28 December 2008

Weekly sampler 21

Well, it's the first sampler since June, but I won't try to make up for lost time.

1. Todd Wood has started a blog, and it's excellent. His slant is unique -- he's a young-earth creationist -- but his writing is superb and his expertise in genetics and genomics is world-class. My favorite entry so far: a commentary on a recent report describing genetic variation among humans. The most recent post deals with the principle of accommodation and one of its Enlightenment defenders, one John Wilkins. Todd hasn't activated comments, so expect a journal and not a conversation. But have a look, and consider the gigantic difference between Todd's work and Mike Behe's. There's just no comparison, and Todd is an example of why one should not grant respect based solely on someone's willingness to accept an ancient universe or universal common descent.

2. Okay, best segue ever. Speaking of John Wilkins, Evolving Thoughts (a blog at ScienceBlogs run by a philosopher of biology) has some very interesting recent posts defending "theistic evolutionists" like me. Back in September, he discussed "Darwin, God and chance" and concluded:

Why does this matter beyond a bit of mental gymnastics, especially since I am not a theist? Well it has one rather significant implication: it means that those who criticise theistic evolutionists (like Asa Gray) for being inconsistent or incoherent are wrong: it is entirely possible to hold that God is not interventionist, and yet hold that God desired the outcomes, or some outcomes, of the world as created. In simpler terms, there's nothing formally wrong with believing the two following things: 1, that God made the world according to a design or desired goal or set of goals; and 2, that everything that occurs, occurs according to the laws of nature (secondary causes). In other words, it suggests that natural selection is quite consistent with theism, solving a problem I discussed earlier.
Read the whole post to see how he arrived at this conclusion, and don't miss the work of his collaborator, one Phil Dowe. More recently, Wilkins has summarized the "theistic evolution" position as he sees it, and reiterated his contention that the position is not incoherent. (Well, duh, but there are plenty of axe-grinding nitwits who assert just that.) I'll discuss these ideas in a separate post soon; in the meantime, pay Wilkins a visit.

3. Steve Martin's blog An Evangelical Dialogue on Evolution has become the blogospheric world headquarters for multilateral discussion of evangelical approaches to the theological understanding of evolution. The most recent series tackled questions of evolution and original sin, centered on an article by George Murphy and featuring responses by Terry Gray, Denis Lamoureux and David Congdon. Congdon's blog, The Fire and the Rose, is one of my favorites.

Left, the human eye as sketched by Descartes. Right, the eye of a fruit fly as revealed by scanning electron microscopy. Courtesy of Wellcome Images, Creative Commons license.

4. The most recent issue of Evolution: Education and Outreach is devoted to the evolution of eyes. And it's all free. Includes an introduction by Ryan Gregory, who also points us to an issue of The Lancet that focuses on evolution. Sheesh, is there some kind of anniversary coming up? :-)

5. Illusions of various kinds are something of a hobby of mine. Hence my interest in an online collection of kinetic optical illusions at Scientific American (meaning that the images produce an illusion of movement). Something else that's cool about the collection: some of the illusions were created (or discovered) by Donald MacKay, a Christian neuroscientist who has influenced me and many of my colleagues through his vigorous and uncompromising approach to the relationship between science and Christian faith. (We read part of his Science, Chance and Providence in our randomness reading group.) Make sure you look at the third image -- it's the infamous Enigma illusion.

6. Here's another kind of illusion that is interesting and informative: synesthesia, in which a perception (such as smell or color) becomes associated with a seemingly unrelated experience (a number or a different sensation). V.S. Ramachandran devoted one of his Reith Lectures to this phenomenon, which he described as "mingling of the senses." A new report describes a new version: touch-emotion synesthesia, in which certain textures evoke particular emotions. The proposed explanation for how these peculiarities is worth a look, too.

7. Using bumps in the road to make music. It'll be a clue in National Treasure 3, you just wait. Note that this link comes courtesy of Very Short List, which is a delight.

8. Deb and Loran Haarsma's excellent book Origins got a nice review at the Reports of the NCSE. I'll write one of my own sometime this spring. When the next issue of RNCSE goes online, I hope it will include my review of Gordon Glover's Beyond the Firmament.

9. The most recent (January 2009) issue of Scientific American is all about evolution. Larry Moran has some typically excellent comments over at Sandwalk, addressing pop evolutionary psychology [gag], testing natural selection, and why everyone should learn evolution.

10. Now off to enjoy one of our family's holiday traditions, this time with a mix of Scotch and rum.

16 November 2008

Critiquing Nature's Destiny by Michael Denton, Part I

I've mentioned before that we've had an intelligent design proponent (code named Timaeus) as an official guest on the ASA email list. The discussion has been mostly useful. One thing that became clear early on was the fact that Timaeus is not a scientist and has not read much science outside of the works of ID defenders. His repeated and enthusiastic citation of Michael Denton led some to request commentary on Denton's work, by knowledgeable scientists. This is my contribution.

Timaeus has made frequent mention of the work of Michael Denton, who has written two books that are popular among ID sympathizers. The first, Evolution: A Theory in Crisis, was published in 1985 and is regarded as a major influence on the early ID movement. The second, Nature's Destiny, was published in 1998 and seems to be far less influential. I recently read Nature's Destiny, and offer here a review in two posts. In this post, I present an overview of the book and its arguments, with a general critique and comments on the portrayal of the book by Timaeus. The second post (if I find time to collate it) will contain more detailed comments on technical aspects of Denton's claims in areas of my expertise. In separate posts, I will comment on Evolution: A Theory in Crisis (henceforth abbreviated as ETC).

Overview

Reading Timaeus' characterizations, one might reasonably suppose that Michael Denton has written books that demolish "Darwinian evolution," in ways not seen before and not answered (or answerable) by evolutionary biologists. Timaeus asserts, for example, that Denton "rips the Darwinian mechanism to shreds, armed with thousands of references to the latest knowledge in biochemistry, genetics, embryology, physiology, comparative anatomy, etc." And that quote clearly refers to Nature's Destiny.

This is a very serious mischaracterization of Denton's work. Denton did attempt, in ETC, to undermine "Darwinian evolution" – unsuccessfully, as I will explain elsewhere. In Nature's Destiny, his project is wholly different. Nature's Destiny seeks to defend a law-based, teleological view of cosmic history in which the development of humanity is the ultimate goal. The view is non-Darwinian for sure, in the sense that such strong teleological conceptions are non-Darwinian by definition. But any claim that Nature's Destiny does damage to modern evolutionary biology is a significant distortion. In fact, I would be most interested in a conversation with Michael Denton, both because I find his work intriguing and because I would be quite curious to hear his response to Timaeus' triumphalistic pronouncements regarding his ideas. Specifically, I wonder if Denton believes that he has "shredded" the "Darwinian mechanism," and whether he would acknowledge that many of the challenges he raised in his first book have failed completely in the face of vast amounts of data arising from completely new biological subdisciplines. (More on this in a future post on ETC.) My point is not that I think Denton is a fool, but that on the contrary I'm pretty sure he'd be embarrassed by the propagandistic ends toward which his ideas are being employed. (Perhaps there is a clue here regarding his divestiture from the Discovery Institute.)

I found Nature's Destiny to be mostly interesting, occasionally informative, occasionally exasperating, and ultimately unpersuasive. Ominously, I found that the chapters I judged to be the weakest were the chapters on topics I know the best. I suspect that cosmologists, physicists, biophysicists and perhaps chemists would feel the same way. In any case, I hasten to add that I have not concluded that Denton is wrong or that his failure to assemble a convincing case is somehow evidence to the contrary. His book is far stronger than Behe's Edge of Evolution, and unlike that unacceptably misleading and inaccurate work of folk science, Denton does not invite speculation that he is willing to abuse science in the course of metaphysical argumentation. Nevertheless, there are times when he's clearly trying too hard, and this is one of my main criticisms of the work.


Nature's Destiny does not attempt to destroy "Darwinism." It attempts to defend a "teleological religious concept of the cosmos as a specifically designed whole, with life and mankind as its primary goal and purpose." (p. xi) As Denton describes in his autobiographical account in Uncommon Dissent and in the prologue, the book can be viewed as an updating and expanding of a classic work by Lawrence Henderson (The Fitness of the Environment, 1913) that describes the ways in which the cosmos (specifically its chemistry) is remarkably fit for life. As Denton puts it in Uncommon Dissent (p. 168), Henderson demonstrated that

there is clear evidence that some adaptive fitness is given from within. This is adaptation "for free" arising out of the intrinsic properties of matter...
It may be that some forms of "Darwinism" cannot abide such talk, but those who think that consideration of nature's "eerie perfection" is somehow "anti-Darwinian" should read Simon Conway Morris. In fact, Conway Morris' Life's Solution is the book that every ID proponent should read after reading Nature's Destiny. Conway Morris' project overlaps with Denton's in obvious ways, and Conway Morris cites Denton twice, approvingly. But one never hears an ID propagandist brag that Conway Morris has "shredded the Darwinian mechanism." This, to me, is telling. I urge those who take Denton seriously to read Life's Solution. It simultaneously affirms Denton's basic view (that life is an inevitable result of the "laws" of the cosmos) while putting the lie to any claim that Denton or anyone else has undermined the theoretical foundation of modern evolutionary biology. If there is hope for ID as a serious intellectual movement, it lies in the deep cosmic concepts that unite the work of Simon Conway Morris and Michael Denton. But as long as ID propagandists believe that Denton has wrecked evolutionary explanation, they will purvey ignorance and confusion, and prolong the degeneration that gives us Casey Luskin and the disastrously bad Edge of Evolution.


Critique

1. As the articulation of a certain metaphysical view of the cosmos, Nature's Destiny works fairly well. As a defense of that view, it is wholly unconvincing, and I suspect that Michael Denton would understand my criticism. Nature's Destiny explores the notion of fine tuning and deep direction at every level of organization; it is not primarily a book about biological evolution. It begins with a standard retelling of the physics fine tuning story, then turns to some special examples of proposed fine tuning in chemistry. These chapters are fun to read, and contain very nice historical and scientific summaries on topics such as the properties of water, carbon and other elements, and gases. But even in these better chapters, and frequently in later chapters, careful readers will detect numerous instances of special pleading, and scores of arguments that go like this:
X is a really good thing for life. It is likely that X must be this way to enable biological function.
Or like this:
X is a really good thing for life. It seems there is no other way to do it, but somehow the cosmos found that way.
The key word is "seems." That word occurs over and over and over again, as do "likely" and "appears" and "perhaps" and "it may be," and in one sense it is a credit to Denton that he is careful not to overstate his case. (His admirers often lack this wisdom.) For this reason, it felt somewhat strange to read the book after seeing Timaeus' chest-beating.

The main impression I got from Nature's Destiny was this: Michael Denton is a Platonist who has a strong preference for typology and for teleological conceptions of the universe. To him, the universe seems to exist just for humans. And so everything he looks at is made to conform to this view. Now, this isn't meant to be an insult or a particularly damning criticism. I have some preferences and predilections of my own (I am decidedly not a Platonist, for example), and I would be a fool to claim that my views are unaffected by these precommitments. My point is that those of us who don't share Denton's somewhat odd viewpoint are able to see just how often his arguments and his choices are strongly affected by the momentum of his cause. To Denton, a lot of things "seem" to be extraordinary. Everything, to Denton, appears to be supremely and perfectly optimized, to the point that he must look for perfection (more accurately, fitness) in every aspect of biology and biochemistry. To me and to others, life just doesn't look like this at all.

And so I see much of Nature's Density as weird and extreme, containing speculations that range from reasonable to utterly off-the-wall, forced by a view of cosmic perfection that I don't embrace for various reasons. In chapter 13, "The Principle of Plenitude," the argument reaches a crescendo when Denton embraces the pre-Darwinian notion that all – or nearly all – possible life forms have been actualized on Earth. Phrases like "seems likely" and "difficult to see" appear multiple times on each page. The equivocation does not, to me, mask the odor of special pleading, which is strongest in the sections on biological evolution.

2. When critiquing "Darwinian" evolutionary mechanisms, Nature's Destiny offers nothing more than standard arguments from ignorance. Again, Nature's Destiny is not the demolition of Darwinism of Timaeus' caricature, but it does occasionally touch on the plausibility of Darwinian explanation. Denton offers nothing new or creative here, simply repeating arguments of the "it is difficult to see how" type. His descriptions of "spectacular adaptations" are enjoyable, but the argument is tiresome and weak. It should be unnecessary to make this point: one does not demolish – or even damage – evolutionary explanations by confessing one's personal incredulity.

This would be a good place to address another aspect of Timaeus' claim that Denton's work in Nature's Destiny "rips the Darwinian mechanism to shreds, armed with thousands of references to the latest knowledge in biochemistry, genetics, embryology, physiology, comparative anatomy, etc." The book contains about 600 notes, at least 1/4 of which are ibids. A few notes refer to more than one reference, but scores are to historical sources such as Darwin, Cuvier and Henderson, all of which are cited repeatedly. And more than half of the book is on fine-tuning topics (water, carbon, etc.) that didn't make Timaeus' list and don't concern the "Darwinian mechanism" as he obviously implies. To call Timaeus' statement an exaggeration is to be generous. The truth is that Denton makes relatively little reference to current science, and when he does he creates a mixture of interesting scientific commentary and shameless cherry-picking.

3. Like Behe, Denton peppers his descriptions of nature with effusive metaphors and confessions of wonder and awe. Cherry-picking and inaccuracies aside, these narratives are entertaining, educational and even inspiring. But they cannot take the place of the argument that needs to be made, namely the argument that adaptations, however spectacular or wonderful, are inexplicable outside of the preferred metaphysical framework. Denton overplays his hand in places, creating the impression that he is willing to substitute "shock and awe" for careful argument. Of course biology is cool. Of course it inspires awe. Not even Richard Dawkins would disagree with that.

So in summary, I found the book to be a bemusing and mostly unsuccessful attempt to defend a view of the cosmos built completely on commitments to typology, teleology, and law-based design. Unlike Behe's Edge of Evolution, the book lacks the sinister implication of deliberate duplicity, and contrary to certain propagandistic pronouncements, it neither attempts nor achieves a damaging critique of evolutionary theory. I recommend that Nature's Destiny be read as a metaphysical treatise, written with a distinctly apologetic angle, and that readers understand that it is characterized by special pleading. And I recommend that anyone who reads it follow up by reading Life's Solution by Simon Conway Morris. Both the overlap and the contrast are striking.

23 October 2008

How evolution can inspire faith

It is understandably typical for Christians to consider evolution as something that confronts and challenges faith. To say that North American evangelicals consider evolution to be largely incompatible with Christian belief is to state the painfully obvious. An evangelical who will just admit that common descent might be true is a progressive thinker, and much of the current discussion is dominated by attempts to push back on evolution by suggesting that it really isn't a completely accurate – or even minimally accurate – description of the development of life in God's world. Almost certainly because of perceived "incompatibilities," evangelical theological reflection on the implications of various scientific conclusions, specifically with regard to biblical interpretation, is regularly decried as dangerously inadequate. (Consider Peter Enns' recent review of a new book on the age of the earth by two of my most excellent colleagues. HT: David Opderbeck.) In other words, many thinking evangelicals are concerned about the lack of serious evangelical engagement of evolutionary theory.

But help is on the way. I've already mentioned Gordon Glover's wonderful Beyond the Firmament (and I reviewed it for the forthcoming issue of the Reports of the NCSE). I haven't seen Denis Lamoureux's Evolutionary Creation yet, but if it's as good as Mike Beidler says, then the landscape is looking a lot less barren. And now we have a very significant new voice in the conversation: my friend Daniel Harrell, associate minister at Park Street Church in Boston, a brilliant reformed preacher and gifted thinker whose ministry had a profound impact on myself and my family at a critical juncture in our spiritual lives. Daniel has written an excellent and interesting book on evolution and Christianity, and I give it my highest possible recommendation.

It's called Nature's Witness: How Evolution Can Inspire Faith, and you can buy it at Amazon or CBD right now. I read it a few months ago and blurbed it, and sometime in the next few months I hope to review it here. In the meantime, look for occasional comments and quotes. But for now, here's an excerpt from the Introduction, presented with permission from the publisher. In fact, this is the bulk of the Introduction, but the final paragraph is the paragraph I would have chosen to capture the essence of Daniel's approach and his project.

Walking across the Boston Common one cold winter’s eve, I was approached by a gentleman, somewhat agitated, who recognized me from church. “Are you the minister who’s writing the book on evolution?” This didn’t sound good. “Uh, ... yes?” I replied, bracing myself. “Do you believe in the word of God? Do you believe that God created the heavens and the earth in six days, like the Bible says?” His articulation was semiautomatic—as was his tone. I assured him that yes, I believed the Bible says that God created the heavens and the earth in six days. I also believe that rivers clap their hands and that mountains sing (Ps 98:9) because the Bible says that too. But I don’t think that the Bible means six twenty-four-hour days any more than I believe that the Bible means that rivers have literal hands. He worried that I suffered from delusion (which as far as I am concerned is never outside the realm of possibility). However, I reminded him that there are two types of delusion. There is the delusion that believes something that is not true, and there is the delusion that fails to believe something that is true. If evolution is an accurate description of the emergence of life, as science attests, then believing it alongside the Bible should pose no threat. There’s no need to fear any honest search for truth because in the end, all honest searches for truth inevitably lead back to God. Historically, religious faith, particularly Christianity, served as the loom onto which the discoveries of science were woven. It was within a Christian theological framework that scientific disclosure found its transcendent meaning. Descartes, Bacon, Galileo, Kepler and Newton, believers all, saw their work not as replacements for faith, but as extensions of it. The idea was that the best of science and the best of theology concerted to give human beings deeper insight into the workings of the universe and, subsequently, into the divine character. Scientific discovery was received with gratitude to the Almighty for the wonder of his creation. Scientists, alongside the psalmist, would proclaim, “The heavens declare the glory of God; the skies proclaim the work of his hands” (Ps 19:1 NIV). The balance between faith and science (or reason) was established in the Middle Ages by Thomas Aquinas. Aquinas, building on Augustine, established a delicate equilibrium between theology (reasoning down from faith) and philosophy, analogous to science (reasoning up from sensory data). Aquinas, unlike the Reformers who would follow, taught that human senses and rational faculties, as made by God, were competent for understanding reality, albeit from a limited standpoint. The limits were filled in by theology. Aquinas asserted that God acted through “secondary causes,” creating the world according to his laws and then giving nature room to unfold in accordance with God’s laws. Whatever was good science was good as far as God is concerned; science simply described what God had already done. However, if God operated mostly behind the scenes as the prime cause, then it wasn’t long before people started wondering whether he was there at all. In time, reliance upon divine revelation gave way to human reason in its Enlightenment form, and soon the supernatural was rendered superfluous. As science advanced, Christians reacted by retreating into a sort of Manichean dualism whereby science was demonized and faith grew reliant on a super-supernatural world where any ordinary explanation raised suspicion. With battle lines so starkly drawn, scientists were left to assume that any move toward Christian faith was akin to committing intellectual suicide. Conversely, the faithful relied on science for their medicine or the weather forecast, but much more than that was to attempt spiritual suicide. Let a spark of evolution in the door and you were liable to catch the whole house on fire. The controversy between Christian faith and evolution is exacerbated by increasing mounds of scientific data that lend weight to evolution. Paleontology, biochemistry, cosmology, physics, genetics—you name the discipline—each regularly puts forth newly discovered evidence in support of Darwin’s simple idea of descent with modification. While some people of faith choose to keep their doors closed, shutting out science is not necessary. Christian faith by definition defies human conceptions of reality (1 Cor 3:19). Its claims are grounded in extraordinary events that defy scientific explanation (most importantly the incarnation and resurrection of Jesus). But God is not only present where science is silent; he remains present even where science speaks loudest. The expansiveness of the universe, the beauty and complexity of organic life and the remarkable makeup of human consciousness—naturally explicable occurrences—are also interpreted by Christians as manifestations of God (Rom 1:20). Christianity consistently asserts that all truth is God’s truth, implying that faith and science, despite differences when it comes to explaining why, nevertheless should agree in regard to what is. Why bother talking about God if God has no relation to observable reality? An avalanche of books has been devoted to the controversy between Christianity and evolution. Don’t expect a contribution to that debate here. There are plenty of other places where that conversation occurs. Instead, I’d like to look at Christian faith in the face of evolution as essentially true as most scientists assert. Now I know that just because a particular theory makes sense of the way something could have happened, it doesn’t necessarily mean that it actually happened that way. But if evolution truly provides an accurate description of life on earth, and things did happen the way evolution describes, how might we rethink the way we think about what the Bible says? To rethink what we think about the Bible is not to rewrite Scripture, nor is it to capitulate to Christianity’s detractors. Instead, rethinking and reworking our theology in light of accurate data results in a more dependable and resilient theology. To be a serious Christian is to seek truth and find it as revealed by God both in Scripture and in nature. If God is the maker of heaven and earth, as we believe, then the heavens and earth, as science describes them, have something to say about God. Natural selection need not imply godless selection. To be reliable witnesses of creation can’t help but make us more reliable witnesses to the Creator.
I hope you're intrigued. Go buy the book—you'll love it—then look for occasional conversations here about some of Daniel's ideas.

Steve Matheson, Calvin College

19 October 2008

Why I'm not a Behe fan: conclusion and a challenge

About 2 months ago, I finished a series on Michael Behe's latest book, The Edge of Evolution. I concluded that it was a terrible book, displaying significant errors of both fact and judgment. The book's main argument is a population genetics argument, and Behe seems to have little knowledge or understanding of that difficult subject. The book is a joke, and I believe it will someday be seen as one of the more disastrous mistakes made by the ID movement. But I think it's important to distinguish between Behe's errors (which reflect on his scientific credibility and on his decision-making habits) and his thesis. His book is full of mistakes, but that doesn't mean that his proposal is known to be false. So I'd like to make it clear what my verdict on his book actually is, then present an outline of one way to actually test Behe's hypothesis.

1. In The Edge of Evolution, Behe correctly identified a biological process – the generation of genetic variants that lead to evolutionary change – as a likely focus of deliberate design. Having concluded that common descent is true, he reasoned that the trajectory of change through the tree of life might be expected to show evidence of non-random direction. Design, as he and others in the ID movement conceive it, might be manifested in the pattern by which the tree of life came to be. (Some might go as far as to say that it must be manifested in such a way, but I don't think Behe suggests this.) My point is that there is nothing stupid, irrational, or unscientific about Behe's reasoning. So, Behe conceived a hypothesis, which I will restate as follows:

  • Based on the consideration of life's complexity, specifically on the consideration of the integrated complexity that characterizes the molecular machinery of the cell, it is proposed that random mutation and subsequent selection cannot fully account for the evolutionary development of biological systems.
  • Consequently, it is proposed that the process of mutation is non-random.
Again, I find nothing outrageous or stupid about the hypothesis, or even its rationale. Molecular machines are astoundingly complex and integrated, and I do think it's reasonable to wonder how such things can come about without the aid of a superintelligence. In other words, Behe's proposal is not inherently incoherent or otherwise easily dismissed. Might the machinery of life have emerged through non-random processes? Sure. EoE is a joke, but not because the proposal is a joke.

EoE is a joke because Behe seems not to have even attempted to establish the strength of the hypothesis. Very little of the book is devoted to this central concern, and those sections that take up the task are so laughably wrong that they have led me to question Behe's scientific integrity. (Sorry, no apologies: the errors are too basic, and the proposal too world-altering, to give someone who is vying for scientific immortality a pass on standards of scientific conduct.)

But this is important: Behe's failure to even attempt an honest defense of his proposal does not imply that the proposal has been falsified. It hasn't. It remains possible that the development of biological machines – especially in the early days of the tree of life – was characterized by a non-random, directed trajectory. (I happen to doubt this, but that's not relevant here.) Behe's book is a failure, but his hypothesis stands.

So here we are: an interesting and potentially revolutionary hypothesis has been advanced. It has a certain explanatory appeal, and it has unquestioned relevance for believers of many kinds. It is empirical and rational. And, I maintain, it is testable, at least in principle. And so I'm offering to collaborate on a real effort to test it.

2. Behe's proposal leads to certain types of testable predictions. He claims that the genetic changes that underlie certain levels of evolutionary change occurred non-randomly. In other words, he claims that there is a dramatic mismatch between rates of genetic mutation and rates of evolutionary change. His efforts in EoE were ridiculously inadequate. Here is an outline of an approach that could succeed.
  • One major mistake that Behe made was to devote most of his attention to a "case study" in which significant genetic change did not occur. His case study was poorly suited to his purpose, but even if it had been better conceived it would be worthless. We can't learn about how evolution works by analyzing examples in which it didn't occur. (Well, of course it did occur in Behe's case study, but the changes that he claims are non-random are different by his own definition.)
  • So, any approach to the detection of non-random influences on evolutionary change needs to focus on case studies that actually involve the relevant level of evolutionary change. Examples should be easy to find, by considering the tree of life and the branching levels at which one would hypothesize non-random change.
  • The evolutionary lineage(s) selected for analysis should be fairly well-documented, so that the nature of the relevant common ancestors can be reasonably inferred. This probably means that much deeper lineages (such as eukaryotes or even multicellular eukaryotes) would not make good subjects of analysis. Since Behe is pretty sure that design characterizes differences at the level of class (and deeper), this concern is not a barrier to addressing his hypothesis, at least at those levels of divergence. The tetrapod lineage could serve well, but there are any number of evolutionary trajectories that could be considered.
  • Within the selected lineage(s), one or more evolutionary changes would be selected for genetic analysis. Changes could be simple (such as the molecular evolution of a particular protein of interest) or more complex (such as the development of a particular attribute like teeth or feathers or lungs), and could even include the sum total of the genetic changes in a lineage, but must be amenable to genetic description. Most importantly, the evolutionary changes that are analyzed must be associated with the specific design postulate. The goal is to examine the genetic changes underlying an evolutionary transition that Behe would identify as designed.
  • Once the genetic changes of interest have been identified, analysis can proceed the way Behe pretended to proceed in EoE: inferred mutational trajectories can be considered in the light of estimated mutation rates and estimated generation numbers. If non-random mutation is clearly necessary for the evolutionary changes in question, it should be apparent that even the simplest mutational paths leading to change are well beyond the explanation of random mutation.
My description makes the undertaking sound straightforward, and in principle it is, but of course such examination of even a relatively simple evolutionary change is a significant and demanding project. Inferring the genetic makeup of the common ancestor is a project all by itself, and constructing postulated mutational pathways is the kind of work that occupies many professional biologists full-time. (Consider the work of Joe Thornton and his group, considered among the best analyses of this kind.) Estimates of generation number will span huge ranges even after the most careful consideration of the variables.

But this is the work that any real scientist and scholar would know has to be done. Behe's hypothesis is completely untested, and only the kind of study that I have outlined can change that. I invite any scholar with interest in undertaking this project to contact me. I would be interested in joining a collaborative effort to test the non-random mutation hypothesis, and I have some significant resources that could be brought to bear on the problem. This is a serious offer, and I would encourage readers to forward it to anyone who might be interested in discussing the details.

15 October 2008

And we're back!

Okay, wow, that was a long hiatus. I can explain, really I can. Here's a report on my activities in the last six weeks.

1. I wandered into Telic Thoughts in search of intelligent intelligent design advocates. It went okay -- there was real discussion (because TT actually wants dialogue) but it was painfully difficult to get through some major misconceptions (created by Michael Behe). The painful part was in the thread called Behe's Test, Take 2, in which some of us tried to explain the relevance of some recent work on bacterial antibiotic resistance to "Darwinian" evolution. I'll repost one of my contributions here soon.

2. Some months ago, after hearing Richard Colling give a talk at Calvin (on his ideas set forth in his book Random Designer) my colleague and friend Randy Pruim (of the mathematics and statistics department) and I decided we should get some people together to get serious about this whole question of randomness and God's action. We got a grant from the Calvin Center for Christian Scholarship to fund a yearlong reading group. We've met once already, and it was a blast. I'll separately post on our activities and ideas and my thoughts. Randy, by the way, is also the director of our new HHMI-funded Integrated Science Research Institute (ISRI), and he's devoted a page to our reading group, affectionately known as Random Readers.

3. My blogging buddy over at Clashing Culture, Mike Haubrich, had me as a guest on his cool radio show (Atheists Talk) in the Twin Cities. The subject was "Defending Theistic Evolution," broadcast October 5. It was fun, and I even took an email question from PZ Myers. (Well, it was more like the abstract of a dissertation than a radio show question, but maybe Mike will have me back and we can talk longer.) Some of the questions we discussed:

  • How do you separate your science from your belief?
  • What is your take on theistic evolution?
  • Were humans the goal of creation?
  • "All of the facets that shape evolution involve lots of cruelty and pain only partially tempered by the joy of sex. I have trouble reconciling a loving God with what we know about evolution. How do you defend this view of evolution?"
You can listen to the interview at the Atheists Talk page.

4. I'm not the only one who was dumb enough to think that Uncommon Descent is a place where people might be able to intelligently discuss evolution, design and faith; Ted Davis made the same mistake (and I do think we were mistaken to go there in the first place). Last month, Ted engaged in an interesting discussion there, for a time, with two other commenters, going by the names of Jack Krebs and Timaeus. They were soon all banned, because Uncommon Descent is not, and does not pretend to be, a place where thoughtful adults hold discussions. But Ted persuaded Timaeus to come to the ASA email list instead, for the purpose of examining and addressing the perceived animus held by "theistic evolutionists" toward ID proponents. (Note: if you follow any of the links to read Timaeus' posts, you'll see a lot of odd characters, which result from the unwise use of Microsoft Word (!) to compose email.)

The conversation began about 3 weeks ago, and peaked about a week and a half later. It's not over, but everyone seems to be taking a breather. I would say that it's going better now than it did at first, though it still seems that Timaeus (a defender of ID) is not able to understand the reasons why Christians like me can see no good reason to suppose that Darwin's theory is inherently or necessarily atheistic or a-teleological. Timaeus is (by his own admission) a non-scientist, and it shows when he mentions evolutionary theory or quotes the usual ID suspects. (He repeats the "Darwinists never studied non-coding DNA" myth, and is unjustifiably impressed by Denton, Behe and even Egnor.) He has a penchant for propagandistic rhetoric, exacerbated by his shallow understanding of the science that is misused by ID apologists. At first, I thought it was pretty clear that he had come to the ASA to argue for ID, and not to listen to the responses of people who have thought about all of this before. And it's still not apparent that Timaeus understands or respects the evolutionary creation position, or that he finds any significant value in listening to what knowledgeable scientists say about ID proposals. But the last few exchanges have been quite a bit better. When the subject is just plain design, and not science or religion, actual dialogue seems to happen, and we're currently discussing Del Ratzsch's work on the nature of design and the marks it might leave.

Talking to ID apologists about design itself is hard enough without all the pollution of anti-science propaganda and theological incompetence. But maybe there can be some progress, at least toward peaceful coexistence of Christians who do and don't prefer certain types of explanation. So watch for updates on the Random Readers, and I'll post any further discussion with Timaeus here.

30 August 2008

And I don't even eat mooseburgers

In case your local news hasn't picked up the story yet.

27 August 2008

A pop science book meme

Various book memes have come across my path, and they can be inspiring and interesting. Here's one I chose to pass along because it should result in the evolution of a pretty good list of recommended popular science books. (The originator calls it the "great pop-sci book project.")

If you choose to pass it on, follow the instructions and link to the source, which is Cocktail Party Physics. And thanks to Brian at Laelaps for the heads-up.

The instructions, from Cocktail Party Physics:

1. Highlight those you've read in full
2. Asterisk those you intend to read
3. Add any additional popular science books you think belong on the list
4. Link back to Cocktail Party Physics (leave links or suggested additions in the comments, if you prefer) so I can keep track of everyone's additions. Then we can compile it all into one giant "Top 100" popular science books list, with room for honorable mentions.
And here's the list:

1. Micrographia, Robert Hooke
2. The Origin of Species, Charles Darwin
3. Never at Rest, Richard Westfall
4. Surely You're Joking, Mr. Feynman, Richard Feynman
5. Tesla: Man Out of Time, Margaret Cheney
6. The Devil's Doctor, Philip Ball
7. The Making of the Atomic Bomb, Richard Rhodes
8. Lonely Hearts of the Cosmos, Dennis Overbye
9. Physics for Entertainment, Yakov Perelman
10. 1-2-3 Infinity, George Gamow
11. The Elegant Universe, Brian Greene
12. Warmth Disperses, Time Passes, Hans Christian von Bayer
13. Alice in Quantumland, Robert Gilmore
14. Where Does the Weirdness Go? David Lindley
15. A Short History of Nearly Everything, Bill Bryson
16. A Force of Nature, Richard Rhodes
17. Black Holes and Time Warps, Kip Thorne
18. A Brief History of Time, Stephen Hawking
19. Universal Foam, Sidney Perkowitz
20. Vermeer's Camera, Philip Steadman
21. The Code Book, Simon Singh
22. The Elements of Murder, John Emsley
23. *Soul Made Flesh, Carl Zimmer
24. Time's Arrow, Martin Amis
25. The Ten Most Beautiful Experiments, George Johnson
26. Einstein's Dreams, Alan Lightman
27. *Godel, Escher, Bach, Douglas Hofstadter
28. The Curious Life of Robert Hooke, Lisa Jardine
29. A Matter of Degrees, Gino Segre
30. The Physics of Star Trek, Lawrence Krauss
31. E=mc<2>, David Bodanis
32. Zero: The Biography of a Dangerous Idea, Charles Seife
33. Absolute Zero: The Conquest of Cold, Tom Shachtman
34. A Madman Dreams of Turing Machines, Janna Levin
35. Warped Passages, Lisa Randall
36. Apollo's Fire, Michael Sims
37. Flatland, Edward Abbott
38. Fermat's Last Theorem, Amir Aczel
39. Stiff, Mary Roach
40. Astroturf, M.G. Lord
41. The Periodic Table, Primo Levi
42. *Longitude, Dava Sobel
43. The First Three Minutes, Steven Weinberg
44. The Mummy Congress, Heather Pringle
45. The Accelerating Universe, Mario Livio
46. Math and the Mona Lisa, Bulent Atalay
47. This is Your Brain on Music, Daniel Levitin
48. The Executioner's Current, Richard Moran
49. Krakatoa, Simon Winchester
50. Pythagorus' Trousers, Margaret Wertheim
51. Neuromancer, William Gibson
52. The Physics of Superheroes, James Kakalios
53. The Strange Case of the Broad Street Pump, Sandra Hempel
54. Another Day in the Frontal Lobe, Katrina Firlik
55. Einstein's Clocks and Poincare's Maps, Peter Galison
56. The Demon-Haunted World, Carl Sagan [I've read parts]
57. The Blind Watchmaker, Richard Dawkins
58. *The Language Instinct, Steven Pinker
59. An Instance of the Fingerpost, Iain Pears
60. Consilience, E.O. Wilson
61. Wonderful Life, Stephen J. Gould [I've read most of it]
62. Teaching a Stone to Talk, Annie Dillard
63. Fire in the Brain, Ronald K. Siegel
64. *The Lives of a Cell, Lewis Thomas [I've read excerpts]
65. Coming of Age in the Milky Way, Timothy Ferris
66. Storm World, Chris Mooney
67. The Carbon Age, Eric Roston
68. The Black Hole Wars, Leonard Susskind
69. Copenhagen, Michael Frayn
70. From the Earth to the Moon, Jules Verne [a long, long time ago]
71. Gut Symmetries, Jeanette Winterson
72. *Chaos, James Gleick
73. Innumeracy, John Allen Paulos
74. The Physics of NASCAR, Diandra Leslie-Pelecky
75. Subtle is the Lord, Abraham Pais

Some suggestions and comments:
  • I would probably substitute The Selfish Gene or The Extended Phenotype for The Blind Watchmaker, but The Blind Watchmaker is still a fine choice.
  • Like others, I would include something by Oliver Sacks, probably The Man Who Mistook His Wife for a Hat.
  • I would ditch anything by Carl Sagan, and certainly wouldn't keep The Demon-Haunted World.
  • I wouldn't include two works by one author (e.g., Richard Rhodes) unless they were both surpassingly great.
  • Include The Song of the Dodo by David Quammen and The Beak of the Finch by Jonathan Weiner. Phantoms in the Brain by Ramachandran and Blakeslee gets honorable mention.
  • Any votes for The Fourth Day by Howard Van Till? The Double Helix by James Watson? I'm partial to What Mad Pursuit, Francis Crick's nice memoir. I haven't read Genome by Matt Ridley, but maybe one of his works belongs on the list.
Looking forward to other suggestions.

Summary:
Add The Song of the Dodo, The Beak of the Finch (it won a Pulitzer, people) and The Man Who Mistook His Wife for a Hat. Delete The Demon-Haunted World.

24 August 2008

Should we expect design?

What kind of universe should one expect to see, as a Christian, or as an atheist, or whatever? Is design (conveniently defined by fellows of the Discovery Institute) something that a Christian should expect to see? That's the question I ask over at Clashing Culture, reflecting on some of the weird theological claims of some ID proponents (and of Richard Dawkins). Wander over and weigh in.

23 August 2008

Why I'm not a Behe fan, Part IIB: abusing genetics

In a previous post, I started to explain a fact that some people (who don't know me) seem to find surprising or noteworthy. Michael Behe is a Christian who accepts common ancestry and an ancient cosmos, so you'd think I would be excited about the work of a fellow "theistic evolutionist." But I'm not. Two overall problems come to mind. (Basically, I find his conduct as a scientist to be unacceptable, and I find his proposals to be laughable failures.) I'm addressing the second one here. The discussion is quite long, so I divided it into two sections, Part A and this post, Part B, which will have to be split up. I'm sorry about the length; it would really take a whole book to carefully explain how Behe has misused genetics and probability.

1. Behe's fans say that he's a nice guy, and that the evolutionists are "crucifying" him. Both claims seem to be true, but they can't hide some serious problems with his conduct as a scientist.

Those issues are the subject of the first post.

2. Some of Behe's defenders think that he has effectively answered his critics. He has not, nor has he understood or acknowledged the most important criticisms of his crude claims.

Behe's recent book The Edge of Evolution (henceforth EoE) is the focus of this series, and as I exlained in Part A:

EoE makes exactly one specific scientific claim, accompanied by simplistic genetic assumptions and supported by a "case study." The scientific claim is that the mutations that drive large-scale evolution, and that are thought to underlie all evolutionary change (past and present), are non-random. And the "case study" is a long-winded account of the adaptation of the malaria parasite in the face of drugs intended for its destruction.
Part A dealt with the laughable case study. But the heart of EoE is the claim that random mutation rates are insufficient – spectacularly insufficient – to support step-by-step evolution of complex features. The implication, then, is that the mutations that underlie major evolutionary change did not occur randomly.

First, some important points of clarification:
  • Behe is not denying that common descent is true, or that evolutionary change results from mutation. He acknowledges both. He is saying that the most important mutations – those that led to, say, new cell types – could not have been random.
  • Behe is not saying that the combination of random mutation and natural selection (the "darwinian" mechanism) is not a driving force in evolutionary change. He acknowledges the efficacy of the process in explaining "a number of important details of life," such as drug resistance in bacteria or pesticide resistance in insects, and is willing to attribute the differences between widely divergent organisms to the workings of "randomness." Specifically, he writes that "explicit design appears to reach into biology to a certain level, to the level of the vertebrate class, but not necessarily further." (p. 220) This means that Behe claims to be certain that the major distinctions between goldfish and bats are non-random, but that the major distinctions between bats and people could be accounted for by random mechanisms. (He asserts the "edge of evolution" to lie somewhere between the species level and the class level. [p. 201])
  • Behe does not commit himself to a particular mode of divine intervention whereby the supposedly non-random mutations came about, and in fact he seems to favor a front-loading scenario in which God "was able to specify from the start not only laws, but much more." (p. 231)
These clarifications are important, because much of the criticism of EoE has been botched significantly. The book is bad, really bad, but it can't be honestly characterized as an anti-evolution argument. Ultimately, Behe seeks to prove that evolution had to be guided. That's the way to understand EoE, and as Joan Roughgarden wisely noted in her review, there are some "constructive" aspects of the book, including the abandonment of opposition to – or even ambivalence about – common descent.

So what's so wrong with Behe's argument in EoE? Well, first, here's the argument summarized:
  1. Evolutionary changes in the features of organisms require changes in genomes, changes which occur by mutation.
  2. Many of the most interesting evolutionary changes require multiple changes in the same genome, often in the same gene.
  3. Mutation rates, in terms of number of mutations per generation, are known to be on the order of 1 in 100 million.
  4. Based on this mutation rate, the probability of occurrence of an evolutionary change requiring several mutations is vanishingly small, such that the whole of life's history is not nearly long enough for the change to occur via random mutation.
And here are some ways in which Behe's argument is wrong and/or misleading.

I. Behe's assumption of a particular mutation rate is both absurdly oversimplified and inappropriately extrapolated into the entire tree of life.

The basis of all of Behe's calculations is a mutation rate of 1 in 100 million. This is the estimated rate at which misspelling-type mutation occurs in each generation, averaged over the entire genome, in humans. (The number doesn't consider other types of mutation, now known to be more common than previously thought.) Behe uses this number in all of his (flawed) probability calculations. Even if we knew nothing about mutation rates, the notion of extrapolating from an human (or even mammalian) characteristic to the whole of the biosphere (past and present) is ludicrous enough that it would by itself cast doubt on the credibility of the author.

Rates and characteristics of mutation are the focus of active current research, and many important questions remain unanswered. But we know that there is no such thing as "the mutation rate," in the biosphere or even in particular species. In fact, mutation rates can vary significantly, between types of organisms, between organisms in different states of health, in individual subpopulations of organisms, even between regions of the genome of a particular organism.

More importantly, it is ridiculous to assume that "the mutation rate" has always been the same. Consider a flowchart outlining mutation and its effects, taken from a recent review of the evolution of mutation rates:

Image from "Mutation rate variation in multicellular eukaryotes: causes and consequences," by C.F. Baer et al., Nature Reviews Genetics, August 2007. Click to enlarge (opens in new window/tab).

The idea is that mutations are created in at least two ways: 1) damage to DNA from external influences such as radiation; and 2) errors in the replication process. During the evolution of early life, neither of these influences would be expected to be the same as – or even comparable to – similar influences today. And that's just the beginning of the flowchart. There are error-correction systems that erase mutations before they can be passed on to the cell's descendants; again, only a fool would suppose that these systems have been present throughout life's history; indeed, bursts of mutation that occur today are usually caused by deficiencies in DNA repair and the appearance of "mutator lines" is thought to be an accelerating force in adaptation.

My point is not that we know what the genetic landscape was like during the early evolution of life's toolkit, nor am I claiming that we know whether or not certain mutations were "nonrandom." My point is that the extrapolation of estimated mutation rates in modern humans into the deep past is clearly unjustified, a move so foolish that it can only be the product of folk science.

II. Behe's treatment of adaptation always ignores existing genetic variation, and his arguments seem to assume that multiple mutations must occur simultaneously.

I've mentioned these problems before, and they constitute some of Behe's biggest errors. When he envisions the process of adaptation, in which several genetic changes separate one state from another, he automatically assumes that none of the changes exists at the beginning. Yet even Darwin knew that populations of organisms harbor huge amounts of genetic variation, as evidenced by the profound success of domestication (of plants and animals) by human selection. Most of Behe's critics have noted this, and Behe's response was a lame dodge. But perhaps the critics haven't been clear about why superfast evolution under human selection is such a problem for his ideas. Here's why: since organisms are so profoundly diverse genetically, many of the genetic changes that could be exploited by selection already exist. In fact, current theory predicts that rapid evolution, such as that required after significant environmental change, is much more likely in populations with significant standing variation.

With his simplistic view of genetics and variation in mind, Behe then describes how an adaptation that requires two different changes will be extraordinary unlikely, because the probability of each change is one in 100 million, and the probability of each occurring together is one in 100 million times 100 million. His critics argue, correctly, that his calculations assume that the mutations must occur simultaneously, and that is indeed very improbable. (Although maybe not nearly as improbable as we used to think.) In some of the discussions in EoE, he describes sequential acquisition of mutations (e.g., p. 111), but he calculates probabilities according to simultaneous occurrence (e.g., p. 63). Jerry Coyne explains why this is a gigantic error, and Behe seems unable to understand why.

I've written a separate post about Behe's mishandling of probability. It shows that he is not someone to consult when the subject is population genetics.

III. Behe claims that huge population sizes automatically generate more evolutionary opportunity than smaller ones do. This is incorrect.

It seems so obvious. More organisms means more mutations means more beneficial mutations means more and faster evolution. It's the kind of obvious, simplistic, intuitive claim that forms the bedrock of any folk science. But it's wrong.

On the contrary, very large population sizes lead to a so-called "speed limit" on adaptation that results from competition among beneficial mutations. The phenomenon is called clonal interference and it's particularly well understood in asexual organisms such as bacteria. The basic idea has been around for decades, but measurement and modeling of the phenomenon has been increasing in the last ten years. A very recent report, the subject of an upcoming post here, showed that the beneficial mutation rate in bacteria is 1000 times higher than previously thought – and the underestimation is due entirely to clonal interference.

The effect is not limited to asexual organisms; in fact, the problem of clonal interference is thought to constitute one of the major driving forces behind the evolutionary development and maintenance of sexual reproduction. The idea is that the genetic shuffling that accompanies sexual reproduction can bring beneficial mutations together and increase the effectiveness of selection. One of the few studies to examine this experimentally led to the conclusion that clonal interference is a problem for sexual organisms, and that sex reduces the impact of clonal interference and lowers the evolutionary "speed limit." (Interestingly, the malaria parasite is partly asexual, and reproduction inside a human is completely asexual, so clonal interference is probably a very significant "speed limit" on the evolution of P. falciparum – another reason not to use malaria as a benchmark "case study" for the understanding of all of evolutionary genetics.)

In summary, I find Behe's handling of genetics in EoE to be unacceptable. He seems ignorant of basic evolutionary genetics, and is clearly content to create a folk science alternative to modern evolutionary biology. No one has proven that random mutation generated the wonders of biology, to be sure, and so I'm not saying that Behe's conclusion is known to be false. I'm saying that his attempts to establish his conclusion have failed miserably, as have his responses to his critics, and the result is that he cannot be trusted as a careful, thoughtful, knowledgeable critic of evolutionary science. EoE is folk science, nothing more.

My final post in the series will have closing comments and some ideas for how we might go about posing questions about the processes that yield biological design.

Behe botches basic probability...how likely is that?

In The Edge of Evolution, Michael Behe presents arguments against the role of random mutation in large-scale evolutionary change, using probability calculations that are so utterly mishandled that they call into question his scientific credibility and integrity. To present evolutionary genetics in this way, one must be possessed of both ignorance and arrogance (a nasty combination) and/or of the kind of compromised scientific integrity that gives rise to folk science. The issue I raise here is independent of Behe's many errors regarding the biology of genetics and adaptation. It's all about misusing probability, and it looks suspiciously like a bait-and-switch. Here is one of many places in EoE where Behe makes a very basic mistake in the presentation of probabilities:

Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose during the course of life on earth that required a cluster of mutations that was twice as complex as a CCC? (Let's call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 1020 cells to solve the evolutionary problem, we would need 1040 cells. (pp. 62-63)
What Behe is saying is this: if event A has probability a, and event B has probability b, then the probability of both events happening is a times b. But that is only true if the events must happen simultaneously. That's the only time you multiply two probabilities. And to make matters worse, Behe is confusing two very different probabilities: the probability that the event will happen in any given attempt, and the probability that it will occur at all.

Consider the following example to see how these mistakes (if that's what they are) are so tremendously misleading. Suppose I hand you a pair of dice and ask you: "What is the probability that you will roll snake eyes?" You might immediately ask: "In how many rolls?" And that is quite an important question. The probability that you will roll snake eyes on any given roll is 1/36, which is the probability of getting a 1 on the first die (1/6) times the probability that you will get a 1 on the second die. Because the two events must happen together, we multiply the probabilities of the separate events. And that probability, 1/36, is pretty small.

But what is the probability that you will get snake eyes in, say, 12 rolls? It is in considering the second question that you can begin to see how Behe went badly wrong in his arguments in EoE. When Behe reports on the likelihood of occurrence of a "double CCC," he reports its probability of occurring in a single attempt. That's what the simple multiplication assumes, and Behe knows that this is nonsense.

The real question, then, is this one: what is the likelihood that a certain event will occur given a certain number of attempts? Behe is happy to calculate probabilities based on crude estimates of certain events in a certain organism, but he never takes a whack at the only interesting question: assuming a certain mutation rate, and a certain number of effective generations, what are the probabilities involved in particular mutational trajectories that have led to adaptation? What, for that matter, is the probability of a particular pair of mutations occurring in a human gene over a certain number of generations?

Back to our example of dice rolling. Behe's suggestion that we multiply the probabilities of "independent mutations" assumes that the two mutations occur simultaneously. Using his assumption of 1 in 100 million (108) as the probability of occurrence of a given point mutation, then we would conclude that the probability of a double mutant is 108 times 108, or 1016. But how many attempts do we get? It matters a lot. If you have 12 tries to get snake eyes, your odds improve dramatically – the probability is now 0.29. Not bad, but things get even better when we correct Behe's other colossal error, which was assuming that the mutations must happen at the same time in the same organism. We know that's not true – even Behe knows that's not true (p. 111). This makes the game entirely different. Now I give you the dice and say, "How many rolls do you think it will take till you have a 1 on each die? The 1's don't have to appear together." Well, I did the calculations for one example scenario:
  • You're trying to get two 1's, either together or sequentially.
  • You get 6 rolls, if necessary, to get the first 1.
  • After you get a 1, you get 6 rolls (if necessary) of the remaining die to get the second 1.
The probability that you will get snake eyes in this scenario is 0.60, and note that 12 is the maximum number of rolls here; many of the successes come in far fewer attempts.

It's hard for me to understand why Behe is so careless with such an important aspect of his argument. His whole case depends on probability, and yet the two weakest aspects of his story are his ludicrous extrapolations and his mishandling of probability. Perhaps he's just not a very careful thinker. Or perhaps we're seeing a sophisticated version of old-fashioned folk science, which typically depends on the kind of obfuscation that the EoE bait-and-switch suggests.

16 August 2008

Does religion deserve respect from atheists?

Check out a renewed discussion of PZ Myers' Crackergate stunt and the concept of showing respect for religion, over at Clashing Culture. Mike makes an interesting point about "respect" for Muhammad and Islam in the context of outrage over the desecration of a Eucharistic host, and I've responded with some scenarios aimed at distinguishing respect for religion from respect for other people. Please chime in!

13 August 2008

First blogiversary for Quintessence of Dust

Actually, my first post went up 3 August 2007, a little more than a year ago, but my first real article wasn't posted till 19 August, so I guess today is as good a day as any to celebrate. It's been a fun year, coinciding with my sabbatical, which ends [sniff] in 3 weeks. Once I'm back in my professor routine, I expect that my posting will be less erratic, especially since I requested a new office that's a bit removed from the beaten track. We'll see.

Thanks to all for reading and commenting. (I think I'll do better at responding to comments when my schedule calms down.) I'm especially thankful to Steve Martin at An Evangelical Dialogue on Evolution for being the first to find me and welcome me to the blogosphere. John Farrell was an early encouragement, and Panda's Thumb linked to one of my first journal club articles. The high point was the teosinte article, which was linked at ERV, Pharyngula and PT and which was honored with a place in The Open Laboratory 2007. The blog has about 240 subscribers and gets roughly 100 hits a day. Room to grow, but it's nice to have enthusiastic readers.

To Mike Beidler: thanks for the compliment; it's my favorite link in the one-year life of the project. To Gordon Glover: keep up the fantastic work; your book is a precious gift.

Here's to Year 2 of Quintessence of Dust. More journal clubs, more developmental biology, a little less bitching about lame creationist claptrap. Or your money back.

11 August 2008

Why I'm not a Behe fan, Part IIA: the malaria scam

In my previous post, I started to explain a fact that some people (who don't know me) seem to find surprising or noteworthy. Michael Behe is a Christian who accepts common ancestry and an ancient cosmos, so you'd think I would be excited about the work of a fellow "theistic evolutionist." But I'm not. Two overall problems come to mind. (Basically, I find his conduct as a scientist to be unacceptable, and I find his proposals to be laughable failures.) I'm addressing the second one here. The discussion is quite long, so I'm dividing it into two parts, A and B.

1. Behe's fans say that he's a nice guy, and that the evolutionists are "crucifying" him. Both claims seem to be true, but they can't hide some serious problems with his conduct as a scientist. First, he showed contempt for his (former) colleagues when he avoided the process of peer review. Second, his comment-free blog is lamentably characterized by misleading and disingenuous "responses" to criticism that look to be calculated attempts to protect what is nothing more than folk science.

Those issues are the subject of the first post.

2. Some of Behe's defenders think that he has effectively answered his critics. He has not, nor has he understood or acknowledged the most important criticisms of his crude claims.

There's something interesting about the ID community's response to Jerry Coyne's review of The Edge of Evolution (henceforth EoE). Thomas Cudworth referred to it as "nasty" and Behe dismissed it as just so much ad hominem and "question-begging." Meanwhile, Bilbo (regular commenter here and contributor at Telic Thoughts) thinks that Behe is "carrying the day" on his comment-free Amazon blog.com, where he has responded to critiques by Ken Miller, Richard Dawkins, Sean Carroll and others.

Well, in fact the review is a piece of crap, as is much of what Jerry Coyne has produced lately. (He's an equal opportunity thug, attacking his scientific colleagues with the same lack of grace and intelligence that he displayed in his recent diatribe against faith.) The piece represents at best a missed opportunity (to address Behe's claims in detail for a lay audience) and at worst a windfall for Behe and the ID movement, focused as they are on convincing the public that they are a persecuted scholarly minority. I'm not the only one who was horrified by Coyne's brainless screed; Jason Rosenhouse blasted it for all the same reasons.

As Rosenhouse predicted, the shoddy nature of Coyne's review enabled Behe to avoid a full-scale defense of his folk science. Behe has never bothered to rigorously justify his claims, and has never carefully engaged existing evolutionary data or theory, so Coyne's shallow account gave him a perfect opportunity to continue to pretend that his ideas can withstand real scientific scrutiny. And so we have ID propagandists whining about Behe's mistreatment, and laypersons reading ID blogs and concluding that EoE has sounded an unanswered challenge to evolutionary theory. It's a boon for ID.

The truth is that Jerry Coyne did identify the errors in the book. EoE makes exactly one specific scientific claim, accompanied by simplistic genetic assumptions and supported by a "case study." The scientific claim is that the mutations that drive large-scale evolution, and that are thought to underlie all evolutionary change (past and present), are non-random. And the "case study" is a long-winded account of the adaptation of the malaria parasite in the face of drugs intended for its destruction. Coyne's review addresses both, and Behe's responses failed to defend either.

The scientific claim is unsupported, and all available evidence contradicts it. And the "case study" is laughably misused in a ploy that a high school sophomore could see through. Let's look at the malaria ploy first, then examine Behe's central scientific claim and its implications in the second half of this article (part B, to be posted later this week).

EoE is actually a very small book, with very little to say. Most of the book is devoted to a recounting of the biology of the malaria parasite, Plasmodium falciparum, and the "trench warfare" between the parasite and its host, Homo sapiens. The outcome of the struggle between the parasite and its host has provided a useful case study of evolutionary change, and specifically of the power of natural selection. Behe grants this readily; indeed, he concludes that random mutation and natural selection can account for the divergence of organisms at the species level (at least). In other words, Behe does not deny the reality of common descent, and acknowledges some role in evolution for natural selection acting on random mutation. (He uses the divergence of dog breeds as an example of what random mutation & selection can do (p. 200), leaving one to wonder why Richard Dawkins chose dogs as an example of why Behe is wrong. I'm guessing Dawkins didn't read the book too carefully, what with all his important work as a scholar.) But Behe's reasoning is stunningly dumb. It goes like this.

  • In the fifty years since antimalarial drugs were brought to bear on P. falciparum, more than 1020 (that's 10 to the 20th power, if the superscript isn't working) of the parasites have been born.
  • In that time, the parasite has adapted to the drugs, through selection acting on random genetic variation, but hasn't developed any completely new proteins or biochemical functions.
  • This means that the Darwinian process is unable to generate significant novelty in fewer than 1020 tries.
That's the argument. And Behe uses it to identify the "edge of evolution."

Now, I hope it's already clear to most readers why the argument is spectacularly bad, but here are some comments.
  • Most basically, it should be obvious that demonstrating the failure of X to happen in one particular situation is hardly proof that X cannot happen. To extrapolate from a single negative observation (even if it were representative of the scenario in question) to the blanket impossibility of the phenomenon is a foolish mistake.
  • More specifically, it should be obvious that we need not expect dramatic new functions to appear during adaptation, since we need not even expect adaptation to occur at all. If functional innovation were as inevitable as adaptation, the dinosaurs would not merely have survived, they would have mastered apparation in additional to intergalactic travel (and world peace). Behe wants you to believe that evolutionary biologists expect dramatic evolutionary innovation to occur, at the level of molecular machinery, whenever selection is applied to a population. That's nonsense, and I think he must know that.
  • It is important to keep in mind that Behe solidly affirms common ancestry, and knows that mutations account for the differences between lineages. This means that he acknowledges the existence of a continuous genetic tree of life, which means that he should be able to formulate scientifically credible approaches to his hypothesis. Pointing to the lack of innovation in one special (parasitic) scenario is hardly a substitute for a direct examination of the myriad exemplars of evolutionary novelty. In other words, the way to determine whether gigantic population sizes are needed for the stepwise generation of novel functions via random mutation is to: a) identify examples of such evolutionary innovations and to work on elucidating the genetic trajectories that could have led to their development; then b) work on determining the population sizes, mutation frequencies, and other parameters that apply to the trajectory. (I like to call this "science.")
The questions that I have after reading EoE (besides the disturbing question raised also by Dennis in a comment here) are these: does Mike Behe really think that evolutionary biologists expect P. falciparum to develop new molecular machines while adapting to antimalarial drug assault? Does he really think that the struggle between a primate and one of its parasites is a model for the generation of evolutionary novelty, of whole gene families whose origins often predate the Cambrian? Does he really believe that the failure of P. falciparum to give rise to a magic drug-dodging charm, or a microscopic invisibility cloak, is an argument against random mutation and natural selection in the evolution of biological novelty?

Probably not. He has another really bad idea: that random mutation doesn't provide enough variation for natural selection to generate novelty. And the mistakes are typical for him: sloppy (or non-existent) examination of the facts, and wild extrapolation from those he carefully selects. Part IIB will look at the rest of the mess.