Thursday, July 01, 2004

The World Open Beckons I'm sure all of my loyal readers are dying to read the next installment in my series on what a giant weenie Robert Koons is, and I'm looking forward to getting back to that myself. Alas, I will be driving up to Philadelphia tomorrow to participate in the World Open chess tournament over the weekend. Preparations for the destined-to-be-a-major-assault-on-my-ego trip took more time than I anticipated. Regular blogging will resume when I return next week.

Someone once commented that chess will never appeal to the masses until the masses realize that the joy of removing an enemy's toenail with red-hot pincers pales in comparison with the joy of capturing his pawn on the tenth move, and forcing him, for want of that pawn, to resign on the eighty-seventh.

Someone else once said that the ability to play chess is the sign of high-intellect. The ability to play chess well is the sign of high intellect gone wrong.

I don't actually play all that well, so I guess I'm absolved on that point. The evidence of high intellect gone wrong is that I spend so much time on this blog!

If there are any serious East coast chess players among my readers, and if you're going to be at the World Open, stop by and say hello. I'll be in the U2000 section, muttering about my colossal stupidity in hanging my knight on move 11.

Wednesday, June 30, 2004

More Stupidity from Touchstone Not content to stop with Roberto Rivera's stupidity, Touchstone has published this brain-dead response to the argument from dysteleology. That's the fancy name for the argument that there are so many instances of bad or inefficient design in nature that it is hard to believe that God specifically created animals in their present form. The article's author, Jonathan Witt, takes the “God is whimsical approach” first popularized by Phillip Johnson in Darwin on Trial.

Witt's article deserves a proper fisking, but for now let me just make one point. WItt writes:

But the point here is that these anti-design arguments by Dawkins, Gould, and other Darwinists are not scientific ones. They are aesthetic arguments, expressing an idea of what the universe should look like—that is, that it should satisfy the tidy-minded engineer. But who is to say that the Darwinists’ taste is that of the cosmic designer, if there is one? Who is to say that the designer should value tidiness over, say, whimsy?

This is written in the context of Gould's argument about the panda's thumb and Dawkins' argument about the absurd backward wiring of the mammalian eye.

I find it ironic that ID's freqeuntly accuse scientists of being unwilling to confront the breathtaking complexity of living things. Here Witt seems unwilling to confront the full force of the argument from dystelelogy. Dawkins and Gould used the examples they did because they were really making points about how natural selection operates and only tangentially speculating on what an omnipotent designer would do.

So let's answer Witt's question. Who is to say that the designer should value tidiness over, say, whimsy? Well, does Witt understand that the recipients of God's whimsy are living creatures capable of understanding pain and suffering?

Human beings take in food and air through the same passge. As a result more than three thousand people choke to death every year. Many of them children. That's God's whimsy for you.

How about birth defects? Each year thousands of children are born minus limbs, with brain damage so severe they will never live an indpendent life, with diseases like leukemia or AIDS. Does this reflect God's whimsy?

Extinction is never pretty, but it happens to be the fate of more than ninety-five percent of all the creatures God ever created. That's how refined and sophisticated God's sense of humor is.

The fact is that, it's scientific deficiencies aside, ID has awful theological consequences. No one would start from the premise that the natural world reflects the will of an omnipotent designer and conclude that the designer is benevolent. Until ID proponents are willing to confront that point head-on, they can not claim that the argument from dysteleology has been answered.

Darwinists Hate Pandas, Again Touchstone Magazine has pounced on the “Darwinists Hate Pandas” meme. There feature article, by Roberto Rivera, is entitled “Of Pandas and Men” with the subhead “Roberto Rivera on Darwinism and Why We Let the Pandas Live”. I already dealt with this article when the original version of it was published at Charles Colson's website, but let me remind you of the crucial line:

For those who take their Darwinism, as Thelonious Monk might have put it, straight, no chaser, the logical response to the plight of the giant panda is “tough.” Evolution is, if nothing else, unsentimental. It rewards adaptability and punishes, in the medium-to-long term, overspecialization. If your diet and habitat disappear—and that has happened countless times in Earth’s history—then you do, too.

My Christian friends sometimes take me to task for being over-concerned with the antics of the more extreme elements of American Christianity. They're crazy, sure, but they're in the minority of religious believers, they assure me.

Well, as far as I know Touchstone is considered pretty mainstream in Christian circles (if any of my readers know better I would be happy to hear that I am wrong). They describe themselves as a “Journal of Mere Christianity”.

And here they are promoting an argument so stupid, so utterly disrespectful of people who do not see the world as they do, that I see no reason ever to take them seriously about anything. If they are representative of contemporary Christian thought, then there is no reason to take Christian thought seriously either.

“Is” and “ought” are two different things. Okay? That simple point, obvious to any child, has apparently eluded both Rivera and his editors at Touchstone. Once that is realized there is absolutely nothing left of Rivera's argument. Arguing that Darwinists should not be unhappy if natural selection leads to the extiniction of pandas is like arguing that physicists should not be unhappy if gravity leads to a plane crash.

Rivera is an idiot.

Tuesday, June 29, 2004

Creepy Spend a few moments perusing this website, dedicated to the proposition that Christian parents have an obligation to remove their kids from Godless, government-run schools. Thier feature item is a lengthy resolution enumerating their grievances with the public schools. Here are a few of the whereases:

Whereas, teaching our children everything that Jesus commanded involves their learning to think biblically about all the spheres of human thought, activity, and life (Dt. 6:4-9) so that they take every thought into captivity to the obedience of Christ (2 Cor. 10:5).

Whereas, our thinking is not to be conformed to this world's way of thinking, but our minds are to be renewed and sanctified by the truth of God's Word (Rom. 12:2; Jn. 17:17).

Whereas, the fear of the Lord is the beginning of knowledge (Pr. 1:7) and in Christ are hidden all the treasures of wisdom and knowledge (Col. 2:3), any instruction that does not begin with the fear of the Lord, teaching the centrality of Jesus Christ for understanding all of life cannot properly be said to impart wisdom or knowledge to children.

Whereas, Jesus said, “He who is not with Me is against Me, and he who does not gather with Me scatters” (Lk. 11:23), the government school system that claims to be “neutral” with regard to Christ is actually anti-Christian, so that children taught in the government schools are receiving an anti-Christian education.

Whereas, the Bible says, children are like arrows in the hand of a warrior (Ps. 127:3-5), we must understand that children are weapons (arrows) to be aimed for the greatest impact in the kingdom of God. Just as it would be foolish for the warrior to give his arrows to his enemies, it is foolish for Christians to give their children to be trained in schools run by the enemies of God.

Whereas, the millions of children in government schools spend 7 hours a day, 180 days a year being taught that God is irrelevant to every area of life.

The resolution contains many other provisions along the same lines.

Take every thought into captivity to the obedience to Christ? Children are weapons to be aimed? Creepy.

When I read this sort of extreme rhetoric I am reminded of just how fragile fundamentalist faith really is. The things they believe are in such defiance of all facts, logic and common sense, that merely being exposed to differing viewpoints at too young an age is enough to damage their faith forever. The burden of being a fundamentalist parent must be almost too much to bear. When I was a child, if I told my parents I thought they were wrong about whatever they would just shrug and laugh it off, maybe correcting my grammar along the way. But if the child of a fundamentalist decides his parents are wrong, those parents live with the knowledge that their ineptitude has led to the eternal damnation of their child's soul. Parenting is hard enough without further burdening yourself with such responsibility.

O'Reilly's Lies My disection of Robert Koons' insipid essay will resume tomorrow. For now, enjoy this genial evisceration of the most relentlessly dishonest and obnoxious pundit on television:

Here's what I'm willing to do, right here, in my medium of newsprint. I'll serve up some O'Reilly untruths, courtesy of the media watchdog group Media Matters for America, and you disprove them - in your column, or on your radio or TV show, wherever the truth wants out.

I'm sure Media Matters will be watching.

Example 1: In an April 27 radio debate with a Canadian journalist, you threatened to lead a boycott of Canadian goods if Canada didn't deport two American military deserters, saying that a previous O'Reilly-led boycott of French goods cost that country billions in lost export business. You cited the Paris Business Review as your source for those losses.

In fact, Media Matters found no evidence that a Paris Business Review even exists, and France's export business with the U.S. actually increased during the run-up to the Iraq war.

Example 2: In discrediting philanthropist and John Kerry supporter George Soros, you distorted his account of his feelings about his father's death, deliberately misquoting him from a 1995 New Yorker article to make it appear that he had callous disregard for his father's life.

Example 3: On May 4, in announcing his acquisition of a cable TV channel, Al Gore said: "This is not going to be a liberal network or a Democratic network or a political network in any way, shape or form."

On “The O'Reilly Factor” that night, you said: “Al Gore has announced that he is starting up a new cable channel exclusively devoted to liberal stuff. We wish Mr. Gore good luck. And he'll need it.”

By the way, Bill, the Media Matters people tell me they've offered to go on your show to address these whoppers and others, but that so far, you've been hiding under your desk.

Monday, June 28, 2004

Koons, Part II In yesterday's posting I began discussing Robert Koons' essay from the recent anthology Uncommon Dissent. Koons pretends that natural selection is an abstract principle used by scientists to avoid confronting the complexity of living organisms. In reality scientists use natural selection as a starting point for generating hypotheses about how various structures evolved. Such scenarios must successfully account for all that is known about the operation of a system. Having cleared that explanatory hurdle, such scenarios inevtiably have consequences for what should be found in other, related organisms. When those consequences are seen to obtain, our confidence in the hypothesis grows. This method of reasoning has been so successful in biology that we are justified in saying that natural selection lies behind much of the complexity we see around us.

Koons, good philosopher that he is, completely ignores all of the actual, empirical work biologists have done over the years. Instead he offers his own list of “Five Stages in the Confirmation of Darwinism” (P. 9-11).

  • Stage 0. The original, pre-Darwinin situation, in which the complex functionality of life triggered a natural human disposition to recognize intelligent agency, creating a strong presumption in favor of such agency as the cause of life.

  • Stage 1. An alternative mechanism is proposed, random variation culled by natural selection, and preliminary evidence in favor of the new hypothesis is gathered and systematized.

  • Stage 2. In several paradigmatic cases, hypothetical Darwinistic pathways leading to actual adaptive forms are described in sufficient detail and with sufficient understanding of the underlying genetic and developmental processes that it seems virtually certain that these pathways represent genuine possibilities. These pathways must be possible, not only in the sense of involving no violation of physical or chemical laws, but also in the sense that every step in the path can be assigned an estimated probability that is sufficiently high for the joint probability of the entire pathway to be consistent with a reasonable belief that such a thing might really have happened.

  • Stage 3. For a significant number of hypothetical pathways of the kind described in stage two, we are able to verify that the pathway was probably actualized in history. New evidence from fossils and homologies is found that conforms to our specific expectations, based on the hypothetical pathways, and few if any instances of evidence are found that cannot readily be explained in terms of these pathways. Each hypothetical pathway describes a large number of intermediate steps, leading from some known ancestral form lacking the adaptation in question to some known form possessing it. Each step should be fully described at both the genetic and the morphological level: that is we should be specific about what mutations, lateral gene transfers, or other processes have occurred, and how the new genotype is expressed in morphology. For each step a hypothetical environment needs to be specified, and the tools of population genetics employed to show that the hypothetical new genotype would in fact be selected over its rivals in the hypothetical environment.

  • Stage 4. If nearly every case of apparent design has been successfully explained in Darwinian terms, and in each case we have found an overwhelming body of specific, confirming evidence, we are justified in treating Darwinism as established beyond a reasonable doubt.

Want to guess the stage at which modern evolutionary theory resides?

Where are we today? Leading biologists assure us that we are at stage four. In fact, however, I believe that we are still in stage one.


As is stated in Koons' explanation of Stage 0, his starting point is that some vague notion of ID is the default position. In other words, if scientists can not meet his explanatory hurdles then design should be accepted as the correct explanation. It is a starting point so asinine that it is enough, all by itself, to disqualify anything else he says from serious consideration. Nonetheless, let us consider whether Koons' five stages have any merit.

We begin with a simple observation: Population genetics has no tools to tell us whether a hypothetical new genotype will be selected over its rivals in a hypothetical environment. The determination of whether a particular allele will be selected over its rivals will depend on the effect it has on the organism's phenotype. The selective advantage (or disadvantage) conferred by a new mutant appears as a variable in the equations of population genetics; some determination of its value must be made before these tools can be applied to any real world situation.

I do not claim that only biologists should be allowed to comment on evolution (after all, my training is in mathematics). But I do say that if a non-biologist is going to argue that the community of biologists is all mixed up about the epistemic status of their discipline, then he really must be extra careful to learn the basics of the subject. Do you get the impression that Koons has really made much of an effort to educate himself on the nature of population genetics? Do you think he could give a coherent description of what lateral gene transfer is, or on the various types of mutations and their effects on organisms (other terms he throws around rather loosely)? If he has not mastered these basic elements of biology, then why should we take seriously his assessments of evolution?

Now, back to his list. Koons charges evolution with being mired at Stage One. This is unsurprising, considering that he has rigged Stage Two to make it impossible to reach. Koons expects us to be able to describe specific genetic events that happened millions of freakin' years ago in animals that are currently extinct! He then expects us to perform elaborate probability calculations to determine whether our hypothetical genetic events might actually have happened. Leaving aside the fact that such a calculation would depend on far more variables than we could realisticly estimate, there is also the fact that low probability by itself tells us nothing about whether an event might actually have happened. Even William Dembski understands that point.

What we do know is that every bit of an organism's phenotype is under genetic control, and that changes in genes can, in principle, affect any bit of that phenotype. We also have a large catalog of mutations in modern organisms and the effect those mutations have on the phenotype of the organism. We know enough to assert that any sufficiently small genetic event will almost certainly happen in a large population given enough time. Finally, we can assert that any sufficiently small change in phenotype can be attained by a correspondingly small genetic change.

Ken Miller's scenario for the evolution of blood clotting, mentioned yesterday, provides a good example of these ideas in action. Recall that Miller's scenario does not invoke any sort of genetic mechanism that is not known to occur in modern organisms, he discusses the effect these changes would have on our nascent blood clotting system, and ultimately uses his scenario to derive verifiable (and verified!) predictions about blood clotting in other organisms. Of course, Miller did not specify specific genetic loci that mutated, nor did he isolate specific species in which these changes occurred, because that level of detail is simply impossible to obtain. If Koons believes that Miller's scenario is too vague to be taken seriously, he will have to tell us what more he wants.

To see how Koons treats actual biology, let's consider the only example he discusses: the paper “A Pessimistic Estimate of the Time Required For an Eye to Evolve”, by Nilsson and Pelger. First, here is what Koons says:

Take, for example, Richard Dawkins's attempts to prove that Darwinism is able to explain the emergence of the vertebrate eye. Dawkins refers to a computer simulation by Nilsson and Pelger, showing that one can gardually improve a light-sensitive spot and reach, in 1800 steps or so, a fully-functional, lens-bearing eye. This might be impressive, except that the computer simulation (like every single simulation referred to by Dawkins in the book) entirely omits the two crucial details about real biology: the genotype/phenotype distinction (the distinction between the genetic constitution of an individual or group as opposed to the properties produced by interaction with its environment) and the processes of embryological development. The steps in Nilsson and Pelger's program are phenotypical (that is, they concern changes in gross, morphological feaures in the fully formed adult). We are not given a model in which the successive forms of the eye are determined by successive trajectories of embryological development, nor are we given a model of how these successive trajectories are determined by successive, feasible mutations. Given these limitations, it is, of course, impossible to estimate the probabilities of the mutations required for each of the 1800 steps in the creation of the vertebrate eye. (P. 9)

It is amusing that Koons repeats Dawkins' error in describing what Nilsson and Pelger did as a computer simulation, since his colleague David Berlinski published a much ballyhooed article in Commentary in which he made a big fuss over the fact that there was no computer simulation in the paper. This point is not relevant to discussing the arguments of either Dawkins or Koons, however.

The paper Koons mentions contained two major accomplishments. The authors described a sequence of small steps bridging a light-sensitive spot of the sort possessed by various worms and microorganisms with a vertebrate eye. They then performed a calculation in which they showed that such an eye could evolve in a remarkably short amount of time.

The sequence Nilsson and Pelger described began with a light sensitive spot. At each step, small changes were made in the size or shape of the spot in such a way that the visual acuity of the resulting proto-eye would be an improvment over what came before. Here is a brief quote from the paper:

We let the evolutionary sequence start with a patch of light-sensitive cells which is backed and surrounded by dark pigment, and we expose this structure to selection favouring spatial resolution. We assume that the patch is circular, and that selection does not alter the total width of the structure. The latter assumption is necessary to isolate the design changes from general alterations of the size of the organ. There are two ways by which spatial resolution can be gradually introduced: (i) by forming a central depression in the light-sensitive patch; amd (ii) by a constriction of the surrounding pigment epithelium. Both these morphological changes reduce the angle through which the individual light-sensitive cells receive light. The relative effects that depression and constriction have on the eye's optical resolution are compared in figure 1a. Initially, deepening of the pit is by far the most efficient strategy, but when the pit depth equals the width, aperture constriction becomes more efficient than continued deepening of the pit.

It was a significant accomplishment for Nilsson and Pelger to exhibit a sequence of small steps leading from a light-sensitive spot to a lens-bearing eye. Prior to their work, it was not obvious that such a sequence existed. Their scenario gains strength from the fact that every proto-eye in their sequence can be found in modern organisms. This proves that the eyes they described really would be functional and useful.

Koons asks us to dismiss their work out of hand, on the grounds that they described morphological changes to the eye without specifying which gene mutated when to produce those changes. Is Koons really suggesting that it is too implausible to suggest that a small genetic mutation changed a light-sensitive spot into a slightly invaginated light-sensitive spot? Do we have to describe elaborate processes of embryological development before we accept the contention that natural selection could cause an invaginated spot to constrict itself into a camera eye? Known mutations in known organisms cause precisely those sorts of changes to occur.

The fact is that Koons does not raise these issues because they actually cast doubt on the validity of Nilsson and Pelger's work. He raises them because they allow him to present himself to his scientifically-illiterate readers as the hard-nosed skeptic facing off against ideology-blinded scientists willing to wave their hands to prop up their worldview.

In case after case biologists have gotten their hands dirty understanding the minutiae of complex systems in biology and have emerged with useful scenarios for how these systems evolved. These scenarios have passed every test we can possibly put them to. But Koons prefers to fold his arms and shake his head. Don't bother him with evidence, he has religious assumptions to defend.

Before closing, let me also point out that paleontology has provided us with precisely the sort of new fossils that he asks for in Stage Three. Surely he is aware of, among many other examples, the reptile to mammal transition. This is a sequence of fossils which shows in great detail how the mammalian inner ear bones evolved from similar bones in the reptilian jaw. This transition was once considered so inherently implausible (after all, the intermediates would be unable either to eat or to hear, right?) that creationists used it as exhibit A in their case against Darwin. Yet we now have detailed fossil and ebryological evidence to tell us how it happened. Meanwhile, each new fossil dug up is another opportunity to score a devastating blow against evolution. But no fossil has turned up that is out of place from an evoltuionary standpoint.

As for new evidence from homologies, the various genome projects have been producing them in droves of late. Do you think Koons cares?

Koons also completely ignores the fact that we can have indirect evidence for selection's action, as I discussed yesterday.

The simple fact is that Koons demands a level of detail that is flatly impossible to obtain. Those requirements on his list that actually can be met, have been. In droves. Koons only mentions a single paper from the scientific literature, and his discussion of it is laughably inadequate. It should be evident that Koons hasn't the slightest interest in giving serious thought to the accomplishments of modern biolgy.

Sadly, there is still more to critique in Koons' paper. We will turn to that tomorrow.

Separation Anxiety Facts and Trends magazine, a publication of the Southern Baptist Convention, is reporting the results of a survey of Protestant pastors on the subject of church/state separation. It seems that pastors, by large majorities, believe that separation has gone too far. Surprise!

Most Protestant clergy in the U.S. believe the separation of church and state has gone too far, or in ways it was never intended to go. These are the results of a nationwide research study conducted among a representative sample of 700 senior pastors. The study was done exclusively for Facts & Trends by Ellison Research of Phoenix. Seventy-eight percent of all ministers felt the separation of church and state has gone too far, while 14 percent felt it
is right about where it should be, and 8 percent felt it has not gone far enough. Ministers in the South were particularly likely to feel it has gone too far (84 percent).
Among Southern Baptist pastors, 92 percent felt it has gone too far.

The article goes on to discuss certain specific issues, such as 'Under God' in the Pledge of Allegiance and displays of the Ten Commandments on public land. Happily, teaching creationism was not one of the issues mentioned.

But the most disturbing part of the article is this:

One of the on-going church-state controversies is the display of religious materials, such as nativity scenes, on public property. Ministers in the study were split over this issue. The most common perspective was that Christian displays should be allowed on government property, but not those of any other religion (36 percent). Almost as common was the feeling that religious displays from any major world religion (e.g. Christianity, Judaism or Islam) should be allowed. Twenty-two percent felt no religious displays should be allowed at all, while 11 percent felt displays should be allowed from any religion, including Wicca, Hare Krishna and anything else. Southern Baptist ministers generally felt displays should be allowed only from Christianity (40 percent) or from major world religions (36 percent).

The most common view is that only Christian symbols should be displayed. Great. These are the same people who complain about the lack of balance in science classrooms.

Creationism in York It seems that the small town of York, PA is having a little dust-up about teaching creationism. Pharyngula has the goods here. I have nothing to add to his excellent comments. The following thought pretty much sums up everything:

I don't want to sound like I'm doing nothing but making fun of the rubes in central Pennsylvania, but my point is that these arguments for creationism are all patently false. It's not a matter of me being prejudiced against Bible believers, or having subtle, arcane knowledge beyond the ken of mere yokels; these are trivially erroneous arguments. They are stupidly wrong. And that is a shame.

Sunday, June 27, 2004

Koons, Part One In Wednesday's post I mentioned William Dembski's latest offering Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. The first essay in this anthology is by Robert Koons, a professor of philosophy at the University of Texas. It is entitled “The Check is in the Mail: Why Darwinism Fails to Inspire Confidence”

I have earlier commented that the line-up of contributors to this volume was unimpressive, based on the fact that almost none of them have credentials in biology, and many don't have credentials in any branch of science. Despite this, I was vaguely optimistic that the book would offer something worth mulling over. After all, most ID books are published by Christian publishers and directed at audiences who use “intellectual” as an epithet. My hope was that the tone of the essays would be respectful, and that I would find plausible reasons for why the evidence for evolution, so persuasive to me, is not persuasive to other thoughtful people.

Sadly, that was too much to hope for. Koons' essay is, I'm sorry, awful. It is long on snarkiness and arrogance, but short on serious consideration of just what it is the biological sciences have been doing in the century and a half since Darwin.

Before considering his main argument, let us first make note of one bright spot in the essay. He writes:

Darwin himself contributed to the illicit shift in the burden of proof in his well known challenge to his critics in The Origin: “ If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” It is, of course, impossible to “demonstrate” any such thing. (P.13)

I describe this quote as a bright spot because he is tactily rejecting the fundamental piller in the case for ID: the irreducible complexity of certain biochemical systems. When Michael Behe introduced this idea in Darwin's Black Box he quoted the very same line from Darwin that Koons used. It was Behe's claim that systems which could not be formed by numerous, successive, slight modifications had now been found, and they were precisely those systems involving several, well-matched parts, such that the removal of any one part rendered the system non-functional. Do a google search on Darwin's quote and you will come up with dozens of creationist web sites claiming that Darwin's challenge had been met. Yet here Koons is plainly rejecting this claim. Good for him.

Sadly, that's the only interesting line in Koons' dreary essay. We should point out that Darwin was not shifting any burden of proof and he was not challenging his critics to do anything. He was merely emphasizing the importance of gradualness within his theory. The quote comes at the end of chapter six, “Difficulties on Theory”, in which Darwin discusses potential challenges to his ideas and explains why he finds them uncompelling.

Picking up where the previous quote left off:

How could it be proved that something could not possible have been formed by a process specified no more fully than as a process of “numerous, successive slight modifications”? And why should the critic have to prove any such thing? The burden is on Darwin and his defenders to demonstrate that it is really possible for at least some of the complex organs we find in nature to be formed in this way: that is by some specific, fully articulated series of slight modifications.

Koons offers some rather specific (and laughable) thoughts on what would be required to assert with confidence that natural selection lies behind most of the complexity we see in nature. He also argues that until scientists can meet his ridiculous standards, ID should win by default. I will consider the specific points he makes in this regard in tomorrow's posting. But first, let's take up the general question of why scientists do, in fact, assert with confidence that natural selection crafted most of the complexity we find in the genomes.

The first thing to observe is that there is absolutely no reason in theory to think that natural selection can not craft a complex organ. Critiques based on the fact that natural selection is a mindless process with no foresight that acts on random variations are fundamentally misguided. The mindlessness and lack of foresight of natural selection are totally irrelevant in determining whether a particular complex structure evolved gradually. All that is relevant is whether it is possible to find a series of small steps, each one beneficial (or at least not harmful) to its bearer, leading from some ancestral species that lacked the structure to the modern species that possess it. If such a series exists than selection is a plausible explanation. If no such series exists, then selection is not a viable explanation. This was the point Darwin was making in the quote given above. Richard Dawkins makes the same point in his book Climbing Mount Improbable.

So is Koons right? Is Darwin's requirement so loose that any organ could conceivably have been formed gradually? Hardly.

People like Koons present natural selection as if it were some abstract principle invoked by scientists to avoid having to deal with the enormous complexity of biochemical systems. The reality is quite different. In attributing a complex structure to the action of selection, scientists are imposing severe explanatory constraints on themselves. Any scenario of gradual evolution must be consistent with everything that is known about the system, and inevitably makes predictions about similar systems in related animals.

To see why, let's consider a specific example: Blood clotting. This is one of the systems described by Behe as being irreducibly complex. It is also singled out by Koons in his essay. Biologist Ken Miller described a scenario for the evolution of blood clotting in his book Finding Darwin's God. Here's an excerpt from the original draft of the relevant section (the published version had been shortened due to space considerations):

Even a general scheme, like the one I've just presented, leads to a number of very specific predictions, each of which can be tested. First, the scheme itself is based on the use of well-known biochemical clues. For example, most of the enzymes involved in clotting are serine proteases, protein-cutting enzymes so-named because of the presence of a highly reactive serine in their active sites, the business ends of the protein. Now, what organ produces lots of serine proteases? The pancreas, of course, which releases serine proteases to help digest food. The pancreas, as it turns out, shares a common embryonic origin with another organ: the liver. And, not surprisingly, all of the clotting proteases are made in the liver. So, to “get” a masked protease into the serum all we'd need is a gene duplication that is turned on in the pancreas' “sister” organ. Simple, reasonable, and supported by the evidence.

Next, if the clotting cascade really evolved the way I have suggested, then the clotting enzymes would have to be near-duplicates of a pancreatic enzyme and of each other. As it turns out, they are. Not only is thrombin homologous to trypsin, a pancreatic serine protease, but the 5 clotting proteases (prothrombin and Factors X, IX, XI, and VII) share extensive homology as well. This is consistent, of course, with the notion that they were formed by gene duplication, just as suggested. But there is more to it than that. We could take one organism, humans for example, and construct a branching “tree” based on the relative degrees of similarity and difference between each of the five clotting proteases. Now, if the gene duplications that produced the clotting cascade occurred long ago in an ancestral vertebrate, we should be able to take any other vertebrate and construct a similar tree in which the relationships between the five clotting proteases match the relationships between the human proteases. This is a powerful test for our little scheme because it requires that sequences still undiscovered should match a particular pattern. And, as anyone knows who has followed the work in Doolittle's lab over the years, it is also a test that evolution passes in one organism after another.

There are many other tests and predictions that can be imposed on the scheme as well, but one of the boldest was made by Doolittle himself more than a decade ago. If the modern fibrinogen gene really was recruited from a duplicated ancestral gene, one that had nothing to do with blood clotting, then we ought to be able to find a fibrinogen-like gene in an animal that does not possess the vertebrate clotting pathway. In other words, we ought to be able to find a non-clotting fibrinogen protein in an invertebrate. That's a mighty bold prediction, because if it could not be found, it would cast Doolittle's whole evolutionary scheme into doubt.

Not to worry. In 1990, Xun Yu and Doolittle won their own bet, finding a fibrinogen-like sequence in the sea cucumber, an echinoderm. The vertebrate fibrinogen gene, just like genes for the other proteins of the clotting sequence, was formed by the duplication and modification of pre-existing genes.

This passage comes at the end of a lenghty outline of blood clotting evolution that I recommend to everyone. Miller's writing is excellent, and he makes some rather complex biochemistry easy to understand. What Miller makes clear is that evolutionary biologists do not simply wave their hands, tell just-so stories, and call their job complete.

Miller's discussion also makes clear how we could find evidence that selection was not the crafter of some particualr complex strucure.
For example, he asserts that several of the proteins in the blood clotting cascade arose as the result of a gene duplication event. This explanation is viable only because the proteins in question show a high degree of sequence similarity. If that similarity did not exist, then Miller's scenario would not be viable.

Similarly, Miller's scenario for the formation of human blood clotting proteins has consequences for what we should find when we examine blood clotting in other vertebrates. As he indicates, those predictions are borne out. With each such successful prediction his scenario becomes more likely; just how science is supposed to proceed.

So, do complex biochemical systems in humans give the appearance of having been made from scratch out of materials unique to humans, or do they show evidence of having been cobbled together from parts that were readily available in other, related organisms? Every case studied to date has fallen into the latter category.

There are many other examples of this sort of reasoning. Darwin showed that the elaborate structures orchids use to attract pollinating insects were cobbled together from parts common in flowers. Had he found instead that they were composed of parts entirely unique to orchids, it would be much harder to attribute their formation to selection.

Stephen Jay Gould famously used the panda's thumb to illustrate the same principle.

Evidence of selection's activity comes in many other forms as well. One example that I like (because it is largely mathematical) is the role of game theory in the study of animal behavior. Game theoretic models have rendered comprehensible many formerly puzzling aspects of animal behavior. These models are based explicitly on the assumption that the behaviors in question were formed by selection. The success of these models is evidence of the correctness of that assumption.

Such examples could be multiplied endlessly. The point is that the hypothesis that natural selection is responsible for crafting complex organs has led to enormous progress in all branches of biology. This progress is strong evidence for the correctness of the hypothesis. What I have described does not even scratch the surface of what is out there. Biologists conitnue to invoke the action of natural selection because they find it enormously useful to do so.

ID proponents, unburdened by the repsonsibility of actually entering a lab and making progress on some problem of biological interest, dismiss all of this with a disgusted wave of the hand. They routinely argue that if we can not specify which genetic locus mutated when we can not have confidence that a given complex structure evolved gradually via selection. One ID proponent who argues that way is Koons, as we shall see in tomorrow's posting.