Friday, October 14, 2005

New evidence for evolution

New Analyses Bolster Central Tenets of Evolution Theory

When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins.

But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests.

If Darwin was right, for example, then scientists should be able to perform a neat trick. Using a mathematical formula that emerges from evolutionary theory, they should be able to predict the number of harmful mutations in chimpanzee DNA by knowing the number of mutations in a different species' DNA and the two animals' population sizes.

"That's a very specific prediction," said Eric Lander, a geneticist at the Broad Institute of MIT and Harvard in Cambridge, Mass., and a leader in the chimp project.

Sure enough, when Lander and his colleagues tallied the harmful mutations in the chimp genome, the number fit perfectly into the range that evolutionary theory had predicted.
Of course, there's already an abundance of evidence for evolution, but it's always nice to have more. Gathering evidence that supports a theory by verifying nontrivial predictions of the theory is a concept that aficionados of "intelligent design" haven't begun to understand.
"What makes evolution a scientific explanation is that it makes testable predictions," Lander said. "You only believe theories when they make non-obvious predictions that are confirmed by scientific evidence."

Lander's experiment tested a quirky prediction of evolutionary theory: that a harmful mutation is unlikely to persist if it is serious enough to reduce an individual's odds of leaving descendants by an amount that is greater than the number one divided by the population of that species.

The rule proved true not only for mice and chimps, Lander said. A new and still unpublished analysis of the canine genome has found that dogs, whose numbers have historically been greater than those of apes but smaller than for mice, have an intermediate number of harmful mutations -- again, just as evolution predicts.
It's not clear why this prediction is called "quirky", except that it's simply mathematical, and perhaps therefore more obscure when written in words. It can be restated as follows. Suppose there are N living members of the species, its "population". Then if a given mutation is harmful enough that it has odds of greater than 1 out of N of reducing an indivudual's chance of leaving descendants, the mutation is unlikely to persist.

Stated yet more simply, if less precisely, any mutation which is sufficiently harmful probably won't persist.

A corollary is that species with large populations tend to have fewer harmful mutations. This is because when N is large, the threshold above which a harmful mutation is unlikely to persist is lower, and so a higher percentage are eliminated over time. Consequently, mice would have fewer harmful mutations than dogs, which would in turn have fewer than apes. And humans would have fewer than chimpanzees.
Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.

(In fact, some "junk" DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.) In any case, West said, it is up to Darwinists to prove ID wrong.
Actually, there is "junk" DNA that is found to be functional. There are sequences of DNA that don't code for genes (a more precise way of saying "junk") yet do have functions. For instance, some of these sequences act as "promoters", which facilitate the expression of real genes.

But the interesting thing is, when a DNA sequence really does have a function like this, it strongly tends to persist in related species. But many other "junk" DNA sequences disappear rapidly in related species, which strongly suggests they are random and have no function. This contradicts the ID prediction that all DNA in a genome has some function.

As for the contention that "it is up to Darwinists to prove ID wrong," that's obvious hogwash. It is primarily up to the supporters of a theory to provide evidence for it, and evolutionists have provided lots of proof for evolution. Opponents of a theory may provide contrary evidence to specific predictions of the theory. But if the theory in question doesn't make nontrivial but testable predictions -- which is the case with ID -- there simply isn't any way to prove it wrong. How convenient!

The bulk of this article provides a reasonably clear outline of how evolution actually works, and additional evidence in favor of the thory. Reading the details is quite worthwhile. For example:
It is now clear from fossil and molecular evidence that certain patterns of growth in multicellular organisms appeared about 600 million years ago. Those patterns proved so useful that versions of the genes governing them are carried by nearly every species that has arisen since.

These several hundred "tool kit genes," in the words of University of Wisconsin biologist Sean B. Carroll, are molecular evidence of natural selection's ability to hold on to very useful functions that arise.

Research on how and when tool kit genes are turned on and off also has helped explain how evolutionary changes in DNA gave rise to Earth's vast diversity of species. Studies indicate that the determination of an organism's form during embryonic development is largely the result of a small number of genes that are turned on in varying combinations and order. Gene regulation is where the action is.
In particular, a standard criticism of evolution made by ID proponents is that evolution has no way to make sudden large changes in a species. But that's wrong:
... mutations in regulatory portions of a DNA strand can have effects just as dramatic as those prompted by mutations in genes themselves. They can, for example, cancel the development of an appendage -- or add an appendage where one never existed. This discovery refuted assertions by Intelligent Design advocates that gene mutation and natural selection can, at most, explain the fine-tuning of species.
All in all, this article from the Washington Post is a very good piece of science journalism.

Here's another commentary on the same article: The Post Shows the Way. It's highly critical of an article in the New York Times which also deals with the Kitzmiller et al. v. Dover Area School District trial.

It also links to a very good, thorough article: Plagiarized Errors and Molecular Genetics, which explains a lot of molecular biology and its bearing on evolution in great technical detail. One should be prepared to spend at least an hour or so on this article, but it's worth it. ID supporters who claim that there is no evidence for evolution are simply blowing smoke when they ignore evidence like this. Although reading such an article is hard work, anyone tempted to believe the ID position really needs to do that work before making up their mind.

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