Newton's Binomium

How to spot a crackpot

2009-04-21T06:33:00.000-07:00

I've found a nice follow-up to Dan Graur's latest post. The anthropologist Pascal Boyer has been investigating the wonders of crackpot physics. In this blog post he gives us a flavor for how he is getting on. Interestingly, what he finds is very similar to what goes on in crackpot biology.

Read full post at Evo.Sphere

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.

Redundantia ad absurdum

2006-06-26T09:39:00.000-07:00

[Update: I've fixed and added some links. An argument has been added, in red.]

You might have thought that this discussion was over (see also here and here). However, Salvador has now decided to reply (also here) to parts of my last piece. My immediate responses can be found under the comments cited, but I thought I should bring some of the more interesting points over here for detailed consideration.

Full or partial redundancy?

Salvador has finally clarified what he and Denton were talking about in their repeated claims that the C. elegans vulva "is generated by means of two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva". It turns out that they meant the graded, action at a distance by the EGF-like ligand LIN-3 vs the sequential, non-graded lateral signal mediated by LIN-12. (Note: The earlier ambiguity was a serious failure of communication on their part. When you make a scientific assertion you must be very precise on the details. Mentioning "two mechanisms" in the context of vulval development will be interpreted as referring to "vulval induction and lateral signaling" by any C. elegans biologist. My second guess was the synMuv genes, because Salvador was discussing knockout experiments at the time. How was I supposed to know what Salvador meant?)

They based their arguments on a mini review by Cynthia Kenyon. Here's a crucial passage:

"[...] A simple and attractive model is that the two pathways both operate and are partially or fully redundant. This set-up would enable the vulva to form perfectly in every animal, which it does."

Salvador then decided to go on the offensive:

"I will be interested to see if he affirms or retracts his comments based on Cynthia Kenyon's article which way pits Sternberg (not richard) against others in the debate over nematode vulva development. Ricardo cited sternberg, but not the competing opinion it seems. However, I am willing to stand corrected."

First of all, let me introduce the figures involved. Cynthia Kenyon and Paul Sternberg are both giants of C. elegans developmental biology. Apart from doing classic work on several systems, such as vulval and embryonic development, and Hox genes, Kenyon turned to the genetics of aging and completely revolutionized the field (for example, with her work on the insulin receptor daf-2 and the transcription factor daf-16, or the signal from the germline that inhibits life-span). While I occasionally disagree with some of her evolutionary thinking, I have enormous respect for her work. Paul Sternberg began by resolving the gonadal and nongonadal post-embryonic cell lineages of the nematode Panagrellus redivivus, a classic evo-devo study from before the time it was called that. He then became famous for discovering the EGF receptor / RAS / RAF / MAPK vulval induction signaling pathway. He has also spearheaded the development and evolution of WormBase in recent years (that's the tool that allows me to gene-name-drop so effectively). Sternberg (definitely not Richard) is perhaps the most knowledgeable scientist in the world when it comes to vulval development.

I hate to disappoint Salvador, but it isn't helpful to talk about "competing" opinions here, for three reasons. First, the mechanisms raised by Kenyon are explicitly discussed in Sternberg's review. Second, Kenyon's piece is a small review written over 10 years ago, and it's hardly appropriate to compare it to the latest comprehensive survey of the field. Third, Kenyon was clear about the speculative nature of her proposal. She admitted that the papers she was reviewing did "not indicate which of the two signaling mechanisms plays the predominant role during normal development" (p. 172). Her proposal was described as "a simple and attractive model", not the final answer to the problem.

So what's the answer? My answer is that the two mechanisms are only partially redundant, not fully redundant (you'll notice that Kenyon was open to either possibility), for two reasons. First, the signal from the anchor cell (encoded by lin-3) is necessary and sufficient for vulval development. If the signal from the anchor cell, graded or not, is abolished (for example, by killing the anchor cell), all vulval precursor cells (VPCs) acquire tertiary fates and no vulva is formed at all. Second, lin-12 (lateral signaling) is necessary and sufficient for specification of the secondary fate VPCs. Mutant individuals with null alleles of lin-12 do not generate secondary fate VPCs and, thus, cannot form a vulva. However, lateral signaling cannot form a vulva on its own, in the absence of a signal from the anchor cell. All this means that Denton's contention that the vulva "is generated by means of two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva" is incorrect. And so is Salvador's original contention that got this discussion started:

"One can do a knockout experiment on one of the develomental pathways of a nematode vulva and then an alternative develomental pathway kicks in to create the vulva. There are two independently successful redundant developmental pathways in the vulva."

No. The graded signal is not sufficient to generate a vulva (it cannot generate secondary fate VPCs in the absence of lin-12 activity). I hope Salvador remains "willing to stand corrected".

So does it matter whether any particular biological system shows partial as opposed to complete redundancy? I believe it does. Most biological systems show some redundancy, but full redundancy is relatively rare. Partial redundancy is exactly what you'd expect to appear under natural selection. In contrast, I suspect that if perfect, full redundancy were all around us in biological systems, Salvador would be claiming it as evidence for design (more about this later).

Here's a point by Sternberg which Salvador might appreciate:

"C. elegans VPC patterning involves multiple sources of information each of which would be capable, in principle, of generating a normal pattern. [...] These pathways might act in combination to generate an exquisitely precise pattern. In C. elegans the graded anchor cell LIN-3 signal and LIN-12-mediated lateral signaling are the major players. In other species, the other pathways might predominate."

Surprise, surprise, this Sternberg is talking about evolution.

[Note: Pharyngula has some nice introductions to vulval development and evolution.]

The Platonic vulva

So why are vulval development mechanisms redundant? Apparently, we are all in agreement about that. In Kenyon's memorable phrase "this set-up would enable the vulva to form perfectly in every animal, which it does". Sternberg makes essentially the same argument. Redundancy is for robustness. Where we differ is over whether this redundancy and robustness have evolved (Kenyon, Sternberg, myself, and just about every practicing biologist in the planet) or designed (Salvador, Denton, and a few others). Before getting to that question, let me just make another point.

I suspect that another reason why Kenyon's piece appeals to Denton and Salvador, is the Platonic undercurrent of the concept of a "perfect vulva". As I've argued in the past, this is an old foible of C. elegans biologists; taking the whole "959 somatic cells" thing far too seriously. Christian thinkers have long been attracted to Platonism, of course. Darwin showed that this was the wrong way to look at biology. A better way is to embrace variation -- what Ernst Mayr called "population thinking". So are worm vulvae as Platonic as Kenyon suggests? No, worms do not challenge population thinking in any way. In one of my favorite C. elegans evolution papers of the last decade (i.e., one I wish I had written), Marie Delattre and Marie-Anne Felix showed that the vulva doesn't actually "form perfectly in every animal": they found a few errors here and there when they looked at thousands of individuals. Incidentally, Felix and her co-workers are doing some of the most exciting work on developmental robustness I know of, much of it on the vulva. It's largely unpublished at the moment, but I'll summarize it here when it comes out.

An argument from redundancy?

So why does Salvador believe redundancy supports ID creationism? This is actually a difficult question to answer because the argument hasn't been laid out in sufficient detail (compared to, say, Behe's "irreducible complexity" argument). Indeed, redundancy is the opposite of "irreducible complexity" (see comments here), so it isn't at all clear what Salvador is talking about. However, going back to the original discussion, Salvador did sketch an argument:

"Regarding the issue of redundant functionality, it does pose a problem for natural selection as a mechanism for it's evolution. Since there are frequently circumstances under which the functions may not visible to selection over several generations, this poses a problem for natural selection. I would not say insurmountable, yet, but substantial."

Substantial? Why? You agree that redundancy is for robustness, right? Now, we know that robustness evolves. For example, C. H. Waddington selected in the laboratory on several different kinds of developmental robustness in Drosophila melanogaster and readily observed selection responses. In the 1950s! Since then, robustness has been characterized in different kinds of organisms (e.g., viruses, bacteria) and systems (e.g., genetic code, development, circadian clocks). We know that robustness responds to selection imposed by high rates of mutation, recombination or environmental perturbation. We know it responds to different kinds of selection, such as, stabilizing, directional or fluctuating. We have simulation models and mathematical theory (also here, here, here, ...). The field has been reviewed, re-reviewed and re-re-reviewed. So what is the problem, exactly? Redundancy can be selected for if it promotes robustness, which it obviously does -- no problem!

Salvador then returns to the vulva:

"In the case of the nematode vulva, without some co-option, the independent path way can not be selectively advantaged unless the other develpmental pathway is knocked out. The independent pathway, would have to be pretty much functional when it appears as it is critical to perpetuation."

No. Partial redundancy does not require such an explanation. An initial sloppy pattern can evolve, and then partial redundancy can be added piecemeal to stabilize it. Even complete redundancy could, in principle, have evolved from partial redundancy, making highly suspect any "arguments from redundancy" for ID. In order for you to claim that redundancy implies design, you must show that there is no way the redundancy could have evolved by natural selection. Good luck establishing that for any system.

I'm afraid that against this background Salvador and Denton and Sanford have to be a lot more specific. It isn't good enough to assert that "problems" exist, especially when you give the impression that you haven't done your homework. If anyone is going to pay any attention you also have to explain where exactly the hundreds of earlier studies went wrong.

Salvador's Redundancy II

2006-06-22T15:05:00.000-07:00

[Update: The saga continues.]

Salvador has chosen an strange venue to reply to my recent posts about him. I tried adding another comment there, but it was becoming too long, so I moved it here. I'll focus on three points.

"Junk" DNA

After his comments it's no longer clear (if it ever was) what Salvador is actually arguing on "junk" DNA. The point is that deleting a piece of DNA that we suspect to be "junk" (e.g., because it is a pseudogene) is a scientific test of whether the DNA is "junk". If the deletion doesn't have any detectable effect, then the "junk" hypothesis is supported. That does not mean that we have proven that the DNA is "junk" (we cannot accept a null hypothesis); any number of alternative hypotheses may, conceivably, turn out to be correct in the end. However, it does mean that one cannot simply assert an alternative hypothesis (e.g., unknown interacting regions) and expect everyone to just accept them without further scientific test. Incidentally, many researchers (only a handful of which are connected to ID creationism) have proposed hypothetical functions for "junk" DNA, so Salvador isn't even right in his claim that ID is particularly well suited for thinking outside the 'evolutionary box'. I for one find the ideas of John Mattick on "junk" DNA much more interesting than anything ID supporters have ever said. However, his ideas will have to be tested in the laboratory or the computer -- something he is actively engaged in. I would love to hear about the research efforts of the ID scientists. In other words, we are still waiting for a good example of the supposed superiority of ID as a "framework for scientific investigation".

Redundancy

Salvador writes:

The premise that systems with survival value are sufficiently visible to natural selection for them to be maintained and evolved is a false one. Those issues are theoretically pursued in Cornell Geneticist, John Sanford's book [...]

Salvador is simply hallucinating here. Is this the same John Sanford who declared in the Kansas Evolution Hearings that the earth was probably between 5,000 and 100,000 years old? Is this the Courtesy Associate Professor at the Department of Horticultural Sciences who has never published a peer-reviewed article on evolutionary biology? You'll forgive me if I continue to walk down the corridor (toward Dan Graur's office and lab) for my genome evolution.

C. elegans vulva

Salvador: when will you retract that nonsense about the "independently successful redundant developmental pathways" for making a vulva? Knocking out either the EGF receptor / RAS / RAF / MAPK inductive signaling pathway or the LIN-12 / Notch lateral signalling pathway results in the development of an abnormal vulva (often, no vulva at all). It would appear that your ID colleagues' "never apologize, never explain" attitude is contagious.

Concealed, denied or confused

2006-06-22T09:45:00.000-07:00

The national academies of science of 67 countries have issued a joint statement on the teaching of evolution. It opens with:

We, the undersigned Academies of Sciences, have learned that in various parts of the world, within science courses taught in certain public systems of education, scientific evidence, data, and testable theories about the origins and evolution of life on Earth are being concealed, denied, or confused with theories not testable by science. We urge decision makers, teachers, and parents to educate all children about the methods and discoveries of science and to foster an understanding of the science of nature. Knowledge of the natural world in which they live empowers people to meet human needs and protect the planet.

It goes on to list some basic "evidence-based facts" on cosmology, geology and evolution which we can all agree on. It concludes with a statement on the nature of science. It's not beautiful, but it's pretty good. Hopefully it will have some impact.

There was one disappointing element, though. Going down the list we find:

Albania, Argentina, Australia, Austria, Bangladesh, ..., Nigeria, Pakistan, Palestine, Peru, Philippines, Poland, Senegal, ...

Wait a minute! Where on earth is the Portuguese Academy of Sciences? One wonders what the hell they do all day over there. They should be ashamed of themselves! I'm off to write them an email. I wonder what the excuse will be: concealment, denial or confusion?

[Via Afarensis]

Salvador's Redundancy

2006-06-19T14:23:00.000-07:00

[Update: This discussion is continued here and here.]

When we last met Salvador Cordova, the energetic proponent of intelligent design (ID) creationism, he was saying spectacularly silly things about the robustness of biological systems over at evolgen. Now he's at it again:

"Intelligent design will open doors to scientific exploration which Darwinism is too blind to perceive. The ID perspective allows us to find designed architectures within biology which are almost invisible to natural selection. Thus, the ID perspective is a far better framework for scientific investigation than the Darwinian perspective. What do I mean, and how will I justify my claim?"

Give the man credit: this opening paragraph has flair. But does the rest of the post deliver? Sadly, it's just the same argument that redundancy and robustness are somehow a problem for evolutionary biology. Bizarrely, he chooses to illustrate his point with a press release from Laurence Hurst about his latest paper in Nature. He quotes the following passage with approval:

"Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life [...] This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product [...] Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments."

The point being made is uncontroversial to any biologist who knows her genetics. So what does Salvador conclude from this? Incredibly this is what he writes:

"Knockout experiments have also been used to argue 'junk DNA' is junk. This is out rightly bad science, but it persists because of Darwinist’s eagerness to close their eyes to design and paint various artifacts in biology a the product of a clumsy blind watchmaker rather than an intelligent designer."

This is wrong on so many levels that it's hard to know where to begin. Jason Rosenhouse did a good job debunking this, but I'll make a couple more points. First, where did this connection to "junk" DNA come from? I suspect it arose from the discussion on evolgen. My colleague Dan Graur made the point that experiments where large portions of "gene deserts" (long stretches of nongenic DNA without apparent function) were deleted support the hypothesis that they truly are "junk" DNA. The "Darwinist's eagerness" is entirely in Salvador's imagination. Second, Salvador seems to be suggesting that Darwinists have been getting the wrong end of the stick about knockout experiments. So who is this Hurst fellow? Surely, he must be a rising star at the Discovery Institute. Actually, you'll be shocked to find that that is not the case: Laurence Hurst is one of the brightest young British evolutionary biologists, a disciple of Darwin if ever I've met one. Indeed, the abstract of the paper the press release was about leaves us in no doubt as to what Hurst and his colleagues were doing (I've highlighted a few key concepts in bold):

It is possible to infer aspects of an organism's lifestyle from its gene content. Can the reverse also be done? Here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. The diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. Using an in silico representation of the metabolic network of Escherichia coli, we examine the role of contingency by repeatedly simulating the successive loss of genes while controlling for the environment. The minimal networks that result are variable in both gene content and number. Partially different metabolisms can thus evolve owing to contingency alone. The simulation outcomes do preserve a core metabolism, however, which is over-represented in strict intracellular bacteria. Moreover, differences between minimal networks based on lifestyle are predictable: by simulating their respective environmental conditions, we can model evolution of the gene content in Buchnera aphidicola and Wigglesworthia glossinidia with over 80% accuracy. We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle.

Isn't it strange how ID, with its "far better framework" keeps opening "doors" in blog posts, while the Darwinists keep publishing papers in Nature, despite having their eyes closed.

What about the rest of the post? Interestingly, we learn where Salvador got his misconceptions on nematode vulval development. He quotes the following passage from Michael Denton:

"The development of the female sexual organ, the vulva, in the nematode provides perhaps the most dramatic example to date of redundancy exploited as a fail-safe device at the very highest level. A detailed description of the mechanism of formation of the nematode vulva is beyond the scope of this chapter, suffice it to say that the organ is generated by means of two quite different developmental mechanism, either of which is sufficient by itself to generate a perfect vulva."

Since Salvador seems to have missed my earlier discussions of this example (here and here), I'll repeat it. Here's a good review of vulval development in the nematode Caenorhabditis elegans, by the leader of the field. The abstract gives an overview:

A single cell of the somatic gonad, the anchor cell, organizes the development of the vulva from epidermal precursors as well as the physical connection of the epidermis with the uterus. WNT signaling acting via the HOX gene lin-39 renders six epidermal precursor cells competent to respond to other developmental signals. The anchor cell induces nearby epidermal precursor cells to generate vulval cells via an epidermal growth factor (EGF) signaling pathway. The precise pattern of vulval precursor cell fates involves the graded action of the EGF signaling and LIN-12 (Notch) mediated lateral signaling. EGF promotes the primary fate while LIN-12 promotes the secondary fate. Both EGF and LIN-12 prevent precursor cells from adopting the tertiary fate, which generates non-specialized epidermis.

So what about those "two quite different developmental mechanisms, either of which is sufficient by itself to generate a perfect vulva"? Well, the thing is, the two signaling pathways are not redundant. Of course there is redundancy in the network (I've discussed one kind here), as there is in almost all biological networks known -- it's just that there are no "independently successful redundant developmental pathways" for making a vulva, to use Salvador's earlier description. This shows a recurrent pattern in ID literature, and other pseudoscience -- grandiose claims based on sloppy scholarship, selective quotation and ignoring reality.

So what of the more general claim that redundancy and robustness pose difficulties for evolutionary biologists? As I've argued before, this is a delusion. Redundancy arises readily from a common evolutionary mechanism: gene duplication. And robustness is an exciting active area of research in evolutionary biology. As regular readers of this blog will know, even I work on it.

I should end by quoting a comment made by Mark Perakh to Jason's post:

It would be entertaining to watch a debate between Salvador Cordova and Michael Behe, wherein Salvador would defend his thesis that biological entites possess redundancy which points to design, while Behe would defend his thesis that biological system are irreducibly complex, hence possess no redundancy, which points to design. A moderator (say, Dembski) would dance between them reconciling these two mutually incompatible arguments by means of writing lengthy equations and inventing new terms, say of "irreducibly complex redundancy," as a corollary to a newly discovered Fifth law of thermodynamics: the law of conservation of redundant irreducible complexity. A lot of fun watching Cordovas and his ilk pretending to have (redundant) brains.

In other words, anything is considered evidence for an intelligent designer by these people, no matter how inconsistent. Now, that is what I call a framework!

Portugal!

2006-06-17T19:43:00.000-07:00

Yes, it's happened for the first time since 1966 -- Portugal has moved on to the next stage in the Football World Cup. Figo and Deco showed how it's done (although Deco was lucky not to be sent off early in the second half), and the rest of the team had a great match as well. Now, the question is whether we play Argentina or the Netherlands in the Round of 16. No offense, but I'd prefer the latter right now. I suspect that the way to achieve that will be to win or draw against Mexico...

One for the Team

2006-06-17T10:25:00.000-07:00

Judge John E. Jones III has been speaking out about his experiences after the Kitzmiller decision:

"Because I was a Republican judge appointed by a Republican president, I was supposed to throw one for the home team. What was lost was the role of precedent and the rule of law. My job was to find the facts and apply the law - nothing more, nothing less [...] If the majority thinks we should teach creationism in schools, does that mean judges are supposed to go with the flow?"

For his courage and integrity, Judge Jones got death threats, and was called a "fascist" by none other than Bill O'Reilly!

[Via Red State Rabble]

Counter Coulter

2006-06-15T09:50:00.000-07:00

PZ Myers (here, here) and other evolutionary bloggers (here, here), have been fuming at Coulter's latest pronouncements on evolution. Apparently, the Sir Isaac Newton of information theory helped her along, so we know what to expect.

I'm always amused when creationists accuse natural selection of being simultaneously illogical and tautological (sometimes they make this claim about evolution, for a trifecta of nonsense). Of course, natural selection is not illogical. It's so logical that when you get it it's hard not to share Huxley's sentiment: "how extremely stupid for me not to have thought of that!" The tautology charge is harder to dismiss out of hand. It is easy to see that natural selection is not trivially tautological in the way that the statement "either Dembski is the Isaac Newton of information theory or he isn't" is. Some have argued that fitness does not have to be defined tautologically, but I'm not that bothered. Natural selection may be tautological, but only in the same way (that of being internally consistent) as the whole of mathematics and logic. The point is not whether a theory, such as Newton's laws of motion, is tautological, but whether it is useful scientifically, in the sense of helping us understand how the world works. Only someone who knows nothing about the last 150 years of evolutionary thinking could delude themselves into thinking that natural selection has been a fruitless idea.

The World Cup is Better than the Olympics

2006-06-11T05:47:00.000-07:00

The Economist has a couple of interesting articles about football this week (I refuse to call it soccer, of course). This is unusual because they do not cover sports news, which is one of the reasons why I read it. In a leader ("Let the Games Begin"), they point out that "the World Cup, unlike the Olympics, is wonderfully difficult to manipulate for political purposes":

"Over its long history, success at the Olympics has usually been a fairly accurate measure of global political power. [...] During the cold war, the United States and the Soviet Union repeatedly struggled to gain a symbolic victory, by winning the most medals at the Olympics. Already a similar, politically charged battle for supremacy between America and China looks likely in the 2008 Beijing Olympics.
By contrast, the World Cup has its own hierarchy, which is pleasingly divorced from the global pecking order. There is a sole superpower—Brazil. The Italians and French, apparently doomed to gentle decline in the real world, remain formidable competitors on the football field. And then there are the rising powers—which are more likely to hail from Africa than Asia. America will field a serious team at the World Cup, but nobody expects it to win. The Chinese, who have discovered a passion for football, failed to qualify for the tournament."

Another good excuse to watch some games...

Junk science

2006-04-02T10:10:00.000-07:00

Last week PZ Myers brought the excellent post he wrote about my paper on the evolution of cell lineage complexity back from the archives. In a related post, PZ took the opportunity to remind us of how Paul Nelson, a fellow of the Discovery Institute, claimed our paper offered "a workable (i.e., usable) measure of ontogenetic depth, maybe". Ontogenetic depth was a concept proposed by Nelson in an unpublished discussion paper in early 2003. I first heard of Paul Nelson and ontogenetic depth in Pharyngula. The ignorance, apparently, was mutual, even though our measure had been originally published in 2003. Despite insistent requests for clarification, and repeated assurances that "an omnibus reply" was in the making, Paul Nelson hasn't said anything substantive about ontogenetic depth for two years. PZ concludes:

"Nelson promised us an explanation of his method; months later, after giving us nothing, he showed up to point to a legitimate and interesting science paper that used an interesting technique, apparently nothing like what he was doing, and thinks that's a fair substitution? What a wonderful example of the purely parasitic nature of the Discovery Institute! No work, only promises, and the best they can do is point to the efforts of real scientists!

We're still waiting for Paul Nelson to explain the procedure and utility of "ontogenetic depth". A day wasn't enough, and I can't complain about that. A month was pushing it. A year? That's not looking so good. At two years, we ought to just give up. I'll be patient, though, and give the poor fellow a decade [...]"

Last week I encountered another example of this kind of scientific parasitism by another intelligent design creationist: Salvador Cordova. Cordova, like Nelson, regularly engages in polite discussions with evolutionary biologists. This time, the topic was "junk" DNA. Cordova joined the discussion and steered it towards the topic of robustness. Over a two comments, he wrote:

"One can do a knockout experiment on one of the develomental pathways of a nematode vulva and then an alternative develomental pathway kicks in to create the vulva. There are two independently successful redundant developmental pathways in the vulva. [...]

In the case of the nematode vulva, without some co-option, the independent path way can not be selectively advantaged unless the other develpmental pathway is knocked out. The independent pathway, would have to be pretty much functional when it appears as it is critical to perpetuation."

He then used this example to suggest that robustness cannot evolve. The problem is that his discussion of vulval development in Caenorhabditis elegans is rubbish. The fates of the six vulval precursor cells are determined by the action of two signaling pathways: the EGF receptor/RAS/RAF/MAPK inductive signaling pathway specifies the primary vulval fate, and the LIN-12/Notch lateral signaling pathway specifies the secondary fate. However, these pathways are certainly not redundant.

The redundancy he's thinking about is in the synMuv (synthetic multivulva) genes. These form two functionally redundant classes, A and B (to which a third, C, has recently been added), of regulators of RAS signalling. This class of genes gets its name from the observation that mutants from within a single class show normal vulval development, but double mutants affecting loci in different classes, known as "synthetic", show several ectopic vulvae, a phenotype known as "multivulva". However, the synMuv genes do not constitute "independently successful redundant developmental pathways". This is parasitism of the highest order: the synMuv genes were originally characterized in the lab of the Nobel Prize winner Robert Horvitz. Let's just say that he's no intelligent design creationist. When are you guys going to start doing some actual research, instead of misinterpreting the work of real scientists?

Cordova's other arguments on how robustness evolves (or rather fails to do so) bear no relationship to any real research into this problem -- for a proper review of the subject see, for example, Andreas Wagner (2005), de Visser et al. (2003) or Flatt (2006). For example, commenting on A. Wagner's paper (reviewed here and here) Cordova descended further into his strange world of make-believe:

"Regarding the paper pertaining to circadian oscillators, 'Can these results be generalized to other systems? It's impossible to tell at this stage.' The answer is likely no.
We know from mathematics that evolutionary algorithms can only solve a small fraction of design architectures. That is a given fact in engineering. Some of those architectures which evolutionary algorithms can not solve are already in evidence in biology, such as the turing machine or anything dealing with large scale software such as seen in the cell."

Notice how Cordova skiped over the entire argument from the paper without actually addressing what Wagner set out to test, and then made up some "given facts" about evolutionary biology.

Remember Cordova's prediction that Wagner's result cannot be generalized to other systems. For the record, I'll bet on the opposite outcome. I'll return to this as more evidence comes out. (Something tells me that you won't have to wait for too long.)

The unnecessary hypothesis

2006-04-01T20:03:00.000-08:00

Does prayer work? The New Testament is clear that it should: "Ask and it shall be given you" (Matthew 7:7). Other religions would concur. However, evidence for this prediction has been hard to come by. Francis Galton was perhaps the first to approach this problem scientifically. In his Statistical inquiries into the efficacy of prayer (1872) he wrote:

"The efficacy of prayer [...] is a perfectly appropriate and legitimate subject of scientific inquiry. Whether prayer is efficacious or not, in any given sense, is a matter of fact on which each man must form an opinion for himself. His decision will lie based upon data more or less justly handled, according to his education and habits. An unscientific reasoner will be guided by a confused recollection of crude experience. A scientific reasoner will scrutinise each separate experience before he admits it as evidence, and will compare all the cases he has selected on a methodical system."

Galton, one of the founders of modern statistics, was clear about how to proceed. He began by reducing the problem to "a simple statistical question -- are prayers answered, or are they not?" He then argued that one should "examine large classes of cases, and to be guided by broad averages". In a memorable case study, Galton considered the "longevity of persons whose lives are prayed for":

"The public prayer for the sovereign of every state, Protestant and Catholic, is and has been in the spirit of our own, "Grant her in health long to live." Now, as a simple matter of fact, has this prayer any efficacy? There is a memoir by Dr. Guy, in the (Vol. XXII. p.355), in which he compares the mean age of sovereigns with that of other classes of persons [...] The sovereigns are literally the shortest lived of all who have the advantage of affluence. The prayer has therefore no efficacy, unless the very questionable hypothesis be raised, that the conditions of royal life may naturally be yet more fatal, and that their influence is partly, though incompletely, neutralised by the effects of public prayers."

Many studies have since attempted to detect the effects of prayer in a variety of contexts, using a Galtonian approach.

The results of the largest study to date into the clinical effects of intercessory prayer were published in the American Heart Journal last week. Rhosgobel wrote an excellent summary of the research. Galton would have been proud. The study split over 1800 coronary bypass patients into three groups:

Patients who were prayed for but were told that they "may or may not be prayed for"
Patients who were not prayed for but were told that they "may or may not be prayed for"
Patients who were prayed for and were told that they "will be prayed for"

Patients from the first two groups did not differ in the probability of developing complications within 30 days of the surgery. Patients from group 3 showed a small but statistically significant increase (!) in complications. The study cost approximately $2.4 million, mostly from the Templeton Foundation. "Unscientific reasoners" have already started to make up excuses, in much the same way as defenders of alternative medicine.

After reading Laplace's Mécanique céleste, Napoleon is said to have questioned the author on his failure to mention God. Laplace famously replied: "I have no need for such a hypothesis". I agree.

Last laugh

2006-03-28T14:29:00.000-08:00

You'll forgive me for returning to this, but the aftershocks haven't finished yet. The Houston Chronicle has nice piece about our paper today, even if I say so myself. (Although I probably would have subtitled it "fuel for selection" or "variation engine". Oh, and did I really split that infinitive at the end?) The author, Patrick Kurp, keeps a very interesting literary blog; for example, check out these posts about Darwin's prose and Fernando Pessoa, written after we talked. (As someone keeps telling me, I should write more about literature myself. I'm thinking something about Borges...)

But today I thought I should write about some not so flattering responses to our paper. A few hours after the paper came out in Nature's website, someone wrote me an email titled "Do you believe in God?" It opened with:

Could sexual relations occur because that is the way God intended to have us populate the earth? [...]

Have you ever asked yourself WHY...God made sexual activity so pleasurable...could it be as a gift to both man and woman?

This could be the easiest evolutionary question ever posed: might it be because individuals who find sex unpleasant have tended to leave fewer descendants? Clearly my fan did not taken the time to actually read the paper. It continues in a crescendo of silliness:

Sometimes people over analyze activities... Is it possible that somethings God just loves you so much that he wants you to exsperience [sic] something greater than yourself... greater than what you can truly describe in words. Something that can't be explained...

I wonder what it's like to be God!

Scary... Think about it: this is what a future biology textbook might say if intelligent design creationists get their way in public schools. I'm amazed at how confidently some people express opinions about things they know so little about.

Apparently our paper has made some people laugh as well.

This is what happens when you put all your eggs in the basket of neo-Darwinism: trying to come up with increasingly risible explanations for the most basic instincts of life. Of course, this explanation is a minority view within the scientific mainstream (for the moment), but it's not that far off a lot of other views on particular processes in the development of life.

I wonder what they've been smoking over there. I'd hate to see what they might consider a serious explanation. Obviously, Pipesman has no idea of what the "scientific mainstream" actually is, which is worrying for a journalist. So let me explain it: I belong to it and your pals over at the Discovery Institute do not.

The origin and maintenance of sex really is one of the big problems of biology; that's not just something we say because it sounds cool. And biologists have been working hard to solve it. Let me illustrate how using some citation analysis. Since 1988, two of the classic books on the subject, John Maynard Smith's Evolution of sex (1978) and Graham Bell's The masterpiece of nature (1982), have been cited by 910 and 693 mainstream scientific papers, according to the ISI Web of Science database. The mutational deterministic hypothesis you seem to find so amusing is actually one of the main players in the field, not some fringe idea. It was proposed almost 20 years ago by Alex Kondrashov in, among others, another paper in Nature. That paper has been cited 381 times. Another major contender for explaining the evolution of sex is contained in this classic paper, which has been cited an even 400 times. To put these numbers in perspective, Darwin's The Descent of Man has been cited approximately 3000 times over the same period, whereas Dembski's collected works have been cited 84 times. In other words, theories on the evolution of sex have been formulated, analysed, extended, discussed, reviewed, tested and retested in hundreds of papers. That's about as mainstream as it gets.

Entanglement

2006-03-15T07:56:00.000-08:00

Welcome to all Tangled Bank readers! I thought this would be a good opportunity to write some more about our paper (yes, any excuse!) -- in which I explain how our research came about, and drop a lot of names in the process. The point of this exercise is to cut through the neatness (or "fraud", as Medawar famously put it) of the finished scientific paper, and give a more personal account of how we found what we found.

I met Christina Burch, my collaborator on this project, at the 2004 Evolution meetings in Fort Collins, CO. We had a chat over a beer and found ourselves talking about a paper by Siegal & Bergman which showed that selection for any stable gene expression pattern could lead to greater robustness in whatever specific gene expression pattern a genotype happened to evolve. That paper made a big splash in the robustness field by showing that what we might call classical stabilizing selection was not required for the evolution of robustness. It turns out that Christina had thought more deeply about their paper than I had, and had spotted some things that didn't add up. For example, Siegal & Bergman had incorporated sexual reproduction in their model but did not test for its effect. She'd even ran some preliminary simulations and hadn't been able to replicate all of their original results when she removed sex. We agreed that this was something worth pursuing and that we should try and do some work on it together.

Now such resolutions are common at scientific conferences, but they don't always go anywhere. Scientists constantly get excited about new problems, but they aren't always in a position to take on new projects. In this case, things turned out differently for two reasons. First, I was in the process of completing another project that would soon culminate in a satisfying publication (I was actually working on the resubmission during the meeting), so I was looking for something else to do. One direction I was considering (the next logical step, really) was to connect gene networks to our cell lineage models. When I thought more about it, I thought that the Siegal & Bergman model would be a good way to do that. Second, Rolf Lohaus (on the left in the photo) was about to join my lab to do his PhD. He had visited my lab during the Summer of 2003 while working on his Masters project on a gene network model of C. elegans vulval development, and I thought he would be interested in working on it. I was not disappointed -- Rolf started working on the project as soon as he arrived. Soon, two other students joined the project: Suraj Srinivasan in my lab (on the right in the photo), and Kristen Dang in Christina's lab (whom I have yet to meet in person). The work progressed incredibly quickly (the fastest in our experience), a testament to the quality and commitment of the team we assembled: we submitted a manuscript on it in mid-June 2005.

Let's get back to the science. You might be wondering about what happened to Christina's initial questions about Siegal & Bergman's paper. When I reread it more carefully I agreed with her assessment. What did it for me was the result they showed in Figure 2d -- I couldn't believe that it would be true in asexual populations. When we repeated their simulations we found that we were right on that point -- they had actually missed the effect of sex on the evolution of robustness. However, the main finding of their paper (explained above) was still valid in asexual populations (we show that in our paper, although we present our results in a different way).

So why did we decide to look at directional epistasis and the evolution of sex as well? It turns out that both Christina and I immediately saw the interest of those problems. In her case, this will not surprise you. She had long been interested in directional epistasis, as you can judge from these earlier papers from her lab. I suppose doing her PhD in Lin Chao's lab must have played a role in that. In my case it won't be so obvious but it's an interesting example of how formative influences can have far reaching consequences.

Although I had never before worked on the evolution of sex, I've been close to people working on it ever since my PhD days, so I've been quite familiar with the field. I started my PhD in Edinburgh, and the closest lab to ours, both intellectually and socially, was that of the theoretician Nick Barton. The reason why that was significant is that, although I didn't interact much with Nick himself, I did interact with people who were interested in the evolution of sex who passed through his lab, such as Joel Peck and Mike Whitlock. Alex Kondrashov, the father of the mutational deterministic hypothesis, also visited for several weeks while I was there and I heard him speak a few times. When I moved to London with my PhD lab, I continued to hear about the evolution of sex from Daniel Falush, then a PhD student in Andrew Pomiankowski's lab. Throughout my postdoc in Armand Leroi's lab (warning: his lab webpage has been frozen in time for 6 years -- I'm still listed as a postdoc there!), the closest lab to ours (Austin Burt's, again both intellectually and socially), was also actively working on the evolution of sex. For example, Matt Goddard, who went on to do an excellent evolution of sex experiment on yeast, did his PhD in Austin's lab.

Which brings us back to our work. When we started looking at the evolution of robustness in sexual and asexual populations, we quickly decided to check the response in directional epistasis. Our thinking on this was also sharpened by the fine papers on Avida and RNA folding -- in fact, we were practically scooped by this paper on Avida. The rest, as happens so often in science, was luck, but as Pasteur pointed out long ago "dans les champs de l'observation le hasard ne favorise que les esprits préparés" ("chance favors the prepared mind").

The way of the dodo...

2006-03-10T05:56:00.000-08:00

Yesterday I went over to Rice University to see a screening of Randy Olson's "Flock of Dodos". I was curious to see his "ten things" in practice. I loved it! It was pretty funny at the expense of both sides. Randy managed the rare feat of being incisive [1. intelligently analytical and clear-thinking. 2. accurate and sharply focused] and insightful about intelligent design creationism, without humiliating its proponents (in fact some of them come across quite sympathetically). The scientists were not at their best (the ending is masterful, but I won't spoil it for you), but I found them to be representative of the range of opinions, attitudes and personalities common among my colleagues: from rambly to focused, from introverted to extroverted, from emotional to analytical, etc. I essentially agree with what Carl Zimmer wrote about the movie and, like him, do not want to give too much away and spoil the fun. Just go and watch it!

There was only one problem -- the audience. Apparently the movie has been playing to packed houses in Kansas, Yale, Harvard, etc. Sadly, that was not the case yesterday. I don't know what happened but let's just say that my wife and I, and my four graduate students must have been about 10% of the total. Ironically, there must have been some severe miscommunication on the part of the organizers (not scientists, by the way), because Rice's E&E department first heard about the event a couple of weeks ago when I told Joan Strassmann. After that a couple of emails were sent around, but still I only saw Joan and Dave Queller there (maybe I missed someone else). I have no idea where all the graduate students were -- maybe a free screening isn't enough these days unless there's also free beer and free pizza... If I'd known, I would have offered extra credit to students in my Evolutionary Biology class!

So, the film was excellent, but the discussion afterwards was a bit disappointing. I left before it ended because I was almost fainting from hunger, so I didn't get to congratulate Randy in person as promised. Maybe I can do it the next time he comes to Houston after the movie is released and he becomes famous. Maybe we can even arrange for him to come a give a talk at UH...

Update: "Flock of Dodos" will have it's official World Premiere at Robert De Niro's Tribeca Film Festival on Sunday, April 30 in New York City. Congratulations!

XXX science

2006-03-05T12:39:00.000-08:00

We all knew that sex sells, but it's still fun to see it applied to your own work. Perhaps Randy Olson should add another point to his ten commandments of evolution communication: "make as many references to sex as possible"!

You'll have to excuse the shameless gloating, but I have to highlight some excellent developments:

Re-evolução sexual by Marcelo Leite (Folha de S. Paulo)
Why sex is good (and not for the obvious reasons) by Dan Jones (The Proper Study of Mankind)

But don't trust everything you read about our paper... For example, in this piece we learn that we actually did our work with fruitflies. Yes, the experiments shown in Figure 3a/right (µ=0.002) were actually started back in the VIIth century!

Resistance is not futile

2006-03-02T13:37:00.000-08:00

Our paper is out now, so I can finally explain what it's all about. Unfortunately I haven't had much time between grading tests, speaking to journalists and preparing for a talk tomorrow. It remains to be seen how much noise this will make, but I'm pleased with the initial response. Here are some clippings for you:

Sex: why bother? (UH Press Release)
How sex stays in fashion (Nature, Editor's Summary)
Why we have sex: it's cleansing (Live Science)
Sex: why even educated fleas do it (Ciencia Hoje)
Sexo tem vantagens evolutivas (Público)

If you've read the earlier posts, you're probably wondering what robustness could possibly have to do with the evolution of sex? At first it would seem that positive epistasis, where mutations spontaneous mutations have weaker effects in combination than they do separately, is a "many-mutation" version of robustness. However, in the last few years, scientists working on a range of models of biological systems (such as, RNA folding and virus growth) have found that high robustness to mutation (that is, to one mutation) tends to be associated with more negative (or less positive) epistasis. In other words, it seems that selection for high robustness might lead to the evolution of negative epistasis.

So how does robustness to mutation evolve? The obvious answer is that high mutation rates can select for robustness to mutation. This has been known for a while. A less obvious suggestion is that sex might act as a qualitatively similar perturbation to mutation and lead to the evolution of robustness to mutation. To our surprise when we started working on this problem, although this had been predicted (most clearly in an uncharacteristically obscure paper published by Stephen Stearns in a Polish paleontological journal), it had never actually been tested in real organisms or even modelled in any detail.

To explore these questions we took a simple model of a genetic system from the literature. Briefly, it represents a very simple transcriptional regulation gene network. We then looked at the evolution of a very simple phenotype: the ability to produce a stable gene expression pattern. Population of these digital organisms were allowed to evolve such that those that produced stable gene expression patterns survived, while those that produced unstable patterns died. We found that sexually reproducing populations evolved increased robustness to mutations when compared to asexual ones. In addition, negative epistasis evolved in the sexuals, but not the asexuals. In other words, sexual reproduction created the conditions that favor its own perpetuation. If these results hold for real organisms, sex may be self-reinforcing.

Update: Dan Jones at The Proper Study of Mankind has written an excellent post on our paper.

Climate change

2006-02-22T13:09:00.000-08:00

Viva, to all visitors from Conta Natura...

Which reminds me, Portugal has been unusually cold this Winter. The other day, my friend Manuela sighted this unusual creature in Evora.

I'm feeling Dodoish today...

2006-02-21T08:06:00.000-08:00

The Loom has given a platform to Randy "Flock" Olson where he gives us poor deluded scientists some advice on how to communicate with the public. Although I agree with much of what Olson has to say, and am very much looking forward to "Flock of Dodos" coming to Rice University, I disagree with him on a few points. For example, he opens his list with:

"[S]o much of the mass communication of evolution is so dull and uninspiring. [For example] the 8 part Evolution series by PBS released a few years ago [...]. We ordered the 7th episode of the Evolution series, on God and religion, and found it unwatchable. At one of my recent screenings a member of the audience offered up that she ordered the second episode for a museum display and found the same thing – five minutes into it they shut it off. [...] These sorts of productions need the simple, honest feedback of evolutionists who have purchased their videos, shown them to their neighbors, and watched them fall asleep. Just send them a note and say this is not good enough. Raise the bar. Its that simple. When evolution media looks bad, evolutionists look bad.

Interesting, coming from someone who tells us not to "condescend" and to "lighten up a bit" later on. Just by curiosity, did you actually watch the whole series, or just the last episode? I happen to think that the series is excellent. Some episodes (e.g., the evolution of infectious disease and the sexual selection / evolution of sex ones) are among the best popular science programs I've ever seen. My wife who is a scientist but not an evolutionary biologist (nobody's perfect!) also enjoyed them.

I suppose I just don't buy the argument that we need to aim at the lowest common denominator in order to grab people. That we need to entertain everyone at all times. (Of course, I could be wrong. Newton's Binomium isn't exactly a mass phenomenon.) No matter how flashy you make something some, perhaps most, people will still switch to "Fear Factor" or whatever. I think there's nothing wrong with creating programs aimed at the same public who watch good natural history or technology shows, even if it's only 10% of the total audience. David Attenborough never dumbed anything down, and still got big audiences. I know many biologists who were turned on to the subject by watching his shows. Dawkins' "The Selfish Gene" did the same for me. Steve Gould's prose inspired others still, even if some of Olson's students found it "arrogant, elitist, condescending, verbose". I'd hate to see these voices disappear just because they risk sending someone, somewhere to sleep.

Update: I should add that I largely concur with Olson on his points 3-5 and 7-10.

Blind Watchmaker or Swiss Designer? (Part II)

2006-02-18T20:42:00.000-08:00

Although it seems easy to identify robustness in biological systems, it is usually difficult to give a precise answer to the obvious question: robust compared to what? Ideally one would like to study many different, independently evolved creatures. However, these are rarely available. For example, the number of different, naturally occurring genetic codes is small, and they are not that different from the inaccurately named "universal" code. Instead, we usually have to make do with simulated creatures. This is the approach Andreas Wagner took to study the evolution of robustness in circadian oscillators.

He began by considering one of the simplest models for a circadian oscillator, known as a Goodwin oscillator. In a Goodwin oscillator a gene expresses a mRNA molecule R that is translated into protein P. This protein is then modified (e.g., dimerized or phosphorylated) to generate an inhibitor P' of its own expression.

This model was chosen because it can "exhibit stable circadian oscillations of an appropriate frequency", and because it can correctly predict "the response of circadian rhythms to stimuli such as temperature pulses, light pulses, and an inhibitor of protein synthesis".

Now consider the case of two coupled Goodwin oscillators forming the following two-gene six-product circuit:

Wagner points out that this circuit can take one of 378 different topologies where the six regulatory interactions represented by dashed lines can be activating, inhibitory or non-existent (the interactions represented by the solid arrows are always positive). He then asks two questions:

Do different topologies result in different degrees of robustness?
Can an evolutionary search in a space of possible circuit topologies reach highly robust topologies when starting from circuits with low robustness?

To address the first question, Wagner took each of the 378 circuit topologies and generated 5,000 random parameter combinations "from a parameter space within which circadian oscillations are known to occur for the basic Goodwin oscillator". He then used these parameter combinations to define a measure of robustness:

"For each of these parameter combinations, I examined whether the circuit adopts limit cycle oscillations with a period of ≈24 h [...] The fraction of randomly chosen parameters that yield circadian oscillations is an estimate of the fractional volume (P) of parameter space that admits such oscillations [...] P can serve as a proxy for a circuit's robustness to perturbations: changing parameters at random in a topology with high P is more likely to yield a parameter combination leading to circadian oscillations than in a topology with low P."

Of the 378 topologies, 176 show no random parameter combinations capable of generating circadian oscillations (P less than 1/5,000). Among the 201 topologies producing oscillations, robustness (P) varies by nearly 2 orders of magnitude among circuit topologies. For most of these topologies, only one or a few of the 5,000 randomly chosen parameter combinations produce circadian oscillations (low P). But for a small fraction of topologies, over 5% of parameter combinations yield such oscillations (high P). Here are nine of the topologies with the highest associated robustness:

These circuits show two important properties which give us some clues as to the mechanistic causes of robustness. First, most topologies contain a mixture of transcriptional (fast) and posttranscriptional (slow) regulation. Second, inhibitory interactions are more common than activating ones. "This is not surprising, if one considers that a closed positive regulatory feedback loop may cause the increase of a gene product without bounds, thus preventing stable oscillations".

The most robust circuits are ≈1 order of magnitude more robust (i.e., have a higher P) than a circuit composed of two decoupled Goodwin oscillators. This result suggests "that the increased complexity of interlocking oscillators involving two (or more) oscillating gene products" found in nature "may not be an accident of natural history: it may indeed provide greater robustness to mutation than single oscillators." However, when the first coupled oscillator evolved it was probably not very robust. So, to repeat the second question posed above, is it likely that a robust oscillator evolved by "numerous, successive, slight modifications" (Darwin 1859) to circuit topology? Wagner introduces an original way to attack this problem:

"This question is best posed by considering the following graph or network representation of oscillator topologies. Consider a graph where each node corresponds to an oscillator topology that is capable of displaying circadian oscillations. Connect two nodes (topologies) by an edge if the two topologies differ by only one regulatory interaction [see a, below]. Such neighboring topologies can arise from each other by genetic change that affects only one regulatory interaction. The question whether robust oscillator topologies can be found through a series of such changes, i.e., through gradual evolution, is a question about the structure of this graph. There is a spectrum of possibilities with two extremes. First, the nodes (oscillator topologies) of this graph may be disconnected. That is, a topology capable of circadian oscillations has no neighboring topologies also capable of producing such oscillations. This would mean that robust topologies cannot be reached from less robust topologies, because functional oscillators are isolated islands in this graph. At the opposite extreme, this graph might consist of one densely connected component, where any two topologies are connected by a path of edges. In this case, stepwise evolutionary alteration of a circuit topology could start from any one topology and reach any other topology via intermediate topologies that admit circadian oscillations.

Part b of the figure below shows this metagraph for the 201 topologies capable of producing circadian oscillations (P at least 1/5,000).

Two properties of this metagraph stand out: it consists of a single, highly connected component, and similar topologies also tend to have similar robustness (P). Thus:

"[G]radual evolutionary changes in circuit topology can generate any circuit topology from any other topology within such a component, without transitions through circuits that do not allow circadian oscillations."

The high evolutionary accessibility of robust topologies is not trivial: metagraphs composed of random samples of 201 topologies (i.e., picked independently of their robustness) tend to show, on average, over 20 disconnected components.

In conclusion, Wagner tested whether evolution could, in principle, discover a robust coupled oscillator circuit topologies and found that the answer is yes. This is an excellent example of why the standard position taken by intelligent design creationists when faced with the appearance of design is scientifically vacuous. No doubt Dembski and Behe will come up with some post hoc criticisms of Wagner's study. What I'd like to see are similarly rigorous attempts to test their claims, instead of the usual hand-waving about mousetraps and Mount Rushmore.

Can these results be generalized to other systems? It's impossible to tell at this stage. A recurring problem in the study of robustness is that it is difficult to judge how representative any biological system really is. For example, when Meir and colleagues (Current Biology 12: 778–786, 2002) discovered that the neurogenic network of the fruit fly Drosophila melanogaster is robust against large variations in the initial concentrations of gene products and the rate constants of molecular interactions they wondered:

"Perhaps this is a generic feature of genetic organization, but perhaps it reflects a coevolution between evolved networks, biologists and theorists: modular, robust networks are the easiest to get at experimentally. Thus, they are the best understood and are the best fodder for models."

There is only one way to find out... To keep working!

Even educated water-fleas do it...

2006-02-17T21:38:00.000-08:00

In the current issue of Science, Paland & Lynch report on some new evidence in favor one of the "Weismann-family" theories for the evolution of sex I mentioned the other day. They compared sexual and asexual populations of water-fleas (Daphnia pulex) and found that sexual populations are more efficient at eliminating deleterious mutations than asexuals, as predicted by (among others) the mutational deterministic hypothesis:

"Of the amino acid altering mutations arising in mitochondrial protein-coding genes of D. pulex, we estimate that 73.2% have strongly deleterious effects and are subject to purifying selection irrespective of the population's breeding system, 13.3% have moderately deleterious effects and persist only in asexual populations, 4.4% are mildly deleterious and allowed to persist in the short-term even in sexual populations, and 9.1% are effectively neutral. Thus, the rate of accumulation of deleterious amino acid–altering mutations in asexual lineages, 4.4+13.3=17.7%, is four times as high as that for sexual lineages (4.4%)."

Blind Watchmaker or Swiss Designer? (Part I)

2006-02-17T07:50:00.000-08:00

Another topic I've been working on is robustness, one of the abstract nouns du jour. Robustness is defined as resistance to some kind of perturbation, such as mutation, heat-shock, or a poison. This is an old idea in biology: it is closely related, for example, to CH Waddington's "canalization", and to Claude Bernard's "homeostasis". It also has obvious parallels in other fields, such as the concept of "stability" in community ecology and "control theory" in engineering.

What fascinates biologists is that organisms appear to be riddled with robustness to all sorts of perturbations. This seems to be true at all levels of biological organization, from the genetic code to metabolic pathways, from RNA and protein structure to genetic regulatory networks. This robustness has important evolutionary consequences because it affects the expression of phenotypic variation within populations, the fuel for natural selection. (For a detailed survey of these topics I'd recommend a book I'm reading at the moment: "Robustness and Evolvability in Living Systems" by Andreas Wagner. Some chapters are previewed in his recent papers. Or you can listen to this talk.)

To make some of these issues clearer I'll discuss a concrete example reported in a paper by Wagner ("Circuit topology and the evolution of robustness in two-gene circadian oscillators". PNAS 102: 11775–11780, 2005). One class of biological systems that has been shown to be highly robust are the genetic oscillators underlying circadian rhythms (i.e., endogenous activity cycles with a period of approximately 24h) in a variety of organisms, including cyanobacteria, fungi, insects and mammals. Although some of these clocks may have evolved independently, they tend to share some basic characteristics according to Wagner:

"First, the principal clock mechanism is simple. It minimally involves one gene that is expressed to produce a mRNA and a protein product that may undergo further modification and exerts direct or indirect negative feedback on the expression of its own gene. Examples include the frequency (frq) gene in the fungus Neurospora crassa, the timeless (tim) gene in the fruit fly Drosophila melanogaster, and the kaiC gene in the cyanobacterium Synechococcus spp. This simple mechanism will generate sustained oscillations in protein concentrations only if the negative feedback is slow. That is, there must be a delay between the time at which the gene product's concentration rises because of its expression and the time at which the gene product represses its own expression. [...] The second common feature of many circadian oscillators is that they consist of not one but two or more oscillating gene products whose regulation is linked. This holds in organisms as different as the fungus Neurospora, the fruit fly Drosophila, and mammals."

More interestingly, like Swiss watches, they show remarkable accuracy and precision under a range of conditions. In his paper, Wagner asks:

"[W]hether interlocked circadian oscillators may be an accident of life's history (there are infinitely many ways to obtain limit cycle oscillations in regulatory systems), or whether such interlocking may exist because it provides especially robust oscillations."

There is, of course, another, if less scientific, alternative that Wagner forgot to mention: that an intelligent designer decided to make circadian clocks that way. Maybe the designer was even Swiss! William Paley seems to have been thinking about this problem two centuries ago:

"But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place. [...] When we come to inspect the watch, we perceive [...] that its several parts are framed and put together for a purpose [...]; that, if the different parts had been differently shaped from what they are, of a different size from what they are, or placed after any other manner, or in any other order, than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use that is now served by it. [...] This mechanism being observed [...], the inference, we think, is inevitable, that the watch must have had a maker: that there must have existed, at some time, and at some place or other, an artificer or artificers who formed it for the purpose which we find it actually to answer; who comprehended its construction, and designed its use."

Interestingly, Wagner actually tested all three hypotheses, something that the proponents of intelligent design creationism seem incapable of doing themselves. I'll explain how in the next post.

[Meanwhile, you can check out Circadiana and Pharyngula replying to a creationist's claim that circadian clocks contradict evolution...]

Why do fish need bicycles?

2006-02-16T19:36:00.000-08:00

The evolution of sexual reproduction is one of the great mysteries of evolutionary biology. In fact it is two slightly different problems:

What advantage, if any, did sex offer when it first appeared?
Why does sex persist in modern organisms? That is, what stops them from becoming asexual again?

These questions, although related, might actually have slightly different answers. It may seem strange to ask such questions at all, but the reason is that there are many costs associated with reproducing sexually. I'll give two examples. First, sexually transmitted diseases are widespread in sexually reproducing populations, which makes sex risky. Second, there's the so-called "two-fold cost of sex". As feminists have been telling us for a while, males are pretty useless. Well, this is seems to be true in evolutionary terms as well. A mutant human female able to reproduce asexually and give birth to more females like her, would give rise to a population with twice the reproductive rate per capita of the normal human population, and these mutants would probably become dominant within a few centuries. (Actually, this is extremely unlikely to happen in our case because, due to a genetic quirk of mammals called genomic imprinting, asexual reproduction is very difficult to evolve in humans. However, asexuality can and has re-evolved many times in other animals, such as reptiles, fish and insects.)

Evolutionary biologists have been grappling with these questions for over a century and many hypotheses (over 20 by a recent count) have been proposed to explain the origin and maintenance of sexual reproduction. However, there is still a lot of debate, partly because many of the hypotheses are not mutually exclusive and are difficult to test. Many of the hypotheses that are currently favored have in common a central idea originally proposed by August Weismann over a century ago. This is that the benefits of sex are not direct (in the sense that the offspring of sexually reproducing individuals have a higher mean fitness than those of asexually reproducing ones) but indirect such that the offspring of sexually reproducing individuals have a higher variance in fitness than that of asexually reproducing ones. In other words, according to Weismann, sex makes natural selection more efficient, thus allowing sexual populations to adapt better to their environments. This can be achieved in many ways (hence the different hypotheses), such as eliminating deleterious (bad) mutations or allowing the spread of beneficial (good) mutations.

One of the main hypotheses from the Weismann "family" is the mutational deterministic hypothesis (MDH), developed by Alex Kondrashov and others. MDH postulates that sexual reproduction confers an advantage by helping natural selection remove bad mutations from the population. The MDH is very attractive because, in order for sexual populations to overcome the two-fold cost of sex, only two things must be true, and these can, in principle, be tested using data from real organisms.

The rate of production of bad mutations must be relatively high, such that each individual acquires on average one or more bad germline mutations not inherited from their parents. This has been observed in some species, but not all. For example, humans have an even higher deleterious mutation rate than the one required by the MDH. The jury is still out over whether this assumption is generally valid in the real world -- there's a lot more work to be done there.
The bad mutations must interact in a special way, called negative epistasis, such that adding more and more bad mutations makes you disproportionately sicker and sicker. For example, imagine that a single bad mutation lowers your fitness by 5% on average. If bad mutations don't interact, adding successive mutations should lead to a progressive decline in 5% steps. Negative epistasis would occur if, for example, the second mutation decreased fitness by 10%, the third by 15%, and so on. The evidence for this second assumption is also equivocal, partly because it is even more difficult to measure than the deleterious mutation rate.

In the next post I'll introduce the other concept needed to understand our paper: robustness.

The Nature of My Blogging

2006-02-16T19:02:00.000-08:00

Nature has a lot to do with my blogging. It all started last year when I got a paper into it -- apologies for the shameless self-promotion. One of the most interesting consequences of that was that two bloggers picked up on the article. One of them was PZ Myers. It's an example of Pharyngula at its best: in a few paragraphs it cuts through ideas that took several years to develop in our collective minds (and were then compressed into the highly compact Nature style) and hits the nail on the head. (The other blog post, in Catalan, is also excellent.)

This was my first real introduction to blogs and I was impressed. I started reading PZ regularly, one thing led to another (literally, or perhaps better, virtually) and I've been hooked ever since. A few months later I decided to give it a try myself. Unfortunately, I quickly found that I rarely have time to write on the blog. When I do, I feel guilty about all the other things I should be doing instead, such as replying to that friend's email, writing the next paper or grant application, planning next week's lecture, ... or reading the latest issue of Nature (authors get a nice subscription discount, you see).

Fortunately, one of the reasons for my low blog output is coming out in two weeks in, well, Nature. I think it's pretty exciting stuff, so I'm going to try and explain what it's all about here. (After all, PZ may have something better to do that week... Dawkins may send him another DVD or something.) Because of their embargo policy, I'll have to limit myself to background for the moment: the evolution of sex and robustness. Sounds kinky, doesn't it?

Bioethics

2006-02-15T19:28:00.000-08:00

Spot the differences! (Via Conta Natura.)

Good news from Ohio

2006-02-14T19:35:00.000-08:00

In a memorable passage from his landmark ruling, Judge Jones argued that science could not be defined differently for "students than it is defined in the scientific community as an affirmative action program". Ohio seems to have followed this sound advice. Could Kansas be next?

On Pattern and Process

2006-01-17T14:17:00.000-08:00

PZ Myers has provided an excellent summary of West-Eberhard's ideas on what evolutionary theory is currently lacking (RPM offered a population geneticist's perspective). This is a topic close to my own interests -- I too dream of an extended evolutionary synthesis, one integrating population genetics, development and phenotypic evolution. This is a major problem, which will likely occupy evolutionary biologists for decades, if not centuries, to come.

Here I would like to consider a follow up question: will current trends in evolutionary developmental biology (evo-devo) finally lead to the solution of the problems raised by West-Eberhard and others? I would like to put forward a controversial view. Although there has been spectacular progress in evo-devo, I believe that most of it will leave evolutionary theory relatively untouched. The problem is that most of current evo-devo, concentrates on what might be called pattern evo-devo (from an evolutionary perspective): the study of what the developmental mechanisms underlying a given trait are, and how these mechanisms have changed in evolution. This work has enriched our understanding of evolution immensely. However, I believe that an overhaul of evolutionary theory will require progress in the more difficult questions of process evo-devo: how do evolutionary forces, such as mutation, environmental change and natural selection, operate on developmental mechanisms, and, conversely, how does development interact with these forces to direct, bias and constrain phenotypic evolution? Many such questions have been well articulated by, among others, Gould, Arthur, Raff, West-Eberhard and the "developmental systems theorists", but progress in answering them has been slow. These questions are hard to tackle using present techniques of developmental genetics, molecular evolution and experimental evolution, but ultimately they will have to be faced if we want to usher in a "new and general theory of evolution", to borrow Gould's phrase.

On Wolfram and Dembski

2006-01-02T08:38:00.000-08:00

Jeffrey Shallit has written an interesting post in his new blog comparing Dembski and Wolfram in their "never retract, never explain, never apologize" approach to science. I've been meaning to say something about Wolfram's New Kind of Science (NKS) for a while. It is true that Wolfram, like Dembski, does have a very high opinion of himself. For example, while Dembski had someone compare him to Newton, Wolfram compares himself to Newton. This makes reading NKS (the main text) a much more irritating experience than it ought to be -- and no, I didn't find Wolfram's explanation for his Nietzschean "tone" convincing.

However, Wolfram is no Dembski, even when it comes to evolutionary biology: I believe Wolfram's work to be much more interesting and substantive. I have read most of NKS carefully, as well as many reviews of it (I quite like Weinberg's), and I have never seen any criticism that is nearly as damaging as, say, Shallit and Elsberry's critique of Dembski (see, for example, pp. 13-17). Although Wolfram is not as interested in biology as he is in computation, mathematics or physics, I still found what he had to say on complexity very interesting in the context of biological complexity and, therefore, don't agree with Shallit's conclusion that: "if he did use a more formal definition -- let's say Kolmogorov complexity -- then his claims become incoherent, trivial, or wrong." Also, Wolfram's work, unlike Dembski's, has stimulated a fair amount of research in several areas of science -- whether it will all turn out to be as "New" as Wolfram so passionately believes remains to be seen, but it should not be dismissed.

What I find most disturbing about Wolfram is his suggestion that just because some of the simplest programs imaginable can produce complexity, therefore it will be helpful to model complex systems using these simple programs even when there is no reason to believe that there is any correspondence between the mechanics of the models and that of the actual processes involved. As a biologist I have generally found this "model in search of a question" approach (common in other physical scientists, by the way) very unproductive. I also don't agree with some of Wolfram's ideas on evolution, but I think he got more flack on that from my colleagues than he deserved. I'm actually working on something which is relevant to this discussion, so I'll come back to it at some point.

Brave New Year

2006-01-01T18:31:00.000-08:00

Apologies for the long silence! Has it really been over two months? Oh well, I should say something about that. Initially I had to work on a paper, and that took all my time in between teaching. Eventually it got into Nature, so that was time well spent. I'll post about it when it comes out, probably sometime next month. Then my laptop had to be repaired, so I did not have a computer to blog from home and at work I had to actually, well, "work". Then, I kept waiting for a good opportunity to get back into it, and... here I am. I guess procrastination doesn't end in graduate school. Sadly I won't be able write much over the next couple of weeks because I have to work on a grant application (talk of procrastination).

There have been some interesting developments in the favorite topics of this blog. First, Science judged recent developments in Evolution to be the most important scientific breakthrough of the year. So maybe it wasn't such a bad idea to dedicate my scientific life to it... Maybe that will help in selling Evolutionary Biology to the next cohort of students. Second, Judge Jones ruled! In so doing he handed the first major legal defeat to Intelligent Design Creationism, one that should have far-reaching implications. I'm still reading the decision (that grant proposal again...) but I can already see that it's a thing of beauty. Hopefully it will help to keep creationism out of science classes in other places. Curiously, perhaps as a result of the Jones decision, Dembski, the Stephen Wolfram of Intelligent Design Creationism has decided to stop blogging. I suppose that means I should keep at it to even things out a little in the struggle against the army of the night.

I'll leave you with two reading suggestions. First, Neal Stephenson's Cryptonomicon, one of the best scientific novels I have ever read. If you have an interest in the history of computer science, cryptography and the Second World War, you should read it. It's great fun as well... Second, I've spent large chunks of the last few reading another great novel: the Shadow of the Wind by Carlos Ruiz Zafon. From the Borgesian opening I was hooked. Enjoy!

Tempo and Mode

2005-10-27T10:10:00.000-07:00

The original "Gould on the Beach" (see below) story has generated a fair amount of attention from evolutionary blogs (e.g. Panda's Thumb, Evolutionblog, Dispatches from the Culture Wars, Red State Rabble). Most of the posts have justly castigated the inanity of Pivar's and O'Leary's comments. Gould was certainly no friend of intelligent design creationism, and no amount of quote mining will make it so.

However, it does not automatically follow that Gould was "clear, consistent, and unambiguous" on the subject, as Jason Rosenhouse (and others) have suggested. At least his thinking was never that clear to me. I hate to admit it, but I think that Gould was indeed something of an "equivocator" as Dembski suggests (without noticing the irony of such a charge, apparently). Since others seem to be oblivious to this aspect of Gould's thinking, I should illustrate what I have in mind.

Here is Gould at the height of his powers, writing about saltation in his classic "Is a new and general theory of evolution emerging?" (Paleobiology 6, 119-30; 1980):

[...] the other alternative, treated with caution, reluctance, disdain or even fear by the modern synthesis, now deserves a rehearing in the light of renewed interest in development: perhaps, in many cases, the intermediates never existed. I do not refer to the saltational origin of entire new designs, complete in all their complex and integrated features -- a fantasy that would be truly anti-Darwinian in denying any creativity to selection and relegating it to the role of eliminating old models. Instead, I envisage a potential saltational origin for the essential features of key adaptations. [...] Yet Darwin, conflating gradualism with natural selection as he did so often, wrongly proclaimed that any such discontinuity, even for organs (much less taxa) would destroy his theory.

(Note how he directly contradicts the statement attributed to him by Pivar.) This is typical of Gould's writings of the time, where he tended to muddle the time scale over which to apply his punctuationism and Darwin's natura non facit saltum. In the end, we're left wondering over exactly what is being proposed that would require the emergence of a "new and general theory", if it isn't Goldschmidtian "hopeful monsterism" (I sense a new religion coming...).

In the same paper he also discussed whether macroevolution can be explained by extrapolating from microevolutionary processes, another of Gould's leitmotivs from that period:

But if species originate in geological instants and then do not alter in major ways, then evolutionary trends cannot represent a simple extrapolation of allelic substitution within a population. Trends must be the product of differential success among species. In other words, species themselves must be inputs, and trends the result of their differential origin and survival. Speciation interposes itself as an irreducible level between change in local populations and trends in geological time. Macroevolution is, as Stanley argues, decoupled from microevolution. [...]

As a final point about the extrapolation of methods for the study of events within populations, the cladogenetic basis of macroevolution virtually precludes any direct application of the primary apparatus for microevolutionary theory: classical population genetics. I believe that essentially all macroevolution is cladogenesis and its concatenated effects. What we call 'anagenesis' and often attempt to delineate as a separate phyletic process leading to 'progress,' is just accumulated cladogenesis filtered through the directing force of species selection [...]

(My emphasis. Bibliographic references removed.)

Not exactly an endorsement of natural selection's ability to shape macroevolution, is it?

Gould on the Beach...

2005-10-25T12:41:00.000-07:00

Now, there's an opera I wouldn't mind seeing! It could be written entirely with passages from his "Natural History" essays. It would have leitmotivs for "contingency" and "constraint", "Bauplan" and "Baseball"...

Andrea Bottaro, over at The Panda's Thumb, brings us a particularly bizarre example of second-hand Gould exegesis, bordering on channeling. A certain Stuart Pivar, ominously described as "a chemical engineer as well as an art collector", thinks of himself as something of an authority on Gould "because Gould used to spend time at his beach house"! Apparently Pivar believes that Gould would never have "signed the statement of the National Center for Science Education’s list of Steves" because:

His message was that natural selection was merely an eliminative force with no creative role, capable of choosing for survival among preexisting forms which are produced by other natural structural processes.

This is, of course, utter nonsense, as Andrea demonstrates in his post. He concludes that:

In other words, Gould saw structuralist principles, together with the role of contingency and developmental contraints, as applying on top of a solid Darwinian theoretical foundation, not to supplant natural selection as a major creative force in evolution, but to influence its outcome. This is a view consistent with the Steves' statement, and most certainly shared, with accommodations for varying emphasis on this or that aspect, by the vast majority of modern biologists.

For those who have read Gould's primary scientific works this is really nothing new, since - misunderstandings and histrionisms aside - his views on the matter did not change very much over time [...] his legacy as a scientist should be found in his own articles and books, not on the web site of some beach buddy, no matter how close.

Although I agree with the main points of Andrea's post, I would be more guarded in my evalutation of Gould's thinking. On this subject, Gould was often insightful and provocative, but was certainly not a model of clarity, as even a cursory inspection of his massive "Structure" will reveal. Although his "message" was emphatically not "that natural selection was merely an eliminative force with no creative role", he did show a longstanding ambivalence towards natural selection, and ostensibly attempted to demote it (subjugate it, even) relative to other forces, such as, contingency, constraints, or species selection.

Not only did Gould have a "penchant for staking debates in rather extreme terms, and sometimes caricaturing his opponents’ positions", as Andrea puts it, but he was often hard to pin-down on his positions. For example, in his writings on punctuated equilibrium he repeatedly equivocated on the time scale he had in mind when contrasting punctuationism and gradualism, to the frustration of his critics. As he well knew, "fast" does not mean the same thing in terms of generation or geological time. Gould would echo Goldschmidt's attacks on the modern synthesis, and would then be extremely vague on the nature of the putative novel genetic / evolutionary mechanisms that needed to be incorporated into evolutionary theory to account for punctuated equilibrium. Similar objections can be (and have been) raised to his writings on adaptationism and the Cambrian explosion. Critics of evolution have been quick to exploit these inconsistencies in Gould's thinking. For example, much of the nonsense spouted by creationists of all stripes on the distinction between micro and macroevolution can be traced directly to "misunderestimations" of Gould's primary articles.

Even if Gould did not usher in the emergence of "a new and general theory of evolution", as he would have liked (time will tell), I still think there's an opera in there somewhere. Maybe PhaWRONGula will take up the challenge...

The Other Prize

2005-10-09T14:40:00.000-07:00

After the prizes from Stockholm all scientists dream about, it's time for their light-hearted counterpart, the Ig Nobel Prizes. Sir Bob May (of "chaos" fame) will probably be even more upset this time given the enviable performance of scientists from both Australia and the UK.

One of my favorites is the Peace prize:

Claire Rind and Peter Simmons of Newcastle University, in the U.K., for electrically monitoring the activity of a brain cell in a locust while that locust was watching selected highlights from the movie "Star Wars." (Rind FC & Simmons PJ, 1992. Orthopteran DCMD Neuron: A Reevaluation of Responses to Moving Objects. I. Selective Responses to Approaching Objects. Journal of Neurophysiology 68, 1654-66.)

Good things...

2005-10-08T16:23:00.000-07:00

This made me laugh.

(OK, OK, the dolphins are off, but it's still pretty funny...)

The William Paley of Young Earth Creationism

2005-09-25T12:35:00.000-07:00

In recent years, William Dembski has risen in prominence within the intelligent design creationism movement. Dembski and his supporters have tried hard to persuade a largely oblivious scientific community that his work is nothing short of revolutionary. For example, six years ago the philosopher Robert Koons declared that "William Dembski is the Isaac Newton of information theory, [...] one of the most important thinkers of our time". So, is Dembski to information theory, what Newton was to physics and mathematics? Is he even what Newton's arch-enemy Leibniz was to algorithmic information theory? Are his ideas on the design inferrence, complex specified information, and the No Free Lunch theorems to Darwin's theory of natural selection, what Einstein's General Theory of Relativity was to Newton's theory of gravitation? Frankly, I doubt it.

One problem is that he has published almost no peer-reviewed, primary research papers, the standard way to contribute to the scientific process since... well, around Newton's time. A more serious problem is that the few substantive arguments he has advanced have been criticized repeatedly, and he has been inept in his responses (I say this as someone who is genuinely interested in some of the questions he raises) -- typically he will challenge the scientific credentials or the character of his critics, while avoiding or misrepresenting many of the serious questions they raise. (For example, see his exchange with Thomas Schneider.)

Dembski can also write some remarkably stupid (telling?) things. Pharyngula and Panda's Thumb have picked up a steady stream of these. Here's one I have just read in Philosophy of Biology on the relative merits of young earth creationism and evolutionary biology:

"[...] young earth creationism is at worst off by a few orders of magnitude in misestimating the age of the earth. On the other hand, Darwinism, in ascribing powers of intelligence to blind material forces, is off by infinite orders of magnitude."

This is particularly interesting coming from a mathematician!

Perhaps this was the aspect of Dembski's output that Koons had in mind when he drew the parallel with Newton -- he was thinking of Newton the alchemist or Biblical interpreter, not Newton the physicist or mathematician.

Waiting for Rita...

2005-09-23T12:32:00.000-07:00

I'm in downtown Houston waiting for the storm to hit. The winds have picked up a bit, although I don't think they are quite "tropical stormish" yet. The skies are also still disquietingly clear. Of course this will change over the next few hours. Our greatest fear is that our windows will not resist the winds or some flying debri.

The city is largely deserted, although we still managed to find open business. We didn't feel like sitting at home for two days, so we decided to out for lunch. My wife's parents arrived from Sweden on Tuesday... After driving for a while through downtown, midtown, West Gray, Riveroaks and Kirby, we found that most restaurants were closed -- I remember just one open greek restaurant early on. Just as we were beginning to think about going back home, we decided to try Rice Village. It was almost completely deserted, but one restaurant was open -- Prego. Not my favorite and a bit pricey for my taste, but yesterday it felt great!

Another island of sanity in these tense days has been SciGuy's blog, written by Eric Berger, a science writer for the Houston Chronicle. His posts have been one of the best news sources around, consistently informative, clear, succint, and not overly dramatic; a wonderful antidote to the hysterical drivel from local and cable news. No wonder so many people have decided to leave town... Thank you!

Talking of science blogs, if you want to take your mind off the Rita madness you should check out Carl Zimmer's latest posts: one on whale evolution, the other on science blogging. Now I think I'm going to turn to some evolutionary biology of my own, as I prepare to resubmit my latest manuscript. The clouds are getting darker.

Update: It's over now. It lasted some 12h but, as you know by now, Houston was lucky. It was hard to sleep because one of our windows thought it was in a bad horror movie and howled and whistled all night.

Extrapolation

2005-09-21T14:27:00.000-07:00

I don't like it.

At Sea

2005-09-05T12:41:00.000-07:00

If further evidence were needed that the federal government made a dog's breakfast of their response to Hurricane Katrina I could point to this item from yesterday's Chicago Tribune:

While federal and state emergency planners scramble to get more military relief to Gulf Coast communities stricken by Hurricane Katrina, a massive naval goodwill station has been cruising offshore, underused and waiting for a larger role in the effort.

The USS Bataan, a 844-foot ship designed to dispatch Marines in amphibious assaults, has helicopters, doctors, hospital beds, food and water. It also can make its own water, up to 100,000 gallons a day. And it just happened to be in the Gulf of Mexico when Katrina came roaring ashore.

The Bataan rode out the storm and then followed it toward shore, awaiting relief orders. Helicopter pilots flying from its deck were some of the first to begin plucking stranded New Orleans residents.

But now the Bataan's hospital facilities, including six operating rooms and beds for 600 patients, are empty. A good share of its 1,200 sailors could also go ashore to help with the relief effort, but they haven't been asked. The Bataan has been in the stricken region the longest of any military unit, but federal authorities have yet to fully utilize the ship.

Captain ready, waiting

"Could we do more?" said Capt. Nora Tyson, commander of the Bataan. "Sure. I've got sailors who could be on the beach plucking through garbage or distributing water and food and stuff. But I can't force myself on people.

"We're doing everything we can to contribute right now, and we're ready. If someone says you need to take on people, we're ready. If they say hospitals on the beach can't handle it ... if they need to send the overflow out here, we're ready. We've got lots of room."

My Bit

2005-09-04T12:51:00.000-07:00

Long before I became a scientist, I learned a more basic kind of skepticism from my mother. She would tell me to pay more attention to what people actually did than to what they said should be done. It's not enough to say you're a Christian, a Socialist or a Communist (common where I grew up), and to talk movingly about the suffering of the poor or the working class, if then you do little to help any actual people around you. On Friday, my wife reminded me of that lesson, when she told me that it was all very well to criticize George Bush or the federal government when we weren't actually doing anything to help the victims of Katrina.

So yesterday we took some clothes to the Salvation Army, and then spent the afternoon volunteering at the Houston Convention Center, where one of the large shelters for victims of Katrina was being set up. I spent my time in a long line of a hundred or so people passing bags of clothes from the entrance (where they were dropped off by a steady stream of locals driving by) into a huge pile inside the Center, where other volunteers sorted the clothes. I did this for over 4 hours stopping only to take a few quick gulps of water now and then. It was easy work, although I couldn't keep my eyes open by 9:30 last night (~3h early) and today I feel as if I played an unfamiliar sport for a long time. My wife spent her time playing a different kind of "sport": making beds.

The experience was humbling in many ways, and not just because there was nothing two scientists with PhDs were obviously "good for". The amount of donations was enormous. I believe that, at some point, people were told to stop dropping clothes off, because we were no longer able to process them. We were obviously an insignificant part of a huge operation that, despite much confusion, did manage to achieve something in the end.

United States of Wal-Mart

2005-09-04T11:36:00.000-07:00

It's hard not to say something trite at times like these. From the comfort of my living room, it's easy to talk about some people's suffering or another's incompetence. However, there's a general feeling that the federal government did much to aggravate this tragedy. Here's Aaron Broussard, president of Jefferson parish, Louisiana, talking to Tim Russert this morning in Meet the Press:

Broussard: We have been abandoned by our own country. Hurricane Katrina will go down in history as one of the worst storms ever to hit an American coast, but the aftermath of Hurricane Katrina will go down as one of the worst abandonments of Americans on American soil ever in U.S. history. I am personally asking our bipartisan congressional delegation here in Louisiana to immediately begin congressional hearings to find out just what happened here. [...]

It's not just Katrina that caused all these deaths in New Orleans here. Bureaucracy has committed murder here in the greater New Orleans area, and bureaucracy has to stand trial before Congress now. It's so obvious. [...] FEMA [Federal Emergency Management Agency] needs to be empowered to do the things it was created to do. It needs to come somewhere, like New Orleans, with all of its force immediately, without red tape, without bureaucracy, act immediately with common sense and leadership, and save lives. Forget about the property. We can rebuild the property. It's got to be able to come in and save lives. [...]

Russert: Shouldn't the mayor of New Orleans and the governor of New Orleans bear some responsibility? Couldn't they have been much more forceful, much more effective and much more organized in evacuating the area?

Broussard: Sir, they were told like me, every single day, "The cavalry's coming," on a federal level [...]. The cavalry's still not here yet, but I've begun to hear the hoofs, and we're almost a week out.

Let me give you just three quick examples. We had Wal-Mart deliver three trucks of water, trailer trucks of water. FEMA turned them back. They said we didn't need them. This was a week ago. FEMA--we had 1,000 gallons of diesel fuel on a Coast Guard vessel docked in my parish. The Coast Guard said, "Come get the fuel right away." When we got there with our trucks, they got a word. "FEMA says don't give you the fuel." [...] Sheriff Harry Lee said that if America--American government would have responded like Wal-Mart has responded, we wouldn't be in this crisis. [my emphasis]

[...] And I want to give you one last story and I'll shut up and let you tell me whatever you want to tell me. The guy who runs this building I'm in, emergency management, he's responsible for everything. His mother was trapped in St. Bernard nursing home and every day she called him and said, "Are you coming, son? Is somebody coming?" And he said, "Yeah, Mama, somebody's coming to get you. Somebody's coming to get you on Tuesday. Somebody's coming to get you on Wednesday. Somebody's coming to get you on Thursday. Somebody's coming to get you on Friday." And she drowned Friday night. She drowned Friday night.

Nobody's coming to get us. Nobody's coming to get us. The secretary [Chertoff] has promised. Everybody's promised. They've had press conferences. I'm sick of the press conferences. For God sakes, shut up and send us somebody.

He then broke down crying. The last few sentences are now being shown repeatedly in MSNBC. But before the emotion got the better of him, he put forward a persuasive, non-partisan argument for "good government". Although this sounds almost intuitive to a European like me, it obviously needs to be repeated here in the US. American politicians, Republican ones in particular, have spent decades decrying the evils of "big government". I don't know whether the government needs to be bigger, but I do know that it needs to be better. When it is easy to find $231 million to build a bridge for a small, uninhabited Alaskan island, but the $105 million requested by the Army Corps of Engineers for hurricane and flood programs in New Orleans last year had to be cut, then something is seriously wrong. Denying that problems exist, be they social or environmental, be they in the Gulf Coast or the Persian Gulf, or saying that "stuff happens", is not good enough.

A Whiff of the BS Model

2005-09-01T08:32:00.000-07:00

I thought it would be useful to compile a summary of the problems with the Behe & Snoke (2004) paper (BS). Note, however, that despite my criticisms I commend BS for their willingness to publish in a high-profile peer-reviewed journal (albeit one that does not often publish on molecular evolution). I wish other proponents of intelligent design creationism (ID) would do the same -- I'm thinking particularly of the mathematician thought by some to be "the Isaac Newton of information theory". (Curiously, this feeling is apparently shared by at least one proponent of ID.)

Here's the beginning of the list, largely based on and Musgrave, Reuland & Cartwright's review in Panda's Thumb (MRC) and the Lynch (2005) paper (L05):

"Darwinism" is tested using a non-Darwinian model.
"The flavor of BS’ paper may be gauged by the fact that the authors are skeptical of Darwinian processes to produce complex structures, yet use a model which largely ignores Darwinian processes." (MRC)
"Although the authors claim to be evaluating whether Darwinian processes are capable of yielding new multiresidue functions, the model that they present is non-Darwinian [...]. Contrary to the principles espoused by Darwin, that is, that evolution generally proceeds via functional intermediate states, BS consider a situation in which the intermediate steps to a new protein are neutral and involve nonfunctional products." (L05, p 2217)
The base population is constructed in a bizarre way. BS (pp 2651-2) assume:
"that newly duplicated genes encode a full-length protein with the signals necessary for its proper expression. It is further assumed that all duplicate genes are selectively neutral. [...] Any given organism in the population may be thought to have anywhere from zero to multiple extra copies of the gene; that is, duplicate copy number is considered to have no selective effect. However, the model presupposes that there are a total of N duplicate copies of the gene, equal to the number of organisms in the population".
This problem is corrected in L05's simulation (p 2218):
"the model presented here starts with a more realistic base population harboring a single locus in all individuals. A duplicate gene then arises in a single random member of the population [...]"
Note that the L05 approach is actually expected to increase the time to neo-functionalization, when compared to BS' approach. (See also points 4 and 5.)
Only one advantageous target sequence is considered possible. This is acknowledged in BS' discussion (p 2661, their emphasis):
"the simulation looks for the production of a particular MR [multi-residue] feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively."
However, they completely ignore this caveat, despite its large potential effect on the effective population size and fixation time estimates. L05 (p 2220) corrected this problem in their simulations by introducing a new parameter: "the number of potential contributory sites to the new function (n)".
The mutational advantage of duplication is ignored. L05 (p 2223) point out that BS:
"failed to realize that a completely linked pair of duplicate genes has a mutational advantage equal to the mutation rate to null alleles (µ), owing to the fact that both members of a linked pair must be inactivated before the viability of the carrier is affected".

This implies that, when the population size "N is moderately large (2Nµ>1), the fixation probability approaches 2µ" (L05). (See also point 2.)
Intermediate alleles are excluded from the base population. L05 (p 2222) note that BS:
"assume that the evolution of a multi-residue function requires the origin of a full set of mutations previously kept absent from the population [...]."

Since BS assume that "the intermediate steps toward the evolution of a selectable multi-residue function are entirely neutral [...]" intermediate alleles could be present in the population before duplication. This is allowed in L05's model. (See also point 2.)
The value of ρ used throughout is unrealistically high. BS define ρ as the ratio of the number of null mutations to mutations compatible with the novel function. They set the parameter to ρ=1000 in all their simulations and justify this choice by asserting that (pp 2652-3):
"The majority of nonneutral point mutations to the gene will yield a null allele (again, by which we mean a gene coding for a nonfunctional protein) because most mutations that alter the amino acid sequence of a protein effectively eliminate function (Reidhaar-Olson and Sauer 1988, 1990; Bowie and Sauer 1989; Lim and Sauer 1989; Bowie et al. 1990; Reidhaar-Olson and Sauer 1990; Rennell et al. 1991; Axe et al. 1996; Huang et al. 1996; Sauer et al. 1996; Suckow et al. 1996)."

This assumption is not supported by the studies cited by BS (see MRC, "Rho-Oh!" section and the L05 passage quoted in my earlier post). By their own admission, the value of ρ has a profound effect on the outcome of their model (p 2661):

"The model is more sensitive to the value of ρ [...]. If ρ were less by a factor of 10 (100 instead of 1000), then the population size needed to fix the feature in the preceding example in 10^8 generations would decrease from 10^22 to 10^16."

I'll continue to add to this list over the next few days. If you let me know of other issues, I'll add them to the list as well.

Update: Two more points have been added.

Update 2: One more point has been added.

BS Model Gets "Lynched"

2005-08-31T06:59:00.000-07:00

Protein Science has released their latest issue. It features Michael Lynch's answer to Behe & Snoke's (BS) 2004 paper, along with a response from BS themselves, and an editorial explaining what happened behind the scenes. Lynch's abstract is fairly clear:

A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multiresidue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

The main difference between the Lynch and BS models is over the issue of whether intermediate mutations on the way to a novel multi-residue feature of a protein are deleterious (BS) or neutral (Lynch). Here's what Lynch has to say about this problem:

[...] Behe and Snoke assume that all mutational changes contributing to the origin of a new multi-residue function must arise after the duplication process. They justify this assumption by stating that the majority of nonneutral point mutations to a gene yield a nonfunctional protein. To stretch this statement to imply that all amino acid changes lead to nonfunctionalization is a gross mischaracterization of one of the major conclusions from studies on protein biology—most protein-coding genes are tolerant of a broad spectrum of amino acid substitutions (Kimura 1983; Taverna and Goldstein 2002a,b). For example, in a large mutagenesis screen, Suckow et al. (1996) found that >44% of amino acid positions in the Lac repressor of Escherichia coli are tolerant of replacement substitutions. Axe et al. (1998) found that only 14% of amino acid sites in a bacterial ribonuclease are subject to inactivation by some replacement substitutions, with only one site being entirely nonsubstitutable. For human 3-methyladenine DNA glycosylase, ~66% of single amino acid substitutions retain function (Guo et al. 2004). Even for the highly conserved catalytic core regions of proteins, approximately one-third of amino acid sites can tolerate substitutions (Materon and Palzkill 2001; Guo et al. 2004). Many other studies (e.g., Kim et al. 1998; Akanuma et al. 2002), including all of those cited by Behe and Snoke, have obtained results of this nature. A deeper understanding of the fraction of amino-acid-altering mutations that have mild enough effects to permit persistence in a population comes from observations on within- and between-species variation in protein sequences (Li 1997; Keightley and Eyre-Walker 2000; Fay and Wu 2003), which generally indicate that 10% to 50% of replacement mutations are capable of being maintained within populations at moderate frequencies by selection-mutation balance and/or going to fixation. Because there is strong heterogeneity of substitution rates among amino acid sites (Yang 1996), these average constraint levels should not be generalized across all sites, many of which evolve at rates close to neutrality. Thus, most proteins in all organisms harbor tens to hundreds of amino acid sites available for evolutionary modification prior to gene duplication.

Here's BS' response:

Experimental studies contradict Lynch’s assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function.

Lynch’s and our models are not mutually exclusive. Some evolutionary pathways might involve both deleterious and neutral mutations.

Lynch writes in the section "The Model" that we "imply that all amino acid changes lead to nonfunctionalization." We imply no such thing. Although we assumed that intermediate mutations required for a new feature decreased function, we wrote, "it can be calculated that on average a given position will tolerate about six amino acid residues and still maintain function." Our estimation of explicitly takes into account the tolerance of sites for substitution.

In "The Model," Lynch writes, "As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein..." We made no such assumption. In our model, the final mutation might restore and enhance the original function.

Compare the argumentation. Lynch examines many lines of evidence (including a study by Axe, another advocate for intelligent design) and concludes, reasonably, that a large fraction of aminoacid substitutions are neutral. This means that BS' original model is fatally flawed. And how do BS respond? They merely assert that they are right, and quibble about definitions. A wonderful demonstration of faith-based science in action.

Lynch's paper includes many other valid criticisms of the BS model. Interestingly, some of the points raised by Musgrave, Reuland & Cartwright in their early review have not yet appeared in print -- I think they should still do it.

Irreducible Differences

2005-08-30T15:55:00.000-07:00

Michael Behe, one of the few credible research scientists to defend intelligent design creationism, has just been disowned by his own department at Lehigh University:

Department Position on Evolution and "Intelligent Design"

The faculty in the Department of Biological Sciences is committed to the highest standards of scientific integrity and academic function. This commitment carries with it unwavering support for academic freedom and the free exchange of ideas. It also demands the utmost respect for the scientific method, integrity in the conduct of research, and recognition that the validity of any scientific model comes only as a result of rational hypothesis testing, sound experimentation, and findings that can be replicated by others.

The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of “intelligent design.” While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

I particularly like the scare quotes. An "official disclaimer" also features prominently in Behe's own web page. To add insult to injury, his colleagues have also invited Ken Miller for a seminar.

I suspect that Behe's week is going to get even worse because Michael Lynch's paper is about to appear in Protein Science. I wonder if the events are related.

[Via Pharyngula and Red State Rabble]

Midwestern Sensibility

2005-08-29T18:22:00.000-07:00

I have to confess that I often watch The McLaughlin Group (TMG). I know it's vaguely masochistic of me, and my wife thinks I'm crazy, that I'm trying to spite her ("the shouting match" she calls it), but I find the loud, friendly banter strangely soothing at the end of the week. (Maybe it's because it reminds me of a radio program I used to listen to in Portugal -- Flashback, which later became the TV program A Quadratura do Círculo or Squaring the Circle.) However, last Friday, I was driven, for the first time, to turn off the TV in the middle of "Issue Two" (it was either that or throwing the thousand-odd page A New Kind of Science at the the lot of them).

The issue in question was ominously titled "Bible vs Biology" by John McLaughlin. His opening statement set the tone:

The debate between the Bible and biology is raging. Was man created full-blown by God, or did the human race develop from primates, as followers of Charles Darwin evolution theory say? Today's debate in America's public schools is a re-run. This summer marks the 80th anniversary of the 1925 Scopes "monkey trial," the historic legal battle in which a Tennessee court threw out Tennessee's law against the teaching of evolution.

Over the years, the United States Supreme Court has also ruled against teaching Bible-based creationism in public schools. What's different today is the "intelligent design" theory. Those who believe in intelligent design say public schools should also be able to teach that man is far too complex to have evolved from primates. Many scientists and educators scoff at the intelligent design theory as a leaner, meaner form of creationism.

Intelligent design supporters say that Americans are open to other ideas besides Darwinian evolution. And poll numbers back the intelligent designers. When asked, 54 percent say they don't believe that human beings did develop from an earlier species. And a whopping 64 percent in the same poll believe that, quote, "human beings were created directly by God," unquote.

Where to begin? "Intelligent design" is not a "theory". "Many scientists" doesn't even begin to do justice to the situation: "the vast majority of scientists" would be closer to the truth. And since when do scientific questions get settled by opinion poll? How many Americans even understand what evolution is?

McLaughlin then asked Eleanor Clift: "Question: Is evolution a scientific theory or a scientific fact?" The answer, of course, is that evolution is both a scientific fact and a scientific theory. The theories that populations of organisms change over time, that new groups successively split from earlier groups, and that all life on Earth has descended from a single common ancestor, are all as well supported as the theories that the Earth is approximately spheroidal and that it revolves around the Sun, and are, therefore, accepted as facts by the vast majority of scientists. The mechanisms of evolution, such as mutation, natural selection and genetic drift, although well established, are still widely referred to as theories. (As happens with other major scientific theories such as general relativity and plate tectonics.) Intelligent design creationism (ID), on the other hand, is neither a scientific fact nor a scientific theory. Therefore, ID should not be taught in schools.

Although Eleanor Clift did not say this, exactly, she did manage the only sensible intervention of the whole segment:

I believe there is enough scientific evidence to support evolution. And the fact that we have an American president challenging evolution and suggesting that intelligent design belongs on the curriculum along with science is absolutely absurd. Intelligent design is a nice religious theory, and that's where it belongs, in a religious class.

Spot on! McLaughlin and Tony Blankley then exchanged a few words of wisdom:

MCLAUGHLIN: Do you think we're descended from primates? Of course we are!
BLANKLEY: I've looked monkeys in the eye and I see a relative. (Laughter.)
MCLAUGHLIN: You know, those words may come back to haunt you.
BLANKLEY: They all do.
[...]
MCLAUGHLIN: You know, the problem with primates, that is an order, and in that line or order there are apes and monkeys and related simians. Does that make us a simian?
BLANKLEY: It makes us a hominoid.
MCLAUGHLIN: So we're all simians in the line, and arguably, if you believe that it is an order, then we are part of that species, are we not?

Now, it is hard to convey to a non-biologist just how painful this exchange is. The level of ignorance of basic science displayed by McLaughlin is so egregious, that if it were in the area of politics or foreign policy he would not invite himself to the show ever again. By this point I picked up the remote and started debating whether I should go to bed and read NKS. Then Blankley said this:

Let me make a point. A theory in science is a proposition supported by scientific evidence. I think Eleanor is right that evolution --

Wrong! Supporting evidence counts for very little. (Of course, this is particularly ironic given that there is no supporting evidence for ID whatsoever.) All kinds of pseudo-scientific ideas, from astrology to psychoanalysis, can marshal supporting evidence. The hallmark of science is testability or falsifiability. "A theory in science is a proposition" for which one could, in principle, find evidence that would disprove it. Evolution is a scientific proposition (for example, finding human fossils in the Cambrian would disprove it). ID is not. But it gets worse:

MCLAUGHLIN: Empirical evidence?
BLANKLEY: Scientifically measured evidence.
MCLAUGHLIN: That's empirical.
BLANKLEY: I believe that there is sufficient evidence to support aspects of evolution. Now --
MCLAUGHLIN: Is it overwhelming? Is it overwhelming?
BLANKLEY: Within a species, it is overwhelming. As between species, there are lacunas in scientific knowledge.
BUCHANAN: Exactly.

(Curiously, I'm beginning to find this amusing in writing. A bit like reading the scripts of a Monty Python's episode.) Yes, the evidence is empirical. Yes, it's overwhelming. And yes, it's for both evolution within and among species. Now Blankley decides that we have already heard enough about evolution:

BLANKLEY: The intelligent design people make two points. One, they say the theory doesn't explain itself sufficiently scientifically. That's a valid debate to have on the scientific basis.
BUCHANAN: John?
BLANKLEY: The second piece they argue is that the explanation is intelligent design. That's an attempt to do Thomas Aquinas's argument number five. And I think that is, in fact, theology.
BUCHANAN: John?

Actually, Blankley was not nearly as bad as I feared (maybe it's his British background...). However, he just let through the first bogus argument for ID! Even if there are "lacunas in scientific knowledge" in evolutionary biology -- and name an area of science where that isn't true -- it absolutely does not follow that the lacunas are to be filled by some mysterious "designer". How pathetic would that be?

Clarence Page, however, was much, much worse than I expected:

MCLAUGHLIN: Does intelligent design mean to you that Adam and Eve as described in Genesis are literally true and that full-blown human beings were brought into existence quickly without the passage of any serious time?  
PAGE: No. Intelligent design is not the same as creationism. You're describing creationism, and we should not use those two interchangeably. We fall into that danger, especially in the --   
MCLAUGHLIN: All right. What is intelligent design?  
PAGE: Intelligent design is really what we were taught when I was growing up in southern Ohio -- maybe it's in our Midwestern sensibility -- but that is that there is evidence to support evolution, as Tony  said. There are also questions about whether or not intelligence may have been involved at some stage in this --  
MCLAUGHLIN: Well, why --   
PAGE: -- whether it explains everything, as what you described --  
BUCHANAN: John, let me get in on this.  
PAGE: -- or whether it merely describes, say, you know -- to go back to "Star Wars," "May the Force be with you," that there's some intelligence out there that got it all started.  
MCLAUGHLIN: Why -- are we not really in semantics, rather than we are in concept? (Cross talk.)  
PAGE: Hopefully not in semantics, John. (Cross talk.)  
MCLAUGHLIN: You can concurrently have intelligent design managing evolution. Correct?

Halfway through this I went to bed. Perhaps PZ Myers can explain what the Midwestern sensibility has to do with any of this. It went even further downhill from here. As you can see at this point Pat Buchanan was dying to get in. No prizes for guessing what he wanted to say:

There is no -- you're exactly right. Does the universe manifest intelligent design? Of course it does. It works like a clock.   And to dispute Tony here, Aquinas was not talking theology there. He was talking natural law and reason.  

From then on they interrupted each other a lot, Buchanan repeated "It's reason!" a few times (where is Pirate Mode when you need it?), Clift squeezed in another sensible comment, and Page concluded with:

PAGE: I believe the president said there ought to be room for discussion of it, which sounds pretty benign. Maybe it was pandering. Maybe it was a sincere expression of his belief. But -- I'm not opposed  to discussion, but if you say that "Hey, this is definitely true, and you've got to believe this," then I'm opposed to that.  
MCLAUGHLIN: Right.  Intelligent design, as described by the host of this program a few precious minutes ago --  
PAGE: Yes, sir. (Chuckles.)  
MCLAUGHLIN: -- if he meant that, he's perfectly okay.  

Again, I have no idea what any of this means. They talked and talked and didn't even address the substance of the president's comments.

As usual with these exchanges, I don't know whether to laugh or cry. Here I lean towards the latter. After all, these are supposed to be this nation's intellectuals, and yet they are scientifically illiterate. Could you imagine sports commentators being so ignorant about their subject?

Update: What did I say about sports commentators? For more idiocy from the media, we have Larry King, Deepak Chopra, the LA Times, ... And it's not only in America: there's also Bryan Appleyard in The Sunday Times (London). Help!

Don't Show Me the Money

2005-08-28T18:13:00.000-07:00

"Show Me the Science", demands the philosopher (and honorary evolutionary biologist) Daniel Dennett from intelligent design creationism (ID) in today's New York Times. He's right.

Dennett reminds us of how genuine scientific controversies play out:

In just about every field there are challenges to one established theory or another. The legitimate way to stir up such a storm is to come up with an alternative theory that makes a prediction that is crisply denied by the reigning theory - but that turns out to be true, or that explains something that has been baffling defenders of the status quo, or that unifies two distant theories at the cost of some element of the currently accepted view.

But ID doesn't play by the rules:

To date, the proponents of intelligent design have not produced anything like that. No experiments with results that challenge any mainstream biological understanding. No observations from the fossil record or genomics or biogeography or comparative anatomy that undermine standard evolutionary thinking.

Instead, the proponents of intelligent design use a ploy that works something like this. First you misuse or misdescribe some scientist's work. Then you get an angry rebuttal. Then, instead of dealing forthrightly with the charges leveled, you cite the rebuttal as evidence that there is a "controversy" to teach. [...]

In short, no science. Indeed, no intelligent design hypothesis has even been ventured as a rival explanation of any biological phenomenon. This might seem surprising to people who think that intelligent design competes directly with the hypothesis of non-intelligent design by natural selection. But saying, as intelligent design proponents do, "You haven't explained everything yet," is not a competing hypothesis. Evolutionary biology certainly hasn't explained everything that perplexes biologists. But intelligent design hasn't yet tried to explain anything. [...]

For now, though, the theory they are promoting is exactly what George Gilder, a long-time affiliate of the Discovery Institute, has said it is: "Intelligent design itself does not have any content."

Exactly.

A Meeting of Minds

2005-08-28T09:23:00.000-07:00

Sean Nee, in his obituary of the great evolutionary theorist (and I mean theorist) John Maynard Smith (Trends in Ecology and Evolution 19: 345-6, 2004), retells his "favorite JMS story":

One day, Haldane brought a visitor to JMS’ lab and asked him to explain to the visitor the aerodynamic problem he was working on. JMS began going through the equations on the blackboard when the visitor’s hand reached out, grabbed some chalk and started correcting the equations. JMS asked, ‘Sorry, I did not quite catch your name?’. The visitor answered, ‘Alan Turing’.

Positive Discrimination

2005-08-24T06:13:00.000-07:00

Pharyngula has been hosting a discussion (also here) on the New York Times series on intelligent design creationism (ID). Many of the arguments have already been aired. Let me just say that I maintain my opinion that Kenneth Chang's piece was terrible, even though I understand his arguments. Just because the piece wasn't written for me, doesn't mean I can't criticize it for its unfair balancing of positions. As poke commented in that discussion, the problem is that the piece treats the "debate" as if it was occurring within science.

To illustrate this, let's analyse the list of scientists featured in the article on each side. How influential are they really? One way to judge is to look at how many papers they've written and how many times these papers have been cited. Here's the data from ISI Web of Science since 1988. Note that this includes all kinds of papers, not just ones on evolution.

In the case of the IDers we have:

Axe: 8 papers, 169 citations
Behe: 33 papers, 317 citations
Dembski: 5 papers, 4 citations
Meyer: 3 papers, 4 citations

(Have you noticed how they are always referred to as "theorists"? I wonder why that is?)

On the evolution corner, we have:

Bottjer: 62 papers, 791 citations
Doolittle: 110 papers, 4719 citations
Erwin: 58 papers, 989 citations
Lenski: 115 papers, 4314 citations
Miller: 18 papers, 388 citations

As for Darwin and Paley, here's a simple comparison of their stature in modern science. Paley's Natural Theology has been cited 141 times since 1988. Darwin's Origin alone (in either the 1859 or 1872 editions), has been cited 2632 times.

I believe the NYT should do better when they report on a disagreement between Behe and Doolittle or Lenski, or between Meyer and Erwin or Bottjer. Equal time just doesn't cut it.

The Doubters

2005-08-23T05:52:00.000-07:00

Yesterday, the New York Times released the second installment in their series on the so-called "evolution debate". Unfortunately it was terrible (for example, see Cosmic Variance, Pharyngula and The Light of Reason). Evolutionary biologists were called "Darwinists", which is bad enough. To make matters worse intelligent design (ID) creationists were referred to as "doubters". Does this mean that they have finally embraced the Royal Society's motto "Nullius in Verba" ("On the words of no one") and become real scientists? No, not really. Apparently, evolution is the only thing they doubt. The piece is filled with the "doubts" of Behe, Meyer and Axe: the same discredited claims about the clotting cascade, the Cambrian explosion, the evolution of antibiotic resistance... The NYT should be ashamed.

The end is interesting, as Mike the Mad Biologist has pointed out:

Dr. Behe, however, said he might find it compelling if scientists were to observe evolutionary leaps in the laboratory. He pointed to an experiment by Richard E. Lenski, a professor of microbial ecology at Michigan State University, who has been observing the evolution of E. coli bacteria for more than 15 years. "If anything cool came out of that," Dr. Behe said, "that would be one way to convince me."

Dr. Behe said that if he was correct, then the E. coli in Dr. Lenski's lab would evolve in small ways but never change in such a way that the bacteria would develop entirely new abilities.

In fact, such an ability seems to have developed. Dr. Lenski said his experiment was not intended to explore this aspect of evolution, but nonetheless, "We have recently discovered a pretty dramatic exception, one where a new and surprising function has evolved," he said.

Dr. Lenski declined to give any details until the research is published. But, he said, "If anyone is resting his or her faith in God on the outcome that our experiment will not produce some major biological innovation, then I humbly suggest they should rethink the distinction between science and religion."

Dr. Behe said, "I'll wait and see."

No prizes for guessing who will come out on top. But that hasn't stopped Behe in the past. I'm confident that he'll continue giving interviews on his pathetic "doubts" for years to come.

The Institutional Love Child of Ayn Rand and Jerry Falwell

2005-08-21T08:55:00.000-07:00

The New York Times has published a piece about the Discovery Institute (DI), the "think" tank behind most intelligent design creationism (ID) "related activities". There are some instructive passages, apart from the one that made it to the title of this entry -- which invokes an image my brain didn't really need. For example, Thomas H. McCallie III, executive director of the MacLellan Foundation, a major funder of DI, reveals that they "give for religious purposes", and adds: "this is not about science, and Darwin wasn't about science. Darwin was about a metaphysical view of the world." He obviously knows very little about Darwin, but at least he's being honest. Now we know where we stand, don't we? I was also interested to find another reason to dislike Bill Gates: apparently, not only is he behind some terrible software, but he also gives about $1,000,000 a year to DI.

But there is more:

Since its founding in 1996, the science center has spent 39 percent of its $9.3 million on research, Dr. Meyer said, underwriting books or papers, or often just paying universities to release professors from some teaching responsibilities so that they can ponder intelligent design. Over those nine years, $792,585 financed laboratory or field research in biology, paleontology or biophysics, while $93,828 helped graduate students in paleontology, linguistics, history and philosophy.

Carl Zimmer was quick to point out that this is surprising given that:

A search for "Intelligent Design" on PubMed yields 22 results--none of which were published by anyone from the Discovery Institute. There are a few articles about the political controversy about teaching it in public schools, and some papers about constructing databases of proteins in a smart way. But nothing that actually uses intelligent design to reveal something new about nature.

Is that all? A similar search using a more comprehensive database, the Institute for Scientific Information's (ISI) Web of Science, did reveal 227 hits for the expression "intelligent design". Alas, most of these are not about what the DI means by ID. Here are a couple of examples:

Strom G (2004) The lack of intelligent design in mobile phones. Lecture Notes in Computer Science 3160: 512-516.
Jacob E, et al. (2004) Intelligent design of feeders for castings by augmenting CAD with genetic algorithms. Journal of Intelligent Manufacturing 15: 299-305 .

Most of the hits on ID, are actually not primary research papers in scientific journals, but reviews, letters or news pieces, many in Theology, Philosophy or Law journals. The ISI reveals that the most prominent "scientists" in the ID movement have published remarkably little primary research in peer-reviewed, science journals in the last 10 years. For example, William Dembski (touted as "the Isaac Newton of information theory") has not published a single peer-reviewed scientific paper over that period.

This is confirmed by the DI's own website. Under the category "Articles Supportive of Intelligent Design Published in Peer-Reviewed Scientific Journals" we find 7 articles:

Meyer SC, “The Origin of Biological Information and the Higher Taxonomic Categories,” Proceedings of the Biological Society of Washington, 117 (2004): 213-239.
Behe MJ and DW Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, 13 (2004): 2651-2664.
Lönnig WE & H Saedler, “Chromosome Rearrangements and Transposable Elements,” Annual Review of Genetics, 36 (2002): 389-410.
Chiu DKY & TH Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4 (2002): 766-775.
Denton MJ & JC Marshall, “The Laws of Form Revisited,” Nature, 410 (2001): 417.
Denton MJ, JC Marshall & M Legge, (2002) “The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology 219 (2002): 325-342.
Mims SA & FM Mims III, “Fungal spores are transported long distances in smoke from biomass fires,” Atmospheric Environment 38 (2004): 651-655.

Of the above papers, the first was more of a review and was later retracted by the journal, the third is a review article, and the fifth is an opinion piece. That leaves 4 research papers, although I'm not familiar with all of them. The ISI actually lists another paper by Denton, on a topic similar to that of paper #6:

Denton MJ, PK Dearden & SJ Sowerby, “Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law,” Biosystems 71 (2003): 297-303.

So let's just say that ID has produced approximately 5 peer-reviewed, primary scientific papers in the last 10 years, after spending $3,600,000 on "research". I wonder how the conservative politicians that keep complaining about federal spending on scientific research would feel about that level of productivity. That much money is equivalent to what the National Science Foundation might give to about 8 biology research laboratories over 3 years. Suffice it to say that if the output, over 3 years, of only one of those 8 hypothetical labs was similar to that of the entire DI over 9 years, it would probably never get federal funding again.

Of the above papers, Behe & Snoke's is, arguably, the most substantive. Interestingly, it does not contain any of the following words, or their close relatives: intelligent, design, or creation. Carl Zimmer notes that Behe & Snoke's paper has never been cited, and concludes that, therefore, it cannot be very "influential". I believe that this judgement is premature given that the paper has been out for less that a year, and citations typically take a while to get going. First scientists need to "discover" the paper: for example, I only found out about it a few weeks ago, partly because Behe & Snoke chose to publish it in a specialist protein biochemistry journal (albeit a respectable one), and not in one more appropriate to its subject matter (e.g., Molecular Biology and Evolution, Evolution, or Genetics). I also feel that to compare its reception to that of the paper announcing the completion of the human genome project was unfair. A more appropriate comparison would be to a theoretical, evolutionary biology paper:

Force A, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545. [pdf]

This paper, which proposed a new mechanism for the preservation of duplicate genes, has been cited 532 times in 55 different journals, a powerful illustration of the impact of good evolutionary biology on the rest of science.

We should remember that criticisms of a paper show up as citations as well, so a paper may be influential for the wrong reasons. I suspect that this will be the fate of Behe & Snoke's paper. Musgrave, Reuland and Cartwright were quick to point out some of the paper's major deficiencies, and I would be surprised if they don't publish a version of their critique in the future. I know that other researchers are working on independent responses.

All this is should not discourage the DI from its mission. I sincerely hope that DI spend more money on primary research in the future.

Update: For other analyses of this piece see Cosmic Variance, The Light of Reason, Pharyngula and stranger fruit.

What's in a Theory?

2005-08-13T10:33:00.000-07:00

Red State Rabble has an interesting post on the relative "theoryness" of Evolution and Intelligent Design. (See Coyne's excellent piece in The New Republic for a more detailed discussion of the same problem.) Hayes hit the nail on the head with his analysis of why Darwin, and not Empedocles or your favorite proto-evolutionist, is given the lion's share of the credit for discovering evolution:

There were others, many others, who observed the fact of evolution and wrote about it, as well.

Why then, does Darwin get all the credit?

The answer is really quite simple. The name of Charles Darwin and the theory of evolution, which he called descent with modification, will always be inextricably linked because he explained how evolution works.

A similar phenomenon occurred in Geology. Alfred Wegener proposed continental drift (CD) a good 50 years before it gained widespread acceptance within the scientific community. It took the development of the theory of plate tectonics in the late 1960s, which provided a plausible mechanism for CD, for geologists to accept it. In fact, CD had long provided a better explanation for some of the data, such as patterns in biogeography, and the shapes of the continents had CD written all over them, but that wasn't enough. Similarly, Lamarck's reasonable arguments failed to persuade the majority of the naturalists of his time that evolution had happened. However, in both cases, the scientific consensus changed almost overnight. Huxley famously remarked upon reading "On the Origin of Species": "how stupid of me not to have thought of that." That feeling has recurred ever since.

Naturally, some proponents of ID would like to think that ID is the new CD. (Orac has noted that this is a line of argument favored by various pseudo-scientists and cranks -- he calls it the Galileo Gambit and he Knows...) That is pure wishful thinking on their part. As I said, there was plenty of evidence in favor of CD before it was adopted. In contrast, as Coyne points out:

Insofar as intelligent-design theory can be tested scientifically, it has been falsified. Organisms simply do not look as if they had been intelligently designed. Would an intelligent designer create millions of species and then make them go extinct, only to replace them with other species, repeating this process over and over again? Would an intelligent designer produce animals having a mixture of mammalian and reptilian traits, at exactly the time when reptiles are thought to have been evolving into mammals? Why did the designer give tiny, non-functional wings to kiwi birds? Or useless eyes to cave animals? Or a transitory coat of hair to a human fetus? Or an appendix, an injurious organ that just happens to resemble a vestigial version of a digestive pouch in related organisms? Why would the designer give us a pathway for making vitamin C, but then destroy it by disabling one of its enzymes? Why didn't the intelligent designer stock oceanic islands with reptiles, mammals, amphibians, and freshwater fish, despite the suitability of such islands for these species? And why would he make the flora and fauna on those islands resemble that of the nearest mainland, even when the environments are very different? Why, about a million years ago, would the designer produce creatures that have an apelike cranium perched atop a humanlike skeleton? And why would he then successively replace these creatures with others having an ever-closer resemblance to modern humans?

There are only two answers to these questions: either life resulted not from intelligent design, but from evolution; or the intelligent designer is a cosmic prankster who designed everything to make it look as though it had evolved. Few people, religious or otherwise, will find the second alternative palatable. It is the modern version of the old argument that God put fossils in the rocks to test our faith. [...]

Herbert Spencer could have been describing ID when he declared that "those who cavalierly reject the Theory of Evolution as not being adequately supported by facts, seem to forget that their own theory is supported by no facts at all. Like the majority of men who are born to a given belief, they demand the most rigorous proof of any adverse belief, but assume that their own needs none."

ID has to come up with some evidence and testable predictions. Until it manages to do so, it cannot be considered a scientific theory at all.

Distributed Intelligent Design?

2005-08-12T08:01:00.000-07:00

As I've said before, Intelligent Design (ID) is not a scientific theory. Interestingly, this view is shared by President Bush's scientific advisor, John Marburger. However, despite such enlightened advice, the President recently told reporters that "both sides ought to be properly taught, so people can understand what the debate is about". It would seem that Bush doesn't talk often enough to his advisor; or maybe he doesn't really listen. (Red State Rabble has an interesting analysis of the hypocrisy of Bush's statement when applied to other debates.)

So why do scientists remain unconvinced? Perhaps it's because ID is just the old argument from design warmed up, and this argument was demolished nearly 150 years ago with the publication of Darwin's "On the Origin of Species". Scientists don't particularly enjoy flogging a dead horse.

Alas, flog it we must until we succeed in removing its rotten corpse from science classrooms everywhere. (See, for example, what's going on in Kansas and Pennsylvania.) Today I won't bother to come up with any new arguments, but will, instead, attack ID by reheating another old argument -- indeed, I think there is a certain poetic justice to it. To do so, I turn to JBS Haldane's classic essay "The Argument from Design", written in 1944. I was recently introduced to it by my colleague Dan Graur, who is a great fan of JBS'. (And not just scientifically, as you might expect from a population geneticist. They also share a peculiar sense of humor -- you can get an idea of what this means by reading JBS' bizarre ode to rectal carcinoma).

In his essay, Haldane develops an argument that I haven't come across recently. He begins by conceding that we should consider arguments from design:

The chemical organisation of a cell is immensely complicated, and it is hard to see how an organism could work at all unless it were of extreme chemical complexity. I think, therefore, that a reasonable man should be prepared to examine arguments which assume a measure of design in living creatures, even though I do not personally think that they are cogent.

(Remarkably prescient of ID arguments, wouldn't you say?)

Next, he summarizes the argument from design, in the form of Paley's famous analogy:

Paley imagined an intelligent savage picking up a watch and concluding that it had been designed. He then argued that animals show far more evidence of design than watches. And he next argued that the designer had many of the characteristics of the God whom he worshipped.

JBS then points out a major weakness in the argument:

Now the most conspicuous features of animal organisation are those which are designed (if they are designed) for competition with other living creatures, and often for their destruction. All animals live by eating other animals or plants. They may kill them [...] or merely eat parts of them [...] The plants generally compete by pushing, rather than biting. [...] Though only a few higher plants [...] actually eat other living things, they are all engaged in a merciless struggle for life.

Of course biologists have devoted much of their time to the internal co-ordination of organisms. If this is attributed to a designer it shows very great ingenuity and no malice. However, a tank resembles a motor-car or a tractor in many of its features, buts its essential function is to carry a gun for the purpose of destruction. And when we consider animals, not in terms of the relations of their parts but of their relations to other animals, the same is true of them.

If, then, animals were designed, they were designed for mutual destruction. If there was one designer, he is or was a being with a passion for slaughter, like that of the ancient Romans, and the world is his Colosseum. A much more reasonable consequence of the hypothesis of design is Polytheism. If each one of the million or so animal species were the product of a different god, their mutual struggle would be intelligible. [...]

Wherever Paley's argument leads, it does not lead to Christianity. If pushed to its logical conclusion it forces us to believe in a malignant creator or, more probably, in a number of malignant creators. Certainly this creator or these creators are not wholly malignant. The world of life contains a great deal of beauty and pleasure, but one can admire the beauty only by closing one's consciousness to the pain and injustice which are bound up with it.

So the next time you hear a proponent of ID harping on about the "intelligent designer" (guess who they mean?), you should reply: "surely you mean designers!"

Murky Waters

2005-08-10T09:06:00.000-07:00

In 1996, John Paul II surprised the world when he declared that evolution was "more than just a hypothesis" and that (I'm paraphrasing here) Catholics just had to deal with it. Given that it took the Catholic Church 400 years to offer a grudging apology for burning Giordano Bruno at the stake (for good measure, they also nailed Bruno's tongue to his jaw to prevent him from speaking), evolutionary biologists had no choice but to be pleasantly surprised.

However, about a month ago, Cardinal Schönborn of Vienna announced that things were about to change. In an Op-Ed piece for the New York Times titled "Finding Design in Nature", Cardinal Schönborn concluded that:

Now at the beginning of the 21st century, faced with scientific claims like neo-Darwinism and the multiverse hypothesis in cosmology invented to avoid the overwhelming evidence for purpose and design found in modern science, the Catholic Church will again defend human reason by proclaiming that the immanent design evident in nature is real. Scientific theories that try to explain away the appearance of design as the result of "chance and necessity" are not scientific at all, but, as John Paul put it, an abdication of human intelligence.

Despite being unmitigatingly stupid and unoriginal, the article is significant given that Cardinal Schönborn was a student of the Pope formerly known as Cardinal Ratzinger. So is the Catholic Church really joining forces with its North American Evangelical brethren to fight "materialistic" science in all its splendour? Not so fast. Apparently, not everyone in the Church shares Schönborn's views. George Coyne, the Director of the Vatican Observatory and a distinguished astronomer, counter-attacked this week in the British Catholic newspaper The Tablet.

I found much to agree with in Coyne's essay:

There appears to exist a nagging fear in the Church that a universe [...] evolved through a process of random genetic mutations and natural selection, escapes God's dominion. That fear is groundless. Science is completely neutral with respect to philosophical or theological implications that may be drawn from its conclusions. Those conclusions are always subject to improvement. That is why science is such an interesting adventure and scientists curiously interesting creatures. But for someone to deny the best of today's science on religious grounds is to live in that groundless fear just mentioned.

He goes on to outline his view of how the universe evolves and concludes that "there are marvelous opportunities to renew one's faith in God's relationship to his creation". Coyne then tries to redefine creationism along more Augustinian / Aquinian lines. If he got rid of the God bit, then we would be in almost complete agreement.

[Via What's New]

Commanding the Army of the Night

2005-08-02T07:31:00.000-07:00

This will come as no surprise to those following the issue, but it is still an important event. Yesterday, Bush decided to weigh in on the problem of whether "Intelligent Design" (ID) should be taught in U.S. public schools. His answer was that 'schools should teach both theories on the creation and complexity of life'. Displaying his usual mastery of doublespeak, Bush then 'declined to state his personal views on ID'. This way Bush narrowly avoided joining other world leaders, like Joseph Stalin and Pope Benedict XVI, in their rejection of evolution and natural selection.

I could point out many problems with Bush's statements, not least that ID is no scientific theory. But I prefer to illustrate just how tiring this debate is by repeating the words of another scientist, writing over 20 years ago:

To those who are trained in science, creationism seems like a bad dream, a sudden reliving of a nightmare, a renewed march of an army of the night risen to challenge free thought and enlightenment (Isaac Asimov, 1981)

Asimov was writing about a similar debate over the predecessor of ID, called "scientific creationism" by people who knew nothing about science. However, the parallels are all too clear:

The creationist leaders [...] have to borrow the clothing of science, no matter how badly it fits [...]. We cannot, however, take this sheep's clothing seriously. However, much [they] might hammer away at their "scientific" and "philosophical" points, they would be helpless and a laughing stock if that were all they had.

It is religion that recruits their squadrons. Tens of millions of Americans, who neither know nor understand the actual arguments for - or even against - evolution, march in the army of the night with their Bibles held high. And they are a strong and frightening force, impervious to, and immunized against, the feeble lance of mere reason.

It would seem that we evolutionary biologists are locked in a kind of Red Queen effect: "it takes all the running" we "can do to keep in the same place".

Update: For more critical posts on this see Pharyngula.

The Designs of Nature

2005-05-18T07:52:00.000-07:00

Three weeks ago today, Nature devoted some attention to intelligent design. The results were mixed, to say the least. A clever cover and a sensible editorial were offset by an outrageous News Feature. As usual, Pharyngula was quick to point out two egregious problems with the piece. First, it is largely devoted to Salvador Cordova. I'm not one to only argue from authority, but this is too much. Who is this "scientist" exactly? Has he ever published a scientific paper in a peer-reviewed journal? Apparently not, according to the ISI and PubMed databases. If Nature thinks his work is so great, why don't they publish one of his papers? Second, the article talks of the efforts of poor, well-meaning "intelligent design supporters" to get a fair hearing at University campuses. Apparently they are being persecuted by evil, intolerant "Darwinists". This is all very telling because "Darwinist" is a term that, at present, you are most likely to hear from creationists and their compagnons de route. (Not that I have any problem with the term itself. I happen to think that Darwin's contributions to biology are among the greatest scientific achievements of all time, and would be honored to be considered among one of his intellectual descendants. It's just that the word is not one commonly used by evolutionary biologists.) Naturally, the intelligent design supporters were delighted with the article.

What I found to be most disappointing was that in four pages (rather long for a News Feature) there was essentially no discussion of the evidence for or against evolution (or intelligent design for that matter). Are we supposed to accept that intelligent design should be taught in Universities because it makes some students feel better? And this from Nature!

This week's issue features some counter-attacks from the forces of reason. Dan Graur, my next-door neighbor here at the University, managed to get some delightfully scathing remarks past the editors. Sarcasm may be the lowest form of wit, but the nonsense of intelligent design deserves no more.

Update: I agree with everything this distinguished panel of "Darwinists" (which includes my PhD supervisor) wrote.

Defending Evolution

2005-05-17T05:27:00.000-07:00

Apologies for not posting in over a week, despite such interesting developments as the Kansas show trials. In fact, I was defending evolutionary biology in other ways: from the students in my class. The final, it turned out, was very tough. But now it's all over so I have the time to write again.

This weekend I bought a copy of a book called Science and Creationism, a collection of essays edited by Ashley Montague and published in 1984 (a nice Orwellian coincidence), two years after the trial which reversed Arkansas' decision to give equal time to evolution and "creation science" in the state's classrooms. The book contains some excellent essays by the likes of SJ Gould, Isaac Asimov, Gunter Stent and Sidney Fox. However, it makes for depressing reading because it shows that the debate has not progressed in over 20 years. Sure, Dembski and Behe are marginally more sophisticated (emphasis on sophistic) than Gish, Whitcomb and Morris, but that is no consolation. To borrow the World Wide Rant's beautiful turn of phrase, the trials have been like concentrated stupid people. To see that I'm not exagerating, check out the posts from last week here and here (avoid CNN at all costs). Here's what Gould had to say back then (he's alluding to the Scopes trial of 1925):

When I think that we are enmeshed again in the same struggle for one of the best documented, most compelling and exciting concepts in all of science, I don't know whether to laugh or cry.

I couldn't agree more.

As another antidote to the stupidity and lies peddled by creationists, I recommend PZ Myers' wonderful essay about the Niobrara Chalk, the famous Kansas geological formation.

Dawkins, God's Epidemiologist

2005-05-01T21:53:00.000-07:00

Richard Dawkins has just given a long interview to Salon where he discusses his recent book "The Ancestor's Tale" and gives a taste for his forthcoming "The God Delusion". As usual it is a pleasure to read. Here are a few juicy bits:

You won't find any opposition to the idea of evolution among sophisticated, educated theologians. It comes from an exceedingly retarded, primitive version of religion, which unfortunately is at present undergoing an epidemic in the United States. Not in Europe, not in Britain, but in the United States. [...]

A delusion is something that people believe in despite a total lack of evidence. Religion is scarcely distinguishable from childhood delusions like the "imaginary friend" and the bogeyman under the bed. Unfortunately, the God delusion possesses adults, and not just a minority of unfortunates in an asylum. [...]

A delusion that encourages belief where there is no evidence is asking for trouble. Disagreements between incompatible beliefs cannot be settled by reasoned argument because reasoned argument is drummed out of those trained in religion from the cradle. Instead, disagreements are settled by other means which, in extreme cases, inevitably become violent. Scientists disagree among themselves but they never fight over their disagreements. They argue about evidence or go out and seek new evidence. Much the same is true of philosophers, historians and literary critics. [...]

[How would we be better off without religion?] We'd all be freed to concentrate on the only life we are ever going to have. We'd be free to exult in the privilege -- the remarkable good fortune -- that each one of us enjoys through having been being born. An astronomically overwhelming majority of the people who could be born never will be. You are one of the tiny minority whose number came up. Be thankful that you have a life, and forsake your vain and presumptuous desire for a second one. The world would be a better place if we all had this positive attitude to life. It would also be a better place if morality was all about doing good to others and refraining from hurting them, rather than religion's morbid obsession with private sin and the evils of sexual enjoyment.

Apart from being the creationist movement's public enemy #1, Dawkins also has the dubious distinction of being largely responsible for my having dedicated my professional career to evolutionary biology. For some of my generation it was David Attenborough's "Life on Earth" documentary; Dawkins' "The Selfish Gene" (immediately followed by "The Blind Watchmaker") did it for me. The following year I began studying Biology at the University of Lisbon.

Hey, I'm half as Republican as PZ Myers!

2005-05-01T08:39:00.000-07:00

I am:
1%
Republican.

"You're a complete liberal, utterly without a trace of Republicanism. Your strength is as the strength of ten because your heart is pure. (You hope.)"

Are You A Republican?

The 1% must be the Lincoln part. PZ Myers, on the other hand, is a lot more Republican than I am and he doesn't like it one bit. There's a serious point here, though -- I mean besides the "how to lie with statistics" one -- American politics is insane! In Europe I would be considered center-right or center-left on a range of political issues. But in the US I consider myself 0% Republican. I wish I could be as optimistic as Dawkins.

Unintelligent Analogies

2005-04-28T13:24:00.000-07:00

PZ Myers has written an interesting post denouncing the use of analogy by proponents of "intelligent design" (ID). Now, analogies are routinely used by scientists in the process of developing and explaining their ideas. Some might even argue that scientific reasoning is mostly analogical in nature, although I think that largely misses the point. The point is that IDers spend most of their time developing, defending, and arguing about analogies between biological systems and everything from clocks to outboard motors, and little or no time actually studying biological systems in the field, the lab or at the computer. IDers are particularly enamored with analogies between organelles (organs of cells) and machines. For example, Michael Behe, one of the few biological scientists in the ID movement, used it in a recent Op-Ed article in the New York Times. He even tried to give the impression that mainstream cell biologists, like Bruce Alberts (President of the National Academy of Sciences and author of perhaps the most widely read textbook on cell biology), shared his half-baked ideas. That turned out to be a mistake, of course: Alberts was quick to dismiss Behe's claims. Behe is also famous for proposing an analogy between biological systems and mousetraps to illustrate the idea of "irreducible complexity" (IC). The analogy (and the whole concept of IC) is obviously flawed: for example, look at this priceless demonstration of how a single piece of wire could, in principle, evolve into a full featured mousetrap. So what did Behe do? Dash to the lab and do some experiments to demonstrate that there actually is such a thing as an IC organ or organelle or molecule? No, he went and wrote increasingly confusing (and confused) justifications of the analogy.

And this is precisely why scientists have no time for the drivel that comes out of the Discovery Institute and other creationist organizations, no matter how many PhDs, MDs or lawyers are behind it. If I tell you that a certain protein has evolved under the action of positive natural selection, any analogies I might make to windsurfing or mountain climbing are completely irrelevant. If I don't show you data on dN/dS ratios, McDonald Kreitman tests, gene genealogies, structural predictions, analyses of mutant forms, etc, you have every right to dismiss my assertions. Until IDers spell out how we might go about telling "intelligently designed" molecules from those evolved through the action of mutation, natural selection and genetic drift, don't expect me to pay any attention to what IDers have to say. Until then.

What's In a Name?

2005-04-27T19:43:00.000-07:00

This blog is named after a poem written in 1926 by Álvaro de Campos, the Futuristic heteronym of Fernando Pessoa. Here's the original poem, in Portuguese:

O binómio de Newton é tão belo como a Vénus de Milo.
O que há é pouca gente para dar por isso.

óóóó—óóóóóóóóó—óóóóóóóóóóóóóóó

(O vento lá fora.)

And here's a rough translation:

Newton's binomium is as beautiful as the Venus de Milo.
The problem is that precious few people notice.

oooo—ooooooooo—ooooooooooooooo

(The wind outside.)

I love this poem because it places science firmly within our culture. As a scientist myself, I couldn't agree more. (Regrettably, Pessoa engaged in a good deal of pseudo-science and mysticism himself, but I like to think that Campos was above all that.)