Showing posts with label Book Reviews. Show all posts
Showing posts with label Book Reviews. Show all posts

24 April 2010

Signature in the Cell: Chapters 9 and 10

"He..strikes at randome at a man of straw."
– Richard Saunders, A Balm to heal Religious Wounds, 1652. Quoted in the Oxford English Dictionary, 2nd Edition

"An imaginary adversary, or an invented adverse argument, adduced in order to be triumphantly confuted."
– Second definition entered for "man of straw" in the Oxford English Dictionary, 2nd Edition

Chapter 9 is called "Ends and Odds." Chapter 10 is "Beyond the Reach of Chance." Between them, they advance a straw man so idiotic that I wonder whether Meyer will be able to reclaim any significant intellectual integrity in the chapters that follow. I've already noted that this is not a book of science or of serious scholarship. Now it seems that it doesn't even merit the distinction of popular science or pop philosophy. These two chapters have purely propagandistic aims, and they do serious damage to the book's credibility and to the author's reputation. Meyer has shown his cards.

18 April 2010

Signature in the Cell: Chapter 8

It's been a month and a half since my last post in this series, and recently a friend asked me why I stopped. I can think of two reasons: first, I spent the month of March teaching a graduate course for the first time; second, I'm worried about how this is going to go. I'm worried because I can see that the book is poor scholarship – Meyer is either underinformed or overcommitted to his cause – and I can see that my critique will be considered within a religious milieu that hinders straightforward criticism and analysis. Ergo, I think this might not be very pretty. It would be a lot more fun to blog about any of 15 different papers from the last two issues of Nature.

But we need to finish, partly because I'll be on a panel of critics at an event with Stephen Meyer himself in Los Angeles next month. (Not just critics: "a powerful group of credentialed critics." More later.)

Chapter 8 is called "Chance Elimination and Pattern Recognition." It deals first with the notion of chance and then with subjects that are at the very heart of design thought – the dual consideration of improbable events and the genesis of phenomena that exhibit "patterns." The chapter is pretty good, but seems to contain seeds of significant future confusion.

04 April 2010

Behe and probability: one more try

Almost two years ago, I reviewed Michael Behe's latest book, The Edge of Evolution, here on the blog. I was unimpressed, to say the least, and remain of the opinion that Behe should not be considered a serious scientific thinker given his failure in that ludicrous book.

Since then, my posts have been referenced occasionally in the blogosphere, typically by people trying to explain Behe's surprisingly crude mishandling of probability in the context of genetics. One particular point has been singled out as a mistake on my part, and some ID defenders want that mistake to rescue Behe's argument. Let me describe the so-called mistake, then explain why I'm right.

27 February 2010

Signature in the Cell: Chapter 7

The chapter is called "Of Clues to Causes" and it's about scientific explanation. That's an interesting and important topic, one that opponents of evolutionary theory rarely understand. Meyer's summary is predictably fluffy but not inaccurate. Those seeking an introduction to philosophical questions pertaining to scientific explanation should look elsewhere, since Meyer says little in the 22-page chapter. His main points:

  1. There are indeed legitimately scientific means of understanding and seeking explanation for past events.
  2. These approaches validate ID as a "possible scientific explanation for the origin of biological information."
I don't disagree with either assertion. But neither is particularly helpful to ID in its quest for explanatory relevance. (Well, the main quest of the ID movement is to undermine naturalism by any means necessary, but its scientific challenge is to demonstrate that it can provide useful explanation.)

21 February 2010

Signature in the Cell: Chapter 6

The chapter is called "The Origin of Science and the Possibility of Design." It's short, unimportant and uninteresting. Its purposes, along with Chapter 7, are twofold: 1) to counter the claim that ID theory is "not science" and 2) to establish that "historical science" (that which deals with the past) is not all that different from "operations science" (as defined by Charles Thaxton and others), specifically because the theorizing of "historical science" can be considered testable.

14 February 2010

Signature in the Cell: Chapters 4 and 5 - errors and problems

Meyer's basic idea in chapters 4 and 5 is reasonably coherent. But I find further evidence in both chapters that Meyer is careless and underinformed on the subjects he addresses. (I explained before why I think this matters. If you think I'm not being nice enough to Meyer, consider providing me with the Rules of Engagement that apply when criticizing culture warriors who are proposing world-shifting new ideas.)

13 February 2010

Signature in the Cell: Chapters 4 and 5 - major themes

Chapter 4 is called "Signature in the Cell." It's an important chapter for two reasons. First, along with chapter 5 ("The Molecular Labyrinth") it lays out Meyer's central question by pointing to the specific features of cellular information systems in need of explanation. Second, it exemplifies an aspect of ID thought that I want to highlight. I'll discuss these two themes here, then add some further critiques in a second post.

06 February 2010

Signature in the Cell: Chapter 3

The chapter is called "The Double Helix," and there's not much to say about it. Meyer provides a fairly standard narrative of the discoveries that led to Watson and Crick and molecular biology. Anyone who's read The Eighth Day of Creation, along with a decent genetics textbook and/or a memoir by one of the principals (What Mad Pursuit by Francis Crick is a personal favorite) will already know everything here. Two observations.

03 February 2010

Signature in the Cell: Chapter 2

The chapter is called "The Evolution of a Mystery and Why It Matters." It's interesting and engaging, and I enjoyed reading it. The "mystery" in question is first described on page 35:

...most philosophers and scientists have long thought that Darwin's theory of evolution by natural selection destroyed the design argument. Yet I also discovered that Darwin himself admitted that his theory did not explain the origin of life itself. [...] His theory assumed rather than explained the origin of the first living thing. Since this limitation of Darwin's theory was widely recognized, it raised a question: Why were nineteenth- and twentieth-century biologists and philosophers so sure that Darwin had undermined the design argument from biology?

26 January 2010

Signature in the Cell: Chapter 1

The chapter is called "DNA, Darwin, and the Appearance of Design." It's a poor start. Meyer sketches some key themes of the rest of the book in this sloppy chapter. Here are those themes (in my words) and some comments.

1. DNA stores information, using a code that is similar to that of a computer. We know a lot about how that works.

2. Life gives the appearance of design. No one disputes that. But the source of the design is, of course, controversial.

09 January 2010

Signature in the Cell: preliminary observations and prologue

There's not much point in "reviewing" a prologue, so let's start instead with some impressions gleaned from reading the prologue and the first chapter while leafing through the rest of the book.

1. This is clearly a pop-science book and not a serious work of scholarship. That's not an insult, just an observation.

07 January 2010

Signature in the Cell: other reviews

Interestingly, Meyer's book is getting a lot of attention right now. At the Jesus Creed, the excellent RJS is also blogging through the book. At Biologos, a guest piece by Francisco Ayala focuses mostly on theological issues. (I like Ayala a lot. I dislike his post a lot.) The ASA has finally decided to establish some blogs, one of which will host discussions of books. The first book under consideration is Signature in the Cell. (Unfortunately, only ASA members can comment, and that excludes me.) And PZ Myers is reading the book right now. He has already concluded that "there's no poetry in creationism." Well, that's a low blow. Meyer mentions Donne on page 16. What more did PZ expect? A personalized limerick? The Digital Cuttlefish?

06 January 2010

Signature in the Cell: beginning the review

So Stephen Meyer of the Discovery Institute, a founder of the ID movement, wrote a book called Signature in the Cell: DNA and the Evidence for Intelligent Design. It came out last summer, and I ignored it. I ignored it because it didn't seem interesting or important or new, and there's always something interesting and important and new to read. (I recently finished The Road. Wow.) It didn't matter to me that the ID people said it was "groundbreaking" or "seminal" or "a blueprint for twenty-first-century biological science" since they said things like that about Behe's last book. And that is a terrible book, one that reflects very poorly on its author. It seemed reasonable to assume that the ID movement wasn't going to generate any serious new arguments, and that if they did it would be obvious. Signature in the Cell gave no indication that it contained anything new.

20 December 2009

Weasels, clouds and biomorphs, part III

The Blind Watchmaker is a superb book by a masterful science writer. It's not just a book about evolution, or even about how evolution works. It's a book about how evolution explains design, and more specifically how natural selection accounts for design. As I wrote before, I consider chapter 3 to be the most important chapter of the book. The chapter is called "Accumulating small change" and it features two different computer programs that Dawkins uses to teach readers about the effectiveness of selection in evolution. Before we play with the Biomorph program in the next post, allow me to set us up by discussing the importance of the program in Dawkins' argument, and by outlining the logic of the program's design.

First let me try to convince you that chapter 3 really is the heart and soul of the book. The chapter is about gradual, step-by-step evolution resulting from natural selection. And as you might already know, natural selection is what Dawkins considers to be The Big Idea, the idea that answered Paley's seemingly insurmountable challenge. In chapter 2, Dawkins makes this clear. Here's how he starts.

Natural selection is the blind watchmaker, blind because it does not see ahead, does not plan consequences, has no purpose in view. Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning. The purpose of this book is to resolve this paradox to the satisfaction of the reader....
–The Blind Watchmaker, page 21
Chapter 2 famously focuses on echolocation in bats, and I would buy the book just to read Dawkins' description of the engineering feat that is the little brown bat. (He gleefully recounts the utter incredulity of an audience of biologists when the mere existence of such biological phenomena was first described.) And here's his conclusion.
I hope that the reader is as awestruck as I am, and as William Paley would have been, by these bat stories. My aim has been in one respect identical to Paley's aim. I do not want the reader to underestimate the prodigious works of nature and the problems we face in explaining them. Echolocation in bats, although unknown in Paley's time, would have served his purpose just as well as any of his examples. Paley rammed home his argument by multiplying up his examples. He went right through the body, from head to toe, showing how every part, every last detail, was like the interior of a beautifully fashioned watch. In many ways I should like to do the same, for there are wonderful stories to be told, and I love storytelling. But there is really no need to multiply examples. One or two will do. The hypothesis that can explain bat navigation is a good candidate for explaining anything in the world of life, and if Paley's explanation for any one of his examples was wrong we can't make it right by multiplying up examples. His hypothesis was that living watches were literally designed and built by a master watchmaker. Our modern hypothesis is that the job was done in gradual evolutionary stages by natural selection.
–The Blind Watchmaker, page 37
Chapter 4 builds on chapter 3, and the rest of the book deals with how it might all work. Chapter 3 is Dawkins' attempt to show us the power of cumulative selection, and cumulative selection is The Blind Watchmaker. This is the heart of the matter, and Dawkins' argument (and his world) hinges on the success of this idea.

And so Dawkins tackles the concept of cumulative selection in chapter 3, and as we've already seen, he immediately faces a serious problem: the end result of an evolutionary process is the generation of design, of biological machines that are complex and, more importantly, wildly improbable. In other words, such things "can't just happen." The human mind is prone to a serious error when faced with this challenge. The error is to envision complexity arising spontaneously from chaos, in a single step, and thus to conclude that such things cannot be explained naturally. The error is in bold, and Dawkins addresses it first with the simple and effective Weasel illustration. The illustration is highly effective as a corrective for that error, but it fails as a model of evolution, as I explained in the previous post.

The Biomorph program was Dawkins' more serious attempt at modeling the development of complex structures by cumulative selection. It's important to understand just how central the program really is, and thus why it's so silly to make a big deal out of the Weasel exercise. Chapter 3 is the heart of the book, and the Biomorph program is the soul of chapter 3. The Biomorph program improves on Weasel in two very important ways:

1. It models evolutionary unfolding without a specific goal. The Weasel program "homed in" on a particular goal; the Biomorph program has no such constraint.

2. The entities that evolve in the Biomorph program, called biomorphs, "develop," and their development is controlled by a number of factors ("genes") which change (i.e., mutate) in each generation, so that mutations result in alterations to development and thus to new forms.

The biomorphs are tree-like structures, and they are drawn according to simple rules. (This post is decorated with a few that I made using a nice Java applet.) The rules control the branching of the trees (branch at a certain angle or at a certain point on the existing branch, or branch of a certain length, or whatever). The drawing of a biomorph, then, is a representation of embryonic development. And the rules represent the various processes in development.

It should be fairly easy to see how to model the effects of genes: a gene will influence a rule, by assigning a number to the rule (e.g., branch at a bigger or smaller angle). Reproduction is simple: the biomorphs are redrawn, based on the parent's structure, using the same rules influenced by the same genes. Boring? No: mutation acts to change the numeric value of the genes, randomly changing the value by either +1 or -1. The result is a set of offspring, each differing slightly from the parent by virtue of a single mutation.

So it goes like this. A parent is selected. The subroutine REPRODUCTION runs, and generates random mutations in each of the genes of the parent (there are 9 genes); the new genes are passed to the subroutine DEVELOPMENT, which draws new biomorphs based on the new genes. The result is a set of 9 offspring, each with a different version of one of the parent's genes. One is selected to be the parent of the next generation. Keep doing this, over and over and over, and you get the program EVOLUTION.

But how does selection work in this program? Recall that the major problem with the Weasel illustration was its goal-directed nature. In the Biomorph program, things are different:
...the selection criterion is not survival, but the ability to appeal to human whim. Not necessarily idle, casual whim, for we can resolve to select consistently for some quality such as 'resemblance to a weeping willow'. In my experience, however, the human selector is more often capricious and opportunistic. This, too, is not unlike certain kinds of natural selection.
The Blind Watchmaker, page 57
Selection, in other words, is done by you, the human who is "playing God."

That's the Biomorph program. Next time: what it demonstrates about evolution.

08 December 2009

Weasels, clouds and biomorphs, part II

Back in September I wrote about the silly preoccupation on the part of various anti-evolutionists with the so-called Weasel program, a simple exercise created more than 20 years ago by Richard Dawkins to illustrate the efficacy of cumulative selection in evolutionary scenarios. My main point was that the Weasel program had one very simple purpose (comparing "single-step selection" – which is purely random – to cumulative selection) and constitutes a trivial fraction of the argument in Dawkins' The Blind Watchmaker.

One might think that Dawkins' basic message – that random one-step flying-together of a Shakespearean phrase or a hemoglobin molecule is impossibly unlikely compared to cumulative selection of intermediate stages – is so elementary that no intelligent person would need to consider it more than once. (Once seems like a lot to me in this case, but never mind.) And yet the error (if that's what it is) is shockingly common. (It forms one pillar of poor Cornelius Hunter's whole enterprise, for example.)

Dawkins understood this problem when he wrote The Blind Watchmaker, so before he unveiled the fascinating program that forms the heart of his case for the power of selection, he took one last stab at making the basic outline clear by going back to clouds. Wait...clouds? (Fans of Hamlet are already sighing blissfully; those who don't get the connection between weasels and clouds should read either Act III, Scene II of Hamlet or Chapter 3 of The Blind Watchmaker.) Yep. Dawkins pointed back at what makes cumulative selection work: the things that are evolving must be able to generate related offspring. And that's what clouds can't do.

Clouds are not capable of entering into cumulative selection. There is no mechanism whereby clouds of particular shapes can spawn daughter clouds resembling themselves. If there were such a mechanism, if a cloud resembling a weasel or a camel could give rise to a lineage of clouds of roughly the same shape, cumulative selection would have the opportunity to get going. Of course, clouds do break up and form 'daughter' clouds sometimes, but this isn't enough for cumulative selection. It is also necessary that the 'progeny' of any given cloud should resemble its 'parent' more than it resemble any old 'parent' in the 'population'... It is further necessary that the chances of a given cloud's surviving and spawning copies should depend on its shape.
The Blind Watchmaker, pages 50-51, italics in the original
Hence the Weasel program.

But I noted last time that Dawkins spent a tiny amount of time and text on the Weasel program, and that he declared it to be "misleading in important ways." The most important, by far, is this: the selection that drove the Weasel program was goal-directed. A better simulation of evolution would be one in which selection is more capricious, more "in the moment." (Survival can be capricious; reproduction happens rather decisively "in the moment.")

Dawkins came up with just such a program, and I mentioned it in the previous post. It's a wonderfully simple simulation of the basic aspects of selection-driven evolution: it includes development, reproduction, genes, and selection, and generates "organisms" with shapes instead of a phrase in all caps. We'll look at that program in the next and final post. But if you want to play with a modern version, you'll find plenty of nice implementations out there. So much more fun than studying...or grading.

07 September 2009

Weasels, clouds and biomorphs, part I

There's usually no point in piling on when the minions of the ID movement get their just deserts after some typically brainless culture-war test launch. Consider the responses (by, most notably, Ian Musgrave at the Panda's Thumb) to the most recent rendition of the ID movement's hilariously idiotic fixation on a particular computer program written by Richard Dawkins. It seems there is little to add. But I think something important is being lost in this conversation, probably because the level of the "conversation" is the level of the ID movement. So let's start with a little quiz.

1. True or false: Richard Dawkins' 1986 classic The Blind Watchmaker used a computer model (a simulation) as a key teaching device while explaining the effectiveness of cumulative selection in evolution. The program is the main focus of chapter 3 ("Accumulating small change") of the book.

Answer: True.

2. True or false: the computer program used for this purpose was made available to the public and has since been adapted for free use on the web.

Answer: True.

3. True or false: the computer program in question is called WEASEL (or similar) and it demonstrates the stepwise generation of a famous phrase from Hamlet.

Answer: False.

Now if this surprises you, then either you haven't read The Blind Watchmaker or you haven't read it in a long time. Because even if you've been influenced by the hysterical antics of the ID crowd, you could not long believe its claims about the Weasel program if you had recently read the book. If you haven't recently read The Blind Watchmaker, you might consider a stroll through some representative ID musings on WEASEL followed by a visit to Chapter 3 of the book (and, if you have a copy from 1989 or later, a visit to the two appendices.) The experience could be jarring for those who have a positive view of these arguments by ID apologists.

But if you don't have a copy of The Blind Watchmaker handy, I can help. First, in this post, I'll discuss the Weasel program and its place in the thesis of The Blind Watchmaker – in the context of the current ID fixation on the program. Then I'll introduce the program that Dawkins really did emphasize in the book, a program called EVOLUTION (or later, when it was expanded and made commercially available, The Blind Watchmaker Evolution Simulation program) but commonly known as the biomorph(s) program. In the second post I'll talk more about the biomorph program and its usefulness.

Chapter 3 of The Blind Watchmaker is a tour de force of expository scientific writing. Called "Accumulating small change", the chapter has a single and simple thesis, laid out in the first paragraph:

We have seen that living things are too improbable and too beautifully 'designed' to have come into existence by chance. How, then, did they come into existence? The answer, Darwin's answer, is by gradual, step-by-step transformations from simple beginnings, from primordial entities sufficiently simple to have come into existence by chance. Each successive change in the gradual evolutionary process was simple enough, relative to its predecessor, to have arisen by chance. But the whole sequence of cumulative steps constitutes anything but a chance process, when you consider the complexity of the final end-product relative to the original survival. The purpose of this chapter is to demonstrate the power of this cumulative selection as a fundamentally nonrandom process.
The Blind Watchmaker, page 43, italics in the original
Dawkins immediately tackles the crazy misconception of evolution as a process that is akin to the impossibly improbable flying-together of the parts of a machine in a single step. Echoing Isaac Asimov, he calculates the probability of the spontaneous assembly of a hemoglobin molecule in a single step, and arrives at a number of predictably indescribable magnitude. It can't just happen.

In a 1987 BBC television show , he uses a much better metaphor: the opening of a safe by entering a combination. To open the safe, a banker (or thief) must correctly enter all of the correct numbers, in order, at the same time. His point is: of course it can't "just happen." The concept that Dawkins aims to communicate is this: from an evolutionary perspective, "success" doesn't happen all at once; it is accumulated. Evolutionary change is cumulative change; it's as though the safe opens a little when one correct number is entered, and allows the banker to reach in and get a little money. ("Small change" is the topic, remember.)

This is a very basic and very important aspect of the Darwinian mechanism, and yet it is maddeningly common to see it ignored or completely misunderstood. So in the first few pages of Chapter 3, Dawkins looks for an illustration of the difference between "randomly getting the whole thing right in one fell swoop" and "accumulating random improvements till the whole thing is assembled." He starts with the old saw about monkeys, typewriters and Shakespeare. Choosing a single phrase from Hamlet, "Methinks it is like a weasel," he first calculates the probability of a random character generator (a monkey) spontaneously banging out Hamlet's phrase. The calculation charmingly indicates that there isn't enough time in the universe for such a thing to occur. Yeah, yeah, yeah. Now, it's easy enough to get a computer (even a 1986-vintage machine) to churn out 28-character strings randomly, and so Dawkins describes a program that can do this. Then he introduces the occurrence of cumulative selection in the program, to illustrate its profound effectiveness compared to mere randomness.
We again use our computer monkey, but with a crucial difference in its program. It again begins by choosing a random sequence of 28 letters... It now 'breeds from' this random phrase. It duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase... the procedure is repeated, again mutant 'progeny' are 'bred from' the phrase, and a new 'winner' is chosen.
The Blind Watchmaker, pages 47-48, italics in the original
Dawkins shows that this procedure can get from a random monkey-phrase to "Methinks it is like a weasel" in mere seconds. And the point is simply this: cumulative selection is more effective than mere "randomness" by incomprehensibly gigantic magnitudes. Dawkins makes it very clear that the Weasel program is meant to demonstrate nothing more than that. After pointing out that single-step selection would take a near eternity to type the phrase, he reiterates the simple purpose of the comparison, and the whole weasel exercise:
Actually it would be fairer just to say that, in comparison with the time it would take either a monkey or a randomly programmed computer to type our target phrase, the total age of the universe so far is a negligibly small quantity, so small as to be well within the margin of error for this sort of back-of-an-envelope calculation. Whereas the time taken for a computer working randomly but with the constraint of cumulative selection to perform the same task is of the same order as humans ordinarily can understand, between 11 seconds and the time it takes to have lunch.
The Blind Watchmaker, page 49, italics in the original
Folks, that's all the silly weasel thing was ever about. So what's all the fuss then?

Well, some ID partisans are all agitated about whether Dawkins' program allowed mutations in positions of the string where the correct letter had been hit upon. They wonder: if cumulative selection had gotten us "Methinks it is like a measel", could 'measel' mutate back to 'measer' and thus take the program a step away from the target? And why does this matter? Well, for Dawkins' purposes it really doesn't matter, but the ID scholars seem to think there's a big speed difference. If you're interested you can read some nice work by Wesley Elsberry or Anders Pedersen that shows clearly that it simply doesn't matter.

But. Here's what's lost in all this. Dawkins never intended the silly little weasel exercise to be a persuasive argument for evolution as it actually occurs in the world. In fact, he is quick to point out why it's deficient (remember Bohr models of the atom in grade school?), noting that it is "misleading in important ways." And at that point, he abandons the Weasel program in favor of a simulation that is far better. That simulation, the Biomorph program, is the topic of the entirety of the rest of Chapter 3 of The Blind Watchmaker (and of my next post).

The absurdity of the ID fixation on the Weasel program is hard to capture with mere words. Perhaps this table will help put the two programs into better perspective.

WeaselBiomorph
Number of times program is mentioned* on Uncommon Descent4442
Number of pages devoted to program in The Blind Watchmakerless than 5 45, including two appendices

*All I did was Google the word 'weasel' or 'biomorph' at uncommondescent.com. The two uses of 'biomorph' were in comments by ID critics (one being Wes Elsberry). The uses of 'weasel' surely include insults that aren't references to the program.

The real focus of Chapter 3 of The Blind Watchmaker is the biomorph program. Seven figures, 23 pages, 22 more pages in two appendices which include a small user's manual for the program. The biomorph program constitutes the heart of Dawkins' book and his argument, so much so that the program is named The Blind Watchmaker. The Weasel program was a tiny stepping-stone for Richard Dawkins, a simplistic teaching tool meant to illustrate a single simple point. It's a hill to die on for the ID movement, and that says a lot about the state of that confused community.

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.

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.