Friday, March 14, 2003

MUW Update On Thursday I reported on the case of Dr. Nancy Bryson, the Mississippi University for Women professor who was asked to step down after teaching some ill-defined sort of creationism in her class. Agape Press is now reporting that she has been reinstated. The story can be found here.

Bible Code Madness From The New York Times comes this item about the lengths to which intelligence officials are willing to go in their search for Osama Bin Laden. It seems they granted an audience to Michael Drosnin, author of the bestsellers The Bible Code and The Bible Code II, who claims that hidden codes in the Bible can be helpful in locating bin Laden.

The Bible Codes first became big news in 1994 with the publication of the paper "Equidistant Letter Sequences in the Book of Genesis" by Israeli mathematicians Doron Witztum, Eliyahu Rips and Yoav Rosenberg. The paper appeared in the highly regarded journal Statistical Science. Equidistant Letter Sequences, or ELS's, refer to sequences of letters taken from the text of Genesis in which the letters are spaced at equal intervals. Thus, we might start at some arbitrary letter and look at every third letter thereafter, or every seventh letter, or every 24th letter. When we do this we sometimes find that a coherent word or sentence is spelled out. Witztum, Rips and Rosenberg performed an experiment in which they compiled a list of famous rabbis together with their birth or death dates, and looked for ELS's corresponding to their list. For most of their rabbis they were able to find an ELS spelling the rabbi's name, with a second ELS corresponding to the birth or death date located nearby.

Of course, a moment's thought reveals that in any sufficiently long text there will be so many possible ELS's that simply by chance some of them will form coherent words. The significant part of the original paper was the claim that its findings were far beyond anything that could plausibly be attributed to chance. If this claim was correct the implication was obvious. If the sequences were not attributable to chance and if no human author could have been clever enough to plant them himself, we are led to the conclusion that some supernatural intelligence planted them there.

Drosnin exploited this idea in his books, arguing that these codes could be used to predict future events, an idea that Witztum, Rips and Rosenberg wanted no part of. Drosnin's claim would have had more merit had he actually predicted a surprising event on the basis of his analysis of the codes. Alas, all he actually did was take events that had already occurred, and retroactively find ELS's in the Bible that corresponded, often roughly, to them. In fairness, Drosnin sent this letter in reply to the Times' piece. Suffice it to say that his claim that "the Bible Code keeps coming true" is open to debate.

The Codes Explained Due to the extravagant nature of the claims, the paper went through an unusually thorough process of peer review. All the referrees came to the same conclusion: They were pretty sure there was some flaw in the experimental design, but there was no obvious flaw and therefore the paper merited publication. Subsequent research by Brendan McKay, Dror Bar-Natan, Maya Bar-Hillel, and Gil Kalai found the elusive flaw. Briefly, there were some idiosyncrasies in the way the list of famous rabbis was compiled. There is a certain amount of freedom in how a name or a date is spelled out in Hebrew characters, and it seems that this flexibility was exploited in ways that made the results seem more statistically significant than they were. It must be said that there is no allegation of fraud here, only a certain amount of carelessness. When the experiment was repeated with this flexibility taken into consideration, researchers were able to reproduce the original results in non-religious books like War and Peace. These results were subsequently published in Statistical Science as well. Which leads us to conclude either that the codes are not good evidence for the divine origin of the Bible, or that War and Peace was authored by God as well.

This site contains the original paper, the published refutation, and several other resources as well.

Religious Bias?Incidentally, note that the referrees recommended publishing this paper despite their reservations and despite its religious overtones. This shows that the creationist complaint that scientific journals are too closed-minded to accept papers with religious themes is not corrrect.

Thursday, March 13, 2003

Challenging Evolution From Agape Press, a self-described Christian news service, comes this article about Mississippi University for Women science professor Nancy Bryson. According to the article, Bryson was asked to resign from her position as head of the Division of Mathematics and Science for teaching "...alternate views on evolution including intelligent-design." The article does not give any specifics concerning what, precisely, she taught, but it does give lots of indignant quotes from Bryson about academic freedom.

Without knowing the specifics of what was taught it is difficult to comment on this, but the tone of the article does not make me optimistic. Academic freedom does not allow you to teach any crackpot theory you like, and if Bryson was presenting information that any biologist should know to be false then it was entirely appropriate to ask her to step down. I suspect that few people would want to defend a biologist who was teaching that disease is best explained via demon possession, or a physicist who argued for the luminiferous ether.

The trouble is that "alternate views on evolution" is usually code for some form of creationism, and there are simply no good scientific arguments to be made in defense of this view. If Bryson was teaching ID, then she probably repeated arguments to the effect that modern evoluionary theory can offer no account of the formation of so-called irreducibly complex machines, or that natural processes can not account for information growth in the genome. Both of these arguments are patently false, and a biologist who prsented such arguments favorably would deserve the condemnation of his/her peers.

Wednesday, March 12, 2003

How do Complex Systems Evolve? The March 4, 2003 issue of the Proceedings of the National Academy of Sciences contains this article addressing the evolution of circadian clock genes in prokaryotes. This refers to a cluster of three genes that regulate certain physiological processes that occur at regular, often daily intervals. Prokaryotes are cells that lack internal organelles, such as a nucleus. Bacteria are the most common examples of such cells. They are contrasted with the more complex eukaryotic cells, which contain nuclei and other organelles. Clock genes are ubiquitous in eukaryotes, but until recently they were found only in one small group of prokaryotes, the cyanobacteria.

The article presents compelling evidence that homologs of the cyanobacteria clock genes exist in other prokaryotes, namely the Archaea and Proteobacteria. Their research enabled them to reconstruct a plausible scenario for how these genes evolved from simpler precursors via familiar processes such as natural selection, gene duplication and lateral gene transfer.

Another Blow for Intelligent Design The latest wave of creationism known as "Intelligent-Design" Theory (ID) offers two main scientific arguments in defense of their views. One is that certain biological structures exhibit "irreducible complexity", meaning that they are built from several parts in such a way that the removal of any one part causes the structure to cease functioning. This is said to pose an insurmountable challenge to evolution by natural selection, because such a structure allegedly could not form by gradual improvements in smaller, precursor systems. The second argument is that natural processes can not substantially increase the information content of the genome, a feat that would be required for evolution to be a viable theory.

Critics have pointed out numerous flaws in both arguments, and the present paper gives further empirical support to these critiques. The researchers studied a particular, three-gene complex, the kai genes, that regulates circadian rhythms in prokaryotes. They observe that "Comprehensive study of the kaiABC cluster expression in Synechococcus sp. PCC7942 showed that all three kai genes are essential for circadian rhythmicity, and inactivation of any of them completely abolishes it." Thus, this system satisfies the definition of irreducible complexity. Nonetheless, they go on to observe that the present indispensability of the three parts in modern prokaryotes does not imply that simpler systems could not have existed in earlier organisms, and they provide evidence to back up this assertion.

As for how information grows, the researchers argue forcefully that gene duplication with subsequent divergence accounts for part of the formation of the three-gene system from precursors possessing one or two parts. An impressive increase in information by anyone's standards. This is just one more example of why the arguments offered by ID proponents are flawed both in theory and in practice. It also illustrates how evolutionary theory continues to produce results in quotidian scientific work.

Bush and Providence Fine op-ed in The New York Times today, by Jackson Lears. He discusses the various ways American politicians have used religious rhetoric to win popular support for their agendas. He argues convincingly that Bush's overuse of such rhetoric does more harm than good.

One argument against our impending war with Iraq is the danger of having it appear that we are beginning a new Crusade. If this is seen as a war of Christianity against Islam, one consequence could be a massive increase in anti-American sentiment, with a corresponding increase in acts of terrorism. The administration's hawks downplay this fear. But with Bush invoking Christian rhetoric in nearly every public speech on this subject, people wishing to vew our forthcoming intervention as a religious war have plenty of ammunition for doing so. In this country Bush's extravagant religiosity scores him high marks, even in secular publications like Newsweek (who recently did a laudatory cover story on "Bush and God"). Overseas, it only contributes to anti-American sentiment.

Tuesday, March 11, 2003

Is Evolution a Religion? The March 7, 2003 Issue of Science features a characteristically insightful
article by Florida State philosophy professor Michael Ruse. A favorite taunt of creationists is to accuse scientists of using evolution as a prop on which to support an atheistic worldview. Evolution, in this view, is just as much a religion as their own preferred brand of fundamentalism. No doubt this will come as news to the thousands of scientists who see evolution as an effective tool for guiding their research. Ruse argues that today evolutionary biology is primarily a rigorous science, complete with mathematical models and experimental protocols. However, in popular writing, some writers stray too far into the realm of metaphysics, thereby providing some fuel for the Creationist complaint. Ruse supports his thesis by outlining the history of the field, and tracing its development from the sloppy reasoning of early proponents like Lamarck and Erasmus Darwin (grandfather of Charles) through Darwin, Huxley, Fisher, Haldane, Dobzhansky and others.


Ruse overstates his case a little, however. The handful of prominent scientists such as E.O. Wilson (specifically mentioned in the article) who can plausibly be said to be using evolution to undergird a materialist worldview are a tiny minority of the biological community generally. When Creationists level their canard, their intent is to paint evolution as the foundation of a world view that smiles upon promiscuity, immorality, homosexuality, and everything else they find undesirable. They then contrast this worldview unfavorably with the benevolent Christian fundamentalism they prefer. There is no sense in which evolution actually plays this role. Ruse states this bluntly, but then writes, "But, if we wish to deny that evolution is more than just a scientific theory, the Creationists do have a point." Of course evolution has greater implications for how we view ourselves than, say relativity, and in that sense it is more than just a theory. Indeed, that is why mainstream publishers routinely print books about evolution, but not about quantum physics. But this weak claim bears no relation to any point the Creationists are making, and it was unwise of Ruse to phrase his argument in this way. We can now look forward to Creationist misuse of Ruse's statement; they will make it appear as if Ruse supports their strong point, when he does not.


Pigliucci's Book For a book length treatment covering many of these issues in more detail, from the perspective of a professional evolutionary biologist, check out Massimo Pigliucci's magnificent Denying Evolution: Creationism, Scientism, and the Nature of Science, available here.

Monday, March 10, 2003

Let's see if I can produce a link. Link to my web site here.

This is a test of my nifty new blog. Will it work?