Simulation is not science

“Reliabilities of identifying positive selection by the branch-site and the site-prediction methods” is merely one piece of evidence indicating that TENS rests on much shakier empirical foundations than most scientists realize:

“Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions,” said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team’s leader…. To demonstrate the faultiness of the statistical methods, Nei’s team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments.

“In some cases, statistical method completely failed to identify the true sites where natural selection occurred,” said Nei. “This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection.”

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes — genes that are genealogically identical among different species — and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher’s exact test, but this test did not detect any selection.

“The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives,” said Nozawa.

“These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences,” said Nei. “But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time.”

Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

In other words, scientists usually do not bother to do science because it is difficult and it takes too long. But, non-scientists should still trust their results because on those rare occasions that scientists actually do make use of the scientific method, it works rather well. And, of course, one should trust biologists because physicists get amazingly accurate results.

Needless to say, the quality of their rationalizations tends to indicate that scientists don’t often make use of logic either.

Bad banker logic

I’ve seen variants of this argument in defense of permitting bailout banks to pay massive bonuses from various parts of the political spectrum, but it makes no sense at all:

We cannot legislate to cap bonuses or pay. There is no room in a free society for a law that curbs the pay proffered in private companies.

This may be true, the problem is that a society that hands over billions of dollars in public money to private companies is no longer a free society. If the government can hand money to the banks, it can take money away from the banks just as easily. So, this is a bogus and illogical line of defense.

Proof of evolution disproved… as expected

You may recall that I viewed the announcement of the landmark discovery of Darwinius masillae in May as an ideal candidate for the falsification of Darwinism as well as the Neo-Darwinian Theory of Evolution by Natural Selection. Or, at least, in the scientific basis for many individuals belief in such things. After all, “Ida” was described “in no uncertain terms as the missing link between us humans and our primate kin. In news reports, team members called her ‘the eighth wonder of the world,’ ‘the Holy Grail,’ and ‘a Rosetta Stone.'” And who can forget how researchers said that “proof of this transitional species finally confirms Charles Darwin’s theory of evolution, and the then radical, outlandish ideas he came up with during his time aboard the Beagle.”

Of course, it didn’t take long for other scientific skeptics to cast doubt on the significance of this supposed wonder of the scientific world. And now, the ever-mutable scientific consensus appears to be in the process of concluding that Darwinius masillae is of little more significance to the theory of human evolution than Piltdown Man or any other of the many scientific frauds and exaggerations of the past.

Critics concur that Ida is an adapiform, but they dispute the alleged ties to anthropoids. Robert Martin of the Field Museum in Chicago charges that some of the traits used to align Ida with the anthropoids do not in fact support such a relationship. Fusion of the lower jaw, for instance, is not present in the earliest unequivocal anthropoids, suggesting that it was not an ancestral feature of this group. Moreover, the trait has arisen independently in several lineages of mammals—including some lemurs—through convergent evolution. Martin further notes that Ida also lacks a defining feature of the anthropoids: a bony wall at the back of the eye socket. “I am utterly convinced that Darwinius has nothing whatsoever to do with the origin of higher primates,” he declares.

I will now await with interest for the various devotees of the cult of Darwin to admit one of the three logical possibilities that stem from this entirely predictable – and predicted – outcome:

1) The Darwinius masillae incident means that the theory of human evolution by natural selection remains unproved.

2) The Darwinius masillae incident proves that scientific assertions about the factual scientific basis for the theory of human evolution by natural selection are not intrinsically reliable.

3) The Darwinius masillae incident is irrelevant because your belief in the theory of human evolution by natural selection is not based on science.