What is Population Genetics?

At the end of Wednesday's post I commented that there was one more aspect of “The tautology objection” that is worth discussing.

The basic argument was that “the survival of the fittest” is an empty tautology because the term “fittest” is simple defined as “those that survive.” We have already seen two reasons why this is wrong: (1) There is no abstract principle of natural selection used by biologists. There is nothing tautological about saying, for example, that moths possessing certain sorts of coloration leave more offspring than those lacking that coloration. (2) There are, in fact, criteria of fitness independent of mere survival. Bethell has simply confused the definition of fitness with how it is measured in certain circumstances.

But what about those abstract, mathematical formulations of evolutionary principles that fall under the rubric of population genetics? Is there anything helpful to Bethell there?

In his 1976 essay “Darwin's Mistake”, written for Harper's magazine, Bethell wrote:

The bold act of redefining selection was made by the British statistician and geneticist R. A. Fisher in a widely heralded book called The Genetical Theory of Natural Selection. Moreover, by making certain assumptions about birth and death rates, and combining them with Mendelian genetics, Fisher was able to qualify the resulting rates at which population ratios changed. This was called population genetics and it brought great happiness to the hearts of many biologists, because the mathematical formulae looked so deliciously scientific and seemed to enhance the status of biology, making it more like physics. But here is what Waddington recently said about this development:

The theory of neo-Darwinism is a theory of the evolution of the population in respect to leaving offspring and not in respect to anything else...Everybody has it in the back of his mind that the animals that leave the largest number of offspring are going to be those best adapted also for eating peculiar vegetation, or something of this sort, but this is not explicit in the theory...There you do come to what is, in effect, a vacuous statement: Natural selection is that some things leave more offspring, and there is nothing more to it than that. The whole real guts of evolution - which is how do you come to have horses and tigers and things - is outside the mathematical theory [my italics].

Before getting to the meat of the issue, we should pause to mock Bethell for syaing “qualify” when he surely meant “quantify.”

Bethell is so confused here it's hard to know where to start. Take the italicized portion of Waddington's quote, which Bethell seems to think is so important. Of course the question of how we came to have “horses and tigers and things” is outside the mathematical theory! Who ever said otherwise?

Bethell does not tell us where Waddington made this remark. I'd be curious to see the full context. But for the moment, let's think about mathematical models in general, and population genetics in particular.

The objects that mathematicians study have no physical existence at all. They are abstractly defined quantities or objects that possess only those properties mathematicians choose to bestow upon them. In defining their abstractions mathematicians typically have some real-life situation in mind. There may be no perfect circles in nature, but there are things that are sufficiently circle-like to amount to the same thing.

Students often object that it is precisely this level of abstraction that makes mathematics difficult. They have a point, but in another sense abstraction is what makes mathematics doable at all. It's understanding the real world that's difficult! Abstraction is where you say you're going to ignore most of the complicating factors that make physical phenomena difficult to predict, and instead focus on a handful of variables that you hope are the most important ones.

In population genetics the goal is to understand the short-term flow of genes in a population. In particular, suppose you find that a particular population of organisms possesses a gene we shall call A. What percentage of the organisms in the next generation will possess A?

To build a mathematical model for this situation we would ask what variables are crucial in determining A's representation in the next generation. A few things might occur to you immediately. We would want to know what percentage of organisms currently possess A, for example. We would also want to know what sort of selective advantage or disadvantage A confers on its bearers. If organisms possessing A are generally more fecund than those lacking A, for example, that will certainly be relevant to determining A's representation in the next generation.

Here are some things that are not relevant: What kind of organisms we're studying (in other words, does A occur in a population of monkeys? zebras? lions? Who cares!), or the precise phenotypic effect A has on its possessors (does A cause certain peppered moths to have darker coloration than their competitors? does A lead to more bristles on the legs of a fruit fly? Again, who cares?)

There are other factors we could mention as well.

Thus, within the mathematicla theory of population genetics a “gene” does not refer to a particular strand of DNA found in an actual critter. A gene is simply an abstract, undefined quantity, rather like the notion of a point in geometry. What we know about a gene is that it appears with a certain frequency in a population and that it competes with some number of alternative genes for representation in the next generation. We have certain other assumptions about mating behavior and fitness and so on.

Then we ask, given the assumptions we have made about these genes, what does logic and mathematics tell us about the representation of the gene in subsequent generations? Of course, any assumptions you make about selective advantages and the like are going to be highly time-sensitive. Environments are constantly changing, after all. This means that models of the sort I am describing are only likely to be applicable over relatively short time periods.

Once you begin to understand the abstract nature of mathematical models, you begin to see the absurdity of Bethell italiczing the last part of Waddington's statement. Horses and tigers are real world entities made from large numbers of genes. They evolved over millions of years in changing environments. How could a simple mathematical model that focusses on a handful of genes over short periods of time possibly tell us anything about why we have horses and tigers, as opposed to centaurs and unicorns? The mathematical models were never intended to answer such questions.

So what, then, did Fisher accomplish in The Genetical Theory of Natural Selection? It's almost a sure thing that Bethell never read the book, would not have understood it if he had, and has no sense of its historical significance. Hence his silliness about biologists requiring a handful of mathematical formulae to make them feel good about their subject.

At the time Fisher was writing there was no widespread agreement that natural selection was an important mechanism of evolution. Lamarckism in particular was still a popular contender. The principles of Mendelian genetics were still a new thing. And the origins of genetic variation were not well understood.

As a result evolutionary biology was foundering a bit. It was clear what the questions were, but answers seemed as distant as ever. So part of what Fisher accomplished was to show that the abstract machinery of mathematics could shed some light on what had previously been seen as purely empirical questions. The book actually begins with a discussion of blending versus particulate inheritance. When Darwin wrote blending inheritance was still a viable option. Darwin recognized that it was diffuclt to reconcile his theory of natural selection with blending inheritance, since it implied that new variations would quickly be diluted. But particulate inheritance, which is at the core of Mendelian genetics, is quite different. Thus, natural selection is a viable theory under a Mendelian scheme, but not viable (barring some mechanism for producing vast quantities of new variation) under a blending scheme.

Nowadays that's a commonplace observation, but at the time it was much overlooked. And Fisher put these casual observations onto a firmer footing than had previously been accomplished.

Fisher subsequently devised notions of natural selection and fitness that were amenable to inclusion in mathematical equations. Contrary to the assertions of the tautology mongers like Bethell, he did not define the fittest organisms as being those which survived. Actually, he never talked about the fitness of an organism at all, but rather the fitness of a particular gene. In his equations the greater fitness of one gene relative to another was represented as an increased probability of being represented in future generations.

The result of all this mathematizing was to show that natural selection was unique among proposed evolutionary mechanisms in being able to explain the gradual accumulation of small variations. He was also able to give a precise meaning to the idea of a population increasing its fitness over time. The result of all this was a previoulsy unknown level of rigor in drawing conclusions about evolution, coupled with a demonstration that the then proposed non-Darwinian mechanisms of evolution were theoretically inadequate.

More than this, he inaugurated a new way of thinking about biological questions. Fisher established the field of population genetics, which remains a major area of study today. It provided powerful analytical tools for pracitcing field biologists, and you can find numerous applications of its techinques in any textbook on the subject.

And now we can come full circle and see precisely why Bethell is so full of it. First, Fisher did not redefine selection. Selection meant exactly the same thing after Fisher that it meant beofre Fisher. He merely provided a formulation of it that was amenable to mathematical analysis. He was not trying to explain the origins of specific organisms or even specific adaptations. Rather, his intent was to explore the theoretical implications of Mendelian genetics for various theories of evolution. And even within the mathematical theory, he did not define anything in tautologous ways.

One final point. In applying the theories of population genetics, it is true that the fitness of a gene is measured by its representation in future generations. But this is far different from saying that fitness is defined that way. Fitness refers to a statistical tendency for certain organisms to bear more young than others. There is nothing tautological in that definition. Furthermore, it is a standard result in probability theory that if your sample size is sufficiently large, the measured freqeuncy of the particular gene in the next generation will be a good approximation to its theoretical value. (That's known as the law of large numbers, but that's a separate post). So there's nothing logiclally suspect either in the theory or the practice of population genetics.

Bethell closes his 1976 essay by writing:

Darwin, I suggest, is in the process of being discarded, but perhaps in deference to the venerable old gentleman, resting comfortably in Westminster Abbey next to Sir Isaac Newton, it is being done as discreetly and gently as possible, with a minimum of publicity.

It is now almost exactly thirty years later and even Bethell would have to concede that both evolution in general, and natural selection in particular, are going strong. Ignorant bombast will lose out to simple truth every time.

The War on Christmas

So far I have not commented on the supposed war on Christmas. The very idea that saying Happy Holidays rather than Merry Christmas constitutes an affront to anything is so clearly ridiculous that I didn't feel the need to actually comment to that effect. Fox News, and Bill O'Reilly in particular, seemed like the only ones promoting the idea, and their motives were so plainly opportunistic that I was inclined to just ignore the whole thing.

Then I read this disgusting column, from the lovely folks at Town Hall. Its author is Brad Prelutsky.

Whereas O'Reilly and company were content to lay this made-up war at the feet of the same godless, atheistic, religion-hating, liberal, securlarist, blah blah blahs who get blamed for everythng else, Prelutsky sees a new villain in the war on Christmas: Jews.

He writes:

That has changed, you may have noticed. And I blame my fellow Jews. When it comes to pushing the multicultural, anti-Christian, agenda, you find Jewish judges, Jewish journalists, and the ACLU, at the forefront.

Being Jewish, I should report, Christmas was never celebrated by my family. But what was there not to like about the holiday? To begin with, it provided a welcome two week break from school. The decorated trees were nice, the lights were beautiful, “It’s a Wonderful Life” was a great movie, and some of the best Christmas songs were even written by Jews.

But the dirty little secret in America is that anti-Semitism is no longer a problem in society; it’s been replaced by a rampant anti-Christianity. For example, the hatred spewed towards George W. Bush has far less to do with his policies than it does with his religion. The Jews voice no concern when a Bill Clinton or a John Kerry makes a big production out of showing up at black Baptist churches or posing with Rev. Jesse Jackson because they understand that’s just politics. They only object to politicians attending church for religious reasons.

My fellow Jews, who often have the survival of Israel heading the list of their concerns when it comes to electing a president, only gave 26% of their vote to Bush, even though he is clearly the most pro-Israel president we’ve ever had in the Oval Office.

I feel no particular desire to reply to this, beyond pointing out that America has never had, and never will have, an anti-Israel President. I would further point out that supporting Israel and being a rubber stamp for the Sharon administration are two different things.

Prelutsky is not finished:

I happen to despise bullies and bigots. I hate them when they represent the majority, but no less when, like Jews in America, they represent an infinitesimal minority.

I am getting the idea that too many Jews won’t be happy until they pull off their own version of the Spanish Inquisition, forcing Christians to either deny their faith and convert to agnosticism or suffer the consequences.

Again, no comment.

For the record though, if I must have strangers braying at me as I leave a Target or a Wal-Mart, I prefer to be wished Happy Holidays.

Have They Tried Open-Mindedness?

Have a look at this vaguely distrubing article from Current Magazine. It discusses the plight of students brought up with creationist pseudoscience having to confront the real thing when they get to college.

Rich Scott’s first few days on the West Chester University campus in suburban Philadelphia were spent worrying—and not just because he was nervous about getting along with his roommate. A recent graduate of a Christian high school, Scott had grown up with parents, teachers and pastors telling him that God created the earth in six days and that evolution is a myth. “Make sure you know what you believe,” Scott’s teachers had said in class as they encouraged their pupils to defend and explain their beliefs about the origin of humankind. And so Scott went to college armed with a firm belief in intelligent design and a determination not to let his years in school affect his conviction in God.

Yes, certainly. I mean, what could experts in biology, physics and chemistry possibly contribute to a discussion about the origin of humankind? Surely your high school teachers have already told you everything of relevance on that subject.

I have told this story before, but I think it is worth repeating. I used to listen to a fundamentalist Christian radio station during the time I spent in Kansas. One time they aired a call-in show for parents seeking Christian advice for dealing with various child-related problems. At one point an obviously distraught mother called in and said, “Like one of your previous callers my family has recently suffered a devastating setback. My son wasn't killed, but to me it feels just as permanent. He just called home from college and told me he had become an atheist.”

These stories are a good reminder that many Christians live in absolute terror of having their faith challenged. This terror is only doubled when they think about their children leaving home. For them, rival ideas and theories are not interesting starting points for stimulating discussion. They are threats to be defeated or avoided.

I find it difficult to imagine being brought up in such an environment. In a previous post I commented that I feel a kinship with other Jews despite the fact that I am an atheist. This is one place where that kinship manifests itself. If you scoured the country I think you'd be hard-pressed to find a Jewish family raising their children to be as closed-minded as Mr. Scott. Jews are famously argumentative, and the idea of closing one's mind to certain ideas without giving them proper consideration is anathema. Jews, in my experience, have far more sophisticated attitudes about faith than many Christians.

For most people it is not considered a triumph to leave college believing exactly what you believed as a freshman. For students like Mr. Scott, it is the goal.

From here the article goes on to describe the familiar statistics about the low rate of acceptance for evolution among many Americans. We have this somewhat comforting pargaraph:

“Many students have, over the years, come to me at church to express concern that a professor is opposed to Christianity and the basis for their concern is that the professor talks about evolution,” David Buchanan, a professor of animal science at Oklahoma State University, said in an e-mail. He has frequently taught seminars on the origin of life and estimates that “more than half” of his students would, if asked, “assert quite a conservative view of Genesis 1:11,” the portion of the Bible that outlines the Judeo-Christian creation story. Buchanan himself is an evangelical Christian and believes that it is important to discuss origin theories that contradict evolution, because “in science, we are always looking at alternatives.” He cautions, however, that the current incarnation of intelligent design theory has not reached the viability necessary to be taught in a college science class.

I'm not sure what alternatives Buchanan has in mind, but otherwise this sounds good.

But I'm not so sanguine about this one:

Scott, despite his initial fears, found no such discrimination in any of West Chester's science departments. Once his professors found out that he believed in intelligent design, they strove to help him find ways to write his papers without sacrificing either scientific knowledge or his personal beliefs. “They were very impressed that I was willing to take a stand and they helped me a lot.” Heartened by his own experience, Scott found other Christian geology majors through facebook and sent them supportive messages. “You might think it’s going to be hard the next few years, but keep praying, keep close to God, and He’ll help you through it,” he encouraged them.

If your personal beliefs are in direct conflict with scientific knowledge, it seems that something has to be sacrificed.

It's all well and good to say that professors should be respectful of student's beliefs. The problem is that I never hear any imprecation for the student to reciprocate this respect. Is the student expected to respect the fact that his science professors are experts in the relevant branches of science? Shouldn't the student be expected to take seriously the idea that professional scientists have good reasons for accepting evolution and rejecting creationism, reasons their religious instructors probably never explained to them? Yes, of course, students should not be ridiculed or threatened for their beliefs and of course professors should avoid indoctrination. But students have to hold up their end of the bargain by recognizing that much of what they were told about science in their religious education was not correct. They have to understand that it is not the professor's job to coddle them when they claim to believe things that are patently untrue.

That last sentence sure is creepy. Learning things that challenge your preconceived notions is, for many people, something to be endured, not something to benefit from. I can't imagine what it's like to be that confident that, as a teenager, you have successfully resolved the fundamental mysteries of existence. I don't care if Mr. Scott learns to accept evolution. But I do hope he will learn to be a bit more open-minded, and a bit more willing to accept that things he heard in high school should be the beginning, not the end, of his education.

The Tautology Objection

In yesterday's post I criticized this article, by Tom Bethell, from National Review Online. However, I left one of his arguments unanswered.

The argument is that natural selection is completely vacuous as a scientific principle. Bethell attempts to make this argument in two different ways. First he writes:

We have been trained to be blasé about the marvels of creation. “Oh, evolution did that,” we say. “It was just a matter of random mutation; nothing surprising there.” “These things arose by accident and were selected for.”

That phrase — “it was selected for” — is regarded as a sufficient explanation for . . . everything. The same mundane phrase is given as the explanation for everything under the sun. How did the bats get sonar? “It arose by an accidental mutation of the genes and was selected for. Next question?” How did the eye develop? “Piecemeal. There was a random mutation and it conferred an advantage so it was selected for. Then the same thing happened over and over again. Next question?” How did the camel get its hump? “Random mutations conferred some advantage and so they were selected for. Next question?”

This is the science before which all knees must bend? These explanations are no better than “Just-So stories” (as one or two Harvard professors have rightly said). No actual digging in the dirt is needed: The theorist merely contemplates the trait in question and makes up a plausible story as to how it might have been advantageous.

If I write about this subject for a hundred years I will never understand what could make a person that arrogant. Both the professional and popular level literature on evolution is chock-full of detailed analyses for how specific adaptations evolved gradually via selection. Biologists base these scenarios on in-depth studies of data from paleontology, genetics, anatomy, and embryology. But Bethell simply ignores it all, preferring instead to promote vicious stereotypes of his intellectual betters.

For example, when paleontologists dig up a detailed series of fossils showing how reptilian jaw bones evolved into mammalian ear bones, and when the scenario suggested by the fossils is subsequently backed up with evidence from embryology and anatomy, are scientists really out of line in saying the mammalian inner ear evolved gradually? (See Stephen Jay Gould's essay “An Earful of Jaw” from his anthology Eight Little Piggies for a good explanation for this.)

Or when we find that the numerous proteins involved in human blood clotting have just the form they ought to have if they formed via a series of gene duplication events starting from a common pancreatic enzyme, when we observe that invertebrates such as lobsters make do with a blood clotting system bearing a striking resemblance to the final stages of our own, and when the scenario of blood clotting evolution suggested by these observations is then used to make further predictions about critters not yet studied (predictions subsequently born out by further research), is it the scientists who are being unreasonable in calling the problem solved, or the creationists for demanding more evidence? (See Ken Miller's excellent description of blood clotting evolution for more details).

The fact is that examples like this could be multiplied endlessly. Bethell either lacks the knowledge or the integrity to comment seriously on this subject.

But Bethell has another argument up his sleeve:

George Will has made one accurate criticism of the idea he so dislikes: “The problem with intelligent design is not that it is false but that it is not falsifiable. Not being susceptible to contradicting evidence, it is not a testable hypothesis.” This is true; but he should have added that Darwin's theory of evolution by natural selection is not falsifiable either. Darwin's claim to fame was his discovery of a mechanism of evolution; he accepted “survival of the fittest” as a good summary of his natural-selection theory. But which ones are the fittest? The ones that survive. There is no criterion of fitness that is independent of survival. Whatever happens, it is the “fittest” that survive — by definition. This, just like intelligent design, is not a testable hypothesis. As the eminent philosopher of science Karl Popper said, after discussing this problem that natural selection cannot escape: “There is hardly any possibility of testing a theory as feeble as this.” Popper was the first to propose falsification as the line of demarcation between theories that are scientific and those that are not; both intelligent design and natural selection fall by this standard. (Emphasis Added)

And there it is. The tautology objection. It has been a mainstay of anti-evolution writing for decades. Bethell himself devoted an entire article in Harper's Magazine to it in 1976. David Berlinski used it in his manifesto “The Deniable Darwin.&rdquo. And Phillip Johnson used it in Darwin on Trial.

Curiously, Answers in Genesis includes this argument among those that creationists shouldn't use, which is one more piece of evidence that young-Earth creationists actually have more integrity than their cousins in ID. (But then again, twice nothing is still nothing).

Apparently Bethell does not aspire to the high standards of AiG. Even before getting to the substance of the argument, such as it is, we should pause to note something very odd. Stephen Jay Gould said it well in his refutation of Bethell's 1976 article:

Bethell's argument has a curious ring for most practicing scientists. We are always ready to watch a theory fall under the impact of new data, but we do not expect a great and influential theory to collapse from a logical error in its formulation.

Indeed. I often tell people that in many cases you can sniff out a bad scientific argument even if you know little of the actual science. Any argument that requires you to believe that several generations of scientists have overlooked a simple logical fallacy can be dismissed out of hand.

Another curious feature of this argument is that it is not clear what, exactly, it is meant to prove. The phrase “survival of the fittest” is catchy and captures the essence of how natural selection works, but it is not something that comes up much among biologists. Contrary to Bethell's preposterous caricature, no scientist has ever moved on the next question after asserting that a particular structure evolved gradually.

I suppose the idea is to show that natural selection is vacuous, and therefore can't be used to explain anything. But this argument shows no understanding of how selectionist reasoning is actually used in routine scientific work. When you have finished playing whatever word games amuse you, it will still be true that there is nothing tautological about saying, for example, that industrial pollution made it advantageous for certain moths to have a dark, rather then light coloration. Selectionist thinking is used to generate testable hypotheses about actual organisms.

The most direct way of refuting Bethell's argument is simply to point out that the bold-faced statement above, upon which Bethell's entire argument rests, is actually quite false. There are criteria of fitness independent of survival. This is the approach Gould took, and he made the obvious point:

My defense of Darwin is neither startling, novel, nor profound. I merely assert that Darwin was justified in analogizing natural selection with animal breeding. In artificial selection, a breeder's desire represents a “change of environment” for a population. In this new environment, certain traits are superior a priori; (they surive and spread by our breeder's choice, but this is a result of their fitness, not a definition of it). In nature, Darwinian evolution is also a response to changing environments. Now, the key point: certain morphological, physiological and behvioral traits should be superior a priori as designs for living in new environments. These traits confer fitness by an engineer's criterion of good design, not by the empirical fact of their survival and spread. It got colder before the wooly mammoth evolved its shaggy coat.

Not a difficult point, but one that Bethell has apparently failed to grasp.

Actually, there is one more angle to this worth discussing, but we sill save that for the next post. Stay tuned!

Giberson on ID

Do I sense a shift in the discussion? In yesterday's post I discussed a New York Times article whose author emphasized the total lack of scientific accomplishments coming from ID. Now we see the same theme in this article from Karl Giberson at Science and Theology News

Giberson takes for his starting point a piece of Michael Behe's testimony from the recent Dover trial. Apparently Behe made a comparison between ID and the Big Bang. Scientists are confident the Big Bang is correct, even though they can not yet give a precise explanation of what caused the bang to happen. Similarly, we can be confident that some bilogical structures must have resulted from intelligent design, even if we can not yet give a clear explanation of how the designer did its work.

An interesting analogy, but one that collapses when you compare the activities of early Big Bang proponents with those of the ID folks. Let me hand the reins over to Giberson:

However, this analogy breaks down when you look at the historical period between George Lemaitre’s first proposal of the big-bang theory in 1927 and the scientific community’s widespread acceptance of the theory in 1965, when scientists empirically confirmed one of the big bang’s predictions.

If we continue with Behe’s analogy, we might expect that the decades before 1965 would have seen big-bang proponents scolding their critics for ideological blindness, of having narrow, limited and inadequate concepts of science. Popular books would have appeared announcing the big-bang theory as a new paradigm, and efforts would have been made to get it into high school astronomy textbooks.

However, none of these things happened. In the decades before the big-bang theory achieved its widespread acceptance in the scientific community its proponents were not campaigning for public acceptance of the theory. They were developing the scientific foundations of theory, and many of them were quite tentative about their endorsements of the theory, awaiting confirmation.

Physicist George Gamow worked out a remarkable empirical prediction for the theory: If the big bang is true, he calculated, the universe should be bathed in a certain type of radiation, which might possibly be detectable. Another physicist, Robert Dicke, started working on a detector at Princeton University to measure this radiation. Arno Penzias and Robert Wilson ended up discovering the radiation by accident at Bell Labs in Murray Hill, N.J., in 1965, after which just about everyone accepted the big bang as the correct theory.

Unfortunately, the proponents of ID aren’t operating this way. Instead of doing science, they are writing popular books and op-eds. As a result, ID remains theoretically in the same scientific place it was when Phillip Johnson wrote Darwin on Trial — little more than a roster of evolutionary theory’s weakest links.

Well said. I would only add that all of the arguments in Johnson's book were complete nonsense. The points he made did not reveal any weak links in evolution. Instead they only revealed weak links in Johnson's understanding of the subject.

Giberson concludes with a simple question:

After more than a decade of listening to ID proponents claim that ID is good science, don’t we deserve better than this?

Indeed we do. But don't hold your breath.

Fisking Bethell

With the conservative Charles Krauthammer bashing ID in The Washington Post and the liberal Bob Beckel dissing evolution in USA Today, I was beginning to fear I might have to revise my views on politics and evolution.

But now things seem to be returning to normal. National Review Online has recently run this awful article from Tom Bethell, author of The Politiclly Incorrect Guide to Science. It goes without saying that no one with actual scientific credentials would publish a book with so hackneyed a title.

After plugging his book and describing the rift among conservatives on this subject (in which a generally anti-evolution rank-and-file is pitted against the pro-evolution “chattering classes”), Bethell gets down to business. First up is antibiotic resistance, briefly mentioned by Krauthammer. Bethell writes:

But what actually happens in the Petri dish? Some of the bacteria are naturally equipped with enzymes that give them immunity to the antibiotic. So they survive, while most of the bacteria die. Nutrients remain in the dish, and the resistant strain now has an ample food supply and multiplies. Before, it could hardly compete with the far more abundant strain, now wiped out. So the (pre-existing) resistant strain becomes more numerous. There is a multiplication of something that already existed. But as the famous geneticist Thomas Hunt Morgan said about 100 years ago — he spent years studying fruit flies at Columbia University and was rewarded with the Nobel Prize — evolution means making new things, not more of what already exists.

Nonetheless, if you define evolution as a change of gene ratios, well, yes, there has been such a change of ratios in the population of bacteria. So, if your definition of evolution is sufficiently modest, then you can call evolution a fact. Others define evolution as “change over time.” That's a fact, too.

It is around here that an experienced reader begins to suspect that Bethell doesn't really know what he is talking about. His second paragraph directly contradicts the first. Even in the narrow situation he described in his first paragraph, selection has, indeed, made something new. It has tranformed a population of non-resistant bacteria into a population of resistant bacteria.

In a single round of variation and selection like this you obviously won't see major changes taking place. But the variations preserved by selection in this round will serve as a platform for subsequent variations that do not yet exist. Of course selection by itself can only cause preexistant variations to become more numerous. Who ever said otherwise? It's the genetic variations themselves that are constantly being created anew.

Consider the evolution of the eye. The familiar scenario is that some primitive organism possessed a simple light-sensitive spot. Over the generations selection preserved a long series of genetic variations that improved the ability of the spot to draw information about the environment from the available light. Eventually this led to modern eyes. No doubt Bethell would take each step in isolation and remark that, in every case, selection merely caused preexisting variations to become more numerous. But the fact remains that most of the variations that led to the eye did not exist when the process began. The end result of all this variation and selection was something entirely new.

Bethell talks about hypothetically defining evolution as a change in gene ratios, as if anyone has ever defined it as anything else. Even Darwin, who did not know about genes, described evolution as descent with modification. The thing being modified, as he makes clear in The Origin of Species, were the average characteristics of a population. Nowadays that average is expressed in terms of genes.

Bethell has other arguments, of course. Apparently fossil bats are hard to come by:

So let's look at the evidence adduced for evolution. The fossil record is sparse. Bats, for example — the only mammals capable of powered flight — appear suddenly in the fossil record, with their sonar systems already fully developed. “There are no half bats,” as a world expert on bats once said. The experts have no idea what animal gave rise to the first bat.

As I've said before, what's significant about the fossil record is that with tens of millions of fossils dug up and categorized, not one is out of place from an evolutionary standpoint. To put in language Bethell might understand, we have examples of creatures that are half-fish, half-amphibian; half-amphibian, half-reptile; half-reptile, half-mammal; half reptile, half-bird; half-land based carnivore, half-whale; and, of course, half-ape, half-human. We have impressively gradated sequences of fossil horses, elephants and rhinos. And these are just the high profile examples that don't include less glamourous creatures like trilobites and snails. In Bethell-land we're supposed to ignore all this because bats don't fossilize well.

And then there's all that complexity anti-evolutionists are so fond of:

The creatures that evolution purports to explain are fantastically complex. The cell, thought at the time of Darwin to be a “simple little lump of protoplasm,” is as complicated as a high-tech factory. We have no actual evidence that it evolved — and yet we are asked, indeed obliged, to believe that it did.

Actually, there is very clear evidence that the modern eukaryotic cells (the ones with well-defined nuclei and all those amazing organelles) evolved from simpler precursors. We can be pretty certain that the mitochondria and the chloroplasts arose via symbiosis, for example. But the cell is hardly the main focus of evolution. The first cell, after all, came into existence billions of years ago. Explaining its existence is the job of origin of life researchers, not evolutionists.

But once again we see the familiar style of argument. We have vast amounts of evidence from fossils, anatomy, biochemistry, genetics and so on that tells us that evolution happened. In many cases we can provide convincing explanations for how specific structures evolved. Bethell would have us dismiss all that because certain aspects of the cell are a bit mysterious. This is a luxury that armchair science critics have that actual scientists do not.

Apparently having run out of mysteries for evolution to solve, Bethell decides to widen his search:

In the human body, there are 300 trillion cells, and each “knows” what part it must play in the growing organism. To this day, embryologists have no idea how this happens — even though they have been trying to figure it out for 150 years.

This is hardly an evolutionary question at all. Once we have a better grasp on the mechanism by which cells differentiate themselves in the course of embryological development, then we'll worry about explaining the evolution of that mechanism.

From here Bethell spends most of the his remaining space waxing poetic about the marvelous things that living creatures do. Since there is no discernible argument in any of this gushing, I will not respond to it here.

What becomes clear from all this is that Bethell is content to point to a few biological mysteries, and on that basis conclude that evolution should be thrown out the window. As I said, he has that luxury because no one expects him to enter a laboratory and come out with actual results.

Actually, Bethell does have one additional argument to make. It's a creationist classic! Bethell argues that natural selection is a meaningless tautology. Natural selection is sometimes defined as the survival of the fittest, you see. But the fittest individuals are simply the ones that survive. It's just a a tautology! QED!!

One wonders how scientists have overlooked for so long this simple logical fallacy. Actually, this argument is singularly brain-dead. But it is also interesting enough to merit it's own blog entry. Stay tuned!

Is ID Dying?

Over the weekend The New York Times published this interesting article, by Laurie Goodstein. After breifly summarizing the recent goings-on in Kansas, Pennsylvania, and the Catholic church, Goddstein writes:

Behind the headlines, however, intelligent design as a field of inquiry is failing to gain the traction its supporters had hoped for. It has gained little support among the academics who should have been its natural allies. And if the intelligent design proponents lose the case in Dover, there could be serious consequences for the movement's credibility.

I would go even further. If the decision in Dover goes against ID, I think that will effectively kill ID as a scientific enterprise. With decisions against them in Cobb County, GA and Dover, PA (assuming those decisions don't get overturned on appeal), few school boards will have the stomach to include the subject in their science classes. And with their prospects of getting ID into science classes reduced to effectively zero, there will be no incentive to maintain the fiction that ID is about producing scientific results.

ID will find itself reduced to the same position as creation science in the late eighties. Once it became clear that the courts weren't buying the subterfuge, creation science prety much stagnated. Nowadays you hear very little about it. In the early eighties creation science was sufficiently menacing that high-powered scholars like Niles Eldredge, Phillip Kitcher and Douglas Futuyma though it worthwhile to write books on the subject. Who would bother doing likewise today?

So it will be with ID. If it fails as a strategy for introducing creationism in the public schools, its usefulness will be gone. ID exists solely for the purpose of creating a constitutionally acceptable form of creationism, after all. Of course, people like William Dembski will continue to peddle their gobbledygook to their handful of admirers, just as representatives of ICR and Answers in Genesis do today. But everyone else will just go back to ignoring them.

The article goes on to describe the chilly reception of ID at many Christian colleges.

P.Z. Myers offers some typically insightful comments in reply:

Really. This is the funniest thing I've read in days. When Baylor and Wheaton dismiss you, when Templeton rejects you, when the major evangelical colleges start backing away from you, maybe it's time to realize that your little Wedge strategy isn't working, and the only thing getting split away from the mainstream is your freaky-weird useless ideology.

John Lynch also wieghs in here:

There you have it. A bunch of people - who had previously funded ID - wanted to give money for research and the ID supporters couldn’t even put together a research proposal. Why? Well ID does not have a positive research proposal merely a definition of design that sees it within the “gaps” of evolutionary explanation.

Meanwhile, William Dembski has offered a whiny little reply to the article here:

I know for a fact that Discovery Institute tried to interest the Templeton Foundation in funding fundamental research on ID that would be publishable in places like PNAS and Journal of Molecular Biology (research that got funded without Templeton support and now has been published in these journals), and the Templeton Foundation cut off discussion before a proposal was even on the table. What has disillusioned Templeton about ID is not that it failed to prove its mettle as science but that it didn’t fit with Templeton’s accommodation of religion to the science of the day and Templeton’s incessant need to curry favor with an academic establishment that by and large thinks religion is passé.

Bitter much?

Pro-ID articles in the PNAS and the Journal of Molecular Biology? News to me, and I follow these things pretty closely.

Ed Brayton has a thorough smackdown of Dembski's claims. His conclusion:

Dembski has crossed over a line at this point, I think. I don't think it's any longer possible to maintain that he is merely an ideologue undergoing cognitive dissonance, or that he's just engaging in wishful thinking of the type we are all probably prone to when defending ideas we have a personal stake in. He is now simply lying outright, and he has to know that.

Well said.