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Signature in the Cell is a 2009 intelligent design book by Stephen C. Meyer. In order to inspire himself to finish his review of Meyer's book, Nick Matzke is typing his review/commentary into this page.

Links to reviewsEdit

Matzke's review: Of Revisionism and Repetition: Creationism, the Origin of Life, and the Origin of 'Intelligent Design'Edit

IntroductionEdit

The origin of the first life has been a major scientific puzzle ever since the question became distinct from the origin of species (and of the planet and universe). This distinction only became really obvious and important in the 19th century, after geologists had established the great age of the earth, Darwin and other biologists showed that extant species shared common ancestry, and Pasteur finished off spontaneous generation (a conclusion supported by Darwin; Lazcano et al. 2009). Except for his "warm little pond" speculation in a private letter, Darwin thought the problem basically insoluble in his time ("one might as well think of the origin of matter") and seems to have been reasonably content to leave the terra incognita to the special creationists for the time being. Of course, later scientists were attracted to the problem, and throughout the 20th century research into the topic the origin of life gradually accelerated, so that what was an almost imponderable mystery at the beginning of the century had become a vigorous empirical research field 100 years later. In the 21st century, the field appears to be moving from strength to strength, with progress being reported each year.

Surely, we are well past the point where the special creation is a serious contender as a scientific explanation for the origin of life. Or are we? Obviously, there are still plenty of fundamentalists about -- a great many in the general public, and a few amongst scientists (though usually engineers), although virtually none in the relevant scientific specialities, unless you count those with positions at Bible Colleges. But these are typically people who are so committed to Biblical inerrancy that they think that the Earth is only thousands of years old ("young-earth creationists", or YECs). Or, if they deign to accept the findings of geology and invent some improbable hermeneutic that reconciles Biblical inerrancy and the old earth -- I am speaking here of the "old-earth creationists", or OECs -- then they still deny common ancestry. This latter group will assert, proudly (Ross 200x) or somewhat quietly (the ID movement) that God has miraculously intervened thousands or millions of times in the history of life, specially creating each major group or "kind" of organism. (Although these groups are supposed to be totally distinct and separated by gaps far too large for evolution to cross, creationists have had no success in rigorously defining the created kinds -- see Scott & Matzke, 2007.)

So, does fundamentalist/creationist/intelligent design advocacy of special creation for the origin of life count as serious academic opposition to the mainstream? Not really. Creationists who deny the age of the earth or common ancestry are so far off the scientific map, and engage in such drastic mistreatment of scientific data to defend their conclusions, that it is reasonable for most scientists to simply dismiss them as cranks and be done with it. They have shown such unreasonableness on so many issues already that they have effectively lost the right to be taken seriously as participants in serious academic discourse on topics like the origin of life. Life is short, so unless one is engaging in the public service of debunking creationists for the purposes of public education or defending good science education policy -- a valuable form of public service, it should be said -- many will be satisfied to note that, on something like common ancestry, the evidence is in, it has been presented in accessible summaries ( Theobald, Prothero, Matzke hominids), and the creationists are wrong and flagrantly so. Thus, arguing about the origin of life with them is like arguing about the causes of the fall of the Roman Empire with someone whose historical judgment is so poor that they think the moon landings were faked. Once this decision is reached, there is nothing further for scientists to do but send our annual donation to the National Center for Science Education and be done with it (full disclosure: I was an employee of the NCSE from 2004-2007).

Zen and the Art of Analyzing and Rebutting Creationists Edit

Perhaps, though, despite everything, one wishes to persist and engage creationists on the origin of life question -- for purposes of public education, for instance, or out of perverse instinct to defend truth, or an idealistic (actually naive) notion that despite their sins, the creationists deserve the benefit of the doubt, or out of sheer bloody-mindedness. In these cases, the unsuspecting academic can rapidly encounter fundamental difficulties that they might not suspect based on regular academic discourse. It is easy for academics to forget this, but words and phrases that mean one thing in an standard academic discussion can mean something substantially different in the head of a creationist. Examples are legion (Rosenhouse 2010), but the case on point is the phrase "origin of life." In an academic context, "origin of life" generally refers to the long series of events that led to the origin of the common ancestor of extant life. But the creationists not only don't believe in a natural origin of the first life, by and large they don't even believe that life traces back to a single supernatural origin. They have no truck with the idea that life's ancestry resembles Darwin's Tree of Life, or Gould's refined metaphor, the bush of life (Gould 198x), or even Doolittle's model of a tree of life with a network of gene-trading unicells representing the Last Common Ancestor. Instead, creationists think that the ancestry of life resembles not a tree but a forest, with life having thousands of separate supernatural origins, one for each of their scandalously poorly-delineated of "kinds" or "basic types." In other words, one can argue with the creationists about the origin of the first life, but any such standard academic argument will draw on a great deal of inference about the Last Common Ancestor and the capabilities of the natural evolutionary processes that got life from the earliest proto-replicators to the Last Common Ancestor -- and the creationists have no truck with those inferences in the first place.

Similar difficulties occur with other crucial topics -- e.g., the meaning of the term "information", creationists' incompetent understanding of probabilities and their calculation, and their wildly inconsistent rules of inference. On top of that can be added creationists' essentially universal inability to fairly review and summarize the scientific literature on any particular point. Thus far it may sound like I am arguing that even if one decides to spend time rebutting the creationists, the task is pointless because there is no common ground on which to have a discussion. Though there is much truth in all of the above, there are some reasons for spending some time to review creationist arguments, even those pertaining to remote and technical topics like the origin of life.

First, and most importantly, there is always the bare possibility, however unlikely, that generations of experts are have missed something crucial, and the creationists have somehow stumbled on something truly brilliant and scientifically revolutionary somewhere in their "conferences" (apologetics seminars) and "research" (trade books and articles, predominantly published by evangelical presses). Maybe this is like hoping pigs will fly, but some scientist, somewhere, should occasionally look into the reports of pigs flying, just to make sure they aren't.

Second, while rebutting creationist arguments is unlikely to convince the committed creationists to change their minds -- the best a really skilled opponent of creationism can usually do is embarrass a creationist enough to shut them up for awhile on a particular issue -- there is some value in having rebuttals to creationist arguments assembled and in print somewhere. There are great many people amongst the general public, and a fair number in academia, who are not rigid creationists, but who have some initial sympathy for creationist arguments, especially those of the vaguer-sounding "intelligent design" sort. The sources of this are diverse. Some have a religious background and think of ID, innaccurately, as a compromise between the extreme fundamentalists and atheists who dominate the news. "I agree it's silly to think that dinosaurs lived with humans like in The Flintstones, but I believe in God, so I must like ID!", they will say to themselves. Some philosophers -- Thomas Nagel and Jerry Fodor are recent examples -- have idealistic and dualist tendencies, and are opposed to the reductionist tendencies found in much (but by no means all) evolutionary science. Many people have an almost instinctive sympathy for the "fairness argument" (Scott 2008) -- the notion, particularly prevalent in America, that if there appears to be an argument going on, and both sides have advanced degrees and use big technical words, then the truth must be somewhere in the middle, or at least both sides deserve a place in news coverage and classrooms -- whether or not the advanced degrees are in the right areas, whether or not one of the sides understands the big technical words, and whether or not the actual academic state of affairs has all of the relevant actual experts on one side of the question. And finally, there will always be a few academics that are just contrarians, inclined to doubt the mainstream view out of postmodern fervor, sheer bloody-mindedness, or (most commonly) simply because they developed their opinion of ID without reading and interacting with the really detailed, devastating critiques that already exist (e.g., see the literature references in Scott & Matzke 2007).

Thomas Nagel, a well-known philosopher, provides an example of several of the above tendencies. His main entry into the ID issue was a critique of the Kitzmiller decision (Nagel 2008) -- a critique based mostly on a reading of the bare decision, without any followup into wealth of science and history referenced in the trial testimony and in the evidentiary exhibits, or any of the numerous detailed works of the experts who testified against ID -- Miller (), Padian (), Pennock (), and Forrest (), for example. It is as if Nagel heard somewhere that the Kitzmiller decision was the definitive rebuttal of ID -- which is true in some senses and not others -- but then mistakenly assumed that a court decision is the kind of document that would, by itself, answer all of the questions, introductory and advanced, that might occur to an academic philosopher with little prior experience in the previous 30 years of the battle between evolutionary science and creationism. The resolutely cynical and skeptical view that many academics have of ID/creationism has been developed through decades of hard experience in correcting creationist arguments, only to see them rise from the dead again and again with only cosmetic alterations. Those new to the issue do not have this experience, and are sometimes led astray by the rosy picture, bold assertions, and breezy confidence exhibited by creationists. Sometimes their skepticism of the mainstream view is heightened when they find that whatever single anti-creationist publication they happen to pick up, usually a nontechnical work aimed at a nonspecialist audience, does not answer all of their questions. For people like Nagel, at least, it is valuable to make available hard-hitting critiques of the latest prominent creationist publications. Even if they cannot be bothered to get up to speed on the ID/creationist issue before publishing on it, at least they can be corrected in prominent venues. Hopefully this will improve their arguments in later works, and also be of benefit to other readers.

Everyone makes mistakesEdit

A third reason to give some serious attention to the project of rebutting creationist arguments is that, while the case is overwhelming that the creationists are basically wrong, this does not guarantee that every argument made against the creationists is the best available. There are many potential sources of error. The science involved can concern pretty esoteric regions of evolution and biology, and there is no guarantee that even eminent scientists will get all the details correct, if they have not made a specific study of the topics in question. One example involves the bacterial flagellum and the eukaryotic cilium. Both are structures that stick out of cells, wiggle in some fashion, and thus produce swimming. Michael Behe, and creationists before him (Scott & Matzke 2007), claimed that these structures that were "irreducibly complex" and thus could not have evolved in a stepwise fashion, and therefore must have come together all at once in some miraculous event. Unfortunately, a number of scientists commenting on the issue for popular publications (Pigliucci, Coyne, Wilson) have gotten the bacterial and eukaryotic structures mixed up, even though the eukaryotic structure is 20 times larger, is built out of entirely different (non-homologous) proteins, operates on fundamentally different principles (undulation rather than rotation), and has entirely different evolutionary relatives. Part of the problem is that the eukaryotic structures have a number of names in the scientific literature, including cilium, undulipodium, kinetosome, and, for maximum confusion, flagellum. This has created confusion for generations of introductory biology students, but also evidently for some professors. Obviously an anti-ID treatise loses a bit of authority if the IDist seems to know the differences between the flagella, and the ID skeptic doesn't. The problem is not universal: Kenneth Miller, for instance, the lead scientific witness against ID in Kitzmiller, and a cell biologist, always gets it right.

Perhaps this example is trivial, but more serious problems can occasionally be found by an alert reader. For example, Prothero's book on the fossil evidence for evolution (Prothero 2007) is truly excellent. It is undoubtedly the best, most systematic review of the fossil evidence for the general public produced to date. But flaws can be found. For example, Prothero endorses Margulis's endosymbiotic hypothesis for the origin of the eukaryotic cilium, which proposes that the cilium descends from a free-living spirochete bacterium. Margulis has heavily promoted her hypothesis in a variety of professional and popular publications (Margulis 1967, 199x, 200x), and gained endorsement in general works by a number of scientists (Sagan, Maynard-Smith, Maynard-Smith and Szathmary, Prothero). But the actual relevant experts have leveled devastating criticisms that have never been answered (Cavalier-Smith 1987, 199x), and none of Margulis's specific pieces of evidence claimed in support of the hypothesis (i.e., that the core cilial protein, tubulin, is found in spirochetes) have held up. Instead, core cilial proteins are all homologous to the mitochondrial apparatus, as long predicted and explained by the endogenous theory for the origin of cilia (Cavalier-Smith, Satir, etc.). Regarding the bacterial flagellum, several popular publications (Science, Ayala, Avise) have endorsed a highly flawed paper which proposed that the flagellum was reducible because all flagellar proteins descended from a single common ancestral protein, even though this conclusion was based primarily on an error (failing to enable a low-complexity filter in protein homology searches, and failing to correct their statistical test for homology for the fact that conducting thousands of tests increases the probability of random false positive hits by thousands of times). Again, the experts in the specialty in question (Snyder, Pallen, Doolittle) and the real wonks of ID criticism (Miller, Matzke) get it right, but they have less of a megaphone, so the mistake can propagate in the anti-ID literature.

Scientific details are difficult, and it should not be surprising or unduly worrying that errors creep in occasionally, especially when the arena of argumentation is all of biology. They will eventually get corrected in due course. More concerning are the sorts of errors that occur when critics of creationism commonly, and often unconsciously, share some premise with ID advocates that is debatable or mistaken.

The "Appearance of Design" is debatableEdit

A prominent example of a debatable premise is the notion that many biological structures exhibit the "appearance of design." This is emphasized most famously by Dawkins in his popular polemics against creationism and the Paleyist Argument From Design (Dawkins 1986, 1996), but also by a wide variety of other evolutionists (Crick, Simpson), in a strong tradition going right back to Darwin. Dawkins, for his part, has an agenda beyond explaning how natural selection accounts for the appearance of design: Dawkins says in addition that the Argument From Design was the best argument that the theists ever had, and thus by defeating the Design Argument, Dawkins claims to defeat God as a serious intellectual proposition. Dawkins is thus out to fry a much bigger fish than one might initially think.

Strangely, a similar argument is also popular with those with theistic evolutionist sympathies (Ayala, Avise, Miller, Conway Morris). For them, natural selection also shows how you can get "design" without an immediate designer -- but they will maintain, nonetheless, that the design is real, and suggest that evolution could have just been God's method of enacting it (although they will correctly hasten to add that this is a theological view, not a scientific position). One advantage of this position, from their point of view, is that common difficulties for the theist position, i.e. the existence of bad, incompetent, or even malicious designs, are caused not by the direct creative intention of God, but as a by-product of God's general decision to produce creation through the action of natural law. This does not by itself solve the famous problem of evil, but it does seem to make it less acute. (Somewhat flippantly, one is tempted to describe this as the "At least it's not personal!" view of natural evil.) Furthermore, this view allows for a solution insofar as theologians can provide arguments about why a good God would allow the action of natural laws to sometimes produce evil results, which is a question that theists of all stripes, special creationists included, have to deal with, due to the manifest existence of earthquakes, tornados, etc.

So, there are theological/atheological reasons why some scientists emphasize "appearance of design" language. But even those who are not grinding those axes will sometimes emphasize "appearance of design" -- perhaps to emphasize their wonder about some fantastic adaptation in of biology, perhaps to explain the history of evolution and natural selection and how it overturned Paley's Design Argument (although it was already on the way out -- xxx), and perhaps just because they think that's the way everyone has always thought about it. But there are some reasons to be skeptical of the whole "appearance of design" language and framework. First, it is well known in certain evolutionary circles (macroevolution, Gould) but often not others (behavioral biology, biomechanics, biomimetics, parts of biochemistry) that "design" terminology and thinking leads to a number of mistakes and quandaries in biology -- panadaptationism, anthropomorphism, and a habit towards unintended and easily-misunderstood teleological language (Gould, Mayr, etc.).

Second, as Ruse and others have pointed out, it just isn't historically true to say that human views of biology have all been dominated by the alleged "appearance of design" in living organisms. The prominent counterexample Ruse points out is the tradition of idealist morphology and comparative anatomy, as represented by e.g. Goethe (and Cuvier?) and other continental figures. (This tradition emphasized the "Unity of Type" -- i.e. homologous structures -- shared between organisms. The patterns are not immediately viewable as adaptations to the organism's immediate "Conditions of Existence", as Owen pointed out -- and thus there is no immediate need for either a Design-for-function or natural selection explanation for these similarities. At the end of chapter x of the Origin, Darwin famously -- or at least it should be famous -- synthesized Unity of Type and Conditions of Existence, by using common ancestry to explain homology and natural selection to explain adaptation or "analogy".) Biologists heavily influenced by this tradition, even prominent "Darwinians" such as T. H. Huxley, and Dobzhansky, did extremely important Darwinian biology, but without giving prominence to rhetoric about "design."

Third, it is far from clear that the "appearance of design" viewpoint of biology is any kind of "primitive" or "obvious" observation that human societies have made. There is a strong argument to be made that "design" or "appearance of design" characterizations of biology have only been popular in highly specific cultural contexts -- notably, those cultures which for other reasons have become familiar with and fascinated with machines, and with a mechanistic view of nature, and with making a "scientific" argument for the existence of God. Of course the obvious example of this is the early scientific revolution, particularly in England, and particularly as influenced by Newton, Harvey, etc. Even in the European culture, we have the counterexample of the morphologists, mentioned above. For many other cultures at other times, "appearance of design" does not appear to have been at all obvious. I have yet to see any strong argument that it appears in the Old Testament or New Testament, for example, despite the fact that it goes without saying that Biblical authors thought that God created animals and plants. The concept of "machine" simply isn't present, and thus there is no basis for viewing organisms as having machine-like qualities that require explanation in engineering terms. Similarly, inspection of the origins legends of various tribal, non-technological cultures seems to reveal no tendency towards viewing organisms as machines that thus had to be "designed." Organisms may well have been "made" by someone, just as humans make clay figurines, for instance, but they are not machines or tools, even though they may have use for humans. And such legends are equally likely to attribute the origin of organisms to a birthlike process -- sex and birth being much more obvious similarities between human and animal experience. And other possibilities exist -- the origin of animals and plants may be viewed as not fundamentally different than the origin of inorganic nature. Or animals and plants will be interpreted in personal and psychological terms -- having spirits, personalities, thoughts, intentions, and perhaps even the ability to speak, either literally, in some stories, or at least metaphorical "speech" or the conveyance of messages to those humans wise enough to listen.

The point can be made even more strongly when it is realized that it is not even clear that the "appearance of design" view of biology is altogether superior to the various prescientific alternatives mentioned above, even in a modern scientific context. The primitive concept of "birth" has profound application throughout biology, beyond organismal birth. We have computational birth-and-death models for understanding phylogenies and gene families, for instance, and of course the concept of replication is fundamental to everything in biology. The primitive view of organisms as having personalities and intentions is (a) often literally true, in the case of animals with reasonably complex nervous systems, (b) metaphorically true for organisms that can learn different responses to different stimuli, conscious or not, and (c) metaphorically true as a characterization of the different behaviors of different species. It is true that there is scientific danger in anthropomorphizing organisms, but it is also true there is danger in not doing so. If you were stranded in Alaska and surrounded by grizzly bears, which would be more useful to you: a mechanistic understanding of bear neurochemistry, or a knowledge of which bears were feeling hungry, protective of young, or otherwise aggressive?

Finally, the "appearance of design" terminology has the problem of simply being confusing. What scientists like Dawkins really mean when they say that biology, or at least some biological adaptations, have the "appearance of design", is not that that biological objects look exactly like objects literally designed by humans. Rather, they mean to say that some similarities are shared with human-designed objects, namely the fit of form to function. Furthermore, they obviously don't mean to say that biology "appears designed" to everyone -- rather, they mean that biology appears design in a superficial sense, to someone who is not informed of the immense body of fact and theory known to evolutionary biology. The whole point of the argument of Dawkins and numerous others is that, once one if fully informed, biology does not, in fact, "appear designed" in the literal sense that human artifacts "appear designed." Rather, as I have said elsewhere (Matzke 2006?), what "appearance of design" scientists are actually saying is that biology "appears designed" in the same way that the Earth "appears flat." The earth only "appears flat" from a very limited, particular perspective of certain naive humans. Once the full picture is in view, the appearance disappears.

None of this is meant to argue that "appearance of design" language necessarily should be completely abandoned in all contexts: that is a stronger position than I need to take here. All we need for the moment is to understand that a large part of science is about understanding the familiar by analogizing it to the familiar. All analogies used to describe biology have strengths and weaknesses; the key thing is that these are understood by conversants. In particular, the design analogy should not be overemphasized relative to others available, both those mentioned above and others (such as Woese's analogy of organisms as eddies in an energy flow (Woese; Scott & Matzke). The losability of context should be actively avoided, e.g. by the "appearance of flatness" comparison. Because of history and because of its involvement in metaphysical disputes, design language in particular should be treated with extra care by scientists. Currently a bizarre situation in which the creationists almost treat Richard Dawkins as if he were a founder of the intelligent design movement, because of his "appearance of design" quotes. It should be made much more clear by scientists that a favorite creationist argument -- "If Dawkins (or whomever) says biology appears designed, maybe it is!" -- is worthless and facile, for the reasons discussed above. It is extremely problematic to use the fact that some biologists use design language as any kind of evidence for actual literal design. I conclude by noting that, completely independently, another biologist has argued at length and convincingly that evolutionary biology should abandon not just "design" but "appearance of design" as the phrases bring more confusion than clarity to the science (Weiss 2009).


Of Fundamentalists and Funhouse MirrorsEdit

The above discussion of "appearance of design" language highlights a fourth and final reason why scholars of evolution, even specialists, can learn some things from examining and rebutting creationist arguments. Not, I hasten to add, in the way that creationists would like: my experience with creationist arguments has been extensive, and I feel safe in asserting that virtually the entire lot of creationist literature boils down to ignorant misinterpretation of real science, question-begging, and pious wishful thinking, all driven by fears of having to grow up and deal with a world in which evolution is real. In other words, creationist literature is academic drivel. (Even most of the creationists' fears are imaginary and unnecessary, but that is another topic.) For all their flaws, though, creationist arguments do have a few interesting features. Although it is impossible to be well-informed about creationist arguments and think that their objections are really based on objective analysis of data rather than religion, it is true that since the advent of "creation science" in the 1960s, creationists have put an extraordinary amount of effort into assembling arguments that have the superficial appearance of being based on science. Commonly, for example, creationists assemble arguments based on quotes and misquotes of scientists and science journalists -- think Dawkins and "appearance of design." The practice is so common that it has been given an epithet by creationism watchers -- "quote-mining" -- and it is even possible to trace the history of the practice back to the "Reformed" (Calvinist, often conservative Presbyterian), inerrancy-based view of the Bible, in which theology is a science, the data is the Bible, and Truth is determined by assembling Bible verses supporting each side of a question, and going with the majority vote (Mark Noll, George Marsden).

The end result of this creationist method of argumentation, annoying as it is, can be somewhat interesting for the scholar of evolution. Creationists will take whatever appealing tidbits of mainstream science they can find -- quotes stripped from their original context, misquotes, summaries of science from innaccurate press releases, simplifications and uncritical analogies made by popular science writings, misunderstandings of evolution put forward by academics speaking outside their field of expertise, and various mundane bits of science -- and piece together an alternate reality, sometimes one almost unrecognizable from a neutral, thorough review of the relevant scientific literature. Looking at a scientific topic in this way -- or the history of science, or the philosophy of science pertaining to that topic -- through the eyes of creationists is like looking at yourself in a circus funhouse mirror. Certain features are grossly inflated, others are squished down to nothingness, and resulting image, while vaguely recognizable, is an essentially monstrous representation of reality. So it is with the creationist representation of scientific topics. Professional creationists spend their days and years scouring the literature and the general culture for publications and especially quotes that support their point of view -- or at least seem to do so to a naive, hopeful reader, one poorly informed about the details of the relevant specialty, which creationists virtually always are.

How could this possibly be useful to the evolutionist? In their misbegotten quest to disprove evolution, creationists will vacuum up from the literature every statement of uncertainty, every ambiguity of terminology, every offhand statement that is useful to their cause. In the process, they often identify, usually unintentionally, areas where different subdisciplines are talking past each other, or where different schools of thought are using the same words in different ways, or where analogies are being used uncritically, even unthinkingly. The creationist quote mines also sometimes identify where scientists are relying on analogies or assumptions that, while they may work well enough for the specific paper the scientist is writing, may cause confusion when extrapolated to broader domains in biology. Creationists inevitably will so extrapolate, and the resulting picture, bizarre in the context of the overall state of the biological evidence, can give a hint about where concepts and terms are going awry. Even if the terminology and analogies are not causing serious problems amongst the experts in a particular field -- they usually have a sophisticated view of what they mean and don't mean by their language -- the creationist funhouse-mirror can show us where confusion is arising amongst science popularizers, textbooks, journalists, educators, and the public at large.

Very often, the creationist portrayal of a biological issue is substantially just a mistaken or oversimplified view common to science popularizers or the public at large, making sense according to "naive common sense" -- i.e. what a member of the public might think is reasonable when giving it a moment's thought before breakfast, and no careful critical study -- and then gripped tightly by the creationist, uncritically extrapolated, and built upon to a pathological degree. Examples include the "appearance of design" notion discussed above, and also idea that transitional forms must be direct ancestors and that the "missing links" are missing, that evolution is progressive and linear, that evolution is random, that foolish scientists once thought much DNA was "junk", but we now know better, and the idea that the genome is a computer program full of "information." [and xxxx as I come up with them!!]

These notions play a prominent part in the recent arguments of the "intelligent design" (ID) movement. They are also notions that can be found prominently in many popular sources, and even sometimes get uncritical support, mistakenly, in certain places in the mainstream scientific community. Some of them have received substantial critical attention from scientists. For example, after 30 years of battles between creationists and evolutionists, the transitional fossils issue has been sufficiently hashed out that, even giving creationists the maximum benefit of the doubt, the discussion should be over. Fossils with transitional morphologies are now known that bridge the gaps that used to exist regarding the origin of land vertebrates, mammals, birds, turtles, and numerous placental mammal groups, including whales and modern humans. Even a few creationists -- those with actual training in paleontology -- admit this (Wise, Wood). The science not only exists, it has been summarized, popularized, and gift-wrapped for any reader who has any remnant of an ability to be objective and to actually read about the science (Prothero, Padian; see table). These sources also effectively explain that collateral ancestors -- side branches -- are just as much evidence of common ancestry as are direct ancestors, and they explain how cladistic methodology does not need or attempt to assign direct ancestry, even though in certain cases it may be possible on other grounds (Prothero 2007). In short, to paraphrase one of the fundamentalists' favorite passages from Romans (1:20), the evidence has been clearly seen, and the creationists are without excuse.

However, there are other areas of biology where, even though the science is also clear, the process of collation, synthesis, and gift-wrapping for general audiences and creationists is less complete. One of these areas concerns biological "information." The "information" argument has been invoked by creationists for decades, but recently a leading "intelligent design" creationist, Stephen C. Meyer, has devoted an entire book solely to the information argument. His title, Signature in the Cell: DNA and the Evidence for Intelligent Design, is apt: Meyer thinks that the information in DNA, all by itself, is strong evidence for an intelligent (subtext: supernatural) origin of life. In Meyer's book, the sorts of popular misunderstandings discussed above are mixed together with beknighted creationist arguments, common and rare, to produce kind of creationist stew in support of the idea that the origin of life through natural processes is effectively impossible, and that "intelligent design", i.e. supernatural special creation, is the best explanation. I will offer rebuttals to Meyer's basic arguments, and while so doing, comment on places where evolutionary scholars and biologists in general can learn some things from analyzing the problems in Meyer's arguments, and his sources. It will be particularly useful to discuss how certain common biological concepts and terms break down when the gradual origin of life is being considered. Meyer gets a large amount of mileage out of taking certain commplace concepts and terms and inappropriately assuming that they apply uncontroversially to natural explanations of the origin of life. This sort of confusion is not unknown in mainstream treatments of the origin of life, so the exercise should be of general benefit.


Meyer's book and the information argumentEdit

Signature in the Cell is a strange melange of several genres. The book is advertised as a "revolutionary new scientific argument for design", but the "scientific" argument, which is at a pop-science at best, is diluted by several distracting themes. Signature is framed in a first-person, authobiographical format, which has as a subtle undercurrent the idea that Meyer has a claim equal to Thaxton, Behe, Dembski, and Johnson in being a scientific leader in the origins of the ID movement. It is partially a rebuttal of the Kitzmiller decision and an expression of Meyer's frustration that he was unable to get his view of events accepted by the press or the Kitzmiller court -- both of which concluded firmly that the six-week Kitzmiller trial had established that ID was warmed-over creationism, and not science. It is partially a history of the ID movement, a history written with the aim of showing that ID is science, not creationism. To that end, the history of the ID movement is interwoven with a generic history of molecular biology, and origin-of-life studies. It is partially a treatise on philosophy of science, wherein Meyer proposes what purports to be a complete philosophy of the science of past events, and in so doing he gives the ID movement's argument for why its claims regarding scientific issues add up to the position that ID is science, not creationism. And finally, it is an apologetic argument for the existence of God, and the importance of having science support the existence of God. And not just any God, but the interventionist God of conservative evangelicalism and fundamentalism, the one who specially created life, specifically humans, and who gives purpose and direction to human life and the universe.

To someone who has long experience with the ID movement, very little in this book comes across as new. The only new parts are some historical tidbits about the ID movement which Meyer drops in passing, and some minor new twists on the ID movement's history and philosophy of itself. However, Signature is somewhat new in that it combines all of these topics into one coherent treatise. Probably the only ID works with comparative levels of integration are the educational materials (e.g. Of Pandas and People) and law review articles put out by the ID movement, both of which attempt cover all the bases. That is, Signature and these works attempt not just to convince readers that ID is plausible, but to convince them that it fits into the cultural and legal category of "science," that it definitely isn't that discredited, unconstitutional religious thing called "creationism," and that it thus deserves a serious position in popular discourse, scientific discourse, and especially in public school science classrooms.

All of these aspects of Signature will be discussed, but the only issue of fundamental importance is whether or not there is any truth to Meyer's "scientific argument." So we will start there. Meyer adequately sums up his argument in his Conclusion:

Since the intelligent-design hypothesis meets both the causal-adequacy and causal-existence criteria of a best explanation, and since no other competing explanation meets these conditions as well -- or at all -- it follows that the design hypothesis provides the best, most causally adequate explanation of the origin of the information necessary to produce the first life on earth. Indeed, our uniform experience affirms that specified information -- whether inscribed in hieroglyphics, written in a book, encoded in a radio signal, or produced in a simulation experiment -- always arises from an intelligent source, from a mind and not a strictly material process. So the discovery of the specified digital information in the DNA molecule provides strong grounds for inferring that intelligence played a role in the origin of DNA. Indeed, whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source. It follows that the best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source. Intelligent design best explains the DNA enigma.

By the late 1990s, I had become convinced -- at least provisionally -- that intelligent design was the only known cause of specified information. As a result, I began to sketch out the case for intelligent design as the best explanation for the DNA enigma. In the years that followed (1998-2003), I published a series of articles arguing that intelligent design provides a better explanation than any competing chemical evolutionary model for the origin of biological information. Since then I have continued to examine additional hypotheses and simulations such as the RNA world and genetic algorithms. The case for intelligent design has grown only stronger. Not only have these new approaches failed to provide an adequate explanation for the origin of biological information; they have strengthened the positive case for design that I had previously formulated.

–Meyer 2009, p. 347, italics original

We can already see some of the repetitiveness that pervades Meyer's book here, as he asserts the same thing, slightly rephrased, several times. But no matter. Meyer's argument is fundamentally quite simple and direct, so we can lay it out as syllogism.

[As I do so, I will also point out which claims are positive claims (arguments for some proposition), and which are negative claims]

1. Something called "specified information" exists in biology, particularly in the DNA genome and its derivatives (like proteins). This "specified information" is the same sort of stuff that exists in human communication -- language, writing, radio signals, computer code. It is complex, i.e. aperiodic and incompressible, and the sequence is specific to function.

2. A nonmaterial source, mind or intelligence, can produce specified information. This is known by direct observation.

3. Natural processes, and simulations of them, cannot produce specified information. In cases where the causal story is known for sure (Meyer seems to mean cases where the cause has been directly observed by humans), intelligence is the cause.

4. Therefore, intelligence is the only known explanation "causally adequate" and "causally existent" for the specified information in DNA.

5. Thus the "best explanation" for the specified information in the DNA is intelligent design.

Supporting point 3 takes up the heart of Meyer's book, chapters 8-14, and will be summarized later on.

Initial comments on the argumentEdit

Meyer's argument is simple enough to be understood by the general reader, and has been promoted heavily by the ID movement as strong enough to effect a scientific revolution, or at least it would be if those mean scientists weren't unfairly biased against ID because of their atheism, methodological naturalism, or other inappropriate biases.

I think it is fair to say that the argument for the conclusion (point #5), as phrased, would be convincing, if assertions #1-4 were clearly true. And this would indeed be scientifically revolutionary. However, even if we thought assertions #1-4 were reasonably probable, there would still remain some significant reasons, from a scientific point of view, to at least be worried about the argument. By the phrase "from a scientific point of view", I don't mean at this juncture to engage in an elaborate philsophy of science. Rather, I will just point out some general considerations and scientific intuitions about why many scientists would "sniff trouble" in Meyer's argument. This is worthwhile, as Meyer surrounds his argument for ID with an extensive defense of the notion that his ID argument qualifies as "science."


SparenessEdit

One reason that scientists might "sniff trouble" in Signature is that Meyer's actual argument, despite the length of his book, is annoyingly spare. Just to illustrate what I mean by a "spare" argument, compare the 5 points of Meyer's argument with a sometimes-popular argument for the existence of God, the Kalaam Cosmological Argument for the existence of a First Cause of the Universe:

1. Whatever begins to exist has a cause. 2. The universe began to exist. 3. Therefore, the universe has a cause.

This argument is strangely reminiscent of Meyer's argument, in that, although hundreds of pages can be spent discussing each term, premise, and logical step, it boils down to a grand conclusion that is held to result from simple logical deduction from a very few premises.

Some philosophers seem to like spare arguments, but scientists generally don't. Spare arguments are annoying for several reasons. First, scientists would prefer that the same conclusion be indicated by a variety of different lines of argument, relying on different sets of probably true premises. This is particularly desirable if the conclusion is particularly grand, and there is a lot relying on it. There are several ways to argue for the desirability of multiple lines of argument starting from different sets of premises, but a simple one is just that humans are limited and flawed creatures, and any particular observation-based premise or logical inference might be mistaken. A single line of argument might be sunk by some dumb mistake somewhere. But if 10 different lines of argument all reach the same conclusion, all 10 lines of argument would have to have mistakes in their different premises or logic, and all 10 mistakes would have to coincidentally result in the same conclusion, for the conclusion to be mistaken. All the grand overarching explanatory theories in science -- evolution, plate tectonics, germ theory of disease, relativity, etc., have this kind of broad support. Even if the theories are mistaken in some fashion -- e.g., the physicists tell us that quantum mechanics and general relativity are in conflict -- they are already positively known to be very good approximations of reality over very broad domains, and this will not change even if they are superceded by another theory. Spare arguments, however, often seem to be doomed to intellectual limbo, debated for millenia but with no sign of progress or resolution.

A second reason to be annoyed with spare arguments is that what you get out of them is not all that useful. For instance, the Kalaam Argument, if true, established nothing but the very abstract idea of a "First Cause." At best, the concept of a "First Cause" is vague and extremely remote from human and scientific experience. It would be much more satisfying, scientifically, if the origin of the Universe were attributed to an entity with substantial detail, say, Homer Simpson. At least we have a very detailed and specific idea of what Homer is, his capabilities, limitations, motives, tendencies, color, weight, etc. These details are what would give scientists something to study. "Homer exists" provides a wealth of specific, detailed empirical expectations. "A First Cause exists" does not. Which is annoying, scientifically.

Meyer's spare argument, even if it succeeds, only gets us to the conclusion that "intelligence was the cause" of specified information. But Meyer, officially at least, gives us virtually no detail, or any account of any kind, of what the bare cause of "intelligence" means. The book contains no definition of "intelligence" or "Mind." About all the reader is told is that intelligence can have purposes, produce specified information, and that intelligence is "not strictly...material" (p. 4xx), but that's about it. If the inferred cause was "human intelligence", that would be a reasonably specific result, humans having a variety of detailed and well-known capabilities, limitations, motives, tendencies, properties, etc. An even better result would be if the cause was a specific human culture, or a specific human -- each of these adds additional detail to the hypothesized cause, and detail in hypotheses provides detailed empirical expectations, and thus empirical tests that scientists can perform. But the bare conclusion of "intelligence" produces little to nothing along these lines. That may not prove Meyer worry, but it is scientifically worrisome. And annoying.

Finally, a related reason that spare arguments are scientifically annoying is that they put a tremendous amount of argumentative weight on a few key concepts. This makes it possible for huge logical or empirical problems to be hidden from view, often unintentionally, by conceptual ambiguity. This, again, can result in millenia of unresolved debate, with none of the empirical progress that scientists would prefer to see. In the Kalaam argument, the key concepts are "universe", "cause", "exist", and "begin." All of these terms have a noncontroversial and unproblematic usage, and we all pretty much agree what they mean in everyday life, at least to a reasonable degree of approximation. But it is another matter entirely to rely on these concepts to carry us to the extreme edge of human inference, and beyond it. All four of these concepts become extremely problematic in the context of relativity, quantum mechanics, and the Big Bang. What does "cause" mean "before" "time" or even "existence" (the universe) have begun to "exist"? Do quantum events have a "cause"? Don't particles and antiparticles continually pop into and out of "existence" without a "cause"? I am sure some philosophers and theologians get their kicks from knocking around these questions, but it's all, well, annoying from a scientific point of view.

So it is with Meyer's argument. The key terms here are "specified information", "function", "intelligence", "causal adequacy", and "explanation." At first glance, these concepts seem reasonable and easy to understand, and for some of them, Meyer even takes some care in explaining what he means. But his argument is spare, and thus our confidence in the argument is seriously impacted if we discover ambiguities in the concepts he is hanging his argument on. By itself, this is just scientifically annoying. But as we shall see, serious examination shows that just these sorts of problems emerge for each of Meyer's key concepts.

Specified informationEdit

FunctionEdit

That's an interesting take Nick. We know that Meyer was principally focused on the origin of information. The origin of information and the origin of function are inextricably interconnected. Back to the chicken-egg dilemma. If function is whatever tends to give a selective advantage then we need criteria indicating what would be selected on planets where conditions are hospitable to life but where no life exists. What approach would you take Nick to discern what is selected prior to a point in time when a self-replicator can be observed much less defined with respect to its properties? Is it any wonder that OOL research has such a difficult time making a breakthrough? If function and selection are intertwined then a break in symmetry exists at an historic moment. What's a theorist to do?

This, finally, is a worthwhile question. And it is the fundamental issue in Meyer's book. And I agree that <a href="http://telicthoughts.com/the-signature-in-the-cell-challenge/#comment-250162">pointing out Meyer's self-contradictions about the genome</a> or <a href="http://telicthoughts.com/are-stereochemical-explanations-causally-sufficient/">pointing out that Meyer is wrong about stereochemistry and the genetic code</a> do not strongly debunk this core argument. However, the existence of those problems should raise worries about the correctness of Meyer's core argument.

Regarding Bradford's favorite, almost only, question, the origin-of-the-first-replicator question:

There are a number of things that would have to be taken into account in a reasonable, thorough scientific consideration of the question of whether or not it is likely that the first replicator originated through a natural process, or through intelligent/divine intervention. In no particular order:

1. Even if absolutely no natural explanation currently existed, that would not necessarily be good evidence for the proposition that no natural explanation is likely to exist. Making such an argument is just intrinsically difficult, given limited human knowledge.

2. As it happens, a decent chunk of an explanation for the origin of the first replicators does exist, and appears to be growing bit-by-bit every year through progress in the origin-of-life field.

3. In particular, progress in the OOL field is shown by the fact that several difficulties that used to be prominent, "unsolvable" chicken-and-egg puzzles, have in fact been solved. E.g. RNA world solved the DNA/protein chicken/egg puzzle. There is of course still some origin-of-the-RNA-world puzzle, but this is a smaller puzzle than the DNA/protein puzzle.

4. The RNA World wasn't just a handy solution to a problem, it has turned out to be a highly successful research paradigm, with all kinds of spinoff research and practical benefits. This is just the sort of thing that encourages scientists to think they are on the right track.

5. Origin-of-genetic-code studies have also been highly productive, there are thousands of articles on this and many research successes, thus getting from RNA World to RNA-protein world is on reasonably strong ground.

6. The creationist method of argumentation in the OOL arena is similar to their argumentation in the fossil arena. I.e. (a) start with a gap, (b) find an intermediate, (c) creationist takes the new, smaller gaps and proclaims "I've discovered more gaps!" and also claims the new gaps are insoluble, just like the old one was supposed to have been. This whole approach is bankrupt, it is essentially a Xeno's paradox, where there is continual retreat, but science is never allowed to cross the finish line. (I like that. Copyright 2010 Nick Matzke.)

7. Apart from the progress of OOL science, there are some positive reasons to think that the natural origin of replicators is likely.

7a. When we trace the ancestors of modern extant life as far back as we can, we get to something much, much simpler than the modern biosphere. This didn't have to be true. A fuller argument on this point is here: http://pandasthumb.org/archives/2008/07/what-critics-of.html

7b. It just so happens that the fundamental biochemical basis of replication, i.e. semiconservative templating, ended up being fundamentally pretty simple. It turned out to be the kind of thing that just might maybe be within the reach of a chemical process. I think an argument can be made that e.g. it turned out to be simpler than Darwin thought it would be. This also didn't have to be the case.

7c. The barrier between life and non-life doesn't appear to be absolutely distinct. In decreasing complexity, we have viruses, parasitic DNA elements, prions, and short, "naked" RNA parasites. From the other end, we have a variety of natural nonbiological phenomena that exhibit some lifelike qualities, if not all of them at once. This kind of thing weakens the claim that there is a fundamental metaphysical discontinuity in the life/nonlife distinction.

7d. The barrier between replication and nonreplication is also not absolutely distinct. All replication is somewhat imperfect anyway, but there are various ways to have something between high-quality replication and just random assembly. Keywords are things like e.g. "statistical replicators", "compositional inheritance" (e.g. when a membrane vesicle splits, the daughters will inherit approximately the same percentage composition).

8. Meyer's argument is basically that (a) natural processes haven't been observed to create new information, (b) intelligence has been observed to do this, (c) therefore intelligence. (a) is just wrong, it is disproven by e.g. the fact that gene duplication + mutation/selection for divergent function produces new functional sequence, i.e. new information on any reasonable definition. Therefore natural processes can create new information, therefore "information" is not some magical special thing requiring, basically, mystical intervention by Mind to produce, therefore Meyer's deductive argument fails.

9. Even if we reduce Meyer's argument to (a) natural processes haven't been observed to create self-replicating chemical sequences, (b) intelligence has been observed to do this, (c) therefore intelligence must have created life, we have problems. (a) is called into serious question by points #1-7. Also, it is far from clear that (b) is even true at the moment, apart from trivial examples. Humans may find it trivial to "create information" of certain sorts, but it is definitely not trivial for humans to create chemical replicators. The sorts of stuff humans have produced that get closest either some from selection experiments, i.e. humans using evolutionary processes, or they come from basically "hacking" living systems.

10. Another problem is that the evidence Meyer inputs into his argument more naturally supports the following: (a) natural processes can't produce information/replication, (b) humans can, (c) therefore humans caused life. There are no known examples of intelligence besides humans, what justification is there for extrapolating the existence of a general category called "intelligence", when we have but one example? The problem, of course, is that this argument is (a) more justifiable from Meyer's rules of inference (relying on observation and uniform experience), but (b) clearly wrong, since we have many positive reasons to think that humans have only recently come into existence.

11. Meyer's rules of inference also lead to other problems. E.g., we could equally well argue, using Meyerian logic, that (a) natural processes haven't been observed to create structures taller than 1400 feet (the biggest observed natural structure is Paricutin volcano in Mexico, grew from 0 to 1,391 feet between 1942 and 1953), (b) intelligence has (Burj Khalifa tower in Dubai is 2720 feet tall), (c) therefore intelligence created all mountains higher than 1400 feet.

There's more to say, but I'm going to bed!


Hi nullasalus,

Re: supernatural and natural. People get them confused when they try and define these from first principles. E.g. the philosopher Sober tries to argue that "numbers" are supernatural, according to the very odd definition of "supernatural" he comes up with.

Where the terms make sense is history of western thought. Natural = things operating by the laws of physics that appear to be universally (or almost universally) operating now and in the past. This includes very complex products of the interaction of various laws, including stochastic/chance processes. Supernatural = miracles, basically, requiring the suspension of the aforementioned physical laws, typically by the action of God or a similar entity.

You can pretty much boil down a supernatural event to violation of the First Law of Thermodynamics, which states that mass and energy can change form, but not be created or destroyed. All miracles I can think of violate this. Even if whole critters aren't poofing into existence, and if mass is conserved, e.g. God just rearranges some preexisting DNA base pairs to give them "information", then conservation of energy is still being violated, as it takes energy to rearrange those base pairs in that specific way.


It is a difficult problem. An Andrea Bocelli CD in a world where the CD player hasn't been invented might be considered to be without function, without purpose, and therefore extremely low information content.

And this would be utterly wrong.

I kind of agree, but look at it in two other ways.

(1) from the perspective of biology, this might be the way things actually are. E.g., if a gene loses function (e.g., primates didn't need the gene to synthesize Vitamin C, since they got it from their fruity diet), then it decays through mutation and neutral drift in *exactly the same way* that random, nonfunctional sequence does.

(2) Imagine if you were a primitive illiterate tribesman with no concept of complex technology, codes, etc. and came across the CD. Would it have any "information" from your perspective? Would you think it was obviously "designed"? Or would you use it as a plate?

(3) Imagine you are modern scientist, but you come across a piece of alien technology, but so advanced and so remote from your experience, that you are in about the same relative position as a tribesman looking at a CD. Would you even conclude that the item was a piece of technology? Would you successfully perceive the "information"?

Tough questions. I suspect that all "information" in the creationist "meaning" sense is context-dependent, i.e. meaningful in one context and not others. But this means that in biology, "information" is whatever sequences function, and if this is so, then Meyer is screwed, because natural processes can clearly produce this sort of information, so his negative generalization about natural processes is sunk.


Thus, molecular biologists beginning with Francis Crick have equated biological information not only with improbability (or complexity), but also with "specificity," where "specificity," or "specified", has meant "necessary to function."

Thus, in addition to a quantifiable amount of Shannon information (or complexity), DNA also conrains information in the sense of Webster's second definition: it contains "alternative sequences or arrangements of something that produce a specific effect." Although DNA does not convey information that is received, understood, or used by a conscious mind, it does have information that is received and used by the cell's machinery to build the structures critical to the mainrenance of life. DNA displays a property -- functional specificity -- that transcends the merely mathematical formalism of Shannon's theory.

[p. 110]

Is this significant? In fact, it is profoundly mysterious. Apart from the molecules comprising the gene-expression system and machinery of the cell, sequences or structures exhibiting such specified complexity or specified information are not found anywhere in the natural -- that is, the nonhuman -- world. Sequences and structures exhibiting either redundant order or mere complexity are common in the chemical substrate of nature. But structures exhibiting specified complexity are completely unknown there apart from DNA, RNA, and proteins. As the origin-of-life biochemist Leslie Orgel observes: "Living organisms are distinguished by their specified complexity. Crystals . . . fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity." Nevertheless, human artifacts and technology -- paintings, signs, written text, spoken language, ancient hieroglyphics, integrated circuits, machine codes, computer hardware and software -- exhibit specified complexity; among those, software and its encoded sequences of digital characters function in a way that most closely parallels the base sequences in DNA.

Thus, oddly, at nearly the same time that computer scientists were beginning to develop machine languages, molecular biologists were discovering that living cells had been using something akin to machine code or software all along. To quote the information scientist Hubert Yockey again, "The genetic code is constructed to confront and solve the problems of communication and recording by same principles found ... in modern communication and computer codes." Like software, the coding regions of DNA direct operations within a complex material system via highly variable and improbable, yet also precisely specified, sequences of chemical characters. How did these digitally encoded and specifically sequenced instructions in DNA arise? And how did they arise within a channel for transmitting information? (pp. 109-110, italics original)


As noted, biological information, such as we find in DNA and proteins, comprises two features: complexity and functional specificity. Computer codes and linguistic texts also manifest this pair of properties ("complexity" and "specificity"), what I have referred to throughout this book as specified information. Although a computer program may be similar to DNA in many respects and dissimilar in others, it exhibits a precise identity to DNA insofar as both contain specified complexity or specified information. (p. 386, italics original)

Of course, insofar as the term "information" connotes semantic meaning, it does function as a metaphor within biology. That does not mean, however, that the term functions only metaphorically or that origin-of-life biologists have nothing to explain. Though information theory has a limited application in describing biological sysrems, it has succeeded in rendering quantitative assessments of the complexity of biomacromolecules. Further, experimental work has established the functional specificity of the base sequences in DNA and amino acids in proteins. Thus, the term "information" as used in biology refers to two real and contingent properties: complexity and functional specificity. (p. 387, italics original)

The origin of specified complexity, to which the term "information" in biology commonly refers, therefore does require explanation, even if the concept of information connotes only complexity in Shannon information theory and even if it connotes meaning in common parlance, and even if it has no explanatory or predictive value in itself. Instead, as a descriptive (rather than an explanatory or predictive) concept, the term "information" (understood as specified complexity) helps to define an essential feature of life that origin-of-life researchers must explain "the origin of." So, only where information connotes subjective meaning does it function as a metaphor in biology. Where it refers to complex functional specificity, it defines a feature of living systems that calls for explanation every bit as much as, say, a mysterious set of inscriptions on the inside of a cave. (p. 388, emphasis original)

The premises themselves are usually themselves exceedingly grand generalizations.

spare are ones that make broad, but very vague, conclusions, based





The arguments ar as follows in various chapters of the book:

3a.

3b. Chance alone cannot produce specified information, because the probability of random assembly of this information is far too low (Chapters 8, 9, and 10).

3c. "Necessity" -- or natural laws, such as the rules of chemical bonding, cannot produce specified information, because they can only produce regular patterns, not the aperiodicity found in DNA, and besides the necessary chemical preferences do not exist between amino acids or between nucleotides (Chapter 11).

3d. "Necessity" in the form of self-organization in an energy flow can produce order -- simple patterns, but not complexity. Kauffman's model of self-organization can produce complexity, but it fails as an explanation for specified information because the analogy to biology is too vague, and the products are not constrained to function (Chapter 12).

3e. The combination of chance and necessity -- i.e. natural selection acting on randomly-generated sequences -- cannot produce specified information, at least not the specified information required for the origin of life, because natural selection requires replication, but replication already requires substantial amounts of specified information. Natural selection before there is a replicating system is impossible. This requirement sinks protein-first, DNA-first, and older models for the origin of life, as well as Eigen's hypercycles, because they all require a combination of specified nucleotide sequences (DNA or RNA) and amino acid sequences (proteins) to be in place to get replication started (Chapter 13).

3f. Genetic algorithms run on computers also do not provide a counterexample, as they presuppose replication and information, both of which are programmed in by the programmers. Simpler programs (Dawkins' Weasel algorithm, and Schneider's Ev program) input a sequence-specific target ahead of time and reward incomplete progress towards that future goal. Even the more sophisticated simulations, such as Avida, don't work, even merely as an example of the increase of information in an already-replicating system, for a complex list of reasons (Chapter 13, especially footnote 46 on pages 533-535).

3g. The RNA World hypothesis for the origin of self-replicating system fails because (1) the building blocks are hard to synthesize, (2) ribozymes don't work as well as proteins, (3) RNA can't handle all the tasks that are necessary to evolve beyond an RNA world, (4) getting the specified information required to have self-replicating RNA is too improbable, (5) ribozyme engineering experiments rely on intelligent experimenters providing the information necessary for replication (Chapter 14).


summarize the terms lay out the argument criticize each of the terms/assertions/premises -- particularly where the argument fails on its own terms


The argument isn't newEdit

Ever since the creationists got wind of the molecular biology revolution in the 1960s, with the understanding that DNA sequences code for amino acid sequences to make proteins and build living things, they have instinctively and entirely uncritically concluded that this was obvious evidence of divine intervention -- how could "random" processes possibly create a code, and the information encoded by a code? For instance, almost at random I had a look at the Creation Research Society Quarterly. The CRSQ is the journal established in 1964 by Henry Morris and other members of the Creation Research Society -- the nucleus of the group that would later (in about 1970 -- Numbers) came up with the "creation science" terminology and movement. The CRS members were not just creationists (believing in special creation, i.e. divine intervention in the history of life) and fundamentalists (i.e., those who believe in the inerrancy of the Bible), they were specifically extreme Biblical literalists and young-earth creationists who interpret the "days" in Genesis as literal 24-hour days.

Volume 1, Issue "0" of the CRSQ (the first issue of the CRS journal was evidently published before the decision was made to make it a quarterly, thus it the 2nd issue is the one that was labeled as "issue 1.") contains an article making arguments that seem eerily familiar to those dealing with modern creationist arguments:





Despite the strong evolutionary dogma against teleology, design is evident in living organisms. Twenty amino acids are commonly found in proteins. ... Only four organic bases occur in the nucleic



director of the "Center for Science and Culture (formerly the Center for the Renewal of Science and Culture, with the "Renewal" part dropped in 200x, probably to appear more secular)

But it highlights the fact that even the those taking a fundamentally correct position can benefit from critical review.

Sometimes criticisms are just wrong, as can happen when critics venture into areas outside their specialities, without doing the necessary homework

This is particularly the case


Example of typical creationist silliness, and how it highlights some issues in science (e.g. fossils, punk eek, cladistics, etc.)Edit

A concrete example is provided by the example of the concepts of "transitional forms" and "intermediate fossils." If evolution is true, then there should be substantial evidence of this in the fossil record, at least among groups that have a good fossil record, and indeed there is (Prothero 2007). However, creationists can find quotes that appear to say that no transitional fossils exist at all! For example:

[Maybe: "In any case, no real evolutionist, whether gradualist or punctuationist, uses the fossil record as evidence in favour of the theory of evolution as opposed to special creation."

Who Doubts Evolution?, New Scientist, 25 June 1981, p. 831 ]

[fossil discussion]

After 30 years, the transitional fossils issue has been sufficiently hashed out that, even giving creationists the maximum benefit of the doubt, the discussion should be over. Fossils with transitional morphologies are now known that bridge the gaps that used to exist regarding the origin of land vertebrates, mammals, birds, turtles, and numerous placental mammal groups, including whales and modern humans. Even a few creationists -- those with actual training in paleontology -- admit this (Wise, Wood). The science not only exists, it has been summarized, popularized, and gift-wrapped for any reader who has any remnant of an ability to be objective and to actually read about the science (Prothero, Padian; see table). In short, to paraphrase one of the fundamentalists' favorite passages from Romans (1:20), the evidence has been clearly seen, and the creationists are without excuse.



What is intelligent design?Edit

subsidiary questions behind the book

  • ID wants to be science, not religion
  • It wants to be in the public schools and courts
  • revisiting the Kitzmiller case
  • It really is creationism
  • Let's not have silliness about ID accepting common ancestry
  • J. Scott Turner, and why some people think like him
  • History of ID
  • Meyer a disinterested investigator
  • Meyer an intellectual leader of the movement

"Information" and what we can infer from itEdit

What is "information", anyway?Edit

matching coastlines

broken up rocks -- high specificity

this sort of template matching is precisely what is at the heart of biological replication

Functional informationEdit

Is information dense in the genome?Edit

Meyer says that "information" -- sequence-specific function -- is densely concentrated in the DNA genome:


Thus, far from being dispersed sparsely, haphazardly, and inefficiently within a sea of nonfunctional sequences (one that supposedly accumulated by mutation), functional genetic information is densely concetrated on the DNA molecule.

–Meyer 2009, p. 461


Far from containing a preponderance of "junk" -- nonprotein-coding regions that supposedly perform no function -- the genome is dominated by sequences rich in functional information.

–Meyer 2009, p. 461


Furthermore, says Meyer, not only is this established truth, but it is a prediction of ID theory, and furthermore it was predicted by ID advocates a decade or more ago:


The genome does display evidence of past viral insertions, deletions, transpositions, and the like, much as digital software copied again and again acumulates errors. Nevertheless, the vast majority of base sequences in the genome, and even the many sequences that do not code for proteins, serve essential biological functions. Genetic signal dwarfs noise, just as design advocates would expect and just as they predicted in the early 1990s.

–Meyer 2009, p. 461


However, at numerous places in the book, Meyer notes (correctly) that repetitive sequences have little information:


"Since information and improbability are inversely related, high-probability repeating sequences like ABCABCABCABCABCABC have very little information (either carrying capacity or content). And this makes sense too. Once you have seen the first triad of ABCs, the rest are "redundant"; they convey nothing new. They aren't informative. Such sequences aren't complex either. Why? A short algorithm or set of commands could easily generate a long sequence of repeating ABCs, making the sequence compressible.

–Meyer 2009, p. 107


Unfortunately for Meyer, he seems to not realize that 40-50% of the human genome (and most animal genomes of similar size) consists of LINEs, SINEs, segmental duplications, and other repeating elements. In other words, there is no way that in "the vast majority" of the genome genetic information is "densely concentrated" -- as proven by his own arguments!

Although it is true that it doesn't logically discredit Meyer's other arguments, this sort of mistake should make people suspicious of his competency to get his other biological facts, and his reasoning from them, correct. This error is pretty simple and obvious. Why didn't the various ID proponents, and positive reviewers like Thomas Nagel, find it?

This particular criticism of Meyer does not lose any force if it turns out that repetitive DNA should happen to have a function. That said, even if you are just worried about "function" in some general, information-poor sense (Meyer explicitly connects specified complexity, i.e. coding, language-like, information-dense sequence, to function, throughout the entire book!!!! So good luck disconnecting those!!), keep in mind (a) the fact that function -- or more commonly some kind of detectable biochemical effect -- has been discovered for a LINE or SINE here or there in no way proves or even implies (b) the idea, extremely common with poorly-informed ID advocates, that ALL or almost all of these sequences must have a function. In fact, we have a lot of positive evidence AGAINST the idea that most LINEs and SINEs have some kind of sexy function -- notably, (c) they are known to be the byproducts of retrotransposons and thus their presence has an easy, obvious, completely straightforward nonfunctional (for the organism) cause, and (d) the number of repetitive elements varies widely between very similar species, and doesn't appear to correlate with organismal complexity. E.g. some onions have genomes 5 times bigger than humans (mostly due to more repetitive elements), other onions have genomes 25 times bigger, and some fishes have genomes 10 times smaller than humans (but the same amount of genes, mostly the same developmental and hox genes, etc.).

These variations in DNA amount may have some kind of functional significance in bulk (one theory, much debated, is that large cells need large nuclei, and the amount of DNA physically determines the size of the nucleus) -- but we pretty much know for sure that there isn't a lot of complex coding information in these variations.

Can natural processes produce information?Edit

No undirected process will demonstrate the capacity to generate 500

bits of new information starting from a nonbiological source

–Meyer 2009, p. 496


Meyer has a bizarre strategy, wherein he claims ad nauseum throughout the book that only intelligence can create new information, therefore information proves intelligence even without any other evidence of motive/means/opportunity/ actual designer presence -- but he claims this while excluding by fiat all the examples of new information arising in biology e.g. via gene duplication & modification etc. (which are barely discussed, just as they are barely discussed within the entire ID movement). He is aware of the problem on some level, because he (inconsistently) puts in the "nonbiological source" qualifier in a craven attempt to avoid falsification. But somehow, despite all his tedious detail about the logic of his argument, he never gives this issue a serious treatment. Of course, once you accept that natural processes can create new information, then Meyer's generalization is totally shot to hell, probably more "information" (meaning functional sequence) has been generated by biology (all the genomes in the biosphere throughout time) than by humans (all the texts in world; I haven't done a calculation though), and endless quotation of Quastler 1960-whatever about how information is habituality associated with intelligences is worth jack squat.

Key question is really replicationEdit

What Meyer has discussedEdit

Origin of replicationEdit

This is really the key questionEdit

Due diligence and how creationists, and Meyer, don't do itEdit

RNA world improvementsEdit

Genetic code studiesEdit

OOL amino acid pool simplerEdit

semi-replication, statistical replicationEdit

kinetics vs. thermodynamicsEdit

flow of molecules vs. static poolEdit

The real questionEdit

Whole planet, totally sterile, billions of places for reactions, producing some chemicals with a kinetic advantage


PhilosophyEdit

Positive and negative argumentsEdit

Meyer converting negative arguments into positive onesEdit

"Best explanation" vs. testing hypothesesEdit

Meyer likes "best explanation" because it creates the appearance of a rigorous argument to cover what is really just an argument from personal incredulity

How real science actually works with designEdit

  • rarefied design inferences are completely or almost completely impossible
  • e.g. Del Ratzsch's bulldozer-on-Mars example -- "bulldozer" imports a vast array of connected concepts

The problem with supernatural hypothesesEdit

  • What do we mean by supernatural? Miracles, suspension of the laws of physics. E.g. conservation of matter/energy,
  • Or anything dealing with a designer sufficiently vague to include an intelligent designer
  • Alternatives are weak. Not Sober's e.g. math.
  • Rigorous method for inferring the supernatural might be possible, but no one has done it yet, and doing it would require constraining the supernatural entity

Disingenuousity: History of Meyer and History of IDEdit

Meyer's annoying autobiographical styleEdit

Playing fast-and-loose with the historyEdit

Signature is written in the exasperating framework of Meyer's first-person account of his involvement in the ID movement and his own thoughts about the topic. Normally, I don't mind writing on scientific topics written in the first person -- it can make for better writing, including increased clarity about who did what, who thinks what, and what are taken as facts versus what are opinions and interpretations. But Meyer's narrative is positively distracting. Just about every time the reader is getting settled into the argument about some particular mainstream proposal, Meyer-the-narrator will pop in and talk about his own views on it in the past tense. In some cases, he more-or-less claims that he independently figured out the problem with the proposal, even though the proposal in question was discussed within the scientific community and rejected decades before. In other cases, he will take a creditable, live hypothesis, and portray it as already discredited. And quite often, Meyer portrays his ideas as actual important discoveries, when in fact all he's got is a barely warmed-over version of the creationists' fallacious "tornado in a junkyard" argument about the origin of life and genetic information.

It is one thing to write an autobiography after you've become a famous scientist, one who has had many of your hypotheses, facts, guesses, and discoveries confirmed by the data and by the scientific community. It is especially appropriate if you have changed the mind of the scientific community on some fundamental issue. At that point, your personal history and thoughts are of some actual academic and historical value. But it is quite another thing to stick your autobiography right into your hopefully revolutionary book. Even Darwin would have been annoying if his Autobiography had been mixed into the Origin of Species. (Imagine that Darwin wrote and researched like Meyer does. It would have gone something like this: "There is grandeur in this view of life, which by the way I discovered, because I'm quite clever, you know." Or: "When hanging out intermittently in the Cambridge library, as a philosopher, I was much struck with certain facts in the origin of life literature, which not only threw some darkness on the origin of life, but which proved that the whole subject was essentially hopeless and that the informed opinions of generations of empirical biologists were easily dispensed with.")

Chutzpah aside, Meyer's history might be interesting to those of us who have followed and written on the history and origins of the ID movement. But unfortunately, Meyer's history is systematically distorted to make it appear as if the ID originated as a secular scientific hypothesis. Every time Meyer refers to an anonymous correspondent or an unnamed meeting, or describes a collaborator or journal in less-than-specific terms, it is likely that he is hiding some embarrassing bit of history. The examples are legion. Here are some highlights:

The 1985 meeting that started Meyer on his questEdit

In the early 1980s, after college, Meyer spent several years working as a geophysicist for oil companies in Texas. On pages 24-25, Meyer describes a meeting he attended in 1985 which got him interested in the origin of life:


I first encountered the DNA enigma as a young scientist in Dallas, Texas.... On February 10, 1985...I found myself sitting in front of several world-class scientists who were discussing a vexing scientific and philosophical question: How did the first life on earth arise? As recently as the evening before, I had known nothing about the conference where this discussion was now taking place. I had been attending another event in town, a lecture at the Southern Methodist University by a Harvard astronomer discussing the big-bang theory. There I learned of a conference taking place the following day that would tackle three big scientific questions -- the origin of the universe, the origin of life, and the nature of human consciousness. The conference would bring together scientists from competing philosophical perspectives to grapple with each of these issues. The next morning I walked into the downtown Hilton where the conference was being held and heard an arresting discussion of what scientists knew and what they didn't.

I was surprised to learn -- contrary to what I had read in many textbooks -- that the leading scientific experts on the origin of life had no satisfactory explanation for how life had first arisen. These experts, many of whom were present that weekend at Dallas, openly acknowledged that they did not have an adequate theory of what they called "chemical evolution," that is, a theory of how the first living cell arose from simpler chemicals in the primordial ocean. And from their discussions it was clear that DNA -- with its mysterious arrangements of chemical characters -- was a key reason for this impasse.

The discussion changed the course of my professional life. By the end of the year, I was preparing to move to the University of Cambridge in England, in part to investigate questions I first encountered on that day in February.

–Meyer 2009, pp. 24-25


All well and good. Most readers would gather that Meyer got interested in this topic at scientific meeting, and move on to the next passage. A reader who has read more than his fair share of ID literature, however, might be cynical enough to wonder why a book with 742 endnotes taking up 52 pages had no space for a brief citation of meeting of what turned out to be the most important meeting in Meyer's professional life. A reader deeply familiar with the history of the ID movement will remember that early ID/creationists used to cite a 1985 meeting in Dallas, but that they described it in a somewhat different way than Meyer gives in 2009.

To cut to the chase, the meeting was actually called "Christianity Challenges the University." The subtitle, "A Dialogue of Theists and Atheists," identifies the "competing philosophical perspectives" eluded to (or elided?) by Meyer. The "scientific meeting" was sponsored by Dallas Baptist University. It was co-organized by DBU philosophy professor James Parker and Roy Abraham Varghese -- the latter a computer consultant-turned-apologist, now well-known, who "for a quarter-century...has been assembling God proofs." Varghese's hallmark appears to be organizing -- and especially funding -- conferences and books that support the view that science proves the existence of God, or at least support the view that notable scientists and academics say that science proves the existence of God.

(In 2007 Varghese was at the center of a scandal concerning the on-again, off-again conversion of the elderly atheist philosopher Antony Flew to deism. Varghese and another apologist basically wrote the book There is a God under Flew's name. All details concerning the case are hotly disputed, but my sense of it is that Flew has become very vulnerable to suggestion, and even the most innocent versions of the evangelists' interactions with Flew indicate a pretty severe lack of character on their part. Anyhow, Varghese met Flew for the first time at that 1985 meeting.)

  • Kenyon
  • Thaxton
  • Bradley and thermodynamics/information
  • origins science, uniform experience, information, and Geisler
  • Meyer himself
  • 1984 conference
  • late-1980s and Pandas
  • early 1990s
  • Meyer before 1998
  • KvD case

It really is all about religion in the endEdit

End of the book, "Why it matters."

What it would take for ID to have a chance of being taken seriously as anything more than a pernicious nuisanceEdit

  • serious lit review
  • serious ID hypothesis
  • serious about its own history

stuff to refer to: themes: Dembski- and Behe-rebuttals not mentioned Del Ratsch, bulldozers SETI rebuttal archeology rebuttal Meyer quote on how an informative DVD weighs same as a less informative one Pennock paper on repetitiveness of Meyer, 2004 article copied from previous articles

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