TalkDesign: Modernized Preview

First static modernization candidate for TalkDesign.

TalkDesign Critical analysis of the Intelligent Design movement. TalkDesign collects articles, FAQs, and archive material responding to Intelligent Design claims from the standpoint of mainstream science. This static candidate preserves the old content while replacing brittle table, Drupal, and PHP-era surfaces with a modern reader path. Start with the introduction Browse articles Sister Site Part of the TalkOrigins family TalkDesign remains focused on Intelligent Design while linking back to the broader TalkOrigins Archive and Foundation search surfaces. 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. Talkdesign.org provides links to the best and most Open Modernization Status FAQ browser Generated from the first canonical FAQ/article route set. Drupal archive browser Clean routes from the captured Drupal-era archive. Migration workbench Operator view for route inventory, redirect planning, and quality review. Translation queue Planned-language status without implying completed coverage.


Browse TalkDesign Articles

article_index Browse TalkDesign Articles Generated article browser for the first modernization candidate. Home Translation status Generated Surface 55 routes listed This page is generated from the modernization route inventory, not hand-maintained legacy navigation. 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


Browse TalkDesign FAQs

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


Drupal-Era TalkDesign Archive

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


Introduction to the TalkDesign.org Site

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


About Us

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


TalkDesign Volunteers

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


Request for Submissions

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.


Acknowledgements

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


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


Evolution of the bacterial flagellum

A detailed and testable scenario for the evolutionary origin of the bacterial flagellum.

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


Background

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 .