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239. by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry [The views and statements expressed here are our own and not necessarily those of NCSE or its supporters.] “Intelligent design” (ID) advocate Stephen C. Meyer has produced a “review article” that folds the various lines of “intelligent design” antievolutionary argumentation into one lump. The article is published in the journal Proceedings of the Biological Society of Washington . We congratulate ID on finally getting an article in a peer-reviewed biology journal, a mere fifteen years after the publication of the 1989 ID textbook Of Pandas and People , a textbook aimed at inserting ID into public schools. It is gratifying to see the ID movement finally attempt to make their case to the only scientifically relevant group, professional biologists. This is therefore the beginning (not the end) of the review process for ID. Perhaps one day the scientific community will be convinced that ID is worthwhile. Only through this route — convincing the scientific community, a route already taken by plate tectonics, endosymbiosis, and other revolutionary scientific ideas — can ID earn a legitimate place in textbooks. Unfortunately, the ID movement will likely ignore the above considerations about how scientific review actually works, and instead trumpet the paper from coast to coast as proving the scientific legitimacy of ID. Therefore, we would like to do our part in the review process by providing a preliminary evaluation of the claims made in Meyer’s paper. Given the scientific stakes, we may assume that Meyer, Program Director of the Discovery Institute ’s Center for Science and Culture , the major organization promoting ID, has put forward the best case that ID has to offer. Discouragingly, it appears that ID’s best case is not very good. We cannot review every problem with Meyer’s article in this initial post, but we would like to highlight some of the most serious mistakes. These include errors in facts and reasoning. Even more seriously, Meyer’s paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature. Summary of the paper Meyer’s paper predictably follows the same pattern that has characterized “intelligent design” since its inception: deny the sufficiency of evolutionary processes to account for life’s history and diversity, then assert that an “intelligent designer” provides a better explanation. Although ID is discussed in the concluding section of the paper, there is no positive account of “intelligent design” presented, just as in all previous work on “intelligent design”. Just as a detective doesn’t have a case against someone without motive, means, and opportunity, ID doesn’t stand a scientific chance without some kind of model of what happened, how, and why. Only a reasonably detailed model could provide explanatory hypotheses that can be empirically tested. “An unknown intelligent designer did something, somewhere, somehow, for no apparent reason” is not a model. Meyer’s paper, therefore, is almost entirely based on negative argument. He focuses upon the Cambrian explosion as an event he thinks that evolutionary biology is unable to account for. Meyer asserts that the Cambrian explosion represented an actual sudden origin of higher taxa; that these taxa (such as phyla) are “real” and not an artifact of human retrospective classification; and that morphological disparity coincides with phyletic categories. Meyer then argues that the origin of these phyla would require dramatic increases in biological “information,” namely new proteins and new genes (and some vaguer forms of “information” at higher levels of biological organization). He argues that genes/proteins are highly “complex” and “specified,” and that therefore the evolutionary origin of new genes is so improbable as to be effectively impossible. Meyer briefly considers and rejects several theories proposed within evolutionary biology that deal with macroevolutionary phenomena. Having rejected these, Meyer argues that ID is a better alternative explanation for the emergence of new taxa in the Cambrian explosion, based solely upon an analogy between “designs” in biology and the designs of human designers observed in everyday experience. The mistakes and omissions in Meyer’s work are many and varied, and often layered on top of each other. Not every aspect of Meyer’s work can be addressed in this initial review, so we have chosen several of Meyer’s major claims to assess. Among these, we will take up the Cambrian explosion and its relation to paleontology and systematics. We will examine Meyer’s negative arguments concerning evolutionary theories and the origin of biological “information” in the form of genes. An expanded critique of this paper is in preparation. Playing with Dynamite: The Cambrian Explosion The Cambrian explosion is a standard topic for antievolutionists. There are several reasons for this: many taxa make their first appearance in the Cambrian explosion; the amount of time within the period of the Cambrian explosion is geologically brief; and we have limited evidence from both within and before the Cambrian explosion on which to base analysis. The first two factors form the basis of an antievolutionary argument that evolutionary processes are insufficient to generate the observed range of diversity within the limited time available. The last factor is a general feature of the sorts of phenomena that antievolutionists prefer: not enough evidence has yet accrued to single out a definitive scientific account, so it is rhetorically easy for a pseudoscientific “alternative” to be offered as a competitor. In Meyer’s closing paragraph, he mentions “experience-based analysis.” The consistent experience of biologists is that when we have sufficient evidence bearing upon some aspect of biological origins, evolutionary theories form the basis of explanation of those phenomena (an example where much evidence has become available recently is the origin of birds and bird flight; see Gishlick 2004). Problems with Meyer’s discussion of the Cambrian Explosion: 1. Meyer tries to evaluate morphological evolution by counting taxa, a totally meaningless endeavor for investigating the evolution of morphology. Most paleontologists gave up taxa-counting long ago and moved on to more useful realms of research regarding the Cambrian (see Budd and Jensen 2000). This is perhaps why most of Meyer’s citations for this section are to his own articles (themselves not in relevant scientific journals). 2. Meyer repeats the claim that there are no transitional fossils for the Cambrian phyla. This is a standard ploy of the Young-Earth Creationists (see Padian and Angielczyk 1999 for extended discussion of this tactic and its problems). Meyer shows a complete lack of understanding of both the fossil record and the transitional morphologies it exhibits (even during the Cambrian explosion; for a recent example of transitional forms in the Cambrian explosion see Shu et al. 2004) as well as the literature he himself cites. (This topic has been dealt with before, as with DI Fellow Jonathan Wells. See Gishlick 2002 at http://www.ncseweb.org/icons/icon2tol.html .) 3. Meyer attempts to argue that the “gaps” in the fossil record reflect an actual lack of ancestors for Cambrian phyla and subphyla. To support this, Meyer cites some papers by University of Chicago reasearcher Mike Foote. However, of the two papers by Foote cited by Meyer, neither deals with the Cambrian/Precambrian records (one concerns the Middle and Late Paleozoic records of crinoids and brachiopods, the other the Mesozoic record of mammal clade divergence), or even transitional fossils. Foote’s papers deal with issues of taxonomic sampling: How well does a fossil record sample for a given time period reflect the biodiversity of that period? How well does a given fossil record pinpoint divergence times? Foote’s conclusions are that we have a good handle on past biodiversity, and that divergence times probably match appearance in the fossil record relatively closely. But Foote’s work utilizes organisms that are readily preserved. It doesn’t deal with organisms that aren’t readily preserved, a trait that almost certainly applies to the near-microscopic, soft-bodied ancestors of the Cambrian animals. According to Meyer’s argument, which doesn’t take into account preservation potential, microscopic metazoans such as rotifers must have arisen recently because they entirely lack a fossil record. Neither of Foote’s papers supports Meyer’s contention that the lack of transitional fossils prior to the Cambrian indicates a lack of ancestors. Lastly, it appears that fossils of the long-hypothesized small, soft-bodied precambrian worms have recently been discovered (Chen et al. 2004). Information and Misinformation For some, “information theory” is simply another source of bafflegab. And that appears to be the only role Meyer sees for “information theory”. After brief nods to Shannon and algorithmic information theory, Meyer leaves the realm of established and accepted information theoretic work entirely. 1. Meyer invokes Dembski’s “specified complexity”/”complex specified information” (SC/CSI) as somehow relevant to the Cambrian explosion. However, under Dembski’s technical definition, CSI is not just the conjoint use of the nontechnical words “specified” (as in “functional”) and “complexity”, as Meyer erroneously asserts. According to Dembski’s technical definition, improbability of appearance under natural causes is part of the *definition* of CSI. Only after one has determined that something is wildly improbable under natural causes can one conclude that something has CSI. You can’t just say, “boy, that sure is specific and complicated, it must have lots of CSI” and conclude that evolution is impossible. Therefore, Meyer’s waving about of the term “CSI” as evidence against evolution is both useless for his argument, and an incorrect usage of Dembski (although Dembski himself is very inconsistent, conflating popular and technical uses of his “CSI,” which is almost certainly why Meyer made this mistake. See here for examples of definitional inconsistency.). 2. Meyer relies on Dembski’s “specified complexity,” but even if he used it correctly (by rigorously applying Dembski’s filter, criteria, and probability calculations), Dembski’s filter has never been demonstrated to be able to distinguish anything in the biological realm — it has never been successfully applied by anyone to any biological phenomena (Elsberry and Shallit, 2003). 3. Meyer claims, “The Cambrian explosion represents a remarkable jump in the specified complexity or ‘complex specified information’ (CSI) of the biological world.” Yet to substantiate this, Meyer would have to yield up the details of the application of Dembski’s “generic chance elimination argument” to this event, which he does not do. There’s small wonder in that, for the total number of attempted uses of Dembski’s CSI in any even partially rigorous way number a meager four (Elsberry and Shallit, 2003). 4. Meyer claims, “One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93)” (p.217). This may be an estimate of something, and at least signals some sort of quantitative approach, but we may be certain that the quantity found has nothing to do with Dembski’s CSI. The quantitative element of Dembski’s CSI is an estimate of the probability of appearance (under natural processes or random assembly, as Dembski shifts background assumptions opportunistically), and has nothing to do with counting numbers of cell types. Of Text and Peptides 1. Meyer argues that “many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins” (p. 218). He makes statements to this effect throughout the paper. Meyer does not say who these scientists are, and in particular does not say whether or not any of them are biologists. The origin of new genes and proteins is actually a common, fairly trivial event, well-known to anyone who spends a modicum of effort investigating the scientific literature. The evolution of new genes has been observed in the lab, in the wild, inferred in great detail between closely-related modern species, and reconstructed in hundreds of cases by comparing the genomes from organisms sequenced in genome projects over the last decade (see Long 2001 and related articles , and below). 2. Meyer compares DNA sequences to human language. In this he follows Denton’s (1986) Evolution: A Theory in Crisis . Denton (1986) argued that meaningful sentences are isolated from each other: it is usually impossible to convert one sentence to another via a series of random letter changes, where each intermediate sentence has meaning. Like Denton (1986), Meyer applies the same argument to gene and protein sequences, concluding that they, like meaningful sentences, must have been produced by intelligent agents. The analogy between language and biological sequence is poor for many reasons; starting with the most obvious point of disanalogy, proteins can lose 80% or more of their sequence similarity and retain the same structure and function (a random example is here ). Let’s examine an English phrase where four out of five characters have been replaced with a randomly generated text string. See if you can determine the original meaning of this text string: Tnbpursutd euckilecuitn tiioismdeetneia niophvlgorciizooltccilhseema er [1] Eighty percent loss of sequence identity is fatal to English sentences. Clearly proteins are much less specified than language. 3. Meyer cites Denton (1986) unhesitatingly. This is surprising because, while Denton advocated in 1986 that biology adopt a typological view of life, he has abandoned this view (Denton 1998). Among other things, Denton wrote, “One of the most surprising discoveries which has arisen from DNA sequencing has been the remarkable finding that the genomes of all organisms are clustered very close together in a tiny region of DNA sequence space forming a tree of related sequences that can all be interconverted via a series of tiny incremental natural steps.” (p. 276) Denton now accepts common descent and disagrees with the “intelligent design” advocates who conjecture the special creation of biological groups, regularly criticizing them for ignoring the overwhelming evidence (Denton 1999). 4. Meyer’s case that the evolution of new genes and proteins is essentially impossible relies on just a few references from the scientific literature. For example, Meyer references Taylor et al. 2001, a paper entitled “Searching sequence space for protein catalysts” and available online at the PNAS website. But Taylor et al.’s recommendation for intelligent protein design is actually that it should mimic natural evolution: “[A]s in natural evolution, the design of new enzymes will require incremental strategies…”. There is a large mass of evidence supporting the view that proteins are far less “specified” than Meyer asserts. Fully reviewing this would require an article in itself, and would be somewhat beside the point since Meyer’s claim is categorically disproven by the recent origin of novel genes by natural processes. (Another way in which “experience-based analysis” leads one to conclusions other than those Meyer asserts.) However, some idea of the diversity of protein solutions to any given enzymatic “problem” is given at the NCBI’s Analogous Enzymes webpage , which includes hundreds of examples. There is more than one way to skin a cat, and there are many more ways to evolve a solution to any given functional “problem” in biology. The origin of novel genes/proteins Meyer makes his case that evolution can’t produce new genes in complete neglect of the relevant scientific literature documenting the origin of new genes. 1. A central claim of Meyer’s is that novel genes have too much “CSI” to be produced by evolution. The first problem with this is that Meyer does not demonstrate that genes have CSI under Dembski’s definition (see above). The second problem is that Meyer cites absolutely none of the literature documenting the origin of new genes. For example, Meyer missed the recent paper in Current Opinion in Genetics and Development with the unambiguous title, “Evolution of novel genes.” The paper and 183 related papers can be found here . Many other references can be found linked from here . It is worth listing a few in-text to make crystal-clear the kinds of references that Meyer missed: Copley, S. D. (2000). “Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.” Trends Biochem Sci 25(6): 261-265. PubMed Harding, M. M., Anderberg, P. I. and Haymet, A. D. (2003). “‘Antifreeze’ glycoproteins from polar fish.” Eur J Biochem 270(7): 1381-1392. PubMed Johnson, G. R., Jain, R. K. and Spain, J. C. (2002). “Origins of the 2,4-dinitrotoluene pathway.” J Bacteriol 184(15): 4219-4232. PubMed Long, M., Betran, E., Thornton, K. and Wang, W. (2003). “The origin of new genes: glimpses from the young and old.” Nat Rev Genet 4(11): 865-875. PubMed Nurminsky, D., Aguiar, D. D., Bustamante, C. D. and Hartl, D. L. (2001). “Chromosomal effects of rapid gene evolution in Drosophila melanogaster.” Science 291(5501): 128-130. PubMed Patthy, L. (2003). “Modular assembly of genes and the evolution of new functions.” Genetica 118(2-3): 217-231. PubMed Prijambada I. D., Negoro S., Yomo T., Urabe I. (1995). “Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution.” Appl Environ Microbiol. 61(5):2020-2. PubMed Ranz, J. M., Ponce, A. R., Hartl, D. L. and Nurminsky, D. (2003). “Origin and evolution of a new gene expressed in the Drosophila sperm axoneme.” Genetica 118(2-3): 233-244. PubMed Seffernick, J. L. and Wackett, L. P. (2001). “Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase.” Biochemistry 40(43): 12747-12753. PubMed 2. Meyer cites Axe (2000) as a counter to the evolutionary scenario of successive modifications of genes leading to new protein products. But Axe (2000) is not in any sense about “successive modifications”; Axe modified proteins in several locations at a time. ID advocates love to cite certain Axe papers that indicate that functional proteins are rare in sequence space, but not others that indicate the opposite (Axe et al., 1996). Axe apparently said in 1999 that his work had no relevance to intelligent design. 3. Meyer portrays protein function as all-or-nothing. But protein function is not all-or-nothing. Recent research highlights several evolutionary mechanisms “tinkering” with existing genes to arrive at new genes (Prijambada et al. 1995; Long 2001). But you won’t learn about that from Meyer. 4. As far as we can tell, Meyer uses the word “duplication” or something similar only twice in the entire 26-page article. One of these usages is in the references, in the title of an article referring to cent", "text_length": 20000, "text_sha256": "b244768746e4926623f4c288c099399ab0c58934cf962598d7057862d61c69b7" }, { "route": "/cs/moonshine/", "title": "Moonshine: Why the Peppered Moth Remains an Icon of Evolution", "description": "Matt Young takes up the criticisms that \"intelligent design\" advocates make about peppered moths and the studies showing that natural selection acted on their populations. The peppered moth example is still an excellent example of natural s", "content_kind": "drupal_article", "text": "Legacy route: /cs/moonshine/ Moonshine: Why the Peppered Moth Remains an Icon of Evolution Matt Young takes up the criticisms that \"intelligent design\" advocates make about peppered moths and the studies showing that natural selection acted on their populations. The peppered moth example is still an excellent example of natural selection in action. by Matt Young Department of Physics Colorado School of Mines www.mines.edu/~mmyoung Version 1.0, Copyright © 2004 by Matt Young [Posted: February 11, 2004] Contents Introduction Kettlewell's Experiments Table 1: Kettlewell's release-and-recapture data Figure 1: The number of moths Kettlewell recaptured as a function of the number he released the previous night. Figure 2: Kettlewell's recapture rate as a function of time. Mathematical Model Figure 3: A mathematical model fitted to Kettlewell's data. Moonlight Figure 4: Kettlewell's daily recapture rate as a function of relative exposure to moonlight. Conclusion References Introduction ernard Kettlewell did not cheat, or, more precisely, the evidence does not support the insinuation, widely repeated on the Internet, that he cheated. Kettlewell was a distinguished naturalist whose studies on predation in peppered moths were a landmark in demonstrating natural selection in the wild. His studies are widely quoted and often used in textbook accounts of natural selection. Judith Hooper (2002), a journalist, strongly suggests, however, that Kettlewell fraudulently altered the results of his famous studies, and others have uncritically accepted her suggestion. Reviews of Hooper's book in the scientific literature are at best mixed (Coyne 2002, Grant 2002, Shapiro 2002), and experts on moth behavior remain convinced that the story of the peppered moth is sound (Cook, 2000, 2003; Grant 1999; Majerus 1998, 2003; Mallet 2004). More pertinently, Kettlewell's data are completely consistent with normal experimental variation, and Hooper's insinuations are groundless. Kettlewell's Experiments What did Kettlewell do, and why does Hooper think he fudged his data? Beginning in the mid-1800's, successive generations of peppered moths ( Biston betularia ) in Britain gradually darkened in response to the air pollution in the industrialized parts of the country. Specifically, a genetically determined dark, or melanic, form of the moth replaced the lighter form as industrial pollution killed lichens on the barks of trees and also coated the bark with a layer of soot. The effect has come to be known as industrial melanism, and its existence is not in dispute (see [Forrest and Gross, 2004: 107-111] for a review). Kettlewell (1955, 1956, 1959) showed that the melanic form of the moth predominated primarily because of predation by birds. He did not think that predation was the only cause of industrial melanism and in fact speculated as to the relative strengths of other causes. Briefly, he performed a number of experiments (Musgrave 2004, Grant 1999, Kettlewell 1959): Release-recapture experiments. Kettlewell marked and released both light-colored and melanic moths early in the morning, and recaptured some the next night. In polluted woods, he and his assistants recaptured more melanic moths than light-colored (1955, 1956), whereas in unpolluted woods they captured more light-colored than melanic (1956). Direct observation (1955, 1956) and filming (1956). Kettlewell and others observed birds eating moths directly off trunks of trees. Camouflage. Kettlewell visually ranked the effectiveness of camouflage of moths on different backgrounds and compared the effectiveness of camouflage with predation rates both in an aviary and in the field. He did not know that birds had ultraviolet vision, which his observers lacked, but got nevertheless a good correlation between camouflage and predation. Later research has shown that the moths are camouflaged in the ultraviolet as well as in the visible (Musgrave 2004). Geographical distribution. He noted that the distribution of the melanic moths in the country closely matched the areas of industrialization (Bishop and Cook 1957). I will discuss only the release-recapture experiments reported in (Kettlewell 1955), because these are the experiments that are under fire and because (unlike Kettlewell's critics) we can bring quantitative tools to bear. For a more general analysis, see (Musgrave 2004; Grant 1999). Kettlewell reported releasing and recapturing moths during an 11-day period in 1953. His data are reproduced in Table 1 (1955: 332). The numbering of the days is mine. Table 1: Kettlewell's release-and-recapture data. Day Date a Number released Number recaptured 0 25 June 32 - 1 26 June 0 5 2 27 June 59 2 3 28 June 63 4 4 29 June 0 9 5 30 June 102 2 6 1 July 114 23 7 2 July 98 34 8 3 July 83 29 9 4 July 79 25 10 5 July 0 16 Totals 630 149 a Recaptures reported as 26 June took place between the evening of 25 June and the morning of 26 June. Hooper has noted that the number of recaptures increased sharply on 1 July, the same day that E. B. Ford sent a letter to Kettlewell. Ford's letter commiserated with Kettlewell for the low recapture rates but suggested that the data would be worthwhile anyway. The letter is unremarkable, and two facts militate against a finding of fraud. First, Kettlewell finished collecting data in the wee hours of the morning and therefore could not have received the letter before collecting his data on 1 July. He markedly increased the number of moths he released on 30 June, the day before the letter was mailed, not 1 July. Additionally, as Hooper admits, he continued to release more moths after 30 June. Not surprisingly, he also captured more moths: more moths released, more captured. Figure 1: The number of moths Kettlewell recaptured as a function of the number he released the previous night. The relationship is linear with a high correlation. Indeed, Figure 1 plots recapture rate as a function of the number of moths released on any day. The line is a line of best fit constrained to pass through the origin on the assumption that no moths are recaptured if none are released. Figure 1 shows that the recapture rate is very nearly a linear function of the number released. The square r 2 of the correlation coefficient is 0.80 and suggests that most of the variation of the number of recaptures is accounted for by variation of the number of releases. The fit improves only slightly if the line is not constrained. Why did Kettlewell release more moths beginning on 30 June? He released both moths he had reared and moths he had captured. Because the moths were just hatching, he had limited control of the number he could release on any given day. There is no reason to suspect that the increased numbers of releases reflect anything other than the number of moths that were available. At any rate, Ford's letter could not have influenced his decision to release more moths because it arrived after Kettlewell's first big release on 30 June. Figure 2: Kettlewell's recapture rate as a function of time, ignoring the 2 days following 0 releases. Note that, owing to the vagaries of graphing programs, the days are not numbered correctly. Still, his recapture rate, as well as the absolute number of moths recaptured, increased from 12 % over the first 3 days of his experiment to 26 % over the last 3 days. More pointedly, if we plot his recapture rate as a function of time, as in Figure 2, we find what looks to the eye as a sudden increase. Figure 2 omits those days, 27 June and 30 June, that were preceded by 0 releases. It is hard to make much out of a mere 8 data points, but the recapture rate certainly appears to the casual observer to increase sharply after 1 day of inactivity. Biological field data, however, display significant random variation, and the eye often infers patterns in random data, so let us perform a quantitative analysis to see whether Kettlewell's data are what we would expect given normal experimental variations. Specifically, let us construct a mathematical model and see how well it describes Kettlewell's data. Mathematical Model Kettlewell recaptured most of his moths after they had been in the wild for only 1 day, but he recaptured some after 2 days. Let us therefore define a 1-day recapture rate R 1 and a 2-day recapture rate R 2 as the ratios of the numbers of moths recaptured after 1 and 2 days in the wild. Kettlewell reported no 3-day recaptures. We may estimate the 2-day recapture rate by looking at the 4 moths captured on days 2 and 5. No moths were released on the preceding days, but 2 days before, a total of 63 -- 32 = 95 moths had been released, so R 2 = 4/95, or approximately 4 %. The overall recapture rate is given by the row labeled \"Totals\" and is R = 149/630, or approximately 24 %. The 1-day recapture rate is the difference R 1 = R - R 2 between the two values, or about 19 % (the numbers do not add exactly because of round-off error). R 2 is very nearly equal to the square of R 1 , as we would expect if the model is appropriate. Our mathematical model is straightforward: The number of moths captured on any given night is equal to the number of moths released the day before times the 1-day recapture rate, plus a similar term, the number of moths released 2 days before times the 2-day recapture rate. The results of a calculation based on this model are shown as the solid curve in Figure 3. Note that I have made no artificial assumptions, such as adjusting the recapture rates to get a good fit to the data, in constructing Figure 3. The points in Figure 3 are Kettlewell's data, and the solid curve is the model. How well does the model fit the data? To answer that question, we have to estimate the normal range of variability in the data. In statistical terms, we calculate the standard uncertainty of the data points. The standard uncertainty is a number that tells us, in this case, how much variation we might expect if we repeated the experiment many times. Figure 3: A mathematical model fitted to Kettlewell's data. The points are the experimental data; the solid curve is the model, and the error bars are 95% confidence. The dashed curve is the model corrected for exposure to moonlight. By way of introduction, suppose that you toss N marbles at a hole in a table. Count the number of marbles that fall through the hole, and repeat the experiment many times. Suppose that the average number of marbles that fall through the hole is M . You will not count M marbles every time you perform the experiment; to the contrary, the number will vary about M and very possibly will never exactly equal M . Thus, we talk of the probability p that any one marble passes through the hole and set it equal to the ratio M / N . The mean number of marbles that pass through the hole is equal to Np . How much will any one toss differ from M ? Assume that the number of marbles that pass through the hole is described by a binomial distribution. Then the standard deviation of M is . On approximately 19 tosses in 20, you will record a number that is between M - 2 σ and M + 2 σ , so 2 σ is most commonly used as a measure of uncertainty. The uncertainty 2 σ can be surprisingly large. For example, if p is 0.24 (the average recapture rate in Kettlewell's experiment) and N is 102 (the number of moths Kettlewell released on 30 June), then M is 24 and 2 σ is about 8. You can expect anywhere between 16 and 32 marbles to fall through the hole on any given toss. You should not be especially surprised by any number unless it is much less than 12 or much more than 36. Thus, the day-to-day variation in an experiment such as Kettlewell's can easily be 100 % or more. This fact alone should militate against a charge of fraud. On any given day, Kettlewell released N moths and recaptured M moths. Because the 2-day recapture rate is small, the statistics are essentially the same as those of the marble example. The number M is highly variable, as we have seen; on another day, he might capture a substantially different number, even if conditions were unchanged. The standard uncertainty u estimates the probable variation of M quantitatively (ISO 1993). It is given by , where the recapture rate R replaces the probability p . We apply this formula to each data point, using the overall recapture rate R for most days but the 2-day recapture rate R 2 for the 2 days that were preceded by 0 releases. The result is shown in Figure 2 as a series of error bars. The error bars represent ±2 u , an interval called the 95 % confidence interval. If we take a single measurement, then we may estimate that the true value (the average of a great many measurements) falls within the error bars, with 95 % probability. Inasmuch as the model (the solid curve) passes through virtually every error bar, it may be said to be a nearly perfect fit to the data, however poor it might appear in the absence of error bars. The points on days 7, 8, and 9 lie noticeably above the curve. If the data were completely unbiased, then we would expect about a 50-50 chance that any one of those points lay above the curve. The odds that 3 consecutive points lie above the curve are 1 in 8, exactly the same as the odds against tossing 3 heads in a row and by no means improbable enough to base a charge of cheating. Even if 5 points lay above the curve, the odds against would be 1 in 32, again, not very impressive in its improbability. Additionally, 2 consecutive data points lie noticeably below the curve. In summary, the last 5 of Kettlewell's data points are higher than the first 5. This meager fact, combined with the anecdotal evidence of Ford's letter, is all that led Hooper (2003) to infer that Kettlewell cheated. In reality, the timing of Ford's letter belies Hooper's inference, and Kettlewell's data are completely consistent with normal experimental variation. Moonlight The differences between the data and the curve are not statistically significant; the observed variation very probably is the result of chance. It is, however, possible that the deviations from the curve are \"real\", that is, due to some systematic effect, or systematic error, not due solely to random error. It is very hard, unfortunately, to track down a source of systematic error when that error is itself less than the standard uncertainty of the data set; the systematic error is said to be lost in the noise. Hooper tells us that the weather was stable and could not have accounted for the increase in the number of recaptures (though her description suggests somewhat variable winds). We have, nevertheless, a strong candidate that can account for the systematic deviations of our simple model from the curve: the phase of the moon. Shapiro (2002), in his review of Hooper's book, suggests that moonlight interferes with moth trapping, a possibility that Hooper and her informant, biologist Ted Sargent, should have investigated. The moon was full on 27 June (that is, the night of 26-27 June). By 2 July, the moon was 5 days past full but visible for only part of the night. Thus, the total exposure to the moon, the product of illuminance (brightness) and time, was approximately one-quarter what it was during the full moon, and it dropped steadily over the next few days. Clarke and his colleagues (1990) have investigated the effect of the phase of the moon on capture rates of peppered moths in a single environment over 30 years and concluded that the moon does not affect capture rates. Unfortunately, theirs was a retrospective study, and they did not record weather data, that is, did not control for cloudy or rainy days. They averaged the data over 5-day periods surrounding the full moon and did not use the actual exposure to the moonlight (as defined above). All of these factors will reduce the correlation between capture rates and exposure to moonlight. Even so, they calculated a small but not statistically significant correlation that suggests a slight increase of capture rate around the full moon. In addition, when they checked the new moon against the full moon, they calculated a small, barely significant increase, which they discounted. Possibly the effect is due to the presence of streetlights, to which they refer obliquely, and which may attract moths away from the stronger mercury vapor light only when the moon is dark. At any rate, they conclude that moonlight does not affect capture rates. Kettlewell worked on clear days only; I do not think that the conclusion of Clarke and colleagues is necessarily pertinent. Figure 4: Kettlewell's daily recapture rate as a function of relative exposure to moonlight. The equation is a line of best fit that relates exposure to recapture rate. Thus, I examined Kettlewell's data in hope of quantifying the effect of the moon on his recapture rates (1955: 332, Table 5). I obtained data that gave the moon's magnitude (an astronomical term that is related to its brightness) and the duration during which the moon was visible each night during Kettlewell's experiment. I plotted Kettlewell's daily recapture rate as a function of the exposure to the moon (the product of brightness and time, as defined above). I made no effort to control for the elevation of the moon. The result is shown in Figure 4, which plots Kettlewell's daily recapture rate as a function of lunar exposure normalized to the value 1 on the night of the full moon. The equation in Figure 4 is the equation of the line of best fit to the data. The daily recapture rate rises by a factor of 3 as the brightness of the moon decreases. (We could perform a similar calculation using Kettlewell's total captures [1955: 333, Table 6], but such a calculation is complicated by the fact that the moths emerge from their cocoons haphazardly, whereas the recapture rate is based on a known distribution of released moths. Still, the calculation based on total captures yields much the same result as that outlined below.) Using the line in Figure 4, I adjusted the calculated recapture rates according to the equation, , where R represents the nightly recapture rate used in the model that led to Figure 3, R ' is the nightly recapture rate modified to include the effect of lunar exposure, is the average daily recapture rate, and E is the nightly exposure to moonlight. The result of the calculation is shown in Figure 3 as the light, dashed curve. It demonstrates a somewhat better fit to the data than the solid curve, especially during the first few days. Instead of asking why Kettlewell's recapture rate was high on 1 July and thereafter, Hooper should have asked why it was so low on 30 June and before. Conclusion Kettlewell's data are simply accounted for by the unsurprising fact that you can recapture more moths when you release more, that and normal experimental variation. When the effect of moonlight is included in the calculation, the calculated curve fits even closer to Kettlewell's data. We have no need of Hooper's perverse, ad-hoc hypothesis. Hooper's claims are moonshine; they are based on a lack of understanding of Kettlewell's experiments in particular and experimental science in general. Hooper evidently did not consider the most likely cause of the changes she saw, exposure to moonlight, let alone realize that the change in recapture numbers began before Kettlewell could have read the letter that supposedly triggered this change. Hooper and Sargent should have performed a careful analysis before Hooper presumptuously insinuated fraud. Kettlewell's conclusion, that predation by birds was a major factor in promoting industrial melanism, was based on at least 4 lines of inquiry, as detailed above. It did not rely on the release-recapture experiments alone. It is also supported by at least 30 studies of different moth species that also developed melanic forms (Grant, 1999). In other words, an enormous body of evidence supports Kettlewell's conclusion. Even if Kettlewell's release-recapture experiments were ruled out, we would still b", "text_length": 20000, "text_sha256": "f70ce328cdc86bf0c139e9aec159fa14e862e75258465b8acd9b85f1d9db8cb3" }, { "route": "/cs/pigdid_intro/", "title": "Introduction", "description": "Reed Cartwright provides an introduction to the series of chapter reviews of Jonathan Wells's book.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_intro/ Introduction Reed Cartwright provides an introduction to the series of chapter reviews of Jonathan Wells's book. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: Introduction Posted by Reed A. Cartwright on August 25, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. Jonathan Wells is one of the most notorious activists of the political ad campaign known as “intelligent design”. He is most well known for his attacks on modern biology, specifically his 2000 book, Icons of Evolution , which was panned by the scientific community for its fraudulent presentation of modern biology. Does Jonathan Wells, aiming once again at the popular market, restore his scientific and academic reputation with his latest book, The Politically Incorrect Guide to Darwinism and Intelligent Design , or is it just old trash in a new bag? To find out, you will need to read our multi-part review, which begins tomorrow. One thing is for sure, Jonathan Wells is too modest. His recently published, The Politically Incorrect Guide to Darwinism and Intelligent Design , is not only politically incorrect but incorrect in most other ways as well: scientifically, logically, historically, legally, academically, and morally. Jonathan Wells has a Masters of Religious Education from Unification Theological Seminary, a Ph.D. in Religious Studies from Yale University, and a Ph.D. in Molecular and Cell Biology from the University of California: Berkeley. His scientific output is nearly non-existent, consisting of a couple co-authored papers from his days as graduate student and postdoc. However, he was highly motivated to get advanced degrees, as he wrote in an article about his education: [Rev. Sun Myung Moon’s] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle…. As a graduate student at Yale, I studied the whole of Christian theology but focused my attention on the Darwinian controversies. I wanted to get to the root of the conflict between Darwinian evolution and Christian doctrine…. When I finished my Yale Ph.D., I felt confident that I understood the theological basis of the conflict between Darwinism and theism. But Darwinism was clearly winning the ideological battle in the universities, the public schools, and the mass media, largely because it claimed to be supported by scientific evidence. I knew enough about biology to know that this claim was quite shaky, but few scientists were willing to challenge it. Those who did were often lumped together with young-earth biblical fundamentalists and thereby discredited in the eyes of most scholars. I eventually decided to join the fray by returning to graduate school in biology. I was convinced that embryology is the Achilles’ heel of Darwinism; one cannot understand how organisms evolve unless one understands how they develop. In 1989, I entered a second Ph.D. program, this time in biology, at the University of California at Berkeley…. ( Wells J. “Darwinism: Why I Went for a Second Ph.D.” ) Did You Know? Hundreds of scientific articles are published every month on evolution. There is no scientific controversy over evolution. The scientific community considers “intelligent design” to be unscientific. Furthermore, Jonathan Wells is a Senior Fellow with the Discovery Institute’s Center for the Renewal of Science and Culture, a public policy think tank located in Seattle, Washington. The Discovery Institute is the epicenter of “intelligent design” activism, which took a major blow when Kitzmiller v. Dover Area School District effectively declared it religiously motivated pseudoscience, unfit for public schools. Now in this first year after Dover, the “intelligent design” activists have been busy picking up the pieces, trying to hide their defeat in Dover behind a “new” marketing campaign. The Politically Incorrect Guide to Darwinism and Intelligent Design , for which the Discovery Institute is holding a party , is part of this marketing campaign, and because of all this, one might reasonably argue that, in addition to the author and the publisher, the Discovery Institute bears responsibility for the poor quality of this book. Now, an interesting thing about The Politically Incorrect Guide to Darwinism and Intelligent Design is that it is fat with specious criticisms of modern biology but nearly emaciated when it comes to “intelligent design”. Nowhere can one find any information on when a designing agent might have designed or how a designing agent manufactured its designs in matter and energy. In fact there is not a single, clear statement of what was and wasn’t designed. So while the title is modest in some respects, it’s also incorrect in one more: there’s no guide to “intelligent design” in The Politically Incorrect Guide to Darwinism and Intelligent Design . Ah, well. Maybe next year. Or the year after that. Or the year after … pigs fly. That is it for this brief introduction. Be back tomorrow for the first installment of our mutli-part review of The Politically Incorrect Guide to Darwinism and Intelligent Design , “Why Should Words Have Meanings? (Chapter 1)” by Burt Humburg .", "text_length": 5578, "text_sha256": "a9dc6c83ad599e9f7d34c292905c78359e1a372e1d32f7e0576ebeec7973ca30" }, { "route": "/cs/pigdid_ch01/", "title": "Review of Chapter One", "description": "Burt Humburg examines Chapter 1, and finds that Jonathan Wells has a severe case of Humtpy-Dumptyism. Wells just can't seem to bring himself to use words in a consistent manner.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch01/ Review of Chapter One Burt Humburg examines Chapter 1, and finds that Jonathan Wells has a severe case of Humtpy-Dumptyism. Wells just can't seem to bring himself to use words in a consistent manner. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: Why Should Words Have Meanings? (Chapter 1) Posted by bhumburg on August 26, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. By titling his first chapter “Wars and Rumors”, Jonathan Wells invokes a snippet of scripture in which Jesus describes the end times And ye shall hear of wars and rumours of wars: see that ye be not troubled: for all [these things] must come to pass, but the end is not yet. ( Matt 24:6 ) Wells uses such dramatic quotations and general martial language because the struggle between “intelligent design” and science is very much a culture war, at least to him and other creationists. In order to advance his thesis, Wells has to convey the idea that “Darwinism” pits itself against traditional Christianity: to allow pupils to learn it is to give them up to atheism, decadence, liberalism and to lose the culture war. Note that Wells does not wage war against evolution. In fact, he is at pains to make it (somewhat) clear that he wages war against “Darwinism”, which in context might sound like the sort of thing any sensible Christian would want to guard against. Unfortunately, Wells isn’t exactly clear what he means by Darwinism as opposed to evolution. In this chapter and chapter fifteen, “Darwinism’s War on Traditional Christianity”, we find many references to “Darwinism”. Assuming that even creationist words have meaning, let us set those invocations in series while adjusting the language only to merge them syntactically. Presumably there is consistency of meaning, and this will hopefully help us gain a greater understanding of what this nasty Darwinism thing is. “[There] is a fundamental conflict here [but] it is not between religion and science, or even between Christianity and evolution, but between traditional Christianity and Darwinism. Although the latter may allow for the existence of a deity, [that deity would not be] the God of traditional Christianity” (p. 173). Darwinism differs from evolution because it explains “the origin of not just one or a few species, but all species after the first—in short, all the diversity of life on Earth” (p. 3). Wells does not disagree with evolution itself or even its attendant conclusions of descent with modification or even perhaps common descent; his objection is that scientists haven’t found any direction to evolution (pp. 2,3,5). It is this failure to perceive direction in evolution that defines Darwinism, which might be considered unguided or undirected evolution (p. 6). This distinction between evolution and “Darwinism” is quite important because at some point after Darwin published his work, “Darwinism declared war on traditional Christianity” (p. 170). Did You Know? No scientific society has endorsed “intelligent design” as science. Most scientists view “intelligent design” as religion. Under oath “intelligent design” activists believe that ID is at best fringe science. But Wells also writes, “[Intelligent] design is compatible with some aspects of Darwinian evolution” (p. 8). Note that he did not write “evolution” but “Darwinian evolution”, presumably “Darwinism”. According to the stated definition on page six, Darwinism requires a component of undirectedness or unguidedness—the idea that any apparent design must be illusory—to distinguish itself from mere evolution. So intelligent design, a philosophical perspective that makes evolution compatible with “Traditional Christianity” by imputing design and direction to its inputs or outcomes, is compatible with perspectives of evolution that declared war on “Traditional Christianity” and considers any perceived design in the outcomes of evolution illusory. Confused yet? One gets the distinct impression that, despite the time Wells spent pondering the material in his book, a better working definition for Darwinism would have been, “everything about evolution to which creationists like me object”. This definition, unlike the one Wells offers, at least would have made sense in context. Easily, one of the prominent faults of Wells’s screed is a pervasive confusion between terms. Words, like “Darwinism” and “Traditional Christianity”, seem to mean whatever Wells wants them to mean for that specific sentence. In many cases words are used without regard for his own stated definitions and usually without regard to usage elsewhere in his book. There are several possible reasons for this confusion in terms. First, Wells confusion may be by design. I have argued elsewhere that creationists intend to confuse their audiences when they argue . Second, if you review the acknowledgements page, you’ll read how Wells used many authors to help him prepare this text. It is possible that Wells’s editorship was so insufficient that he allowed a term that makes up part of the book’s very title to have a flexible meaning. My suspicion is that there was both disparity between the understanding of key terms by different authors as well as an intention to confuse. Wells doesn’t spend a great deal of time defining intelligent design. This is in keeping with creationist strategy. As federal Judge John E. Jones III of the Middle District of Pennsylvania noted: ID’s backers have sought to avoid the scientific scrutiny which we have now determined that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in science class. ( Kitzmiller v. Dover Area School District ) Wells does not actually define “intelligent design” and thus does not lock “intelligent design” down into a form that could actually be scrutinized. Instead he chooses to list to list a few things “worth noting” about “intelligent design”. Throughout chapters one and fifteen, Wells defends ID creationism as the sort of thing that “traditional Christians” should support. But in this section, presumably in an effort to accommodate the obvious imperfections in biological structures or the lack of justice or beneficence in competing organisms, Wells writes, “ID does not claim that the design must be optimal; something may be designed, even if it is flawed. When automobile manufacturers recall defective vehicles, they are showing that those vehicles were badly designed, not that they were undesigned” (p. 8). We here at the Thumb support Wells’s freedom to believe in a God or gods of his choosing, but we aren’t so sure that the consideration of God as incompetent is a feature of “Traditional Christian” beliefs. This is yet another example of words meaning whatever Wells wants them to mean. The real meaning of “intelligent design”, for the most part, is left unclear. Again, this is likely by design, since it is in keeping with creationist strategy: One consistency among the Dover School Board members’ testimony, which was marked by selective memories and outright lies under oath, as will be discussed in more detail below, is that they did not think they needed to be knowledgeable about ID because it was not being taught to the students. ( Kitzmiller v. Dover Area School District ) Indeed a popular talking point by creationists is that they need not necessarily have an alternative to “Darwinism” in order to know that “Darwinism” is wrong. (c.f. Jeremy Paxman’s interview with Ann Coulter around 2:00: “I can be a restaurant critic without opening up a restaurant.”) Darwin considered that the evolution that he was noting in organisms affected humans as well and that man had a phylogenetic history just like the beetles he was studying. It is instructive that this is likely Wells’s biggest objection against Darwin. Wells quotes Darwin as writing, There seems to be no more design in the variability of organic beings, and in the action of natural selection, than in the course which the winds blow. [Although] I cannot look at the universe as the result of blind chance, yet I can see no evidence of beneficent design, or indeed design of any kind, in the details. The reader will recall Darwin’s previous intention to become a country pastor and his schooling in the ministry (short as it was) and impute sorrow to the words Darwin wrote above. Darwin mourned the lack of evidence of design in the evolution he discovered. Like all scientists with the courage to discard a favored hypothesis, Darwin had to admit to himself that which he would have preferred to not: there was no evidence of design in the world he was observing and measuring with the tools of science and what happened to the beetles and orchids was happening and had happened to humans and to our progenitor species as well. The idea that man is an animal must be offensive to Wells, who appears not to tolerate any view of our specie’s emergence other than an immaculate conception. What was Darwin’s fault according to Wells? “He set out to explain the origin of not just one or a few species, but all the species after the first.” What a scoundrel that Darwin was! One can almost hear Wells saying to himself, “Had Darwin simply stopped at beetles or orchids, that would have been one thing. But to suggest that even humans share a deep kinship with all the living things on the planet or that man is an animal as well? That’s just beyond the pale.” Perhaps instead of reading Genesis 1 so much, Wells should have read Ecclesiastes 3 . Tune in tomorrow, when PZ Myers deals a mortal blow to Jonathan Wells’s thoughts on embryos and development. (How may mortal blows can one hack take?) Those who visit Pharyngula know that PZ has already posted this portion of the review over there and the Thumb is poised to simply re-air his essay. Now you know what life is like on the West Coast.", "text_length": 10007, "text_sha256": "eab5bf90a6d320fa065a9637515e4929d5c53851ad1d95728c8458fd9cee6cf6" }, { "route": "/cs/pigdid_ch03/", "title": "Review of Chapter Three", "description": "PZ Myers reviews Chapter 3, which takes up developmental biology. Consistently, Jonathan Wells has to serve up a mishmash of the biology in order to dismiss it.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch03/ Review of Chapter Three PZ Myers reviews Chapter 3, which takes up developmental biology. Consistently, Jonathan Wells has to serve up a mishmash of the biology in order to dismiss it. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: Simply Incorrect Embryology (Chapter 3) Posted by PZ Myers on August 27, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. Jonathan Wells is a titular developmental biologist, so you’d expect he’d at least get something right in his chapter on development and evolution in The Politically Incorrect Guide to Darwinism and Intelligent Design , but no: he instead uses his nominal knowledge of a complex field to muddle up the research and misuse the data to generate a spurious impression of a science that is unaware of basic issues. He ping-pongs back and forth in a remarkably incoherent fashion, but that incoherence is central to his argument: he wants to leave the reader so baffled about the facts of embryology that they’ll throw up their hands and decide development is all wrong. Do not be misled. The state of Jonathan Wells’s brain is in no way the state of the modern fields of molecular genetics, developmental biology, and evo-devo. Here’s my shorter version of Wells’s chapter 3, titled “Why you didn’t ‘evolve’ in your mother’s womb.” It may sound familiar to many of you. The strongest evidence for Darwin’s theory was embryology, but Karl Ernst von Baer, who laid out the laws of development, did not think they supported evolution, and Ernst Haeckel twisted and distorted von Baer’s laws and faked his data to support Darwinism. He was wrong, and the earliest stages of vertebrate embryos do not resemble one another at all, so Darwinism was built on a false foundation, and they’re still using Haeckel’s faked data in our textbooks. Oh, and mutant fruit flies are still just flies. That’s right, it’s a rather boring rewrite of a premise of his book, Icons of Evolution , which I hammered on over three years ago . He hasn’t learned a thing since, and he’s making exactly the same arguments. I’ll take a different tack this time and expose the sleight of hand he’s pulling. Here’s the centerpiece of his ploy. It’s a basic concept in evo-devo, proposed in the early 1990s by Duboule and Raff as a summary of 150 years worth of observations, called the developmental hourglass. What it illustrates is that we have great diversity in the earliest stages of development, in the blastula and gastrula and neurula, but that they all converge on a more similar form, the pharyngula, at what’s called the phylotypic stage…and then they diverge once again to achieve the diversity of adult forms. This is a great opportunity for a creationist. You see, when you dig into the developmental biology literature, you will find some papers taking about the similarities of embryos at the neck of the hourglass, and you will also find other papers talking in some detail about the great differences before and after that stage. You will also find marvelous possibilities for confusion in the vague and malleable term “early”—to me, for instance, anything before the pharyngula stage is early, and everything after is late and relatively uninteresting. To put that in perspective, though, humans reach that stage at the 4 th or 5 th week of pregnancy—so I’m basically declaring month two and later of the human pregnancy to be late development. We do tend to throw around the terms early and late as relative measures of the timing of events, but we also name specific stages and processes…the fine details of which Wells leaves out, to make everything that much more confusing. This is the heart of Wells’s strategy: pick comments by developmental biologists referring to different stages, which say very different things about the similarity of embryos, and conflate them. It’s easy to make it sound like scientists are willfully lying about the state of our knowledge when you can pluck out a statement about the diversity at the gastrula stage, omit the word “gastrula”, and pretend it applies to the pharyngula stage. Literally. He is actually that dishonest. Here’s how Wells quotes William Ballard (a well known elder developmental biologist, who has done a lot of work on fish and is therefore familiar to me): It is “only by semantic tricks and subjective selection of evidence,” by “bending the facts of nature,” that one can argue that the early embryo stages of vertebrates “are more alike than their adults.” (pp. 30,31) Always be suspicious when you see partial phrases quoted and strung together by a creationist. Little alarm bells should be going off like mad in your head. This is from a paper in which Ballard is advocating greater appreciation of the morphogenetic diversity of the gastrula stage—that is, a very early event, one that is at the base of that hourglass, where developmental biologists have been saying for years that there is a great deal of phylogenetic diversity. Here’s what Ballard actually said: Before the pharyngula stage we can only say that the embryos of different species within a single taxonomic class are more alike than their parents. Only by semantic tricks and subjective selection of evidence can we claim that “gastrulas” of shark, salmon, frog, and bird are more alike than their adults. (Ballard WW (1976)) See what I mean? He has lifted a quote from a famous scientist that applies to the gastrula stage, stripped out the specific referents, and made it sound as if it applies to the pharyngula stage. It’s a simple game, one he repeats over and over in this chapter. One might argue that maybe Ballard also thought these semantic tricks applied to the pharyngula stage, and so Wells was representing his general views accurately. Alas, this cannot be. The paragraph before his mangled quote says this, rather plainly: All then arrive at the pharyngula stage, which is remarkably uniform throughout the subphylum, consisting of similar organ rudiments similarly arranged (though in some respects deformed in respect to habitat and food supply). After the standardized pharyngula stage, the maturing of the structures of organs and tissues takes place on diverging line, each line characteristic of the class and further diverging into lines characteristic of the orders, families, and so on. It’s a classic quote mine. Wells has edited the quote to suit his ends, and has also utterly ignored the sense of the paper, which directly contradicts his claims, to produce a grand lie and tie it to the reputation of a distinguished senior scientist. I could stop here. With that one example, Wells is exposed as a disreputable scoundrel, a sloppy ideologue whose “scholarship” is untrustworthy and willfully distorted. You simply cannot believe one word he says. I will go on a little further, though, and try to explain some of the ideas he has treated so shabbily. The developmental hourglass There is a fair amount of debate in the evo-devo community about the reality of the developmental hourglass, but Wells doesn’t seem to touch on the actual arguments at all—merely these strawman complaints and garbled chronologies that he uses to cast false doubt on the evolutionary process. One serious question is about how wide the waist of the hourglass actually is: an overzealous Haeckelian interpretation would be that it is very narrow indeed, but serious embryology (none of which seems to be done by “intelligent design” proponents) demonstrates that there is a significant amount of variation within the phylotypic period. Michael Richardson relaunched a critical reevaluation on the basis of morphology, and there have been a number of attempts to analyze the molecular basis of the model (several papers are cited at the end of this article; some find no detectable evidence of a consistent molecular pattern, others do.) If it does pan out as a universal and coherent property of developing embryos that they should have a conserved stage, the next question is “why?” What is it that shelters the phylotypic stage to some degree (as yet unquantified) from the evolutionary divergence so common in other developmental processes? I actually rather like Raff’s explanation: that it is a matter of scope. The diagram to the right below outlines this idea. Development is a process of increasing complexity (the grey line). The assembly of an integrated body plan requires, at some time, a pattern of global interaction—there has to be information generated at some point to specify where the head will be relative to the tail, etc., and some processes operate over large areas of the animal. For instance, somites, one of the body elements characteristic of the phylotypic stage, form under the influence of a somitic clock, rhythmic waves of molecular activity that sweep the length of the trunk and tail. One idea is that these “whole body” specification events are conserved and are difficult to uncouple from one another, so all the features for which they are responsible tend to appear together in a coordinated fashion…and that coordination is what we call the phylotypic period. Other processes are more modular and more local, not needing that level of global interaction, and are more free to diverge. The dark line in the graph indicates a peak time of long range interactive processes (and again, the real argument is about how broad that peak might be, and how much are the different fundamental processes, such as myotome and branchial arch formation, unlinked), and how subsequent developmental events become more independent. That there are active, open questions in this particular area of developmental biology, though, does not suggest the field of evo-devo is wrong. It means that biologists are working on interesting problems, and a survey of the field would show that evolution is the productive framework of choice. “Intelligent design” activists like Wells are reduced to irrelevant carping from the sidelines…and even their criticisms are all wrong. Darwin’s debt to embryology Another feature of Wells’s book, and creationists in general, is the obsession with Charles Darwin. I like the guy, I think he was brilliant, and it was his insights that launched modern evolutionary biology. But come on—he’s been dead for 124 years. He didn’t have all the tools we do now: no genetics, no molecular biology. Science has moved on well beyond Darwin’s day, but not for the creationists, who still think they can whimper and whine about errors in a book almost 150 years old and thereby dent work that nowadays depends in large part on molecular and genetic and population genetics…fields that didn’t even exist for Charles! Darwin did argue that embryology was an important piece of the evidence for evolution, a fact that is still true and probably even more so than in his time. What Wells does, though, is again mislead his readers about Darwin’s views. He claims that: …von Baer’s view “was confounded with and then transformed into” the evolutionary doctrine that the embryos of higher organisms pass through the adult forms of lower organisms in the course of their development. It was this evolutionary distortion of von Baer’s work that Darwin considered the strongest evidence for his theory. In the 1860’s, German Darwinist Ernst Haeckel (pronounced “heckle”) made some drawings to illustrate this distorted view, and Darwin relied on the drawings in later editions of The Origin of Species and in The Descent of Man (1871). (p. 27) There’s that Wells sleight of hand again. Haeckel’s ideas about recapitulation (this idea of embryos passing through the adult forms of ‘lower’ organisms, which even Haeckel did not hold as simple-mindedly as Wells pretends) would be very difficult to find in the Origin of Species , which was published in 1859…note the date of Haeckel’s work. Pore through the Origin , and you won’t find reference to Haeckel’s theory (later editions cite him once), and you certainly won’t find any reliance on his drawings. Darwin refers to embryology as the “strongest single class of facts” in favor of a change of forms in a letter to Asa Gray , and even there we don’t see the kind of adherence to recapitulation that Wells proposes. It is curious how each one, I suppose, weighs arguments in a different balance: embryology is to me by far the strongest single class of facts in favour of change of forms, and not one, I think, of my reviewers has alluded to this. Variation not coming on at a very early age, and being inherited at not a very early corresponding period, explains, as it seems to me, the grandest of all facts in natural history, or rather in zoology, viz. the resemblance of embryos. Hmmm. He’s talking about the timing of the onset of accumulation of variation, not that there is some constraint to follow adult forms. The description above actually fits very well with von Baer’s ideas of development proceeding from the general to the specific, not the “evolutionary distortion” (which is not part of evolutionary theory, anyway!) Wells describes. In the Origin , we see even more nuance. We can see why characters derived from the embryo should be of equal importance with those derived from the adult, for a natural classification of course includes all ages. But it is by no means obvious, on the ordinary view, why the structure of the embryo should be more important for this purpose than that of the adult, which alone plays its full part in the economy of nature. Yet it has been strongly urged by those great naturalists, Milne Edwards and Agassiz, that embryological characters are the most important of all; and this doctrine has very generally been admitted as true. Nevertheless, their importance has sometimes been exaggerated, owing to the adaptive characters of larvae not having been excluded; in order to show this, Fritz Muller arranged by the aid of such characters alone the great class of crustaceans, and the arrangement did not prove a natural one. But there can be no doubt that embryonic, excluding larval characters, are of the highest value for classification, not only with animals but with plants. Thus the main divisions of flowering plants are founded on differences in the embryo,- on the number and position of the cotyledons, and on the mode of development of the plumule and radicle. We shall immediately see why these characters possess so high a value in classification, namely, from the natural system being genealogical in its arrangement. Notice: no claim that embryos recapitulate adult forms, an acknowledgment that the importance can be exaggerated and that there are confounding characters, and the citation of well-known authors (Agassiz, by the way, was an opponent of evolutionary theory) that embryology is important for analysis in systematics. This doesn’t resemble Wells caricature in the slightest. What about later editions? I mentioned that Haeckel was cited once, and here it is: Professor Haeckel in his Generelle Morphologie and in other works, has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters, but receives aid from homologous and rudimentary organs, as well as from the successive periods at which the various forms of life are believed to have first appeared in our geological formations. He has thus boldly made a great beginning, and shows us how classification will in the future be treated. Again, no mention of recapitulation of adult forms, and in fact, the emphasis is on using multiple lines of evidence to build a phylogeny: embryological characters, homologous and vestigial organs, and paleontology. That sounds reasonable to me. Does Wells disagree? Wells’s treatment of the historical relationship of Darwin and Haeckel is as shoddily done as his discussion of the phylotypic stage. He relies entirely on mangled chronologies and the dishonest attribution of ideas to the targets of his slanders. Modern developmental genetics and evo-devo Did You Know? Modern biologists don’t think embryos are most similar at their earliest stages. Wells objects to showing students photos of embryos. Scientists have routinely demonstrated major morphological changes in embryos caused by mutations, and have even enumerated the genetic changes underlying the differences between some species. At the end of the chapter, Wells throws away several pages in a common creationist complaint, that mutant flies are still flies, not shrimp or horses. In particular, he focuses on work by McGinnis and colleagues, who have been working out the details of how Hox genes affect morphology; in one well-known work a few years ago, they demonstrated that a fly gene, Ubx, had evolved limb-suppressing properties that are not present in the crustacean version of Ubx. Flies, of course, only have legs on their thoraxes, not their abdomens (where Ubx is expressed), while shrimp do have abdominal limbs. It’s great stuff: it demonstrates how large-scale morphological properties of organisms are regulated by fairly small changes in the sequences of key genes. Wells’s response? …even if they had shown how ancient shrimp lost a few legs, their experiment would not have even begun to explain how a water-dwelling shrimp-like animal could acquire the ability to breathe air and fly. (p. 35) It’s a classic example of goalpost shifting. The “intelligent design” activists are always demanding step-by-step explanations for the evolution of an organism, but when a legitimate researcher uncovers one step, they immediately resort to demanding a grand explanation of the whole leap. McGinnis explained one piece in the process; his goal wasn’t to explain the respiratory system or wings, but the pattern of limbs, and he did an experiment to test his ideas. Wells wants to criticize a study on legs because it didn’t look at wings, but you know that if it had looked at wings, he would have just complained that it didn’t explain legs. What we have in evo-devo is a promising, exciting field of study that is revolutionizing our understanding of life on earth, and all Wells has to offer is the vapid sophistry of “intelligent design” (the “designer did it”) and no experimental work at all, while making the same crude and ignorant arguments— “mutant fruit flies are still just fruit flies” —that creationists have been making for decades. It’s all of a piece. I keep looking for a word to summarize this book, and I keep coming back to “dishonest”; devious, unethical, deceitful, underhanded, shifty, false, and untrustworthy would also fit. I predict that in the coming reviews of other chapters in The Politically Incorrect Guide to Darwinism and Intelligent Design by my colleagues at the Panda’s Thumb , they’re all going to be using permutations of that concept of contemptible fraudulence to express their feelings about Wells. It’s the kind of book that makes knowledgeable people want to wash their hands obsessively. Tune in tommorow for Andrea Bottaro’s review of Chapter 9. References Ballard WW (1976) Problems of gastrulation: real and verbal. Bioscience 26(1):36-39. Bininda-Emonds OR, Jeffery JE, Richardson MK (2003) Inverting the hourglass: quantitative evidence against the phylotypic stage in vertebrate development. Proc Biol Sci. 270(1513):341-6. Hazkani-Covo E, Wool D, Graur D (2005) In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer’s third law. J Exp Zoolog B Mol Dev Evol304(2):150-8. Poe S, Wake MH (2004) Quantitative tests of general models for the evolution of development. Am Nat 164(3):415-22. Richardson MK Hanken J Gooneratne ML Pieau C Raynaud A Selwood L & Wright GM (1997) There is no highly conserved embryonic stage in ", "text_length": 20000, "text_sha256": "ebc61f868785ccf80349d601ca28757d4c35950935014dacc0d3743e17fb4aec" }, { "route": "/cs/pigdid_ch09/", "title": "Review of Chapter Nine", "description": "Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch09/ Review of Chapter Nine Andrea Bottaro provides this review of Chapter 9. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: The Secret is Lies (Chapter 9) Posted by Andrea Bottaro on August 28, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. Chapter 9 in Wells’s Politically Incorrect Guide to Evolution and Intelligent Design , “The Secret of Life”, is like previous chapters, a rehash of well-known creationist arguments. This time the topics are DNA, the genetic code, and the origin of biological information. In addition, Wells uses up a third of the chapter with some excuse-making for the lack of peer-reviewed papers supporting “intelligent design”, and with a completely misleading account of the purported “persecution” of an ID-friendly scientist by the “Darwinist orthodoxy”. As far as the scientific arguments go, after giving an overview of DNA structure and function, Wells presents three main objections to the current scientific understanding of evolution at the DNA level, which in a nutshell go like this: Since all information-containing systems whose origins are known are produced by intelligent agents, the best current scientific explanation must be that those whose origin is still unknown are also the product of intelligent agents, instead of unintelligent processes. The sequence of bases in DNA “is not predetermined by the laws of physics or chemistry”, and therefore, implicitly, it must be cause by something outside such laws. (Note that “intelligent design” activists believe that intelligence, even human intelligence, is outside of the laws of nature.) All available scenarios for the origin of life are sorely incomplete, in particular those that currently enjoy widest support in the scientific community, which hypothesize that short molecules of RNA (a nucleic acid similar to DNA) may originally have acted both as information-bearers and as direct mediators of chemical reactions (a job done today mostly by proteins). This is know as the “RNA World” hypothesis. Wells complains that we don’t have a clear idea how such RNAs may have originated in the primordial Earth conditions and that, although experiments have shown that small, randomly generated RNAs can have intrinsic specific chemical functions, in all those experiments the RNAs were generated by intelligent investigators. (Hence the origin of the information they contain can again be tied to intelligent agents.) Finally, Wells grumbles, even if such experiments could be construed to indicate that short RNAs can harbor non-intelligently-derived information, all known living systems contain much more information, and there is no evidence that that much information can arise naturally—so there. I don’t think it’s too hard to spot the flaw in the first claim: by the same logic, one could say that all information-rich structures whose origins are known were designed by humans, therefore DNA must have been designed by humans. Of course, this is impossible; however DNA originated, humans as we know them could not have been around then. In science, a proposed explanation is generally considered appropriate when it is corroborated by alternative lines of evidence. Appeals to unknown, unverified and unverifiable entities, as proposed by “intelligent design” activists in this case, are not explanations in any scientific sense but are at best conjectures in wait of validation. Wells tries to support this argument by citing Bill Gates, who once stated that “DNA is like a computer program but far, far more advanced than any software ever created”. Hey, he’s Bill Gates; he should know! And if DNA is a computer program, there must a programmer, right? In reality, however, DNA is not really like a computer program in any but the most superficial way. It also doesn’t look or work like any of the other common metaphors used to describe it: an “instruction book”, a “recipe”, a “floor plan”. Truth be told, DNA looks nothing like any of the designed objects humans use to direct assembly of any product. But let’s not get the evocative power of a metaphor stand in the way of reality, Wells would suggest. Did You Know? RNAs can perform a stunning variety of chemical reactions. In your body, all proteins are created by enzymatic RNAs. The genetic code is linked to the chemical properties of amino-acid binding RNAs. The second of Wells’s argument is more slight of hand than anything else. In one sense, the statement that the sequence of DNA is “not predetermined” by natural laws is trivially true, and in another, it is utterly false. Wells just hopes the reader will get confused between the two. It is true that the sequence of DNA is “not predetermined”, but that doesn’t mean anything at all. The shape of a mountain is equally not predetermined by the laws of physics or geology, but only a crank would argue that therefore the shape of a mountain is not the historical product of physical forces, geological processes, and chance. The sequence of DNA in any living organism, like the shape of a mountain, is the result of a long historical process in which physical and chemical laws, biological mechanisms and chance intertwined to yield a specific result which could not have been predicted or predetermined at the onset, based on the simple knowledge of the underlying laws. And yet, there are also some aspects of DNA coding that do follow the laws of chemistry in ways that must be most uncomfortable for Wells. For instance, it has been found that certain nucleotide triplets in RNA can physically bind to the very same amino acids their respective counterparts in DNA code for. But DNA is a digital code (“just like a computer program”, remember?), and there really is no need nor reason to expect that a physical-chemical correspondence of this kind should exist. It’s as if you were analyzing the code in a face recognition program and found that the subroutines involved in nose shape discrimination physically stuck to your nose . The “computer program” metaphor has no way to make sense of such a finding, other than attribute it to the whim of the programmer. Biologically, though, such an observation would make sense if one assumed that originally the code was not digital, as it is now, but simpler: analog . At some point, early during the origin of life, when directed protein synthesis arose, the correspondence between nucleic acid sequence and protein sequence may have been not digital, but chemical . And like a molecular fossil, even billions of years after the onset and stabilization of the digital genetic code, remnants of this pre-digital age still remain with us. Which brings me to the third argument. This is a perfect illustration of the strategy of arguing from ignorance and goalpost-moving which characterize the creationist literature. The “RNA World” hypothesis, that life arose as complexes of RNAs which both contained information and carried out the chemical reactions necessary for proto-life, was formulated in the 1980’s based on the unexpected observation that some short RNAs could perform specific chemical reactions (“ribozymes”). Although still debated among scientists, since its original formulation the hypothesis has accumulated a number of notches on its belt, in the form of verified predictions (either ignored or glibly dismissed by Wells). Among these one can count three important findings. The empirical verification that short RNAs can perform a stunning variety of chemical reactions, including, to some extent, self-replication, a step that would have been essential for the origin of life. The finding that certain conditions and chemical “facilitators” likely present in the primordial Earth allow the spontaneous formation and persistence of RNA chains from individual constituent components. The discovery that certain basic biological processes, once thought the exclusive realm of proteins, can in fact be mediated by RNA molecules. Most spectacularly, it has been shown that the machinery for protein synthesis is, at its core, a ribozyme. This of course doesn’t mean that we have solved the problem of the origin of life (or that we even can, for that matter), but it illustrates the differences between a priori “explanations”, based on lack of evidence and negative argumentation, and actual scientific research, which proceeds by proposing testable explanations and actually doing the experiments required to test them. The last part of this chapter recounts the controversy surrounding the publication of an article by Wells’s Discovery Institute colleague Stephen Meyer in the taxonomy journal Proceedings of the Biological Society of Washington , which was followed, according to “intelligent design” lore, by the persecution by “Darwinists” of Richard Sternberg, the journal editor, for allowing the paper to appear in the peer-reviewed literature. Without going into much detail on the story, these are some things Wells “forgets” to mention in his description: The journal itself is a minor publication, with a minimal circulation, that usually deals with topics like description of new invertebrate species. It does not deal at all the kind of broad, general issues discussed by Meyer’s paper. Indeed, it is extremely unlikely that Meyer ever even would have known of the existence of the journal (I certainly didn’t, before the brouhaha), except that…. The editor, a position held on rotation by one of the Smithsonian investigators, happened to be at the time an acquaintance of Meyer’s. This scientist had extensive previous contacts with “intelligent design” and creationist circles, had presented at closed conferences with leading “intelligent design” activists, had contributed to creationist journals, and was even invited to speak at an “intelligent design” conference in Finland (with Wells) at the time the controversy broke out. Contrary to Wells’s claims, the journal has officially stated that the editor failed to follow the journal’s guidelines in handling the review of the submitted paper by choosing to personally manage the process, without sharing editorial duties with other members of the editorial committee, a most unfortunate decision, given the potential conflict of interest arising from the circumstances outlined above. Because the identity of the paper reviewers are anonymous, and the reviewers themselves have not come forward, it is impossible to say whether Sternberg chose reviewers that would be friendly to Meyer’s position, by selecting them among the small circle of known creationism and “intelligent design” sympathizers. Again, contrary to the impression given by Wells, the “preliminary investigation” by the Office of Special Counsel regarding the alleged workplace harassment of the editor following the article’s publication was in fact entirely based on Sternberg’s own allegations, with no possibility of defense by the accused Smithsonian investigators, and on internal Smithsonian e-mails improperly obtained and selectively divulged by a politically appointed OSC lawyer. Despite this obvious imbalance, which gave the accused no chance of countering the accusations, the OSC lawyer could not find any evidence of retaliation or professional damage to Sternberg, except of course for the distrust and spurning he elicited in his colleagues because of the suspicious circumstances in which Meyer’s article was published, and his creationist sympathies. The OSC admitted that it never had jurisdiction on the case, and the editor chose not to pursue his allegations in more appropriate venues. This did not stop creationist organizations, like Wells’s Discovery Institute, from mounting media campaigns aimed at discrediting and sullying the reputation of Smithsonian investigators, and Sternberg supervisor’s in particular, in national papers and news outlets. Lastly, Wells claims that this supposedly illustrates a “Catch 23” rule: “intelligent design” is not considered science because it is not published in the peer-reviewed scientific literature, and cannot be published in the scientific literature because it is not considered science. This is really just a lame excuse: “intelligent design” is not published in the literature simply because it has no science to publish. The few articles that have been produced by “intelligent design” activists in the scientific literature invariably are either rather debatable, repetitive philosophical/theoretical works, or do not in fact support an “intelligent design” position at all. Most damningly, in January 2002 “intelligent design” activists initiated their own online journal “Progress in Complexity, Information and Design”, with the stated aim “to advance the science of complexity by assessing the degree to which teleology is relevant (or irrelevant) to the origin, development, and operation of complex systems” (profoundly sounding jargon for “intelligent design”), where they could have published any research free of “censorship” or editorial pressures. Meant initially to be a quarterly publication, as of today only 8 issues of the journal have appeared in over 4 and a half years (the last in November 2005). None of the articles published contains any research or scientific finding based on “intelligent design”. Neither have “intelligent design” activists published any research papers in other venues available to them, such as the peer-reviewed journal “Rivista di Biologia/Biology Forum” , which routinely harbors fringe anti-evolution papers thanks to its editor, the Italian creationist Giuseppe Sermonti, who was one of the pro-creationism “experts” at the Kansas anti-evolution “show trial”. Any “intelligent design”-based research would definitely be welcome in Rivista —a theoretical paper by Wells himself was published there several months ago. Its absence speaks louder than any of Wells’s unfounded censorship accusations.", "text_length": 14051, "text_sha256": "ed43de55135556928e05bb6fe189bdfe85d0c75a2cd7491b29bbc6ba26a7cd63" }, { "route": "/cs/pigdid_ch10/", "title": "Review of Chapter Ten", "description": "Ian Musgrave critiques Chapter 10 of PIGDID in this essay, titled \"IC is not nice\".", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch10/ Review of Chapter Ten Ian Musgrave critiques Chapter 10 of PIGDID in this essay, titled \"IC is not nice\". The Politically Incorrect Guide to Darwinism and Intelligent Design Review: IC is not nice (Chapter 10) Posted by Ian Musgrave on September 8, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. No book on “intelligent design” would be complete without a mention of the concept of irreducible complexity . Jonathan Wells’s The Politically Incorrect Guide to Darwinism and Intelligent Design does not disappoint in this regard; it is the actual discussion of irreducible complexity that is very disappointing and down right misleading. After a cute introduction with outboard motors [ 1 ], Wells moves into Michael Behe’s use of irreducible complexity. Irreducibly complex systems as defined by Michael Behe are: a single system composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system effectively to cease functioning. (Behe 1996, p. 39) This has been redefined a couple of times , but in the end the original definition is the one “intelligent design” activists continue to return to and the one used by Wells. To illustrate the “IC” concept, Wells uses Behe’s example of a mousetrap. Remove one component, and the mousetrap cannot function. Unfortunately for Wells and Behe, a cottage industry has sprung up making reducibly complex mousetraps , so this illustration has lost its force. Even more so since we have experimental and “in the wild” systems that have evolved “IC”. The fact that there are complex systems that don’t work when you remove bits is in itself unremarkable. Behe’s contention is that systems that are “irreducibly complex” are unevolvable, and Wells presents this contention as fact. However, IC systems are far from unevolvable. Firstly, way back in the 1930’s Muller (1936) showed that evolution would produce such “IC” systems by incrementally adding parts that were dispensable at first but later became indispensable. In the 1970’s Cairns-Smith showed that systems could be assembled around scaffolding, which when removed left an “IC” system. Indeed there are several mechanisms whereby “IC” systems can come into being. The clear flaw in Behe’s contention is the fact that just because a modern system is not decomposable into smaller parts does not mean that it was not initially constructed from smaller parts. There are other practical issues. Behe’s definitions of “part”, “system”, and “function” are arbitrarily flexible, making it easy for Behe to elide between different definitions and evade counter examples, as it suits him. For Behe, in the clotting system “part” means single enzymes, whereas for the flagella it is entire assemblies of proteins. We’ll see the implications of this later. However, Wells does not address any of these highly pertinent issues. Then there is Behe’s admission that irreducibly complex systems may evolve indirectly, indeed, indirect evolution of systems by co-option is extensive in evolution . A beautiful example is this is the pentacholrophenyl (PCP) degradation pathway in bacteria. PCP is a highly toxic chemical which is not present in nature; it is only produced by humans and has only been present in any concentration in the environment within the last 60 years as an industrial waste product. Recently some bacteria have evolved the ability to metabolise PCP. The PCP pathway is irreducibly complex, in that removing any one of the three enzymes needed to break down PCP stops degradation, with subsequent cell death (Copley, 2000). Yet the PCP pathway was cobbled together out of two enzymes that broke down dicholrophenol (which is produced by fungi), and a mutation of maleylacetoacetate isomerase, that normally metabolizes amino acids. The mutation of maleylacetoacetate isomerase spontaneously formed a irreducibly complex degradation pathway from pre-existing intermediates (Copely 2000). An irreducibly complex system developed literally under our feet. As well as having real, biological systems with irreducibly complexity evolving in front of us, we also have evidence from studies of computer models that IC systems can evolve . Yet you won’t find any of this in Wells’s book. You will only find a brief, irrelevant reference to the Kitzmiller trial , where Behe’s claims that the irreducibly complex immune system was unevolvable were systematically shredded , but no reference to the substantial biological evidence tendered in the trial. Some old favorites do get trotted out: the visual system, the clotting system and the bacterial flagellum. The real biological evidence is ignored, and tall tales are spun, so lets look at what Wells says in the light of evidence. Speaking of light, lets start with Wells misrepresentation of the visual system. A little light on the subject Wells wrote: When light strikes the human retina it is absorbed by a molecule [retinal] which alters an attached protein [opsin], which then initiates what biochemists call a “cascade”—a precisely integrated series of molecular reactions that in this case causes a nerve impulse to be transmitted to the brain. If any molecule in this cascade is missing or defective, no nerve impulse is transmitted, the person is blind. Since the light sensing mechanism doesn’t function unless every part is present, it is irreducibly complex. The fossil record cannot tell us, and no evolutionary biologist has explained, how all these molecules assembled themselves to produce the light sensitive spot that was the starting point for Darwin’s speculation. (p. 111) To start off with, Wells’s statement “If any molecule in this cascade is missing or defective, no nerve impulse is transmitted, the person is blind” is flat out wrong, arrestin and retinoid binding protein can be completely absent in vertebrates with no effect or mild night blindness (Gonzalez-Ferdanez, 2000). Other proteins can be damaged with only mild effects on vision. But nonetheless Wells is still using the flawed concept that if a modern system breaks if a component is damaged, it couldn’t have evolved. Lets see about that. Did You Know? Evolutionary biologists worked out how evolution can make irreducibly complex systems over 40 years ago. Irreducibly complex systems have evolved under our very feet. Evolutionary biologists have made successful predictions about what pieces of the clotting system would be missing from particular organisms. A light spot does not need to be as complicated or as tightly regulated as a vertebrate (or cephalopod) eye. One of the iconic light spots is that of the eukaryotic single-celled organism Euglena . The Euglena signal transduction cascade consists of a single protein, the light harvesting protein and the protein that generates the single signaling molecule are one and the same (Iseki 2002). Incidentally, this gives an insight into how signaling cascades develop. If gene duplication of the light sensing enzyme were to occur, and with subsequent mutation so that one copy remains light sensitive, and the other just signals, then you have a mini-cascade happening. Duplication and divergence underlies a large amount of evolutionary novelty. But to return to light spots. As we saw, Euglena has a single-protein system, which is not irreducibly complex at all, and we can see how systems could be tacked on to it to form a cascade. Vertebrates use the molecule opsin, rather than the Euglena protein. Opsin is a very old molecule; bacteria have their own version, bacteriorhodopsin, which in its simple form is a single molecule that pumps ions across a membrane (Spudich 1998). Furthermore, changing ion concentrations in cells is a classic way to modify cells excitability and function. Once again we have a one step “cascade”, and a light spot based on this bacteriorhodopsin is something eminently evolvable. In more advanced systems, bacteriorhodoposin is linked to the chemosenory signaling pathway. No new system was involved; an old one was co-opted. This theme of co-option is present in the visual system of multi-cellular organisms. Both invertebrate and vertebrate eyes, from simple to complex, use opsin to capture light. But in non-chordate invertebrates, opsin is linked to an enzyme called phospolipase C, and in chordates and vertebrates, it is linked to a phosphodiesterase enzyme (Nilsson 2004). In both cases, the light sensing molecule has co-opted existing signaling systems to work through (Nilsson 2004, Hisatomi 2002). You may ask how the phospholipase C and phosphodiesterase cascades were put together. These are relatively simple and highly flexible systems cobbled together from proteins with other functions. (See Nilsson 2004, Hisatomi 2002; we have already seen that you can mess around with these cascades quite a bit.) Of course, you will learn none of this from Wells. Rather than go to the effort of finding out what researchers do know about visual system evolution, he spends his time criticizing Jerry Coyne because Coyne had the temerity to use an anatomical analogy to demonstrate how irreducibly complex systems could evolve. Wells blandly reproduces Behe’s fulmination that anatomy is quite irrelevant to molecular evolution. This is ironic, since Behe’s canonical example of irreducible complexity is a mouse trap . Coynes point is valid because it is the logic of part assembly, rather than the nature of the parts themselves, that is important. A modern human eye acts as an irreducibly complex system, remove a lens, for example, and you are effectively blind. But in simpler organisms, lensless eyes work adequately, and the modern human eye can be reached by minor modification of these systems. Having one photosensitive enzyme is inadequate for modern mammalian vision, but it is quite adequate for a simple photospot such as in Euglena , and subsequent enzymes can be tacked on. This misunderstanding that modern dependence means systems are unevolvable extends to the clotting system. The reducibly complex clotting system Now before I go on, I’ll remind you of Behe’s definition of “irreducible complexity”: “a single system composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system effectively to cease functioning”. I’d like to emphasize that the blood clotting system did not evolve in modern terrestrial vertebrates, as it sometimes seems to be implied in Behe’s writings. Instead it evolved in far more primitive organisms with low pressure blood systems, where a cut is less lethal than in vertebrates with high pressure circulatory systems. Clotting in the chordate lineage (the group of animals that includes vertebrates) arose somewhere between chordates and the earliest jawless fish. Primitive chordates such as the sea squirt have no clotting system; they plug up any wounds with mobile blood cells called haematocytes. Their equivalent in humans, platelets, are quite important in clotting but get left out of Behe’s descriptions (Jiang & Doolittle, 2003, Davidson et al., 2003, Yong & Doolittle 1987). This turns out to be important later on. Have a look at the diagram of the clotting systems for a variety of chordates. The reducibly complex clotting system. Jawed fish lack the extrinsic clotting system, hagfish lack factor X and other components of the vertebrate system, and the primitive chordate Amphioxus has no fibrinogen, but a thrombin like enzyme that produces a clot. Sea Squirts have no coagulation system, but plug holes with haematocytes. Click on the image for a full scale version. The first thing you see is that several chordates have very much reduced clotting systems. Jawed fish lack the entire intrinsic pathway and have much less than the dozen proteins that Wells claims are essential for clotting to occur. Jawless fish, such as the hagfish, lack Factor X and some of the accessory enzymes and probably have only half of Wells’s “essential” proteins (Davidson et al. 2003). Without a complete genome of Amphioxus , we don’t know how many of the vertebrate clotting components it has but certainly less than jawless fish. We do know that it has an enzyme that forms clots and acts like thrombin in vertebrate coagulation assays, and we do know it lacks fibrinogen. However, it still forms clots. It is thus very clear that the clotting system is reducible. Why would Wells think otherwise? He is merely parroting Behe (as he does all the way through this chapter), without realizing Behe’s deep misunderstanding of biology. Here’s an example of how badly Behe misunderstands things from his chapter in Of Pandas and People : Why is the blood clotting system incompatible with a nonintelligent evolutionary view of nature? Macroevolution means a change from a simpler to a more complex state. Let us try to envision such a change for blood clotting. Assume that we initially start with an organism that contains just a primitive version of thrombin and fibrinogen. The thrombin would immediately cut all the fibrin, causing a massive clot and the speedy death of the organism. (Behe 1993, p. 145) Several issues with Behe’s account immediately arise. A “primitive version” of thrombin would hardly chop up fibrinogen with the spectacular efficiency of our modern ones. Furthermore, it is the amplification of thrombin activity by the cascade that results in spectacular fast clotting in advanced vertebrates. Without the cascade, there would be no massive, system wide clot. Clotting would proceed in a more leisurely fashion, but this is no problem for organisms with low-pressure blood systems like Amphioxus . Behe is either being disingenuous or lacks even basic understanding of clotting physiology. If Wells was really investigating the clotting system, rather than parroting Behe, he would have noticed these points. Such a simple “one step” system is not just theoretical speculation. Shrimp and some crustaceans have a one-step clotting enzyme, and they singularly fail to have lethal, system wide coagulation. Many other crustaceans operate with a simple two-component system (Theopold et al., 2004). We know that the Amphioxus thrombin-like system is much reduced compared to jawless fish and jawed fish, let alone vertebrates, although the full details of the system are not clear. We do know about the trypsin-stimulated polyphenoloxidase system though (Pang et al., 2004), and this can serve as a model for primitive clotting systems in chordates. When Amphioxus is wounded, tissue damage causes local calcium levels to be high. This activates trypsin released from the tissue (as well as circulating trypsin). The activated trypsin in turn activates polypheoloxidase in the circulation of Amphioxus , which the produces cross-linked melanin. While everyone knows that melanin is the pigment that makes our skins brown (and go browner after exposure to sunlight), fewer will be aware that it is an important component of the innate defense system in invertebrates. Furthermore, sticky masses of melanin are used to entangle and immobilize bacteria and can also help plug the wound (Pang et al., 2004). Hmmm, a trypsin-like molecule, activated by high calcium on tissue injury, that makes gluggy stuff. That sounds just like thrombin! (Thrombin appears to be derived from tryspin-like molecules.) Fibrinogen is also used to limit bacterial invasion. Thrombin is not just used in the clotting system (despite Behe’s claim that it is—see Wang et al., 2005); it plays an important role in tissue remodeling and activating immune cells. It is highly plausible that a proto-thrombin was released during tissue damage and initially initiated wound repair, then started making gluggy stuff that limited bacterial invasion, and then was modified to make gluggy stuff that sealed blood vessels. (There are parallel examples seen in modern invertebrates). Given there is a calcium-activated trypsin that activates polyphenol oxidase locally, without glugging up the entire circulation with melanin, this suggests that locally released calcium could control a proto-thrombin easily (and calcium is critical to modern thrombin) conta Behe and in agreement with invertebrate “one step” systems. From such a simple calcium-activated system, it is not too far to the simple hagfish system, and thence to the more complicated jawed fish system , and thence to us. Behe (1996) wrote: In fact, having a primitive, poorly controlled clotting system would probably be more dangerous to an animal, and therefore less advantageous, than having no such system at all! Tell that to sea-squirts or Amphioxus (or any number of crustaceans), who handle clotting with a small component clotting system. (As noted above, sea squirts just use haemocytes, a very, very primitive precursor of platelets.) Of course, you won’t find a discussion of this reducible clotting system from Wells. He chooses instead to misquote Russell Doolittle. But (Doolittle claimed) “when these two lines of mice were crossed … [then] for all practical purposes, the mice lacking both genes were normal! He concluded: “Contrary to claims about irreducible complexity, the entire ensemble of proteins is not needed.” (p. 112) But this is not what Doolittle said; Wells leaves out Doolittle’s very important qualifier. And what do you think happened when these two lines of mice were crossed? For all practical purposes, the mice lacking both genes were normal! 6 Contrary to claims about irreducible complexity, the entire ensemble of proteins is not needed. Music and harmony can arise from a smaller orchestra. No one doubts that mice deprived of these two genes would be compromised in the wild , but the mere fact that they appear normal in the laboratory setting is a striking example of the point and counterpoint, step-by-step scenario in reverse!” I have written a long article about Behe’s misquotation of Doolittle, and as Wells blindly follows Behe I direct you to this article (try and guess which one is the fibrinogen knockout mouse). But both Behe and Wells ignore a key point. Mice that have no fibrinogen, the key final step in the clotting cascade, still form clots. These aren’t good clots by any means, but the mice live as long as normal mice, and heal wounds as fast as normal mice, so they are good enough for the purpose in a laboratory setting. If clotting was really as irreducibly complex as Wells claims, clotting should utterly fail, and the mice should die at or shortly after birth, as we need the clotting system to keep our blood vessels intact. So if a mouse, with a modern, high pressure circulation system, can form clots without fibrinogen, then a primitive, low pressure clotting system would work quite well, just as it does in the fibrinogen free Amphioxus . But of course Wells ignores this crucial aspect and proceeds to “the” bacterial flagellum. In a spin with Flagella The flagellum is beloved of ID promoters, as, at least in diagrams, actually looks like a human-built machine. But looks are deceptive, and there is a wealth of information to show that they evolved. The relation ship of Type II secretory systems to type IV secretory/motility systems and the archebacterial flagellum. Homologous proteins are indicated by colour, the GspM/FlagG homolg Y1 has been omitted due to uncertainly as to its location in the membrane (modified from Musgrave 2004). Click to enlarge. Again, Wells simply re-iterates Behes’ arguments. Behe’s contention is that the flagellum consists of a “motor”, a “shaft”, and a “propeller”. (Note that these “parts” are complexes of molecules, so when you demonstrate a flagellum with fewer proteins, Behe just says, “it’s still got a shaft”, whereas he insists that the “parts” of the clotting system are individual proteins and must all be pr", "text_length": 20000, "text_sha256": "9499957f1a06d9500483a572d00952209505635f9ba98787ee38eaedebac5b86" }, { "route": "/cs/pigdid_ch15/", "title": "Review of Chapter Fifteen", "description": "Burt Humburg points out the irony of Jonathan Wells, Unification Church sanctioned theologian, setting himself up as a defender of traditional Christianity in this review of Chapter 15.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch15/ Review of Chapter Fifteen Burt Humburg points out the irony of Jonathan Wells, Unification Church sanctioned theologian, setting himself up as a defender of traditional Christianity in this review of Chapter 15. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: \"Traditional Christianity,\" Ersatz Revolutionaries, and the Culture War (Chapter 15) Posted by bhumburg on August 30, 2006 01:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. Chapter 15 is entitled “Darwinism’s War on Traditional Christianity”. For much of this chapter, the reader will find Wells on his soapbox about this or that aspect of, you guessed it, “Traditional Christianity”. And, like “Darwinism” in the first chapter , Wells struggles to find a definition for his term. Wells chooses a current version of the Nicene Creed as the sort of “creedal affirmations that” traditionally unite Christians. (Apparently the litmus suggested by Jesus was inadequate.) Wells almost approaches clarity when he implies that if one doesn’t adhere to the tenets of the (current?) Nicene Creed, one cannot seriously consider him or herself as a Christian. (No word yet on the apparently non-Christians who affirmed a prior version of the Nicene Creed.) There are two important things to say about Wells’s definition of a “Traditional Christian”. First, the commitment to the tenets of the Nicene Creed is hardly a universal litmus for determining who is and who is not a Christian. A Protestant, even one who subscribes to every tenet of the Nicene Creed, who thinks that Wells is right is encouraged to try to obtain the sacramental elements from a Catholic communion and see how far he gets. (According to Catholic tradition, Protestants cannot receive Catholic communion.) The second important thing to note is that Jonathan Wells is styling himself as a defender of “Traditional Christianity.” Read that again: Jonathan Wells, Traditional Christianity. Not to be impolite, but to us here at the Thumb Wells defending “Traditional Christianity” reads as queer as Ann Coulter defending “traditional values”. Jonathan Wells has testified that he is a Unificationist , a follower of the Reverend Sun Myung Moon, and a member of the Grand Unification Church. According to Wikipedia, among other things, Reverend Moon published a document in 2002 that claimed all the leaders of the world’s five major religions (and several communist leaders besides) all voted Moon to be the Messiah and pledged their support to him. Wikipedia also describes that, according to Unification Church theology, when Reverend Moon marries couples in a mass marriage ceremony, he cleanses those believers of original sin. For those not versed in “traditional Christianity”, original sin is the reason why people need to be born again; according to traditional Christian theology, absent original sin, we would have no need for a savior or forgiveness. (For those interested in more information on Reverend Moon or his Grand Unification Church, John Gorenfeld and Mark Levine’s interviews regarding Reverend Moon here and here are highly recommended.) As I wrote in my review of Chapter 1, we here at the Thumb defend Wells’ right to say and publish anything he wants. However, words must have meanings and any definition of “Traditional Christianity” sufficiently plastic to accomodate Unificationist theology would really be expected to accomodate verified observations like evolution. So the definition of “Traditional Christianity”, like “Darwinism”, is a word that means whatever Wells wants it to mean, but Wells doesn’t stop with just new definitions for words. When Wells writes, “Before Darwin, science and theology in Christendom generally got along quite well. Indeed, most of the time they were mutually supportive. Serious conflict erupted only after 1859, and then only because Darwinism declared war on traditional Christianity” (p. 170), he’s also inventing a new history of the interaction between religion and science. We here at the Thumb would remark that readers should Google, at their convenience and presumably after they have replaced their irony meters, “Galileo”. Snark aside, the onset of the science and religion war is not linked in any way with Darwin. Whether by politics (as suggested by this Wikipedia article on Science and Religion ) or by an inherent immiscibility between its philosophies, science and religion have had periods during which they didn’t get along. As Scott Liell notes in a NY Times Essay entitled “ Shaking the Foundation of Faith :” At the end of the day, it was never faith per se that stood in opposition to science; Franklin was ultimately as much a believer as Thomas Prince. Many people of faith - Unitarians, Quakers and those who, like most of the founding fathers, were deists - were prominent members of the scientific community. Rather, it was (and is) a specific type of belief that consistently finds itself at odds with science, one that is not found merely in America and is not limited to Christianity. It is the specific brand of faith that devalues reason and confers the mantle of infallible, absolute authority upon a leader or a book. It is only the priests of these sects, as Jefferson said, who “dread the advance of science as witches do the approach of daylight.” ( Excerpt from “Shaking the Foundation of Faith” from the NY Times ) Wells’s claim that science and religion were chummy up until Darwin is ahistorical nonsense, as preposterous as the idea that the South won the Civil War. Still on his soapbox, Wells moves to reject theistic evolution in a section tellingly entitled, “Surrendering on Darwin’s Terms”. After describing how philosopher Michael Ruse considers Darwinism, “so well established that Christians should accept it as fact” (p. 173), Wells quotes Ruse as saying, “‘It is still open to you to accept that God did the job. More likely, if you accept God already, it is still very much open to you to think of God as great inasmuch as He has created this really wonderful world’” (p. 174). Wells then sneeringly writes, “In other words, a Darwinian who really, really [emphasis in original] wants to be a Christian can be a Christian of sorts—just not a traditional one” (p. 174). Or take Wells’s contempt for biologist and Kitzmiller trial expert witness Kenneth Miller. (No, not just Miller’s theology but also for him as a person; please see Mark Perakh’s review .) Wells quotes Miller as believing “in Darwin’s God”. For those who have not read Miller’s Finding Darwin’s God Amazon , I highly recommend it. It’s the kind of easy read that just about anyone can pick up and enjoy. Take, for example, this excerpt . “Look at the beauty of a flower,” [Father Murphy, Kenneth Miller’s priest during childhood] began. “The Bible tells us that even Solomon in all his glory was never arrayed as one of these. And do you know what? Not a single person in the world can tell us what makes a flower bloom. All those scientists in their laboratories, the ones who can split the atom and build jet planes and televisions, well, not one of them can tell you how a plant makes flowers.” And why should they be able to? “Flowers, just like you, are the work of God.” I was impressed. No one argued, no one wisecracked. We filed out of the church like good little boys and girls, ready for our first communion the next day. And I never thought of it again, until this symposium on developmental biology. Sandwiched between two speakers working on more fashionable topics in animal development was Elliot M. Meyerowitz, a plant scientist at Caltech. A few of my colleagues, uninterested in research dealing with plants, got up to stretch their legs before the final talk, but I sat there with an ear-to-ear grin on my face. I jotted notes furiously; I sketched the diagrams he projected on the screen and wrote additional speculations of my own in the margins. Meyerowitz, you see, had explained how plants make flowers. ( Excerpt from Finding Darwin’s God, by Kenneth Miller ) Miller goes on in that chapter to talk about the biology regarding how plants evolved flowers, the theological implications of this, and in general holds forth on a view of science and religion in which they interact, not wage war. Agree or disagree with Miller’s perspectives, for Christians on just about any side of the evolution debate, it’s a fascinating read and begs discussion in coffee shops or Bible study groups. Wells chose a different portion to quote, thereby introducing the reader to Miller’s book: Miller argues that the inherent unpredictability of evolution was essential to God’s plan to create human beings with free will. “If events in the material world were strictly determined,” he writes, “then evolution would indeed move toward the predictable outcomes that so many people seem to want…. As material beings, our actions and even our thoughts would be preordained, and our freedom to act and choose would disappear.” (p. 174) Wells moves quickly to disavow Miller’s perspectives by writing in the very next sentence, “In the Christian tradition, however, human freedom is an attribute of our non-material souls rather than a product of material evolution. Darwin’s God is not the God of traditional Christianity” (p. 174). Then he moves on to Steven Jay Gould. No discussion about Father Murphy or Meyerowitz. No acknowledgement or analysis of the rich detail of Miller’s book. Instead, Miller’s patiently argued point, that putting faith in God because of scientific failures represents poorly placed faith (described a bit later in this essay), is simply lost on Wells; he’s already handwavingly dismissed it on other, highly questionable grounds. Did You Know? Mainstream Christianity has no problem with theistic evolution. More religious scientists support evolution than “intelligent design”. Jonathan Wells, self-styled defender of “Traditional Christianity”, is a follower of Rev. Moon and not a traditional Christian. I write “questionable” because there are serious flaws with Wells’s logic. When Wells retorts that our decisions are the exclusive ken of our spiritual bodies, does he seriously not think that coffee in the morning tends to make those decisions sharper for many people (even Christians who fully adopt the Nicene Creed)? Is Wells honestly not aware that children born with certain combinations of abnormal chromosomes or genes can predictably have problems with cognition or demonstrate maladaptive behaviors, even in mild cases? From a theological and sociological perspective, it must be an excuse to simplemindedly say, “my genes made me sin”, but genes and other physical factors do matter . No understanding of theology that completely rejects these materialistic influences is likely to be convincing to those with even a pedestrian understanding of neurobiology. Wells’s dismissal of Miller’s attempt to describe his understanding of God is just that: an anti-intellectual, handwaving, supercilious, and simpleminded dismissal. We here at the Thumb would caution Wells that Behe’s dismissal of evidence didn’t work too well at the Kitzmiller trial. Wells then turns his hatred of theistic evolution to Father George Coyne, cosmologist and former director of the Vatican Observatory. Coyne is quoted, “‘… Science is completely neutral with respect to philosophical or theological implications …. It is difficult to believe that God is omnipotent and omniscient in the sense of many of the scholastic philosophers. For the believer, science tells of a God who must be very different from God as seen by them’” (p. 178) Again, Wells moves quickly to rebuke: “This logic-challenged priest—science is theologically neutral yet leads to a different God—has the arrogance to lecture a pope and a cardinal on Catholic doctrine” (p. 178). To put these dismissals of theistic evolution into perspective, the reader must understand that there is a venerable history of enthusiasts of science trying to find peace with religion and vice versa. Throughout history and forever into the future, whenever the conclusions of science conflict with contemporary theological understanding, believers have struggled and will struggle to reconcile them. Miller provided an example of that kind of conflict: Father Murphy believed in God because of scientific ignorance in a problem. In the fullness of time, that problem was solved by science, in this case by Meyerowitz. Stated in slightly different language, the elucidation of the evolution of flowers undermined the logic behind Father Murphy’s theology. As Miller writes in his book: Like [Father Murphy, the creationists who use God of the Gaps thinking ] have based their search for God on the premise that nature is not self-sufficient. By such logic, just as Father Murphy claimed that only God could make a flower, they claim that only God could have made a species. Both assertions support the existence of God only so long as they are shown to be true, but serious problems for religion emerge when the assertions are shown to be false. If a lack of scientific explanation is proof of God’s existence, the counterlogic is unimpeachable: a successful scientific explanation is an argument against God. That’s why this reasoning, ultimately, is much more dangerous to religion than it is to science. Eliot Meyerowitz’s fine work on floral induction suddenly becomes a threat to the divine, even though common sense tells us it should be nothing of the sort. The reason it doesn’t, of course, is because the original premise is flawed. The Western God created a material world that is home to both humans and daffodils. God’s ability to act in that world need not be predicated on its material defects. There is, therefore, no theological reason for any believer to assume that the macromolecules of the plant cell cannot fully account for the formation of a flower. Life, in all its glory, is based in the physical reality of the natural world. We are dust, and from that dust come the molecules of life to make both flowers and the dreamers who contemplate them. The critics of evolution have made exactly the same mistake, but on a higher and more dangerous plane. They represent no serious problem for science, which meets the challenge easily. Their claims about missing intermediates and suspect mechanism can be answered directly by providing the intermediates and demonstrating the mechanisms. Religion, however, is drawn into dangerous territory by the creationist logic. By arguing, as they have repeatedly, that nature cannot be self-sufficient in the formation of new species, the creationists forge a logical link between the limits of natural process to accomplish biological change and the existence of a designer (God). In other words, they show the proponents of atheism exactly how to disprove the existence of God—show that evolution works, and it’s time to tear down the temple. As we have seen, this is an offer that the enemies of religion are all too happy to accept. All of this logic is lost on Wells, who dismisses Miller’s theology because it accomodates the obvious influences on our decisions by physical and material things. Like Behe on the witness stand in the Kitzmiller trial, Wells waves away this inconvenient theology with which he disagrees. Father Coyne doesn’t get much more respect. Wells tries to earn schoolyard snark points by identifying an apparent logical contradiction: how can science be neutral to theology and yet inform our understanding of God? When one reads Father Coyne’s entire essay, one almost gets the feeling that Coyne knew about the apparent contradiction beforehand and published it regardless. Look what Coyne writes in his final paragraph: These are very weak images, but how else do we talk about God? We can only come to know God by analogy. The universe as we know it today through science is one way to derive an analogical knowledge of God. For those who believe modern science does say something to us about God, it provides a challenge, an enriching challenge, to traditional beliefs about God. God in his infinite freedom continuously creates a world that reflects that freedom at all levels of the evolutionary process to greater and greater complexity. God lets the world be what it will be in its continuous evolution. He is not continually intervening, but rather allows, participates, loves. Is such thinking adequate to preserve the special character attributed by religious thought to the emergence not only of life but also of spirit, while avoiding a crude creationism? Only a protracted dialogue will tell. But we should not close off the dialogue and darken the already murky waters by fearing that God will be abandoned if we embrace the best of modern science. ( Final paragraph from God’s Chance Creation by Father Coyne, former director of Vatican Observatory ) Humility and honesty, that’s what I’m struck by when I read these words. “Apparent grammatical contradictions be damned”, Coyne might be saying to us. “We need to have an honest discussion about God and talk about what’s really going on.” Here’s a priest seeking to reconcile the science he understands and the things he wants to believe. Miller is a scientist seeking to do the same. Both of them are doing their best and both want to dialog with believers who find the answers provided and verified by science threatening. Apparently Wells isn’t too impressed by their efforts. Indeed, he’s scornful of the fact that these scientists who are Christians are thinking and endorsing thoughts that diverge from “Traditional Christianity”, or at least Wells’s elastic version of it. And the method with which he expresses his scorn—calling Father Coyne arrogant for daring to have an opinion that is in variance with his superiors in the Church—is noteworthy because it brings up an important thing to understand about Wells’s book. Wells’s screed certainly purports to be a subversive and revolutionary book that advocates “intelligent design” using freethinking arguments: the title is The Politically Incorrect Guide to Darwinism and Intelligent Design , the pages are peppered with callouts like “Books You’re Not Supposed to Read” and “Websites You’re Not Supposed to Visit”, and much verbiage is spent positioning “intelligent design” as this underdog, upstart idea that just needs a fighting chance and reasonable people willing to think forbidden thoughts to support it, thereby allowing “intelligent design” creationism to get a foothold and find its success over the inferior “Darwinism”. This book is not revolutionary . Wells is writing in a highly conservative fashion . Wells is not a freethinker . When Father Coyne put forward what he stated to be an inarticulate best effort to describe his feelings about God, feelings which were in keeping with the best available science but necessarily conflicted with Schöenborn’s anti-evolutionary position, Wells derided him as one who had “the arrogance to lecture a pope and a cardinal on Catholic doctrine”. Frankly, it is inconsistent of Wells to beg for open-minded thinking and posture as a revolutionary when it comes to “intelligent design” and turn right around and disagree with that person’s theology on the basis that the person was arrogant for disagreeing with a religious leader in the first place. The chapter in its entirety endorses “Traditional Chrisitanity”, implicitly and explicitly belittling those who somehow fall outside of Wells’ elastic definition. Wells writes, “Although [Darwinism] may allow for the existence of a deity, it is not the God of traditional Christianity, who created human beings in his image. The contradiction couldn’t be sharper, and most attempts to blunt it end up abandoning traditional Christianity” (p. 173). This is not revolutionary thinking. It is highly conserva", "text_length": 20000, "text_sha256": "4e2caf97896716471516d03677c3e934dd6d7e3f3aed5e089abade8fac92114b" }, { "route": "/cs/pigdid_ch15_legal/", "title": "Critique Concerning Legal Issues", "description": "Tim Sandefur takes on statements by Wells concerning legal issues surrounding the lawsuit over the Understanding Evolution website.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch15_legal/ Critique Concerning Legal Issues Tim Sandefur takes on statements by Wells concerning legal issues surrounding the lawsuit over the Understanding Evolution website. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: ID's Newspeak Posted by Timothy Sandefur on September 6, 2006 12:00 PM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. If there’s something embarrassingly dumb to be done or said, it’s probably going to be done or said in the name of “political incorrectness”. That term was first used to bring attention to the political censoriousness at leftist epicenters in the 1990s, but it has mutated into an excuse for saying stupid, outlandish, misleading things. The Politically Incorrect Guide to American History was full of misrepresentations, politically-motivated elisions, and a neo-Confederate interpretation of the Constitution that embarrassed serious constitutional scholars . The Politically Incorrect Guide to Science was full of silly pro-“intelligent design” notions, and now The Politically Incorrect Guide to Darwinism and Intelligent Design by Jonathan Wells has come along to carry this tradition forward—if “forward” is the right term. An indication of the astonishing degree of misrepresentation and outright lying that The Politically Incorrect Guide to Darwinism and Intelligent Design employs comes in Chapter 15 when discussing the controversy over an evolution website supported by a grant from the National Science Foundation. The Thumb covered this pseudo-controversy pretty thoroughly at the time. But here’s how Jonathan Wells describes it: In 2005, a California resident sued the NSF and University of California for violating the First Amendment, but district court judge Phyllis J. Hamilton dismissed the lawsuit. So the governments of the United States and California now officially endorse religious views—and only those religious views—that are acceptable to Darwinists. (p. 179) The citations provided for this statement are to the Discovery Institute’s blog and a report on ( quelle suprise! ) World Net Daily . The paragraph does not mention that the “resident” was the wife of an “intelligent design” activist and serial plaintiff Larry Caldwell. Nor does it even mention why Judge Hamilton dismissed the case. That decision, Caldwell v. Caldwell , 420 F.Supp.2d 1102 (N.D. Cal. 2006), was based on Caldwell’s lack of standing—a procedural matter having nothing to do with the religious issue at all. According to Judge Hamilton, “the court need[ed] not, and [did] not, reach the merits of the Establishment Clause claim” Id. at 1108. Furthermore, Wells claims that the First Amendment “clearly prohibits the government from favoring the views of one religious group over another” (p. 178), which isn’t quite accurate. More precisely, the First Amendment prohibits the government from endorsing a religious viewpoint. The distinction is important because the First Amendment does allow the government to endorse a great many truth claims. The government can say “X is true” except and only except in those cases where X is a religious claim and only a religious claim. If for example the government wishes to state that it is true that a match can start a fire, the government is free to do so, even if a particular religious group agrees with that statement. But the government is not allowed to declare that the doctrine of papal infallibility or reincarnation is true. The government is allowed to teach that some people believe in papal infallibility , or that some people believe in the trinity , because these are not religious claims; they are descriptions of fact that can or might be empirically verified to some degree. The website about which Wells complains was funded at least partly by government dollars, and it declared that “most religious groups have no conflict [sic] with the theory of evolution or other scientific findings. In fact, many religious people, including theologians, feel that a deeper understanding of nature actually enriches their faith”. Now, whether or not a person agrees that religion and evolution are compatible—I don’t.—is not the same as saying that some people do believe this thing . And the fact that some people believe this thing is not a religious statement. There is nothing in the First Amendment prohibiting the government from saying it. Yet according to Wells, “Political scientist John G. West[ 1 ] wrote in 2004: ‘Taxpayers might wonder why it’s the government’s business to tell them what their religious beliefs about evolution should or shouldn’t be’” (p. 179). That, of course, is not what the website did. It said only that some people believe this thing or that thing. Yet even this easy distinction is too much to demand of The Politically Incorrect Guide to Darwinism and Intelligent Design . In Chapter 13 Wells focuses on the legal issues of teaching “intelligent design” in the classroom, and it too is full of this kind of misleading writing. The chapter begins by describing the case of public school teacher Roger DeHart, who “supplemented” his science classes with readings from Of Pandas And People , an “intelligent design” textbook that began life as a biblical creationism textbook. But Wells describes it this way: For several years, biology teacher Roger DeHart had been teaching students the required curriculum about evolution, but he had also been mentioning intelligent design…. DeHart had the support of his school administrators and local school board, but the American Civil Liberties Union (ACLU) claimed that his practice amounted to religious proselytizing and “violates both state and federal laws.” The school district caved in to pressure from the ACLU, the National Center for Science Education (NCSE) and local atheists. DeHart was ordered to stop mentioning intelligent design, though he was told in 2001 that he could request approval to use supplementary materials critical of some of the evidence for Darwinian evolution. (pp. 143,144) You see, he was just mentioning “intelligent design” and was railroaded by a conspiracy of “local atheists”. And note the scare quotes around “violates both state and federal laws”. Wells doesn’t explain which laws those would be (e.g. the Establishment Clause of the First Amendment to the Constitution) or how they would apply in a case where a government employee is teaching religion to students. DeHart was careful to use the “intelligent design” movement’s best tactics, e.g. claiming that they are seeking only “free debate” and “teaching the controversy”. Because evolution as a scientific matter is true and because there is no genuine controversy over it, these tactics are simply mechanisms for sneaking religion into the public school classroom—a fact well covered on the Thumb . Wells’s portrayal of DeHart as a martyr, chewed up in the great maw of atheist science, is typical of the doublespeak of “intelligent design” activists and is related to activists desire to portray themselves as an oppressed minority. We’re told that “Darwinism has serious problems with the evidence” (p. 147), which isn’t true, and that “Darwinists are opposed to mentioning scientific problems with their view” (p. 147), which isn’t true, and that “ID theorists are given no opportunity to respond” (p. 149) to their critics, which is amusing to find in a book by written a leading “intelligent design theorist” and released by a major publishing house. DeHart, in fact, chose to go to another school, a religious school, in fact, where he is perfectly free to teach the religious concept of “intelligent design”, without any oppression by the atheistic cabal that “intelligent design” activists like to pretend is ruthlessly suppressing dissent. There are few legal claims in Wells’s The Politically Incorrect Guide to Darwinism and Intelligent Design ; in fact, the book is so unserious as to quote from an episode of Friends in one marginal notation (p. 155). But Chapter 13 includes a brief whine about the Kitzmiller decision. The passage opens by claiming that the Discovery Institute “urged the [school] board to rescind the policy” of requiring that science students listen to a disclaimer about evolution (p. 154). (It doesn’t note that the district’s science teachers refused to read the disclaimer to their students.) This, of course, is not entirely honest; it would be more honest to say that the Discovery Institute abandoned the Dover School Board as soon as it became clear that that ship was sinking . That, at least, was the view of the Thomas More Law Center’s Richard Thompson, who said, [The Discovery Institute] wrote a book, titled “Intelligent Design in Public School Science Curricula.” The conclusion of that book was that … ‘school boards have the authority to permit, and even encourage, teaching about design theory as an alternative to Darwinian evolution’ … and I could go further. But, you had Discovery Institute people actually encouraging the teaching of intelligent design in public school systems. Now, whether they wanted the school boards to teach intelligent design or mention it, certainly when you start putting it in writing, that writing does have consequences. In fact, several of the members, including Steve Meyer, agreed to be expert witnesses, also prepared expert witness reports, then all at once decided that they weren’t going to become expert witnesses, at a time after the closure of the time we could add new expert witnesses. So it did have a strategic impact on the way we could present the case, cause they backed out, when the court no longer allowed us to add new expert witnesses, which we could have done…. So that caused us some concern about exactly where was the heart of the Discovery Institute. Was it really something of a tactical decision, was it this strategy that they’ve been using, in I guess Ohio and other places, where they’ve pushed school boards to go in with intelligent design, and as soon as there’s a controversy, they back off with a compromise. And I think what was victimized by this strategy was the Dover school board, because we could not present the expert testimony we thought we could present. But Wells simply writes, “the Dover School Board ignored the Discovery Institute’s advice” (p. 155). In a lovely example of ad hominem , Wells says that Dover citizens suing the school board were represented by “[t]he American Civil Liberties Union (ACLU)—the same organization that defends the right of Nazis to march publicly in support of their racist and anti-Semitic policies” (p. 155). Ah, yes, because ACLU is really a group of evil racists doing the leg-work for the Great Atheist Conspiracy. No mention of the ACLU’s defense of Christians, conservatives, and other generally pro-intelligent-design groups, as Ed Brayton has well documented . Jonathan Wells claims that Judge Jones “was so impressed by the testimony and materials presented by the Darwinists that he apparently didn’t bother to read much of the material presented by their critics” (p. 155). Of course, it’s a very serious matter to accuse a judge of such misbehavior, but the opinion itself belies that fact. The long decision (58 pages in the final version) contains many citations of the record and discusses at length the credibility of the pro-intelligent-design witnesses—or rather the lack thereof. One need merely read the decision—which is too much, alas, for many people—to see this point refuted. As Craig Venter once noted, it’s common for people who lose a race to say “oh, I wasn’t really racing after all”. So, too, it’s common for those who lose a case to say the judge was just a schmuck anyway. After all, as Wells claims, Judge Jones was “[a]pparently not burdened with an excess of judicial restraint” (p. 155). Ah, judicial restraint, the last refuge of the scoundrel. I’ve written before about the meaninglessness of such terms. But so, too, did Judge Jones, whose refutation speaks for itself: Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred as this is manifestly not an activist Court. Rather, this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the Board to adopt an imprudent and ultimately unconstitutional policy. ( Kitzmiller v. Dover Area School Dist. , 400 F.Supp.2d 707, 765 (M.D. Pa. 2005)) This decision, Wells concludes, “intimidated” legislators in Ohio “into surrendering [their] critical analysis of evolution” (p. 156). Translated into plain language, this means that Judge Jones’s enforcment of the First Amendment persuaded Ohio officials not to start promulgating a religious viewpoint in government schools. It’s telling, really, that “intelligent design” activists have to play such word games. “Intelligent design” is really a word-game anyway: a word game that replaces “religion” with “scientific theory”, “creation” with “design”, “miracle” with “irreducible complexity”, and so forth. This sad little shell game is all that anti-science activists have to offer. But it’s sad that they continue to find publishers willing to sell such pseudo-intellectualism to the public for a quick buck. As the great John Fogerty put it , The little pig knows what to do, he’s silent and quick, just like Oliver Twist; Before it’s over, your pocket is clean, A four-legged thief paid a visit on you. Notes The PIG commonly fails to disclose the fact that quoted authorities are allied with the Discovery Institute. This is one example.", "text_length": 13823, "text_sha256": "b87622675ae4a3ac219ce82713fd56c6e18ff762e27abb9239907b87d630e090" }, { "route": "/cs/pigdid_ch16/", "title": "Review of Chapter Sixteen", "description": "Mark Perakh reviews Chapter 16, wherein Jonathan Wells engages in a massive fit of projection to try to smear evolutionary biologists with the heritage of Trofim D. Lysenko.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch16/ Review of Chapter Sixteen Mark Perakh reviews Chapter 16, wherein Jonathan Wells engages in a massive fit of projection to try to smear evolutionary biologists with the heritage of Trofim D. Lysenko. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: Whose Head is Ugly? Jonathan Wells and Lysenkoism (Chapter 16) Posted by Mark Perakh on August 29, 2006 12:00 AM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. I’ll address in this article chapter sixteen, “American Lysenkoism”, in Jonathan Wells’s Politically Incorrect Guide to Darwinism and Intelligent Design . As Wells (1994) explained, he went to study biology at the behest of his spiritual “father” the Reverend Sun-Myung Moon, with an explicit goal to devote his life to “destroying Darwinism”. Since he set out to destroy “Darwinism” before having sufficiently familiarized himself with it, this immediately points to his lack of impartiality when dealing with “Darwinism.” Wells’s goal was not to evaluate “Darwinism” on its merits but to search for any arguments, regardless of their merits, which would serve his goal set in advance. This alone is a strong warning to the consumers of Wells’s literary output: take Wells’s arguments with a good dose of salt; he is not an unbiased judge of evidence, but a partisan of an anti-evolution effort whose goal is not to find the truth but to prove his viewpoint regardless of means. In a box in the margin of chapter sixteen Wells writes: “Lysenkoism is now rearing its ugly head in the US, as Darwinists use their government positions to destroy the careers of their critics.” Really? Thousands of biologists in the USSR at the time of Lysenko’s reign were arrested, exiled to Siberia, and many of them shot in the basements of the notorious Lubyanka prison, while intelligent design advocates in the US thrive on lavish donations from ultra-religious sources, have their own publishing outlets, lecture all over the country without any interference from genuine scientists, endlessly appear on TV and radio shows, and enjoy support from the extreme right-wing pundits and commentators? Readers having even a minimal knowledge of the actual situation immediately see that no reasonable discourse can be expected from a writer so brazenly misrepresenting the reality. Which “government positions” does Wells have in mind? Are “Darwinists” holding all (or most) positions in the present Republican administration? Are they in command of the Congress? Perhaps Wells wanted to really say that “Darwinists” occupy many positions of authority in universities. This is certainly true. By the same token the “Newtonists”, and “Einsteinists”, and “Maxwellists”, and “Boltzmannists” occupy positions of authority in universities as well, while Wells would perhaps like to see “Moonists” in such positions instead. If indeed “Darwinists” (Wells’s term for modern biologists) are predominant in biological science, it is for good reason. Evolutionary biology is a robust science whose fruits are proven to be of great use in technology, medicine, agriculture, and many other fields. On the other hand Wells’s co-travelers, the “intelligent design” activists, have yet to show any, even very modest, contribution to science. Why should they get any position of authority anywhere besides their own outlets such as the infamous Center for Science and Culture at the Discovery Institute of Seattle? Despite the abject lack of any positive contribution to the society from the CSC, which “Darwinists” have ever “destroyed careers” of its fellows, such as Wells? Wells and his colleagues in the anti-evolution enterprise thrive despite their destructive activity aimed at “destroying” biological science. They receive good salaries and grants, travel all over the globe assaulting biological science, and often also occupy positions in legitimate universities despite the egregious lack of substance in their favorite “intelligent design” “theory”. This is still a free country, and there is no alleged nefarious activity by scientists aimed at muzzling “intelligent design” activists, who are free to spread their nonsense as suggested by Wells, along with the proponents of a flat earth or of astrology, or of geomancy, palm reading, “creation science”, and all other fads and fallacies which usually are much more popular than genuine science. There is indeed an “ugly head rearing in the US”, and it is that of “intelligent design” activism. I shall discuss now specific notions in Wells’s screed used by Wells to mislead his readers. The chapter in question deals with the alleged manifestations of “Lysenkoism” in the US. This term stems from the sad story of the destruction of the thriving biological science in the USSR under the guidance of Trofim Denisovich Lysenko (Трофим Денисович Лысенко), which started in the late twenties of the 20 th century and ended in the seventies. Lysenko was a poorly educated but politically savvy agrobiologist, who for decades managed to get an unconditional support from the tyrannical ruler of the USSR, first Joseph Stalin and later Nikita Khrushchev. He indeed used his power to “destroy the careers” of many scientists, who either held views differing from those of Lysenko or just earned his hostility for arbitrary reasons. “Destroying” careers often extended to arrests and exiles of Lysenko’s victims, who were sometimes even killed. At a minimum they were deprived of their jobs and of any means to conduct their research. Wells wants his readers to believe that the “Darwinists” allegedly occupying “government positions” in the USA treat the critics of “Darwinism” the same way Lysenko treated the biologists in the USSR. Of course, Wells cannot support such an assertion by any factual evidence, therefore he resorts to a rather transparent shenanigans to somehow “prove” his point. He uses several means to achieve his goals, including misquotations and sometimes bold lies. Quotemining Here is an example. Wells refers to my essay (Perakh 2004a) wherein I described my personal experience regarding the “Lysenkoism” in the USSR. The essay in question is a part of an article co-authored by Wesley R. Elsberry and myself. The article consists of two separate parts: a part written by Elsberry and a part written by myself. While I do not wish to appear to be promoting my own essay, readers who really want to know what was written there instead of relying on Wells’s misrepresentation can easily verify my words by looking up my essay. It can be accessed either in an HTML version (Perakh 2004a) or in a PDF version (Perakh 2004b). Wells provides a quotation from my essay and gives it in a rather peculiar form, amounting to a deliberate distortion of my thesis. Here is how Wells quotes from my essay: Retired physicist Mark Perakh, who grew up in the former Soviet Union, writes: “The anti-Lysenkoist stand of the ID advocates is … ludicrous given the similarity of their denial of Darwinian biology to the denial of the neo-Darwinian synthesis by the Lysenkoists.” Perakh continues :” From my experience both with Marxism and with the realities of the Soviet system, I can assert that … it is ID advocates whose behavior is reminiscent of the oppressive Soviet regime” since they subject Darwinists to “continuous denunciations, verbal assaults, derision, and ultimately to dismissal from their positions.” (p. 182) A brief look at the actual text of my essay immediately reveals that the alleged quotation has been constructed by Wells by means of some tricks. He transposed various sentences from my essay, placing those that occur somewhere later in the text, ahead of some other that in fact occur earlier in the text. He used ellipsis in several cases, apparently to hide from readers the exact wording of my essay. He combined partial quotes taken from different parts of my essay in an allegedly single sentence thus fraudulently attributing to me something I did not say. Here are some details. The sentence in the above quotation, starting with the words “The anti-Lysenkoist stand” and ending with the words “synthesis by Lysenkoists” occurs in my text several pages later than the sentence starting with the words “From my experience both” and ending with the words “oppressive Soviet regime.” Wells has transposed these two sentences, placing a sentence that occurs much later in the text, ahead of a sentence, which in fact precedes it by several pages. He inserts the words “Perakh continues” thus exacerbating his distortion by falsely asserting the order in which my sentences appear, opposite to their actual order of appearance. This way he creates a false impression that the latter sentence is a continuation of the former, which it is not. The insertion by Wells of his own words “Perakh continues” is a testimony to Wells’s intentionally contrived misleading of readers. Since both sentences are nevertheless indeed present in my text (but in an opposite order), some readers may try to justify Well’s “creative quoting” by pointing out that this is a minor infraction that does not affect the gist of his argument. Perhaps this is indeed a minor point, but being contrary to the common rules or proper quotations, it is indicative of the overall doubtful reliability of Wells’s quotation habits, where the strict adherence to facts is not of paramount importance. I will not discuss here the parts of my actual text replaced by Wells with ellipsis, but will rather point out now to a really egregious example of quote mining by Wells, which amounts to a direct fraud. Here is how Wells quotes from my text: From my experience both with Marxism and with the realities of the Soviet system, I can assert that … it is ID advocates whose behavior is reminiscent of the oppressive Soviet regime” since they subject Darwinists to “continuous denunciations, verbal assaults, derision, and ultimately to dismissal from their positions.” And here is the actual text in my essay: From my experience both with Marxism and with the realities of the Soviet system, I can assert that in the dispute between the Intelligent Design advocates and their opponents, including pro-evolution scientists, it is ID advocates whose behavior is reminiscent of the oppressive Soviet regime. Comparing Wells’s quotation with the actual text of my essay, we immediately notice that my actual text ends with the words “Soviet regime” and a period, whereas Wells quotation contains additionally the words: “since they subject Darwinists to ‘continuous denunciations, verbal assaults, derision, and ultimately to dismissal from their positions.’” While readers may be confused by this discrepancy, I’ll clarify now how Wells’s shenanigan works. First, the words “since they subject Darwinists to” are inserted by Wells; they are not part of my text. As to the rest of the added words, they are indeed found in my text but are taken by Wells from a page in my text which is many pages further in the text than the preceding phrase ending with “Soviet regime.” Where these words occur, they relate to a different topic, having nothing to do with “intelligent design” advocates. By fraudulently combining in one sentence two unrelated quotations, plus inserting several words of his own, Wells misleads readers, apparently aiming to create a false impression that I accuse “intelligent design” advocates of subjecting “Darwinists” to “dismissal from their positions.” In fact the second quoted phrase describes not the behavior of “intelligent design” advocates but rather the behavior of the Soviet authorities at the time of Lysenko’s reign. Of course “intelligent design” activists do not “subject evolutionary biologists to dismissal from their position”. They certainly would be happy to do so (see the proof of that statement in my essay, Perakh 2004a), but their hands fortunately are too short for that. They must limit themselves to verbal assaults. Misquotation is a device used when no arguments of substance are available, as is the case of Wells fighting modern biology. While Wells’s “creative quoting” is in itself a telltale testimony to the dismal level of his unscrupulous discourse, it is just a secondary component of his narration which is substandard all over. Lamarckism One of Wells’s theses is his asseverations that, first, “Darwinism” includes elements of Lamarckism, and, second, that Lysenko’s pseudo-biology, officially approved in the USSR, was “Darwinist” throughout. Did You Know? Lysenkoism was anti-Darwinian. Lysenkoism rejected the modern synthesis because it didn’t fit with “Marxism-Leninism”. There are more similiarities between “intelligent design” activists and Lysenkoists than between modern biologists and Lysenkoists. With a sufficient desire, it is always possible to find signs of similarity between any, even drastically opposite, systems of views. Wells provides a quote from Darwin which, in his view, is in harmony with Lamarckism. First of all, although Lamarck’s main ideas have been largely abandoned by biological science, it does not mean that everything Lamarck believed was necessarily wrong. In fact Lamarck was a serious scientist, unlike Wells and his friends at the Discovery Institute. There were positive elements in Lamarck’s views, so it is no wonder Darwin, who worked in the pre-genetics age, could find some elements of Lamarckism to be in tune with his own views. However, to assert that Darwin’s theory of natural selection is in any way analogous to Lamarckism is absurd. While Well’s interpretation is his privilege, he seems to be not aware of the most principal difference between the views of Lamarck and Darwin. The inheritance of acquired characteristics was considered “common knowledge” in Darwin’s time, when there was yet no knowledge of genetics, of Mendel’s work and of any other elements of the “modern synthesis”, which is an important part of biological science in our time. Darwin did in fact believe that the transmission of acquired traits could occur, as explicated in his “pangenesis” theory. I am not sure if he thought it was a significant component of heredity, but he indeed postulated that the environment could affect changes both at the “germinal” level and at the “somatic” level, the latter of which would have been “lamarckian” sensu latu . It was a secondary point in Darwin’s system of views, which was discarded many years later with the advent of the modern synthesis. In fact, Darwinian theory differed from Lamarck’s in a very principal way, and no cherry-picked quotations by Wells can prove otherwise. What differentiated Lamarck’s theory of evolution from Darwin’s was that Lamarck believed all species arose and evolved separately and sequentially, i.e. with no (or very limited) common descent, and there was a “vital force” that pushed organisms to evolve along certain lines (very much teleologically). Darwin certainly disagreed with both, and adhered to the view that evolution is given “direction” by the action of selection, and not by intrinsic mechanisms. Creative Darwinism Regarding the allegedly Darwinian essence of the Soviet Lysenkoist pseudo-biology, here Wells displays the same level of ignorance as he demonstrated in his infamous utterance (Wells 2002) wherein he compared evolutionary biologist Kenneth Miller to Heinrich Himmler (the notorious Chief of SS in the Nazi Germany), who, in Wells’s uninformed mind, was the chief of the Nazi propaganda machine (thus confusing Himmler with Goebbels). Wells seems to be unaware of the simple facts of history. In the Soviet system, words rarely were used to denote what their direct meaning implied. Given the expertise of Wells’s colleagues in an Orwellian “newspeak”, he should appreciate the virtuosity achieved by the Soviet doubletalk, in particular in its ostensible adherence to Darwinism. Yes, Darwinism was acclaimed in the USSR as the officially adopted doctrine, allegedly the only one compatible with Marxism-Leninism. There was an important nuance, however. The term “Darwinism” in the USSR was used with a qualifier, “creative Darwinism”, which was in line with the more general but equally ubiquitous term of “Creative Marxism”. The latter term simply meant the most recent decisions of the Communist Party’s leadership, which in Stalin’s time was just Stalin’s personal view. Most often it had nothing to do with the legacy of Marx, or even of Lenin, but whenever Stalin announced his opinion, it was automatically referred to as the great achievement of the “creative Marxism-Leninism”. The succinct expression asserted that “Marxism is not a dogma but a manual for action”. Likewise, whatever Lysenko announced as the new achievement was automatically praised as the further development of “creative Darwinism” for which an alternative term was “Michurinian biology” (Perakh 2004a). More often than not, it had nothing in common with the real Darwinism. Wells seems to be blissfully unaware of all those facts of history. His assertions that Lysenko was a Darwinist are either naively uninformed or deliberately misleading. Wells mentions Lysenko’s notorious experiments with “yarovizatsiya” (i.e. vernalization) of winter crops, without explaining its relation to “Darwinism”. (There was none.) He seems to be unaware of other theories by Lysenko. For example, the omnipotent academician fervently propagated his pet theory asserting that there is no competition for resources within individual species. This idea was radically incompatible with Darwin’s natural selection, although spin experts from the Discovery Institute probably can apply their acrobatic abilities to “prove” that Lysenko’s theory also was Darwinian. (Indeed, they likewise “prove” that Hitler’s racist ideas were based on “Darwinism.” Of course, this assertion has little to do with facts—see, for example Flank 2006 or Walker undated ). On the basis of his theory, Lysenko recommended to plant fruit trees and other cultured plants in packs, so that several plants were planted at the same spot in the soil. Since, as Lysenko claimed, the plants, being members of the same species, will not compete for food and light, they will actually help each other to grow and thrive. Khrushchev fell for Lysenko’s bait and ordered to follow Lysenko’s recommendation, based on “Marxism-Leninism”, according to which members of the same class in the human society are never antagonistic to each other but are united by common interests in the struggle of classes, only the latter being antagonistic. The result was of course disastrous, as the plants stubbornly refused to convert to Marxism and competed for resources despite belonging to the same species and despite the decisions of the “Politburo”. Perhaps Wells simply is not cognizant of these features of Lysenkoism, in which case he should have abstained from proclaiming a judgment on Lysenkoism’s alleged Darwinian roots. Lysenkoism in the US? Isn’t this story reminiscent of the attitude of the “intelligent design” activists like Wells and his colleagues in the “intelligent design” enterprise. Like Lysenko, they stubbornly adhere to their views regardless of facts and evidence. Recall Wells’s admission that his life is devoted to destroying “Darwinism”, whereas the possibility of evidence being in favor of modern biology is never mentioned. The word of the Reverend Moon obviously takes precedence for Wells against all the huge accumulation of empirical material testifying for evolutionary theory. Of course, Wells’s main thesis is not that the “ugly head” of Lysenkoism “is rearing in the US” because evolutionary scientists in any way share Lysenko’s views . Such an assertion would apparently be too much even for Wells. On the other hand there is indeed a lot of similarity between Lysenko’s pseudo-science and “intelligent design”. Lysenkoists re", "text_length": 20000, "text_sha256": "c031c109ac75fe609fbeb06debd1aa87b765c7a458acdc3ddec9ae03bddfc77e" }, { "route": "/cs/pigdid_ch16_ohio/", "title": "Ohio", "description": "Richard B. Hoppe takes Wells to task over Wells's misleading version of events in Ohio.", "content_kind": "drupal_article", "text": "Legacy route: /cs/pigdid_ch16_ohio/ Ohio Richard B. Hoppe takes Wells to task over Wells's misleading version of events in Ohio. The Politically Incorrect Guide to Darwinism and Intelligent Design Review: PIG Ignorant About Ohio Posted by Richard B. Hoppe on August 31, 2006 12:00 PM Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design . Regnery Publishing, Inc. Washington, DC. Amazon Read the entire series. Jonathan Wells has recently written The Politically Incorrect Guide to Darwinism and Intelligent Design . Wells’s book is stuffed full of misrepresentations, distortions, and plain falsehoods. My Thumb colleagues are reviewing whole chapters, but my purpose here is to focus in some detail on just one of Wells’s claims to illustrate his scurrilous tactics. The claim I focus on is from Chapter 16, “American Lysenkoism”. Mark Perakh has already documented how Wells manipulated partial quotations from Perakh’s earlier essay on Lysenkoism to create misrepresentations of what Perakh actually wrote. Here I will describe Wells’s dishonesty about a specific episode in Ohio last year. In chapter 16 Wells wrote … some Darwinist professors at Ohio State University (OSU)—a public institution—are now trying to destroy another student’s career by preventing him from getting his doctorate. (p. 189) This is the infamous Bryan Leonard affair that I described on the Thumb as it was happening; see “ID vs. Academic Integrity: Gaming the System in Ohio” for the full story. Wells accuses three Ohio State University professors of torpedoing Leonard, saying Although Leonard had gone through normal procedures and received proper approval to conduct his research … [the three professors] accuse Leonard of “unethical” conduct primarily on the grounds that his research was predicated on “a fundamental flaw: there are no valid scientific data challenging macroevolution”. (p. 189) The next sentence in the letter was “Mr. Leonard has been misinforming his students if he teaches them otherwise”. As noted below, what Leonard was teaching was Wells’s Icons of Evolution trash, so he was indeed misinforming his students. Furthermore, Wells claimed The OSU Darwinists then invoked some procedural techicalities—widely ignored in the case of other Ph.D. candidates—to demand that Leonard’s dissertation defense be postponed. (p. 190) Like all creationists, Wells stuffs his screed with false claims (a tactic immortalized as the Gish Gallop , each claim expressed in a sentence but requiring paragraphs to rebut). With respect to the Leonard affair, Wells makes two specific claims, that the professors accused Leonard of unethical behavior and that he failed to follow some “procedural technicalities” that are allegedly widely disregarded at Ohio State. Both of Wells’s claims are misrepresentations, and in making them he also produces some peripheral garbage that requires examination. As background one must know that the three professors—an evolutionary biologist, a paleoanthropologist, and a mathematician—all have appointments as Members of the Graduate Faculty of the Ohio State University. As such, they have specific responsibilities with respect to that university (for the ‘umbrella’ University policy governing those responsibilities see here , especially 3335-5-30 (B)). If they have reason to believe that the regulations of the graduate school are not being followed, as part of their affirmative duty to their employer they must bring that to the attention of the Graduate School. Just as a police officer has the affirmative duty to enforce the law and a physician has the affirmative duty to treat a patient with the patient’s best interests in mind, the members of the graduate faculty have an affirmative duty to ensure that the policies and regulations of the Graduate School are followed. When they become aware of a violation of those policies and regulations they are bound to report it. Failure to do so would violate the terms of their appointment to the graduate faculty. The Ethics Question Now consider the ethics question regarding Leonard’s research. As a graduate student, Leonard had already thrust himself into a policy-making environment as a member of a committee writing lesson plans to instantiate the new state science standards in Ohio, in particular 10 th grade biology. He drafted a lesson plan that contained classic creationist objections to evolutionary theory (the misnamed “ critical analysis of evolution ”). As originally submitted to the State Board of Education the lesson plan contained nine “aspects of evolution” to be “critically analysed”. Eight of the nine came straight out of Wells’s Icons of Evolution , a collection of misrepresentations, distortions, and flat falsehoods. The lesson plan also contained irrelevant “web resources”, including a number of creationist web sites, and at least one outright fake reference, a paper allegedly in Nature that has no existence outside creationist web sites. It was a shoddy piece of creationist propaganda masquerading as a lesson plan. In the Kansas creationism hearings Leonard claimed to have been teaching that creationist trash for years and that his doctoral research focused on whether doing so influenced students’s learning about evolution. When Leonard drew public attention to his work at the Kansas creationist hearings, the three OSU professors, aware of Leonard’s status as a graduate student, asked whether Leonard’s dissertation research had been properly reviewed and approved by OSU’s Institutional Review Board (IRB). Operating under federal laws and regulations, IRBs are charged with ensuring that research performed with human subjects are ethical and meet legal requirements for informed consent, among other things. Failure to conform to requirements can have substantial negative effects on a university. IRBs are particularly vigilant about the use of minors as subjects of research. Given that Leonard’s lesson plan draft contained a series of falsehoods about evolutionary biology, and given that in Kansas Leonard testified about his (as yet unpublished) research, the question arose as to whether Leonard had appropriately informed the IRB and the parents of his students that he was teaching scientific trash in order to assess its effects on their children and whether he had received appropriate permissions to do so. To my knowledge that question has still not been answered. The “Procedural Technicalities” Question As noted, Wells claimed that in addition to the IRB question, the three OSU professors “invoked some procedural technicalities—widely ignored in the case of other Ph.D. candidates—to demand that Leonard’s dissertation defense be postponed” (p. 190). What “procedural technicalities” did the professors raise? Simple: They pointed out that contrary to Graduate School requirements, Leonard’s dissertation defense committee had no members from the program in which he was seeking a degree . That is, while Leonard was seeking a degree from the program in science education, no one from that program was on his committee. Instead, there was a member from the technology education program (his advisor), one from entomology, one from human nutrition, and a “graduate school representative” from the Department of French & Italian! It’s as though Leonard were seeking certification in neurosurgery before an examining committee consisting of a dermatologist, a ob/gyn, a chiropracter, and a truck driver. Not even Leonard’s advisor is in the program from which he sought a degree! As one commenter on my earlier post remarked, looking just at that committeee one has no idea where Leonard was supposedly seeking a degree. Two of the members of Leonard’s committee have one property in common: they are “intelligent design” activists. Glenn Needham and Robert Disilvestro are publicly self-identified with the “intelligent design” movement. DiSilvestro testified (note his denial of common descent ) in the Kansas creationism hearings with Leonard ( who also denied common descent ), and Needham testified to the validity of Leonard’s lesson plan at the Ohio State Board of Education. In addition, until the brouhaha erupted Leonard’s advisor, Paul E. Post, had links to a variety of Christian sites, including at least one “intelligent design” site, on his personal OSU web site, When the fiasco became public those links immediately disappeared. The fourth member of Leonard’s committee, an assistant professor of French & Italian, had never before served as graduate school representative on a defense committee and had no qualifications appropriate to Leonard’s area of research. The three professors who brought the anomalies to the attention of the graduate school did not “… demand that Leonard’s dissertation defense be postponed”, as Wells falsely claims, but rather requested that the Graduate School look into very serious questions surrounding the conduct of Leonard’s research and the composition of his defense committee. An administrator in the Graduate School and the head of the program from which Leonard was seeking a Ph.D. began inquiries regarding the anomalous composition of Leonard’s committee. At that, the graduate school representative (the assistant professor of French & Italian) withdrew, and a replacement—the Dean of the College of Biological Sciences, who was qualified to evaluate a dissertation on the teaching of evolution—was appointed. Within 24 hours of that replacement, Leonard’s defense was postponed at the request of his advisor . The graduate school did not postpone Leonard’s defense, his advisor did so when a qualified person was appointed to the defense committee. Finally, Wells’s claims that this “procedural technicality”—not having any qualified examiners on a dissertation defense committee—is “… widely ignored in the case of other Ph.D. candidates …”. Wells is here claiming that the Ohio State University routinely awards Ph.D.s to students whose committees are unqualified to assess the students’s work! That is a breathtaking accusation to make about the Graduate School of the Ohio State University. Wells provides no evidence whatsoever for this extraordinary claim. It merely stands in unsupported thin air. Wells flatly libels a distinguished research university in aid of his sectarian agenda. Conclusion I have to say it must be easy to write as Wells does. Need a “fact”? Make it up. Find an inconvenient fact? Ignore it. Need a quotation? Quotemine a genuine scientist, pasting together bits and pieces from pages apart in the original to make it say something the original wouldn’t recognize. Wells has no shred of intellectual honesty, and has a true soulmate in Salvador Cordova, who was quoted in Nature as saying The critical thinking and precision of science began to really affect my ability to just believe something without any tangible evidence. Wells hasn’t been affected one whit by the precision and critical thinking of science. He blatantly misrepresents an episode for which documentation exists in the public domain that flatly contradicts his distortions. He wholly ignores that documentation in favor of a tissue of misrepresentations and plain falsehoods, and libels a distinguished university to boot. But Wells can’t be bothered with that. He has an agenda: to destroy Darwinism for purely religious reasons, and the facts—and the Ohio State University—be damned. Did You Know? The Ohio State University requires that faculty members on dissertation defense committees be qualified in the subject matter of the dissertation? Wells calls that requirement a “procedural technicality”. Did Wells have anyone qualified on his committee?", "text_length": 11710, "text_sha256": "0b78a0b92080a8f256e3e74163bef31c3bc42ef3c256e4714bcf7e4c604157a9" }, { "route": "/cs/pt_reviews_pigdid/", "title": "PT Reviews \"The Politically Incorrect Guide to Darwinism and Intelligent Design\"", "description": "A number of the contributors to the Panda's Thumb weblog review chapters from \"intelligent design\" advocate Jonathan Wells's 2006 book, The Politically Incorrect Guide to Darwinism and Intelligent Design . The book proved to be a farrago of", "content_kind": "drupal_article", "text": "Legacy route: /cs/pt_reviews_pigdid/ PT Reviews \"The Politically Incorrect Guide to Darwinism and Intelligent Design\" A number of the contributors to the Panda's Thumb weblog review chapters from \"intelligent design\" advocate Jonathan Wells's 2006 book, The Politically Incorrect Guide to Darwinism and Intelligent Design . The book proved to be a farrago of quote mines, obfuscation , misleading rhetoric, and just plain false claims. Introduction Review of Chapter One Review of Chapter Three Review of Chapter Nine Review of Chapter Ten Review of Chapter Fifteen Review of Chapter Sixteen", "text_length": 591, "text_sha256": "a1fe88f41108c7a8c805dfe5cf603b41b6297331ae09318f8c29bbc47e5e028d" }, { "route": "/cs/qrefs/", "title": "Quixotic References", "description": "[1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID move", "content_kind": "drupal_article", "text": "Legacy route: /cs/qrefs/ Quixotic References [Return to The Quixotic Message ] [1] The claim that scientists by the thousands are joining the ID movement, and that it's just a matter of time before the rest see the light, is a propaganda technique known as inevitable victory , and is frequently employed by the ID movement. Very strange it is then that IDist press releases and newspaper articles keep mentioning the same handful of names over and over again, year after year, particularly Dembksi, Wells, and Behe, as if these guys just happen to be a sample of the thousands who are joining in the movement. (Just for clarity, Behe is the only one out of those three who can fairly be called a scientist.) For numerous examples of IDist/creationist proclamations of imminent success, see The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism by Glenn Morton: \"In recent reading of Dembski and other ID proponents I saw them make a claim which has been made for over 40 years. This claim is one that the young-earthers have been making. The claim is that the theo ry of evolution (or major supporting concepts for it) is increasingly being abandoned by scientists, or is about to fall. This claim has many forms and has been made for over 162 years.\" [2] IDists are very keen to protect their image by claiming that they're not creationists, and that they're not even anti-evolutionists. But then their latest tactic for getting ID into public schools is to \"teach the evidence against evolution\". Consider the crowing that they've done about a poll in Ohio: Darwin Would Love This Debate : \"Which option (\"A\" or \"B\") represents your view? \"A. Biology teachers should teach only Darwin's theory of evolution and the scientific evidence that supports it.\" \"B. Biology teachers should teach Darwin's theory of evolution, but also the scientific evidence against it.\" \"Only 15 percent of adults nationally, according to a 2001 Zogby poll, agree with \"A,\" while 71 percent agree with \"B.\" (Not sure: 14 percent.) \" This is a perfect example of a loaded question, because it makes people think that there actually is evidence against evolution, and if this is true, then how can it be objectionable to teach it? IDists also say that what they want is for \"origins science\", as they call it, to be taught \"objectively\". When they say \"objective\" what they really mean is giving equal weight to ID arguments, as if a truly objective and knowledgeable person would find them legitimate. George Orwell would be proud. In a sense though, they're right about one thing: referring to ID as \"the evidence against evolution\" is somewhat appropriate, since it really is nothing more than a collection of criticisms, albeit bad ones. [3] There is very little consistency in IDist beliefs, even among the prominent leaders of the movement. Michael Behe, for example, accepts an ancient Earth and common descent, but does not believe that natural processes can account for all of evolution. In contrast, Philip Johnson staunchly denies common descent. Paul Nelson, in further contrast, is a young Earth creationist. Obviously, at least two of these people are seriously wrong about one or more major aspects of their beliefs, yet the ID movement does everything it can to downplay these differences. Amazingly, they claim that drawing conclusions about these scientific issues, which are precisely what they've been arguing about all along, is not even relevant! To the best of my knowledge, Behe is the only prominent IDist who unequivocally accepts evolution (although he heaps praise upon those who argue against it). Most of the others can be safely classified as creationists, or they're much too circumspect for anyone to know just what they believe. But don't call them creationists -- they'll go bonkers and accuse you of misrepresentation. In fact, the ID movement gets a lot of rhetorical mileage out of claiming that they're being stereotyped by \"Dogmatic Darwinists\" who are trying to persecute and discredit them by linking them to creationism. But not only is it true that most of them are creationists, it's also true that the ID movement uses essentially the same tactics and has the exact same overriding goals as those of the old-school movement: Religious apologetics and \"cultural renewal\". [4] This is a major part of the \"Wedge strategy\" formulated by Philip Johnson. The idea is to advocate a scientific theory (or more correctly, an objection to an existing theory) by avoiding the details at all costs, thereby allowing numerous mutually exclusive viewpoints to exist under the same \"Big Tent\". The details, according to Johnson, can be worked out later, after the Evil Empire has been defeated. Won't that be fun to watch. The Wedge strategy is purely political. A real scientific movement would vigorously debate the differences held among its members, as do evolutionary biologists. The irony is that it's hard to know just what if anything the IDists are objecting to, because they refuse to go into specifics. This has the added benefit of making them extremely slippery in debate. See this interview with Johnson for more: \"So the question is: \"How to win?\" That's when I began to develop what you now see full-fledged in the \"wedge\" strategy: \"Stick with the most important thing\"-the mechanism and the building up of information. Get the Bible and the Book of Genesis out of the debate because you do not want to raise the so-called Bible-science dichotomy. Phrase the argument in such a way that you can get it heard in the secular academy and in a way that tends to unify the religious dissenters. That means concentrating on, \"Do you need a Creator to do the creating, or can nature do it on its own?\" and refusing to get sidetracked onto other issues, which people are always trying to do. They'll ask, \"What do you think of Noah's flood?\" or something like that. Never bite on such questions because they'll lead you into a trackless wasteland and you'll never get out of it.\" [5] Creationists and neo-creationists absolutely love the argument from authority, presumably because it fits in well with their authoritarian world-view. The irony is that scientific authority is almost universally against them when it comes to evolution. The Discovery Institute has made a big deal about its 100 scientists, even though the statement that they signed does not mention ID, and it's language is largely noncontroversial: Discovery Institute pdf Doubting Darwinism Through Creative License. (NCSE) Compare their list to a poll of Ohio scientists , or a letter opposing ID sent by 80 scientific organizations . The predictable IDist retort is to claim that the scientific community is too biased to judge things fairly, which makes one wonder why they seek scientific authority in the first place. [6] See Becoming a Disciplined Science: Prospects, Pitfalls, and Reality Check for ID by Bill Dembski. This was a keynote speech of his at the 2002 RADIP conference in which he proposes ways for ID to be become a \"disciplined science\". His proposals for \"scientific research\" are nothing more than suggestions on how the ID movement can sharpen its polemical skills: \"Building a design curriculum is educational in the broadest sense. It includes not just textbooks, but everything from research monographs for professors and graduate students to coloring books for preschoolers. [...] \"Do the same names associated with intelligent design keep coming up in print or are we constantly adding new names? Are we fun to be around? Do we have a colorful assortment of characters? Other things being equal, would you rather party with a design theorist or a Darwinist? \"These, then, are my recommendations for turning intelligent design into a disciplined science.\" To answer his question, I would much rather party with a design \"theorist\". Anyone who can do what they do with a straight face has got to be good at telling jokes. :-) [7] Time and time again we're told that evolutionary theory is somehow sorely lacking, but when asked how well ID \"theory\" can stack up to it in terms of explaining the natural world, we're told that ID doesn't have to, because, well, just because. This makes it not only a \"different kind of theory\" than evolution, it makes it different from any scientific theory, past or present. See this ISCID Brainstrorms thread containing posts by Bill Dembski; many other examples could be given: \"You've charged me with moving the goalposts and adjusting the definition of irreducible complexity because I require of evolutionary biologists to \"connect the dots\" in a causally convincing way. The dots here are functional precursors that could conceivably have evolved into the final system of interest. [...] \"As for your example, I'm not going to take the bait. You're asking me to play a game: \"Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.\" ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots.\" [8] Here's an excerpt from The Truth, the Whole Truth, and Nothing but the Truth? by Brian Spitzer, which is a critical review of Philip Johnson's Darwin on Trial : \"It is useless to try to explain science to someone who isn't interested in what the facts have to say. And it's useless to try to learn anything from such people. If they are clever, as Johnson is, they can find a way to claim that almost any fact supports their position. If evolutionists agree on something, it's a dogmatic orthodoxy; if they disagree, they're squabbling about every detail of evolutionary theory. ...\" This tactic is frequently encountered on debate fora as well, though it's probably unintentional most of the time. An ID advocate will pull out a \"maverick\" scientist who takes a different view on things, and then claim that this is somehow evidence of evolutionary theory's deficiency. But why are all of these scientists against ID? Dogmatic orthodoxy, of course... [9] The ID movement's claim that Darwinists are driven by religious and/or ideological motivations is so glaringly hypocritical, it serves as its own parody. The leaders of the movement are very careful to do what they can to downplay their own biases, at least for public mass consumption (they tend to be a bit less coy in front of religious audiences). Here are the two specific examples alluded to: Evolving Banners at the Discovery Institute . (NCSE) The Center's Name Change (C(R)SC) [10] Lest anyone thinks this is an exaggeration, simply check out Bill Dembksi's forward to Discovery Institute Fellow Benjamin Wiker's book, Moral Darwinism: How We Became Hedonists . This article is a masterpiece of hypocrisy, even by Dembski's standards. (And the title of Wiker's book should tell you a thing or two as well.): \"Understanding this movement [Darwinism] is absolutely key to understanding the current culture war. Believers in God often scratch their heads about western culture's continual moral decline. What was unacceptable just a few years ago is today's alternative lifestyle and tomorrow's preferred lifestyle. Abortion, euthanasia, divorce, sexual preference, and drug abuse are just a few of the moral issues that have undergone massive changes in public perception. [...] \"Epicurus's most prominent disciple is without question Charles Darwin. Darwinism is not only the most recent incarnation of Epicurean philosophy but also the most potent formulation of that philosophy to date. Darwinism's significance consists in the purported scientific justification it brings to the Epicurean philosophy. But the science itself is weak and ad hoc. As Wiker shows, Darwinism is essentially a moral and metaphysical crusade that fuels our contemporary moral debates. Furthermore, Wiker argues that the motivation behind Darwinism today is its alternative moral and metaphysical vision rather than the promotion of science. \"Wiker's project has nothing to do with scapegoating Epicurus, Darwin, or anyone else for that matter.\" Sure Dr. Dembski, sure . Blaming the all of the world's problems, real or perceived, on just one scientific theory isn't scapegoating. Nah ... [11] To be fair, disparaging the contradictory philosophies that Darwinian evolution has supposedly spawned has been a long-standing staple of the old-school creationists, and it is far easier to find examples of this coming from them than it is to find it from the neo-creationists. But ID's big tent has welcomed the old-schoolers with open flaps, so the IDists have little right to complain if people have a hard time telling who's who. Furthermore, the type of IDists commonly found in online debate fora, who, unlike the national movement, do not all share a common metaphysical viewpoint, will tend to contradict each other far more often. Thus a far left anarchist type will blame Darwin for contributing to capitalism, while the more common far right types will try to blame Darwin for Communism. Nevertheless, the consequentialist fallacy -- that Darwinism causes \"bad things\" and thus can't be true -- is high on the ID movement's list of propaganda techniques. It's extremely easy to cull such examples from \"regular\" creationists or online debaters, but just to be sporting, I've only provided references from leading members of the ID movement: On Liberalism: Nihilism and the End of Law by Philip Johnson. \"The primary answer is that modernist thinking assumes the validity of Darwinian evolution, which explains the origin of humans and other living systems by an entirely mechanistic process that excludes in principle any role for a Creator. In the word of the neo-Darwinist authority George Gaylord Simpson, the meaning of \"evolution\" is that \"man is the result of a purposeless and natural process that did not have him in mind.\" For modernist intellectuals, belief in evolution in precisely this sense is equated with having a scientific outlook, which is to say, with being a modernist. The price for denying \"science\" is to be excluded from modernist discourse altogether. [...] Greenawalt defends a limited role for religious convictions in a jurisprudential culture whose ruling paradigm, called \"liberalism,\" is roughly identical to what I have been calling modernism. Or Benjamin Wiker's article, Playing Games with Good & Evil: The failure of Darwinism to explain morality : \"Allow me (since we are going to be playing games for rather high stakes) to lay my own cards on the table. I find this sort of talk absurd. Darwinian game theory is not new but simply a rehash of liberal political theory disguised as cutting-edge science. Give it a few vigorous scratches and we find Thomas Hobbes, the very father of modern political liberalism, back to haunt us from the 17th century. Hobbes was also the father of modern materialism, and his political liberalism was rooted in his mechanistic account of nature and human nature.\" On Racism : Not Just in Kansas Anymore by our friend Philip Johnson: \"In short, Congress contemplated that biology classes should explore matters that Darwinists would prefer to ignore, such as criticisms of classic textbook examples like the faked drawings of embryonic similarities, and even the possible role of Darwinian concepts in encouraging the scientific racism embodied in eugenics programs.\" More Johnson: Domesticating Darwin . \"This explanatory project carried some extremely racist implications, however. Because he was determined to establish human continuity with animals, Darwin frequently wrote of 'savages and lower races' as intermediate between animals and civilized people. Thus Degler observes that it was as much Darwin himself as any of the so-called \"social Darwinists\" who set the evolutionary approach to human behavior on a politically unacceptable course. 'Thanks to Darwin's acceptance of the idea of hierarchy among human societies,' he tells us, 'the spread and endurance of a racist form of social Darwinism owes more to Charles Darwin than to Herbert Spencer.' \"Nor is a scientific grounding for racism the only unsavory heritage of nineteenth-century Darwinism. Degler also cites Darwin's theories about the intellectual inferiority of women, and describes how Darwin's cousin, Francis Galton, employed Darwinian logic in favor of an ambitious eugenics program to improve the breed.\" (Note also the charge of sexism.) And then there is this truly deplorable letter by John Calvert (of the Kansas \"ID Network\") to the local paper in response to one written by KCFS (Kansas Citizens for Science) about teaching ID in public schools: What were we fighting against in Bastogne? We were fighting against a Nazi regime that used the philosophy of Naturalism to justify a eugenics program of terrifying proportions. Naturalism is the belief that all phenomena result only from the laws of chemistry and physics and that teleological or design explanations are not valid. Naturalism is not science. It is a belief system. (You can read a reply to Calvert's letter here .) On Capitalism (and other rightist thought): As reported by CBN news : [Philip] Johnson explained, \"Andrew Carnegie, John D. Rockefeller, they loved Darwinism because it said they were right to amass all the money in the world, you know. And if other people didn't have as much money, it was because they were inferiors.\" Richard Weikart, Discovery Institute Fellow, in The Roots of Hitler's Evil . \"Second, since Hitler believed that nothing exists beyond nature, he tried to find his purpose in life in obeying the iron laws of nature. Darwinian biology was especially significant in this regard, as he tried to apply its lessons to politics and society. Darwinism especially forms of it often disparagingly called Social Darwinism today taught him that life is a constant struggle for existence leading to biological progress. Hitler embraced eugenics and racial extermination of allegedly inferior races as means to improve the human species and foster progress.\" H-Ideas archived post by Weikart: \"It is, of course, true that many distorted Darwin's views, but Darwin's own work reflected laissez-faire economic views and propagated racial inequality (he claimed \"savages\" were inferior mentally and morally).\" In fairness, from what little is available from him online, Weikart tends to dispel some common myths about Darwin's link to Social Darwinism, and has himself pointed out that people from completely opposite political viewpoints have tried to find support in Darwinism (much like the Bible, I suppose). Yet he puts more blame on Darwin than traditional scholars, such Robert Bannister, whose 1979 treatise on the subject Weikart calls \"revisionist\" . The next book he has planned, apparently with Discovery Institute backing, is to be titled, From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Devaluing Human Life in Germany . Given the typical style of books published by the DI Fellows, it will be interesting to see how Weikart presents this one. Regardless of its content, you can bet the DI will use it as an ad hominem against evolutionary theory. Ironically, Weikart's published dissertation is titled Socialist Darwinism: Evolution in German Socialist Thought from Marx to Bernstein , which brings us to... Socialism (and other leftist thought): The most infamous of ID writings is known as the Wedge Document , which is the de facto manifesto of the ID movement, having been unintentionally leaked from the Discovery Institute: \"Finally, materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promised to create heaven on earth.\" Here is a", "text_length": 20000, "text_sha256": "a3f54b2af278cb6a9cf3dde36569bc7f67517fd1ad0bbf36c5ec6fd906af4dc4" }, { "route": "/cs/quixotic_message/", "title": "\"The Quixotic Message\", or \"No Free Hunch\"", "description": "Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates.", "content_kind": "drupal_article", "text": "Legacy route: /cs/quixotic_message/ \"The Quixotic Message\", or \"No Free Hunch\" Steve Reuland (aka \"theyeti\") takes a humorous but well-referenced look at the inconsistencies of the Intelligent Design movement and its advocates. by theyeti * [contributed January 22nd, 2003] [Author's note: This collection of contradictions and absurdities was originally composed and posted to the antievolution.org discussion board. It was later decided to put it up on the web so that it can be exposed to a larger audience. This collection is meant to be lighthearted and funny, though it does highlight some serious issues in the ID debate. If this presents a problem for you, then go read something else. Furthermore, at the urging of several readers, I decided to make a references page to document these inconsistencies. It can be reached by clicking on any one of the numbered references below. If you feel that this would detract from the humor, then feel free to skip it. But as Dave Barry would say, I'm not making this up ...] IDists... On Intelligent Design... ID is whatever we say it is, and we don't agree. Greater and greater numbers of scientists are joining the ID movement, which is why we keep referring to the same three year after year. [ 1 ] ID is not creationism, and can be perfectly compatible with evolution. This is why we're asking schools to teach the \"evidence against evolution\".[ 2 ] We're not creationists, except for those of us who are, but the rest of us won't confirm that we're not. But if you call us creationists, we'll complain to no end. [ 3 ] The correct stance on issues like an ancient Earth, the common ancestry of organisms, and natural selection can be worked out later, after we've convinced the public that they should be rejecting at least one of these. [ 4 ] ID is a widely accepted theory in the scientific community. Just last year, over 100 scientists signed a statement which does not support ID, but does say that they are \"skeptical\" of Darwinism. The opinions of tens of thousands of other scientists don't count, because they're all biased. [ 5 ] ID is a program for research into the science of design, nothing more. Part of our research plans are to produce coloring books for preschoolers, and to make ourselves more likeable at parties. [ 6 ] ID is a scientific theory for detecting purpose and teleology in nature. But don't ask us what that purpose is, because that's a religious question that's separate from ID. The Designer could be anything from God to a space alien. But the Raelians, who believe it was a space alien, are being illogical. On Darwinism... Darwinism can't explain the evolution of life in every single detail, therefore it's wrong. But don't ask IDists to explain these things, because that's not the kind of theory ID is. [ 7 ] Mainstream scientists dare not disagree with the monolithic block that is Darwinian orthodoxy. However, here are a number of mainstream scientists who disagree with each other on some issues, which means that they can't agree on anything. [ 8 ] Darwinists are driven by religious and ideological motivations. But since we've removed the picture of God and the phrase \"Cultural Renewal\" from our website, everyone knows this isn't true of us. [ 9 ] Absolutely everything wrong in society is caused by dogmatic Darwinian atheistic materialists. Including stereotyping, demonizing, and scapegoating. [ 10 ] Darwinists are responsible for both socialism and laissez-faire capitalism. Both racism and liberalism. Both feminism and sexism. Both animal research and the animal rights movement. And Commie-Nazism. [ 11 ] On philosophy... Philosophers cannot agree on exactly where the line between science and non-science lies. Therefore, anything can be considered science if we say so. If a living system looks well designed, it's evidence for ID. If it looks poorly designed, that's just because we have no way of knowing what constitutes good and bad design. Afterall, we can't tell that it's bad design because we have no way of knowing what the Designer really intends. But we do know that ID will revolutionize culture, society, and law, according to what the Designer intends. [ 14 ] Methodological naturalism is an unfair rule that keeps us from considering supernatural explanations. But this would mean that detectives couldn't consider an intelligent agent in a person's death, because as we all know, murderers are supernatural. [ 15 ] A good scientific theory like ID should be vague and ambiguous, and refuse to propose any specific details about mechanism or history. Some unspecified being \"designed\" something, somewhere, at some point in time, somehow, is a perfectly good explanation. The argument from design is not a theological argument, because we aren't necessarily talking about God. But any rebuttal of the design argument is theological, because it requires us to say \"God wouldn't do it this way\", and this is not legitimate. [ 16 ] On the Evidence... Since the peppered moth case has been proven problematic, natural selection is disproven. The other 1,582 studies of natural selection in the wild, as well as the numerous laboratory studies, don't count. [ 17 ] And peppered moths don't rest on tree trunks. The actual datasets of moths found in natural positions in the wild, off but also on trunks, are irrelevant because researchers have captured thousands of moths over the years in their moth traps, and not once has a moth in a trap been found on a tree trunk. [ 18 ] Since moths don't rest on tree trunks but instead higher up in the branches, this means that birds can't get to them, because there is a magic barrier preventing birds from visiting tree branches. As demonstrated above, moths don't rest on tree trunks, which means that the photographs showing the contrasting conspicuousness of moths on tree trunks found in textbooks are FRAUDS, FRAUDS, FRAUDS. All the other staged animal photos in textbooks are however unobjectionable. The fact that more inclusive groupings, such as phyla, appeared before more specific groupings, such as genera, is evidence against evolution. Likewise, the fact that Europeans first appeared before Tony Blair is evidence against shared human ancestry. [ 19 ] Evolution can't produce novel information, because any change to an enzyme that increases substrate specificity reduces the reactivity of the enzyme with other compounds, which is a loss of information. Similarly, any change which increases the enzyme's generality is a loss of information because the enzyme has lost some specificity. [ 20 ] Life could not come about by natural means because it has Specified Complexity. Specified Complexity means something that cannot come about by natural means, therefore life must exhibit Specified Complexity. [ 21 ] It was very nice of our loving Designer to design an immune system to protect us from the deadly diseases He designed. The fundamental unity of living things means that there is only one Designer. The extraordinary variation among living things, including their tendency to kill each other, just means that our singular Designer is very creative and whimsical. [ 22 ] Lateral gene transfer, which is a powerful mechanism of evolution, is evidence against evolution. The fact that the laws of the universe are perfect for life is evidence for a Designer. The fact that the laws of the universe can't produce life is evidence for a Designer. [ 23 ] Irreducibly Complex structures require multiple parts. Therefore they can't evolve. If someone demonstrates how a structure that requires multiple parts could have evolved, that just means that it wasn't Irreducibly Complex. IC structures must be molecular systems. Except mousetraps. \"Indirect\" pathways are wildly unlikely and as hard to find as leprechauns, and are therefore only a \"bare\" possibility but not a realistic one and can be safely disregarded, despite the detailed attention paid to them by every major biologist from Darwin to Dawkins. [ 26 ] The ID hypothesis, on the other hand, bears no resemblance to leprechauns. [*] \"theyeti\" is a pseudonym of Steven Reuland. Comments, suggestions, additions, or threats of eternal damnation can be sent to reulansn@musc.edu.", "text_length": 8220, "text_sha256": "4a1bd242e9353d3254faa9872845271b5077583d40ecad7edbb24761896fee9e" }, { "route": "/cs/spitzer_dot_review/", "title": "The Truth, the Whole Truth, and Nothing but the Truth?", "description": "Brian Spitzer's review of Phillip Johnson's Darwin on Trial tells why it and the \"Intelligent Design\" movement are neither science—nor Christian.", "content_kind": "drupal_article", "text": "Legacy route: /cs/spitzer_dot_review/ The Truth, the Whole Truth, and Nothing but the Truth? Brian Spitzer's review of Phillip Johnson's Darwin on Trial tells why it and the \"Intelligent Design\" movement are neither science—nor Christian. Why Phillip Johnson's Darwin on Trial and the \"Intelligent Design\" movement are neither science—nor Christian by Brian Spitzer DRAFT, Version 1.1 email author for comments and feedback [Contributed July 15, 2002; Last Modified: July 18, 2002] Introduction Darwin on Trial Lawyer games Just the facts, ma'am How science isn't done Did they really say that? Colin Patterson Steven Jay Gould Nature on the British Museum of Natural History Tricks of the trade Distortions and inventions The tautology argument The missing links which aren't, and other examples The log in your own eye Selective use of evidence The moving target Johnson's response Conclusions Additional examples Bait-and-switch Selective use of evidence Ad hominems and innuendo Misrepresentations of science Quote mining Begging the question \"Straw man\" arguments Conspiracy theory Introduction Lawyers are not the best-respected professionals in our society. Being a lawyer gives one a certain prestige because law requires expertise, like medicine or science, but we tend to put lawyers in the same shady box as salesmen and politicians. We don't trust them. And—perhaps—there are good reasons not to. Courtroom lawyers are called upon to represent the guilty as often as the innocent, and they are duty-bound to build the best case that they can. It follows logically that a courtroom lawyer will spend half of his or her time trying to convince a jury of the truth; the other 50% of the time, they are trying to persuade the jury to believe something which isn't the truth. This is not only permissible in the courtroom, it's necessary for our justice system to work. It's ironic that a system of justice requires what could be called 'injustice' from its participants, but that's what the law demands: lawyers playing parts which they may not even believe. Our law dictates that even the guilty should be represented in court, and most of us would agree that this curious tangle of competing fictions turns out to make our justice system more just. Because of this, it is entirely acceptable for a lawyer to play his or her false part in court, just as it is acceptable for an actor to play someone fictional on the stage. But when people assume false identities offstage, we call them impostors. I would argue that when a lawyer plays lawyer games outside the courtroom, it is just as morally wrong. Of course, you can't have a debate without having debating tactics. It's entirely fair, inside the courtroom or out, to showcase the facts that are most favorable to you. In the same way, it's perfectly fair to write a radio ad pointing out that your brand of widgets is cheaper and more reliable than your competitor's—if those favorable facts are actually true. But we're all aware of sleazy sales pitches where the tactics are used to obscure or distract attention from the relevant facts. I am not claiming that the line between these two is crystal-clear. But I am claiming that those who try to sway public opinion—especially if they are laying claim to the moral mantle of Christianity—are ethically bound to stick to the fair methods and leave the lawyer games in court. Back to top 1. Darwin on Trial Darwin on Trial , the book by Phillip Johnson which founded the neocreationist movement of \"intelligent design\", was written in 1991. I first encountered it in 1996. At the time I knew nothing at all about creationism. A friend-like me, a serious Christian as well as a scientist—suggested that I take a look at it, and I was curious enough to do so. There are certainly things about the book which I applauded, at the time. I've always been irritated by pop-science works which try to make statements about God (or the lack thereof) as though these statements are supported by scientific fact, and I was glad to see someone taking on Richard Dawkins. But even without much training (I had only a B.A. in biology), while reading through Johnson's book I began to notice some puzzling things. At first, they were quite small: a claim in one place which contradicted a different claim in another. A strange lapse of logic-perhaps excusable on account of the author's inexpertise? Statements which didn't fit with what I knew firsthand about science and scientists. I was naive. I assumed that a Christian writing to other Christians would provide a scrupulously fair and accurate account of the facts [1] . But the deeper I got into Darwin on Trial , the less naive I became. And the clearer it became that the driving force behind Johnson's book was neither fairness nor accuracy. A few years passed with this troubling thought at the back of my mind. I entered graduate school and started doing real science myself. And, the more I learned, the less I trusted Darwin on Trial . I finally challenged myself to put my mistrust to the test. Perhaps Johnson was merely confused about some things. What I should do, I told myself, is look at the sources he actually used in writing Darwin on Trial , and see what they say. Perhaps part of what Johnson says is accurate; perhaps his sources misled him in places. So I went to the campus library and started checking his claims. I was a lot less naive when I finished that task. I found that almost every scientific source cited by Johnson had been misused or distorted, in ways ranging from simple misinterpretations and innuendos to the construction of what appears to be outright fiction. The more closely I examined Darwin on Trial , the more inaccuracies I found, until it became almost impossible to catalogue all of the misleading statements in Johnson's work. This book-upon which the \"intelligent design\" movement is trying to hang a program of social reform and public education-is perhaps the ugliest and most deceptive book I have ever seen. It may seem irrelevant to critique a book over a decade since it was published. But Darwin on Trial was the work which founded the \"intelligent design\" movement, and Phillip Johnson is still regarded as the \"godfather\" of that entire school of thought. Later \"intelligent design\" creationists have adopted many of his exact arguments, as well as many of the questionable tactics and strategies used in Darwin on Trial . Perhaps most importantly, nobody in the \"intelligent design\" movement has, to my knowledge, ever criticized or disavowed any of the claims in Darwin on Trial . As I will show, this book is so full of questionable tactics that it would be hard for any informed reader not to notice any of the inaccuracy. All of the stars of the \"intelligent design\" movement, by their silent approval of these tactics, stand under a cloud of suspicion at the very least. Many Christians have welcomed the \"intelligent design\" creationists in the belief that they are fighting for God and truth. But, as the televangelism scandals of the 1980's should remind us, there are some more unsavory reasons for seeking celebrity in the Christian community: money, fame, applause, or power, especially political power. In short, there are a wealth of reasons why Christians need to be careful about trusting the stars of the \"intelligent design\" movement. And even well-intentioned debaters, if they let their desire to win the argument outstrip their respect for the facts, will turn out a product which is grossly misleading. Integrity is important. If—as I will show in this essay—the claims of \"intelligent design\" are more a product of debating tactics and tricks than they are a fair and honest presentation, Christians need to seriously consider whether they can support this movement in good faith. Back to top 2. Lawyer games To understand a lawyer's book, talk to another lawyer. Darwin on Trial has been reviewed by, among other people, a practicing lawyer by the name of Thomas C. Sager. In his review, Sager makes some very interesting points about the legal profession which he and Johnson share. He puts it succinctly: \"The job of a lawyer is not to find the truth, (that is the job of the judge or jury) but to defend (or prosecute) the client.... The standard is to vigorously argue on behalf of one's client, rather than to pursue an abstract 'truth' or even 'justice'.\" Sager goes on to note: \"In supporting the client, the lawyer may use any ethical means available. It is perfectly ethical for a lawyer to make ad hominem attacks on the opposing witnesses, to present incomplete information to a jury, to bring in irrelevant data, and of course to use a wide panoply of rhetorical skills and tricks. Science, obviously, has different goals. But the lawyer's orientation should be kept in mind when analyzing Johnson's book, because he is a lawyer, he has titled his subject a trial, he pursues it as a trial, and his job is to prosecute Darwinism. Lots of things are 'fair', from his point of view.\" [2] Johnson might protest that none of these tactics— ad hominem arguments, half-truths, and rhetorical sleight-of-hand-are technically lies . I am not interested in quibbling over fine shades of meaning in such definitions; in my view, deliberately misleading people does not become more acceptable because it goes under a different name. To a certain extent, it does not even matter whether these inaccuracies are deliberate or not. If Johnson is being intentionally misleading, that is an ethical and intellectual crime. If he is merely letting a desire to attack evolutionists override his concern for careful and accurate research, that indifference to fairness is also a crime, though a lesser one. In either case, Darwin on Trial cannot safely be trusted at face value as a guide to the facts. Back to top 3. Just the facts, ma'am Phillip Johnson, perhaps even by his own admission, is not terribly interested in facts. Indeed, the heart of the argument against evolution which is presented in Darwin on Trial —and echoed throughout the \"intelligent design\" movement up until the present day—is that science isn't actually about facts. According to Darwin on Trial , it's about \"ideology.\" The accusation is that evolutionary scientists are all hopelessly biased, wedded to an atheistic ideology, and that the only reason they support evolutionary theory is that they need some way to explain the marvels of biology without bringing up God. This is a clever strategy, because a number of well-known and outspoken scientists are in fact atheists, and the Christian community in America has long had a vein of simmering resentment against a few individuals, like Richard Dawkins, who have preached atheist ideology while calling it science. Johnson taps into this vein skillfully, claiming that \"Darwinism\" is not only the view that natural forces created biology as we see it today, but also the insistence that God is a mere fable, uninvolved in evolution or—for that matter—anything else. The problem is that this argument isn't true. The truth is that biologists are overwhelmingly convinced that the theory of evolution really does explain the natural world accurately. That's why they support it, not some \"ideology.\" Johnson and the other \"intelligent design\" creationists are aware that a large number of evolutionists maintain a deep faith in God. However, if the \"intelligent design\" creationists acknowledged them, they would have to admit that there are other reasons besides ideology to agree with the theory of evolution. Their strategy has been to deny that these people exist. A Gallup poll conducted in 1982 [3] found that only about 10% of Americans think that \"Man evolved over millions of years from less developed forms. God had no part in this process.\" 90% of us, then, reject \"Darwinism\" as Johnson defines it, and the \"intelligent design\" creationists are fond of quoting this statistic. What they avoid mentioning is the other half of the poll, in which Gallup went not to the average American but to the average American scientist. About 40% of scientists declared their belief in both evolution and in an actively intervening God very much in control of the process. Either 40% of the scientists in America are fighting tooth and nail in defense of an ideology which they actually reject , or-based on the very poll which Johnson likes to cite-Johnson's argument about ideology is bunk. There is plenty of other evidence suggesting that Johnson should know this argument to be just that: bunk. Upon reading through the sources cited in Darwin on Trial , I found that the distinction between science and atheism was drawn quite clearly on a number of occasions It is made repeatedly by theologian Langdon Gilkey ( Creationism on Trial , pp.34-35, 97, 175-176) [4] and scientist Douglas Futuyma ( Science on Trial , p.217) [5] , both of whom are cited by Johnson. While Darwin on Trial points out that evolutionists like Dawkins, Julian Huxley, and Steven Jay Gould claim or imply that God is dead, it neglects to mention that all these figures have been criticized harshly and publicly by evolutionary biologists for muddying the line between scientific conclusions and metaphysical preferences. Johnson has a ready excuse: he claims that any time scientists say that they are not atheists, it is only to fool the public—or, as he puts it in one of his nastier moments, \"for fear of jeopardizing the funding for scientific research\" (p.127). However, Darwin on Trial gives no evidence to back up this accusation. That's because no such evidence exists. If Johnson wants to convince us that his accusations of atheism are not just conspiracy theory, he has had plenty of opportunity to do so. Several reviews of his book have criticized him for pretending that the personal views of a few inflammatory scientists are the consensus view of the scientific community, but Johnson has made no attempt to correct his claims or provide evidence for them. To my knowledge, neither have any of the other leaders of \"intelligent design\" creationism. There can be no denying it: stereotypes are rhetorically handy. But they aren't honest. The attempts by a few scientists to clothe their personal philosophies in the authority of science are certainly deplorable, and I believe that Christians are right to deplore them. But is the correct response to meet one mistruth with another? The way science works—methodological naturalism, to call it by its highbrow name [6] —is to try to explain the world in terms of ideas which can be empirically tested. The tests can be experimental, or one may posit an hypothesis and then look for those empirical signs which would follow logically if that hypothesis were true. Johnson's strategy is to claim that this is the same as atheism (see, for example, pp.116-117 of Darwin on Trial ). This argument does not stand up for long under scrutiny. We may not call it by such an elaborate name, but when a plumber tries to find out why your sink is clogged, or when police try to solve a crime, or when an engineer tries to design a bridge—in fact, whenever anyone tries to figure out pretty much anything about the physical world we live in—they are using methodological naturalism. You yourself use it every day. So do the \"intelligent design\" creationists. Scientists aren't precommitted to atheism. They're precommitted to a scientific method that can actually work. The only alternative to methodological naturalism—that is, to trying to understand the world in terms of ideas which can be empirically tested—is to try to understand the world in terms of ideas which can't be tested at all. See if you can unclog your sink that way. Johnson should, by now, be painfully aware that this argument does not hold up. He has been challenged clearly and publicly (for instance, by Robert Pennock) [7] to present a working alternative to methodological naturalism. Despite the fact that he has had over a decade to work out a method for what he calls \"theistic science\", Johnson has had nothing to say. Writes Pennock: \"This is not surprising, for he has consistently refused to say anything positive about how a theistic science is supposed to work.\" If Johnson really feels that scientists have other options—if we really do have a choice other than methodological naturalism in science—he should give us a hint about what those options are. Until the intelligent design creationists explain to scientists what other methods they could be using, I find it very hard to blame the scientists for considering methodological naturalism to be a limited but indispensable tool. Back to top 4. How science isn't done Darwin on Trial misrepresents science just as it misrepresents scientists. Johnson seems to suggest that any event which has not been directly observed may be dismissed as \"pure philosophy\", but inferential evidence-as he should know from law-can prove a point as well as direct observation. Essentially all modern science, including particle physics, astrophysics, geology, microbiology, and chemistry, relies on inferential evidence. He claims that scientists disagree over \"every detail\" of evolutionary theory, but Douglas Futuyma, on p.171 of Science on Trial (again, a book cited in Darwin on Trial ) explains accurately and clearly what is and is not in dispute in the scientific community. On p.30 of Darwin on Trial , Johnson dismisses evolutionary mechanisms such as developmental constraints and pleiotropy—despite the fact that they are proven, genuine mechanisms that are not only compatible with Darwinian theory but are practically logical outgrowths of it. Darwin on Trial claims on pp.72-73 that, because developmental processes are different in different classes of tetrapods, the resulting traits cannot be homologues of one another; but this is only true if evolution adheres strictly to the principle of recapitulation [8] , a principle which was rejected decades ago by modern science. It suggests on p.80 that Archaeopteryx is just a mosaic along the lines of the platypus (it isn't); suggests on p.94 that the isolation of present-day taxa is at odds with the theory of evolution (this is incorrect); and on pp.95-96 claims that neutral theory is incompatible with Darwinian theory (a conclusion soundly rejected in at least one paper actually cited on the subject in Darwin on Trial ) [9] . After examining the sources which Johnson himself used in writing Darwin on Trial , I find it very difficult to understand how a writer with a serious concern for fairness could have reached the conclusions which are stated in Darwin on Trial . Serious misunderstandings of science pervade Darwin on Trial . For example, Johnson suggests that all scientists stick to the Darwinist party line out of self-interest—apparently unaware that scientific careers are made not by conformity but by coming up with radical new ideas. Any working scientist could have told him that. He does not understand basic scientific terminology (such as the word \"tentative\", for example, an error which he has not corrected even after being informed of it), or how the \"self-correcting\" nature of the scientific enterprise works. Many of these misunderstandings are so basic that Johnson seems to have done little or no research on the topic. In short, rather than do the work involved in understanding how science actually works, Johnson apparently made up a picture of modern biology which he finds useful for rhetorical purposes. Is this really the sort of work on which a true intellectual movement can be founded? Is this the sort of ethics with which the Christian community wants to ally itself? Back to top 5. Did they really say that? a. Colin Patterson Most damning of all is the way in which Darwin on Trial represents the views of other individuals. In several cases, Johnson cites the published opinions of scientists on various matters; it is therefore possible to set his book side-by-sid", "text_length": 20000, "text_sha256": "3dd16d574e76244be9236494c7882c33bd437ee5690c499c2556c3c0164e26f6" }, { "route": "/cs/syn_dembski_dodges/", "title": "The Design Revolution? How William Dembski Is Dodging Questions About Intelligent Design", "description": "Mark Perakh's essay on the tactics used by William Dembski in responding to, or not responding to, criticism and critics.", "content_kind": "drupal_article", "text": "Legacy route: /cs/syn_dembski_dodges/ The Design Revolution? How William Dembski Is Dodging Questions About Intelligent Design Mark Perakh's essay on the tactics used by William Dembski in responding to, or not responding to, criticism and critics. Read the full article PDF (off-site) .", "text_length": 287, "text_sha256": "2bde9cd21212a30b177d62820f09e723203fc5ad68e6c8420b032d67c7806122" }, { "route": "/cs/syn_stormtroopers/", "title": "How Intelligent Design Advocates Turn the Sordid Lessons from Soviet and Nazi History Upside Down", "description": "Wesley R. Elsberry and Mark Perakh examine the invidious comparisons made by \"intelligent design\" advocates where they liken evolutionary biologists to Soviet and Nazi leaders. In particular, the bizarre misuse by ID advocates of the exampl", "content_kind": "drupal_article", "text": "Legacy route: /cs/syn_stormtroopers/ How Intelligent Design Advocates Turn the Sordid Lessons from Soviet and Nazi History Upside Down Wesley R. Elsberry and Mark Perakh examine the invidious comparisons made by \"intelligent design\" advocates where they liken evolutionary biologists to Soviet and Nazi leaders. In particular, the bizarre misuse by ID advocates of the example of Trofim D. Lysenko, pseudoscientist extraordinaire, is examined. Read the full article in PDF (off-site) .", "text_length": 485, "text_sha256": "425585b1c15599d75ee3a9a52227a2103cf75acfc284293531ee38e91c2c8753" }, { "route": "/cs/td_volunteers/", "title": "TalkDesign Volunteers", "description": "Mark Perakh, PhD Dr.Sci, Professor of Physics Emeritus California State University Fullerton perakh@bigfoot.com www.nctimes.net/~mark, www.talkreason.org Wesley R. Elsberry, Ph.D. Wildlife and Fisheries Sciences, Texas A&M University http:/", "content_kind": "drupal_article", "text": "Legacy route: /cs/td_volunteers/ TalkDesign Volunteers Mark Perakh, PhD Dr.Sci, Professor of Physics Emeritus California State University Fullerton perakh@bigfoot.com www.nctimes.net/~mark, www.talkreason.org Wesley R. Elsberry, Ph.D. Wildlife and Fisheries Sciences, Texas A&M University http://www.antievolution.org/ John S Wilkins, Ph.D. - jointly between History and Philosophy of Science, and Botany University of Melbourne Topic: Species concepts Jack Krebs Vice-President Kansas Citizens for Science www.sunflower.com/~jkrebs Liz Craig President, Kansas Citizens For Science www.kcfs.org Freelance writer lizard6849@yahoo.com Randy Bennett Associate Professor, Biology Juniata College Evolutionary Developmental Biology http://faculty.juniata.edu/bennett/ James H. Swan, PhD Professor Public Health Sciences Wichita State University jim.swan@wichita.edu Board Member, Kansas Citizens for Science Burt Humburg Resident in General Surgery University of Minnesota Minneapolis, MN Matt Young Department of Physics Colorado School of Mines www.mines.edu/~mmyoung", "text_length": 1064, "text_sha256": "260d6020e8be994ef494a2d3d66378c6965fedb95d187eda644e4ffb993e28d7" }, { "route": "/cs/theft_over_toil/", "title": "The advantages of theft over toil: the design inference and arguing from ignorance", "description": "John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few p", "content_kind": "drupal_article", "text": "Legacy route: /cs/theft_over_toil/ The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by \"intelligent design\" advocate William A. Dembski for his \"explanatory filter\". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few papers in the peer-reviewed literature that is explicitly about \"intelligent design\". John S. Wilkins 1 , Wesley R. Elsberry 2 Unedited version. Published as: Wilkins, John S, and Wesley R Elsberry. 2001. The advantages of theft over toil: the design inference and arguing from ignorance. Biology and Philosophy 16 (November):711-724. Abstract Intelligent design theorist William Dembski has proposed an \"explanatory filter\" for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design. Keywords Intelligent design, Bayesian inference, natural selection, Darwin, Dembski Sam Spade enters his office to find \"Fingers\" Finagle, a reformed safecracker, standing in front of his open safe holding the priceless artifact the Cretan Sparrow that Spade was looking after for a client. \"Fingers\" insists he did not crack the safe, but merely spun the combination dial a few times idly, and it opened by itself. Spade knows from the promotional literature that came with the safe when he bought it at the Chump end-of-season sale that is has over 10 billion (1010) possible combinations, and that only one of these will open it. Moreover, he knows that the dial must be turned in alternating directions, not - as \"Fingers\" claims he did - in the same direction repeatedly. What does Spade know about this situation? Is the safe open by design, or by accident? William Dembski (1998) thinks he can answer this question definitively. Dembski has proposed an \"explanatory filter\" (EF) which, he claims, enables us to reliably distinguish events that are due to regularities, those that are due to chance, and those that are due to design. Such a filter is needed, he believes, to determine the reason for cases like Spade's safe, the discrimination of signals by the Search for Extra-Terrestrial Intelligence project (SETI) that are due to intelligent senders from those that are caused by ordinary phenomena like quasars, and most critically, whether all or some aspects of the biological world are due to accident or design. In other words, Dembski's filter is a reworking of Paley's design inference (DI) in the forensic manner of identifying the \"guilty parties\". We will argue that Dembski's filter fails to achieve what it is claimed to do, and that were it to be adopted as a scientific heuristic, it would inhibit the course of science from even addressing phenomena that are not currently explicable. Further, the filter is a counsel of epistemic despair, grounded not on the inherent intractability of some classes of phenomena, but on the transient lacunae in current knowledge. Finally, we will argue that design is not the \"default\" explanation when all other explanations have been exhausted, but is another form of causal regularity that may be adduced to explain the probability of an effect being high, and which depends on a set of background theories and knowledge claims about designers. Spade's immediate intuition is that \"Fingers\" has indeed burgled the safe, but Spade is no philosopher and he knows it. He has, however, read The Design Inference by the detective theoretician, Dembski, and so he applies the filter to the case in hand (literally, since he has \"Fingers\" by the collar as he works through the filter on the whiteboard). The EF is represented as a decision chart (p37): HP events are explained as causal regularities. If it is very likely that an event would turn out as it did, then it is explained as a regularity. IP events are events which occur frequently enough to fall within some deviation of a normal distribution, and which are sufficiently explained by being between those extremes. The rolling of a \"snake eyes\" in a dice game is an IP event, as is the once-in-a-million lottery win. SP events come in two flavours: specified and unspecified. Unspecified events of small probability do not call for explication. An array of stones thrown will have some pattern, but there is no need to explain exactly that pattern, unless the specifiable likelihood of a pattern is so small that its attainment calls for some account. If an array of stones spells out a pattern that welcomes travellers to Wales by British Rail, then that requires explanation; to wit, that the stones were placed there by an employee of British Rail, by design. The minuscule probability that a contextually significant message in English would occur by chance is ruled out by the specified complexity of that sentence. This Dembski calls the Law of Small Probabilities - specified events of small probability do not occur by chance. 3 Spade, though not given to deep reflection, nevertheless studied statistics at the Institute of Forensic Studies, and so he wishes to be thorough. He traverses the filter step-by-step. E: the safe door is open. HP? No, the door regularly remains locked without intervention, and \"Fingers\" did not know the combination. IP? No, there is no significant chance that random spinning of the dial would happen on the combination. Even had \"Fingers\" chanced to spin the dial the right directions - an IP event - the chance is one in ten billion (10-10) that he would have happened on the combination. The chance is effectively zero, using the Law of Small Probabilities. SP? Yes, the event has a very small probability. sp/SP? Yes, the prior probabilities are exactly specified in addition to being very small. Conclusion: \"Fingers\" opened the safe by design, not by accident. \"Fingers\" is duly charged and arraigned for burglary. He engages the renowned deep thinking lawyer, Abby Macleal, and she defends him with skill. Before we get to the courtroom scene, however, let us go back in time, over a century, to the musings of a young naturalist. This naturalist - call him Charles - is on a voyage of discovery. He has read his Paley; indeed, he might almost have written out Paley's Evidences with perfect correctness by memory. Although he has not heard of Dembski's filter, he knows the logic: whatever cannot be accounted for by natural law or chance must be the result of design. Young Charles encounters some pattern of the distribution and form of a class of organisms - let us suppose they are tortoises - on an isolated archipelago and the nearest large continent. Each island has a unique tortoise most similar to the autochthon of the neighboring island and the island closest to the continent is most similar to that species. On the basis of the biological theories then current, he knows that there is no known process that can account for this pattern. It is so marked that one can draw a tree diagram from the continental form to the islands, and it will match a diagram showing the similarity of each form to the others. What should Charles rationally infer from this? Let us assume for comparative purposes that Charles is in possession of the filter; he will therefore reason like this: E: Species are distributed such that morphological distance closely matches geographic distance. HP? No, there is no regularity that makes this distribution highly probable. IP? No, the likelihood of such a distribution is extremely low. SP? Yes, it is a very small probability (made even smaller as more variables are taken into account). sp/SP? Yes, the problem is (more or less) specified. Conclusion: The tortoises have the biogeographic distribution and formal distribution they do by design. By Dembski's framework, Rational Charles should have ascribed the tortoises' situation to intelligent agency, and his subsequent research should have been directed to identifying that agency, perhaps by building balsa rafts to test the likelihood that continental sailors might have taken varieties now extinct on the continent and placed them each to an island according to some plan. An even more parsimonious explanation, and one more agreeable to the Rev. Paley's natural theology, might be that a single agent had created them in situ, along a plan of locating similar species adjacent to each other, which has the added virtue of explaining a large number of similar distributions known throughout the world, as Alfred, a later young voyager, was to note. Unfortunately for the progress of rational science, Actual Charles is not rational in this manner. He infers that some unknown process accounts for this distribution as a regularity, instead of inferring design. He irrationally conjectures that all the variants are modified descendants of the continental species, and that the morphological and geographical trees are evidence of a family tree of species evolution; and thus the theory of common descent is born. Charles is, rightly, castigated by his friends for irrationality and lack of scientific rigor. His leap to an unknown process is unwarranted, as is his subsequent search for a mechanism to account for it. Were his ideas to be accepted, perhaps out of fashion or irreligion, science would be put back for more than a century until Dembski came along to put it right. Lest this seem to be a parody of Dembski's views, consider his treatment of the evolution versus creation debate and the origins of life. Dembski (wrongly) conflates the two, treating the origins of life as a test case for the validity of evolutionary theory (it isn't - even if the major groups of living organisms had separate origins, or were created by an agent, their subsequent history could and would have an explanation in terms of \"undesigned\" evolution). Creationists - the actual ones that do reject evolutionary theories in the way that Rational Charles should have in the 1830s - challenge what Dembski putatively does not, that species share common ancestors with their closest relatives and that natural selection accounts for adaptation. As an adjunct to their arguments, they also, along with Dembski, give credence to the \"calculations\" of the probability that prebiotic processes would spontaneously form the building blocks of life (the LIFE event), especially of genetic molecules, that various authors have given. Dembski discusses Stuart Kauffman's (and others') blocking of the design inference (Kauffman 1993, 1995) with the following argument: Premise 1: LIFE has occurred. Premise 2: LIFE is specified. Premise 3: If LIFE is due to chance then LIFE has small probability. Premise 4: Specified events of small probability do not occur by chance (the Law of Small Probabilities). Premise 5: LIFE is not due to a regularity. Premise 6: LIFE is due to regularity, chance, or design (the filter). Conclusion: LIFE is due to design. Of Dawkins' arguments (Dawkins 1986: 139, 145-146) that there is a lot of \"planetary years\" available because there are a very large number of planets in the universe in which LIFE might have occurred and a lot of time available on each, Dembski says \"... because Dawkins never assigns an exact probability to LIFE, he never settles whether LIFE is a high probability event and thus could legitimately be attributed to a regularity\" (p58, italics added). Therefore, he says, we may infer that Dawkins accepts Premise 5! But what Dawkins actually says is that the improbability of life occurring had better not exceed the probability that it arose by chance on any one of the available number of planets on which it might have done. This sets a minimum bound to the probability of life, and Dawkins says that on (then) current knowledge, he doesn't know how probable life is. For all he knows, life is indeed due to a regularity. Kauffman's work on the dynamics of autocatalytic polymer sets supports the notion that the upper bound to the probability of life occurring is very high indeed, and life is to be \"expected\" in appropriate conditions. Dembski's comment? This is a \"commitment\". The implication is that it is a mere belief or act of faith on Kauffman's part. In fact, it is considerably more than that, and the real problem for origins of life researchers is not to find a possible scenario, but to decide which of a growing number of them holds the most promise, or which combination. But Dembski's filter makes it unnecessary to even try. 4 So, let us return now to the courtroom drama in time to hear Abby Macleal rebut prosecutor Pearl E. Mason's case. Abby calls retired Chump engineer Lachlan (Locky) Smith to the stand, and elicits from him the information that the Chump safe Spade owns has an inherent design flaw. If the tumbler is spun five times or more, centrifugal force will cause the lock to spontaneously open. Spade suddenly realizes why he got it so cheap. \"Fingers\" is acquitted, and initiates civil action for mental anguish and loss of reputation. Clearly, the background information has changed the probability assignments. At the time Spade found \"Fingers\" at the open safe, he was in possession of one set of background information, Bi. The probability of the event E requiring explanation led to a design inference. After Smith's testimony, a different set of background information, Bj, comes into play, and so the filter now delivers a \"regularity\" assignment to E. Suppose, though, that Smith had delivered yet another background set, Bk, by testifying that the model in question only actually used two of the five cylinders in the lock. Given that there are 100 possible numbers that might match the successful open state for each cylinder, the probability of a random opening is now 10-4, which is a much higher probability, given the number of Chumps of that model in use in the Naked City (particularly after Chump's massive sell-off of that model to clear the faulty stock). Now the same filter delivers us a chance explanation given Bk. The point is that Dembski's filter is supposed to regulate rational explanation, especially in science, and yet it is highly sensitive to the current state of knowledge. One single difference of information can change the inference from design to regularity to chance. This goes to the claim that Dembski's explanatory filter reliably finds design. Reliability, Dembski tells us, is the property that once an event is found to have the property of \"design\", no further knowledge will cause the event to be considered to have the property of \"regularity\" or \"chance\". What the filter lacks that real-world design inferences already have is a \"Don't know\" decision. If we can say of a problem that it is currently intractable or there is insufficient information to give a regularity or chance explanation now, then the Filter tells us we must ascribe it to design if it is specifiable. But it can be specifiable without the knowledge required to rule out regularity or chance explanations. This is clearly a god of the gaps stance, and it can have only one purpose: to block further investigation into these problems. Supposing we do insert a \"don't-know\" branch: where should it go? There is an ambiguity in Dembski's treatment of his argumentative framework. The Explanatory Filter is written about as if it describes a process of analysis, but Dembski's further argumentation is cast in terms of a first-order logical calculus. In a process, we would come to a \"don't-know\" conclusion after some evaluation of alternatives, but in a logical framework, there is no temporal dependency. We will here ignore the demands of process and concentrate on the logic. As Dembski's filter eliminates hypotheses from high probability to low probability, clearly an inability to assign a probability in the first place makes the decision the first branch point. So if, on Bi, the probability of E is undecidable, that needs to be worked out first: Undecidable probabilities lead us to a blocking of the inference at all. No further inferences can be drawn, and no design is required to explain any event for which there is no assignment. However, even if E is decidable on Bi, that in no way licences the expectation that on Bj or Bk those probabilities will remain fixed. For example, when Dawkins wrote in 1986, the state of knowledge about prebiotic chemical reactions was sparse; the range of possible RNA codes and molecular alternatives was not properly understood. As knowledge has grown, our estimate of the probability that some ribonucleotides, or perhaps ribonucleoproteins, or even polyaminoacids, might enter into protobiotic autocatalytic cycles has become much higher. Some even think that in a geologically short time after the cooling of the earth's surface, with the right conditions (themselves now expected to be of reasonably high probabilities on earth) life is almost certain to arise. Perhaps, then, we need another branching at each decision, leading to \"Don't-know-yet\". As Dembski's probabilities are Bayesian assignments made on the basis of a set of prior knowledge and default hypotheses, this seems to be a perfectly reasonable move. However, it has one glaring problem - it blocks any inferences of design, and that is too much. There are well attested cases of design in the world: we humans do things by design all the time. So an explanatory filter had better not exclude design altogether. How can it be included here? When is a design inference legitimate? The problem with a simple conclusion that something is designed, is its lack of informativeness. If you tell me that skirnobs are designed but nothing else about them, then how much do I actually know about skirnobs? Of a single skirnob, what can I say? Unless I already know a fair bit about the aims and intentions of skirnob designers, nothing is added to my knowledge of skirnobs by saying that it is designed. I do not know if a skirnob is a good skirnob, fulfilling the design criteria for skirnobs, or not. I do not know how typical that skirnob is of skirnobs in general, or what any of the properties of skirnobs are. I may as well say that skirnobs are \"gzorply muffnordled\" 5 , for all it tells me. But if I know the nature of the designer, or of the class of things the designer is a member of, then I know something about skirnobs, and I can make some inductive generalizations to the properties of other skirnobs. The way we find out such things about designers is to observe and interact, and if we can, converse, with them. In this way we can build up a model of the capacities and dispositions of designers. Experience tells me that a modernist architect will use certain materials to certain effect. Lacking any information about modernist architects leaves me none the wiser knowing that an architect is modernist (in contrast to other architects). Once we have such knowledge of designers, though, what we can say about them is that they generate regularities of outcomes. We know, for example, what the function of the Antikythera Device, a clockwork bronze assembly found in an ancient Greek shipwreck, was because we know the kinds of organisms that made it, we know the scientific, religious and navigational interests they had, we know about gears, and we know what they knew about the apparent motions of the heavens. Hence we can infer that the Antikythera Device is an astrolabe, used for open sea navigation by the stars, or a calendrical calculator, or both (de Solla Price 1974). But suppose it was found by interstellar visitors long after humans went extinct. What would they know about it? Unless they had simil", "text_length": 20000, "text_sha256": "b5526e4ff28c2cdc72f0a4dbcf80f6fdb0456dddc1d666fd14a5fd7207162e72" }, { "route": "/cs/theory_is_as_theory_does/", "title": "Theory Is As Theory Does", "description": "Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright examine the claims of the Michael Behe and David Snoke paper published in Protein Science in 2004. While the goal of the Behe and Snoke paper is to generate impressive-looking improbabi", "content_kind": "drupal_article", "text": "Legacy route: /cs/theory_is_as_theory_does/ Theory Is As Theory Does Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright examine the claims of the Michael Behe and David Snoke paper published in Protein Science in 2004. While the goal of the Behe and Snoke paper is to generate impressive-looking improbabilities for the evolutionary development of a class of biochemical features, it turns out that use of biologically realistic numbers in their model shows that evolution is almost certain to develop them. Posted by Reed A. Cartwright on October 11, 2004 11:06 AM by Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright “There’s precious little real biology in this project,” Mr. Behe said. For example, he said, the results might be more persuasive if the simulations had operated on genetic sequences rather than fictitious computer programs. Michael J. Behe was commenting in The Chronicle of Higher Education (Kiernan 2003) on a paper reporting that digital organisms could evolve irreducibly complex systems without intervention (Lenski et al. 2003). Ironically, Behe has just coauthored a theoretical paper with David W. Snoke on the evolution of complex molecular adaptations that has “precious little real biology” in it. William Dembski has already stated that Behe and Snoke’s research “may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution” (Dembski 2004). Despite the common claim made by “intelligent design” activists that evolution is in trouble, they have so far been unsuccessful in presenting their arguments to the scientific community. Is this the long-awaited peer-reviewed publication which will finally do it? No. Although some in the “intelligent design” community tout Behe and Snoke’s paper as the long-awaited theoretical paper (Discovery Institute 2004) , it contains no “design theory”, makes no attempt to model an “intelligent design” process, and proposes no alternative to evolution. In reality Behe & Snoke (2004) is an unmemorable investigation of neutral drift in protein and nucleic acid sequences. As we will show, the paper cannot even support the modest claims it does make. Behe has argued that certain biochemical systems or structures have a property he calls “irreducible complexity” (Behe 1996). Irreducible complexity is an update on the old anti-evolutionist argument of “What good is half a wing?” Simply put, the idea is that all the components of a system must be present before the system can accomplish its current function, and, therefore, there is no gradual, step-by-step way for natural selection to construct the system being considered. Behe’s arguments have attracted significant criticism , and Behe has recast his definition of “irreducible complexity” from time to time to attempt to deal with these criticisms. One of these re-definitions of “irreducible complexity” introduces the notion of unavoidable gaps in a stepwise progression of adaptive evolutionary intermediates of a system, such that the only means of bridging the gap is via neutral evolution (Behe 2000). The current paper is apparently an attempt to quantify just how improbable this process of bridging gaps via neutral mutation might be, and thus we may expect that when Behe makes arguments along these lines in the future he will point to this paper as the justification for saying that evolution does not have the time available to fashion “irreducibly complex” structures. Although Behe and Snoke are “skeptical” of the ability of “Darwinian processes” to account for the evolution of complex biochemical systems (Behe & Snoke 2004), there is substantial scientific evidence for the conclusion that complex biochemical systems can and have evolved on earth. There is direct experimental research (Hall 2003). There are observed instances of it occurring in nature (Copley 2000, Seffernick & Wackett 2001, Johnson et al. 2002). There is also much evidence from comparative studies (Melendez-Hevia et al. 1996, Cunchillos & Lecointre 2003 as two examples). However, we don’t have enough space to fully explore the large amount of data that Behe and Snoke’s “skepticism” must overcome. We have our hands full just explaining some of the manifold ways in which Behe and Snoke’s model fails to represent molecular evolution. The flavor of Behe and Snoke’s paper may be gauged by the fact that the authors are skeptical of Darwinian processes to produce complex structures, yet use a model which largely ignores Darwinian processes. In the following sections we will examine some of the more questionable aspects of Behe and Snoke’s paper. Contents Contents One True Sequence? Evolution of DPG Binding Subfunctionalization vs. Neofunctionalization Rho-Oh! How unlikely is the evolution of MR features? Applying Behe & Snoke’s equations to the DPG binding site example Conclusion Acknowledgements References One True Sequence? Theory is rather hard to review, and it is not uncommon for problematic theory to get published. For this reason, post-publication review is very important to sifting good theory from bad. We cannot emphasize this enough. The theoretician among us only trusts theory that either has withstood the test of time or has been satisfactorily replicated by him. (This paper satisfies neither.) There are two issues in creating good theory: (1) getting the modeling right and (2) using assumptions relevant to nature. Sometimes the former dooms theory, but in most instances it is the latter. We believe there are some issues with the modeling in the paper, but investigating them is too complex for this essay. However, even a rough reading of the paper makes it clear that Behe and Snoke’s work and the conclusions they draw are not relevant to nature. Behe and Snoke are attempting to estimate how long and how large of a population it would take for a protein in the absence of selection to evolve a new binding site or other complex feature. They assume up-front that multiple amino acid substitutions would be required before the new feature can be preserved by natural selection. They call this a “multiresidue” feature (MR). Behe and Snoke are modeling the formation of a completely new binding site in a duplicated protein. While this process is important in generating some kinds of new function, in the majority of duplicated proteins, existing binding sites are either modified to act on new substrates (for example the expansion of the protein kinase (Manning et al. 2002, Caenepeel et al. 2004, Waterston et al. 2002) and G-protein coupled receptor families in vertebrates) or new catalytic mechanisms (the TIM family of proteins; Schmidt et al. 2003, Gerlt & Babbitt 2001). (See Musgrave 2003 for more discussion about the evolution of binding sites. See Musgrave 2004 for a discussion on disulfide bonds.) Duplication of enzymes and modification of their existing binding sites can produce quite complex pathways; for example the clotting cascade is due to duplication of proteolytic enzymes with a subsequent change in substrates (Miller 1999 and the references therein). Behe and Snoke use five parameters to model the neutral evolution of their sequences: the number of mutations needed for the multi-residue feature (λ), the ratio of null mutations (ones that create a pseudogene) to needed mutation (ρ), the number of duplicate genes in the population (N), the selection coefficient of the multi-residue feature (s), and the instantaneous rate of point mutation per site (ν). (Contrary to what Behe and Snoke claim, ν is not a per generation rate of nucleotide mutation.) In the model, selection only acts upon a duplicate gene’s multi-residue feature when it has acquired the particular λ “compatible” mutations and none of the λρ mutations that would nullify it. Behe and Snoke implement nullification by assuming that the duplication is deleted when the first “compatible” mutation (forward or backward) occurs after the first null mutation occurs. The deleted duplication is instantly replaced by a new gene that has no compatible and no null mutations. We call this “reset on null.” After a bit of math and some simulations Behe and Snoke estimate the average time to first appearance (T f ) and the average time to fixation (T fx ) of a multi-residue trait under various parameter sets. They use these results to conclude that point mutations plus selection cannot explain the evolution of multi-residue traits. However, the model has many restrictive assumptions that prevent it from supporting the conclusion that Behe and Snoke make. In reality, the paper says that if you have a protein function that requires two or more specific mutations in specific locations in a specific gene in a specific population, and if the function is not able to be acted on by natural selection until all mutations are in place and if the only form of mutation is point mutation, and if the population of organisms is asexual, then it will take a very large population and very long time to evolve that function. This is not unexpected. Furthermore, this paper follows the fallacious fascination with the “one true sequence” that is popular in the “intelligent design” community (for example Meyer 2004). Behe and Snoke end their paper with the following conclusion: Although large uncertainties remain, it nonetheless seems reasonable to conclude that, although gene duplication and point mutation may be an effective mechanism for exploring closely neighboring genetic space for novel functions, where single mutations produce selectable effects, this conceptually simple pathway for developing new functions is problematic when multiple mutations are required. Thus, as a rule, we should look to more complicated pathways, perhaps involving insertion, deletion, recombination, selection of intermediate states, or other mechanisms, to account for most [multi-residue] protein features. (Behe & Snoke 2004 p11) No matter how much Behe and Snoke want to make this conclusion, it is simply not warranted by any work presented in the paper. The evolution of new functions is not a process that requires a certain target to be hit. There can be multiple new functions that any starting protein can acquire. Likewise, there can be multiple ways of acquiring any given function. And finally, evolution doesn’t happen in a single population; it happens in multiple populations at the same time. Calculating that it would take a long time for a specific new function to evolve from a specific gene with a specific set of mutations in a specific population in no way suggests that it would take a long time for any new function to evolve in any gene from any set of mutations in any population. Behe and Snoke’s work attempts to show the former, but in their discussion they conclude the latter. Their conclusion simply does not follow. Behe and Snoke do mention this early in their discussion: … because the simulation looks for the production of a particular MR feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively. Although we see a particular disulfide bond or binding site in a particular protein, there may have been several sites in the protein that could have evolved into disulfide bonds or binding sites, or other proteins may have fulfilled the same role. For example, Matthews’ group engineered several nonnative disulfide bonds into lysozyme that permit function (Matsumura et al. 1989). We see the modern product but not the historical possibilities. (Behe & Snoke 2004 p11, emphasis original) Unfortunately Behe and Snoke ignore their own caveat in the rest of their discussion, resulting in an entirely unjustified conclusion. At the very least, it biases their estimates of population sizes and generations considerably upward. A more realistic scenario, in which multiple targets could be reached, would result in a much smaller number of generations and/or smaller required population sizes. (To be fair, it would be more difficult to model such a scenario.) At worst, the fact that they only consider specific changes at specific locations makes their model meaningless because it assumes a fundamentally different process than the one that occurs in nature. The rest of this essay will be divided into two parts. The first part will explore the assumptions that Behe and Snoke use to build their model, and why those assumptions bias their model toward their favored conclusion. The second part will discuss the likelihood of MR features evolving, and will include a calculation for Behe and Snoke’s flagship example using realistic parameters. Evolution of DPG Binding Let us now look at one of Behe and Snoke’s own examples, the evolution of β-hemoglobin’s 2,3-diphosphoglycerate binding site. Hemoglobin is the protein that caries oxygen in vertebrate blood. In most vertebrates, hemoglobin is a tetramer composed of two α and two β protein chains. There is much evidence that the α and β chains evolved from duplicates of an ancestral globin chain (Li 1997 pp289-292). In mammals, frogs, and reptiles there is a small pocket which binds the organic phosphate molecule 2,3-diphosphoglycerate (DPG) at the interface between the two beta chains. (Reptiles use inositol pentaphosphate (IPP) as the physiological modulator, but their site binds DPG very effectively.) If a molecule of DPG is bound to hemoglobin, it helps stabilize the tetramer, reducing the hemoglobin’s affinity for oxygen. Therefore, DPG regulation allows hemoglobin to release more oxygen in capillaries. DPG is produced by a shunt pathway that prevents glycolysis (the pathway that “burns” glucose to produce energy) from producing the energy molecule ATP when levels of ATP are high. This means that DPG levels are positively correlated with the oxygen levels. When oxygen levels are high, ATP levels are high, and DPG levels are also high. When oxygen levels are low, ATP levels are low, and DPG levels are also low. Therefore, low levels of oxygen favor increased oxygen affinity of hemoglobin. In sum, DPG regulation ensures that hemoglobin can work efficiently even when oxygen levels are low. Behe and Stoke refer to DPG binding as an example of a function that must have involved multiple neutral mutations, citing Li (1997). At the beginning of their discussion, Behe and Stoke state: Some features of proteins, such as disulfide bonds and ligand binding sites, … are composed of multiple amino acid residues. As Li (1997) points out, the evolutionary origins of such features must have involved multiple mutations that were initially neutral with respect to the MR feature. (Behe & Snoke 2004 p7, emphasis added) However, this is simply not supported by Li (1997): The emergence of a new function in a DNA or protein sequence is supposedly advantageous and is commonly believed to have occurred by advantageous mutations. However, acquiring a new function may require many mutational steps, and a point that needs emphasis is that the early steps might have been selectively neutral because the new function might not be manifested until a certain number of steps had already occurred. (Li 1997 p427, emphasis added) Note the change from “might have been” to “must have involved.” Li (1997) in fact never says early mutational steps “ must have been.” He points out that at least one mutation to form the DPG binding site was selectable, the one that generated histidine at position 2. He also says “Of course one cannot rule out the possibility that either Lys82 or His143 or both have evolved because of a selective advantage other than DPG binding” (p 428). As we shall see below, this is in fact the case. Behe and Snoke overemphasize must , creating a misleading impression that there is authoritative support for the concept that all amino acids of a site must be in place for a selectable function to occur. This is exactly the opposite of current knowledge. It is interesting to point out that in their introduction Behe and Snoke actually quote from this section of Li (1997), yet manage to misread it. As Li (1997) noted, the binding site for diphosphoglycerate in hemoglobin requires three residues. The population size required to produce an MR feature consisting of three interacting residues by point mutation in a duplicated gene initially lacking those residues would depend on the number of nucleotides that had to be changed—a minimum of three and a maximum of nine. (Behe & Snoke 2004 p10) This gives the misleading impression that Li (1997) states that the DPG binding site requires all 3 amino acids, and only those amino acids, in place before selectable binding occurs. Unfortunately for Behe and Snoke, the DPG binding site is a good example of plasticity and redundancy which highlights a key flaw in their “one true sequence” assumption. Li (1997), the very article they quote, gives examples of alternate sequences that work well, thus invalidating the assumption that only their “one true sequence” will have that function. The modern mammalian DPG binding site is formed from 3 amino acids on the beta chain. Histidines (H in the single amino acid code ) at position 2 and 143, and lysine (K in the single amino acid code) at position 82. All these amino acids are basic; we can call these amino acids responsible for DPG binding the HKH triad. Behe and Snoke imply that you must have the HKH triad in place for both binding and selection to take place. Now, while all of these sites are required for good binding, there are mammals without these 3 that do quite nicely. You can replace basic histidine with basic arginine ® and a functional DPG binding site is obtained at either position 2 or 143 (Bonaventura et al. 1975). So you can have R KH and HK R and still get DPG binding with selectable function. There are even more variants with selectable function. Mice have an asparagine (N) at position 2, giving an N KH triad. Lemurs make do with leucine ( L KH). Ruminants have methionine (M) at position 2. The M KH variant is much less sensitive to DPG, but still has binding and selectable function (Angeletti et al. 2001). Even with a limited number of vertebrates, we can show that the actual example cited by Behe and Snoke, the DPG binding site, does not in fact follow their “one true sequence” model. But it gets more interesting than that. As one example, Li (1997) has argued that the precursor to modern hemoglobins that can bind diphosphoglycerate did not have any of the three amino acid residues involved in the interaction. (Behe & Snoke 2004 p11) This is true, but highly misleading. DPG binding is at the end of a sequence of development of allosteric modulation by anions and organic phosphates paralleling the development of tetrameric hemoglobin. While most vertebrate hemoglobins are α 2 β 2 tetramers, most species of hagfish, a primitive jawless fish, have monomeric hemoglobin. In other species of hagfish, the oxygenated form of hemoglobin is a monomer, and the deoxygenated form is a dimer. In all known species of lamprey, another primitive jawless fish, the oxygenated form of hemoglobin is a monomer, and the deoxygenated form is either a dimer or tetramer. In sharks, the oxygenated form is the αβ dimer, and the deoxygenated form is a tetramer. In bony fish, frogs, lizards and mammals hemoglobin is the familiar α 2 β 2 tetramer. In most vertebrates, organic phosphates modulate the oxygen affinity of hemoglobin, but most vertebrates use ATP, the energy bearing phosphate produced by oxidative metabolism, to modulate hemoglobin oxygen affinity (Nikinmaa 2001, Coates 1975a). Mammalian DPG binding evolved not from scratch, as implied by Behe and Snoke, but from an ATP binding site. Lamprey hemoglobin is not modulated by organic phosphates, it has PSS (proline, serine) at the equivalent posit", "text_length": 20000, "text_sha256": "8627ef076416f1fd318c1246d94d59f7f490f93d2ed7a9bd387bed7ff7c150e0" }, { "route": "/cs/wein_nfl_review/", "title": "Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch", "description": "Richard Wein's review of No Free Lunch argues that Dembski's case is nothing more than a god-of-the-gaps argument dressed up in misleading pseudoscientific mumbo jumbo.", "content_kind": "drupal_article", "text": "Legacy route: /cs/wein_nfl_review/ Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch Richard Wein's review of No Free Lunch argues that Dembski's case is nothing more than a god-of-the-gaps argument dressed up in misleading pseudoscientific mumbo jumbo. Read the full article PDF (off-site) .", "text_length": 335, "text_sha256": "ef97db14dc7b1d9e956139acc6458059b11fa19057230e0189dd0e44631d22c4" }, { "route": "/cs/wein_what_response/", "title": "Response? What Response?", "description": "Richard Wein replies to William Dembski's reply to Wein's Not a Free Lunch But a Box of Chocolates.", "content_kind": "drupal_article", "text": "Legacy route: /cs/wein_what_response/ Response? What Response? Richard Wein replies to William Dembski's reply to Wein's Not a Free Lunch But a Box of Chocolates. How Dembski has avoided addressing my arguments by Richard Wein Copyright © 2002 Version 1.1 [Last Modified: May 28, 2002; change to section 5.1, concerning the LCI] Permission is given to copy and print this page for non-profit personal or educational use. Contents 1. Preamble 2. Peer Review 3. Argument from Ignorance 4. Tornado in a Junkyard 5. Short Responses 5.1 Uniform Probabilities 5.2 The No Free Lunch Theorems 5.3 Specification 5.4 Algorithmic Information Theory 5.5 Predictive Power of Darwinian Evolution 5.6 Explanatory Power 5.7 Wein's Acknowledgment 6. Conclusion he Talkorigins Archive recently posted my critique of William Dembski's book No Free Lunch , entitled Not a Free Lunch But a Box of Chocolates , in which I thoroughly analyzed and refuted his arguments. Dembski quickly responded with an article entitled Obsessively Criticized But Scarcely Refuted: A Response To Richard Wein . Although that article purports to be a response to my critique, it is in fact largely a recapitulation of arguments from No Free Lunch which ignores my refutations of them. In the few instances where Dembski has made a serious attempt to address my arguments, he almost invariably misconstrues them. Not one of my arguments has been satisfactorily addressed. I invite any skeptical reader to cross-check my original critique with Dembski's response. To facilitate such a cross-check, this article uses the same section names and numbers as Dembski's and I provide links to the relevant sections of my critique. All quotations labelled \" Wein: \" are from my critique and those labelled \" Dembski: \" are from his response, unless otherwise indicated. 1. Preamble I begin, like Dembski, with some peripheral issues, before getting down to the technical issues in section 3 below . Since he thinks it will work to his advantage here, Dembski makes some appeals to authority. He correctly points out that I have little authority, possessing only a humble bachelor's degree (in statistics). I am happy to let my arguments be judged on their merit, and would not ask anyone to accept them on my authority. Dembski should be wary of casting stones, however, since he himself criticizes experts in fields where he has no qualifications at all, such as biochemistry. He also asks how the eminent endorsers of No Free Lunch can \"think NFL is the best thing since sliced bread\" if it is as bad as I argue it is. Perhaps he should ask himself how the far more eminent and numerous supporters of evolutionary theory can be so convinced by it if it is as bad as antievolutionists say. The antievolutionist is ill-placed to make appeals to authority when the overwhelming weight of scientific authority is against him. Regrettably, advanced academic qualifications are no safeguard against falling into the trap of pseudoscience, especially when powerful dogmatic convictions are at stake. 2. Peer Review For all the length of his discussion of peer review, Dembski fails to refute any of the facts that I presented ( critique section 8 ). Most important, he is unable to name even one statistician or information theorist who approves of his work in their fields, confirming my suspicion that there are none. While remaining completely silent on the subject of information theorists, Dembski attempts to explain the lack of support from statisticians by suggesting that his statistical claims are more appropriately judged by philosophers of science. I do not dispute that some philosophers have expertise in the field of statistics. But I note that he preferred to claim the support of statisticians when he thought he could get away with it: Interestingly, my most severe critics have been philosophers (for instance Elliot Sober and Robin Collins...). Mathematicians and statisticians have been far more receptive to my codification of design inferences. [NFL, p. 372n2, and \" Intelligent Design Coming Clean \"] Will he now retract his claim that statisticians have been receptive to his work? In his article, Dembski claims that his method of calculating perturbation probabilities constitutes \"a contribution to the applied probability literature.\" Has he submitted it to a journal of applied probability? Or is this yet another claimed contribution to a technical field that is best judged by philosophers? 3. Argument from Ignorance Dembski begins this section by repeating the claim that his eliminative method of design inference is \"inductively sound\", based on the same absurd argument which I have already refuted ( critique section 3.6 ). He makes no attempt to address my argument. Next, he repeats his claim that it is possible to rule out unknown material mechanisms: Dembski: Specified complexity can dispense with unknown material mechanisms provided there are independent reasons for thinking that explanations based on known material mechanisms will never be overturned by yet-to-be-identified unknown mechanisms. In No Free Lunch an attempt to dispense with unknown material mechanisms was known as a \"proscriptive generalization\", but that term appears nowhere in Dembski's current article. It is unclear whether this is just a matter of inconsistency, or whether he now feels the term was an unwise one, suggesting a degree of certainty that he cannot justify. Since he has not acknowledged any change in his argument, I will continue to use his old term for the sake of consistency. I will also assume that his \"material\" mechanisms are synonymous with the \"natural\" mechanisms of No Free Lunch . Dembski's frequent unacknowledged changes of terminology do nothing to enhance the clarity of his arguments. The proponent of an argument from ignorance always believes he has sufficient reasons for thinking that his explanation will not be overturned by a yet-to-be-identified unknown mechanism. So the fact that such reasons exist does not save the argument from being one of ignorance. It is an argument from ignorance because it is based not on evidence for the proposed explanation but on the purported absence of any other explanation. In No Free Lunch , Dembski defined arguments from ignorance as being arguments of the form \"not X therefore Y\" (p. 111). But this is just the type of purely eliminative argument that he is making: not material, therefore design. Whether he eliminates material mechanisms by eliminating known mechanisms individually or by trying to rule out unknown mechanisms through proscriptive generalizations, this is still a purely eliminative argument. Dembski continues by giving an example of a proscriptive generalization against alchemy. But the point is made needlessly, since I have already agreed with Dembski that proscriptive generalizations can be used to rule out some categories of possibilities ( critique section 3.2 ). The point is irrelevant, since these are arguments against possibilities not arguments for a hypothesis. In terms of Dembski's \"not X therefore Y\", they are a \"not X\"; they are not a \"therefore Y\". Scientists did not argue \"not alchemy, therefore modern chemistry\". Next, we have the example of a combination lock, which I did not discuss in my critique, so I'll consider in some detail here. Dembski argues as follows: Dembski: The geometry and symmetry of the lock precludes that material mechanisms can distinguish one combination from another--one is as good as any other from the vantage of material mechanisms. Not at all. There may be a flaw in the mechanism which causes it to favour some combinations over others. Or the lock may be flawed in some other way. No matter how carefully the lock has been inspected, we cannot completely rule out that possibility. Consider an imaginary scenario in which a safe's combination dial is randomly rotated by natural forces. Let's say the safe is on a rowing boat at sea, and the rolling of the boat is sufficient to make the dial rotate. Now suppose that, while the sole occupant of the boat looks on, the safe springs open. For good measure, suppose that the rower is a locksmith who has thoroughly inspected the lock, found it to be flawless, closed the safe, and thoroughly randomized the dial, all since he has been alone on the boat. How will he explain the spontaneous opening of his safe? Let us say that he appreciates the sheer improbability of the safe opening by pure chance if it was operating to specification, and he rejects that explanation. Does he infer design? Or does he infer that, despite his thorough check, there was a flaw in the mechanism that caused it not to operate correctly? Even though it may seem implausible that the safe sprang open spontaneously, he will surely consider it even more implausible that someone boarded his boat and opened the safe while he was watching it, without him noticing, and he will prefer the former explanation. This is an \"inference to the best explanation\", or comparative inference. I discussed such inferences at some length ( critique section 3.5 ). Dembski has completely ignored that discussion, and continues to insist that his eliminative inferences are the only option. According to Dembski's logic, the rower should have inferred design, no matter how certain he was that no human agent could have been responsible, even if it required him to posit an unembodied designer. Dembski may respond that the hypothesis of a flawed mechanism is another relevant chance hypothesis which must be eliminated before inferring design. If he does so, he admits the fallacy of his argument that it is possible to \"guarantee the security of the lock.\" I should add that this discussion of proscriptive generalizations has no relevance to Dembski's argument for design in biology, since I have refuted his claim of a proscriptive generalization against Darwinian evolution of irreducibly complex systems (more on this below ). The remainder of Dembski's section is not a response to my critique at all, but is a long passage cut and pasted from one of his articles, with trivial changes. The article in question is the text of his recent talk at the American Museum of Natural History, which he has posted to the Internet under the title \" Does Evolution Even Have a Mechanism? \" Most of this is a rehash of arguments from No Free Lunch , and does not even belong in a section which purports to be addressing the \"Argument From Ignorance\" issue. I will address only the parts dealing with that issue. Dembski: Isn't arguing for design on the basis of specified complexity therefore merely an argument from ignorance? Two comments to this objection: First, the great promise of Darwinian and other naturalistic accounts of evolution was precisely to show how known material mechanisms operating in known ways could produce all of biological complexity. So at the very least, specified complexity is showing that problems claimed to be solved by naturalistic means have not been solved. Biologists have never claimed to know precisely how every biological structure evolved. So Dembski is attacking a straw man. Dembski: Second, the argument from ignorance objection could in principle be raised for any design inference that employs specified complexity, including those where humans are implicated in constructing artifacts. An unknown material mechanism might explain the origin of the Mona Lisa in the Louvre, or the Louvre itself, or Stonehenge, or how two students wrote exactly the same essay. But no one is looking for such mechanisms. It would be madness even to try. Intelligent design caused these objects to exist, and we know that because of their specified complexity. Once again, Dembski assumes that all our inferences of design use his eliminative approach. I have already addressed this claim ( critique section 3.5 ). He has not responded. I note that this section of Dembski's article contained not one direct response to any argument of mine. He made no attempt at all to refute my argument that his method of design inference is a purely eliminative argument, an argument from ignorance, and a god-of-the-gaps argument ( critique section 3.3 ). He did not provide definitions of these terms and attempt to show that his method does not match them. He did not even attempt to challenge my definitions of these terms. Nor did he address my argument that the term \"specified complexity\" is an unnecessary middleman. Let me make that argument even simpler: why not replace all relevant chance hypotheses eliminated --> specified complexity --> design with all relevant chance hypotheses eliminated --> design ? 4. Tornado in a Junkyard I pointed out ( critique section 4.1 ) that Dembski's only probability calculation for a biological system is based on a hypothesis of purely random combination, or what I called a \"tornado in a junkyard\" scenario. Since such hypotheses are already universally rejected by biologists, I argued that the calculation was addressing a straw man hypothesis, and was therefore irrelevant. Dembski responds: Dembski: Wein therefore does not dispute my calculation of appearance by random combination, but the relevance of that calculation to systems like the flagellum And why does he think it irrelevant? Because co-optation is supposed to be able to do it. Dembski has not read my article carefully enough. I wrote: Wein: No biologist proposes that the flagellum appeared by purely random combination of proteins--they believe it evolved by natural selection--and all would agree that the probability of appearance by random combination is so minuscule that this is unsatisfying as a scientific explanation. Therefore for Dembski to provide a probability calculation based on this absurd scenario is a waste of time. There is no need to consider whether Dembski's calculation is correct, because it is totally irrelevant to the issue. There is nothing here about co-optation. I did not mention co-optation until the following section (where I called it \"change of function\"). So Dembski has entirely failed to address my argument. Nevertheless, I thank him for confirming that his calculation is based on a hypothesis of random combination. At this point, let me interject a passage from Dembski's talk at the American Museum of Natural History, which he included in his section 3: Dembski: Convinced that the Darwinian mechanism must be capable of doing such evolutionary design work, evolutionary biologists rarely ask whether such a sequence of successful baby-steps even exists; much less do they attempt to quantify the probabilities involved. I attempt that in chapter 5 of NFL (to which I'll return shortly). There I lay out techniques for assessing the probabilistic hurdles that the Darwinian mechanism faces in trying to account for complex biological structures like the bacterial flagellum. The probabilities I calculate--and I try to be conservative--are horrendous and render natural selection utterly implausible as a mechanism for generating the flagellum and structures like it. There is no mention here that the probabilities were calculated under a hypothesis of random combination. On the contrary, there is a distinct implication that they were calculated under a hypothesis involving natural selection. We know this to be untrue, but listeners at the AMNH may have been misled by it. A reader unfamiliar with the tactics of antievolutionists might have thought that it did no harm to include an irrelevant calculation in No Free Lunch . But those of us familiar with antievolutionist rhetoric foresaw that it would be abused in the way we see here. In my next section ( critique section 4.2 ), I refuted Dembski's claim to have found a proscriptive generalization against the Darwinian evolution of irreducible complexity. Since this is an important point, I'll repeat the passage here: Wein: Let us accept, for the sake of argument, that Dembski's definition is tight enough to ensure that IC systems cannot evolve by direct pathways. What has he said on the vital subject that Behe failed to address--the subject of indirect pathways? The answer is nothing. The crux of his argument is this: Dembski [NFL]: To achieve an irreducibly complex system, the Darwinian mechanism has but two options. First, it can try to achieve the system in one fell swoop. But if an irreducibly complex system's core consists of numerous and diverse parts, that option is decisively precluded. The only other option for the Darwinian mechanism then is to try to achieve the system gradually by exploiting functional intermediates. But this option can only work so long as the system admits substantial simplifications. The second condition [that the irreducible core of the system is at the minimal level of complexity needed to perform its function] blocks this other option. Let me stress that there is no false dilemma here--it is not as though there are other options that I have conveniently ignored but that the Darwinian mechanism has at its disposal.[p. 287] Wein: But there is indeed an option that Dembski has overlooked. The system could have evolved from a simpler system with a different function. In that case there could be functional intermediates after all. Dembski's mistake is to assume that the only possible functional intermediates are intermediates having the same function. For once, Dembski appears to have read and understood my argument, but he makes no attempt to refute it. His proscriptive generalization is therefore dead. That leaves him with only appeals to ignorance and red herrings: Dembski: For Wein to account for systems like the flagellum, functions of precursor systems must co-evolve. But that means the space of possible functions from which these co-evolving functions are drawn is completely unconstrained. This provides yet another recipe for insulating Darwinian theory from critique, for the space of all possible biological functions is vast and there is no way to establish the universal negative that no sequence of co-evolving functions could under co-optation have led to a given system. Dembski is not required to establish a universal negative. He just needs to show that a design hypothesis is better, given the available evidence, than the hypothesis of purely natural evolution. But he rejects inferences to the best explanation, insisting on a purely eliminative mode of inference, and that puts him in the unenviable position of either establishing a \"universal negative\" or admitting there is a category of possibilities he has not eliminated. Since he cannot do the first and does not wish to do the second, he equivocates, first claiming that he has ruled out all Darwinian possibilities (his proscriptive generalization) and then, when it is shown he has not done so, complaining that the expectation was unreasonable. In short, he wants to have his lunch and eat it too! Dembski: Let me suggest that there are further reasons to be deeply skeptical of Wein's co-optation scenario. First, specified complexity is used to nail down design in cases of circumstantial evidence, so if there should happen to be design in nature, specified complexity is how we would detect it. Thus, my probability calculation for the flagellum, in the absence of a counter-calculation by Wein, is prima facie evidence of biological design. This may not provide sufficient reason for convinced Darwinists to abandon their paradigm, but it gives evolution skeptics reason to consider other options, including design. This is the crude argument from ignorance: having eliminated the absurd hypothesis of purely random assembly, we must infer design unless biologists can give an alternative hypothesis detailed enough to allow a probability calculation. Dembski: Second, there is a whole field of study developed by Russian scientists and engineers known under the acronym TRIZ (Theory of Inventive Problem Solving) that details patterns of technological evo", "text_length": 20000, "text_sha256": "478dbe57af5961d63db399bbe73bb75e85ea3dc0991b61c952f633b358192edb" }, { "route": "/cs/without_arguments/", "title": "A Presentation Without Arguments", "description": "Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002.", "content_kind": "drupal_article", "text": "Legacy route: /cs/without_arguments/ A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. How William Dembski defeats skepticism, or does he? By Mark Perakh [Contributed June 29, 2002, Last Modified July 3, 2002] Starting on June 20, 2002 and through June 23, the 4 th World Conference of Skeptics took place in Burbank, CA. Its main organizer in the USA was CSICOP, which stands for Committee for the Scientific Investigation of Claims of the Paranormal. Although the forum in question was designed as a meeting of skeptics, whose participants are all squarely on the side of genuine science and opponents of all incarnations of creationism regardless of the disguises the latter employs (such as Intelligent Design, Irreducible Complexity, etc) one not quite common feature of that meeting's program was that its organizers invited two prominent proponents of modern modifications of creationism, William Dembski and Paul Nelson, to give talks and to defend their views in an open dispute with two opponents of the anti-evolution movement, Wesley Elsberry and Kenneth Miller. I cannot remember a single conference of creationists wherein the opponents of creationism were scheduled to give talks in an open discussion. The proponents of creationism sometimes accuse their detractors of being doctrinaire adherents of anti-religious bias whose motivation is not pursuing the truth but assaulting the religious faith. Although this may be not the most important point, still it seems worth mentioning that both Elsberry and Miller have asserted that they are not atheists. Professor of biology Miller is a faithful Catholic, and Elsberry, while vigorously defending the theory of evolution, has also said that he is a \"theistic evolutionist.\" Hence, both Dembski and Nelson were given a chance to argue in favor of their position using arguments of substance, based on facts rather than on ideology, in a dispute with opponents who had no reason to assault Dembski's and Nelson's religious beliefs In this brief essay I will discuss only the presentation by Dembski. The text of Dembski's presentation [1] is notable by the almost complete absence of any arguments relevant to the gist of the dispute between ID advocates, like he himself, and the opponents of that theory. Indeed, the only instance of Dembski's touching on the substance of the dispute seems to be a paragraph on page 4 in [1] where Dembski mentions his term of Specified Complexity and unequivocally defines it as a synonym for \"specified improbability.\" Of course, there is nothing new in that statement. Dembski's interpretation of complexity as \"disguised improbability\" was expressed by him in various forms in many of his articles and books (for example, in [2,3]). This interpretation has been criticized more than once as being contrary to logic and to the accepted mathematical notion of complexity (see the partial list of references at the end of this essay). Dembski's statement illustrates once again his disdainful dismissal of all and every criticism directed at his work. Dembski does not bother to offer any reply to the critique of his interpretation of complexity and steadfastly adheres to his concept which is viewed by many critics as deficient. Continuing in the same vein, Dembski repeats his thesis, suggested by him many times before, that what he calls \"specified complexity\" is a necessary indicator of design. The fallacy of that statement was demonstrated more than once (for example in [4,5]). Indeed, consider an example discussed several times before. Imagine a pile of pebbles found on a river shore. Usually each of them has an irregular shape, its color varying over its surface, and often its density also varying over its volume. There are no two pebbles which are identical in shape, color and density distribution. I guess even Dembski would not argue that the irregular shape, color and density distribution of a particular pebble resulted from intelligent design, regardless of how complex these shapes and distributions may happen to be. Each pebble formed by chance. Now, what if among the pebbles we find one which has a perfectly spherical shape, with an ideally uniform distribution of color and density? Not too many people would deny that this piece in all likelihood is a product of design. However, it is much simpler than any other pebble, if, of course, complexity is defined in a logically consistent manner rather than in Dembski's idiosyncratic way. A logically consistent definition of complexity is given, for example, in the algorithmic theory of randomness-probability-complexity (and is often referred to as Kolmogorov complexity). Kolmogorov complexity of a perfectly spherical piece of stone is much lower than it is for any other pebble having irregular shape and non-uniform distribution of density and color. Indeed, to describe the perfectly spherical piece one needs a very simple program (or algorithm), actually limited to just one number for the sphere's diameter, one number for density and a brief indication of color. For a piece of irregular shape, the program necessarily must be much longer, as it requires many numbers to reproduce the complex shape and the distributions of density and of color. This is a very simple example of the fallacy of Dembski's thesis according to which design is indicated by \"specified complexity.\" Actually, in this example (as well as in an endless number of other situations) it is simplicity which seems to point to design while complexity seems to indicate the chance as the antecedent cause of the item's characteristics. That is about all Dembski chose to discuss in his presentation with regard to the substance of the dispute. Instead, Dembski dabbles in prophecy. His argument in favor of ID mainly boils down to the references to polls which show that the majority of Americans believe in some form of creationism. This may be true. However, Dembski himself gives an example of astrology which is no less popular in America than ID, but this by no means makes astrology plausible. Dembski is not arguing in his presentation that ID will win the minds because it is true. It will win, predicts Dembski, because the American public is predisposed to believe in ID. The same may be true though for astrology and other fads and fallacies he himself listed as being widespread despite their contradicting scientific data. One more argument by Dembski is that young people are inclined to take the side of innovators, and, since ID-ists are the new guys in town, the sympathy of the younger generation will be with them, thus ensuring their victory. Maybe so. What does it have to do with the merits of ID \"theory?\" If scientific theories were accepted or rejected by a popular vote, or just by the vote of young people, quantum mechanics, the general theory of relativity and a whole bunch of other great achievements of the human mind would never have had a chance to take their legitimate place in the progress of humankind. On page 4 Dembski argues that his ID theory is \"not a crank theory (at least not one that is obviously so).\" The sole argument Dembski offers in favor of that statement is that Paul Davies \"thinks that it's onto something important,\" thus disagreeing with those who, like Wesley Elsberry, \"think it merely codifies the argument from ignorance.\" This seems to be a rather weak argument, even by Dembski's standards. The reference to Davies can be interpreted in various ways and is far from endorsing ID as a real scientific theory. Moreover, so what if Davies or any other writer has indeed said something which can somehow be interpreted charitably regarding Dembski's ideas? The position whose strength can be sustained only by such ambiguous references is weak indeed and can be suspected of being crank science with a high degree of likelihood. If all Dembski can say in support of his views is that somebody thinks it has \"something to it,\" it raises a suspicion that he has no factual evidence favoring his suppositions. To show that certain ideas or theories indeed belong in real rather than crank science, one has to subject those ideas to merciless tests, wherein evidence supporting these ideas can be reproduced and independently verified. Dembski and his colleagues in the ID \"movement\" not only did not ever produce such evidence which could be independently verified, but in fact offered no evidence at all despite having a substantial financial support and a substantial fighting force at their Discovery Institute of Seattle. Instead of supporting his theory by factual evidence and arguments of substance, all Dembski was able to do was to resort to a dubious reference which proves nothing and is largely irrelevant. That is the tenor of Dembski's entire presentation. In a similar manner, Dembski plays with other quotations allegedly supporting his thesis, like a quotation from Mencken on page 2, juxtaposed with a quotation from Gould, which, Dembski implies, contradict each other. These two quotations may or may not contradict each other (and actually they were relating to different situations and therefore their juxtaposition was meaningless). It is, however, always possible to mine a host of quotations on every subject and pretend that they prove something even if they are not relevant to each other in any way. Such play with mutually irrelevant quotations confirms the suspicion that Dembski has no real arguments which would be necessary in a talk to an audience not consisting of such ID adherents who would happily swallow anything seemingly confirming their already held preconceptions. One the main points stressed by Dembski in his presentation is the assertion that Intelligent Design, unlike such fringe pseudo-science as astrology and the like, has by now become firmly \"mainstream\" in science. In this, Dembski depicts the desired as if it is real. So far, the overwhelming majority of mainstream scientists ignore ID as can be seen by searching through the scientific literature. Practically no scientific magazine has published articles by scientists wherein a discussion of ID and related matters could be found. No references to ID can be found in the mainstream peer-reviewed scientific publications. The ID advocates either publish their productions as popular or semi-popular books and collections by non-scientific publishers or in their own periodicals mostly connected to their Discovery Institute. The only exception seems to be Dembski's monograph [2] published by the Cambridge University Press. Even this book, reportedly, was Dembski's doctoral dissertation in philosophy rather than in science. Regardless of how many times Dembski will repeat his mantra about \"mainstreaming\" ID, the scientific community has not and will not accept the claims by ID-ists unless and until he and his colleagues present real data supporting their contentions. So far no such data have been presented. The overall level of Dembski's acerbic assault on skeptics can be exemplified by his comment that the letters COP in the abbreviation CSICOP are \"not accidental.\" Is this so? In the absence of real arguments, they may be sometimes replaced with attempts at being witty by using irrelevant puns. Dembski wants the readers to believe that the organization of skeptics is like police trying to muzzle its opponents. Somehow he does not notice the absurdity of such an accusation given the fact that he and his cohort Nelson are freely presenting their views at the meeting organized by the same CSICOP which allegedly is out to prevent the IDists from presenting their views. Maybe in his actual talk Demski said something beyond the irrelevant discussion of the prospects for ID versus evolution to win the minds of masses? It does not seem to be the case. According to the reports by the attendees of the conference, in his actual talk Dembski did not say anything beyond the immaterial quasi-arguments of his posted piece [1]. (This can also be verified by viewing the video tape of the session in question, available from CSICOP). Let me list some of the items that were discussed by Dembski's critics (a partial list of critical reviews of Dembki's literary production includes, but not limited to [4,5,6,7,8,9,10,11,12,13,14,15,16,17]). To some of his critics Dembski never replied in any form. To some others he responded (for example in his latest book [3]) with superficial and largely irrelevant arguments, but he never really replied to the substance of a number of points listed below, which constitute essential elements of his theory. Dembski asserted that complexity is tantamount to low probability. This assertion was rebuffed more than by one of the listed critics. Dembski never replied to that critique. Dembski asserted that his Explanatory Filter never produces \"false positives.\" This assertion was rebuffed by several of the listed (as well as by some not listed) critics. Dembski never replied to them. (It can be argued though that in his latest book [3] Dembski by implication concedes that false positives can be produced by his Explanatory Filter after all but he still does not admit this explicitly). Dembski announced a supposedly new important law – the so-called Law of Conservation of Information. More than one critic argued that the law in question does not exist. Dembski never replied to those critics. Dembski widely used a concept of what he called Specified Complexity. More than one critic argued that the concept in question is meaningless in the sense it has been used by Dembski. The latter never replied to this critique. The same can be said about Dembski's concept of Complex Specified Information (CSI). Dembski insists that design can be reliably inferred if low probability of an event is combined with its specification. More than one among the listed critics argued that the specification as defined by Dembski has no reasonable interpretation. Dembski never responded to that critique. There are other items claimed by Dembski, subjected to critique to which Dembski never responded while he continues to promote the same criticized concepts and assertions. In his presentation, Dembski condescendingly suggested a program of action for skeptics if the latter wish to defend their position against ID. In his uncompromising self-confidence Dembski seems not to realize that if he suggests a new, allegedly revolutionary theory, the burden of proof is on him and on his colleagues in the ID camp. It is ID-ists who need to provide evidence, any evidence, in support of their position. It is precisely the absence of evidence for the ID theory that makes skeptics (read: mainstream scientists) to reject ID as an unsubstantiated attempt to overturn the facts established by science. If Dembski or any of his colleagues showed any reasonable evidence supporting their views, then, beyond doubts, scientists would be much more receptive in regard to their theory. So far this has not happened. Therefore, rather than suggesting what skeptics should do to defend their views from the assault by ID, Dembski should better think of how to search for any believable proof of his own so far arbitrary and dubious assertions. By inviting Dembski and Nelson to give talks at the 4 th World Skeptics Conference, its organizers offered Dembski a chance to reply to his critics on the matters of substance and to defend his position in front of a diversified audience, mostly not very friendly to his views. By taking the floor at the conference in question, Dembski put himself in an unenviable position of denying a simple fact obvious to all – he was complaining about skeptics suppressing his views while speaking to the same skeptics who provided to him the forum. Acknowledgements I would like to thank Brian Spitzer, Pete Dunkelberg, and Wesley Elsberry for constructive remarks regarding the initial version of this article. References [1] William A. Dembski, [online], Skepticism's Prospects for Unseating Intelligent Design , http://www.iscid.org/papers/Dembski_SkepticismsProspects_062102.pdf , accessed on June 22, 2002. [2] William A. Dembski, The Design Inference , (Cambridge University Press, 1998). [3] William A. Dembski, No Free Lunch – Why Specified Complexity Cannot Be Purchased without Intelligence , (Rowman and Littlefield, Lanham, Maryland, 2002). [4] Mark Perakh, A Consistent Inconsistency, [online], www.talkreason.org/articles/dembski.cfm , accessed on June 22, 2002 [5] Mark Perakh, A Free Lunch in a Mousetrap, [online], www.talkreason.org/articles/dem_nfl.cfm , accessed on June 22, 2002 [6] Richard Wein, [online], http://website.lineone.net/~rwein/skeptic/whatswrong.htm , accessed on November 22, 2001 [7] Richard Wein, Not a Free Lunch But a Box of Chocolate, [online]. www.talkreason.org/articles/choc_nfl.cfm , accessed on June 22, 2002. [8] Matt Young, [online], www.pcts.org/journal/young2002a.html , accessed on March 10, 2002. [9] Victor J. Stenger, [online], http://spot.colorado.edu/~vstenger/Found/04MessageW.pdf , accessed on January 17, 2002. [10] Robert T. Pennock, Tower of Babel (Cambridge, MA: The MIT Press, 2000). [11] Taner Edis, [online], www.csicop.org/si/2001-03/intelligent-design.html , accessed on January 17, 2002. [12] Eli Chiprout, [online], http://members.aol.com/echiprt/dembski.htm . Accessed on July 25, 2001 [13] Wesley R. Elsberry, [online], www.infidels.org/library/modern/science/creationism/dembski.htm , accessed on November 22, 2001 [14] Wesley R. Elsberry, [online], www.talkreason.org/articles/inference.cfm , accessed on June 22, 2002. [15] Thomas D. Schneider, [online], www.lecb.ncifcif.gov/~toms/paper/ev/dembski/claimtest.html , accessed on November 22, 2001. [16] Branden Fitelson, Christopher Stephens and Elliott Sober, Philosophy of Science , 66, (1999): 472. [17] John S. Wilkins and Wesley R. Elsberry, The Advantages of Theft over Toil: The Design Inference and Arguing From Ignorance, Biology and Philosophy, v.16, 711 (2001).", "text_length": 18100, "text_sha256": "fe718c475dd03a3eb79eac31a0712cee2bb4c782386a8113186c153c96cb47b0" }, { "route": "/cs/you_missed_a_spot_dr_dembski/", "title": "You Missed a Spot, Dr. Dembski", "description": "William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design . The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to t", "content_kind": "drupal_article", "text": "Legacy route: /cs/you_missed_a_spot_dr_dembski/ You Missed a Spot, Dr. Dembski Original: You Missed a Spot, Dr. Dembski William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design . The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to the effect that Dembski covers herein all the criticisms that have been offered about \"intelligent design\" and Dembski's particular contribution, \"specified complexity\". This is untrue, as I will attempt to demonstrate. Dembski has gone so far as to challenge critics to find criticisms that he missed entirely. I responded earlier , pointing out various difficulties in proving a negative as Dembski had asked for. At that point, I had not read the whole text of TDR carefully, and thus did not wish to offer something that might be discussed on pages I had not yet gotten to. But now I have read the whole thing, and one rather glaring omission is evident to me. Throughout the book, Dembski touts \"specified complexity\" as a reliable marker of \"intelligent design\" and says that certain biological systems, such as the flagellum of E. coli bacteria (please note, Dr. Dembski, that the species name is NOT capitalized) have \"specified complexity\". This completely sidesteps and ignores a criticism I raised at the CTNS/AAAS \"Interpreting Evolution\" conference at Haverford College, June 17th, 2001, in a presentation on Dembski's ideas. I pointed out that Dembski's program of submitting events of known design and unknown cause to his \"explanatory filter/design inference\" were no test at all of the reliability of his apparatus, calling it a \"verificationist program\". To actually test his methodology Dembski and other ID advocates would have to examine cases where we had biological systems with a sufficiently detailed evidential record that even the ID advocates would agree beforehand that natural causes were sufficient to explain their deveolpment. Only then would running them through Dembski's \"explanatory filter/design inference\" place the EF/DI at hazard of showing a \"false positive\" result. I suggested that Dembski and his comrades at the (then) Discovery Institute Center for Renewal of Science and Culture concentrate upon systems like the impedance-matching system of the mammalian middle ear and the Krebs citric acid cycle, which exemplified complex systems for which biologists have accumulated a strong set of empirical data concerning their development. I reiterated the criticism in a web page critiquing Dembski's book, \"No Free Lunch\". TDR is bereft of any hint that this criticism impinged upon Dembski's mental processes at all. At least, there's no hint that I see. To the contrary, there are still the explicit statements that the EF/DI is somehow verified by Dembski's program of feeding it examples that cannot possibly put it at risk of failure. The bogus and completely unfounded \"reliability\" that Dembski claims thereby is used in several places in TDR to assert strong claims about the need to incorporate Dembskian notions of \"design\" into biology. That seems to me to be avoiding a tough question about \"intelligent design\". Further links: Haverford conference video: William Dembski's presentation My presentation Dembski and Elsberry panel Dembski and Elsberry audience Q&A My PowerPoint file for presentation", "text_length": 3413, "text_sha256": "28fbbf75c3930d017affd964c64d1620f3a410d9c3e927f316e408c794b35dd0" }, { "route": "/people/mgrey/", "title": "ID-Commentaries", "description": "A collection of commentaries on ID-texts, written by Morgan Grey.", "content_kind": "article", "text": "Legacy route: /people/mgrey/ ID-Commentaries This is a collection of my weekly ID-Commentaries, originally posted on the DebunkCreation discussion group . ID-Commentary: \"Who's Got the Magic?\" (10/21 2001) ID-Commentary: \"Disbelieving Darwin -- And Feeling No Shame!\" (10/12 2001) Dembski `retracts' comments about Dennett (10/20 2001) ID-Commentary: \"Another Way to Detect Design?\" (10/7 2001) ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" (10/2 2001) ID-Commentary: \"Explaining Specified Complexity\" (9/16 2001) Other on-line articles. Some of the articles I refer to in my ID-commentaries have been placed on-line here, due to the ever-changing structure of the internet.", "text_length": 710, "text_sha256": "c0c04c9b2adf49e57bee494046afcd24bdaa4205225582b3885cba7b8da6c5c1" }, { "route": "/people/mgrey/IDC.html", "title": "ID-Commentaries", "description": "A collection of commentaries on ID-texts, written by Morgan Grey.", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC.html ID-Commentaries This is a collection of my weekly ID-Commentaries, originally posted on the DebunkCreation discussion group . ID-Commentary: \"Who's Got the Magic?\" (10/21 2001) ID-Commentary: \"Disbelieving Darwin -- And Feeling No Shame!\" (10/12 2001) Dembski `retracts' comments about Dennett (10/20 2001) ID-Commentary: \"Another Way to Detect Design?\" (10/7 2001) ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" (10/2 2001) ID-Commentary: \"Explaining Specified Complexity\" (9/16 2001) Other on-line articles. Some of the articles I refer to in my ID-commentaries have been placed on-line here, due to the ever-changing structure of the internet.", "text_length": 718, "text_sha256": "569b16e9302af0e5067d691bcb0d892771cc806d3e940ae517e71c1d1ccf7fcf" }, { "route": "/people/mgrey/IDC/001.html", "title": "ID-Commentary: \"Explaining Specified Complexity\"", "description": "A commentary of William Dembski's", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/001.html ID-Commentary: \"Explaining Specified Complexity\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sun Sep 16, 2001 8:36 pm Message: 21453 Subject: ID-Commentary: \"Explaining Specified Complexity\" This is my first of what I hope to be many weekly posts, in which I post a document by one of the leaders of the ID-movement, together with my comments on it. I hope this feature will spark increased discussion in the group, and, in particular, that any lurking IDers will see this as an oppurtunity to argue the validity of ID. My first such commentary will be on Dembski's \"Explaining Specified Complexity\", posted on Metanexus at < http://www.metanexus.org/archives/message_fs.asp?&listtype=Magazine&ARCHIVEID=3066 >, and reproduced at < http://www.leaderu.com/offices/dembski/docs/bd-specified.html > [also online here ]. Although I have already made a few comments about this article ([ online here ]), I feel that it still contain some material, and also since I've read all of Dembski's TDI since then, thereby having clearified some misunderstandings on my own part about what Dembski is saying. (Note: The Meta is badly formated, and contains all kind of annoying \"=20\"'s, which I've removed. If anyone doubt my integrity in reproducing the text, they are welcome to refer back to the original.) ------------------------------------------------------- Meta 139: Dembski on \"Explaining Specified Complexity\" < grassie@VOICENET.COM > William Grassie Meta 139. 1999/09/13. Approximately 1883 words. BG> Below is a column entitled \"Explaining Specified BG> Complexity\" by William Dembski at Baylor BG> University in Texas. Dembski discusses whether BG> evolutionary algorithms can generate BG> actual \"specified complexity\" in nature, as BG> opposed to merely the appearances thereof (i.e., BG> unspecified or randomly generated complexity). BG> Dembski believes these problems in probability BG> make plausible a concept of intelligence involved BG> in evolution. Your comments are welcome on BG> < reiterations@meta-list.org >. BG> BG> -- Billy Grassie BG> WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=- EXPLAINING WAD> SPECIFIED COMPLEXITY WAD> WAD> William A. Dembski WAD> WAD> Michael Polanyi Center Baylor University Waco, WAD> Texas 76798 Dembski has a long record of claiming that \"[a]lgorithms and natural laws are in principle incapable of explaining the origin of information\" (see for example \"Intelligent Design\", pp. 160), and in a response to a review of \"The Design Inference\", he directs readers to two Meta-posts, claiming that these would show \"that the Darwinian mechanism -and indeed any non-telic mechanism- is incapable of generating specified complexity\" (see < http://www.arn.org/docs/dembski/wd_responsetowiscu.htm >). He identifies these two posts as \"Explaining Specified Complexity\" and \"Why Evolutionary Algorithms Cannot Explain Specified Complexity\", and it will be interesting to see if \"Explaining Specified Complexity\" or \"Why Evolutionary Algorithms Cannot Explain Specified Complexity\" (which I'll be commenting on next week) really do contain the scathing critique that Dembski claims they do. WAD> In his recent book The Fifth Miracle, Paul Davies WAD> suggests that any laws capable of explaining the WAD> origin of life must be radically different from WAD> scientific laws known to date. The problem, as he WAD> sees it, with currently known scientific laws, WAD> like the laws of chemistry and physics, is that WAD> they are not up to explaining the key feature of WAD> life that needs to be explained. That feature is WAD> specified complexity. Life is both complex and WAD> specified. The basic intuition here is WAD> straightforward. A single letter of the alphabet WAD> is specified without being complex (i.e., it WAD> conforms to an independently given pattern but is WAD> simple). A long sequence of random letters is WAD> complex without being specified (i.e., it WAD> requires a complicated instruction-set to WAD> characterize but conforms to no independently WAD> given pattern). A Shakespearean sonnet is both WAD> complex and specified. Notice Dembski's use of \"specified complexity\" as well as his claim that \"[l]ife is both complex and specified\" and that seeing this is \"straightforward\". About a week ago, when I had started reading TDI, I thought that the only difference between it and Dembski's popular writings was that TDI couldn't detect agency ([ online here ]), a thing I already knew from Wesley Elsberry's excellent posts. However, after having read the rest of TDI, as well as other critiques of it, I have noticed several other inconsistencies in Dembski's representation of his explantory filter. Take \"specified complexity\". While this term is nowhere to be found in TDI, Dembski often claims that the presence of this is a reliable indicator of design (intelligent or not). And, as Dembski claims above, \"specified complexity\" really *is* \"straightforward\" to recognize. All one need to do is to check whether the feature in question \"conforms to an independently given pattern\" and if it \"requires a complicated instruction-set to characterize\". Of course, given this, few people would object that a DNA molecule contains \"specified complexity\". Contrast this with Dembski's treatment of design in TDI. To \"make a successful design inference\" regarding an event E, one needs to calculate the propability of E, with regard to *all* \"relevant chance hypotheses\" (see pp. 50-1 in TDI), as well as determining that E is specified. This is of course a huge operation, not at all as simple as recognizing \"specified complexity\", as it is advocated by Dembski above. Indeed, in all of TDI, there is not a *single* example of Dembski applying his explanatory filter to anything, let alone a DNA molecule. Not even in his discussions of Caputo does he regard any other chance hypothesis than \"Caputo using an urn model with two balls, one ball for each party\". In TDI, Dembski implores us to \"Do the propability calculation!\" Yet, nowhere in any of his writings has he actually *done* the calculation. Instead, in poular writings, he points to the fact that the DNA molecule contains \"specified complexity\" without at any time informing his readers that this doesn't mean that his explanatory filter would label it \"design\". This is, IMHO, a far graver inconsistency than his muddlement of design and agency. [...] WAD> I submit that the problem of explaining specified WAD> complexity is even worse than Davies makes out in WAD> The Fifth Miracle. Not only have we yet to WAD> explain specified complexity at the origin of WAD> life, but evolutionary algorithms fail to explain WAD> it in the subsequent history of life as well. WAD> Given the growing popularity of evolutionary WAD> algorithms, such a claim may seem ill-conceived. WAD> But consider a well known example by Richard WAD> Dawkins (The Blind Watchmaker, pp. 47-48) in WAD> which he purports to show how a cumulative WAD> selection process acting on chance can generate WAD> specified complexity. Dembski has promised us to show that natural selection is *in principle* incabable of creating specified information. Yet, when push comes to show, he's only going to look at a particular evolutionary algorithm, namely Dawkins' famous \"Weasel applet\", that, in Dawkins' own words, was \"misleading in important ways\": \"Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that each generation of selective \"breeding\", the mutant \"progeny\" phrases were judged according to the criterion of resemblance to a *distant ideal* target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution.\" (Dawkins, R., 1996, \"The Blind Watchmaker\", pp. 50, original emphasis) In other words, Dembski has simply chosen a \"misleading\", albeit popular, version of natural selection, instead of dealing with the *real* models used by researchers in evolutionary algorithms. For example, Dembski could have chosen to deal with how an evolutionary algorithm solves the \"500 city Traveling Salesman Problem\", like Wesley has asked him to do for years ([ online here ]). WAD> He starts with the following target sequence, a WAD> putative instance of specified complexity: WAD> WAD> METHINKS*IT*IS*LIKE*A*WEASEL Dembski's use of \"putative\" indicates that Dembski thinks that METHINKS*IT*IS*LIKE*A*WEASEL really isn't an instance of specified complexity. However, after having followed Dembski's (often confusing) advice on how to calculate specified complexity, I have reached the conclusion that METHINKS*IT*IS*LIKE*A*WEASEL really *is* an instance of \"specified complexity\". Anyone interested in the calculations as well as the reasons for them can consult the not-so-technical appendix. But since, as we have seen, \"specified complexity\" is *not* the same as \"design\", it is still a possibility that METHINKS*IT*IS*LIKE*A*WEASEL will not be labelled \"design\" by the explanatory filter. WAD> (he considers only capital Roman letters and WAD> spaces, here represented by bullets-thus 27 WAD> possibilities at each location in a symbol WAD> string). WAD> WAD> If we tried to attain this target sequence by WAD> pure chance (for example, by randomly shaking out WAD> scrabble pieces), the probability of getting it WAD> on the first try would be around 10 to the -40, WAD> and correspondingly it would take on average WAD> about 10 to the 40 tries to stand a better than WAD> even chance of getting it. Thus, if we depended WAD> on pure chance to attain this target sequence, we WAD> would in all likelihood be unsuccessful. As a WAD> problem for pure chance, attaining Dawkins's WAD> target sequence is an exercise in generating WAD> specified complexity, and it becomes clear that WAD> pure chance simply is not up to the task. I consider it interesting that while the propability of the sequence is considerably lower than Dembski's own bound of 500 bits (see the appendix), he still thinks that \"pure chance simply is not up to the task\" of generating it. This indicates that not even Dembski takes his probability bound serious. WAD> But consider next Dawkins's reframing of the WAD> problem. In place of pure chance, he considers WAD> the following evolutionary algorithm: (i) Start WAD> out with a randomly selected sequence of 28 WAD> capital Roman letters and spaces, e.g., WAD> WAD> WDL*MNLT*DTJBKWIRZREZLMQCO*P WAD> WAD> (note that the length of Dawkins's target WAD> sequence, METHINKS*IT*IS*LIKE*A*WEASEL, comprises WAD> exactly 28 letters and spaces); (ii) randomly WAD> alter all the letters and spaces in this initial WAD> randomly-generated sequence; (iii) whenever an WAD> alteration happens to match a corresponding WAD> letter in the target sequence, leave it and WAD> randomly alter only those remaining letters that WAD> still differ from the target sequence. This is a complete misrepresentation of Dawkins' \"Weasel applet\". I refuse to believe that anyone who has read \"The Blind Watchmaker\" can write the above. The \"Weasel applet\" does *not* \"randomly alter all the letters and spaces\", and since it has no way of knowing which alterations \"happens to match a corresponding letter in the target sequence\", there is no way it can \"leave it and randomly alter only those remaining letters that still differ from the target sequence.\" Dawkins' \"Weasel applet\" \"breeds\" a number of \"progeny\", in every case randomly changing *some* of the letters, then seeing what \"progeny\" has the closest *overall* match with the target sequence. As though the \"Weasel applet\" wasn't misleading enough, Dembski has made it even more so, making it in no way a representive of the process (natural selection) he's criticizing. WAD> In very short order this algorithm converges to WAD> Dawkins's target sequence. In The Blind WAD> Watchmaker, Dawkins (p. 48) provides the WAD> following computer simulation of this algorithm: WAD> WAD> (1)WDL*MNLT*DTJBKWIRZREZLMQCO*P WAD> WAD> (2)WDLTMNLT*DTJBSWIRZREZLMQCO*P WAD> ... WAD> (10) MDLDMNLS*ITJISWHRZREZ*MECS*P WAD> ... WAD> (20) MELDINLS*IT*ISWPRKE*Z*WECSEL WAD> ... WAD> (30) METHINGS*IT*ISWLIKE*B*WECSEL WAD> ... WAD> (40) METHINKS*IT*IS*LIKE*I*WEASEL WAD> ... WAD> (43) METHINKS*IT*IS*LIKE*A*WEASEL WAD> WAD> Thus, Dawkins's simulation converges on the WAD> target sequence in 43 steps. In place of 10 to WAD> the 40 tries on average for pure chance to WAD> generate the target sequence, it now takes on WAD> average only 40 tries to generate it via an WAD> evolutionary algorithm. WAD> WAD> Although Dawkins uses this example to illustrate WAD> the power of evolutionary algorithms, the example WAD> in fact illustrates the inability of evolutionary WAD> algorithms to generate specified complexity. We WAD> can see this by posing the following question: WAD> Given Dawkins's evolutionary algorithm, what WAD> besides the target sequence can this algorithm WAD> attain? This is nothing but a red herring. Nowhere in TDI, as well as in any of his popular writings, has Dembski identified \"ability to attain anything besides the target sequence\" as a requirement of having specified complexity. And if this criterion was applied to humans doing things as well, it is doubtful how much of what we do could be considered exhibiting \"specified complexity\". If by \"target sequence\" Dembski means \"what one set one's mind to doing before doing it\", it would only be people with nerve or brain damages, being unable to do what they wanted, who could be considered producers of specified complexity. WAD> Think of it this way. Dawkins's evolutionary WAD> algorithm is chugging along; what are the WAD> possible terminal points of this algorithm? WAD> Clearly, the algorithm is always going to WAD> converge on the target sequence (with WAD> probability 1 for that matter). An evolutionary WAD> algorithm acts as a probability amplifier. WAD> Whereas it would take pure chance on average 10 WAD> to the 40 tries to attain Dawkins's target WAD> sequence, his evolutionary algorithm on average WAD> gets it for you in the logarithm of that number, WAD> that is, on average in only 40 tries (and with WAD> virtual certainty in a few hundred tries). WAD> WAD> But a probability amplifier is also a complexity WAD> attenuator. For something to be complex, there WAD> must be many live possibilities that could take WAD> its place. Notice Dembski's terminological sleight-of-hand here. First, he determines that the sequence indeed *does* contatin \"specified complexity\". Then, he conflates \"specified complexity\" with \"design\" (which, as we have seen, there is no basis for doing). And finally, he submits it to the explanatory filter, which labels it \"regularity\", since it is a high-propability event (see Section 2.1 of TDI). This, of course, leads to a contradiction, since specified complexity is *not* \"design\". Therefore, Dembski must now forget what he initially claimed, namely, that the sequence exhibits specified complexity. How this is done will become \"appearant\"... [...] WAD> It follows that Dawkins's evolutionary algorithm, WAD> by vastly increasing the probability of getting WAD> the target sequence, vastly decreases the WAD> complexity inherent in that sequence. As the sole WAD> possibility that Dawkins's evolutionary algorithm WAD> can attain, the target sequence in fact has WAD> minimal complexity (i.e., the probability is 1 WAD> and the complexity, as measured by the usual WAD> information measure, is 0). In general, then, WAD> evolutionary algorithms generate not true WAD> complexity but only the appearance of complexity. WAD> And since they cannot generate complexity, they WAD> cannot generate specified complexity either. Now, we also have \"appearant\" and \"actual specified complexity\", where \"appearant specified complexity\" is anything produced by an evolutionary algorithm, while \"actual specified complexity\" is that produced by intelligent agents. But since \"specified complexity\" is supposed to be what divides the product of intelligence from that of other processes, the only way we can determine if the sequence METHINKS*IT*IS*LIKE*A*WEASEL is produced by an evolutionary algorithm is to see... if it was made by an evolutionary algorithm. WAD> This conclusion may seem counterintuitive, WAD> especially given all the marvelous properties WAD> that evolutionary algorithms do possess. But the WAD> conclusion holds. What's more, it is consistent WAD> with the \"no free lunch\" (NFL) theorems of David WAD> Wolpert and William Macready, which place WAD> significant restrictions on the range of problems WAD> genetic algorithms can solve. According to Wesley, Dembski has seriously distorted Wolpert and Macready's \"No Free Lunch\" theorems: \"NFL says that when you average the performance of an algorithm over all \"cost functions\" of a problem, it performs no better on average than blind search. That is for *any* algorithm, not just evolutionary computation (which Dembski likes to imply). This goes to early claims that certain forms of evolutionary computation could be considered as general problem-solvers that could be deployed without much domain knowledge of a problem. NFL says that if you are concerned about the relative efficiency of getting a solution, you have to apply domain knowledge of the problem and cost function to select an algorithm with good performance on that problem and cost function. NFL isn't about essential capacity of an algorithm to produce a solution; it is about comparative efficiency of algorithms in producing solutions. It's my opinion that Dembski misconstrues or misunderstands what the NFL theorems say. I've passed word along that Dembski's choice of \"No Free Lunch\" for the title of a book that is due out this fall sets him up for embarrassment. That's still the title, so far as I know. It will be interesting to see how the reviews turn out. The introduction to the book is online at .\" (Wesley R. Elsberry, [ online here ]) WAD> The claim that evolutionary algorithms can only WAD> generate the appearance of specified complexity WAD> is reminiscent of a claim by Richard Dawkins. On WAD> the opening page of his The Blind Watchmaker he WAD> states, \"Biology is the study of complicated WAD> things that give the appearance of having been WAD> designed for a purpose.\" Just as the Darwinian WAD> mechanism does not generate actual design but WAD> only its appearance, so too the Darwinian WAD> mechanism does not generate actual specified WAD> complexity but only its appearance. WAD> WAD> But this raises the obvious question, whether WAD> there might not be a fundamental connection WAD> between intelligence or design on the one hand WAD> and specified complexity on the other. In fact WAD> there is. There's only one known source for WAD> producing actual specified complexity, and that's WAD> intelligence. Of course, if \"actual specified complexity\" is defined as \"that specified complexity that is produced by intelligence\", then the above is *obvious*. But then the claim \"life contains actual specified complexity\" becomes false, since we do *not* know that life was produced by intelligence. Indeed, that is what Dembski's filter is supposed to demonstrate in the first place. WAD> In every case where we know the causal history WAD> responsible for an instance of specified WAD> complexity, an intelligent agent was involved. Of course, if you a priori eliminate all instances of non-intelligent processes producing specified complexity, then you would hardly be surprised in finding that \"[i]n every case where we know the causal history responsible for an instance", "text_length": 20000, "text_sha256": "7c5e7af55eceb9358ed40680fd297df52f6a40f7d066b871458c83d00564d090" }, { "route": "/people/mgrey/IDC/002.html", "title": "ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\"", "description": "A commentary on William Dembski's", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/002.html ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" From: \"Morgan Grey\" < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Tue, 2 Oct 2001 15:00:15 -0700 (PDT) Message: 21796 Subject: [DebunkCreation] ID-Commentary: \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" I appologize for the long delay in posting this, but the last couple of weeks have been rather hectic. This is my second commentary on ID-texts. This week, I'm commenting on Dembski's \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\", Dembski's second post on why evolutionary algorithms can't explain specified complexity, from < http://www.metanexus.org/archives/message_fs.asp?&listtype=Magazine&ARCHIVEID=3080 > (also online at < http://www.geocities.com/evolutionsteori/IDC/3080.html >). My last such post can be found at < http://www.geocities.com/evolutionsteori/IDC/001.html >. Again, note that the original Metaview contains some =20's and a few =9's, which I have removed. And again, readers are invited to check for themselves if I have correctly conveyed the original message by doing so. ------------------------------------------------------- Metaviews 152: \"Specified Complexity\" by William Dembski grassie@VOICENET.COM William Grassie Metaviews 152. 1999/11/1. Approximately 3575 words. BG> Below is another posting from William Dembski at BG> Baylor University in Waco, TX. Dembski BG> continues his discussion of evolutionary BG> algorithms (see Meta 139) and presents a BG> mathematical argument for why such algorithms BG> cannot generate specified complexity Dembski does no such thing. The points of critique launched in this essay are limited to: 1) Evolutionary algorithms always solve their problems, setting the probability of success at 1, and the complexity therefore at 0. 2) Evolutionary algorithms get their \"specified complexity\" from the fitness functions, and thus have not *created* it. None of these are supported by any kind of \"mathematics\", unless one considers any essay with numbers in it to be \"mathematical\". BG> as asserted by Richard Dawkins. Dembski here continues the practice I also critiqued in my previous installment of ID-Commentary: Namely, to only criticize Dawkins' \"misleading\" Weasel program, instead of dealing with *real* problems solved by evolutionary algorithms, as asked by critics of Dembski. This is especially suspect, since \"Why Evolutionary Algorithms Cannot Generate Specified Complexity\" (and its companion-piece \"Explaining Specified Complexity\") is being presented as an *in principle*-refutation of the possibility of evolutionary algorithms producing \"specified complexity\". When speaking to the general public, who only know Dawkins' Weasel program, this tactic might work very well, but leave more informed skeptics wondering why Dembski keeps avoiding the *real* challenges, if his \"explanatory filter\" really is capable of doing what has been attributed to it. BG> A number of equations are presented in the BG> appendix. BG> BG> Dembski concludes that \"all the specified BG> complexity we get out of an evolutionary algorithm BG> has first to be put into the construction of the BG> evolutionary algorithm and into the fitness BG> function that guides the algorithm. Evolutionary BG> algorithms therefore do not generate or create BG> specified complexity, but merely harness already BG> existing specified complexity.\" I am not sure I BG> follow the entire argument, Bill Grassie's confusion is understandable, since Dembski has a wonderful ability to cloak everything he says in a highly techincal and intimidating babble. Therefore, most of my comments will deal with what Dembski is actually *saying*, trying to \"translate\" his impressive-sounding lingo, showing that it often covers simple and uncontroversial statements. BG> but I am certainly reminded of my first BG> programming course as a freshman in college in BG> 1975, when I clocked 70 hours one week in the lab BG> trying to code a quick sort algorithm. Some more BG> teleological interventions would have helped. BG> BG> I will entertain responses on the Metaviews list BG> and try to run some compilation in a week or so. BG> If you want immediate gratification conversation, BG> check out the Reiterations List at for a higher BG> volume, lightly moderated discussion. BG> BG> -- Billy Grassie BG> WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- WAD> =-=-= From: bill@desiderius.com (William A. WAD> Dembski) Subject: Specified Complexity WAD> WAD> WHY EVOLUTIONARY ALGORITHMS CANNOT GENERATE WAD> SPECIFIED COMPLEXITY by William A. Dembski WAD> WAD> In my last piece for META, I asserted that WAD> evolutionary algorithms cannot generate specified WAD> complexity and motivated this assertion by WAD> pointing to the failure of Richard Dawkins's well- WAD> known METHINKS IT IS LIKE A WEASEL example to WAD> generate specified complexity. My point was that WAD> Dawkins's evolutionary algorithm converged on WAD> METHINKS IT IS LIKE A WEASEL with probability WAD> one, and therefore reduced the complexity of WAD> generating this sequence to zero. With reference WAD> to specified complexity, complexity and WAD> probability are inverse notions: High complexity WAD> presupposes many live possibilities and WAD> correspondingly assigns low probability to anyone WAD> of these possibilities. Thus, while it's true WAD> that shaking out random scrabble pieces would WAD> render METHINKS IT IS LIKE A WEASEL highly WAD> improbable (and therefore complex), Dawkins's WAD> evolutionary algorithm renders that sequence WAD> certain and thereby removes its complexity. WAD> WAD> Basically, the problem here is one of setting the WAD> relevant probabilistic context. Within a random- WAD> scrabble-shaking-scenario, this sequence is WAD> complex and specified, but within Dawkins's WAD> evolutionary algorithm it is no longer complex WAD> (though it remains specified). I therefore WAD> concluded my last piece by saying that just as WAD> Darwinian evolution only delivers the WAD> **appearance** of design (an assertion all WAD> Darwinists perforce accept), so too it only WAD> delivers the **appearance** of specified WAD> complexity. Dembski forgets the other half of his conlusion: That his actual/appearant split of \"specified complexity\" makes it considerably more difficult to determine whether life indeed *is* an instance of specified complexity: \"Does nature exhibit actual specified complexity? The jury is still out.\" (Dembski, W.A., 1999, in Meta #3066) [...] WAD> In general terms, the problem of generating WAD> specified complexity via an evolutionary WAD> algorithm can be conceived as follows. We are WAD> given a phase space of possible solutions to a WAD> problem and a fitness function over that phase WAD> space. Our task is to optimize this fitness WAD> function by finding a point in the phase space WAD> that attains a certain level of fitness. Think of WAD> it this way: The phase space is a vast plane, the WAD> fitness function is a vast hollowed-out mountain- WAD> range over the plane (complete with low-lying WAD> foothills and incredibly high peaks). The task of WAD> an evolutionary algorithm is by moving around in WAD> the plane to get to some point under the mountain- WAD> range where it attains at least a certain height WAD> (e.g., 10,000 feet). The collection of all such WAD> places on the plane where the mountain range WAD> attains at least that height (here 10,000 feet) WAD> we will call the **target**. Thus the job of the WAD> evolutionary algorithm is by navigating the phase WAD> space to find its way into the target (see WAD> Appendix 1 below). What Dembski here calls the \"phase space\" is already known to readers of Dawkins as \"genetic space\": \"Imagine a museum with gallaries stretching towards the horizon in every direction, and as far as the eye can see upwards and downwards as well. Preserved in the museum is every kind of animal form that has ever existed, and every kind that could be imagined. Each animal is housed next door to those it most resembles. Each dimension in the museum -that is, each dimension along which a gallary extends- corresponds to one dimension in which the animals vary. For example, as you walk north along a particular gallary you notice a progressive lengthening of the horns of the speciments in the cabinets. Turn round and walk south and the horns shorten. Turn and walk east and that horns stay the same but something else changes, say the teeth get sharper. Walk west and the teeth grow blunter. Since horn length and teeth sharpness are only two out of thousands of ways in which animals can vary, the gallaries must criss-cross one another in many-dimensional space, not just the ordinary three-dimensional space that we, with our limited minds, are capable of visualizing.\" (Dawkins, R., 1996, \"Climbing Mount Improbable\", pp. 200) In the case of Dawkins' weasel program, the \"phase space\" is 28-dimensional (since there are 28 positions that can vary), where each dimension is 27 characters long (since there are 26 letters + space). In the weasel program, the algorithm can move any numbers of characters, but is restricted to moving a certain number of dimensions at a time (kinda' like the tower in chess, which can only move either back-forth or left-right, but can move any number of spaces). WAD> Now, the phase space (which we are picturing as a WAD> giant plane) usually comes with some additional WAD> topological structure, typically given by a WAD> metric or distance function (see Appendix 2). WAD> This topological structure tells us how points in WAD> the phase space are related geometrically to WAD> nearby points. The concept Dembski is trying to convey is that known to the biological community as a \"fitness landscape\", where increasing altitude stands for increasing fitness, as defined in terms of reproductive sucess. In the case of Dawkins' weasel program, the fitness landscape is a 29-dimensional cone, placed \"over\" the 28-dimensional \"chessboard\" (a.k.a. \"phase space\"). On the space directly under the top of the cone, the target sequence (\"methinks it is like a weasel\") is written, while the spaces around it are labelled with sequences very close to it (e.g. \"yethinks it is like a weasel\" and \"methinks it is like a geasel\"). WAD> Also, even though the phase space is huge, it WAD> tends to be finite (strictly finite for problems WAD> represented on computer and topologically finite, WAD> or what topologists call \"compact,\" in general). This is quite uncontroversial. The number of possible 28-letter sequences, each position with 27 possible outcomes (28^27 ~ 10^39) *is* \"huge, [but] finite\". WAD> Moreover, such spaces typically come with a WAD> uniform probability that is adapted to the WAD> topology of the phase space (see Appendix 3). With respect to Dawkins' weasel program, this pretty much means that the very first sequence has no more probability coming up \"jhdhonfybyyeev nzyvqqtiilke\" than \"xgyhsnszciuhanomqtwlpgwaaumu\". I know of no algorithms, where this is not the case. Dembski's reason for mentioning this is unclear. WAD> Basically this means that if you get out your WAD> tape measure and measure off a three by five foot WAD> area in one part of the phase space, the uniform WAD> probability will assign it the same probability WAD> as a three by five foot area in another portion WAD> of the phase space. All the spaces to which I've WAD> seen evolutionary algorithms applied do indeed WAD> satisfy these two conditions of having a finite WAD> topological structure (i.e., they are compact) WAD> and possessing a uniform probability. Moreover, WAD> this uniform probability is what typically gets WAD> used to estimate the complexity/improbability of WAD> the target (i.e., the area of the phase space WAD> under the mountain range where it attains a WAD> certain requisite level -- e.g., 10,000 feet). WAD> WAD> For instance, in Dawkins's WAD> METHINKS*IT*IS*LIKE*A*WEASEL example, the phase WAD> space consists of strings of upper case Roman WAD> letters and spaces (represented by asterisks) of WAD> length 28. A uniform probability on this space WAD> assigns equal probability to each of these WAD> sequences -- approximately 1 in 10^40. It's this WAD> improbability that corresponds to the complexity WAD> of the target sequence and with respect to which WAD> this target sequence constitutes an instance of WAD> specified complexity. Again, Dembski is being very unclear about what *exactly* he means by \"specified complexity\". Judging from the above, one would think that the \"complexity\" (i.e. \"propability\") of a certain event should be calculated only with respect to a single chance hypothesis. But in TDI (pp. 50) Dembski says that his explanatory filter needs to \"sweep the field clear of\" *all* chance hypotheses. This wouldn't be much of a problem, since \"specified complexity\" is never even mentioned in TDI. But since Dembski is constantly referring to specified complexity as a characteristic feature of \"design\", as well as to TDI as his \"scholarly argument\" for his ideas, this is unlikely to be anything *but* a problem. WAD> In general, given a phase space with a target WAD> sitting under those places where the mountain WAD> range attains at least a certain level (e.g., WAD> 10,000 feet), the (uniform) probability of WAD> randomly choosing a point from the phase space WAD> and landing in the target will be very small. In WAD> Dawkins's example, the target equals the WAD> character string METHINKS*IT*IS*LIKE*A*WEASEL and WAD> the improbability is 1 in 10^40. For non-toy WAD> examples the improbability is typically much less WAD> than my universal probability bound of 1 in WAD> 10^150 that I justify in The Design Inference WAD> (Cambridge, 1998; cf. section 6.5). Indeed, if WAD> the probability of the target were not small, a WAD> random search through the phase space would WAD> suffice to find a point in the target, and there WAD> would be no need to construct an evolutionary WAD> algorithm to find it. Again, few people would disagree that \"methinks it is like a weasel\" is too long to find just by randomly selecting letters and spaces. Indeed, Dawkins himself concluded that it \"would be a long time coming\" before this would produce the target sequence (\"The Blind Watchmaker\", pp. 47). WAD> We therefore suppose that the target is just a WAD> tiny portion of the whole phase space; or, in WAD> slightly more technical language, the (uniform) WAD> probability of the target in relation to the WAD> phase space as a whole is exceedingly small. WAD> What's more, the target, in virtue of its WAD> explicit identification, is specified (certainly WAD> this is the case in Dawkins's example where the WAD> target includes but one point and coincides with WAD> the character string WAD> METHINKS*IT*IS*LIKE*A*WEASEL). Thus it would seem WAD> that to find a point in the target would be to WAD> generate specified complexity. But just as Morris and Whitcomb thinks that radiometric datings only show the \"appearent age\" of the Earth, so Dembski believes that the solution produced is only \"appearant specified complexity\". WAD> But let's look deeper. Consider an evolutionary WAD> algorithm that does in fact find the target. An WAD> evolutionary algorithm can be conceived as a WAD> stochastic process that moves around the phase WAD> space some finite number of times (see Appendix WAD> 4). Let's call the evolutionary algorithm E. The WAD> evolutionary algorithm starts at some point E(0) WAD> in the phase space (usually chosen at random). WAD> Then it moves to E(1). Then to E(2). Then to E WAD> (3). Etc. For E successfully to find the target WAD> (i.e., to find a point under the mountain range WAD> where it attains at least a certain level -- WAD> e.g., 10,000 feet) then means that within a WAD> manageable number of steps n, E is very likely to WAD> land in the target -- i.e., some one of E(0), E WAD> (1), ..., E(n) is likely to land in the target WAD> (see Appendix 5). Simply put, the algorithm E has WAD> to get us into the target with high probability WAD> and in a relatively short number of steps. In the WAD> Dawkins example, E(n) rapidly converged to WAD> METHINKS*IT*IS*LIKE*A*WEASEL for n around 40. WAD> WAD> An evolutionary algorithm needs to be contrasted WAD> with pure random sampling. Pure random sampling WAD> treats the phase space as a giant urn from which WAD> we draw items at random according to the uniform WAD> probability. In that case, a random sample from M WAD> of size k will contain a point in the target with WAD> probability better than 1/2 provided that k is WAD> around the reciprocal of the (uniform) WAD> probability of the target. Since we are assuming WAD> that the probability of the target is less than WAD> my universal probability bound of 1 in 10^150 WAD> given earlier, it follows that k will need to be WAD> at least 10^150. This number is enormous and far WAD> exceeds the number of computations conceivable WAD> for any traditional computer. Moreover, it WAD> doesn't seem that quantum computation is going to WAD> render this number tractable either since the WAD> points in phase space need to be made explicit in WAD> any random sampling scheme (implying decoherence WAD> and thus preventing us from exploiting quantum WAD> superposition). Since all of the above is the case, both with respect to Dawkins' weasel program, as well as all examples of evolutionary algorithms that I am aware of, I am puzzled as to why Dembski finds it relevant to mention. WAD> Let's now return to the evolutionary algorithm E. WAD> We're going to allow ourselves a certain number WAD> of steps, call it m, for E to land in the target. WAD> Clearly m is going to have to be much less than WAD> 10^150 if we're going to program E on a computer WAD> and have any hope of E landing in the target. WAD> With m fixed, we can determine the probability WAD> that E will land in any subset of phase space in WAD> m steps (see Appendix 6). For instance, in the WAD> Dawkins example, for m = 100 and the target WAD> sequence METHINKS*IT*IS*LIKE*A*WEASEL and E the WAD> cumulative selection algorithm Dawkins WAD> constructed, the probability of E attaining the WAD> target in m = 100 steps is approximately 1. WAD> WAD> What this means is that even though with respect WAD> to the uniform probability on the phase space the WAD> target has exceedingly small probability, the WAD> probability for the evolutionary algorithm E to WAD> get into the target in m steps is no longer WAD> small. And since complexity and improbability are WAD> for the purposes of specified complexity parallel WAD> notions, this means that even though the target WAD> is complex and specified with respect to the WAD> uniform probability on the phase space, it WAD> remains specified but is no longer complex with WAD> respect to the probability induced by WAD> evolutionary algorithm E. Now Demsbki seems to have returned to claiming that complexity needs to be calculated with regard to *all* relevant chance hypotheses (as opposed to just the \"uniform probability\"). While few would disagree that life is complex with regard to the chance hypothesis of it being assembled by throwing random molecules together, it is quite another matter if it is complex with regard to it having come about through the actualization of heritable modifications, exclusion of certain modifications through differental reproductive success, and specified through the conditions of the environment (i.e. natural selection). In fact, whether this is so is the very point in question, and IDers are just assuming their conclusion when they claim that life contains \"specified complexity\". WAD> Does this mean that the evolutionary algorithm WAD> has in fact generated complex specified WAD> information, but that in referring", "text_length": 20000, "text_sha256": "97c7db01fbdc6362b22e6d67fafa834d54964744ce85682a6870a22001f5f8d3" }, { "route": "/people/mgrey/IDC/003.html", "title": "ID-Commentary: \"Another Way to Detect Design?\"", "description": "A commentary of William Dembski's", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/003.html ID-Commentary: \"Another Way to Detect Design?\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sun Oct 7, 2001 10:29 pm Message: 21866 Subject: ID-Commentary: \"Another Way to Detect Design?\" This is my third commentary on ID-texts. This week, I'm commenting on Dembski's \"Another Way to Detect Design?\", a reply to Fitelson, Stephens & Sober's (FS&S) \"How Not to Detect Design\" (online at < http://www.arn.org/docs/dembski/wd_wisconsinureview.htm >), which I recommend everyone to read. It is a bit technical in passages, but is a sound critique of Dembski's filter. Dembski's reply on Meta-views can be found at < http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=3097 > (and is also online at < http://www.geocities.com/evolutionsteori/IDC/3097.html >). My last such post can be found at < http://www.geocities.com/evolutionsteori/IDC/002.html >. ------------------------------------------------------- 167: Detecting Design? by William Dembski Metaviews 167. 1999/12/29. Approximately 2593 words. BR> Below is another column from William Dembski, now BR> at Baylor University's Polanyi Center . In the BR> piece below, Dembski responds to Elliott Sober BR> review in the Philosophy of Science, September BR> 1999. Dembski concludes: BR> BR> \"We are back, then, to needing some account of BR> complexity and specification. Thus a likelihood BR> analysis that pits competing design and chance BR> hypotheses against each other must itself BR> presuppose the legitimacy of specified complexity BR> as a reliable empirical marker of intelligence. BR> Consequently, if there is a way to detect design, BR> specified complexity is it.\" BR> BR> -- Billy Grassie BR> WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- WAD> =-=-= From: William_Dembski@baylor.edu (William WAD> A. Dembski) Subject: Another Way to Detect WAD> Design? WAD> WAD> In The Design Inference (Cambridge, 1998) I argue WAD> that specified complexity is a reliable empirical WAD> marker of intelligent design. Dembski does no such thing. \"Specified complexity\" is never even *mentioned* in TDI. Only in later writings does Dembski claim that the concept has anything to do with his 1998 dissertation. Furthermore, Dembski's claim that his filter can somehow detect *intelligent* design, is also confined to later, popular writings. In TDI, he writes: \"Thus, even though a design inference is frequently the first step toward identifying an intelligent agent, design as inferred from the design inference does not logically entail an intelligent agent. The design that emerges from the design inference must not be conflated with intelligent agency. Though they are frequently linked, the two are seperate. Whether an event conforms to a pattern is a seperate question from what caused an event to conform to a pattern.\" (pp. 8-9) And this is only the first time Dembski claims this. Other similar attempts to distinguish \"design\" from. intelligent agency can be found in TDI on pp. 19-20, 36, and 226-7. WAD> A long sequence of random letters is complex WAD> without being specified. Here, Dembski is taking advantage of the fact that to the general lay-reader, \"complexity\" is something about consisting of many parts, or being difficult to understand: ------------------------------------------------------- (< http://www.dictionary.com/cgi-bin/dict.pl?term=complex >) [...] complex \\Com\"plex\\, a. [...] 1. Composed of two or more parts; composite; not simple; as, a complex being; a complex idea. [...] 2. Involving many parts; complicated; intricate. [...] Source: Webster's Revised Unabridged Dictionary, © 1996, 1998 MICRA, Inc. ------------------------------------------------------- However, Dembski's notion of complexity is far from that of the lay-reader. In chapter 5 in TDI, Dembski argues that \"[p]robability measures are disguised complexity measures\" (p. 114). Or, as Dembski writes in \"Intelligent Design\": \"It follows, therefore, that how we measure information needs to be independent of whatever procedure we use to individuate the possibilities under consideration. The way to do this is not simply to count possibilities but to assign probabilities to these possibilities.\" (pp. 154) and \"As a purely formal object, the information measure described here is a complexity measure.\" (pp. 158) To illustrate the difference between the general concept of complexity and the concept as proposed by Dembski, consider an atom with nine electrons in its outer shell. While the average observer would probably refer to this system as \"simple\", Dembski's complexity measure would label it \"complex\", due to its low probability of occuring. To the one's who spend their chemistry lessons drawing naked women in their notebooks: Having eight electrons in the outer shell is the \"optimal\" state of atoms, and every atoms \"attemps\" to reach this state (except in the first shell, where the optimal number is two). Finding an atom with *nine* electrons in its outer shell would thus be as unlikely as finding two magnets with their positive poles stuck together. But most of Dembski's audience doesn't know this. They think that \"[a] long sequence of random letters is complex\" because it is long, not because it is improbable. And of course, Dembski never establishes *which* \"long sequence[s] of random letters\" are improbable, let alone informing his audience that this needs to be determined, letting them stay in blissful ignorance. WAD> A short sequence of letters like \"the,\" \"so,\" WAD> or \"a\" is specified without being complex. Again, Dembski very conveniently \"forgets\" to mention that according to his own complexity measure, complexity have nothing to do with the length of the sequence. WAD> A Shakespearean sonnet is both complex and WAD> specified. Thus in general, given an event, WAD> object, or structure, to convince ourselves that WAD> it is designed we need to show that it is WAD> improbable (i.e., complex) and suitably patterned WAD> (i.e., specified). It is only later (and even then, tucked away in parantheses) that Dembski even hints at the connection between propability and complexity. WAD> Not everyone agrees. Elliott Sober, for instance, WAD> holds that specified complexity is exactly the WAD> wrong instrument for detecting design (see his WAD> September 1999 review in Philosophy of Science WAD> titled \"How Not to Detect Design\"). In this piece WAD> I want to consider the main criticisms of WAD> specified complexity as a reliable empirical WAD> marker of intelligence, show how they fail, and WAD> argue that not only does specified complexity WAD> pinpoint how we detect design, but it is also our WAD> sole means for detecting design. Before evaluating if Dembski succeeds in \"consider[ing] the main criticisms of specified complexity\", let us see what FS&S's \"main criticisms\" are. 1) Dembski's filter is much too punctilious, since a design inference can be made with respect to likelihoods of the hypothesis being correct: \"There is a straightforward reason for thinking that the observed outcomes favor Design over Chance. If Caputo had allowed his political allegiance to guide his arrangement of ballots, you'd expect Democrats to be listed first on all or almost all of the ballots. ... The key concept is *likelihood*. The likelihood of a hypothesis is the probability it confers on the observations; it is not the probability that the observations confer on the hypothesis. ... Chance and Design can be evaluated by comparing their likelihoods, relative to the same set of observations.\" (original emphasis) 2) Dembski's terminology and examples are confusing and contradictory: \"Dembski defines the Regularity hypothesis in different ways. Sometimes it is said to assert that the evidence E is noncontingent and is reducible to law (39, 53); at other times it is taken to claim that E is a deterministic consequence of earlier conditions (65, 146n5); and at still other times, it is supposed to say that E was highly probable, given some earlier state of the world (38).\" \"Understanding what \"regularity,\" \"chance,\" and \"design\" mean in Dembski's framework is made more difficult by some of his examples. Dembski discusses a teacher who finds that the essays submitted by two students are nearly identical (46). One hypothesis is that the students produced their work independently; a second hypothesis asserts that there was plagiarism. Dembski treats the hypothesis of independent origination as a Chance hypothesis and the plagiarism hypothesis as an instance of Design. Yet, both describe the matching papers as issuing from intelligent agency, as Dembski points out (47).\" \"The same sort of interpretive problem attaches to Dembski's discussion of the Caputo example. We think that all of the following hypotheses appeal to intelligent agency: (i) Caputo decided to spin a roulette wheel on which 00 was labeled \"Republican\" and the other numbers were labeled \"Democrat;\" (ii) Caputo decided to toss a fair coin; (iii) Caputo decided to favor his own party. Since all three hypotheses describe the ballot ordering as issuing from intelligent agency, all, apparently, are instances of Design in Dembski's sense. However, Dembski says that they are examples, respectively, of Regularity, Chance, and Design.\" 3) There is no reason why regularity needs to be rejected before chance can be accepted, or why both need to be rejected before design can be accepted: \"In the first example, Dembski (39) says that Newton's hypothesis that the stability of the solar system is due to God's intervention into natural regularities is less parsimonious than Laplace's hypothesis that the stability is due solely to regularity. In the second, he compares the hypothesis that a pair of dice is fair with the hypothesis that each is heavily weighted towards coming up 1. He claims that the latter provides the more parsimonious explanation of why snake-eyes occurred on a single roll. We agree with Dembski's simplicity ordering in the first example; the example illustrates the idea that a hypothesis that postulates two causes R and G is less parsimonious than a hypothesis that postulates R alone. However, this is not an example of Regularity versus Design, but an example of Regularity&Design versus Regularity alone; in fact, it is an example of two causes versus one, and the parsimony ordering has nothing to do with the fact that one of those causes involves design. In Dembski's second example, the hypotheses differ in likelihood, relative to the data cited; however, if parsimony is supposed to be a different consideration from fit-to-data, it is questionable whether these hypotheses differ in parsimony.\" 5) With respect to chance and regularity, Dembski's filter is likely to make a wrong inference: \"The fact that the Filter allows you to accept or reject Regularity without attending to what specific Regularity hypotheses predict has some peculiar consequences. Suppose you have in mind just one specific regularity hypothesis that is a candidate for explaining E; you think that if E has a regularity-style explanation, this has got to be it. If E is a rare type of event, the Filter says to conclude that E is not due to Regularity. This can happen even if the specific hypothesis, when conjoined with initial condition statements, predicts E with perfect precision. Symmetrically, if E is a common kind of event, the Filter says not to reject Regularity, even if your lone specific Regularity hypothesis deductively entails that E is false.\" 4) Dembski's specification criterion is useless in helping one formulate patterns of specification (as opposed to those of fabrications). One of the conditions offered by Dembski is far too lenient on chance hypotheses, and the two other even allows tautologies to be formulated as specifications: \"CINDE [one of the conditions] is too lenient on Chance hypotheses -- it says that their violating CINDE suffices for them to be accepted (or not rejected). Suppose you want to explain why Smith has lung cancer (E). It is part of your background knowledge (I) that he smoked cigarettes for thirty years, but you are considering the hypothesis (H) that Smith read the works of Ayn Rand and that this helped bring about his illness. To investigate this question, you do a statistical study and discover that smokers who read Rand have the same chance of lung cancer as smokers who do not. This study allows you to draw a conclusion about Smith -- that Pr(E | H&I) = Pr (E | not-H &I). Surely this equality is evidence against the claim that E is due to H. However, the filter says that you can't reject the causal claim, because CINDE is false -- Pr (E | H&I) [is not equal to] Pr(E | H).\" \"In fact, just writing down a tautology satisfies TRACT and DELIM (165). On the assumption that human beings are able to write down tautologies, we conclude that these two conditions are always satisfied and so play no substantive role in the Filter.\" 5) Dembski is wrong in claiming that one should reject speciefied events of small probability to avoid a \"probabilistic inconsistency\": \"Suppose you know that an urn contains either 10% green balls or 1% green balls; perhaps you saw the urn being filled from one of two buckets (you don't know which), whose contents you examined. Suppose you draw 10 balls from the urn and find that 7 are green. From a likelihood point of view, the evidence favors the 10% hypothesis. However, Dembski would point out that the 10% hypothesis predicted that most of the balls in your sample would fail to be green. Your observation contradicts this prediction. Are you therefore forced to reject the 10% hypothesis? If so, you are forced to reject the 1% hypothesis on the same grounds. But you know that one or the other hypothesis is true. Dembski's talk of a \"probabilistic inconsistency\" suggests that he thinks that improbable events can't really occur -- a true theory would never lead you to make probabilistic predictions that fail to come true.\" I must admit that I, on this particular point, find FS&S's reasoning to be a little strained. First, I think that everyone agrees that, say, a human being being assembled by random atoms banging together as a chance hypothesis is *far* too improbable, and that another explanation for the existence of humans is required. Pointing out that we sometimes must accept hypotheses requiring low probabilities doesn't justify accepting hypotheses requiring *extremely* low probabilities. Second, the example proposed above is only valid if we are absolutely sure that the mentioned buckets are the only possible sources. Given the above event, I would consider the possibility that someone was pulling my leg, and that the balls really came from a bucket, where 70% of the balls were green. 6) Since the explanatory filter requires you to reject *all* chance hypotheses before accepting design, infering design is nigh-impossible, unless you happen to be omniscient: \"Here Dembski is *much* too hard on Design. Paley reasonably concluded that the watch he found is better explained by postulating a watchmaker than by the hypothesis of random physical processes. This conclusion makes sense even if Paley admits his lack of omniscience about possible Chance hypotheses, but it does not make sense according to the Filter. What Paley did was compare a specific chance hypothesis and a specific design hypothesis without pretending that he thereby surveyed all possible chance hypotheses. For this reason as well as for others we have mentioned, friends of Design should shun the Filter, not embrace it.\" (emphasis original) 7) Since it is impossible to eliminate all competing theories, ID-theory can't establish itself merely by eliminating Neo-Darwinistic evolution. Instead, it must be able to make predictions that can be tested: \"To test evolutionary theory against the hypothesis of intelligent design, you must know what both hypotheses predict about observables (Fitelson and Sober 1998, Sober 1999b). The searchlight therefore must be focused on the design hypothesis itself. What does it predict? If defenders of the design hypothesis want their theory to be scientific, they need to do the scientific work of formulating and testing the predictions that creationism makes (Kitcher 1984, Pennock 1999). Dembski's Explanatory Filter encourages creationists to think that this responsibility can be evaded. However, the fact of the matter is that the responsibility must be faced.\" It will be interesting to see if Dembski in fact *has* succeeded in \"consider[ing] the main criticisms of specified complexity\". WAD> Consequently, specified complexity is not just WAD> one of several ways for reinstating design in the WAD> natural sciences-it is the only way. There is no need to \"reinstat[e] design in the natural sciences\": Several natural sciences, like archaeology and anthropology, have already been detecting and studying intelligent designed objects for decades. Perhaps some of the archaeologists on this list (Brian? Anne?) would like to comment on whether they need Dembski's filter to infer that, say, a cave painting is designed? WAD> Specified complexity, as I explicate it in The WAD> Design Inference, belongs to statistical decision WAD> theory. Statistical decision theory attempts to WAD> set the ground rules for how to draw inferences WAD> for occurrences governed by probabilities. Now, WAD> statistical decision theorists have their own WAD> internal disputes about the proper definition of WAD> probability and the proper logic for drawing WAD> probabilistic inferences. It was therefore WAD> unavoidable that specified complexity should come WAD> in for certain technical criticisms simply WAD> because the field of statistical decision theory WAD> is itself so factionalized (cf. Bayesian vs. WAD> frequentist approaches to probability). Dembski is ignoring that most of \"the main criticisms of specified complexity\" didn't deal with the probability-part of his book, but with the philosophical and logical assumptions, as well as his inability to clearly define his terms. For Dembski to claim that \"the main criticisms of specified complexity\" are mostly due to the fact that \"the field of statistical decision theory is itself so factionalized\", is simply misleading. WAD> The approach I take follows the common WAD> statistical practice (popularized by Ronald WAD> Fisher) of rejecting a chance hypothesis if a WAD> sample appears in a prespecified rejection WAD> region. What my complexity-specification WAD> criterion does is extend this statistical WAD> practice in two ways: First, it generalizes the WAD> types of rejections regions by which chance is WAD> eliminated, namely, to what I call WAD> \"specifications.\" Another example of Dembski obfuscating the issue by using vague and impressive-sounding terms to describe even the most simple concepts. Statistical theory is operating with what is known as \"rejection regions\". For example, before taking a statistical sample of the number of people who have been cured of cancer after taking drug X, the statistican might decide that if the result differs from that expected by pure luck by 0.01 or less, the usefulness of drug X in curing cancer should be rejected. Dembski's \"inovation\" is to claim that this \"rejection region\" can be formulated *after* the sample has been taken, in which case it should be called a \"specification\". So when Dembski says that his \"complexity-specification criterion\" \"generalizes the types of rejections regions by which chance is eliminated ... to ... specifications\", he is just saying that it can also eliminate chance *after* the event is known. This is the claim that many reviewers have objected to, and which FS&S's review spends considerable time questioning. WAD> Second, it allows for the elimination of all WAD> relevant chance hypotheses for an eve", "text_length": 20000, "text_sha256": "fcc5f217bf6baefe5fa7b0ac9eef7fca444b8e0704fb6821b95be2c0f94374ca" }, { "route": "/people/mgrey/IDC/004.html", "title": "ID-Commentary: \"Disbelieving Darwin -- And Feeling No Shame!\"", "description": "From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Fri Oct 12, 2001 9:54 am Message: 21889 Subject: ID-Commentary: \"Disbelieving Darwin...\" This is my fo", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/004.html ID-Commentary: \"Disbelieving Darwin -- And Feeling No Shame!\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Fri Oct 12, 2001 9:54 am Message: 21889 Subject: ID-Commentary: \"Disbelieving Darwin...\" This is my fourth commentary on texts written by leading IDers. My last such post can be found at < http://www.geocities.com/evolutionsteori/IDC/003.html >. This week, I'm commenting on Dembski's \"Disbelieving Darwin -- And Feeling No Shame!\", posted to Metanexus at < http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=2581 > (also online at < http://www.geocities.com/evolutionsteori/IDC/2581.html >) In this article, Dembski speculates about dogmatism in science, the public's alleged refusal to accept Darwinism, and also shares a few thoughts about evangical Christianity's new poster-child, Intelligent Design-Theory. ------------------------------------------------------- 027: Disbelieving Darwin and Feeling No Shame, by William Dembski Metaviews 027. 2000.03.16. Approximately 2150 words. BG> Below is a column from William Dembski from the BG> Polanyi Center at Baylor University with the BG> title \"Disbelieving Darwin - And Feeling No BG> Shame!\" Dembski makes a compelling inductive BG> argument from past scientific failures that we BG> should be skeptical about Darwinism. He presents BG> the dominant biological orthodoxy as dogmatic and BG> out of step with the public and the evidence. BG> Dembski develops a tentative case for moving BG> beyond Darwinism. BG> BG> In the end, Dembski presents Intelligent Design BG> Theory as THE alternative to Darwinism, but there BG> are other possibilities to be considered. I would BG> also like to see the terms \"intelligent\" BG> and \"design\" defined in a rigorous manner. BG> Finally, one wonders whether the radical BG> skepticism that Dembski advocates for science BG> would also be applied to his religious beliefs and BG> how. All in all though, we have a poignant BG> counterpoint to Michael Shermer's recent thread. BG> BG> -- Billy Grassie BG> WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From: WAD> William_Dembski@baylor.edu (William A. Dembski) WAD> Subject: Disbelieving Darwin -- And Feeling No WAD> Shame! Dembski starts out by praising the tentativeness of science and warning us of letting dogmatism replace commitment to a certain theory. All well and good, and hopefully something that scientists on both sides of the issue can agree with. And since everyone can read this for themselves in the original document, I have snipped the beginning of Dembski's essay without further comment. [...] WAD> I open with these general remarks about WAD> tentativeness and dogmatism in science because WAD> their importance is too frequently neglected in WAD> discussions of biological evolution. It hardly WAD> makes for a free and open exchange of ideas when WAD> biologist Richard Dawkins asserts, \"It is WAD> absolutely safe to say that if you meet somebody WAD> who claims not to believe in evolution, that WAD> person is ignorant, stupid, or insane (or wicked, WAD> but I'd rather not consider that).\" Nor does WAD> philosopher Michael Ruse help matters when he WAD> trumpets, \"Evolution is a fact, *fact*, *FACT!*\" WAD> WAD> Nor for that matter does Stephen Jay Gould's WAD> protegÇ Michael Shermer promote insight into WAD> natural selection when he announces, \"No one, and WAD> I mean *no one*, working in the field is debating WAD> whether natural selection is the driving force WAD> behind evolution, much less whether evolution WAD> happened or not.\" Let me be entirely clear on this: Dembski has a point. In presenting the neo-Darwinian theory of evolution to the public, many scientists *have* (and still do) presented evolution dogmatically and without the tentativeness that Dembski advocates (and with which I absolutely agree). However, I also believe that this rests as much on YEC's as on evolutionary biologists. In their oft-repeated claims that \"evolution is just a theory\", they have forced the scientific community to make clear that common descent (and to a certain degree the process of evolution) is supported by overwhelming evidence. In doing so, many scientists have emphasized the evidential suppport of the theory to the point of presenting it as something that simply *cannot* be false. Needless to say, members of the ID movement have seized on these statements, pressing the opposite point: That the neo-Darwinian theory of evolution, as the only scientific theory, is being presented as something *other* than \"a theory\". Let me add that not all scientists have fallen to the temptation of presenting the theory as something it is not, as these few examples will hopefully show: \"It would be folly for evolutionists to claim that they have a complete and accurate understanding of the history of life and of the processes that produced that history. Too many major paradigms in science have been overturned for any statement of such absolute confidence to be wise. We should consider alternatives and we should consider the possibility that we might be wrong in at least some parts of the basic framework of evolutionary thinking. And this consideration of alternatives is, in fact, going on in the 1980s with challenges from within evolutionary biology itself to the neo-Darwinian model as it is applied to macroevolution (Lewin 1980).\" (Raup, D.M., \"The Geological and Paleontological Arguments of Creationism\", in Godfrey, L.R. (ed.), 1983, \"Scientists Confront Creationism\", pp. 161) \"Science does not claim to discover the final truth but only to put forward hypotheses based on evidence that is available at the time of their presentation. Well-corroborated hypotheses are often treated as facts, and such a fact is that of organic evolution. If a hypthesis is fairly general in its presentation, it is difficult to test, but a detailed hypothesis like that of organic evolution is readily suspectible to disproof. The evidence for evolution is overwhelming, and there is no known fact that either weakens the hypothesis or disproves it.\" (Campbell, B.G., 1966, \"Human Evolution\", pp. 1) WAD> Such remarks, and especially the attitude behind WAD> them, do nothing to settle the ongoing WAD> controversy over evolution. Gallup polls WAD> consistently indicate that only about ten percent WAD> of the U.S. population accepts the sort of WAD> evolution advocated by Dawkins, Ruse, and WAD> Shermer, that is, evolution in which the driving WAD> force is the Darwinian selection mechanism. The WAD> rest of the population is committed to some form WAD> of intelligent design. Dembski is doing some serious word-spinning here. Gallup's poll doesn't even use the term \"Darwinian selection mechanism\", so any claims of the \"population accept[ing]\" \"evolution in which [this is] the driving force\" must come from Dembski, not from Gallup. According to < http://www.gallup.com/poll/releases/pr010305.asp >, the poll asks people to chose the following statement that best describes their view: \"Human beings have developed over millions of years from less advanced forms of life, but God guided this process.\" \"Human beings have developed over millions of years from less advanced forms of life, but God had no part in this process.\" \"God created human beings pretty much in their present form at one time within the last 10,000 years or so.\" Of the people asked, 37% agreed with the first statement, 12% with the second, and 45% with the third. Since statement no. 2 is tantamount to atheism, it is not at all surprising that only a small minority of the American public agrees with it. In fact, only 1% of the people referring to themselves as \"creationists\" agreed with this statement. And that the 45% agreeing with statement 3 \"is committed to some form of intelligent design\" is also well beyond dispute, given that they are most likely YECs. However, when Dembski choses to classify the 37% who agreed with the first statement as being \"committed to some form of intelligent design\", he is simply imposing *his own* opinion about how \"God guided this process\", in order to make it appear as if the public somehow supports the ID-movement. For example, all Christians who hold some version of theistic evolution, teleological evolution, or fully gifted creation would hardly like being told that they are \"committed to some form of intelligent design\", especially after Dembski told them that \"intelligent design is incompatible\" with their position, and that it \"[t]heistic evolution takes the Darwinian picture of the biological world and baptizes it\" (\"Intelligent Design\", pp. 110). And as far as Gallup is concerned, those 45% \"selected a statement that can be seen as compatible with the scientific findings of evolutionary scholars\". There is absolutely no evidence that the public is particularly committed to the views espoused by members of the ID-movement. In fact, Alan G. Padgett, writing for Christianity Today, a magazine that characterizes itself as believing that \"the Scriptures are the inspired Word of God and that the gospel is the power of God unto salvation\", does \"not think that the intelligent-design folks will win the day\", and even \"accept[s] the notion that life will some day be explained through natural causes\": \"For my part, if I had to predict today how a future Angelic Doctor will reconcile theology and science, I would throw my hat in with O'Hear and Swinburne. I do not believe the intelligent-design folks will win the day. In other words, I accept the notion that life will some day be explained through natural causes, while insisting that God is the origin of all natural things, natural causes, and natural laws. In this way design and evolution are not opposites. Rather, evolution is based upon natural regularities, which in turn are created by God. Evolution is based upon design.\" (Padgett, A.G., 2000, \"Creation by Design\", Christianity Today, < http://www.christianitytoday.com/bc/2000/004/13.30.html >) I am not claiming that the public is particularly hostile to the ID-movement, or that the majority holds those versions of theistic evolution that are compatible with neo-Darwinism, since the options presented by the Gallup-poll are so vague. However, I strongly resent Dembski's attempt to twist those results in order to claim that the majority of the population \"is committed to some form of intelligent design.\" I have hear snipped several paragraphs, in which Dembski advances speculations about \"why the public rejects Darwinism\". I found these speculations irrelevant until Dembski can *show* that \"the public rejects Darwinism\", and have therefore not commented on them. [...] WAD> The public need feel no shame at disbelieving and WAD> openly criticizing Darwinism. Most scientific WAD> theories these days are initially published in WAD> specialized journals or monographs, and are WAD> directed toward experts assumed to possess WAD> considerable technical background. Not so WAD> Darwin's theory. The locus classicus for Darwin's WAD> theory remains his *Origin of Species*. In it WAD> Darwin took his case to the public. Dembski is here \"forgetting\" the fact that in Darwin's time, there was few to none scientific publications dealing with biology, in which Darwin could have published his theory. In fact, Darwin practically *founded* biology as a science, eventually making possible the publication of biological journals like NATURE and SCIENCE, in which studies regarding evolution are published. WAD> Contemporary Darwinists likewise continue to take WAD> their case to the public. There is nothing wrong in \"tak[ing one's] case to the public.\" What is usually advocated is that one *also* \"take[s one's] case to the\" scientific community. So far, the ID-community has not published anything in the scientific litterature, offering any evidence for their claims that certain things (the universe, life, etc.) is intelligently caused. Perhaps Dembski, in his next writing, will assure the public that it \"need feel no shame at disbelieving and openly criticizing\" Intelligent Design-theory? WAD> The books of Richard Dawkins, Daniel Dennett, WAD> Stephen Jay Gould, E. O. Wilson, and a host of WAD> other biologists and philosophers aim to convince WAD> a skeptical public about the merits of Darwin's WAD> theory. These same authors commend the public WAD> when it finds their arguments convincing. But WAD> when the public remains unconvinced, commendation WAD> turns to condemnation. WAD> Daniel Dennett even recommends \"quarantining\" WAD> parents who teach their children to doubt WAD> Darwinism (see the end of his *Darwin's Dangerous WAD> Idea*). In his \"Intelligent Design\" (pp. 289) Dembski makes the same charge, specifying the reference to page 519 in Dennett's book. I assume that Dembski is referring to the following paragraph: \"We should not expect this variety of respect to be satisfactory to those who wholeheartedly embody the memes [fundamentalist Christianity] we honor with our attentive -but not worshipful- scholarship. On the contrary, many of them will view anything other than enthusiastic conversion to their own view as a threat, even an intolerable threat. ... But we have no reasonable alternative, and those whose visions dictate that they cannot peacefully coexist with the rest of us we will have to quarantine as best we can, minimizing the pain and damage, trying always to leave open a path or two that may come to be seen as acceptable.\" (Dennet, D.C., 1995, \"Darwin's Dangerous Idea\", pp. 519) Unless Dembski thinks that \"teach[ing one's] children to doubt Darwinism\" \"dictate that [one] cannot peacefully coexist with\" other people, it seems as if we have another example of Dembski misrepresenting his opponents' views. [...] WAD> Whether intelligent design is the theory that WAD> ultimately overturns Darwinism is not the issue. WAD> The issue is whether the scientific community is WAD> willing to eschew dogmatism and admit as a live WAD> possibility that even its most cherished views WAD> might be wrong. This is, IMHO, a *non*issue. Dogmatig-sounding statements from popularizers of science notwithstanding, there is absolutely no reason for assuming that \"the scientific community is\" *not* \"willing to eschew dogmatism and admit as a live possibility that even its most cherished views might be wrong.\" [...] WAD> William Dembski WAD> META> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Footer META> information below last updated: 1999/12/10. [...] META> Copyright 1999, 2000 by William Grassie. Copies META> of this internet posting may be made and META> distributed in whole without further permission. META> Credit: \"This information was circulated on the META> Meta Lists on Science and Religion META> < http://www.meta-list.org >.\" ------------------------------------------------------- ===== Morgan \"Evolution is to the social sciences as statues are to birds: a convenient platform upon which to deposit badly digested ideas.\" (Steve Jones, 2000, \"Darwin's Ghost\", pp. xxvii) [ More ID-Commentaries ]", "text_length": 15185, "text_sha256": "2f91864c9f56925563cd3a4e510e863f7146815799870680514c1d14b2dce1b5" }, { "route": "/people/mgrey/IDC/005.html", "title": "ID-Commentary: \"Who's Got the Magic?\"", "description": "From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sun Oct 21, 2001 5:44 pm Message: 22008 Subject: ID-Commentary: \"Who's Got the Magic?\" Group, This is", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/005.html ID-Commentary: \"Who's Got the Magic?\" From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sun Oct 21, 2001 5:44 pm Message: 22008 Subject: ID-Commentary: \"Who's Got the Magic?\" Group, This is my fifth commentary on texts written by leading IDers. My last such post can be found at http://www.geocities.com/evolutionsteori/IDC/004.html . This week, I'm commenting on Dembski's \"Who's Got the Magic?\", posted to Metanexus at http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=2595 (also online at http://www.geocities.com/evolutionsteori/IDC/2595.html ). Dembski's post is a response to Pennock's criticism of Johnson's \"supernatural theistic science\", as found in Pennock's \"Tower of Babel\". Following that is a criticism of what Dembski sees as \"bargain-hunting\", where \"scientific naturalists\" are trying to get \"something for nothing\". Pennock has written a reply, which can be found at http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=2645 . Although quite long, it raises some good criticism of Dembski's essay, and should be read by everybody interested in the issue (if only for the fun of being able to say \"hare designer\" out loud). ------------------------------------------------------- 042: Who's Got the Magic? by William Dembski Metaviews 042. 2000.04.25. Approximately 2286 words. BG> In the posting below, William Dembski from the BG> Michael Polanyi Center at Baylor University offers BG> a critical review of Robert Pennock's book \"The BG> Tower of Babel.\" In so doing, he argues again on BG> behalf on \"Intelligent Design Theory,\" which he BG> distinguishes from \"Creationism.\" In my view, the BG> debate would be improved, if both terms were more BG> carefully defined, rather than assumed. BG> BG> In any case, Dembski argues that the \"something BG> for nothing\" thinking which characterizes BG> scientific materialism approach to evolution is BG> akin to \"magic\". \"Pennock and his fellow BG> scientific naturalists,\" writes Dembski, \"are BG> bargain hunters\" (i.e. looking for something for BG> nothing.) \"They want to explain the appearance of BG> design in nature without admitting actual design.\" BG> BG> Dembski and the Polanyi Center have been in the BG> news recently with 1) a very ambitious conference BG> on Naturalism in Science held two weeks ago BG> involving a broad spectrum of thinkers, and 2) a BG> recent vote by the faculty senate at Baylor BG> University seeking to close the one-year old BG> center (see the Chronicle of Higher Education on BG> 4/19/00). BG> BG> I am grateful that these debates can also take BG> place on Meta and welcome your comments and BG> feedback. BG> BG> -- Billy Grassie BG> WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From: WAD> William_Dembski@baylor.edu (William A. Dembski) WAD> Subject: Who's Got the Magic? WAD> WAD> In criticizing Phillip Johnson's \"intelligent WAD> design creationism,\" Robert Pennock raises a WAD> particularly worrisome legal consequence of WAD> Johnson's view. According to Pennock, Johnson WAD> insists \"that science admit the reality of WAD> supernatural influences in the daily workings of WAD> the world.\" But what if the same reasoning that WAD> Johnson is trying to import into science were WAD> adopted in Johnson's own area of specialization WAD> -- the law (Johnson is a law professor at UC WAD> Berkeley)? Here's the concern as Pennock lays it WAD> out in _Tower of Babel_ (p. 295): WAD> WAD> [[indent]] \"For the law to take [Johnson's view] WAD> seriously as well, it would have to be open to WAD> both suits and defenses based on a range of WAD> possible divine and occult interventions. Imagine WAD> the problems that would result if the courts had WAD> to accept legal theories of this sort. How would WAD> the court rule on whether to commit a purportedly WAD> insane person to a mental hospital for self- WAD> mutilation who claims that the Lord told her to WAD> pluck out her eye because it offended her? How WAD> would a judge deal with a defendant, Abe, accused WAD> of attempted murder of his son, Ike, who claims WAD> that he was only following God's command that he WAD> kill Ike to prove his faith?\" WAD> WAD> Implicit in this passage and throughout Pennock's WAD> book is a forced choice between mechanism and WAD> magic: Either the world works by mechanisms that WAD> obey inviolable natural laws and that admit no WAD> break in the chain of natural causation, or all WAD> hell breaks loose and the world admits WAD> supernatural interventions that make a hash of WAD> science and our understanding of the world WAD> generally (and legal studies in particular). This is not \"[i]mplicit\" at all. Pennock is in fact quite forthcoming about the reality of this \"forced choice\": \"Without the binding assumption of uninterruptible natural law there would be absolute chaos in the scientific worldview. Supernatural explanations undermine the discipline that allows science to make progress. It is not that supernatural agents and powers could not explain in principle, it is rather that they can explain all too easily.\" (Pennock, R.T., 2000, \"Tower of Babel\", pp. 294) What might come as a surprise, I partially disagree with Pennock on this point. When Pennock says that \"[s]upernatural explanations undermine [science]\", he is supposing that the there is such a thing as a \"natural explanation\". However, I have often found that since this term has been used by so many authors in so many contexts, its meaning has been diluted to the point of being useless in any discussion about the philosophy of science. Many IDists (most notably, Johnson) have taken advantage of this fact, claiming that since \"science only considers naturalistic explanations\", any form of intelligent design is excluded from considerations a priori, when no such thing is (or should be) the case. Even a wide definition of \"natural\" like \"consisting of a form of matter and/or energy\" is too limiting, since we have no way of knowing if explanations involving other substances will one day be feasible. In the place of \"naturalistic\", I offer \"knowable\". Although not all scientific explanations should necessarily use known mechanisms (dark matter being a substance about which we know very little), they should all use explanations, in which the mechanisms are *knowable*. The reason I only \"partially\" disagree with Pennock, is that for all intents and purposes, \"*super*natural\" equals \"*un*knowable\". Putting aside fortune tellers and mediums, all claiming to \"know the mind of God\", everyone agrees that any knowledge about the supernatural is impossible, even in principle. As Pennock writes: \"God works, as they say, in mysterious ways. We cannot have any privy knowledge of God's will, and those who have tried to claim it are quickly brought back to earth. When the complex Ptolemaic epicycle theory of the planetary system was explained to Alphonso X, King of Castile, with its equant points, eccentrics, deferents, and epicycles -wheels upon wheels within offset wheels- he is reported to have commented that \"if God had consulted him at the creation, the universe should have been on a better and simpler plan.\" Defending the complexity of his theoretical models from another critic who made the same point, Ptolemy is said to have replied, \"You may complain that these models are not simple, but from the point of view of God, who knows what is simple?\" And, of course, Ptolemy was right; we cannot say that our notion of simplicity is at all relevant to what God's might be, or even if God values simplicity at all. Scientific models must be judged on natural grounds of evidence, for we have no supernatural ground upon which we can stand since any such ground is necessarily a mystery to us.\" (Pennock, 2000, pp. 290) WAD> Pennock is offering his readers mechanism. WAD> Johnson is offering them magic. Any reasonable WAD> person knows which option to choose. WAD> WAD> But as with most forced choices, there's a WAD> tertium quid that Pennock has conveniently WAD> ignored, and that when properly understood shows WAD> that the real magician here is in fact Pennock WAD> and not Johnson. The tertium quid here is WAD> intelligent design, which is entirely separable WAD> from creationism. But Pennock, as a trained WAD> philosopher, knows that design is an old notion WAD> that requires neither miracles nor a creator (F. WAD> H. Sandbach's _The Stoics_, for instance, makes WAD> this abundantly clear). That \"intelligent design\" is a \"tertium quid\" is quite correct! And, in this case, also a straw man erected by Dembski. Pennock never claimed that the by Dembski quoted argument was directed at some generic version of \"intelligent design\"; in \"Toder of Babel\", he clearly identifies it as being among \"Prospects for a Supernatural \"Theistic Science\"\" (the *heading* of the paragraph in question). If Dembski doesn't consider \"intelligent design\" to be identical to Johnson's \"theistic science\", he should not set up Pennock's criticism of the latter as a criticism of the former, but instead openly acknowledge the difference. However, there is much evidence that Dembski *doesn't* think that there is such a difference: \"Intelligent design is three things: a scientific research program that investigates the effects of intelligent causes; an intellectual movement that challenges Darwinism and its naturalistic legacy; and a way of understanding divine action. Intelligent design therefore intersects science and theology.\" (Dembski, W.A., 1999, \"Intelligent Design\", pp. 13) \"The crucial breakthrough of the intelligent design movement has been to show that this great theological truth -that God acts in the world by dispersing information- also has scientific content.\" (Dembski, 1999, pp. 233) For the sake of the argument, I have no trouble accepting that inferences to design does not need to involve supernatural or unknown agency (in fact, I often find myself having to remind IDists that archaeologists have been detecting intelligent design for ages without Dembski's filter, and that his attempt to \"reinstate design within science\" is completely unnecessary). However, since the leading members of the ID-movement often seems to \"forget\" that the alleged designer need not be God (especially when talking to their supporter[s]), I feel perfectly justified in pointing out this inconcistency. WAD> Intelligent design is detectable; we do in fact WAD> detect it; we have reliable methods for detecting WAD> it (cf. my _The Design Inference_); and its WAD> detection involves no recourse to the WAD> supernatural. Design is common, rational, and WAD> objectifiable. Dembski is here falling into what Lamoureux calls \"the problem of conflation of ideas\" (although in a situation involving conflation of other ideas): \"A significant factor in the acceptance of Johnson's \"Darwin on Trial\" (1991) and \"Reason in the Balance\" (1995) in the North American evangical community relates directly to the way he presents his arguments. His three foundational principles are so tightly interwoven throughout his writings that it becomes nearly impossible for the reader to distinguish them, and this opens the door for the problem of the conflation of ideas. When this happens a poorly rationalized idea can be \"justified\" simply by being placed alongside a powerful truth. ... This phenomenon of the conflation of ideas is operating in Johnson's writings with regard to his three foundational principles. As I affirmed earlier, with qualification, Johnson's first two principles are powerful and clearly welcomed by all Christians: (1) an attack against naturalism and materialism, (2) support for intelligent design in the universe. However, I caution readers not to conflate these two powerful ideas with Johnson's third foundational principle -the complete failure of the modern theory of biological evolution.\" (Lamoureux, \"Evangicals Inheriting the Wind: The Phillip E. Johnson Phenomenon\", in Johnson, P.E. & Lamoureux, D.O. et al., 1999, \"Darwinism Defeated?\", pp. 25, 26) In Dembski's case, it is the conflation of the reality of detection of design and Dembski's \"explanatory filter\" as a reliable design-detector. It doesn't follow from the fact that we can detect design that Dembski's filter is the most reliable way to do this. In fact, as I argued in my third ID-Commentary, two weeks ago, in most of the cases were we detect intelligent agency, we do so on the basis of the explanatory power in asuming that the object in question was brought about by a specific intelligent agent. E-mails, watches, and the Rosetta stone are all instances where we use our knowledge about specific designers to explain why, say, the three texts, written in three languages on the Rosetta stone all mean the same when translated, or why the symbols on the face of a watch all resemble Arabic nummerals. Even Dembski, when discussing his favorite example of design-detection, the Caputo case, uses knowledge about the designer (Nicholas Caputo) in constructing the pattern needed for his explanatory filter: \"Now consider a human subject S confronted with sequences (A) and (B). S comes to the these sequences with considerable background knowledge which, we may suppose, includes the following: (1) Nicholas Caputo is a Democrat. (2) Nicholas Caputo would like to see the Democrats appear first on the ballot since having the first place on the ballot line significantly boosts one's chances of winning an election. (3) Nicholas Caputo, as election commissioner of Essex County, has full control over who appears first on the ballots in Essex County. (4) Election commissioners in the past have been guilty of all manner of fraud, including unfair assignments of ballot lines. (5) If Captuto were assigning ballot lines fairly, then both Democrats and Republicans should recieve priority roughly the same number of times. Given the background knowledge S is in a position to formulate various \"cheating patterns\" by which Caputo migh attempt to give the Democrats first place on the ballot.\" (Dembski, W.A., 1998, \"The Design Inference\", pp. 16) But no such things is possible when dealing with the unknown designer of the ID-movement. Not only because the designer is unknown, but also since much suggests that it is *unkowable*. As Dembski tells us, \"[w]e cannot predict what an inventor would do short of becoming that inventor.\" (Dembski, 2001, \"Is Intelligent Design Testable?\", http://www.arn.org/docs/dembski/wd_isidtestable.htm ) And this is exactly the point of Pennock's criticism: \"The appeal to supernatural forces, whether these are taken to be divine or occult, is always available for we can cite no necessary constraints upon the powers of supernatural agents. This is just the picture of God that Johnson presents. He says that God could create out of nothing or use evolution if He wanted; God is \"omnipotent.\" He says God creates in the \"furtherance of a purpose,\" but that God's purposes are \"inscrutable\" and \"mysterious.\" A god that is all-powerful and whose will is inscrutable can be called to \"explain\" *any* event in any situation, and this is one reason for science's methodological prohibition against such appeals. Given this feature, supernatural hypotheses remain immune from disconformation.\" (Pennock, 2000, pp. 291-2, original emphasis) WAD> How, then, is Pennock a magician? There are at WAD> least three forms of magic. One is the art of WAD> illusion, where appearance is carefully crafted WAD> to distort reality. As entertainment, this form WAD> of magic is entirely unobjectionable. Another WAD> form of magic is to invoke the supernatural to WAD> explain a physical event. To call this magic is WAD> certainly a recent invention, since it makes most WAD> theists into magicians (Was Thomas Aquinas a WAD> magician for accepting as a historical fact the WAD> resurrection of Jesus? Was Moses Maimonides a WAD> magician for thinking that his namesake had WAD> parted the Red Sea?). Dembski, knowing that he can't contest Pennock's argument against the explanatory power of using supernatural explanations in science, instead starts Appealing to the Gallery (see http://www.infidels.org/news/atheism/logic.html#populum ). And since about 90% of the population in USA are Christians, Dembski will get plenty of support if he can convince his audience that accepting Pennock's argument means that they are inconcistent Christians (curriously absent from Dembski's essay is the mention that Pennock himself is a Quaker). But the validity of an idea has nothing to do with whether we like the consequences or not. All that matters if it is *true*. However, I shall argue that Dembski is wrong in claiming that Pennock's argument \"makes most theists into magicians\", and that Christians in fact have no problem accepting a science using knowable explanations as well as the historical reality of miracles. We must recognize that there is a profound difference between believing in the historic reality of an event and believing that science can explain it. A distinction Dembski blurs when he equates Aquinas' and Maimonides' beliefs in miracles with his own claim that they believed that those events could be scientifically explained by invoking the supernatural. It might very well be the case that a man named Jesus was resurrected, almost two thousand years ago, or that the Red Sea parted to let Moses and the Jews pass, even longer before. A scientist observing those things happening would have no reason to deny the reality of those things. And even if they had not been observed, their historical reality could be inferred from the traces those events had left, as witnessed by YEC flood geologists trying to find evidence for a supernaturally caused Flood in sediments and \"polystrate\" fossils. But, for the reasons outlined above, science would not be able to show that these events was caused by a supernatural entity with an \"inscrutable\" purpose, since such a claim is necessarily untestable. People believing that this really *was* the case, should find support for this elsewhere (theology or philosophy). WAD> According to Pennock, intelligent design WAD> creationism is guilty of this form of magic. Deep WAD> down, though, Pennock must realize that WAD> intelligent design (leaving off the creationism) WAD> can avoid this charge. It is not a coincidence that it is said of Intelligent Design that it \"says one thing one day, and then seems to say a different thing the next.\" ( http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=3512 ) As per the quote above, Dembski has been claiming that ID has shown \"that this great theological truth -that God acts in the world by dispersing information- also has scientific content\", yet now he is saying that his theory need *not* invoke the supernatural. Again, I have no problem with intelligent design not supporting any theologic claims, but I would wish that leaders of the ID-movement themselves would be more forthwright about the things they think ID actually *is*. WAD> Pennock is guilty of his own form of magic, WAD> however. The third form of magic, and the one WAD> Pennock and his fellow scientific naturalists are WAD> guilty of, is the view that something can be WAD> gotten for nothing. Of course, whether or not something is \"from nothing\" is absolutely irrelevant. All that matters is if it is *true*. In determining this, it might be useful if Dembski could bring himself to comment on the evidence that has been presented to him as disproofs of ID-claims about the capability of evolutionary algorithm in solving difficult problems, such as the answer to the 500 city Traveling Salesman Problem, presented by Wesley Elsberry in http://www.geocities.com/evolutionsteori/IDC/5f5blk.html . [...] WAD> Even so, the scientific community continues to be WAD> skeptical of d", "text_length": 20000, "text_sha256": "0d0192ce4cc24bd7a3f6fbe23d5914958e543672a65bf916f197f6a97b747a86" }, { "route": "/people/mgrey/IDC/199811261107.html", "title": "Dembski's Agency Triad", "description": "From: \"Wesley R. Elsberry\" < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 1998/11/26 Message-ID: <199811261107.DAA21334@CX33978-A.DT1.SDCA.HOME.COM>#1/1 Subject: Dembski's Agency Triad [Quote] The actualization of one am", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/199811261107.html Dembski's Agency Triad From: \"Wesley R. Elsberry\" < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 1998/11/26 Message-ID: <199811261107.DAA21334@CX33978-A.DT1.SDCA.HOME.COM>#1/1 Subject: Dembski's Agency Triad [Quote] The actualization of one among several competing possibilities, the exclusion of the rest, and the specification of the possibility that was actualized encapsulate how we recognize intelligent agents. Actualization-Exclusion-Specification - this triad - provides a general scheme for recognizing intelligence, be it animal, human, or extraterrestrial. Actualization establishes that the possibility in question is the one that actually occurred. Exclusion establishes that there was genuine contingency (i.e., that there were other live possibilities, and that these were ruled out). Specification establishes that the actualized possibility conforms to a pattern given independently of its actualization. Now where does choice, that defining characteristic of intelligent agency, figure into this criterion? The problem is that we never witness choice directly. Instead, we witness actualizations of contingency that might be the result of choice (i.e., directed contingency), but that also might be the result of chance (i.e., blind contingency). Now there is only one way to tell the difference - specification. Specification is the only means available to us for distinguishing choice from chance, directed contingency from blind contingency. Actualization and exclusion together guarantee that we are dealing with contingency. Specification guarantees we are dealing with a directed contingency. The Actualization-Exclusion-Specification triad is therefore precisely what we need to identify choice and therewith intelligent agency. [End Quote - WA Dembski, TDI, pp.63-64] Dembski has either shown in the above that natural selection is intelligent, or that there is no conceivable test that will distinguish the action of natural selection from the action of an intelligent agent. That is, the process of natural selection fits the triad listed. Actualization - heritable variation arises. Exclusion - some heritable variations lead to differential reproductive success, so that some heritable variation increases in representation and other heritable variation decreases in representation in the population. Specification - environmental conditions specify which variations are preferred, and thus yields directed contingency. -- Wesley R. Elsberry, Student in Wildlife & Fisheries Sciences, Tx A&M U. Visit the Online Zoologists page ( http://www.rtis.com/nat/user/elsberry ) Email to this account is dumped to /dev/null, whose Spam appetite is capacious. \"All our times have come\\Here but now they're done\" - BOC", "text_length": 2807, "text_sha256": "9a4eb0209560a588c43b18bc4239a445e4007f917530417e188e12a328405941" }, { "route": "/people/mgrey/IDC/200106080021.html", "title": "Re: No free lunch theorems", "description": "From: Wesley R. Elsberry < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 7 Jun 2001 19:10:29 -0400 Message-ID: <200106080021.RAA13020@CX33978-A.DT1.SDCA.HOME.COM> Subject: Re: No free lunch theorems In article <42YT6.1424", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/200106080021.html Re: No free lunch theorems From: Wesley R. Elsberry < wre@cx33978-a.dt1.sdca.home.com > Newsgroups: talk.origins Date: 7 Jun 2001 19:10:29 -0400 Message-ID: <200106080021.RAA13020@CX33978-A.DT1.SDCA.HOME.COM> Subject: Re: No free lunch theorems In article <42YT6.14243$FS6.994617@NEWS6-WIN.SERVER.NTLWORLD.COM>, Dene Bebbington wrote: DB>Does anyone know whether the no free lunch theorems that DB>Dembski refers are applicable to evolutionary algorithms? Yes, they are. DB>Apparently evolutionary algorithms have been successfully DB>used to generate computer programs that solve real DB>problems. That would be genetic programming or evolutionary programming. There are a variety of categories of evolutionary computation; the production of programs is the topic of the above two mentioned classes, and also is prominent in \"artificial life\" simulations. Producing programs via evolutionary computation is a tough field, but some success (defined here as \"working programs\") has been had there. Other evolutionary computation has been applied to various optimization and search problems, with several successful applications (success defined here as \"it found a reasonably good solution\"). DB>It seems to me that if the result of such algorithms are CSI DB>then Dembski must be wrong. NFL says that when you average the performance of an algorithm over all \"cost functions\" of a problem, it performs no better on average than blind search. That is for *any* algorithm, not just evolutionary computation (which Dembski likes to imply). This goes to early claims that certain forms of evolutionary computation could be considered as general problem-solvers that could be deployed without much domain knowledge of a problem. NFL says that if you are concerned about the relative efficiency of getting a solution, you have to apply domain knowledge of the problem and cost function to select an algorithm with good performance on that problem and cost function. NFL isn't about essential capacity of an algorithm to produce a solution; it is about comparative efficiency of algorithms in producing solutions. It's my opinion that Dembski misconstrues or misunderstands what the NFL theorems say. I've passed word along that Dembski's choice of \"No Free Lunch\" for the title of a book that is due out this fall sets him up for embarrassment. That's still the title, so far as I know. It will be interesting to see how the reviews turn out. The introduction to the book is online at < http://www.idurc.org/nofreelunchintro.html >. Dembski's latest foray into invoking NFL can be seen at < http://www.metanexus.net/archives/message_fs.asp?ARCHIVEID=3294 >. It already has a couple of responses from Tom Schneider, which can be seen at < http://www.lecb.ncifcrf.gov/~toms/paper/ev/dembski/rebuttal.html > and < http://www.lecb.ncifcrf.gov/~toms/paper/ev/dembski/claimtest.html >. And don't forget my Dembski page at < http://inia.cls.org/~welsberr/ae/dembski_wa.html#sub_ea >. If anybody has a question that they think should be posed to Dr. Dembski, I'll be sharing the stage with him for a 90 minute workshop session on June 17th. Drop me email by the 13th, and maybe I'll get a chance to bring up your favorite topic. Time to get back to preparing figures for the dissertation... -- Wesley R. Elsberry, Student in Wildlife & Fisheries Sciences, Tx A&M U. Visit the Online Zoologists page ( http://www.rtis.com/nat/user/elsberry ) Co-recipient of \"Most Obnoxious Critic\" status awarded by William A. Dembski \"It's not luck if you can do it consistently.\"-NB [ Other on-line articles ] [ ID-Commentaries ]", "text_length": 3650, "text_sha256": "ce4ecc7e5ef739c44b5a976083a5a95e3213a03879848c6ab874c54915b3fa0f" }, { "route": "/people/mgrey/IDC/21340.html", "title": "Re: Re[2]: [DebunkCreation] Any books on evolution?", "description": "From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Sep 8, 2001 12:10 pm Message: 21340 Subject : Re: Re[2]: [DebunkCreation] Any books on evolution?", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/21340.html Re: Re[2]: [DebunkCreation] Any books on evolution? From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Sep 8, 2001 12:10 pm Message: 21340 Subject : Re: Re[2]: [DebunkCreation] Any books on evolution? --- lflank@ij.net wrote: > On 7 Sep 01, at 12:17, Morgan Grey wrote: > > > I just discovered that my public library caries a > > copy of Dembski's $64.95 \"The Design Inference\". I > > suppose I know what I'm going to spend my weekend > > doing... > > Laughing uncontrollably . . . . . ? No, that is what I'm doing right now. Actually, I find much of what Dembski has to say genuinely interesting. Of course, it *is* his Ph.D. dissertion, so it better not be too silly. But this is propably because Dembski's design inference, as presented in TDI, is very different from how it is presented by most IDers, as well as by Dembski himself in popular books and articles. For one, Dembski doesn't claim that his filter can detect *ingelligent* design: \"Although a design inference is often the occasion for inferring an intelligent agent (cf. the examples in the following sections), as a pattern of inference the design inference is not tied to any doctrine of intelligent agency. The design inference focuses on features of an event that bar it from being attributed to chance, not on the causal story underlying the event. To be sure, there is a connection between the design inference and intelligent agency (see Section 2.4). This connection, however, is not part of the logical structure of the design inference.\" (Dembski, W. A., 1998, \"The Design Inference: Eliminating Chance Through Small Probabilities\", pp. 8) In fact, Dembski defines \"design\" as \"the set-theoretic complement of the disjunction regularity-or-chance\" (pp. 36). Under this definition, I would have no problem with life being \"designed\", with the \"designer\" in part being the process of natural selection. ===== Morgan \"Evolution is to the social sciences as statues are to birds: a convenient platform upon which to deposit badly digested ideas.\" (Steve Jones, 2000, \"Darwin's Ghost\", pp. xxvii) [ Other on-line articles ] [ ID-Commentaries ]", "text_length": 2249, "text_sha256": "a3ba719fb267d85ca4fd228afac92132221479b9a780064d0e02b78b96e22559" }, { "route": "/people/mgrey/IDC/21397.html", "title": "Re: Re[2]: [DebunkCreation] Any books on evolution?", "description": "From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Mon Sep 10, 2001 9:58 am Message: 21397 Subject: Re: Re[2]: [DebunkCreation] Any books on evolution? -", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/21397.html Re: Re[2]: [DebunkCreation] Any books on evolution? From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Mon Sep 10, 2001 9:58 am Message: 21397 Subject: Re: Re[2]: [DebunkCreation] Any books on evolution? --- Dave Oldridge < doldridg@s... > wrote: (snip) > And, while rigorously mathematical, that definition > [i.e. Dembski's] places all events that are produced > by a COMBINATION of regularity AND chance directly > under the heading of \"designed.\" Thus all evolution > IS, by his definition, \"design.\" > > Yet, he and others are quick to equivocate this > definition when they get et outside the academic, > mathematical environment. And such equivocation in > a trained mathematician is either gross incompetence > or a sin. Further equivocation on Dembski's part happens when someone challenges his claims with examples of genetic algorithm producing CSI. He has two similar tactics: Define \"information\" in such a way that it *by definition* cannot be produced by genetic algorithms. I'm at school, and doesn't have it handy, but in his \"Intelligent Design\", most of his discussion about natural selection as a \"designer\" consists of defining his way out of the issue. Of course, if \"information\" is defined so that it depends on how the structure in question came about, Dembski's \"design inference\" is useless, since it attempts to determine the \"design\" of something *without* knowing the causal story of the event in question. The other tactic is similar, and also depends on re-defining \"design\" in such a way that its status suddenly depends on its causal story. In < http://www.leaderu.com/offices/dembski/docs/bd-specified.html >, Dembski introduces a split between \"appearant\" and \"actual CSI\", and claims that \"[j]ust as the Darwinian mechanism does not generate actual design but only its appearance, so too the Darwinian mechanism does not generate actual specified complexity but only its appearance.\" Of course, if something is CSI only if we know it to have not been generated by \"the Darwinian mechanism\", Dembski's claim that life contains CSI is no longer valid, since it is not known that life was not generated by \"the Darwinian mechanism\". Either way, his re-definition of terms used in TDI (or invention of terms not used there) while at the same time referring to TDI as \"the book that supports all of this\", makes me seriously suspicious of his integrity. ===== Morgan \"Evolution is to the social sciences as statues are to birds: a convenient platform upon which to deposit badly digested ideas.\" (Steve Jones, 2000, \"Darwin's Ghost\", pp. xxvii) [ Other on-line articles ] [ ID-Commentaries ]", "text_length": 2753, "text_sha256": "07fffbde38d4c1759137dca1e278a53919b006f1126bebd6b7ec627a5b820acc" }, { "route": "/people/mgrey/IDC/21990.html", "title": "Dembski `retracts' comments about Dennett", "description": "From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Oct 20, 2001 8:04 pm Message: 21990 Subject: Dembski `retracts' comments about Dennett As readers", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/21990.html Dembski `retracts' comments about Dennett From: Morgan Grey < cynical_prophet@yahoo.com > To: < DebunkCreation@yahoogroups.com > Reply-to: < DebunkCreation@yahoogroups.com > Date: Sat Oct 20, 2001 8:04 pm Message: 21990 Subject: Dembski `retracts' comments about Dennett As readers of last week's ID-Commentary -\"Disbelieving Darwin -- And Feeling No Shame!\"- will remember, I took issue with Dembski's claim that Daniel Dennett \"recommends 'quarantining' parents who teach their children to doubt Darwinism\", arguing that Dembski was misrepresenting Dennett. I have just recieved an e-mail from Richard Wein, in which he, among other things, directs my attention to a \"clarification\" made by Dembski in a later post to Metanexus. As a sort of mini-ID-Commentary, here is Dembski's post, as well as my comments on it: ------------------------------------------------------- http://www.meta-list.org/archives/fulldetails.asp?listtype=Magazine&ARCHIVEID=2584 030: Disbelieving Darwin Discussed Metaviews 030. 2000.03.23. Approximately 2693 words. BG> William Dembski's previous posting on Metaviews BG> provoked lots of feedback. This Meta-post contains a number of short texts from various authors, as well as one by Dembski himself. However, I will only comment on the one posted by Dembski. [...] BG> Finally, William Dembski also writes with a BG> partial retraction of a statement made about BG> Daniel Dennett's reputed desire to \"quarantine\" BG> parents who doubt Darwinism. Note that even though Dembski himself refers to his posting as a \"clarification\" and never actually retracts anything, Bill Grassie refers to it as a \"partial retraction\" anyway. BG> Many other messages have also been exchanged on BG> this thread on the Reiterations Discussion List BG> and can be read at < http://www.meta-list.org > in BG> the archives. BG> BG> -- Billy Grassie [...] WAD> =-=-=-=-=-=-=-=-=-=-=-=-=-= From: \"William A. WAD> Dembski\" Subject: WAD> Clarification to \"Disbelieving Darwin and Feeling WAD> No Shame\" WAD> WAD> I'd like to post a clarification to my WAD> essay \"Disbelieving Darwin and Feeling No Shame\": WAD> WAD> In my essay \"Disbelieving Darwin and Feeling No WAD> Shame\" I made the following statement: \"Daniel WAD> Dennett even recommends 'quarantining' parents WAD> who teach their children to doubt Darwinism (see WAD> the end of his *Darwin's Dangerous Idea*).\" This WAD> is not quite accurate. On p. 519 of his book, WAD> Dennett states, \"Those whose visions dictate that WAD> they cannot peacefully coexist with the rest of WAD> us we will have to quarantine as best we can....\" WAD> A few lines later he continues, \"If you insist on WAD> teaching your children falsehoods--that the Earth WAD> is flat, that \"Man\" is not a product of evolution WAD> by natural selection--then you must expect, at WAD> the very least, that those of us who have freedom WAD> of speech will feel free to describe your WAD> teachings as the spreading of falsehoods, and WAD> will attempt to demonstrate this to your children WAD> at our earliest opportunity. Our future well- WAD> being--the well-being of all of us on the planet-- WAD> depends on the education of our descendants.\" WAD> WAD> As Dennett in a private communication has made WAD> clear to me, he does not recommend quarantining WAD> parents who teach their children to doubt WAD> Darwin's theory and takes exception to anyone who WAD> attributes as much to him. I agree that there is WAD> no explicit recommendation here to quarantine WAD> parents who teach their children to doubt WAD> Darwinism. Nonetheless, it seems to me that there WAD> is an implicit recommendation to do just that. If WAD> (1) doubting Darwinian evolution is as silly as WAD> believing in a flat earth and (2) if our future WAD> well-being depends on the [proper] education of WAD> our descendants and (3) if \"at the very least\" WAD> Darwinists will attempt to demonstrate the truth WAD> of Darwinism to our children at their \"earliest WAD> opportunity\" and (4) if \"quarantining\" is WAD> maintained as a live option by Darwinists, then WAD> it is no big stretch to think that quarantining WAD> parents who teach their children to doubt Darwin WAD> is far from Dennett's intention. Dembski just repeats his original claim, adds some numbers, and wraps it up as a \"clarification\". In case Dembski is suffering from a reading disability, Dennett never advocates \"quarantining\" anyone on the basis of their ideas being \"silly\". Unless Dembski thinks that \"teach[ing one's] children to doubt Darwin\" \"dictate that [one] cannot peacefully coexist with the rest of us\", Dembski has absolutely nothing to be afraid of. WAD> Sincerely, Bill WAD> WAD> -- William A. Dembski, Ph.D. Director, Michael WAD> Polanyi Center Associate Research Professor in WAD> the Conceptual Foundations of Science Baylor WAD> University WAD> WAD> Address: William A. Dembski The Michael Polanyi WAD> Center P.O. Box 97130 Baylor University Waco, TX WAD> 76798-7130 WAD> WAD> E-mail: William_Dembski@baylor.edu Web: WAD> www.baylor.edu/~William_Dembski (personal) WAD> www.baylor.edu/~polanyi (Michael Polanyi Center) WAD> META> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Footer META> information below last updated: 1999/12/10. [...] META> Copyright 1999, 2000 by William Grassie. Copies META> of this internet posting may be made and META> distributed in whole without further permission. META> Credit: \"This information was circulated on the META> Meta Lists on Science and Religion META> < http://www.meta-list.org >.\" ------------------------------------------------------- ===== Morgan \"Creationists say--\"Welcome to the war. We are eager to join battle, for we have the truth on our side, and the consequences are as important as life (eternal life) and death.\"\" (Gish, D.T., 1993, \"Creation Scientists Answer Their Critics\", pp. 249) __________________________________________________ [ More ID-Commentaries ]", "text_length": 5964, "text_sha256": "c6c2de78f161a7593f723123db341b04b73e921d3601b8b116d5dbefb3c3bac8" }, { "route": "/people/mgrey/IDC/2595.html", "title": "Who's Got the Magic?", "description": "042: Who's Got the Magic? by William Dembski Metaviews 042. 2000.04.25. Approximately 2286 words. In the posting below, William Dembski from the Michael Polanyi Center at Baylor University offers a critical review of Robert Pennock's book \"", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/2595.html Who's Got the Magic? 042: Who's Got the Magic? by William Dembski Metaviews 042. 2000.04.25. Approximately 2286 words. In the posting below, William Dembski from the Michael Polanyi Center at Baylor University offers a critical review of Robert Pennock's book \"The Tower of Babel.\" In so doing, he argues again on behalf on \"Intelligent Design Theory,\" which he distinguishes from \"Creationism.\" In my view, the debate would be improved, if both terms were more carefully defined, rather than assumed. In any case, Dembski argues that the \"something for nothing\" thinking which characterizes scientific materialism approach to evolution is akin to \"magic\". \"Pennock and his fellow scientific naturalists,\" writes Dembski, \"are bargain hunters\" (i.e. looking for something for nothing.) \"They want to explain the appearance of design in nature without admitting actual design.\" Dembski and the Polanyi Center have been in the news recently with 1) a very ambitious conference on Naturalism in Science held two weeks ago involving a broad spectrum of thinkers, and 2) a recent vote by the faculty senate at Baylor University seeking to close the one-year old center (see the Chronicle of Higher Education on 4/19/00). I am grateful that these debates can also take place on Meta and welcome your comments and feedback. -- Billy Grassie =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From: William_Dembski@baylor.edu (William A. Dembski) Subject: Who's Got the Magic? In criticizing Phillip Johnson's \"intelligent design creationism,\" Robert Pennock raises a particularly worrisome legal consequence of Johnson's view. According to Pennock, Johnson insists \"that science admit the reality of supernatural influences in the daily workings of the world.\" But what if the same reasoning that Johnson is trying to import into science were adopted in Johnson's own area of specialization -- the law (Johnson is a law professor at UC Berkeley)? Here's the concern as Pennock lays it out in _Tower of Babel_ (p. 295): [[indent]] \"For the law to take [Johnson's view] seriously as well, it would have to be open to both suits and defenses based on a range of possible divine and occult interventions. Imagine the problems that would result if the courts had to accept legal theories of this sort. How would the court rule on whether to commit a purportedly insane person to a mental hospital for self-mutilation who claims that the Lord told her to pluck out her eye because it offended her? How would a judge deal with a defendant, Abe, accused of attempted murder of his son, Ike, who claims that he was only following God's command that he kill Ike to prove his faith?\" Implicit in this passage and throughout Pennock's book is a forced choice between mechanism and magic: Either the world works by mechanisms that obey inviolable natural laws and that admit no break in the chain of natural causation, or all hell breaks loose and the world admits supernatural interventions that make a hash of science and our understanding of the world generally (and legal studies in particular). Pennock is offering his readers mechanism. Johnson is offering them magic. Any reasonable person knows which option to choose. But as with most forced choices, there's a tertium quid that Pennock has conveniently ignored, and that when properly understood shows that the real magician here is in fact Pennock and not Johnson. The tertium quid here is intelligent design, which is entirely separable from creationism. No doubt, Pennock's constant conjoining of the two serves a useful rhetorical purpose, rallying the troops, giving Darwinists a single common enemy, and keeping biology safe from teleology (indeed, it has become a point of grammatical correctness with Pennock never to use \"intelligent design\" without \"creationism\" -- \"intelligent design\" properly being an adjective that only modifies \"creationism\"). But Pennock, as a trained philosopher, knows that design is an old notion that requires neither miracles nor a creator (F. H. Sandbach's _The Stoics_, for instance, makes this abundantly clear). Intelligent design is detectable; we do in fact detect it; we have reliable methods for detecting it (cf. my _The Design Inference_); and its detection involves no recourse to the supernatural. Design is common, rational, and objectifiable. How, then, is Pennock a magician? There are at least three forms of magic. One is the art of illusion, where appearance is carefully crafted to distort reality. As entertainment, this form of magic is entirely unobjectionable. Another form of magic is to invoke the supernatural to explain a physical event. To call this magic is certainly a recent invention, since it makes most theists into magicians (Was Thomas Aquinas a magician for accepting as a historical fact the resurrection of Jesus? Was Moses Maimonides a magician for thinking that his namesake had parted the Red Sea?). According to Pennock, intelligent design creationism is guilty of this form of magic. Deep down, though, Pennock must realize that intelligent design (leaving off the creationism) can avoid this charge. Pennock is guilty of his own form of magic, however. The third form of magic, and the one Pennock and his fellow scientific naturalists are guilty of, is the view that something can be gotten for nothing. This third form of magic can be nuanced. The \"nothing\" here need not be an absolute nothing. And the transformation of nothing into something may involve minor expenditures of effort. For instance, the magician may need to utter \"abracadabra\" or \"hocus-pocus.\" The Darwinian just-so stories that attempt to account for complex, information rich biological structures are likewise incantations that give the illusion of solving a problem but in fact merely cloak ignorance. The great appeal behind this third form of magic is the offer of a bargain -- indeed an incredible bargain for which no amount of creative accounting can ever square the books. The idea of getting something for nothing has come to pervade science. In cosmology, Alan Guth, Lee Smolin, and Peter Atkins all claim that this marvelous universe could originate from quite unmarvelous beginnings (a teaspoon of ordinary dust for Guth, black-hole formation for Smolin, and set-theoretic operations on the empty set for Atkins). In biology, Jacques Monod, Richard Dawkins, and Stuart Kauffman claim that the panoply of life can be explained in terms of quite simple mechanisms (chance and necessity for Monod, cumulative selection for Dawkins, and autocatalysis for Kauffman). We have become so accustomed to this something-for-nothing way of thinking that we no longer appreciate just how deeply magical it is. Consider, for instance, the following evolutionary account of neuroanatomy by Melvin Konner, an anthropologist and neurologist at Emory University: \"Neuroanatomy in many species -- but especially in a brain-ridden one like ours -- is the product of sloppy, opportunistic half-billion year [evolution] that has pasted together, and only partly integrated, disparate organs that evolved in different animals, in different eras, and for very different purposes.\" (_IEEE Spectrum_, March 2000.) And since human consciousness and intelligence are said to derive from human neuroanatomy, it follows that these are themselves the product of a sloppy evolutionary process. But think what this means. How do we make sense of \"sloppy,\" \"pasted together,\" and \"partly integrated,\" except with reference to \"careful,\" \"finely adapted,\" and \"well integrated.\" To speak of hodge-podge structures presupposes that we have some concept of carefully designed structures. And of course we do. Humans have designed all sorts of engineering marvels, everything from Cray supercomputers to Gothic cathedrals. But that means, if we are to believe Melvin Konner, that a blind evolutionary process (i.e., Richard Dawkins's blind watchmaker) cobbled together human neuroanatomy, which in turn gave rise to human consciousness, which in turn produces artifacts like supercomputers, which in turn are not cobbled together at all but instead carefully designed. Out pop purpose, intelligence, and design from a process that started with no purpose, intelligence, or design. This is magic. Of course, to say this is magic is not to say it is false. It is after all a logical possibility that purpose, intelligence, and design emerge by purely mechanical means out of a physical universe initially devoid of these. Intelligence, for instance, may just be a survival tool given to us by an evolutionary process that places a premium on survival and that is itself not intelligently guided. The basic creative forces of nature might be devoid of intelligence. But if that is so, how can we know it? And if it is not so, how can we know that? It does no good simply to presuppose that purpose, intelligence, and design are emergent properties of a universe that otherwise is devoid of these. The debate whether nature has been front-loaded with purpose, intelligence, and design is not new. Certainly the ancient Epicureans and Stoics engaged in this debate. The Stoics argued for a design-first universe: the universe starts with design and any subsequent design results from the outworkings of that initial design (they resisted subsequent novel infusions of design). The Epicureans, on the other hand, argued for a design-last universe: the universe starts with no design and any subsequent design results from the interplay of chance and necessity. What is new, at least since the Enlightenment, is that it has become intellectually respectable to cast the design-first position as disreputable, superstitious, and irrational; and the design-last position as measured, parsimonious, and alone supremely rational. Indeed, the charge of magic is nowadays typically made against the design-first position, and not against the design-last position, as I have done here. But why should the design-first position elicit the charge of magic? Historically in the West, design has principally been connected with Judeo-Christian theism. The God of Judaism and Christianity is said to introduce design into the world by intervening in its causal structure. But such interventions cannot be anything but miraculous. And miracles is the stuff of magic. So goes the argument. The argument is flawed because there is no necessary connection between God introducing design into the world and God intervening in the world in the sense of violating its causal structure. Theists like Richard Swinburne, for instance, argue that God front-loads design into the universe by designing the very laws of nature. Paul Davies takes a similar line. Restricting design to structuring the laws of nature precludes design from violating those laws and thus violating nature's causal structure. Design easily resists the charge of magic. Rather, it's the a priori exclusion of design that has a much tougher time resisting it. Indeed, the design-last position is inherently magical. Consider the following remark by Harvard biologist Richard Lewontin in _The New York Review of Books_: [[indent]] \"We take the side of science _in spite of_ the patent absurdity of some of its constructs, _in spite of_ its failure to fulfill many of its extravagant promises of health and life, _in spite of_ the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our _a priori_ adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated.\" If this isn't magic, what is? Even so, the scientific community continues to be skeptical of design. The worry is that design will give up on science. In place of a magic that derives something from nothing, design substitutes a designer who explains everything. Magic gets you something for nothing and thus offers a bargain. Design gets you something by presupposing something unimaginably bigger and thus asks you to sell your scientific soul. At least so the story goes. But design can be explanatory without giving away the store. Certainly this is the case for human artifacts, which are properly explained by reference to design. Nor does design explain everything: There's no reason to invoke design to explain a random inkblot; but a Dürer woodcut is something else altogether. The point of the intelligent design program is to extend design from the realm of human artifacts to the natural sciences. The program may ultimately fail, but it is only now being tried and it is certainly worth a try. Just as truth is not decided at the ballot box, so truth is not decided by the price one must pay for it. Bargains are all fine and well, and if you can get something for nothing, go for it. But there is an alternate tendency in science which says that you get what you pay for and that at the end of the day there has to be an accounting of the books. Some areas of science are open to bargain-hunting and some are not. Self-organizing complex systems, for instance, are a great place for scientific bargain-hunters to shop. Bernard cell convection, Belousov-Zhabotinsky reactions, and a host of other self-organizing systems offer complex organized structures apparently for free. But there are other areas of science that frown upon bargain-hunting. The conservation laws of physics, for instance, allow no bargains. The big question confronting design is whether it can be gotten on the cheap or must be paid for in kind. Design theorists argue that design admits no bargains. Pennock and his fellow scientific naturalists are bargain hunters. They want to explain the appearance of design in nature without admitting actual design. That's why Richard Dawkins begins _The Blind Watchmaker_ with \"Biology is the study of complicated things that give the appearance of having been designed for a purpose,\" whereupon he requires an additional three hundred pages to show why it is only an appearance of design. Pennock and his fellow naturalists have my very best wishes for success in their hunt for the ultimate bargain. They may even be right. But they are not guaranteed to be right. And they certainly haven't demonstrated that they are right. They have yet to pull the rabbit out of the hat. William Dembski Baylor University =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Footer information below last updated: 1999/12/10. Meta is an edited and moderated listserver and news service dedicated to promoting the constructive engagement of science and religion. Subscriptions are free. For more information, including archives and submission guidelines, go to < http://www.meta-list.org >. There are now four separate meta-lists to which you can subscribe: is commentaries and bookreviews posted three to five times per week. is announcements and news and is posted as frequently as needed. is a monthly digest. is a higher volume discussion list which is lightly moderated. You can subscribe to one or all of the meta-lists. If you would like to unsubscribe or change your subscription options, simply go to < http://www.meta-list.org > and follow the links to subscribe or unsubscribe. Note that all subscription changes entered on the web forms, requires your confirmation by email. Copyright 1999, 2000 by William Grassie. Copies of this internet posting may be made and distributed in whole without further permission. Credit: \"This information was circulated on the Meta Lists on Science and Religion < http://www.meta-list.org >.\"", "text_length": 15845, "text_sha256": "0c9618c8fd80161b42a398097b74b9a70a1f2750a1d5f94ea0ccd451000cbcfa" }, { "route": "/people/mgrey/IDC/3066.html", "title": "Explaining Specified Complexity", "description": "Meta 139: Dembski on \"Explaining Specified Complexity\" grassie@VOICENET.COM William Grassie Meta 139. 1999/09/13. Approximately 1883 words. Below is a column entitled \"Explaining Specified Complexity\" by William Dembski at Baylor University", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/3066.html Explaining Specified Complexity Meta 139: Dembski on \"Explaining Specified Complexity\" grassie@VOICENET.COM William Grassie Meta 139. 1999/09/13. Approximately 1883 words. Below is a column entitled \"Explaining Specified Complexity\" by William Dembski at Baylor University in Texas. Dembski discusses whether evolutionary algorithms can generate actual \"specified complexity\" in nature, as opposed to merely the appearances thereof (i.e., unspecified or randomly generated complexity). Dembski believes these problems in probability make plausible a concept of intelligence involved in evolution. Your comments are welcome on reiterations@meta-list.org . -- Billy Grassie =-=-=-=-=-=-=-=-=-=-=-=-=-=-=- EXPLAINING SPECIFIED COMPLEXITY William A. Dembski Michael Polanyi Center Baylor University Waco, Texas 76798 In his recent book The Fifth Miracle, Paul Davies suggests that any laws capable of explaining the origin of life must be radically different from scientific laws known to date. The problem, as he sees it, with currently known scientific laws, like the laws of chemistry and physics, is that they are not up to explaining the key feature of life that needs to be explained. That feature is specified complexity. Life is both complex and specified. The basic intuition here is straightforward. A single letter of the alphabet is specified without being complex (i.e., it conforms to an independently given pattern but is simple). A long sequence of random letters is complex without being specified (i.e., it requires a complicated instruction-set to characterize but conforms to no independently given pattern). A Shakespearean sonnet is both complex and specified. Now, as Davies rightly notes, contingency can explain complexity but not specification. For instance, the exact time sequence of radioactive emissions from a chunk of uranium will be contingent, complex, but not specified. On the other hand, as Davies also rightly notes, laws can explain specification but not complexity. For instance, the formation of a salt crystal follows well-defined laws, produces an independently known repetitive pattern, and is therefore specified; but that pattern will also be simple, not complex. The problem is to explain something like the genetic code, which is both complex and specified. As Davies puts it: \"Living organisms are mysterious not for their complexity per se, but for their tightly specified complexity\" (p. 112). How does the scientific community explain specified complexity? Usually via an evolutionary algorithm. By an evolutionary algorithm I mean any algorithm that generates contingency via some chance process and then sifts the so-generated contingency via some law-like process. The Darwinian mutation-selection mechanism, neural nets, and genetic algorithms all fall within this broad definition of evolutionary algorithms. Now the problem with invoking evolutionary algorithms to explain specified complexity at the origin of life is absence of any identifiable evolutionary algorithm that might account for it. Once life has started and self-replication has begun, the Darwinian mechanism is usually invoked to explain the specified complexity of living things. But what is the relevant evolutionary algorithm that drives chemical evolution? No convincing answer has been given to date. To be sure, one can hope that an evolutionary algorithm that generates specified complexity at the origin of life exists and remains to be discovered. Manfred Eigen, for instance, writes, \"Our task is to find an algorithm, a natural law that leads to the origin of information,\" where by \"information\" I understand him to mean specified complexity. But if some evolutionary algorithm can be found to account for the origin of life, it would not be a radically new law in Davies's sense. Rather, it would be a special case of a known process. I submit that the problem of explaining specified complexity is even worse than Davies makes out in The Fifth Miracle. Not only have we yet to explain specified complexity at the origin of life, but evolutionary algorithms fail to explain it in the subsequent history of life as well. Given the growing popularity of evolutionary algorithms, such a claim may seem ill-conceived. But consider a well known example by Richard Dawkins (The Blind Watchmaker, pp. 47-48) in which he purports to show how a cumulative selection process acting on chance can generate specified complexity. He starts with the following target sequence, a putative instance of specified complexity: METHINKS*IT*IS*LIKE*A*WEASEL (he considers only capital Roman letters and spaces, here represented by bullets-thus 27 possibilities at each location in a symbol string). If we tried to attain this target sequence by pure chance (for example, by randomly shaking out scrabble pieces), the probability of getting it on the first try would be around 10 to the -40, and correspondingly it would take on average about 10 to the 40 tries to stand a better than even chance of getting it. Thus, if we depended on pure chance to attain this target sequence, we would in all likelihood be unsuccessful. As a problem for pure chance, attaining Dawkins's target sequence is an exercise in generating specified complexity, and it becomes clear that pure chance simply is not up to the task. But consider next Dawkins's reframing of the problem. In place of pure chance, he considers the following evolutionary algorithm: (i) Start out with a randomly selected sequence of 28 capital Roman letters and spaces, e.g., WDL*MNLT*DTJBKWIRZREZLMQCO*P (note that the length of Dawkins's target sequence, METHINKS*IT* IS*LIKE*A*WEASEL, comprises exactly 28 letters and spaces); (ii) randomly alter all the letters and spaces in this initial randomly-generated sequence; (iii) whenever an alteration happens to match a corresponding letter in the target sequence, leave it and randomly alter only those remaining letters that still differ from the target sequence. In very short order this algorithm converges to Dawkins's target sequence. In The Blind Watchmaker, Dawkins (p. 48) provides the following computer simulation of this algorithm: (1) WDL*MNLT*DTJBKWIRZREZLMQCO*P (2) WDLTMNLT*DTJBSWIRZREZLMQCO*P ... (10) MDLDMNLS*ITJISWHRZREZ*MECS*P ... (20) MELDINLS*IT*ISWPRKE*Z*WECSEL . .. (30) METHINGS*IT*ISWLIKE*B*WECSEL ... (40) METHINKS*IT*IS*LIKE*I*WEASEL ... (43) METHINKS*IT*IS*LIKE*A*WEASEL Thus, Dawkins's simulation converges on the target sequence in 43 steps. In place of 10 to the 40 tries on average for pure chance to generate the target sequence, it now takes on average only 40 tries to generate it via an evolutionary algorithm. Although Dawkins uses this example to illustrate the power of evolutionary algorithms, the example in fact illustrates the inability of evolutionary algorithms to generate specified complexity. We can see this by posing the following question: Given Dawkins's evolutionary algorithm, what besides the target sequence can this algorithm attain? Think of it this way. Dawkins's evolutionary algorithm is chugging along; what are the possible terminal points of this algorithm? Clearly, the algorithm is always going to converge on the target sequence (with probability 1 for that matter). An evolutionary algorithm acts as a probability amplifier. Whereas it would take pure chance on average 10 to the 40 tries to attain Dawkins's target sequence, his evolutionary algorithm on average gets it for you in the logarithm of that number, that is, on average in only 40 tries (and with virtual certainty in a few hundred tries). But a probability amplifier is also a complexity attenuator. For something to be complex, there must be many live possibilities that could take its place. Increasingly numerous live possibilities correspond to increasing improbability of any one of these possibilities. To illustrate the connection between complexity and probability, consider a combination lock. The more possible combinations of the lock, the more complex the mechanism and correspondingly the more improbable that the mechanism can be opened by chance. Complexity and probability therefore vary inversely: the greater the complexity, the smaller the probability. It follows that Dawkins's evolutionary algorithm, by vastly increasing the probability of getting the target sequence, vastly decreases the complexity inherent in that sequence. As the sole possibility that Dawkins's evolutionary algorithm can attain, the target sequence in fact has minimal complexity (i.e., the probability is 1 and the complexity, as measured by the usual information measure, is 0). In general, then, evolutionary algorithms generate not true complexity but only the appearance of complexity. And since they cannot generate complexity, they cannot generate specified complexity either. This conclusion may seem counterintuitive, especially given all the marvelous properties that evolutionary algorithms do possess. But the conclusion holds. What's more, it is consistent with the \"no free lunch\" (NFL) theorems of David Wolpert and William Macready, which place significant restrictions on the range of problems genetic algorithms can solve. The claim that evolutionary algorithms can only generate the appearance of specified complexity is reminiscent of a claim by Richard Dawkins. On the opening page of his The Blind Watchmaker he states, \"Biology is the study of complicated things that give the appearance of having been designed for a purpose.\" Just as the Darwinian mechanism does not generate actual design but only its appearance, so too the Darwinian mechanism does not generate actual specified complexity but only its appearance. But this raises the obvious question, whether there might not be a fundamental connection between intelligence or design on the one hand and specified complexity on the other. In fact there is. There's only one known source for producing actual specified complexity, and that's intelligence. In every case where we know the causal history responsible for an instance of specified complexity, an intelligent agent was involved. Most human artifacts, from Shakespearean sonnets to Dürer woodcuts to Cray supercomputers, are specified and complex. For a signal from outer space to convince astronomers that extraterrestrial life is real, it too will have to be complex and specified, thus indicating that the extraterrestrial is not only alive but also intelligent (hence the search for extraterrestrial intelligence-SETI). Thus, to claim that laws, even radically new ones, can produce specified complexity is in my view to commit a category mistake. It is to attribute to laws something they are intrinsically incapable of delivering-indeed, all our evidence points to intelligence as the sole source for specified complexity. Even so, in arguing that evolutionary algorithms cannot generate specified complexity and in noting that specified complexity is reliably correlated with intelligence, I have not refuted Darwinism or denied the capacity of evolutionary algorithms to solve interesting problems. In the case of Darwinism, what I have established is that the Darwinian mechanism cannot generate actual specified complexity. What I have not established is that living things exhibit actual specified complexity. That is a separate question. Does Davies's original problem of finding radically new laws to generate specified complexity thus turn into the slightly modified problem of finding find radically new laws that generate apparent-but not actual-specified complexity in nature? If so, then the scientific community faces a logically prior question, namely, whether nature exhibits actual specified complexity. Only after we have confirmed that nature does not exhibit actual specified complexity can it be safe to dispense with design and focus all our attentions on natural laws and how they might explain the appearance of specified complexity in nature. Does nature exhibit actual specified complexity? This is the million dollar question. Michael Behe's notion of irreducible complexity is purported to be a case of actual specified complexity and to be exhibited in real biochemical systems (cf. his book Darwin's Black Box). If such systems are, as Behe claims, highly improbable and thus genuinely complex with respect to the Darwinian mechanism of mutation and natural selection and if they are specified in virtue of their highly specific function (Behe looks to such systems as the bacterial flagellum), then a door is reopened for design in science that has been closed for well over a century. Does nature exhibit actual specified complexity? The jury is still out. William A. Dembski =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Footer information below last updated: 1999/07/12. Meta is an edited and moderated listserver and news service dedicated to promoting the constructive engagement of science and religion. Subscriptions are free. For more information, including archives and submission guidelines, go to < http://www.meta-list.org >. There are now four separate meta-lists to which you can subscribe: [metaviews] is commentaries and bookreviews posted three to five times per week. [metanews] is announcements and news and is posted more frequently. [metamonthly] is a monthly digest. [reiterations] is a higher volume discussion list which is lightly moderated. You can subscribe to one or all of the meta-lists. If you would like to unsubscribe or change your subscription options, simply go to < http://www.meta-list.org > and follow the links to subscribe or unsubscribe. Note that all subscription changes entered on the web forms, requires your confirmation by email. Permission is granted to reproduce this e-mail and distribute it without restriction with the inclusion of the following credit line: This is another posting from the Meta-List < http://www.meta-list.org >. Copyright 1997, 1998, 1999. William Grassie. [ Other on-line articles ] [ ID-Commentaries ]", "text_length": 14043, "text_sha256": "ea594b4e13a16058a18afade05288e579c2bd7363d8f8183f2e26ecb25ef39a5" }, { "route": "/people/mgrey/IDC/5f5blk.html", "title": "Dembski & the TSP", "description": "From: Wesley R. Elsberry < welsberr@orca.tamu.edu > Newsgroups: talk.origins,comp.ai.genetic Date: 1997/02/28 Message-ID: <5F5BLK$LC1@NEWS.TAMU.EDU>#1/1 Subject: Dembski & the TSP William Dembski gave a talk last Saturday at the \"Naturalism", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/5f5blk.html Dembski & the TSP From: Wesley R. Elsberry < welsberr@orca.tamu.edu > Newsgroups: talk.origins,comp.ai.genetic Date: 1997/02/28 Message-ID: <5F5BLK$LC1@NEWS.TAMU.EDU>#1/1 Subject: Dembski & the TSP William Dembski gave a talk last Saturday at the \"Naturalism, Theism, and the Scientific Enterprise\" conference on intelligent design in general, and the results of his information theoretic analyses in particular. As expected, he claimed that functions, algorithms, chance, and natural laws were incapable of generating \"complex specified information\", whether considered seprately or in combination. I would like to thank everyone who sent me or posted possible questions for Dembski. I collated my own points of difference plus those into a handout which I had available that morning. Several of the points brought up in these newsgroups were also brought up in the discussion. Bill Jefferys asked about the proof that Dembski offered concerning gradualness of information acquisition under selection. I brought up genetic algorithms as an empirical disproof. In general, Dembski's response was to claim that his analysis was both general and sound, and therefore his questioners could not be correct. In discussion of my presentation the day before, Dembski had indicated that GAs find solutions to difficult problems because an intelligent programmer had made them. By reference to Dembski's own analysis, I took this to be a claim that the programmer had somehow infused information about the particular solution that a GA finds, and thus tainted the process. I asked Dembski about a specific case, a 500 city Traveling Salesman Problem. I asked where, precisely, the information about the particular tour found was introduced by the programmer. I eliminated the GA population handling routines, since those can be found in general toolkits applicable to many problems, not just 500 city TSPs. I eliminated the evaluation function, since by Dembski's own analysis, no function can produce information. Dembski responded that he objected to the notion that CSI can be gotten on the cheap or for free, and said that the information produced by a GA isn't untainted, since intelligence had to design the hardware, the operating system, the GA program itself, and the problem specification. I don't believe the response during the discussion to have been responsive to the point. Dembski's stated claim is that functions, algorithms, chance, and natural laws cannot *ever* produce CSI. Given an example of what by Dembski's standards is clearly CSI resulting from the application of a GA, what I'm told is that only algorithms which are made by an intelligence can produce CSI. This is a wholly different claim, and much weaker. The conference web site is http://www.dla.utexas.edu/depts/philosophy/faculty/koons/ntse/ntse.html -- Wesley R. Elsberry, 6070 Sea Isle, Galveston TX 77554. Central Neural System BBS, 409-737-5222, 1:385/385, ANNs, GAs, Alife, AI, evolution, and more. Student in Wildlife & Fisheries Sciences. http://www.rtis.com/nat/user/elsberry \"shakespeare and i are frequently coarse\" - archy [ Other on-line articles ] [ ID-Commentaries ]", "text_length": 3201, "text_sha256": "d84a488b24400f1abbfd5f68959d844460ce78eef8f48a897543656376b1f592" }, { "route": "/people/mgrey/IDC/online.html", "title": "Other On-line Articles", "description": "Other On-line Articles These are some of the on-line articles I refer to in my ID-commentaries: Metaviews: Who's Got the Magic? (ARCHIVEID=2595) Disbelieving Darwin -- And Feeling No Shame! (ARCHIVEID=2581) Explaining Specified Complexity (", "content_kind": "article", "text": "Legacy route: /people/mgrey/IDC/online.html Other On-line Articles These are some of the on-line articles I refer to in my ID-commentaries: Metaviews: Who's Got the Magic? (ARCHIVEID=2595) Disbelieving Darwin -- And Feeling No Shame! (ARCHIVEID=2581) Explaining Specified Complexity (ARCHIVEID=3066) Why Evolutionary Algorithms Cannot Generate Specified Complexity (ARCHIVEID=3080) Another Way to Detect Design? (ARCHIVEID=3097) Usenet: Dembski's Agency Triad (Message-ID: <199811261107.DAA21334@CX33978-A.DT1.SDCA.HOME.COM>#1/1) Dembski & the TSP (Message-ID: <5F5BLK$LC1@NEWS.TAMU.EDU>#1/1) Re: No free lunch theorems (Message-ID: <200106080021.RAA13020@CX33978-A.DT1.SDCA.HOME.COM>) Yahoo! Groups: Re: Re[2]: [DebunkCreation] Any books on evolution? (Message: 21397) Re: Re[2]: [DebunkCreation] Any books on evolution? (Message: 21340) [ Back to my ID-Commentaries ]", "text_length": 869, "text_sha256": "3f7793b2cdb4bb038b12eebffea15a0f0dbf9274bd06a1e104a3478b900c6a89" }, { "route": "/pages/wells/who-real-fraud_v2-3.html", "title": "Who's the Real Fraud?", "description": "Short Description of page", "content_kind": "article", "text": "Legacy route: /pages/wells/who-real-fraud_v2-3.html Who's the Real Fraud? Scientific mistakes, distortions, and sleights-of-hand in Wells' book Icons of Evolution by Nic Tamzek Copyright © 2002 [Draft Version 2.3, posted: February 17, 2002] Permission is given to copy and print this page for non-profit personal or educational use. Note: This document was written as a flier (!) for a Wells lecture at UCSD. This is an expanded web version, currently hosted at The Talk.Origins Archive: [ http://home.mmcable.com/faqs/wells ]. It is now a draft web article, and any constructive comments would be welcome (feel free to email me at the above address). A truly thorough refutation of Wells would take an entire book; however, any oversights in this version are the sole responsibility of the author and will be corrected in succeeding versions at the above URL. Contents Introduction A chapter-by-chapter critique of Icons of Evolution : Chapter 2: The Miller-Urey experiment Was there significant prebiotic oxygen? Was the prebiotic atmosphere reducing The RNA world Chapter 3: Darwin's Tree of Life Cambrian explosion Molecular phylogeny The root of the Tree of Life The Chinese paleontologist story Chapter 4: Homology in Vertebrate Limbs Is the definition of homology circular? Complexities of homology; R. A. Raff comments Chapter 5: Haeckel's Embryos More from R. A. Raff Richardson on creationists and Haeckel The vertebrate classes are not all equally related Chapter 6: Archaeopteryx -- The Missing Link Chapter 7: Peppered Moths The natural resting locations of peppered moths -- Majerus' data Peppered moth photographs, staged and otherwise What are the implications if moths rest most often underneath branches? The scientific literature Bruce Grant's review of Wells M.E.N. Majerus' review of Wells Of moths and maps Chapter 8: Darwin's Finches Chapter 9: Four-Winged Fruit Flies Chapter 10: Fossil Horses and Directed Evolution Chapter 11: From Ape to Human: The Ultimate Icon Conclusions What is Icons really about? Acknowledgements References Endnotes Introduction onathan Wells' book Icons of Evolution: Science or Myth? Why Much of What We Teach About Evolution Is Wrong (henceforth Icons ) makes a travesty of the notion of honest scholarship. Purporting to document that \"students and the public are being systematically misinformed about the evidence for evolution,\" (p. XII) via common textbook topics such as peppered moths, embryo similarities, and fossil hominids [1] , Icons in fact contains a bevy of its own errors. This is not original -- creationists have been making mistakes about evolution for years. Newly and more insidiously, however, Icons contains numerous instances of unfair distortions of scientific opinion, generated by the pseudoscientific tactics of selective citation of scientists and evidence, quote-mining, and \"argumentative sleight-of-hand,\" the last meaning Wells' tactic of padding his topical discussions with incessant, biased editorializing. Wells mixes these ingredients in with a few accurate (but always incomplete) bits of science and proceeds to string together (often in a logically arbitrary fashion) a narrative that is carefully crafted to make the semblance of an honest case for Wells' central defamatory accusation: that mainstream biologists are \"dogmatic Darwinists that misrepresent the truth to keep themselves in power\" (pp. 242-243). As is documented below, a picture of Wells' book Icons belongs in the dictionary next to the word \"misrepresentation.\" The central pillar of Wells' case is this: \"Some biologists are aware of difficulties with a particular icon because it distorts the evidence in their own field. When they read the scientific literature in their specialty, they can see that the icon is misleading or downright false. But they may feel that this is just an isolated problem, especially when they are assured that Darwin's theory is supported by overwhelming evidence from other fields. If they believe in the fundamental correctness of Darwinian evolution, they may set aside their misgivings about the particular icon they know something about.\" ( Icons , pp. 7-8) In other words, Wells argues that the specialists know about the problems in their field of expertise, but that everyone thinks that the evidence supporting evolution is somewhere else. This is just plain false, as we shall see -- the experts in each field have explicitly stated that the evidence in their field supports evolutionary theory. If Wells' above contention is false, then Wells' argument collapses. Wells likes asking questions; it is now time for him to answer some. Chapter 2: Miller-Urey experiment Prebiotic Oxygen. A key question in origin-of-life research is the oxidation state of the prebiotic atmosphere (the current best guess is that the origin of life occurred somewhere 4.0-3.7 bya (billion years ago)). Wells wants you to think that there is good evidence for significant amounts free oxygen in the prebiotic atmosphere (significant amounts of free oxygen make the atmosphere oxidizing and make Miller-Urey-type experiments fail). He spends several pages (14-19) on a pseudo-discussion of the oxygen issue, citing sources from the 1970's and writing that (p. 17) \"the controversy has never been resolved\", that \"Evidence from early rocks has been inconclusive,\" and concluding that the current geological consensus -- that oxygen was merely a trace gas before approximately 2.5 bya and only began rising after this point -- was due to \"Dogma [taking] the place of empirical evidence\" (p. 18). None of this is true (see e.g. Copley, 2001 ). Certain minerals, such as uraninite, cannot form under significant exposure to oxygen. Thick deposits of these rocks are found in rocks older than 2.5 bya years ago, indicating that essentially no oxygen (only trace amounts) was present. On page 17 Wells notes that uraninite deposits have been found in more recent rocks, but neglects to mention to his readers that these only occur under rapid-burial conditions, whereas ancient deposits of uraninite occur in slow deposition conditions, for example in sediments laid down by rivers, so that the minerals were exposed to atmospheric gases for significant periods of time before burial. 'Red beds' are geologic features containing highly oxidized iron (rust) indicative of high amounts of oxygen. Wells (p. 17) notes that red beds are found before 2 bya, but fails to mention that the temporal limit of red beds is just a few hundred million years before 2 bya. Wells doesn't even mention the evidence that banded iron formations (incompletely oxidized iron indicative of ultralow-oxygen conditions) are very common prior to 2.3 bya and very rare afterwards. Wells also doesn't mention that early paleosols (fossil soils) from about ~2.5 bya contain unoxidized cerium, impossible in an oxygenic atmosphere (e.g., Murakami et al. , 2001 ). Finally, Wells doesn't mention to his readers that pyrite, a mineral even more vulnerable to oxidation than uraninite, is found unoxidized in pre-2.5 bya rocks, and with significant evidence of long surface exposure (i.e. grains weathered by water erosion; e.g. Rasmussen and Buick, 1999 ). Why does Wells leave out the converging independent lines of geological evidence pointing to an anoxic early (pre ~2.5 bya) atmosphere? Was the prebiotic atmosphere reducing? Are the Miller-Urey experiments \"irrelevant\"? The famous Miller-Urey experiments used a strongly reducing atmosphere to produce amino acids. Current geochemical opinion is that the prebiotic atmosphere was not so strongly reducing, but varies from moderately reducing to neutral. Completely neutral would be bad for Miller-Urey-type experiment, but even a weakly reducing atmosphere will produce lower but significant amounts of amino acids. In the approximately two brief pages of text where Wells actually discusses the reducing question (p. 20-22), Wells cites some more 1970's sources and then asserts that the irrelevance of the Miller-Urey experiment has become a \"near-consensus among geochemists\" (p. 21). This statement is misleading. What geochemists agree on is that if the early earth's mantle was of the same composition as the modern mantle and if only terrestrial volcanic sources are considered as contributing to the atmosphere, and if the temperature profile of the early atmosphere was the same as modern earth (this is relevant to rates of hydrogen escape) then there will be much less hydrogen compared to Miller's first atmosphere (20% total atm.). Even if this worst-case scenario is accepted, hydrogen will not be completely absent, in fact there is a long list of geochemists that consider hydrogen to be present (although in lower amounts, roughly 0.1-1% of the total atmosphere). At these levels of H 2 there is still significant (although much lower) amino acid production. Also, many geochemists think that these conditions do not represent the early earth, contrary to the impression given by Wells. For example, on p. 20, Wells mentions terrestrial volcanos emitting neutral gases (H 2 O, CO 2 , N 2 , and only trace H 2 ), but he fails to mention that mid-ocean ridge vents could have been significant sources of reduced gases -- they are important sources of reduced atmospheric gases even today, emitting about 1% methane ( Kasting and Brown, 1998 ) and producing reduced hydrogen and hydrogen sulfide (e.g. Kelley et al. , 2001 ; Perkins, 2001 ; Von Damm, 2001 ) and potentially ammonia prebiotically ( Brandes et al. , 1998 ; Chyba, 1998 ). Why does Wells exclude oceanic vents from consideration? Another strange omission is that Wells completely fails to mention the extraterrestrial evidence, which is the only direct evidence we have of the kinds of chemical reactions that might have occurred in early solar systems. For example he neglects to mention the famous Murchison meteorite, which contains mixtures of organic compounds much like those produced in Miller-Urey style experiments, and which constitutes direct evidence that just the right kind of prebiotic chemistry was occurring at least somewhere in the early solar system and that some of those products found their way to earth (see e.g. Engel and Macko, 2001 for a recent review). Wells asserts that since the 1970's, non-reducing atmospheres have become the \"near-consensus.\" The latest article that Wells cites supporting this view, however, is a 1995 nontechnical news article in Science ( Cohen, 1995 ). Why doesn't he quote Kral et al. (1998) , who write, The standard theory for the origin of life postulates that life arose from an abiotically produced soup of organic material (e.g., Miller, 1953; Miller, 1992). The first organism would have therefore been a heterotroph deriving energy from this existing pool of nutrients. This theory for the origin of life is not without competitors (for a review of theories for the origins of life see Davis and McKay, 1996), but has received considerable support from laboratory experiments in which it has been demonstrated that biologically relevant organic materials can be easily synthesized from mildly reducing mixtures of gases (e.g., Chang et a l., 1983). The discovery of organics in comets (e.g., Kissel and Kruger, 1987), on Titan (e.g., >Sagan et al. , 1984), elsewhere in the outer solar system (e.g., Encrenaz, 1986), as well as in the interstellar medium (e.g., Irvine and Knacke, 1989) has further strengthened the notion that organic material was abundant prior to the origin of life. None of this is meant to convey the impression that no controversies exist (both Cohen (1995) and the Davis and McKay (1996) article cited by the above-quoted Kral et al. (1998) are about the various competing hypotheses about the origin of life). But textbooks generally mention some of these hypotheses (briefly of course, as there is only space for a page or two on this topic in an introductory textbook), and furthermore generally mention that the original atmosphere was likely more weakly reducing than the original Miller-Urey experiment hypothesized, but that many variations with mildly reducing conditions still produce satisfactory results. This is exactly what is written in the most popular college biology textbook, Campbell et al. 's (1999) Biology , for instance. In other words, the textbooks basically summarize what the recent literature is saying. The original Miller-Urey experiment, despite its limitations, is also repeatedly cited in modern scientific literature as a landmark experiment. So why does Wells have a problem with the textbooks following the literature? Wells wants textbooks to follow the experts, and it appears that they are. The RNA world. Wells writes (p. 22) as if the RNA world is an alternative to failed Miller-Urey-style experimentation. He cites no source for this claim, because the claim is pure obfuscation. The RNA world hypothesis is complementary, not opposed, to Miller-style prebiotic syntheses, as it is meant to explain how genetic replication got going without DNA, several steps down the road after prebiotic syntheses. Wells gives the impression that there are only two possible starts to life on earth, Urey-Miller style syntheses and the RNA world. Wells misleadingly cites several quotes that taken alone suggest that the RNA world is impossible, and that there is no remaining scientific explanations for life on earth. However, most authorities agree that the RNA world was one stage of the origin of life, rather than the very first stage, and that it was proceeded by a pre-RNA world. Indeed, the very authors he quotes to suggest that the RNA world is impossible go on to explain the concept of a pre-RNA world and how an RNA world would arise from that, but Wells omits all mention of this. Wells doesn't bother to cite recent work on precursors to the RNA world, see for example Cavalier-Smith (2001) for an introduction and references to ideas on this such as the 'NA world' and 'lipid world' (for the latter, see e.g. Segre et al. , 2001 ). Chapter 3: Darwin's Tree of Life Wells mixes up several issues in this chapter. As we saw in the previous chapter, he will give several topics each a cursory and incomplete treatment, raising doubts about each subject and connecting them together whether they are logically connected or not. The Cambrian Explosion . Here Wells is running down a path well-worn by his creationist and 'designist' (IDist) colleagues. As a result there is already significant literature available on the \"animal phyla appeared suddenly, and without precursors, and all equally far apart from each other\"-sort of contention. See for example Conway Morris ( Conway Morris, 1998 ) for an authoritative discussion, and Knoll and Carroll (1999) which is freely available online. A particularly interesting perspective is that of Keith B. Miller, geologist, evolutionist and evangelical Christian, who wrote an article (1999) in Perspectives on Science and Christian Faith entitled \"The Precambrian to Cambrian Fossil Record and Transitional Forms,\" ( http://www.asa3.org/ASA/topics/evolution/PSCF12-97Miller.html ) in which he wrote, There is much confusion in the popularized literature about the evidence for macroevolutionary change in the fossil record. Unfortunately, the discussion of evolution within the Christian community has been greatly influenced by inaccurate presentations of the fossil data and of the methods of classification. Widely read critiques of evolution, such as Evolution: A Theory in Crisis by Denton, and Darwin on Trial by Johnson, contain serious misrepresentations of the available fossil evidence for macroevolutionary transitions and of the science of evolutionary paleontology. [...] The implication of much of the evangelical Christian commentary on macroevolution is that the major taxonomic groups of living things remain clearly distinct entities throughout their history, and were as morphologically distinct from each other at their first appearance as they are today. There is a clear interest in showing the history of life as discontinuous, and any suggestion of transition in the fossil record is met with great skepticism. The purpose of this short communication is to dispel some of these misconceptions about the nature and interpretation of the fossil record. On page 38 of Icons Wells quotes page 30 of Simon Conway Morris' (1998) book The Crucible of Creation about the \"sharp demarcation\" at the Cambrian explosion. But Conway Morris writes on the very next page (32-3), \"The term 'explosion' should not be taken too literally, but in terms of evolution it is still very dramatic. What it means is the rapid diversification of animal life. 'Rapid' in this case means a few millions of years, rather than the tens or even hundreds of millions of years that are more typical when we consider evolution in the fossil record.\" And of course one of the central points of Conway Morris' entire book is that the morphological disparity that emerges in the Cambrian, often invoked by Wells & co. via quotation of people like Stephen J. Gould, is not quite as radical as the IDists or even Gould would have it. There is a significant problem in asserting that the animal phyla of the Cambrian are as morphologically diverse as the fauna today -- in large part this perception is due to the somewhat arbitrary concepts of 'phylum' and 'body plan'. Conway Morris writes (p. 170) that \"the strangeness of the problematic Cambrian animals is really a human artifact, a construct of our imagination.\" On pages 185-195 he uses the fossils Wiwaxia and Halkieria as transitionals between phyla (which by Wells' account shouldn't exist) to connect three very 'disparate' major phyla -- Mollusca, Brachiopoda, and Annelida -- to each other. For someone who self-righteously passes judgment on figures in textbooks, Wells' figures are atrocious. His Figure 3.4, \"Actual Fossil Records of the Major Living Animal Phyla\" purports to show when the various animal phyla appear in the fossil record. Note that, again, Wells cites no source in his notes to figure out where his figures came from. However, examining a similar graphic at the online University of California Museum of Paleontology ( UCMP, 2000 ), we see that Wells has left a number of phyla out, namely the dozen or so that have either no fossil record or appear very late relative to the Cambrian phyla. Notably all of the missing phyla are soft-bodied, but if Wells admitted that numerous phyla existed without any fossil record whatsoever, he would severely weaken his argument on page 44 that any small, soft-bodied ancestors of the animal phyla would have been fossilized if they existed. Wells' figure also places Rotifera and Phoronida as having fossil records in the Cambrian, which could be correct if the UCMP page is out of date, but as Wells gives no references for the figure it is impossible to check. Molecular Phylogeny. Wells' second argument against the Tree of Life deals with the 'molecular clock' hypothesis -- namely that DNA or protein sequence divergence is regular enough to date ancient splits between lineages. This hypothesis is indeed being questioned by scientists, as the influence of things like natural selection may well alter the rate of sequence change (e.g. cone snail venoms are a fantastic example of rapid sequence divergence under selective pressure; see Espiritu et al. , 2001 ). And if these changes occur often enough then getting accurate clock dates, particularly for distant events, will be very hard. This is an entirely different thing from determining molecular phylogenies, however, which is what Wells is actually trying to debunk. But unfortunately for Wells, there is considerable evidence that these phylogenies are reliable and in reasonably good accord with phylogenies generated from other data. On the general subject of accuracy in molecular phylogenies see Theobald 2002b and for recent work on phyla evolution and metaz", "text_length": 20000, "text_sha256": "cd88da2d1c671eafb40b379f0121937e10bce099e20e6cb7025592d4d2f699d5" } ] }