Wednesday, August 31, 2005

BS Model Gets "Lynched"

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.

Read on

Tuesday, August 30, 2005

Irreducible Differences

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]

Read on

Monday, August 29, 2005

Midwestern Sensibility

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.
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.
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.


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!

Read on

Sunday, August 28, 2005

Don't Show Me the Money

"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."

Read on

A Meeting of Minds

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’.

Read on

Wednesday, August 24, 2005

Positive Discrimination

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.

Read on

Tuesday, August 23, 2005

The Doubters

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.

Read on

Sunday, August 21, 2005

The Institutional Love Child of Ayn Rand and Jerry Falwell

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:
    1. Meyer SC, “The Origin of Biological Information and the Higher Taxonomic Categories,” Proceedings of the Biological Society of Washington, 117 (2004): 213-239.
    2. 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.
    3. Lönnig WE & H Saedler, “Chromosome Rearrangements and Transposable Elements,” Annual Review of Genetics, 36 (2002): 389-410.
    4. Chiu DKY & TH Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4 (2002): 766-775.
    5. Denton MJ & JC Marshall, “The Laws of Form Revisited,” Nature, 410 (2001): 417.
    6. 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.
    7. 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.

    Read on

    Saturday, August 13, 2005

    What's in a Theory?

    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.

    Read on

    Friday, August 12, 2005

    Distributed Intelligent Design?

    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!"

    Read on

    Wednesday, August 10, 2005

    Murky Waters

    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]

    Read on

    Tuesday, August 02, 2005

    Commanding the Army of the Night

    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.

    Read on