Newton's Binomium

New venue

2008-09-07T14:03:00.000-07:00

After a long break where I dealt mostly with my primary duties (research, writing papers, teaching, presenting at conferences, ...) and got my tenure application in order, I'm back to blogging. I've teamed up with some colleagues at the University of Houston to write on evolution in a blog (Evo.Sphere) sponsored by the Houston Chronicle. Check out my first post there: The Fittest Theory.

The mystery in the comments

2007-10-19T14:18:00.000-07:00

Derek Atkins (apparently my only reader these days) has forced me out of blog inaction by a series of comments to an old piece on Sanford's curiously titled book. You may recall that I started reading it out of politeness after Salvador Cordova gave it to me. I quickly lost interest once I realized just how bad it was and decided to spare you a complete series of negative reviews. After all, I have serious work to do writing papers and grant applications, going to seminars, pushing worms (they've missed me!), analyzing data, mentoring and teaching. Somehow I doubt that my tenure package will look stronger if I waste valuable time refuting bad (really, really bad; failing student bad) population genetic arguments -- a subject which, by the way, I'm teaching right now to a dozen (suffering) undergraduate and graduate students.

Now Atkins has bombarded me with so many comments that I may never get around to answering all of them, but I see a few that are worth responding to, because they are representative of the kinds of arguments that Sanford and other creationists make routinely. After a discussion on how many different kinds of creationists can dance on the head of a pin, Derek gets to what is really bothering him: "What I take exception to is your list of Sanford’s assertions that twists what he really does say. This speaks to your integrity." So I'm in trouble now... Here goes:

[Continue reading below the fold.]

Let’s start with the first assertion to which you’ve taken exception. Analogies are what they are—an attempt to aid the reader (since there may be a wide range of exposure to the materials) in understanding the salient points. It is a device that is effective and is used in all disciplines. [...] The use of differing language/information analogies to the genome does not start nor end with YE or ID proponents (they are not one-in-the-same) but is seen in the analogies of those who are strident evolutionists as well, such as Carl Sagan (1974) when he compares the genome with having more information than contained in the Library of Congress. [...] What I find interesting is not having read any evolutionist being singled out for using these analogies, but anyone who is YE or ID is denigrated for doing so. Unless you have taken non-YE/IDers to task regarding this point, it seems irrelevant to single out Sanford. I credit Sanford for being quite clear about the limitations of the analogy, as quoted above.

Yes, Dawkins used the cake recipe in 1982 in The Extended Phenotype, Dennett used Borges' Library of Babel concept in an interesting analogy for genotypic space in Darwin's Dangerous Idea, and Steve Jones wrote a whole book on The Language of the Genes. Good science writers make their careers on good analogies. Of course to suggest that they never get into trouble over their analogizing is ridiculous: entire volumes of criticism by scientists and philosophers have been devoted to the "gene/meme" and "spandrels" analogies alone. The problem is that, despite his mild disclaimers, the analogy Sandford introduces is a terrible one to discuss the evolution of genomic complexity. So I pointed it out. The reason I did this without hesitation and with what you might perceive as some impatience is that creationists of all stripes use analogies as substitutes for the rigorous scientific work of formulating hypotheses, testing them in the laboratory, or with computer simulations, or with observations from nature, and developing theories based on these activities.

Moving on:

In the second argument you offer as one example the nematode Caenorhabditis elegans, citing de Bono M, Barmann CI,.(1998). In the abstract we read, “A loss-of-function mutation in the npr-1 gene, which encodes a predicted G protein-coupled receptor similar to neuropeptide Y receptors, causes a solitary strain to take on social behavior.” [...] Loss-of-function and various other degradations to the genome is more the rule than the exception to genetic mutations. This is the point Sanford makes clear, though you sidestep this and ask, “Does it matter?” It is an important area of discussion that is not well served with a flippant response. Any gene that mutates causing loss-of-function has certainly lost, not gained usefulness, and by definition the genome has lost information."

This is wrong at so many levels that it is even hard to know where to begin. First of all, it is by no means certain that the genome has lost any information in this case (or any other involving mutations). The main reason is that Sanford and other people who use this argument don't actually define the term in a meaninful way (precisely one of my main criticisms of Sanford). According to any technical meaning of information that I am aware of, a single aminoacid substitution does very little, if anything to it.

The second error you (both) make is that you misunderstand what is meant by the expression "loss-of-function". This has nothing whatsoever to do with information. It also does not mean degradation. de Bono & Bargmann are referring only to the activity of the npr-1 gene product, which is a transmembrane receptor that binds to small peptides outside the cell and creates a signal inside the cell. Loss of function in these cases means that the peptides bind with lower affinity to the receptor or elicit a weaker signal inside the cell. The "social allele" is a loss of function allele when you treat the "solitary allele" of the N2 strain as the reference allele (the reference strain in C. elegans biology). If the Hawaiian strain CB4856 happened to be the standard strain, instead of the English N2 strain, the mutation would be referred to as a gain-of-function mutation. Note that gain-of-function mutations in all kinds of genes are routinely isolated by geneticists (something Sanford neglects to mention). What de Bono & Bargmann are saying is that the NPR-1 receptor from a social worm has a lower activity than the receptor from a solitary worm. But if you look at the level of the behavior, it is not obvious which one has the greater "function": they are both functional, they just have different functions. The irony is that the best information available suggests that the social allele (with lower activity) is actually ancestral to the solitary one in the Caenorhabditis genus, so the mutation most likely occurred in the direction of increased function in the evolutionary history of C. elegans.

So let's recapitulate. On the first point, you did not actually address my substantive, specific criticisms of his analogy. To say that others have also used analogies is beside the point. The question is: where exactly did I twist what Sanford was saying? On the second, until you define information, Sanford's point remains nonsensical. Your misunderstanding of the meaning of loss-of-function does not inspire confidence in your command of the issues at hand. Do yourself a favor and read a population genetics textbook before embarrassing yourself any further: Gillespie's Population Genetics or Hartl & Clark'a Principles of Population Genetics are both pretty good.

Snakes and ladders

2007-05-26T09:25:00.000-07:00

PZ Myers has just written an excellent essay on the evolution of complexity. He makes several interesting points with which I agree. For example, human scientists have long assumed that we (humans) are the most complex organisms in the biosphere. They used to think we had about 100,000 genes. (Kauffman was a bit out of date by 1995, but that number was kicking around. For example, I remember seeing it in the first edition of Jonathan Slack's From egg to embryo from 1983). In 2001, initial estimates from the draft sequence of the human genome put the number of protein-coding genes at 30,000-40,000. It has been shrinking ever since. By 2004, the estimates were down to 20,000-25,000. Of course, this is only the latest in a long series of slights to human delusions of grandeur: from being at the center of the Universe to being in one of many, many, many planets; from being the pinnacle of creation to being genealogically related to every organism on the planet (actually, I find this rather cool, and not demeaning at all, but that's just me...), from being a complexity champion among the metazoa, to being perilously close in genomic complexity to the nematode C. elegans, which has about 19,000 genes and 959 somatic cells.

Like PZ Myers (and Larry Moran), I find most of the current hypotheses that try to do away with the so called genomic paradoxes, unconvincing, bordering on wishful thinking. An understanding of the nearly neutral theory of molecular evolution should makes us intensely skeptical of any claims to deep significance in the non-coding portions of genomes of species with low effective population sizes like us (what counts is the historical population size during our evolution over the last few million years, not the explosion over the last few centuries, in case you're wondering). Just because our genome is crawling with small RNAs (I'll assume it, even though the estimates are not terribly reliable at the moment), and some of them can regulate gene expression, doesn't mean that these RNAs are doing anything terribly important or in any way related to our supposed complexity. Of course, this is no reason to stop looking -- don't take my word for it. I'm just giving you an evolutionary biologist's hunch as to the outcome of this flurry of activity.

Where I have to disagree with PZ (and with others before him, such as SJ Gould in Full House) is in dismissing the problem of increases in complexity.

[Continue reading below the fold.]

On this I'm with Wallace Arthur in his latest book Creatures of Accident (his defense of agnosticism is less persuasive). Just because increases in complexity are not the dominant theme in the evolution of life (more snakes and ladders, than just ladders), does not mean that we should ignore this important feature of the pattern. The fact remains that from simple molecules we got simple prokaryotic cells, then more complex eukaryotic cells, then simple multicellular organisms, ..., then exquisitely complex multicellular creatures like cephalopods, crocodiles and chimpanzees. There are even well-documented cases of generalized increases in complexity across whole groups of animals, such as in the complexity of septal sutures in ammonoids (cephalopods again). Finding out what evolutionary forces could possible drive such increases in complexity is a central problem in biology, and one that has not been adequately addressed yet. Sure, gene duplications are part of the story. But what are the selective pressures on complexity? What are the distributions of mutational effects on complexity?

I have actually been working on the evolution of complexity and have just written a theoretical paper on it. I've been promising to say something about it. Now, that I've started talking about it, I might just get around to doing so.

Publish or perish?

2007-04-07T21:00:00.000-07:00

PZ Myers has just taken the time to reminisce over Paul Nelson's three year long silence on his curious concept of "ontogenetic depth". It so happens that I was first introduced to this IDea through the Pharyngula post about our 2005 paper (mentioned in my last post). Unlike Nelson, we have not been idle since we came up with our measure of lineage complexity. In fact our first follow up paper has just been accepted for publication at the Proceedings of the Royal Society B. I promise to write about the paper in more detail here before it comes out. Now I must finish going over it one more time, and prepare a talk on it for Monday (you can check out the summary).

This walk down memory lane brings to mind a challenge of my own to another intelligent design creationist. The last time I wrote about "ontogenetic depth" here, I warned Salvador Cordova not to be so sure that Andreas Wagner's results on the evolution of robustness of circadian oscillators (see here and here) would not generalize to other systems. Guess what? Andreas Wagner has just proved Salvador wrong for a completely different kind of gene network model (one pioneered by Wagner about a decade ago, and essentially the same model we used in our recent paper on the evolution of robustness).

So, on the one hand you have real scientists at work, publishing their results in peer-reviewed journals, moving their fields forward. On the other hand, you have the pseudoscientific creationists at the Discovery Institute, not doing any original scientific work of their own, not publishing in peer-reviewed journals, criticizing and misrepresenting the work of others, attacking great scientists ad hominem.

Update: For a vivid metaphor of the contrast I made in the last paragraph, check out PZ's brilliant exegesis of 300.

Preaching to the unconverted

2007-03-09T05:48:00.000-08:00

I first came across PZ Myers' posts when I was teaching Evolution of Development in the Fall of 2004. I forget which posts caught my eye initially, but I started checking back occasionally. This was before I started paying regular attention to blogs -- I didn't even know what they were... Then I read his piece about our 2005 Nature paper and was hugely impressed. So I started reading him more regularly, and I've done so ever since. Some two years later, he's still my favorite blogger, the one I read most from. Happy Birthday, PZ!

Update: for more tributes see here, here and here.

What's in a word?

2007-03-01T09:02:00.000-08:00

The Science Cafe on Tuesday was a lot of fun. I got stumped a couple of times -- strangely enough I'm not an expert on penguin homosexuality -- but I'm told I didn't do too badly (although my graduate students may not be good informants). I managed to control myself and not mention negative epistasis... The other speakers were great. I might just have to go over to Salento more often (I was already a fan of their coffee).

Janis Antonovics and friends (Hello, MissPrism! Long time no see. Nice blog, by the way...) have just published a fascinating essay on the use of words related to “evolution” in the context of research into the evolution of antibiotic resistance. Their main finding is disquieting:

The results of our survey showed a huge disparity in word use between the evolutionary biology and biomedical research literature (Figure 1). In research reports in journals with primarily evolutionary or genetic content, the word “evolution” was used 65.8% of the time to describe evolutionary processes [...]. However, in research reports in the biomedical literature, the word “evolution” was used only 2.7% of the time [...]. Indeed, whereas all the articles in the evolutionary genetics journals used the word “evolution,” ten out of 15 of the articles in the biomedical literature failed to do so completely. Instead, 60.0% of the time antimicrobial resistance was described as “emerging,” “spreading,” or “increasing” [...]; in contrast, these words were used only 7.5% of the time in the evolutionary literature [...]. Other nontechnical words describing the evolutionary process included “develop,” “acquire,” “appear,” “trend,” “become common,” “improve,” and “arise.”

They do point out that there was no evidence that the scientists involved were trying to cover up evidence for evolution or anything. Just poor choice of words. And, unfortunately, this does nothing to improve the public understanding of evolutionary biology (see this figure).

Some of their other findings are more encouraging. For example, decided to look at whether the use of the word “evolution” changed in NSF and NIH grant proposals and in papers published in general science journals such as Nature and Science. They report:

The results showed that the use of the word “evolution” was actually increasing in all fields of biology, with the greatest relative increases in the areas of general science and medicine (Figure 3). This reflects the growing importance of evolutionary concepts in the biomedical field, and highlights even more the strange rarity with which the word “evolution” is used in the biomedical literature dealing with antimicrobial resistance.

But they follow this up with a deeply troubling passage for me:

It has been repeatedly rumored (and reiterated by one of the reviewers of this article) that both the National Institutes of Health and the National Science Foundation have in the past actively discouraged the use of the word “evolution” in titles or abstracts of proposals so as to avoid controversy.

I too have heard the similar rumors -- mustn't upset all those scientifically illiterate representatives in Washington! But it gets better:

Indeed, we were told by one researcher that in the title of one proposal, the authors were urged to change the phrase “the evolution of sex” to the more arcanely eloquent wording “the advantage of bi-parental genomic recombination.”

Talk about politically correct evolutionary biology! I wish I'd known of this story before the Science Cafe...

Sex talk

2007-02-16T06:46:00.000-08:00

Sex: Why Bother? Evolution Mysteries

One of the greatest mysteries of biology is why humans need a sexual act to reproduce while some organisms such as bacteria do not, and while others, like plant lice, can reproduce with or without a sexual act. Scientific evidence indicates that sexual reproduction is in fact a much less efficient way of producing new individuals and, consequently, of passing on genes to the next generation. Why then are some species, like humans, only able to reproduce with a sexual act? This is one of the greatest intrigues of evolutionary biology. And science aside, what does sex mean to us after all? Do we mate with the only goal of passing genes onto the next generation? Or is there more to it under the sheets? Come and discuss these questions with outstanding scientist, medical ethicist, and religious studies scholar at the next Science Café.

WHEN: Tuesday February 27, 2007 from 7:30 pm to 9:00 pm

WHERE: Salento Coffee House, 2407 Rice Boulevard in Rice Village

WHO:

Dr. Ricardo Azevedo, Assistant Professor in the Department of Biology and Biochemistry at the University of Houston
Dr. Simon Whitney, M.D. and Medical Ethicist, Medical Director of Baylor Family Medicine at the Baylor College of Medicine
Prof. Jeffrey J. Kripal, J. Newton Rayzor Professor and Chair of the Department of Religious Studies at Rice University. Author of “Esalen: America and the Religion of No Religion”, a book dealing with modern fusions of science, eroticism, and mystical experience
Moderator: Patricia Gras, Senior Producer at HoustonPBS and Host of TV show Living Smart – airing Sundays at 3:30pm and Thursdays at 1:30pm. Living Smart episodes also available on google video

COST: Free to the public. No registration needed.

Open your mind

2007-01-16T12:20:00.000-08:00

Bora Zivkovic, of A Blog Around the Clock, has put together an anthology of the best science blog writing (ever). It has a great name: The Open Laboratory. To my surprise, my two-part post "Blind Watchmaker or Swiss Designer?" (see here and here) was picked for it. I'm delighted to be among such distinguished company.

How selfish is this meme?

2006-11-28T18:55:00.000-08:00

Go ahead, link to this post and do your bit for the new science of memetics.

[Via Pharyngula]

Tangled Bank #67: Giving thanks for science

2006-11-22T06:18:00.000-08:00

Welcome to this Blog Carnival. Since I haven't had time to do much scientific blogging of my own, this is a good opportunity to catch up with other science bloggers' writing.

Looking complexity in the eye

What better way to begin this Carnival than with a reference to the man who came up with the image of the tangled bank in the first place. Halfway through the Origin of Species, Darwin raised the problem of the organs of extreme perfection. The first example he discussed was the eye. As usual, what he had to say on the subject was remarkably clear, sensible and, well, farsighted:

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real [...]

The rest is well worth reading not least because most of Darwin's predictions have been borne out by the data. We have made spectacular progress towards solving even the problems he anticipated would be most difficult to address (e.g., "how a nerve comes to be sensitive to light"). Little did he know, however, that we would still be arguing with creationists over the eye a century and a half later. I suspect Darwin that would have appreciated the following articles, though:

Ian Musgrave, over at The Panda's Thumb explains why if
the vertebrate eye is a product of intelligent design then it doesn't speak well to the skills of the designer. Don't you just wish you had some squid eyes?
Refusing to wallow in cephalopod envy for once, PZ Myers expanded on Ian's post by giving an overview of the diversity of eye types in animals. That he can write so beautifully about photoreceptors and opsins is an example to us all. As usual, contemplating the cellular and molecular details will provide no comfort for creationists.
Last month, Carl Zimmer wrote a wonderful piece for National Geographic on the evolution of organs of extreme perfection -- these days they are known, more prosaically, as complex structures. In his blog, Carl dared the Discovery Institute to respond. Dutifully, Casey Luskin obliged. In three parts! He should have known better: arguing with Carl when you know so little biology is a terrible idea.

Hip medicine

Here's another wonder of intelligent design: the human hip. Dr Kavokin tells us what can go wrong .

A fistful of dollars

Any scientist will tell you that one of the most unpleasant aspects of their work is the constant need to look for money to support their research. (I have met only one person who disagrees with that sentiment.) The NIH is promising to overhaul their procedures. Will it make things any smoother? Orac, perhaps the top NIH-funded science blogger around, gives us his first impressions.

Evolutionary sense and sensibility

No stranger to self-promotion blogging, I was pleased to see Massimo Pigliucci writing about his new book Making Sense of Evolution, written with the philosopher Jonathan Kaplan. Here he gives us a taste for their chapter on adaptive landscapes. I actually heard Kaplan give a very interesting talk about the same problem last year. I will definitely get the book now that it's out.

Sex and evolution

One of the reasons why natural selection is difficult to define and measure is recombination. Fortunately our understanding of the evolutionary consequences of recombination is improving. RPM discusses some recent research into the problem.

Getting old

Aging, like sex, raises some great evolutionary mysteries. If that doesn't ring enough Weismannian bells for you, check out Ouroboros' post on my favorite worm. Reason has been keeping up with some strange aging research from Russia.

Martin Rundkvist has been following in George W. Bush's footsteps. He shares his experiences at the Hanoi historical museum.

Heavenly creatures

Have you ever heard of a bufflehead? Just one of 10,000 birds...

Decidedly less cute are the saltwater crocodiles from the Northern Territory of Australia.

But you can trust humans to make life unpleasant for these great creatures. Here's what we're doing to the waterways of Western Maryland.

Unweaving the spectrum

Phil Plait shows us, once again, that physics too can be beautiful. Next time someone reminds you that "There are more things in heaven and earth [...] than are dreamt of in your philosophy" agree with them and send them this link.

Always Learning, a physician, shares some astrophysical wonder of his own.

But what else can you do with electromagnetic radiation? Past Lessons, Future Theories introduces xDNA.

Prickly science

A graduate student in the lab next door to mine has just had a good reason to celebrate: he's a coauthor in a paper that came out in last week's issue of Science. The only problem is that it's not easy to find him: he's coauthor number 109 out of 226. PZ Myers took a break from his favorite lophotrochozoans to explain why we should care about this deuterostome. And it's not for the obvious reasons.

Migrations points out a recent paper on the role of the Wnt/beta-catenin pathway in sea urchin development.

Eugenomics

Hsien Hsien Lei discusses socialized health care in the genomics age over at Genetics and Health. I suspect these issues will keep coming back.

Good information theory, bad information theory

Those of you wondering what on earth this blog has to do with Newton may have noticed that the words "of information theory" more often than not follow the name of the great scientist around here. That's unfortunate. Well, it's happened again. There was Salvador Cordova, Dembski's co-blogger and a regular commenter here, happily babbling away about the great contributions of intelligent design creationism to science, in that alternate universe of his inhabited by such wondrous theories as the "fourth law of thermodynamics" and the "law of conservation of complex specified information", and Mark Chu-Carroll went and spoiled his fun. Bad news for uncommon descent indeed.

Newtrition

But there is actually a different reason for this blog's name: it's a reference to a classic Portuguese modernist poem. However, I was happy to find a surprising Newtonian connection in Lab Cat's exploration of the many uses of flaxseed.

Vote for me

2006-11-07T13:22:00.000-08:00

No, I'm not campaigning. Here's a good illustration of how I feel on days like this.

Review of "The Mystery of the Genome" (II)

2006-10-10T09:53:00.000-07:00

At the end of the previous installment I began examining Sanford's arguments as to why "random mutations are never good". As we saw, most of these ended up being among some of oldest and most discredited creationist arguments around. But he also had a new (at least to me) and more subtle one: that even if there are beneficial mutations they'll turn out to be nearly-neutral. Although it's nice to see that creationists have caught up with Kimura, albeit several decades late, I'm afraid this argument is also invalid.

The "nearly neutral" theory of molecular evolution was developed by Motoo Kimura and Tomoko Ohta in the 1970s. Basically this relies on an old result by Kimura that requires an explanation. Imagine that we have a diploid population fixed for an allele A at the A locus. What is the probability that a new allele a arising by mutation (A -> a) will go to fixation some time in the future? The answer is that it depends on whether selection is acting on it. To make a long story short, there are three (simple) possibilities:

If the a allele is neutral, that is, the fitnesses of the three genotypes are the same W(AA) = W(Aa) = W(aa), then the probability of fixation of a is P = 1/(2N), where N is the size of the population (number of individuals). In other words, the probability that the a allele will go to fixation due to stochastic effects (or genetic drift) is higher in a small population than in a large one.
If the a allele is beneficial, then the probability that it will go to fixation depends on the selective advantage it confers. If the fitnesses of each genotype are W(AA) = 1, W(Aa) = 1+s, and W(aa) = 1+2s, then the probability that a will go to fixation is approximately P = 2s. Other fitness functions will change the probabilities, but that doesn't matter for the main point I want to make.
If the a allele is deleterious, then the probability that it will go to fixation depends on the selective disadvantage it confers. The formulas are more complicated and need not detain us for the main point I want to make.

What Kimura and others have pointed out is that if the population size N and/or the selective advantage s of an allele are too small, then a beneficial allele (i.e., one with a positive value of s in the above expressions) will behave as if it were neutral. Such an effectively neutral allele will not be under the action of natural selection, but will fluctuate under genetic drift. A quick manipulation of the probabilities given above shows that if the selective advantage s of a beneficial allele is equal to or less than 1/(4N), then the allele is effectively neutral. A similar point can be made for a weakly deleterious allele.

Sanford's main point then is that there are likely to be very few truly beneficial mutations in humans because of this effect. Although this decades-old argument is generally correct for humans, it is misleading for two reasons. First, it neglects to mention that this near-neutrality effect is especially acute in large mammals like humans because of their historically low population sizes. However, most creatures on earth are not subject to this problem to anything near the same extent. How do we know this? There are many lines of evidence, such as the evolution of codon-usage bias. I won't take the time to explain this in full here, but suffice it to say that it can only evolve if selection is able to act on very weakly beneficial mutations. Briefly, we expect to see strong codon bias in species that have large populations. Predictably we find little or no codon bias in humans or mice (in concordance with Sanford's point), but it is present in nematodes (Caenorhabditis elegans and, more strongly, in C. briggsae), cress Arabidopsis thaliana, fruitflies Drosophila melanogaster, and is very strong in microorganisms like E. coli and yeast Saccharomyces cereviseae. Second, Sanford handwaves about the ratio of beneficial mutations to deleterious mutations, when in fact there are no good direct estimates of this number for humans. Direct estimates in other organisms are not abundant either, because it is technically difficult to do so, but there are some for which the picture is not as apocalyptic as Sanford suggests. For example, Sanjuan, Moya & Elena (2004) found that "the proportion of beneficial mutations was unexpectedly high" in the vesicular stomatitis virus. I also know of at least one other study (as yet unpublished, so I cannot say anything else about it) which found that the ratio of beneficial to deleterious mutations in a famous microbe is much higher than previously thought.

Which brings us to the main problem with Sanford's argument. Let's imagine that what he has said in Chapter 2 is right and that there is no evidence for the operation of positive selection (selection for beneficial mutations) in humans. This is precisely where Sanford's argument fails. In fact the opposite is the case: we have strong and abundant evidence that positive selection has occurred in the human evolutionary lineage. To Sanford's embarrassment , there has actually been a steady stream of papers demonstrating positive selection in the last few years, such as, Johnson et al. (2001), Sabeti et al. (2002), Nielsen et al. (2005), Chimpanzee Sequencing and Analysis Consortium (2005), and Voigt et al. (2006). To understand how these estimates work I would recommend evolgen's 7-part series of posts explaining how natural selection can be detected using molecular data (the last one is a good place to start). Only someone completely ignorant in the human population genetics literature could possibly claim that beneficial mutations don't exist in humans.

Since this is one of the central arguments in Sanford's book, I doubt that there is anything else worth discussing. However, I'll check the other chapters and will let you know if this is not the case.

What has Evo-Devo ever done for us? (II)

2006-10-10T09:09:00.000-07:00

This discussion reminds me of a conversation I witnessed a few years ago between a population geneticist (PG) and an evolutionary developmental biologist (EDB) that shall remain nameless.

The EDB was explaining to the PG the significance of a paper that had made the cover of Nature a few years earlier. Those who are familiar with the literature on butterfly eyespots know that this is a classic of the field. It's beautifully written and illustrated. I know of more than one biologist that was turned on to the field of Evo-Devo by reading this paper. It shows how the expression of the regulatory gene Distal-less (better known for its role in limb development in Drosophila) is crucial to the formation of the eyespots of the wing of the African butterfly Bicyclus anynana. They analyse mutants, selection lines and different species to come up with a general hypothesis for how eyespot size and shape evolves in these butterflies. It has been cited 143 times and has sparked an entire research program in Evo-Devo.

The problem was that the PG didn't get what all the fuss was about. The EDB was getting more and more excited in trying to convey the beauty and elegance of the results, and he did so eloquently. At some point the PG said something like: "Of course I knew that some genes were involved. Is it really that important that we now know the identity of one of them?"

I think this exchange illustrates well the attitude of biologists for which the ultimate goal of evolutionary biology is not uncovering the precise steps involved in the evolution of a particular structure, but understanding the general evolutionary processes involved. Of course, evolutionary biology needs both.

Review of "The Mystery of the Genome" (I)

2006-10-09T13:29:00.000-07:00

A few months ago, I had a debate with Salvador Cordova over robustness and redundancy. At some point (in these comments) Salvador decided that I needed enlightening on matters evolutionary and gave me a copy of a book by John Sanford, an agricultural geneticist at Cornell University (Courtesy Associate Professor), suggestively titled Genetic Entropy & The Mystery of the Genome (and ominously subtitled: "the genome is degenerating"). I suppose that courtesy dictates that I should say a few words about it. I finally picked it up and have read the first 30 pages (Prologue and Chapters I and II).

Unsurprisingly Sanford's objective is to demolish what he calls the "Primary Axiom" of evolutionary biology "that man is merely the product of random mutations plus natural selection". This is not a good start for someone who claims professional expertise in biology. Bringing the term axiom from mathematics into a discussion of a theory in the natural sciences is not helpful. What he describes is a summary of a theory, not an axiom. But let's go with it for the moment. So why might Sanford be challenging this "Primary Axiom"? He provides a telling answer:

If the Primary Axiom could be shown to be wrong it would profoundly affect our culture [...] It could change the very way we think about ourselves. (Prologue)

So now we know where he's coming from. What next?

In Chapter 1 ("The genome is the book of life. Where did it come from?") he explains how "the genome is an instruction manual". Although I would put it slightly differently, I don't have a major problem with his description: he talks of DNA, proteins, regulation of gene expression, etc. He then introduces a complicated metaphor -- manuals for constructing wagons -- for the process of mutation and natural selection designed to highlight the improbability of evolution. He goes into full "personal incredulity" mode:

Isn't it remarkable that the Primary Axiom of biological evolution essentially claims that typographical errors plus some selective copying can transform a wagon into a spaceship, in the absence of any intelligence, purpose, or design? Do you find this concept credible?

No prizes for guessing which answer he's counting on. While his wagon metaphor could have been more elegant (and more elegantly expressed) it is not fundamentally wrong. At least he doesn't tell us that natural selection is pure randomness. However, his discussion is misleading in at least two respects. First, it does not convey the immensity of time allowed for evolution to operate. This might be because Sanford is a Young Earth creationist and doesn't believe there has been much time for anything, although I haven't read a statement by him to that effect yet, so I'll give him the benefit of the doubt. Second, he analogizes mutation to spelling mistakes in natural language, which is deeply misleading. Although it is true that randomly altering letters in source code written in a high level programming language is unlikely to produce beneficial mutations, that does not imply that evolutionary computation is impossible, far from it. (Indeed, evolutionary computation raises major problems for evolution deniers, but that's another discussion.) The problem with Sanford's characterization is that point mutations are more subtle than the spelling analogy would suggest. But since no analogy is perfect, we'll let it pass for now.

Chapter 2 ("Are random mutations good?") gets to one of the central points of his argument. According to Sanford the bad news for the "Primary Axiom" is that "it can very reasonably argued that random mutations are never good". If true, this would indeed be a problem. So what about the evidence? Sanford tries to back it up with the following assertions:

Mutations are like misspellings in the "instruction manual".
There no "clear cases of information-creating mutations".
The few beneficial mutations that occur are nearly neutral.
Repeated selection experiments in plant breeding have resulted in "no meaningful crop improvement"
Geneticists never see beneficial mutations.

Most of these are standard, repeatedly refuted creationist claims. I've already explained why the first argument is based on a misleading analogy. The second argument sounds more serious but it is hard to say what Sanford has in mind since he never precisely defines information, and creationists cannot be trusted to do so with any accuracy (see also this). In any event, mutations can create new binding sites, duplicate genes, etc, so whatever he means cannot be meaningful (to use one of Sanford's favorite terms). Let me give you an example from my study organism, the nematode Caenorhabditis elegans. A single aminoacid substitution in the gene npr-1 (neuropeptide Y receptor homologue) can make worms (normally solitary) aggregate on food. Is that an increase or decrease in information? Does it matter?

The fifth argument is completely wrong. Define beneficial and I'll give you many examples. Just in the nematode C. elegans we have mutations that increase or decrease body size, that increase or decrease lifespan, that increase or decrease hermaphrodite self-fertility, that make it easier or more difficult to go into dauer (the worm equivalent of a spore), etc. Many of these mutations can be beneficial in certain environments.

The fourth argument is nothing short of delusional. Artificial selection has succeeded in getting selection responses in the desired direction for "improvement" in practically every instance tried. For example, Ken Weber selected for differences in wing shape on the order of a few cells in the fruitfly Drosophila melanogaster and got a response! Exceptions to this generalization are so few and far between (e.g., changing the primary sex ratio and directional asymmetry in Drosophila) that the existence of constraints is still debated in the pages of Nature. There may have been a few unsuccessful selection experiments in crop species (I'm less familiar with that literature), but I doubt that Sanford's summary is accurate. Indeed I know of at least one case that contradicts it: starting with 163 ears of corn Leng (1962) was able to increase oil content of kernels from 4-6% to about 16% within 60 generations using artificial selection. That may not count as "meaningful crop improvement" in Sanford's book, but it does in mine.

We're left with the third argument. This one is more subtle and will be the subject of the next installment of this review. By then I may have been able to read a couple more chapters as well.

What has Evo-Devo ever done for us?

2006-10-09T08:51:00.000-07:00

All right, but apart from the sanitation, the medicine, education, wine, public order, irrigation, roads, a fresh water system, and public health, what have the Romans ever done for us? (In Monty Python's Life of Brian, 1976)

PZ Myers has just posted a letter by Jason Hodin replying to a review of Sean Caroll's Endless Forms Most Beautiful that appeared in the New York Review of Books (which the NYRB refused to publish). Briefly, Hodin argues that Sean Carroll has hyped the field of Evo-Devo and that the NYRB reviewers (neither of which is trained in biology, apparently), went even further and practically attributed every advance in evolutionary biology from the past 150 years to Evo-Devo. I generally agree with both charges, but I am more interested in the former. While I respect Sean Carroll contributions to the field of Evo-Devo, I do not share his enthusiasm about the magnitude of evo-devo's accomplishments.

Jason Hodin argues :

I don't mean to denigrate my field of Evo Devo, nor do I intend to suggest that no critical insights have come from it. Perhaps the most important contribution of the field is methodological.

I agree with this sentiment. I believe that Evo-Devo has indeed crystalized a novel approach to evolutionary biology that is now changing research into other kinds of phenotypic evolution. However, we should not deceive ourselves into thinking that what Gould called "a new and general theory of evolution" is already here: it isn't. Understanding how certain developmental mechanisms have evolved adds more patterns to our picture of evolution, in much the same way as a new fossil does. Don't get me wrong: I'm in love with the details of the "new natural history" of Evo-Devo. But to trully revolutionize evolutionary biology, development has to be incorporated into the mechanisms of evolution, such as mutation and selection. Our current understanding of contraints, modularity and evolvability, for example, has not yet accomplished that.

That's Avida!

2006-10-06T09:26:00.000-07:00

Mark Chu-Carroll has written an excellent post over at Good Math, Bad Math addressing creationist attacks on some research using the artificial life model system known as Avida. A descendant of Tom Ray's Tierra, Avida is used by several labs around the world, notably those of Chris Adami at Caltech and Richard Lenski at Michigan State University, to study a wide range of problems in evolutionary biology and ecology: from the evolution of robustness to adaptive radiation, from the evolution of sex to phylogenetic reconstruction. And, of course, the evolution of complexity.

On the face of it, work on these digital organisms (think of them as tame computer viruses) has grown into a vibrant research field in its own right, at the intersection between evolutionary biology and computer science. A quick search reveals at least 9 high profile papers on Avida in the last decade, including some of the ones I've already linked to. What do I mean by "high profile"? As a crude benchmark, those are papers with more than 10 citations each in other scientific papers (indeed, they were cited 37 times each on average). To put these numbers in perspective consider that the same database, the Institute for Scientific Information's (ISI) Web of Knowledge, tells us that William Dembski, none other than the Isaac Newton of information theory, has co-authored a total of 5 papers, cited 5 times in total (i.e., once each on average). So, there are Newtons and then there are Newtons...

So what do creationists think about all this work on Avida? Surely they would welcome an actual test of Behe's ideas on irreducible complexity, right? Wrong. They didn't like it one bit. So what did they do about it? Publish a rebuttal in the pages of Nature? Submit their own test to another journal? No. Instead they got Eric Anderson to sneer at the paper in one of their best journals, the Progress in Complexity, Information, and Design.

That might sound fair enough, but only if you don't know your scientific journals. The problem is that PCID, despite its impressive sounding description ("quarterly, cross-disciplinary, online journal that investigates complex systems apart from external programmatic constraints like materialism, naturalism, or reductionism") is not even up to the standard required for listing in the ISI. But is that really so bad? Well, the ISI currently lists 6088 science journals, including such obscure titles as Wool Technology and Sheep Breeding (impact factor 0.02), the Journal of the South African Institute of Mining and Metallurgy (impact factor 0.08) and Hazard Waste Consultant (impact factor 0, yes zero). So, yes, that is pretty bad. Publishing in journals not listed by the ISI counts for next to nothing in tenure decisions which could go some way towards explaining some of the problems Chapman listed in his pathetic apologia for the dismal state of scientific research on intelligent design.

And who, exactly, is Eric Anderson? The paper is not helpful in this respect, as no affiliation is listed. A search in ISI reveals no one of that name with a track record of publication in either evolution or computer science. For all we know, it might be a pseudonym for one (or more) of those "ID-friendly scientists" working at undisclosed locations that populate Chapman's dream world. Of course, anyone, credentialled or not, is entitled to comment on scientific matters. It's just that if you're going to fight evolutionary heavyweights like Lenski, Ofria and Adami, then you'd better make sure that you know what you're talking about. Specially when they have teamed up with Pennock, a philosopher, to make damn sure their argument was watertight. By now you've probably guessed it: Eric Anderson made a dog's breakfast of his critique. Let's turn to Mark for the details. Commenting on the abstract to Anderson's paper he says:

So the authors Avida are at best oblivious to the properties of the work they're doing; at worst, they're liars. And their work is based on on circular assumptions, which support Behe's notion of irreducible complexity. He's making an incredibly strong accusation against the Avida team: that either they're stupid and don't understand their own work; or they're liars.

In other words, not a promising start. And it gets worse. Not only does Anderson adopt an incredibly obnoxious and patronizing tone throughout, but he confuses hypotheses and assumptions and then accuses Lenski et al. of circular reasoning. Here's Mark's summary of the problem:

Now, here's where it gets really interesting. He says that he's going to examine the "key assumptions" built into Avida. But that's not really what he's going to do. What you'll see as I go through his paper is that he repeatedly tries to make it look like Avida is using circular reasoning. In fact, what they're doing is describing an experiment.

How do you do an experiment in real science? You start by developing a hypothesis. Using your hypothesis, you make a prediction. Then you perform the test, and see if the results match the prediction. If they do, then the experiment confirms the hypothesis (note, confirms not proves); if they don't, then the experiment disproves the hypothesis.

What the Avida team did was develop a hypothesis that an evolutionary system, working within the constraints of Behe's model of evolution could produce an irreducibly complex system. They proceed to describe their model, and the predictions it makes. Then they show their results, which confirm their hypothesis. Mr. Anderson tries to argue that because they stated their hypothesis up front, and then the test confirmed it, that they were cheating and being circular. He's pretending that the hypothesis is actually a set of assumptions; and that therefore, the experiment confirming the hypothesis is invalid.

Nicely put, hm? You get the idea.

Now, if you want to learn more about Avida, you could turn to Carl Zimmer's excellent piece in Discover. Here's one of my favorite passages:

One of the hallmarks of life is its ability to evolve around our best efforts to control it. Antibiotics, for example, were once considered a magic bullet that would eradicate infectious diseases. In just a few decades, bacteria have evolved an arsenal of defenses that make many antibiotics useless.
Ofria has been finding that digital organisms have a way of outwitting him as well. Not long ago, he decided to see what would happen if he stopped digital organisms from adapting. Whenever an organism mutated, he would run it through a special test to see whether the mutation was beneficial. If it was, he killed the organism off. "You'd think that would turn off any further adaptation," he says. Instead, the digital organisms kept evolving. They learned to process information in new ways and were able to replicate faster. It took a while for Ofria to realize that they had tricked him. They had evolved a way to tell when Ofria was testing them by looking at the numbers he fed them. As soon as they recognized they were being tested, they stopped processing numbers. "If it was a test environment, they said, 'Let's play dead,'" says Ofria. "There's this thing coming to kill them, and so they avoid it and go on with their lives."

This is yet another example of what has been called Leslie Orgel's Second Law: "Evolution is smarter than you are".

On Fire!

2006-10-02T22:40:00.000-07:00

On a brighter note, C. elegans biology (my own real-life organism of choice) is on a roll. First, there was the Nobel Prize for the complete cell lineage in 2002. Now, the Nobel Prize for RNA interference. Did you know that it took John Sulston and his colleagues longer to complete the cell lineage work, than it took Fire and Mello to get the Nobel Prize since their paper came out. Congratulations!

Coming to a peer-reviewed journal near you... at some point... promise... trust us...

2006-10-02T22:30:00.000-07:00

The Onion couldn't have spoofed the Discovery Institute better than its own President, Bruce Chapman. This statement is pathetic beyond belief.

[Via Red State Rabble]

Long time, no write

2006-09-29T09:31:00.000-07:00

I'm amazed that it's been such a long time since my last post. Here's a quick summary of what I've been up to in the last few months:

Lost my appendix in late July, evidently continuing a disturbing trend among evolutionary bloggers. Intelligently designed indeed... That put me out of action for a few days.
Worked on the first draft of a manuscript on developmental complexity and robustness. It's not bad, but needs a bit more work. That should keep me off the streets in the next few months...
Went to the first Euro-Evo-Devo conference in Prague in mid-August. Talked about modularity and robustness in a symposium on "Modularity". Each speaker talked about a different kind of modularity. It was great fun, but I'm not sure the concept is that helpful (if it ever was)... The rest of the meeting was pretty good.
Participated in a Summer School on "Mathematics in Biology and Medicine" in September in Portugal. A very interesting meeting. By pure coincidence, Martin Golubitsky, my distinguished colleague from the Department of Mathematics, was also invited. We finally got a chance to talk even though we're in adjacent buildings here in Houston -- we agreed that we should talk some more...

More later.

Degeneracy vs Redundancy

2006-07-13T20:22:00.000-07:00

Salvador Cordova and I have been arguing over the significance of redundancy and robustness in living systems. Salvador, has been trying to develop an "argument from redundancy" for ID creationism. It begins in an analogy between biological and engineered systems. As most ID arguments, that's where it stops as well. I'm skeptical mostly because I don't see many examples of perfect redundancy in nature.

I'm actually writing a paper on a related subject (more about that at some point) and came across an article that made the point about the difference between perfect and partial redundancy much better than I did. One of the authors is Gerald Edelman, who won the Nobel Prize for Medicine and Physiology in 1972 for his classic on the structure of antibodies. They argue that there's a difference between degeneracy in biology and redundancy in engineering:

The contrast between degeneracy and redundancy at the structural level is sharpened by comparing design and selection in engineeringand evolution, respectively. In engineering systems, logic prevails,and, for fail-safe operation, redundancy is built into design.This is not the case for biological systems. Indeed, not the leastof Darwin's achievements was to lay the argument by design torest. But, for obvious economic reasons, design is by far themajor component of most technical efforts in modern society. Ingeneral, an engineer assumes that interacting components shouldbe as simple as possible, that there are no "unnecessary" or unplannedinteractions, that there is an explicit assignment of functionor causal efficacy to each part of a working mechanism, and thaterror correction is met by feedback, modeling, or other paradigmsof control theory. Protection can be afforded by planned redundancy,but adventitious compensation for error is neither expected norusual. Irrelevancy is avoided from theoutset.

By contrast, in evolutionary systems, where there is no design, the term "irrelevant" has no a priori meaning. It is possiblefor any change in a part to contribute to overall function, mutationscan prompt compensation, stochastic interactions with the environmentcan lead to strong selection, often there is no fixed assignmentof exclusive responsibility for a given function, and, unlikethe engineering case, interactions become increasingly complex [...]

Now that's what I'm talking about!

Counter Coulter II

2006-07-10T09:24:00.000-07:00

As pointed out before, Ann Coulter has written a book of breathtaking inanity, which is now second on the New York Times non-fiction bestseller list (after topping the list for several weeks, I believe). Among the usual preposterous claims against, you guessed it, liberals (a term of abuse here in the US), she devoted two chapters to "debunking" evolution. People who have actually read the relevant chapters have not been impressed. Here's a representative sample: Darwin Central, Right Wing Professor, Talk Reason, Pharyngula, Media Matters, Loom. After that, I'm not tempted, but I'd like to comment on one passage from Coulter's book that has been quoted often:

Throw in enough words like imagine, perhaps, and might have -- and you've got yourself a scientific theory! How about this: Imagine a giant raccoon passed gas and perhaps the resulting gas might have created the vast variety of life we see on Earth. And if you don't accept the giant raccoon flatulence theory for the origin of life, you must be a fundamentalist Christian nut who believes the Earth is flat.
That's basically how the argument for evolution goes [emphasis in original].

Anyone who knows anything about science will know that this is about as ludicrous a representation of the scientific process that has led to the nearly universal acceptance of evolution as one could come up with (apparently, prompted by a misreading of an essay by Zimmer, of all people). The irony is that Coulter has actually spewed a perfect analogy for creationism, not evolution. For example, here's the Wikipedia entry describing the Zulu creation myth:

The Ancient One, known as Unkulunkulu, is the Zulu creator. He came from the reeds and from them he brought forth the people and the cattle. He created everything that is: mountains, streams, snakes, etc. He taught the Zulu how to hunt, how to make fire, and how to grow food.

Notice any similarities? This is the last one of forty-nine creation myths listed. Most of them are just as well supported by evidence as the giant racoon flatulence creation myth (the other ones are simply too vague). They are also mutually inconsistent.

Coulter should stop writing about things she doesn't understand. Better stick to something she's obviously good at, like plagiarism (for example, see here, here, here, here).

How far we have not come

2006-07-10T07:44:00.000-07:00

A couple of weeks ago, PZ Myers brought to our attention a chilling story of anti-atheism bigotry in Oklahoma. Now, he has posted a first person account by the victim of the ordeal, Chuck Smalkowski. Here's a small excerpt to give you an idea of what his family went through:

The whole family was under constant stress. Police trying to get search warrants to the property by having ex-employees file false statements. Other cops trying to hire ex-cons to beat me up. The whole town knows of it! The Sheriff trying to have my bond pulled by the bail bondsman when there was no legal way to do it. My kids have been out of school since November. Principal's son saying should he get a gun when he sees my daughter and my son. DA has yet to reply to our concerns. The Department of Human Services comes to my place saying they received a complaint that I starve my kids. It was even obvious to them the charge was bogus.
We have become very good at using back roads. The police follow us around. Traffic tickets that when challenged were dropped in court. Not to mention the stares and whispers, the betrayal from employees, one of my healthy dogs dying. Brush fires starting up upwind.

An FBI agent even said, "You aren't kidding". When it was obvious someone followed us and was watching our meeting out in the middle of nowhere. I was told about a few things. All I can say is that some of the crooks out here now charged with crimes wore badges and guns! But he could not help my family and me. Not without witnesses willing to come forward. One scared witness left the state. The last words she spoke to me were, Chuck I don't want to end up dead in a ditch!

Just what you would expect life to be like out here in the Bible belt!

There's more: a corrupt DA, a lawyer having to remind the jury that atheists do not worship the devil, people praying in court for a conviction, whole thing appears to come straight from a Grisham novel. (One set several decades ago...) Just another Salem indeed!

Another Devil's Chaplain

2006-07-02T10:26:00.000-07:00

The few regular readers of this blog will have noticed that I am a great admirer of the blog Pharyngula written by the biologist PZ Myers, with its inimitable mix of evolutionary developmental biology, atheism, liberalism and cephalopods. Not only is PZ refreshing and insightful in most of what he writes, he also sustains an astonishing posting rate. I would have to blog full-time to even approach a similarly substantive output (to say nothing about quality), but perhaps I'm just an unusually slow writer. Although that is unlikely to change in the future, I thought I would improve things by posting on one of the intellectual passions I share with PZ Myers, besides evo-devo: atheism.

Recently, PZ has been tackling the thorny issue of the relationship between atheism and science in two incisive posts (here and here). He addressed the question of whether there is any difference between the scientist's and the atheist's attitudes towards religion. PZ concluded that "the scientist and atheist positions are the same". Here's a summary of his argument:

What should a scientist expect from an idea? That it be a reasonable advance in knowledge; that it be built on a foundation of evidence; that it be testable; that it should lead to new and useful questions and ideas. If we look at religion from that perspective, it doesn't help. At best, the hypothesis of the supernatural and/or a supreme being is vague, unfounded, and inapplicable in any practical fashion—deistic views, for instance, are so abstract and so carefully divorced from risk of challenge that they represent an empty hypothesis, and the most flattering thing you can say about them is that they're harmless. At worst, religion is confused, internally contradictory, and in conflict with evidence from the physical (and near as we can tell, only) world.

Now, this argument appears to upset many people. They would rather scientists keep these thoughts to themselves, and focus on teaching and practicing science at all times. Surely, people should be allowed to believe in God if they chose to. Of course they do! A better question is whether scientist-atheists should hurt people's feelings by articulating their views in public. In fact, all atheistic and agnostic scientists I know focus exclusively on the science most of the time. I certainly don't bring up religion in my Evolutionary Biology course or at my lab meetings (and I suspect, neither does PZ). I'm much more interested in a student's understanding of linkage disequilibrium, or in how the worms (or models) behaved in the latest experiment.

The problem is that scientists are being asked to watch in silence as critics of science attack science by linking it to atheism (e.g., Ann Coulter, and the "Coultergeists" at the Discovery Institute do it all the time), while many defenders of science believe they are doing it a service by distancing science from atheism (e.g., Michael Ruse's disappointing ramblings on "evolutionism", or the talking heads at the end of the otherwise excellent Darwin exhibition). Others, such as Richard Dawkins, EO Wilson, PZ Myers and myself, believe that this is not good enough. Just because some scientists, such as Ken Miller and Francis Collins, manage to do good science while also believing that Jesus of Nazareth was the Son of God, does not mean that there is no conflict between science and religion. By not speaking out, scientist-atheists are helping fuel most people's bigotry towards atheism.

I should note that this debate is peculiar to the US. Just the other day, I was talking to a prominent French biologist who was mystified with my account of the "debate" over evolution in this country. In Portugal, a Catholic country, Mário Soares was twice elected president with absolute majorities, despite being openly agnostic, something pollsters repeatedly show would be impossible in the US. Never before I came to the US did I think twice before including the word "evolution" in the answer to the question of what it is I actually work on. Perhaps people are just more outspoken in the US ("I have a problem with evolution..." is a common reply), but somehow I doubt it.

This debate reminds me of Jerry Coyne's review of a book by another of PZ Myers' fans, Richard Dawkins' (I would recommend "A Devil's Chaplain" to any budding atheist, at least until his new book comes out):

[...] Atheism in early nineteenth-century Britain was blasphemy and thus illegal [...] Thankfully, such strictures are now much rarer, but a subtler form of repression prevails in places such as the United States. Scientist−atheists, bowing to prevalent notions of politically correct social inclusiveness, are unwilling to express their opinions for fear of offending religious sensibilities. But Dawkins makes a strong case that most religions are insidious and dangerous illusions. It's time for those who agree to stand up beside him.

Which I am now doing.