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.

1. Meyer makes a basic error on page 66 while describing the early evidence that DNA is the genetic material. He's describing the classic experiments of Avery, MacLeod and McCarty on Pneumococcus bacteria that can be transformed from one strain into another. The phenomenon of transformation had been discovered by Frederick Griffith in the 1920's.

If a deadly strain of the bacteria was first heated to death, the strain was harmless when injected into mice. No surprise there. The mice were also unharmed when injected with a living but nonvirulent strain of the virus.

Do you see the mistake?

Now, if you're not a biologist, you might think the error is trivial, purely semantic, a typing glitch induced by the proximity of the word 'virulent.' And that last part is probably right. But this biologist finds the error more significant, and I suspect others would agree. The difference, I think, is that I can't imagine mistaking a virus for a bacterium; it's like mistaking a pencil for a sequoia. A person who would make that mistake – and leave it in his awesome, groundbreaking treatise on 21st-century biological science – is a person who doesn't think very much about viruses or bacteria. A person who would make that mistake is a non-specialist. A layperson.

And of course, Stephen Meyer is a layperson. He's clearly not a biologist, or even a person who's particularly knowledgeable about biology. (That paper in the Proceedings of the Biological Society of Washington became infamous due to political disputes; I thought it was most notable for being lame.) This is obvious from my reading of this book and his other work, and the mistake on page 66 just serves to remind me that despite the thunderous praise from fans on the dustjacket and in the ID-osphere, Meyer just isn't all that impressive as a scientific thinker. Call me a jerk, but I expect a hell of a lot more from someone who wants to rewrite science (and its history).

2. Alas, I cut off Meyer's description of Griffith's famous experiment. (You can read a great overview of the work of Griffith and Avery et al. at Nature's cool Scitable site.) What Griffith showed was that the nonvirulent (i.e., nonlethal) strain of bacteria could kill mice if it was injected along with heat-killed virulent bacteria. The nonvirulent bacteria had been transformed into virulent bacteria by being in the presence of dead virulent bacteria. (To this day, the process of introducing DNA into bacteria is called transformation.) Fifteen years later, Avery and colleagues were trying to figure out the nature of the transforming substance. Here's how Meyer sets the stage:

There were two possibilities. Either the dead strain was coming back to life–but this was absurd–or something in the dead strain of bacteria was being transferred to the living strain, making it suddenly lethal.
–pages 67-68

Now I think this is very interesting. Without any further comment and no apparent justification, Meyer dismisses a major hypothesis, even labeling it "absurd." The idea of bacteria "coming back to life" is far-fetched, I'll grant you, but I guess I'm wondering whether the irony of Meyer's casual vacation of the reanimation hypothesis is something that only Shakespeare lovers can detect. Avery, MacLeod and McCarty didn't consider reanimation, as near as I can tell, but that could just be their obvious naturalistic bias, don't you think?

Avery and colleagues did, on the other hand, deal with the possibility that the nonlethal bacteria spontaneously mutated into a lethal strain. Their stubborn naturalism comes through rather clearly in their writing, I must say. Someday I'd love to see an explanation for why Steve Meyer considers the reanimation hypothesis to be absurd. And I'm curious to know whether he would understand why this is important.

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?

Meyer is asserting that scientists in the late 19th century knew that they had no satisfactory naturalistic account of the origin of life. I assume that he's right about that. He's struck by the fact that they weren't shaken by that "small hole in this elaborate tapestry of naturalistic explanation":

Despite the impasse, late-Victorian-era biologists expressed little, if any, concern about the absence of detailed explanations for how life had first arisen. The obvious question for me was, Why?
– page 40

Meyer then begins an interesting discussion of the declining popularity of vitalism during and preceding that time, a decline caused by the relentless advance of effective naturalistic explanation. For example:

During the 1860s and 1870s scientists identified the cell as the energy converter of living organisms. Experiments on animal respiration established the utility of chemical analysis for understanding respiration and other energetic processes in the cell. Since these new chemical analyses could account for all the energy the cell used in metabolism, biologists increasingly thought it unnecessary to refer to vital forces.
–page 41

The following section, "Evolution on a Roll," is quite good. Meyer credits his dissertation mentor, Harmke Kamminga, with the claim that "Darwin's theory inspired attempts at 'extending evolution backward' in order to explain the origin of the first life." He then explains why "Darwin's theory inspired confidence in such efforts." One key reason: his theory "implied that living species did not possess an essential and immutable nature."

The rest of the chapter is a narrative of the development of early OOL theories, ending with the famous Miller-Urey experiment of 1953. Although I'm not well-qualified to assess the accuracy of Meyer's account, I found the section interesting and informative. The chapter ends with this ominous transition:

A seamless and fully naturalistic account of the origin and development of life-forms appeared, if not complete, then at least sketched in enough detail to preclude anachronistic speculations about a designing hand. The problem of the origin of life had at last been solved. Or at least so it seemed, until scientists began to reflect more deeply on the other great discovery of 1953.
–page 57

That "great discovery," of course, is Watson and Crick's description of the structure of DNA. And I call the transition "ominous" because I sense a return to rhetorical tactics that disgusted me in chapter 1. That last sentence suggests that "scientists" share Meyer's seeming awe before "the DNA enigma." And I don't believe that at all.

So, here are two observations that I think will be central to a critique of this book.

1. Meyer finds late nineteenth-century scientists to be "oddly confident," even triumphalistic, about their naturalistic explanations for how life began. It seems to me that he seeks to plant doubt in readers' minds about the utility of such explanations by showing that scientists of that time were enthusiastic about naturalistic explanation. My response goes something like this.

You're right, Steve Meyer. Scientists then, and now, are enthusiastic about naturalistic explanation. It's worked really well, so well that many of us are convinced that it will succeed even in areas that it seems to have barely touched. If your point is that science should remain ruthlessly critical of its ideas, or if you suspect that some scientists are overly credulous when it comes to some aspects of OOL theorizing, then you'll find me in agreement. But if you think there is something fundamentally wrong with assuming that life can be naturalistically explained, then we are at odds, and I will oppose your ideas.

I think it's important to be clear about something here. I don't think that Steve Meyer is stupid or dishonest for expressing his own preference in this matter. It seems to me that he prefers to assume that the origin of life could be – or is even likely to be – refractory to naturalistic explanation. He prefers to assume that the origin of life can be shown to be necessarily dependent on a "designing intelligence," such that it is inexplicable apart from that preexisting mind. I don't have a problem with Steve Meyer's preference for design-based explanation. It will always be a rational and defensible choice, no matter what new data turn up or which new theories – however fantastical or elegant – are proposed.

But I want to point to the nature of our difference. It is a difference of opinion, of preference, even of outlook (Meyer would say "worldview," I think). It seems to me that Meyer believes this difference to be decisive, meaning that it will cause me to miss the things that matter: the enigmas, mysteries and other glaringly obvious indications that naturalistic explanation can't work. But I don't think the difference is all that important. To me, it just means that two Steves, Meyer and Matheson, see the world in two distinct ways. For Steve Meyer to convince Steve Matheson that the mind-first view is vastly superior from an explanatory standpoint, he'll have to do a whole lot more than point to things we don't understand. Until he does that, his writings, even in nicely-crafted chapters like this one, will be little more than quaint explications of the peculiarities of his view of the world. Interesting, even endearing? Maybe. Decisive? No.

2. In this chapter, Meyer continues a theme that he introduced in the first chapter. I'll call it "driving a wedge." The wedge in question is one that seeks to establish a gulf between the idea of design and the idea of naturalistic explanation. Meyer seems to accept the notion that phenomena that can be explained while relying on solely "material processes" are phenomena that do not involve design, intelligence, purpose, guidance. I could be wrong about that; maybe he'll disclaim such a stark dichotomy later in the book. But here's what he writes in a section called "Setting the Philosophical Stage:"

The age-old conflict between the mind-first and matter-first worldviews cuts right through the heart of the mystery of life's origin. Can the origin of life be explained purely by reference to material processes such as undirected chemical reactions or random collisions of molecules? Can it be explained without recourse to the activity of a designing intelligence? If so, then such an explanation would seem to make a materialistic worldview ... all the more credible. Who needs to invoke an unobservable designing intelligence to explain the origin of life, if observable material processes can produce life on their own?
–pages 37-38

I'm a Christian of a particular stripe, and I have an answer to that final question. A believer invokes the hand of God, not because he needs an explanation for those things that can't yet be explained by material processes, but because he believes, and therefore sees God's hand in all the processes he observes.

Steve Meyer has failed to convince me that the origin of life is a true "mystery." And he's failed to convince me, in any case, that it matters. Not because he's a fool or a failure (though both may also be the case). But because I don't see God's world the way he does.

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.

Our commonsense reasoning might lead us to conclude that the information necessary to the first life, like the information in human technology or literature, arose from a designing intelligence. But modern evolutionary biology rejects this idea.

...Lewontin and Dawkins, like evolutionary biologists generally, insist that the appearance of design in life is illusory. Life, they say, looks designed, but was not designed by an actual intelligent or purposive agent.

–pages 17-18

3. We don't know how the information systems arose during very early evolution. This is a mystery, an enigma: the DNA enigma. I hope that Meyer will explain the difference between "unanswered question" and "mystery." If Signature in the Cell is about nothing more than current ignorance regarding certain aspects of abiogenesis, then the book is a joke.

4. There seem to be some distinctive characteristics about the methods and arguments of scientists studying the past, raising the question of whether origin-of-life (OOL) theorizing is fundamentally different from other biological science. Specifically, Charles Thaxton, a founding member of the ID movement and current Fellow of the Discovery Institute, has claimed that OOL theories are inherently untestable and that the uniqueness of the OOL event legitimizes the postulation of "intelligent causes." Meyer aims to critique Thaxton's arguments. Because Meyer wrote his dissertation on historical and philosophical aspects of OOL science, we should have high expectations of his writing on the subject.

It's a fluffy chapter, peppered with personal narrative and reflection. But looking back on the Prologue and this first chapter, we can see the trajectory Meyer is likely to follow. Keeping our instinctive perception of design ever before us, he will establish DNA and genetic information as the uber-example of design, then attempt to convince us that the origin of genetic information systems is inexplicable without reference to an intelligent agent, while reassuring us that this explanatory maneuver is legitimately scientific.

But you probably already knew that.

Further comments on the chapter:

1. Meyer seems to recognize that he needs to offer a design-based explanation for the origins of genetic systems:

It is provocative to claim that the evidence from DNA and our best scientific reasoning points strongly to an intelligent cause of life. It is not very interesting to claim that it is possibly true ("plausible") that DNA owes its origin to such cause. Many statements are merely plausible or possibly true. But that doesn't mean we have any reason to think them likely to be true. Rigorous scientific testing usually provides evidence-based reasons for making such claims or for preferring one hypothesis over another.

–page 30

I'm sure we'll come back to this theme repeatedly as we go through Signature in the Cell, but let's make it really clear. To establish the kind of design claim that Meyer wants to make, one must do more – much, much more – than merely pointing to current scientific ignorance or (worse) confessing personal incredulity in the face of proposed scientific explanation. What one must do is show that the non-design alternative (whatever it is) is unable to provide the expected explanation. If Meyer fails to do this, it won't mean that his design proposal is wrong. It will just mean that it is "merely plausible."

2. Meyer's historical reflections emit a suspiciously propagandistic aroma. While describing the influence of Charles Thaxton, Meyer writes in ways that I find to be unacceptably misleading. Consider his description of a conference in Dallas in February of 1985. After noting that the conference "would bring together scientists from competing philosophical perspectives," Meyer relates how "controversy erupted":

What introduced drama into what might have otherwise been a dry academic discussion was the reaction of some of the scientists to a new idea. Three of the scientists on the panel had just published a controversial book called The Mystery of Life's Origin with a prominent New York publisher of scientific monographs.Their book provided a comprehensive critique of the attempts that had been made to explain how the first life had arisen from the primordial ocean, the so-called prebiotic soup. These scientists, Charles Thaxton, Walter Bradley, and Roger Olsen, had come to the conclusion that all such theories had failed to explain the origin of the first life.

–page 26

According to Meyer, Thaxton et al. then suggested that because information in DNA is "mathematically identical" to information in language and code, it must have an "intelligent cause." Then:

That was where the fireworks started. Other scientists on the panel became uncharacteristically defensive and hostile. Dr. Russell Doolittle, of the University of California at San Diego, suggested that if the three authors were not satisfied with the progress of origin-of-life experiments, then they should "do them." Never mind that another scientist on the panel who had favored Thaxton's hypothesis, Professor Dean Kenyon, of San Francisco State University, was a leading origin-of-life researcher who had himself performed many such experiments. It was clear that Dolittle regarded the three scientists, despite their strong credentials, as upstarts who had violated some unspoken convention.

–page 26

Reading this account makes me worry about the rest of Signature in the Cell. Meyer seems to be carefully manipulating his account in order to give the reader a distorted impression of the "conference" and the book at the center of one of its panel discussions. The "conference" wasn't the scientific conference that you're picturing. It was a dialogue sponsored by Dallas Baptist University and an organization of Christian scholars. It was called "Christianity Challenges the University: A Dialogue of Theists and Atheists" and it was specifically intended to bring "the theistic position" into dialogue with "the atheistic position" on topics from all corners of the academic world. The opening talks were on "Why I am a Christian." I think the event sounds really interesting, and the organizers assembled a superb group of scholars. But do you see how Meyer has misled us about that conference? It wasn't a scientific meeting. It was a dialogue between atheists and theists. Why didn't Meyer just tell us that? The session that Meyer attended was not a meeting of scientists for the purpose of discussing OOL research. It was a religiously-oriented dialogue centered on the new book by Thaxton et al., and the session was chaired by Thaxton himself. (You can read more about the Dialogue in the ASA Newsletter, June/July and August/September of 1985.)

And it gets worse. Meyer's claim that "other scientists became defensive and hostile" is contradicted by the report of Owen Gingerich, the Harvard astronomer and historian of science, who was present at the whole dialogue and wrote that "the entire dialogue was conducted with intelligence and good humor, with each side respecting while disagreeing with the philosophical orientation of their opponents." Meyer wants you to picture the "other scientists" reacting with hostility to a "new idea" from "upstarts" while carefully obscuring the nature of the event, to the point that he writes of a "conference" to "bring together scientists from competing philosophical perspectives." I find that to be disingenuous. And quite sad.

Meyer writes that The Mystery of Life's Origin was published "with a prominent New York publisher of scientific monographs." Well, that publisher is The Philosophical Library, and yes they published a few "scientific monographs" over the decades. A few. I'll let you figure out their main scholarly specialty. Meyer's embellishment is pathetic, and this kind of behavior is so hard to understand. Why would the publisher matter? Does Meyer think that no one will bother to see if The Philosophical Library really is a prominent publisher of science books? Did it occur to him that inquiring minds might visit the publisher's web site? Man, I just don't get it.

Finally, look again at how Meyer identifies the characters in his drama. Dean Kenyon, creationist and Discovery Institute Fellow, is referred to as "Professor Dean Kenyon" and "leading origin-of-life researcher." Russell Doolittle, distinguished evolutionary biologist and biochemist, was elected to the National Academy of Sciences in 1984, the year that The Mystery of Life's Origin was published. Meyer refers to him as "Dr. Russell Doolittle."

This book looks like folk science to me. It's already lowered my regard for its author. I hope it gets better. I really do.

A quick note about a hero

My chapter-by-chapter commentary on Signature in the Cell will resume shortly. But I can't resist writing a little about someone I know who did something extraordinary. Here's the short version.

This friend of mine, we'll call her "Susan," became inspired several months ago while reading accounts of people resisting Nazi occupation during World War II, and especially those who risked their lives (and often lost their lives) working to assist Jews and others targeted by the occupiers. She wondered how/if she would/could do such things.

Subsequently, she read a story in our local paper about a grieving father who, in his son's name and honor, had donated a kidney to someone he didn't know, as part of a kidney donation chain. Susan thought, "I can do that." (She's married and has four kids ranging in age from 17 to 9.)

She contacted the local transplant program and found out that such altruistic donations had not occurred in Grand Rapids and that the center didn't have procedures for such an arrangement. But when the program realized Susan was serious, they put the procedures together and began the testing to determine Susan's suitability as a donor.

It all culminated in the first altruistic kidney donation in West Michigan on Monday, 11 January. Both Susan and the recipient are doing really well.

Susan is my hero. Somehow, I'm lucky enough to be married to her. We celebrated our 25th wedding anniversary a little more than two weeks ago.

Please look into the kidney donation thing. Think of it as an anniversary gift.

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.

2. In discussions at Telic Thoughts over the last week and a half, I got the impression that the book is primarily about DNA and genomics. I was wrong. It's part memoir, part basic overview, part rehash of arguments based on "information." There seems to be little about genomes and their structure here. Again, that's not an insult or a critique. But don't be fooled by claims that this is a work of serious science or that the subtitle ("DNA and the Evidence for Intelligent Design") indicates a systematic examination of genomics.

3. The book includes excellent notes, an extensive bibliography and an exhaustive index. Very nice.

4. Perusing the index, I discovered something very curious. Mike Behe is mentioned exactly three times in the book, solely in discussions of Darwin's Black Box and irreducible complexity. Nowhere in the book does Meyer cite or mention The Edge of Evolution, where Behe tries to create evidence for intelligent design by calculating mutation rates in, you know, DNA. Hmmm. I'll bet that was an interesting meeting of the Fellows.

5. From the prologue, page 8:

This book attempts to make a comprehensive, interdisciplinary argument for a new view of the origin of life. It makes "one long argument" for the theory of intelligent design.

This looks like a mistake to me. The book is, at least in part, a breezy memoir. Does Meyer really want it compared to the Origin of Species?

6. Key passage from page 8:

Thus, Signature in the Cell does not just make an argument; it also tells a story, a mystery story and the story of my engagement with it. It tells about the mystery that has surrounded the discovery of the digital code in DNA and how that discovery has confounded repeated attempts to explain the origin of the first life on earth. Throughout the book I will call this mystery "the DNA enigma."

I wonder if Meyer understands – really understands – how badly his project will turn out if it's all about what we don't yet know. If this book is about building a case for intelligent design by repeatedly restating the fact that we don't yet understand the origin of the first life on earth, then this book is not an argument for intelligent design. It is more likely the death rattle of the movement of the same name.

7. A key question from the final sentences of the prologue:

Even if we grant Darwin's argument in the Origin, does it really follow that he refuted the design hypothesis?

Again, this is a mistake in my view. What is argued by Ayala and others (it is Ayala that Meyer is answering in the close of the prologue) is not that Darwin "refuted the design hypothesis." In other words, the claim is not that "design is wrong." The claim is that design is not a useful explanation. As I would put it, design isn't the answer, it's the question. That's what you get when you grant Darwin's argument. You don't "refute" design; you enfeeble it as an explanation for biological change.

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?

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.

But then last week over at the Panda's Thumb, Nick Matzke posted on some of the weaknesses in the book, and he caught my eye with this:

If you are a sufficient wonk about the ID debate, there is some interesting stuff about Meyer’s highly revisionist account of his own history and the history of the ID movement, and there is an interesting study to be made of the science that Meyer left out of his book, but that makes for a big project, so it will be awhile before I or someone else get it out there.

Seemingly at the same moment, the folks at Telic Thoughts (one ID site that's mostly worthy of respect) called for more reviews of the book by ID critics, and the discussion that followed made it clear to me that this book needs to be carefully reviewed. (Darrel Falk has a nice critique at the Biologos blog, but it's not a detailed review.)

So I'll blog through the book, chapter by chapter. There are 20 chapters, plus a crucial epilogue and two important-looking appendices, but the series won't be as crazy long as it sounds: looking through the book and Meyer's overview in the prologue, I can see that many chapters – about half is my guess – contain basic overviews or memoir-like material that will require little comment or review. I will not dwell on political/philosophical issues such as whether ID is science or stealth creationism. Instead I'll focus on specific scientific claims, and I'll look specifically for new analysis or evidence in favor of ID. That means that some of my entries will be uncharacteristically short. Really.

First up: the prologue.

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.

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.

Resurrection

So there hasn't been a post on Quintessence of Dust in three months. Here are some reasons for this.

1. We're in the midst of a distracting crisis at Calvin College right now. I won't talk about it here, but it's very serious and has already affected my relationship with the college.
2. I recently completed a major writing project, a book that I coauthored with a colleague at Calvin. Not much else to say about that at this point.
3. I've coauthored two recent review articles with my colleagues at the Van Andel Institute, and we have significantly expanded the scope of our collaboration, with a major new grant proposal in the works.

During this hiatus, I enjoyed a wonderful attack (and a flatulent followup) by a poorly-equipped ID demagogue, Cornelius Hunter. God bless him: he said I'm "the best of the worst." There's not much there, so I'll ignore his criticism and work instead on completing two interrupted series, one on deep homology & design and one on Richard Dawkins' biomorph program. Then we'll get back to regular forays into the current literature, and we'll focus on "junk DNA" a bit more. Biomorphs are next. See you soon.