Science makes no assumption of naturalism beyond what intelligent design advocates already accept

Legacy route: /faqs/naturalism.html A Philosophical Premise of 'Naturalism'? by Mark Isaak Copyright © 2002 [posted: Sept. 24, 2002] The main objection some prominent intelligent design (ID) creationists have against evolution is that it is unjustifiably based on the philosophical underpinning of naturalism. "The Neo-Darwinian conclusion about the process of evolution is based on a premise of metaphysical naturalism: that there are no causes except matter in mindless motion." (ARN, 1996) And "The metaphysical assumptions of scientific materialism are not themselves established by scientific investigation, but rather are held a priori as unchallengeable and usually unexamined components of the 'scientific' worldview." (Johnson, 1989) This leads to the claim that evolution excludes God (Johnson, 1999), and that it is only fair to teach an alternative (intelligent design) that allows supernatural influence. This essay, however, will show that the above claims are false. Although science does make some assumptions that might be considered naturalistic in a sense, the assumptions that science is based on are not as restrictive as creationists claim. Furthermore, the proponents of intelligent design make exactly the same assumptions in their own work. Finally, we will see that the complaint about naturalism is applied unfairly to discredit only those parts of science that naturalism's critics oppose on ideological grounds. Naturalism We first must clarify (or try to do so) what is meant by "naturalism." Naturalism is the philosophy that states that explanations for all phenomena must be in terms of natural causes. Some usages of "materialism" are similar, and the two terms are sometimes used interchangeably. The main point that naturalism's critics object to is exclusion of the supernatural. Some people distinguish between philosophical naturalism, which states that natural causes are all there are, and methodological naturalism, which says merely that natural causes are all that is available for science to work with. In either case, the definition invites the question of what "nature" means. A complete definition would have to explain how to distinguish whether something is natural or supernatural. I have never seen that problem addressed satisfactorily, and I will not attempt to do so here. I will use the terms "nature" and "supernatural" in their usual informal senses. "Supernatural" refers to certain inexplicable or inscrutable phenomena that are traditionally given that label, and nature refers to everything else in the universe. Naturalism gets associated with science because natural explanations have such a good track record for explaining observed phenomena. To date, natural explanations have been determined for very, very many previously unknown areas, and supernatural explanations have been determined for none. When exploring another unknown area, the possibility of a natural explanation is the way to bet. Researchers bet that way routinely, and as a result the human race has benefitted with incredible advances in medicine, agriculture, electronics, materials science, and more. Supernatural explanations, on the other hand, have led nowhere. Indeed, many supernatural explanations are rejected not because they are supernatural but because they cannot or do not lead anywhere. It is possible to come up with any number of possible explanations for anything -- lost socks could be caused by extradimensional vortices which our observations prevent from forming; hiccups could be caused by evil spirits inside us trying to escape; stock market fluctuations could be caused by the secret manipulations of powerful extraterrestrials. Scientists reject such claims on the grounds of parsimony. All of those claims are possible, but they require adding complicated entities which there is no adequate evidence for. To make matters worse, the nature of those entities effectively prevents investigation of them, and the impossibility of investigation prevents us from learning anything new about them. We cannot conclude that any of those explanations are wrong. But from a scientific standpoint, they are worse than wrong; they are useless. The naturalism that anti-evolutionists most object to is philosophical naturalism, which insists on natural explanations even outside science -- i.e., that "nature is all there is." Many scientists, however, do not accept philosophical naturalism either. Some are staunch believers in God or other supernaturalism, including major contributors to evolutionary theory, such as Alfred Russel Wallace, Theodosius Dobzhansky, and Ronald Fisher, and active researchers and defenders of evolution today, such as Kenneth R. Miller and Francisco J. Ayala (see also Slack, 1997). In the United States, by one poll, roughly 40% of scientists believe in an active personal God, and there are surely many more who believe in a God fitting a definition less restrictive than the one used in the poll (Larson & Witham, 1999). These scientists would hardly work to support a philosophical position that they are steadfastly opposed to. Right away, then, we see that the main complaint about naturalism is trivially untrue. Critics of naturalism (I will call them ID advocates for short, although some other creationists make the same criticisms) still deny such obvious facts, though. One method of denial is to claim that the God that their opponents believe in doesn't count. For example: "Naturalistic evolution is consistent with the existence of 'God' only if by that term we mean no more than a first cause which retires from further activity after establishing the laws of nature and setting the natural mechanism in motion." (Johnson, 1990) To those of us who know a few evolutionary biologists personally, such assertions are beyond ludicrous. There are likely some people who believe as Johnson describes, but there are many others for whom God is a personal, ever-present force in their life. Several denominations of Christianity and other religions, including Catholics, Methodists, Presbyterians, and Jews, see no conflict between God and evolution. (NCSE, 2000) This could hardly be the case if a naturalism inherent in evolution was inimical to theistic religion. The other common method of denial is to focus attention on the handful of scientists who do support philosophical naturalism, such as William Provine and Richard Dawkins. These scientists, however, do not speak for all of science. Indeed, no scientists do. Part of science's strength is its diversity. Since scientists of many diverse religions are studying evolution, any religious bias one scientist tries to insert into it will soon be rejected by another. Moreover, philosophers of science, who have no stake in actual theories, also scrutinize science for unwarranted assumptions. With these watchdogs, we can be confident that the theory in the end will be virtually free of religious bias. Likewise for various philosophical, political, and cultural views. Some scientists will disagree with some of the things I say below about the supernatural. But the fact remains that there are many scientists who accept supernatural views in their religion -- some who even see their religion as motivating and inspiring their science -- and who are completely accepted in the field of science. Once one understands the basic requirements of science (more on this below), this should not be surprising. Focusing only on the most materialist scientists and disregarding the rest is a propaganda ploy, not an argument. Most scientists would admit that there will always be phenomena that have not been explained. The more we learn, the more areas of ignorance we uncover. The wise person, when looking at these unknown areas, will say simply, "I don't know." The ID advocates, on the other hand, see the unknowns as openings for the supernatural, perhaps even evidence for it. This is the god of the gaps. Many people, including religious scientists, reject the god of the gaps for purely theological reasons, reasons that have nothing to do with naturalism. For example, they see such a position as opposing a belief in a God that is active in all creation; and, as new discoveries fill the gaps in which God is placed, they see the god-of-the-gaps as undermining a reason to believe in God. (Miller, 1998; Lamoureaux, 1999) Far from denying the supernatural, they are denying that human ignorance is a basis for worship. Spirituality expresses itself differently to different people. Some people see their God denied by the theory of evolution. Others see God in the operation of nature, inseparable from the theory of evolution; they see a need for blatantly supernatural evidence of God as effectively denying God. Others have a variety of entirely different views. This range of views exists among scientists as well as the population at large. One may fail to understand all these views, but to pretend they don't exist is the height of insensitivity. A single spiritual view will not apply to everyone, and trying to impose one will benefit nobody but the arms dealers. A related claim is that adherence to naturalism rules out, a priori , the possibility of detecting design (SEAO, n.d.). This claim also is easily seen to be utterly false, and not just because scientists needn't adhere to naturalism. Even when assuming naturalism, detecting design is obviously possible. One example comes from Carl Sagan, who suggests that design can be inferred from a sequence of bits counting out the first few prime numbers. In fact, this is a favorite example of one of intelligent design's main advocates (Dembski, 1998a). Carl Sagan certainly didn't assume exceptions to naturalism when he proposed that indication of design. (It is worth noting that actual SETI researchers look for an entirely different kind of evidence. They aren't looking for any pattern in the signal except a narrow bandwidth, which they consider a likely indicator based on what people would do. (SETI Institute, n.d.)) Evidence could conceivably be found that points to design of biological organisms, too; for example, records from an ancient ET civilization describing their bioengineering on Earth. Detecting design is a routine part of science already; there is no reason to change existing scientific practices to make it possible. What Science is Based On Many people, including some scientists, misunderstand the foundations of science, believing that science assumes naturalism in some form. As noted above, though, science is based on nature, not on naturalism. To explain this more fully, we must say something about what science is and what it is based on. There is disagreement among philosophers over the exact definition of science, but for our purposes, we needn't go into such depth. We will cover only the basic philosophical assumptions that science makes and qualities of science that are generally agreed upon. Some basic philosophical assumptions are necessary, because conclusions can't be made until you have something to make them with. Whether they realize it or not, virtually everybody makes just a few very basic philosophical assumptions; most people would call them common sense. First, we assume that our memories are not altogether faulty; in other words, that the past is (or was) real. Second, we make an assumption about the future, namely that patterns and principles that have held true in the past will probably continue. These two assumptions together may be considered the single assumption of continuity of phenomena. Most people also assume that there is an external reality, and that our senses give at least a partially accurate indication of it. The assumption of a continuity of phenomena is used by everybody. Consider eating, for example. You need to make assumptions about the past and its applicability to the future in order to find food, even if finding food means nothing more than remembering what cupboard it is in. You need the assumptions again to decide, say, that drain cleaner hasn't suddenly become edible today. You need the assumption to decide that this thing that looks and tastes like an apple is, in fact, and apple and not an old shoe. In short, the assumption is so basic that we need it for survival. Those basic assumptions--a memorable past, a predictable future, and an observable external reality--are the only assumptions made by science (and even the assumption of external reality is rejected by some philosophical idealists). Science makes no other assumptions. With perception and memory, we can see that there are certain regularities in the world, and with induction, we can put them to use. In short, we can learn. Science assumes only that there is a past, present, and future that we can know something about. Once we have that, the real world provides the rest. It is worth repeating that those assumption are not limited to science. Everybody makes them. Even if they deny them with their words, they live their lives according to them. Most people make additional assumptions, but they make those basic ones, too. Some people think that science makes additional assumptions, but it really doesn't. It has been suggested, for example, that science assumes that the laws of nature have been constant throughout time (e.g., Morris, 1994). However, that is not an assumption but a conclusion. Uniformity of natural laws is something that scientists actively test. To date, their tests show that there has been little if any change in the last six billion years, but there is some evidence (still relatively weak) that the fine structure constant has changed slightly before that (Webb et al, 1999). The assumption of naturalism is another assumption that science gets falsely accused of. Science does not make this assumption. Science does not assume that gods are necessary, but it does not assume they are absent, either. Science does not assume that miracles occurred, but neither does it assume a priori that they never have. (Miracles and science are discussed more below). Science is in the business of testing assumptions, not adding new ones. Individual scientists may believe one way or the other, but their beliefs are not a basis for science. All science is based on observations of nature, which leads some scientists to say that science must assume methodological naturalism (e.g. Singham, 2002). But a little investigation shows that even this is an overstatement. The observations that science is based on are natural, but that is simply because the things we call supernatural are not observable, at least not directly. Supernatural forces can, in theory, have effects that are observable. Science allows for this possibility. In fact, several scientific studies have been done to investigate phenomena that most people would consider supernatural, including the power of prayer (Benor, 1990; Byrd, 1988; Harris et al, 1999; Cha et al, 2001), divination (Randi, 1982; Enright, 1999), prophecy (Witztum et al., 1994; McKay et al., 1999; Perakh, 2000), life after death (Schwartz et al., 2001), ESP (Wiseman et al., 1996), and more. Some organizations actively encourage scientific investigation of the supernatural (JREF, 2002). Science can hardly be called naturalistic when it actively delves into the supernatural. If a supernatural phenomenon is found to give repeatable, verifiable results, science will study it. For example, if fairies appear where they can be repeatedly observed, measured, and tested, then they will be valid objects of scientific study. Under such circumstances, though, most people would start calling the phenomenon "natural." The fairies that come to be part of normal shared experience will get labelled "natural" even if we don't yet understand how they fly, make the little sparkling lights, and turn some of the researchers into frogs. As I mentioned earlier, delimiting the supernatural is not easy. But what about individual miracles? What about so-called supernatural events that can't be studied? Suppose, for example, an apparition of a dead relative appears and speaks to one person on one occasion, and nothing like it ever happens again. Science has a place for such phenomena as well: that place is outside science. But they are outside science because the observations cannot be verified, not because they are supernatural. Unverifiable natural events are also outside of science. When President Harrison signed the statehood proclamations admitting North Dakota and South Dakota to the United States, he purposely did not let anyone see which he signed first. The question of which state was admitted earlier is, in practice, outside of science, because no verifiable observations can be made to answer it. (However, simply being a one-time event does not place something outside of science. The observations must be repeatable, not necessarily the event being studied. Most events have observable consequences that persist long after the event. The origin of the moon, for example, can be studied scientifically because different mechanisms for its origin imply different modern-day properties such as the chemical composition of moon rocks.) To the extent that a reputed supernatural event leaves lasting evidence, the event can be studied scientifically. And again, we find science actively engages in studying such events. However, where verifiable evidence is lacking, science does not apply. Scientists and philosophers can disagree over other defining features of science, but at least one requirement is clear. For something to qualify as science, the observations must be independently verifiable by others. Perhaps the greatest strength of science is that all its findings are subject to testing, and verifiability of the raw data is foundational to such testing. The effect of this requirement is to remove from scientific consideration subjective impressions and unevidenced phenomena. This does not imply that subjective and unevidenced phenomena aren't important, merely that they cannot be used as the basis for scientific research. Science has never claimed to be all-encompassing. The few people who say otherwise are usually people who want the good reputation of science to apply to their own ideas outside science. Intelligent design proponents fit in this group (Dembski, 1998b). What these people want is more akin to scientism than to science. They want the reputation of science without having earned it. The status of Intelligent Design as science has nothing whatsoever to do with its being natural or supernatural. As we have seen, simply being supernatural doesn't disqualify something from scientific study. Intelligent Design is rejected from science simply because there is no verifiable evidence to support it. Most of Intelligent Design theory is purely subjective, saying little more than "it sure looks designed to me." Only two lines of argument have even a pretense of being scientific. The first, irreducible complexity, is a God-of-the-gaps argument. Certain biological systems, it is claimed, could not have evolved, leaving design as the alternative (Behe, 1996). This argument fails first because a lack of evolution does not imply design, and second because the arguments fail to allow for several biological processes that make the evolution of irreducible complexity not only possible but expected (Muller, 1939). The second supposedly scientific argument for design is specified complexity (Dembski, 1998c). But specified complexity is also a god-of-the-gaps argument. In fact, Dembski's "explanatory filter" for detecting design is really just the god-of-the-gaps expressed as a formal flow-chart; plus, it relies on irreducible complexity for its conclusions. The ID advocates deny that their arguments are god-of-the-gaps, and Dembski's arguments in particular are dressed with lots of rhetoric and confusing and inconsistent terminology to make them look more substantive,


Legacy route: /faqs/demskiscompass.html Content source: /cs/dembskis_compass/ - DR. DEMBSKI'S COMPASS - or, How to lose one's way while looking for misdirection. Andrea Bottaro responds to a criticism made by "intelligent design" advocate William A. Dembski about Bottaro's review of Unlocking the Mystery of Life . Andrea Bottaro University of Rochester School of Medicine and Dentistry [Posted: 10 August 2003] Leading Intelligent Design Creationism (IDC) proponent Dr. William Dembski has quoted my recent critique of the video "Unlocking the Mystery of Life" 1 in "The Myths of Darwinism", the Introduction to his latest edited book "Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing" 2 . Unflatteringly, alas, the quote is meant to illustrate a purportedly common misinformation strategy (the "Myth of Victory Past") used by "Darwinists" to surreptitiously dispatch significant objections. According to Dembski, when a valid criticism to evolutionary theory is leveled, first it is "dismissed without an adequate response", and later defined as a "discredited criticism that was refuted a long time ago", without an adequate refutation in fact ever being offered. I am fingered by Dembski as an example of how this supposed "Darwinist" conspiracy works Here, I wish to specifically address Dembski's charge that I "misdirected" readers of my "Unlocking" critique, and argue that, in fact, it is Dembski's own compass that must be malfunctioning 3 . 1. Setting off... in the wrong direction After describing the "Myth of Victory Past" for his readers, Dembski writes: "It will help to see how this Darwinist technique of "passing the buck" actually plays out in practice. ... Here is what Bottaro says about irreducible complexity: "The crucial argument ... widely discussed in the video, is the concept of "irreducibly complex" systems, and the purported impossibility of conventional evolutionary mechanisms to generate them. Although it was quickly rejected by biologists on theoretical and empirical grounds [ref.#6], "irreducible complexity" has remained the main staple of [Intelligent Design] Creationism. Ironically, this argument was just recently delivered a fatal blow in the prestigious science journal Nature, where a computer simulation based entirely on evolutionary principles (undirected random mutation and selection) was shown to be able to generate "irreducibly complex" outputs [ref.#7]." "This sounds quite impressive and damning until one follows the paper trail. Indeed, what are references #6 and #7 to which Bottaro refers? Reference #6 is to Kenneth Miller's book "Finding Darwin's God". Unfortunately, you won't find the promised refutation of irreducible complexity's challenge to Darwinism there. " 2 Dembski continues with a brief account of some of Miller's counter-arguments in "Finding Darwin's God", and references his own book "No Free Lunch" as the site of refutation of those arguments. Solemnly, Dembski concludes: "Reference #6 is therefore an exercise in misdirection." 2 Well, actually, it isn't. In fact, quite ironically, Dembski has barely set foot on the "paper trail" and he's already lost. His confident statement notwithstanding, my original reference #6 is not to Miller's "Finding Darwin's God". It's unclear how Dembski even reached that conclusion, since my reference, in its entirety, reads: "6. see for instance several articles by Dr. Ken Miller, Brown University: http://www.millerandlevine.com/km/evol/ Accessed 6/30/03" 1 [emphasis added] As anyone can verify at the click of a mouse, that link leads to Dr. Miller's web site, where more links to a number of articles are found. Here, "Finding Darwin's God" is represented by a single excerpt from its concluding chapter, very general in tone and void of any mention of either Behe or irreducible complexity. Oddly enough, Dembski even goes as far as directly quoting Miller from what he says is my own reference, but for the life of me I cannot find that quote on Miller's web page, or any of its side-links. On the other hand, Miller's site does contain several pertinent works, including his original review of "Darwin's Black Box" and a few more articles on irreducible complexity and IDC, written both before and after Dembski's "No Free Lunch". Dembski ignores the articles I referenced, discusses an arbitrarily chosen quote from "Finding Darwin's God" (that I didn't reference), and tells his readers to trust that he already neatly disposed of all these objections in his own book 4 . Without excessively dwelling on this rather straightforward issue, if Dembski wishes to publicly accuse me of "misdirection" in my use of references, at the very least he should discuss, and direct his own readers to the references I actually give, rather than others of his own choosing. 2. A detour OK, fine, wrong reference. Perhaps Dembski might still contend that even my real reference does not contain "the promised refutation of irreducible complexity's challenge to Darwinism" 2 . Except, that'd be wrong as well. As Dembski's own quote of my writing plainly shows, I never "promised" that readers would find some sort of definitive "refutation of irreducible complexity's challenge to Darwinism" in my reference #6, as he implies. What I did in fact was to simply refer readers to a source where they could find examples of the theoretical and empirical arguments based on which biologists rejected Behe's irreducible complexity 5 . Of course, it shouldn't surprise anybody that Dembski finds those arguments insufficient - or he wouldn't be today at the top of yet another list of "Darwinism doubters". Similarly, however, Dembski himself should perhaps consider the real possibility that biologists, such as myself, still find these same objections quite convincing, and his supposed refutations of them inadequate 6 . For someone like Dembski, who has been engaged in essentially the same argument for almost a decade in the absence of any significant rate of "conversion" of his opponents, this shouldn't represent a major revelation. Truthfully, I can't actually tell what point Dembski is ultimately trying to make here. He certainly can't be arguing that biologists did not quickly reject irreducible complexity on several theoretical and empirical grounds, or that some of those grounds are not described in reference #6 (either mine, or his imaginary one). And if this is the case, and my reference accurately reflects what was "promised" in the text, then Dembski's claim to the contrary is manifestly unsupported. 3. Walking in circles Next, Dembski goes on to deal with my reference #7. The Lenski paper 7 , he informs us, "... describes a computer simulation and thus contains no actual biology. ... The validity of this study therefore depends on whether the simulation maps faithfully onto biological reality. Unfortunately, it does not, and the study therefore doesn't prove a thing about real-life biological evolution." 2 There are two separate issues here. The first relates again to my alleged "myth-making". Clearly, I was not referring here to some old paper which failed to really address the issue in question and/or had since been refuted (the forms of "Myth of Victory Past" previously described by Dembski). On the contrary, I was referring to a very recently published paper, which (to my knowledge) had not been formally addressed, let alone refuted, by Dembski or any other prominent ID advocate. Unless in Dembski's eyes I am guilty of misdirection because I did not anticipate a forthcoming refutation, and didn't proactively alert my readers to it, it's hard to understand his objection to this part of my critique and supporting references. Secondly, and more importantly, Dembski's purported refutation of Lenski still has to come. Dembski's entire justification for the dismissal of the Nature paper boils down to his claim that its computer simulation does not "map faithfully onto biological reality". Why it doesn't, however, Dembski forgets to tell us, either in Myths or (as far as I know) anywhere else 8 . Until Dembski does so, of course, he can hardly accuse me of misdirection. At most, he can charge me with incompetence, for not seeing the obvious faults he finds in the paper, but then I'd still be in such company as the paper's own authors (as well as Nature's reviewers and editors). If the alternative is to take Dembski's rain check for a future substantial and convincing refutation 9 , I'll gladly stick with the other "incompetents" for the time being. 4. Conclusion - Dr. Dembski's compass In "Myths of Darwinism", Dr. Dembski levels against me the rather serious accusation that I misled my readers, making me a participant in the pervasive misinformation ploy he alleges "Darwinists" routinely engage in. But, Dembski assures, if his readers follow his steps on the "paper trail", they can find their way back and safely arrive to their truthful destination. Alas, at the end of the road, it is Dembski himself who appears quite off course, having lost his way, along with a chance for restraint and careful scholarship, while looking for signs of deceit in those 2 fateful references. When the facts are examined, one finds that: quite embarrassingly, in his efforts to prove my "misdirection" Dembski seems to have taken the wrong turn himself (intentionally or as a result of plain shoddiness, I can't say), all the way to a reference which is not the one I clearly pointed to; contrary to Dembski's claim, the first of my references leads my readers exactly to the information I said it would; the second reference, Lenski's paper, still seems to represent the fatal blow to "irreducible complexity" I said it is, and will remain so as long as Dembski and fellow IDC advocates fail to provide any meaningful rebuttal of its conclusions. In my critique of "Unlocking the Mystery of Life", I commented on the tendency of that unfortunate "documentary" to create straw-man versions of scientific knowledge to oppose to ID philosophy. Regrettably, in his Introduction to "Uncommon Dissent", Dembski appears to have chosen the very same approach to reach his rhetorical goal: he needed a good example of his purported "Darwinian Myth", and he simply made one up. Notes 1. "Unlocking the Mystery of Life - More Omissions Than Facts", in "Bottaro's Letter to WNYE", at the National Center for Science Education web site: http://www.ncseweb.org/resources/articles/2018_bottaro39s_letter_to_wnye_7_8_2003.asp . Accessed 7/29/03. Reproduced here on Talkdesign.org: http://www.talkdesign.org/faqs/bottaroslettertoWNYE.html 2. http://www.designinference.com/documents/2003.07.UncDiss_Intro_Contrib.pdf , pages 12-16. Accessed 7/29/03 3. My primary concern here is to uphold my professional standards, as well as the contents of my "Unlocking" critique, against Dembski's misguided accusation. However, substantial criticisms can in fact be raised to Dembski's other claims regarding Miller's and Lenski's work. At the risk of being accused of another round of myth-making, I would refer the reader to the comments by Nic Tamzek and others (see http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3f25217b7174ffff;act=ST;f=2;t=72 , and links therein. Accessed 7/29/03). 4. Paradoxically, Dembski seems here to engage in diversion tactics himself: first, my reference of Miller's site turns into a reference to "Finding Darwin's God", then Miller's numerous and complex arguments in that book get distilled into just his 4 counterexamples of "evolved" irreducible complexity. Finally, Dembski simply declares he has definitively shown those to be faulty in "No Free Lunch" - case closed. In fact, whether he successfully did it or not (arguable, but that's beside the point here), that can hardly be considered a wholesale refutation of "Finding Darwin's God", let alone of the many arguments against irreducible complexity raised by biologists I was referring to in my text. 5. For irreducible fans of the controversy, there are luckily many other freely available critiques of irreducible complexity on the web, in addition to Miller's. Among the best are several at www.talkorigins.org and www.talkreason.org (links found here: http://www.talkorigins.org/faqs/behe.html and http://www.talkreason.org/index.cfm?category=0 . I particularly recommend Pete Dunkelberg's recent overview "IC Demystified": http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html , and, closer to my own field of expertise, Matt Inlay's discussion of immune system evolution: http://www.talkdesign.org/faqs/Evolving_Immunity.html ). An often entertaining series of exchanges between several ID advocates, including Dembski, and my U of R colleague H. Allen Orr can be found at the Boston Review web site ( http://bostonreview.net/BR21.6/orr.nclk ; http://bostonreview.net/BR22.1/BR22.1.nclk ; http://bostonreview.net/BR27.3/orr.nclk ; http://bostonreview.net/BR27.5/exchange.nclk ). Al sites accessed 7/29/03 6. I suspect this very inability to accept even the possibility of honest disagreement, out of absolute self-assuredness and/or lack of internal critical feed-back, is in fact the origin of some of IDC's recurrent and often bizarre conspiracy theories about "darwinian censorship" and the likes, such as Dembski's "myth" discussed here. 7. Lenski RE, Ofria C, Pennock RT, Adami C. "The evolutionary origin of complex features." Nature. May 8 2003; 423 (6936):139-44 8. To be fair, Dembski goes on to offer a cursory explanation. The authors, he says, begged the issue of irreducible complexity "by requiring of their simulation that complex features exhibiting complex functions can always be decomposed into simpler features exhibiting simpler functions... There is no evidence that real-life irreducibly complex biochemical machines can be decomposed this way." 2 As pointed out by Tamzek, however, this can't really be Dembski's reason for rejecting Lenski's conclusions, since Dembski himself has previously conceded this very same point: "That an irreducibly complex system may have subsystems that have functions of their own (functions distinct from that of the original system) is therefore allowed in the definition." (from "Still Spinning Just Fine: A Response to Ken Miller", http://www.designinference.com/documents/2003.02.Miller_Response.htm . This is actually just one of several Dembski's statements on the same subject, quoted in the previously linked Antievolution.org thread by Tamzek). 9. Cynics could say they almost see a strategy emerging: "When a valid criticism ... is first proposed, it is dismissed without an adequate response, either on some technicality or with some irrelevancy or by simply being ignored. ... Thereafter, the criticism becomes known as "that discredited criticism that was refuted a long time ago"." 2 But of course, according to Dembski only "Darwinists" do that, so I am looking forward to his forthcoming refutation of Lenski's paper.


Evolving Immunity

Legacy route: /faqs/Evolving_Immunity.html Content source: /cs/evolving_immunity/ Evolving Immunity Matt Inlay responds to the immunity chapter, Chapter 6, of Michael Behe's Darwin's Black Box . < A Response to Chapter 6 of Darwin's Black Box by Matt Inlay Version 1.4 [Contributed June 6, 2002; Last Modified July 17, 2002] email author for comments and feedback Introduction Immune systems are generally characterized by their ability to distinguish between self and non-self cells, tissues, or molecules, and to eliminate the non-self (for review see Janeway 2001 ). The mammalian immune system is an incredibly complex and intricate system that can recognize non-self and provide protection from a wide variety of pathogens. While there is a high degree of interconnectivity between its components, the immune system can be loosely divided into two subsystems, the innate and the adaptive immune systems. In general, innate immunity is a non-specific, inducible response to pathogens. It is immediate in action, yet short-lived. On the other hand, the adaptive immune system is much more specific, but takes longer to activate. It also features immunological memory, and can augment itself to respond more quickly and with greater specificity to future infections of similar pathogens. Both systems work together to provide protection against a diverse and rapidly-evolving array of pathogens. While much is known about the evolution of the immune system, the details of its origin remain to be elucidated. The innate immune system is the more ancient of the two systems, with roots deep in the deuterostome branch of the bilaterians, roughly one billion years ago. Conversely, the adaptive immune system appeared more recently and quite suddenly, around 450 million years ago with the emergence of the gnathostomes, more commonly called the jawed vertebrates. Because of its high degree of complexity and interconnectivity, the mammalian immune system has been labeled as "irreducibly complex", and its evolution and origin through "Darwinian" mechanisms challenged [i] . Michael Behe, in his book Darwin's Black Box ( Behe 1996 ), defines irreducible complexity (IC) as: "[A] single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function." (page 39). Unfortunately, each of the terms "system", "well-matched", "interacting", "parts", and "function" can have multiple meanings, depending on the context, so nonarbitrarily labeling a system as IC is not an easy task. For instance, "system" in Behe's definition differs significantly from the same word in the context of "immune system". His use of "system" refers specifically to biochemical systems. What is the difference? The components, or parts of a biochemical system are molecular in nature, like proteins or complexes of molecules. "System" as is used in immune system refers not just to molecules, but to the cells and tissues involved in conferring immunity. The immune system as a whole contains numerous biochemical systems within it. It is important to note this distinction because Behe only addresses biochemical systems as IC. Systems, whether biochemical or not, are often defined according to their function. However, the term "function" is also nebulous. The "function" of the immune system is rather broad, encompassing any action involved in either immune recognition or response. Even the skin is considered to be part of the immune system. The "function" of a biochemical system is much more specific. Here, function refers to a specific biochemical function, such as the formation of a blood-clot, the spinning of a flagellum to produce locomotion, or the synthesis of a biomolecule from a precursor. This type of function usually consists of a series of biochemical reactions. This is important because Behe is trying to make a specific argument about the origin and evolution of IC biochemical systems. Immediately after defining IC, Behe states: "An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." Behe is trying to suggest that because of the nature of IC, biochemical systems that possess this quality could not have evolved through random mutation and natural selection, or "blind-watchmaking". Essentially, Behe is using IC to disprove evolution. As an alternative, Behe suggests that the only way that IC biochemical systems could have originated is through intelligent intervention. He offers as evidence the fact that all IC systems whose origins are known were designed by intelligent agents, us. There are many problems with Behe's argument. Basically, Behe is saying that because we do not know how an IC system could have evolved, it didn't evolve. This type of argumentation is referred to as an argument from ignorance . The problem with arguments from ignorance is that they make a conclusion based on a lack of knowledge. There is still much we do not know about evolution. What seems like a conundrum right now may be easily resolved in the future. Biology, and science in general, is filled with mysteries and unknowns. The whole point of science is to seek answers to those questions. Secondly, he tries to use arguments against evolution as evidence for intelligent design. Negative arguments against one theory do not necessarily provide evidence for a particular alternative. It would be like trying to show how safe a Honda Civic is by providing evidence that a Toyota Corolla is unsafe. No matter how unsafe the Corolla is, it says nothing about the Civic. Negative argumentation is scientifically useless without an alternative that can be positively tested. These fallacies do not rule out the possibility that Behe has raised an interesting and useful challenge to our current understanding of evolution. However, a closer look reveals he hasn't. In chapter 6 of Darwin's Black Box , entitled "A Dangerous World", Behe outlines three IC biochemical systems in the immune system; clonal selection, V(D)J recombination, and the complement cascade. However, in his analysis of each of these systems, Behe makes critical mistakes. For the process of clonal selection, Behe targets the antibody molecules, which have the ability to rearrange their genes, and to switch from a membrane-bound form to a secreted form. Behe assumes that an antibody molecule missing one of these features would be useless. However, there are many examples of proteins that do not undergo rearrangement, but are able to switch forms. Additionally, there is a gene closely related to antibodies which can also undergo rearrangement, but does not switch forms. Behe neglects to mention either of these intermediate-like molecules. Instead, he scrutinizes the process of antibody gene rearrangement as the second IC system. He describes the numerous features of this system and claims there is no pathway through which it could have evolved. However, he assumes that the only selectable function for the genes involved in rearrangement is rearrangement. There are well-studied systems that bear remarkable similarity to V(D)J recombination that have nothing to do with immunity. He fails to recognize the existence of these other systems, nor realizes that most of the components of recombination are already present there. Finally, in his description of the third IC system, Behe mistakenly assigns a single function to the complement pathway. He fails to realize that the complement system has several different functions, and several mechanisms of activation. This would allow for a gradual, stepwise accumulation of parts and functions. In fact, many other groups of organisms possess a complement system that lacks his primary function. According to Behe's definition of irreducible complexity, those systems shouldn't exist. In each case, Behe claims that a lack of articles in the scientific literature provides evidence that these systems could not have evolved. However, there are hundreds to thousands of articles published on these systems. Much was known about the evolution of each of these systems at the time Darwin's Black Box was published. Additionally, much has been learned since then. This article will attempt to summarize the existing knowledge about the origins of these systems, and propose a possible pathway for their evolution through a Darwinian mechanism. It is not necessary to "prove" that these systems evolved. Because the essence of his argument is "how could this have evolved?", this article merely seeks to provide an answer to that question. One issue that will not be discussed is whether or not these systems are actually irreducibly complex. The term is not very useful to the discussion of origins because of the ambiguities surrounding its definition. In fact, IC as a term has failed to make much of an impression on the scientific community, as a search on the publication database PubMed, fails to turn up any references to "irreducible complexity" [ii] . IC system I: Clonal selection The first system Behe describes in chapter 6 is the process of clonal selection, which is how the adaptive immune system detects non-self molecules and initiates a response. This system focuses on a protein called immunoglobulin (Ig), and the complex it is part of, called the B cell receptor complex (BCR). Immunoglobulins, also called antibodies, are Y-shaped proteins that can recognize and bind foreign molecules (Figure 1a,b). They are produced by lymphocytes called B cells, and are initially expressed on the cell surface. In its membrane-bound form, an immunoglobulin molecule binds to two additional proteins, Ig a and Ig b , to form the BCR (Figure 1c). The target of an immunoglobulin is referred to as its antigen (Ag). Antigen can be essentially any molecule, though there is a preference for proteins. Because of the way in which immunoglobulins are produced, the specific antigen that each Ig recognizes is different in each B cell. This occurs through a process of gene rearrangement called V(D)J recombination, which will be explained later. When an unactivated, or naïve, B cell's Ig recognizes its particular antigen, it sends a signal back into the interior of the cell to initiate activation. This signal is transmitted via a series of modifications through a series of "messenger" proteins, which ultimately trigger the transcription of a panel of genes involved in B cell activation. In order to become fully activated, further interaction with a second class of lymphocyte, called T cells, is required. Once the B cell is activated it proliferates and differentiates into a plasma cell, and the function of the immunoglobulin changes from recognition to response. The immunoglobulin switches from a membrane-bound form (mIg) to a secreted form (sIg), where it can diffuse throughout the tissues of the host organism and there bind its cognate antigen. The only difference between the two forms is at the very tip of the bottom of the Y shape, which corresponds to the very tail end of the gene. The switch from mIg to sIg production results from a switch between two alternative RNA splicing patterns, such that the terminal coding exon directs either the translation of a membrane-bound or soluble C-terminal domain, respectively (Figure 2). The process of amplifying a particular B cell (or subset of B cells) from amongst billions based on its antigen specificity is called clonal selection (Figure 3). This process allows the immune system to choose from which B cell (or subset of B cells) it will mount an immune response. Additional discussion of the clonal selection system in the context of irreducible complexity can be found in the web article: The Evolution of Improved Fitness (http://www.talkorigins.org/faqs/fitness/) Behe summarizes this first system as a group of 3 components (page 125): membrane-bound form of the antibody messenger secreted form of the antibody Behe has this to say about the evolution of the clonal selection system: "A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there's no way to tell if it's doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps." (Page 125) Switch forms or rearrange? So the question is, could the clonal selection system have evolved? Certainly. One thing to realize is that the immunoglobulins are not the only molecules that can undergo gene rearrangement to produce a diverse set of antigen-receptors. T cell receptors (TCRs) are antigen-receptors quite similar to immunoglobulins. However, TCRs exist only in a membrane-bound form, yet are able to carry out their particular function without the need to leave the cell surface. Their receptors are used only for the detection of foreign antigens, and do not directly mediate an effector response. So even if immunoglobulins would be unable to effectively carry out their job if they were restricted to the membrane-bound form, they could have evolved from a TCR-like gene, which does not require secretion. If that occurred, then the ability to rearrange and the ability to switch forms could evolve in separate steps, with each step offering a selectable advantage. It remains unclear whether a TCR-like gene appeared first or an Ig-like gene. However, it is also possible that the ability to rearrange came after the evolution of the alternative splicing pattern, resulting in the ability to switch. This would require that antigen receptors with a single specificity be effective mediators of immunity. Could this have occurred? Absolutely. There are several families of innate receptors that do not rearrange, called pattern recognition receptors (PRRs) ( Medzhitov and Janeway 1997 ). Bacteria possess many unique and essential surface molecules that are distinct from metazoan surface molecules. For example, organisms ranging from insects to humans bear numerous receptors capable of recognizing the bacterial cell wall component lipopolysaccharide (LPS) ( Fenton and Golenbock 1998 ). Examples include the macrophage scavenger receptor, CD14, and the b 2 -integrins. Binding to these receptors induces a variety of responses, from the release of inflammatory agents to the phagocytosis of the LPS-carrying particle. Some of these receptors are membrane-bound and some are secreted. Interestingly, there are some that can exist in both forms, such as CD14. So here we have examples of receptors that do not rearrange, can be membrane-bound, secreted, or both, and can mount an effective immune response. Recently, a gene was discovered in the silkmoth Hyalophora cecropia whose expression is upregulated upon exposure to LPS ( Sun, Lindstrom et al. 1990 ). The gene product, a protein called hemolin, is secreted into the hemolymph (the invertebrate "blood") and can bind to the most toxic region of LPS ( Daffre and Faye 1997 ). This protein is also constitutively expressed in a membrane-bound form on the surface of hemocytes (the invertebrate white blood cell equivalents). Interestingly, the structure of this protein was found to contain 4 Ig domains, and is a member of the Ig superfamily ( Lindstrom-Dinnetz, Sun et al. 1995 ). Ig domains are a type of 3D protein structure first identified in immunoglobulins, consisting of 7 or 8 b -pleated sheets. Additionally, the crystal structure was recently solved and revealed a shape loosely similar to an immunoglobulin arm ( Su, Gastinel et al. 1998 ). However, sequence analysis shows that hemolin most likely does not represent a precursor to immunoglobulins as the type of Ig-domain it possesses (the I-set) is one not found in vertebrates. Hemolin does show similarities both structurally and functionally to cell-adhesion molecules, and also contains some cell-adhesion activity. This dual function, both for immune response and cell-adhesion, suggests that immune molecules arose from cell-adhesion molecule precursors. Hemolin is a clear example of an inducible immune molecule that can exist in both membrane-bound and secreted forms. Immunoglobulin signal transduction When an antibody recognizes an antigen, it sends a signal back into the cell, which "primes" the cell for activation. But what is the nature of this signal? How exactly does the binding of antigen, which occurs on the exterior of the cell, induce a signaling cascade on the interior? The answer lies in the branched nature of the immunoglobulin. As previously stated, immunoglobulins are loosely shaped like a Y, with two arms sticking out into the extracellular space, and the bottom embedded into the membrane. Associated with each Ig molecule are the two accessory proteins Ig a and Ig b . These accessory molecules have long cytoplasmic tails, and contain motifs specialized for attracting the type of kinases required to initiate the cascade. These motifs are called ITAMs ( I mmunoreceptor T yrosine-based A ctivation M otifs). These motifs serve as targets for protein tyrosine kinases, which phosphorylate certain tyrosine residues on the ITAMs. Because most antigens have multiple epitopes (i.e. multiple binding sites for antibodies), and because the immunoglobulins have multiple arms, the recognition of an antigen results in a clustering of immunoglobulins in the area of the membrane where the antigen comes in contact with the B cell (Figure 4). This process is often called crosslinking, and is the key to activating the cell. Visually, it resembles a "hands across America", where each arm of the Ig is linked to an arm of another Ig, and so on and so on. As more and more Igs cluster around the antigen, a family of kinases, called the src family kinases, which are loosely associated with the cytoplasmic tails of Ig a and Ig b , begin to phosphorylate the ITAMs. Because the src kinases bind to phosphorylated tyrosines, this sets up a positive feedback loop, and more and more src kinases are recruited to the site. The phosphorylated tyrosines also bind another kinase called syk. The newly bound syk kinase begins to phosphorylate and activate other syk molecules, which in turn phosphorylate and activate the next molecule in the signaling cascade, thereby propagating and amplifying the signal. The downstream components of this cascade are also expressed in other cell types, and are considered more general signal transducers. In this way, a general transduction pathway can be co-opted by more specific signal molecules. This leads to the activation of transcription factors (TFs), which then enter the nucleus and initiate the transcription of genes involved in cell proliferation and differentiation. In this particular situation, the B cell becomes "primed" for activation by T cells. Most of the "messengers", or components of the BCR signaling pathway are homologous to many other signaling pathways present in other tissues and in other organisms. For instance, one of the final components in the pathway is the activation of the transcription factor NF-


Evolving Immunity

Legacy route: /faqs/Evolving_Immunity1.2.html Evolving Immunity A Response to Chapter 6 of Darwin's Black Box By Matt Inlay Draft 1.2 - email author for comments and feedback created 5/31/02, last modified 6/03/02 Introduction Immune systems are generally characterized by their ability to distinguish between self and non-self cells, tissues, or molecules, and to eliminate the non-self ( Janeway 2001 ). The mammalian immune system is an incredibly complex and intricate system that can recognize non-self and provide protection from a wide variety of pathogens. While there is a high degree of interconnectivity between its components, the immune system can be loosely divided into two subsystems, the innate and the adaptive immune systems. In general, innate immunity is a non-specific, inducible response to pathogens. It is immediate in action, yet short-lived. On the other hand, the adaptive immune system is much more specific, but takes longer to activate. It also features immunological memory, and can augment itself to respond more quickly and with greater specificity to future infections of similar pathogens. Both systems work together to provide protection against a diverse and rapidly-evolving array of pathogens. While much is known about the evolution of the immune system, the details of its origin remain to be elucidated. The innate immune system is the more ancient of the two systems, with roots deep in the deuterostome branch of the bilaterians, roughly one billion years ago. Conversely, the adaptive immune system appeared more recently and quite suddenly, around 450 million years ago with the emergence of the gnathostomes, more commonly called the jawed vertebrates. Because of its high degree of complexity and interconnectivity, the mammalian immune system has been labeled as "irreducibly complex", and its evolution and origin through "Darwinian" mechanisms challenged [i] . Michael Behe, in his book Darwin's Black Box ( Behe 1996 ), defines irreducible complexity (IC) as: "[A] single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function." (page 39). Unfortunately, each of the terms "system", "well-matched", "interacting", "parts", and "function" can have multiple meanings, depending on the context, so nonarbitrarily labeling a system as IC is not an easy task. For instance, "system" in Behe's definition differs significantly from the same word in the context of "immune system". His use of "system" refers specifically to biochemical systems. What is the difference? The components, or parts of a biochemical system are molecular in nature, like proteins or complexes of molecules. "System" as is used in immune system refers not just to molecules, but to the cells and tissues involved in conferring immunity. The immune system as a whole contains numerous biochemical systems within it. It is important to note this distinction because Behe only addresses biochemical systems as IC. Systems, whether biochemical or not, are often defined according to their function. However, the term "function" is also nebulous. The "function" of the immune system is rather broad, encompassing any action involved in either immune recognition or response. Even the skin is considered to be part of the immune system. The "function" of a biochemical system is much more specific. Here, function refers to a specific biochemical function, such as the formation of a blood-clot, the spinning of a flagella to produce locomotion, or the synthesis of a biomolecule from a precursor. This type of function usually consists of a series of biochemical reactions. This is important because Behe is trying to make a specific argument about the origin and evolution of IC biochemical systems. Immediately after defining IC, Behe states: "An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." Behe is trying to suggest that because of the nature of IC, biochemical systems that possess this quality could not have evolved through random mutation and natural selection, or "blind-watchmaking". Essentially, Behe is using IC to disprove evolution. As an alternative, Behe suggests that the only way that IC biochemical systems could have originated is through intelligent intervention. He offers as evidence the fact that all IC systems whose origins are known were designed by intelligent agents, us. There are many problems with Behe's argument. Basically, Behe is saying that because we do not know how an IC system could have evolved, it didn't evolve. This type of argumentation is referred to as an argument from ignorance . The problem with arguments from ignorance is that they make a conclusion based on a lack of knowledge. There is still much we do not know about evolution. What seems like a conundrum right now may be easily resolved in the future. Biology, and science in general, is filled with mysteries and unknowns. The whole point of science is to seek answers to those questions. Secondly, he tries to use arguments against evolution as evidence for intelligent design. Negative arguments against one theory do not necessarily provide evidence for a particular alternative. It would be like trying to show how safe a Honda Civic is by providing evidence that a Toyota Corolla is unsafe. No matter how unsafe the Corolla is, it says nothing about the Civic. Negative argumentation is scientifically useless without an alternative that can be positively tested. These fallacies do not rule out the possibility that Behe has raised an interesting and useful challenge to our current understanding of evolution. However, a closer look reveals he hasn't. In chapter 6 of Darwin's Black Box , entitled "A Dangerous World", Behe outlines three IC biochemical systems in the immune system; clonal selection, V(D)J recombination, and the complement cascade. However, in his analysis of each of these systems, Behe makes critical mistakes. For the process of clonal selection, Behe targets the antibody molecules, which have the ability to rearrange their genes, and to switch from a membrane-bound form to a secreted form. Behe assumes that an antibody molecule missing one of these features would be useless. However, there are many examples of proteins that do not undergo rearrangement, but are able to switch forms. Additionally, there is a gene closely related to antibodies which can also undergo rearrangement, but does not switch forms. Behe neglects to mention either of these intermediate-like molecules. Instead, he scrutinizes the process of antibody gene rearrangement as the second IC system. He describes the numerous features of this system and claims there is no pathway through which it could have evolved. However, he assumes that the only selectable function for the genes involved in rearrangement is rearrangement. There are well-studied systems that bear remarkable similarity to V(D)J recombination that have nothing to do with immunity. He fails to recognize the existence of these other systems, nor realizes that most of the components of recombination are already present there. Finally, in his description of the third IC system, Behe mistakenly assigns a single function to the complement pathway. He fails to realize that the complement system has several different functions, and several mechanisms of activation. This would allow for a gradual, stepwise accumulation of parts and functions. In fact, many other groups of organisms possess a complement system that lacks his primary function. According to Behe's definition of irreducible complexity, those systems shouldn't exist. In each case, Behe claims that a lack of articles in the scientific literature provides evidence that these systems could not have evolved. However, there are hundreds to thousands of articles published on these systems. Much was known about the evolution of each of these systems at the time Darwin's Black Box was published. Additionally, much has been learned since then. This article will attempt to summarize the existing knowledge about the origins of these systems, and propose a possible pathway for their evolution through a Darwinian mechanism. It is not necessary to "prove" that these systems evolved. Because the essence of his argument is "how could this have evolved?", this article merely seeks to provide an answer to that question. One issue that will not be discussed is whether or not these systems are actually irreducibly complex. The term is not very useful to the discussion of origins because of the ambiguities surrounding its definition. In fact, IC as a term has failed to make much of an impression on the scientific community, as a search on the publication database PubMed, fails to turn up any references to "irreducible complexity" [ii] . IC system I: Clonal selection The first system Behe describes in chapter 6 is the process of clonal selection, which is how the adaptive immune system detects non-self molecules and initiates a response. This system focuses on a protein called immunoglobulin (Ig), and the complex it is part of, called the B cell receptor complex (BCR). Immunoglobulins, also called antibodies, are Y-shaped proteins that can recognize and bind foreign molecules (Figure 1a,b). They are produced by lymphocytes called B cells, and are initially expressed on the cell surface. In its membrane-bound form, an immunoglobulin molecule binds to two additional proteins, Ig a and Ig b , to form the BCR (Figure 1c). The target of an immunoglobulin is referred to as its antigen (Ag). Antigen can be essentially any molecule, though there is a preference for proteins. Because of the way in which immunoglobulins are produced, the specific antigen that each Ig recognizes is different in each B cell. This occurs through a process of gene rearrangement called V(D)J recombination, which will be explained later. When an unactivated, or na�ve, B cell's Ig recognizes its particular antigen, it sends a signal back into the interior of the cell to initiate activation. This signal is transmitted via a series of modifications through a series of "messenger" proteins, which ultimately trigger the transcription of a panel of genes involved in B cell activation. In order to become fully activated, further interaction with a second class of lymphocyte, called T cells, is required. Once the B cell is activated it proliferates and differentiates into a plasma cell, and the function of the immunoglobulin changes from recognition to response. The immunoglobulin switches from a membrane-bound form (mIg) to a secreted form (sIg), where it can diffuse throughout the tissues of the host organism and there bind its cognate antigen. The only difference between the two forms is at the very tip of the bottom of the Y shape, which corresponds to the very tail end of the gene. The switch from mIg to sIg production results from a switch between two alternative RNA splicing patterns, such that the terminal coding exon directs either the translation of a membrane-bound or soluble C-terminal domain, respectively (Figure 2). The process of amplifying a particular B cell (or subset of B cells) from amongst billions based on its antigen specificity is called clonal selection (Figure 3). This process allows the immune system to choose from which B cell (or subset of B cells) it will mount an immune response. Additional discussion of the clonal selection system in the context of irreducible complexity can be found in the web article: The Evolution of Improved Fitness (http://www.talkorigins.org/faqs/fitness/) Behe summarizes this first system as a group of 3 components (page 125): membrane-bound form of the antibody messenger secreted form of the antibody Behe has this to say about the evolution of the clonal selection system: "A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there's no way to tell if it's doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps." (Page 125) Switch forms or rearrange? So the question is, could the clonal selection system have evolved? Certainly. One thing to realize is that the immunoglobulins are not the only molecules that can undergo gene rearrangement to produce a diverse set of antigen-receptors. T cell receptors (TCRs) are antigen-receptors quite similar to immunoglobulins. However, TCRs exist only in a membrane-bound form, yet are able to carry out their particular function without the need to leave the cell surface. Their receptors are used only for the detection of foreign antigens, and do not directly mediate an effector response. So even if immunoglobulins would be unable to effectively carry out their job if they were restricted to the membrane-bound form, they could have evolved from a TCR-like gene, which does not require secretion. If that occurred, then the ability to rearrange and the ability to switch forms could evolve in separate steps, with each step offering a selectable advantage. It remains unclear whether a TCR-like gene appeared first or an Ig-like gene. However, it is also possible that the ability to rearrange came after the evolution of the alternative splicing pattern, resulting in the ability to switch. This would require that antigen receptors with a single specificity be effective mediators of immunity. Could this have occurred? Absolutely. There are several families of innate receptors that do not rearrange, called pattern recognition receptors (PRRs) ( Medzhitov and Janeway 1997 ). Bacteria possess many unique and essential surface molecules that are distinct from metazoan surface molecules. For example, organisms ranging from insects to humans bear numerous receptors capable of recognizing the bacterial cell wall component lipopolysaccharide (LPS) ( Fenton and Golenbock 1998 ). Examples include the macrophage scavenger receptor, CD14, and the b 2 -integrins. Binding to these receptors induces a variety of responses, from the release of inflammatory agents to the phagocytosis of the LPS-carrying particle. Some of these receptors are membrane-bound and some are secreted. Interestingly, there are some that can exist in both forms, such as CD14. So here we have examples of receptors that do not rearrange, can be membrane-bound, secreted, or both, and can mount an effective immune response. Recently, a gene was discovered in the silkmoth Hyalophora cecropia whose expression is upregulated upon exposure to LPS ( Sun, Lindstrom et al. 1990 ). The gene product, a protein called hemolin, is secreted into the hemolymph (the invertebrate "blood") and can bind to the most toxic region of LPS ( Daffre and Faye 1997 ). This protein is also constitutively expressed in a membrane-bound form on the surface of hemocytes (the invertebrate white blood cell equivalents). Interestingly, the structure of this protein was found to contain 4 Ig domains, and is a member of the Ig superfamily ( Lindstrom-Dinnetz, Sun et al. 1995 ). Ig domains are a type of 3D protein structure first identified in immunoglobulins, consisting of 7 or 8 b -pleated sheets. Additionally, the crystal structure was recently solved and revealed a shape loosely similar to an immunoglobulin arm ( Su, Gastinel et al. 1998 ). However, sequence analysis shows that hemolin most likely does not represent a precursor to immunoglobulins as the type of Ig-domain it possesses (the I-set) is one not found in vertebrates. Hemolin does show similarities both structurally and functionally to cell-adhesion molecules, and also contains some cell-adhesion activity. This dual function, both for immune response and cell-adhesion, suggests that immune molecules arose from cell-adhesion molecule precursors. Hemolin is a clear example of an inducible immune molecule that can exist in both membrane-bound and secreted forms. Immunoglobulin signal transduction When an antibody recognizes an antigen, it sends a signal back into the cell, which "primes" the cell for activation. But what is the nature of this signal? How exactly does the binding of antigen, which occurs on the exterior of the cell, induce a signaling cascade on the interior? The answer lies in the branched nature of the immunoglobulin. As previously stated, immunoglobulins are loosely shaped like a Y, with two arms sticking out into the extracellular space, and the bottom embedded into the membrane. Associated with each Ig molecule are the two accessory proteins Ig a and Ig b . These accessory molecules have long cytoplasmic tails, and contain motifs specialized for attracting the type of kinases required to initiate the cascade. These motifs are called ITAMs ( I mmunoreceptor T yrosine-based A ctivation M otifs). These motifs serve as targets for protein tyrosine kinases, which phosphorylate certain tyrosine residues on the ITAMs. Because most antigens have multiple epitopes (i.e. multiple binding sites for antibodies), and because the immunoglobulins have multiple arms, the recognition of an antigen results in a clustering of immunoglobulins in the area of the membrane where the antigen comes in contact with the B cell (Figure 4). This process is often called crosslinking, and is the key to activating the cell. Visually, it resembles a "hands across America", where each arm of the Ig is linked to an arm of another Ig, and so on and so on. As more and more Igs cluster around the antigen, a family of kinases, called the src family kinases, which are loosely associated with the cytoplasmic tails of Ig a and Ig b , begin to phosphorylate the ITAMs. Because the src kinases bind to phosphorylated tyrosines, this sets up a positive feedback loop, and more and more src kinases are recruited to the site. The phosphorylated tyrosines also bind another kinase called syk. The newly bound syk kinase begins to phosphorylate and activate other syk molecules, which in turn phosphorylate and activate the next molecule in the signaling cascade, thereby propagating and amplifying the signal. The downstream components of this cascade are also expressed in other cell types, and are considered more general signal transducers. In this way, a general transduction pathway can be co-opted by more specific signal molecules. This leads to the activation of transcription factors (TFs), which then enter the nucleus and initiate the transcription of genes involved in cell proliferation and differentiation. In this particular situation, the B cell becomes "primed" for activation by T cells. Most of the "messengers", or components of the BCR signaling pathway are homologous to many other signaling pathways present in other tissues and in other organisms. For instance, one of the final components in the pathway is the activation of the transcription factor NF- k B. This transcription factor is used in multiple tissues in a wide variety of organisms to transcribe numerous immune-related genes. The DNA sequence recognized by


Honesty in "Darwin on Trial"

Legacy route: /faqs/johnson.html Honesty in "Darwin on Trial" The Truth, the Whole Truth, and Nothing but the Truth? Why Phillip Johnson's Darwin on Trial and the "Intelligent Design" movement are neither science�nor Christian by Brian Spitzer DRAFT, Version 1.1 email author for comments and feedback [Contributed July 15, 2002; Last Modified: July 18, 2002] Introduction Darwin on Trial Lawyer games Just the facts, ma'am How science isn't done Did they really say that? Colin Patterson Steven Jay Gould Nature on the British Museum of Natural History Tricks of the trade Distortions and inventions The tautology argument The missing links which aren't, and other examples The log in your own eye Selective use of evidence The moving target Johnson's response Conclusions Additional examples Bait-and-switch Selective use of evidence Ad hominems and innuendo Misrepresentations of science Quote mining Begging the question "Straw man" arguments Conspiracy theory Introduction Lawyers are not the best-respected professionals in our society. Being a lawyer gives one a certain prestige because law requires expertise, like medicine or science, but we tend to put lawyers in the same shady box as salesmen and politicians. We don't trust them. And�perhaps�there are good reasons not to. Courtroom lawyers are called upon to represent the guilty as often as the innocent, and they are duty-bound to build the best case that they can. It follows logically that a courtroom lawyer will spend half of his or her time trying to convince a jury of the truth; the other 50% of the time, they are trying to persuade the jury to believe something which isn't the truth. This is not only permissible in the courtroom, it's necessary for our justice system to work. It's ironic that a system of justice requires what could be called 'injustice' from its participants, but that's what the law demands: lawyers playing parts which they may not even believe. Our law dictates that even the guilty should be represented in court, and most of us would agree that this curious tangle of competing fictions turns out to make our justice system more just. Because of this, it is entirely acceptable for a lawyer to play his or her false part in court, just as it is acceptable for an actor to play someone fictional on the stage. But when people assume false identities offstage, we call them impostors. I would argue that when a lawyer plays lawyer games outside the courtroom, it is just as morally wrong. Of course, you can't have a debate without having debating tactics. It's entirely fair, inside the courtroom or out, to showcase the facts that are most favorable to you. In the same way, it's perfectly fair to write a radio ad pointing out that your brand of widgets is cheaper and more reliable than your competitor's�if those favorable facts are actually true. But we're all aware of sleazy sales pitches where the tactics are used to obscure or distract attention from the relevant facts. I am not claiming that the line between these two is crystal-clear. But I am claiming that those who try to sway public opinion�especially if they are laying claim to the moral mantle of Christianity�are ethically bound to stick to the fair methods and leave the lawyer games in court. Back to top 1. Darwin on Trial Darwin on Trial , the book by Phillip Johnson which founded the neocreationist movement of "intelligent design", was written in 1991. I first encountered it in 1996. At the time I knew nothing at all about creationism. A friend-like me, a serious Christian as well as a scientist�suggested that I take a look at it, and I was curious enough to do so. There are certainly things about the book which I applauded, at the time. I've always been irritated by pop-science works which try to make statements about God (or the lack thereof) as though these statements are supported by scientific fact, and I was glad to see someone taking on Richard Dawkins. But even without much training (I had only a B.A. in biology), while reading through Johnson's book I began to notice some puzzling things. At first, they were quite small: a claim in one place which contradicted a different claim in another. A strange lapse of logic-perhaps excusable on account of the author's inexpertise? Statements which didn't fit with what I knew firsthand about science and scientists. I was naive. I assumed that a Christian writing to other Christians would provide a scrupulously fair and accurate account of the facts [1] . But the deeper I got into Darwin on Trial , the less naive I became. And the clearer it became that the driving force behind Johnson's book was neither fairness nor accuracy. A few years passed with this troubling thought at the back of my mind. I entered graduate school and started doing real science myself. And, the more I learned, the less I trusted Darwin on Trial . I finally challenged myself to put my mistrust to the test. Perhaps Johnson was merely confused about some things. What I should do, I told myself, is look at the sources he actually used in writing Darwin on Trial , and see what they say. Perhaps part of what Johnson says is accurate; perhaps his sources misled him in places. So I went to the campus library and started checking his claims. I was a lot less naive when I finished that task. I found that almost every scientific source cited by Johnson had been misused or distorted, in ways ranging from simple misinterpretations and innuendos to the construction of what appears to be outright fiction. The more closely I examined Darwin on Trial , the more inaccuracies I found, until it became almost impossible to catalogue all of the misleading statements in Johnson's work. This book-upon which the "intelligent design" movement is trying to hang a program of social reform and public education-is perhaps the ugliest and most deceptive book I have ever seen. It may seem irrelevant to critique a book over a decade since it was published. But Darwin on Trial was the work which founded the "intelligent design" movement, and Phillip Johnson is still regarded as the "godfather" of that entire school of thought. Later "intelligent design" creationists have adopted many of his exact arguments, as well as many of the questionable tactics and strategies used in Darwin on Trial . Perhaps most importantly, nobody in the "intelligent design" movement has, to my knowledge, ever criticized or disavowed any of the claims in Darwin on Trial . As I will show, this book is so full of questionable tactics that it would be hard for any informed reader not to notice any of the inaccuracy. All of the stars of the "intelligent design" movement, by their silent approval of these tactics, stand under a cloud of suspicion at the very least. Many Christians have welcomed the "intelligent design" creationists in the belief that they are fighting for God and truth. But, as the televangelism scandals of the 1980's should remind us, there are some more unsavory reasons for seeking celebrity in the Christian community: money, fame, applause, or power, especially political power. In short, there are a wealth of reasons why Christians need to be careful about trusting the stars of the "intelligent design" movement. And even well-intentioned debaters, if they let their desire to win the argument outstrip their respect for the facts, will turn out a product which is grossly misleading. Integrity is important. If�as I will show in this essay�the claims of "intelligent design" are more a product of debating tactics and tricks than they are a fair and honest presentation, Christians need to seriously consider whether they can support this movement in good faith. Back to top 2. Lawyer games To understand a lawyer's book, talk to another lawyer. Darwin on Trial has been reviewed by, among other people, a practicing lawyer by the name of Thomas C. Sager. In his review, Sager makes some very interesting points about the legal profession which he and Johnson share. He puts it succinctly: "The job of a lawyer is not to find the truth, (that is the job of the judge or jury) but to defend (or prosecute) the client.... The standard is to vigorously argue on behalf of one's client, rather than to pursue an abstract 'truth' or even 'justice'." Sager goes on to note: "In supporting the client, the lawyer may use any ethical means available. It is perfectly ethical for a lawyer to make ad hominem attacks on the opposing witnesses, to present incomplete information to a jury, to bring in irrelevant data, and of course to use a wide panoply of rhetorical skills and tricks. Science, obviously, has different goals. But the lawyer's orientation should be kept in mind when analyzing Johnson's book, because he is a lawyer, he has titled his subject a trial, he pursues it as a trial, and his job is to prosecute Darwinism. Lots of things are 'fair', from his point of view." [2] Johnson might protest that none of these tactics� ad hominem arguments, half-truths, and rhetorical sleight-of-hand-are technically lies . I am not interested in quibbling over fine shades of meaning in such definitions; in my view, deliberately misleading people does not become more acceptable because it goes under a different name. To a certain extent, it does not even matter whether these inaccuracies are deliberate or not. If Johnson is being intentionally misleading, that is an ethical and intellectual crime. If he is merely letting a desire to attack evolutionists override his concern for careful and accurate research, that indifference to fairness is also a crime, though a lesser one. In either case, Darwin on Trial cannot safely be trusted at face value as a guide to the facts. Back to top 3. Just the facts, ma'am Phillip Johnson, perhaps even by his own admission, is not terribly interested in facts. Indeed, the heart of the argument against evolution which is presented in Darwin on Trial �and echoed throughout the "intelligent design" movement up until the present day�is that science isn't actually about facts. According to Darwin on Trial , it's about "ideology." The accusation is that evolutionary scientists are all hopelessly biased, wedded to an atheistic ideology, and that the only reason they support evolutionary theory is that they need some way to explain the marvels of biology without bringing up God. This is a clever strategy, because a number of well-known and outspoken scientists are in fact atheists, and the Christian community in America has long had a vein of simmering resentment against a few individuals, like Richard Dawkins, who have preached atheist ideology while calling it science. Johnson taps into this vein skillfully, claiming that "Darwinism" is not only the view that natural forces created biology as we see it today, but also the insistence that God is a mere fable, uninvolved in evolution or�for that matter�anything else. The problem is that this argument isn't true. The truth is that biologists are overwhelmingly convinced that the theory of evolution really does explain the natural world accurately. That's why they support it, not some "ideology." Johnson and the other "intelligent design" creationists are aware that a large number of evolutionists maintain a deep faith in God. However, if the "intelligent design" creationists acknowledged them, they would have to admit that there are other reasons besides ideology to agree with the theory of evolution. Their strategy has been to deny that these people exist. A Gallup poll conducted in 1982 [3] found that only about 10% of Americans think that "Man evolved over millions of years from less developed forms. God had no part in this process." 90% of us, then, reject "Darwinism" as Johnson defines it, and the "intelligent design" creationists are fond of quoting this statistic. What they avoid mentioning is the other half of the poll, in which Gallup went not to the average American but to the average American scientist. About 40% of scientists declared their belief in both evolution and in an actively intervening God very much in control of the process. Either 40% of the scientists in America are fighting tooth and nail in defense of an ideology which they actually reject , or-based on the very poll which Johnson likes to cite-Johnson's argument about ideology is bunk. There is plenty of other evidence suggesting that Johnson should know this argument to be just that: bunk. Upon reading through the sources cited in Darwin on Trial , I found that the distinction between science and atheism was drawn quite clearly on a number of occasions It is made repeatedly by theologian Langdon Gilkey ( Creationism on Trial , pp.34-35, 97, 175-176) [4] and scientist Douglas Futuyma ( Science on Trial , p.217) [5] , both of whom are cited by Johnson. While Darwin on Trial points out that evolutionists like Dawkins, Julian Huxley, and Steven Jay Gould claim or imply that God is dead, it neglects to mention that all these figures have been criticized harshly and publicly by evolutionary biologists for muddying the line between scientific conclusions and metaphysical preferences. Johnson has a ready excuse: he claims that any time scientists say that they are not atheists, it is only to fool the public�or, as he puts it in one of his nastier moments, "for fear of jeopardizing the funding for scientific research" (p.127). However, Darwin on Trial gives no evidence to back up this accusation. That's because no such evidence exists. If Johnson wants to convince us that his accusations of atheism are not just conspiracy theory, he has had plenty of opportunity to do so. Several reviews of his book have criticized him for pretending that the personal views of a few inflammatory scientists are the consensus view of the scientific community, but Johnson has made no attempt to correct his claims or provide evidence for them. To my knowledge, neither have any of the other leaders of "intelligent design" creationism. There can be no denying it: stereotypes are rhetorically handy. But they aren't honest. The attempts by a few scientists to clothe their personal philosophies in the authority of science are certainly deplorable, and I believe that Christians are right to deplore them. But is the correct response to meet one mistruth with another? The way science works�methodological naturalism, to call it by its highbrow name [6] �is to try to explain the world in terms of ideas which can be empirically tested. The tests can be experimental, or one may posit an hypothesis and then look for those empirical signs which would follow logically if that hypothesis were true. Johnson's strategy is to claim that this is the same as atheism (see, for example, pp.116-117 of Darwin on Trial ). This argument does not stand up for long under scrutiny. We may not call it by such an elaborate name, but when a plumber tries to find out why your sink is clogged, or when police try to solve a crime, or when an engineer tries to design a bridge�in fact, whenever anyone tries to figure out pretty much anything about the physical world we live in�they are using methodological naturalism. You yourself use it every day. So do the "intelligent design" creationists. Scientists aren't precommitted to atheism. They're precommitted to a scientific method that can actually work. The only alternative to methodological naturalism�that is, to trying to understand the world in terms of ideas which can be empirically tested�is to try to understand the world in terms of ideas which can't be tested at all. See if you can unclog your sink that way. Johnson should, by now, be painfully aware that this argument does not hold up. He has been challenged clearly and publicly (for instance, by Robert Pennock) [7] to present a working alternative to methodological naturalism. Despite the fact that he has had over a decade to work out a method for what he calls "theistic science", Johnson has had nothing to say. Writes Pennock: "This is not surprising, for he has consistently refused to say anything positive about how a theistic science is supposed to work." If Johnson really feels that scientists have other options�if we really do have a choice other than methodological naturalism in science�he should give us a hint about what those options are. Until the intelligent design creationists explain to scientists what other methods they could be using, I find it very hard to blame the scientists for considering methodological naturalism to be a limited but indispensable tool. Back to top 4. How science isn't done Darwin on Trial misrepresents science just as it misrepresents scientists. Johnson seems to suggest that any event which has not been directly observed may be dismissed as "pure philosophy", but inferential evidence-as he should know from law-can prove a point as well as direct observation. Essentially all modern science, including particle physics, astrophysics, geology, microbiology, and chemistry, relies on inferential evidence. He claims that scientists disagree over "every detail" of evolutionary theory, but Douglas Futuyma, on p.171 of Science on Trial (again, a book cited in Darwin on Trial ) explains accurately and clearly what is and is not in dispute in the scientific community. On p.30 of Darwin on Trial , Johnson dismisses evolutionary mechanisms such as developmental constraints and pleiotropy�despite the fact that they are proven, genuine mechanisms that are not only compatible with Darwinian theory but are practically logical outgrowths of it. Darwin on Trial claims on pp.72-73 that, because developmental processes are different in different classes of tetrapods, the resulting traits cannot be homologues of one another; but this is only true if evolution adheres strictly to the principle of recapitulation [8] , a principle which was rejected decades ago by modern science. It suggests on p.80 that Archaeopteryx is just a mosaic along the lines of the platypus (it isn't); suggests on p.94 that the isolation of present-day taxa is at odds with the theory of evolution (this is incorrect); and on pp.95-96 claims that neutral theory is incompatible with Darwinian theory (a conclusion soundly rejected in at least one paper actually cited on the subject in Darwin on Trial ) [9] . After examining the sources which Johnson himself used in writing Darwin on Trial , I find it very difficult to understand how a writer with a serious concern for fairness could have reached the conclusions which are stated in Darwin on Trial . Serious misunderstandings of science pervade Darwin on Trial . For example, Johnson suggests that all scientists stick to the Darwinist party line out of self-interest�apparently unaware that scientific careers are made not by conformity but by coming up with radical new ideas. Any working scientist could have told him that. He does not understand basic scientific terminology (such as the word "tentative", for example, an error which he has not corrected even after being informed of it), or how the "self-correcting" nature of the scientific enterprise works. Many of these misunderstandings are so basic that Johnson seems to have done little or no research on the topic. In short, rather than do the work involved in understanding how science actually works, Johnson apparently made up a picture of modern biology which he finds useful for rhetorical purposes. Is this really the sort of work on which a true intellectual movement can be founded? Is this the sort of ethics with which the Christian community wants to ally itself? Back to top 5. Did they really say that? a. Colin Patterson Most damning of all is the way in which Darwin on Trial represents the views of other individuals. In several cases, Johnson cites the published opinions of scientists on various matters; it is therefore possible to set his book side-by-side with the original statements and see if they match up. Time and time again, they do not. Even on a generous reading of t