As part of my daily diet of news sites and blog reading I keep an eye on various creationist websites. This is done partly as opposition research. It’s always good to know what the crazy people are getting excited about. But it is also because they frequently link to interesting articles I might have overlooked otherwise.
Over at Uncommon Descent, Denyse O’Leary helpfully linked to this article by Carl Zimmer from the November 10 issue of The New York Times. The article discusses recent developments in genetics, and how hey are changing long-held notions of what a gene is. It’s fascinating stuff, but O’Leary seemed especially taken with the following excerpt:
But these exceptions did not seem important enough to cause scientists to question their definitions. “The way biology works is different from mathematics,” said Mark Gerstein, a bioinformatician at Yale. “If you find one counterexample in mathematics, you go back and rethink the definitions. Biology is not like that. One or two counterexamples — people are willing to deal with that.”
That seems like an odd thing to say.
In mathematics, a counterexample is something that refutes a proposed conjecture. Someone says, “I believe it’s true that assumptions A, B and C imply that D is true as well.” A counterexample is then an example in which A, B, and C are all seen to hold, but D is sadly false. Presented with such a counterexample, you conclude merely that your intuition is not yet as finely honed as it might be.
There is a sense in which a counterexample might lead you to rethink your definitions. Presumably you have some concrete scenario in mind, and you are devising an abstract model of it. Typically your understanding of the scenario guides your construction of the model, and that includes the definitions of the basic terms you will be using. If you then discover that things that really ought to be true turn out not to follow from your definitions and assumptions, you might then conclude that these definitions need to be tweaked.
This is not really comparable to the situation in biology, or any other science for that matter. There we have some theory that successfully accounts for a great deal of experimental data. That gives us confidence that our theory represents at least some part of the truth about nature. But since even our best scientific theories are mere approximations of reality, as opposed to perfect descriptions of it, there are always anomalies that are not covered by the theory. But a few anomalies are not going to lead scientists to abandon a theory that has consistently proven itself to be useful in the field and the lab.
That aside, the article makes for fascinating reading. It goes without saying, of course, that O’Leary’s description of it is farcically wide of the mark. For example, she writes:
Earlier, I called attention to this longish but very informative article by Carl Zimmer, “Now: The Rest of the Genome” (The New York Times, November 11, 2008). It pretty much blows the genetic reductionism I grew up with out of the water. The “gene” – that little coil of sugar that ran our lives back then – is a dead idea.
In this earlier post she comes to the bizarre conclusion that somehow Lamarck’s ideas are being rehabilitated, and that new research makes it unreasonable to talk about “genes for” various traits.
This is all perfectly absurd. As Zimmer notes at the start of his article, in reference to the word “gene:”
The word was coined by the Danish geneticist Wilhelm Johanssen in 1909, to describe whatever it was that parents passed down to their offspring so that they developed the same traits. Johanssen, like other biologists of his generation, had no idea what that invisible factor was. But he thought it would be useful to have a way to describe it.
Given O’Leary’s rather outre ideas about body/mind dualism, it is possible she thinks heredity is based on some sort of bizarre, nonmaterial whatizzit that somehow interacts with matter. But as long as we are okay with heredity having some physical basis, the idea of the gene is not going anywhere.
What is dying, or, more correctly, is dead, is the idea of one gene one protein, or the idea that merely knowing the sequence of letters in a person’s DNA is enough, if only in principle, to explain their physical form. The idea that a gene is just a stretch of DNA that codes for a protein is no longer adequate. Turns out there are other factors involved in heredity:
But it turns out that the genome is also organized in another way, one that brings into question how important genes are in heredity. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel.
Also interesting is the role evolution is playing in helping scientists understand some of these new findings:
David Haussler, another Encode team member at the University of California, Santa Cruz, agrees with Dr. Birney. “The cell will make RNA and simply throw it away,” he said.
Dr. Haussler bases his argument on evolution. If a segment of DNA encodes some essential molecule, mutations will tend to produce catastrophic damage. Natural selection will weed out most mutants. If a segment of DNA does not do much, however, it can mutate without causing any harm. Over millions of years, an essential piece of DNA will gather few mutations compared with less important ones.
Only about 4 percent of the noncoding DNA in the human genome shows signs of having experienced strong natural selection. Some of those segments may encode RNA molecules that have an important job in the cell. Some of them may contain stretches of DNA that control neighboring genes. Dr. Haussler suspects that most of the rest serve no function.
Go read the whole article. The picture that emerges is the familiar one of scientists gradually devising clearer and clearer pictures of how nature works using current theories as a springboard for further research, as opposed to the last word on the subject.
And off to the side, making noise loud enough to be annoying but not substantive enough to be interesting, are folks like O’Leary, who think that anytime scientists revise some bit of accepted wisdom it is time to argue that the whole edifice is crumbling. She writes, for example:
One thing about this article, it is mercifully free of rubbish about evolution.
We actually don’t know what most of the stuff in the genome does. So why not wait until we do know before we begin to describe its history? That will save a lot of rewrites down the road, maybe inconvenient ones.
Apparently she missed the part I quoted above. More to the point, however, is that evolutionary theory, at least in the big picture, actually doesn’t care all that much about the precise physical mechanisms of heredity. The difference between “Heredity is governed entirely by DNA,” and “Heredity is governed not just by DNA but also by other physical factors linked to DNA,” is not the difference between “Evolution proceeds largely through the accumulation of small, inherited variations,” and “Evolution is nonsense that must be replaced by the Magic Man theory.”
The old notion of genes mutating, leading to new variations, that are then sifted by natural selection, is not going anywhere. As Zimmer notes, those ideas have been marvelously successful at explaining a great many things. They are simply being supplemented with many new ideas as well. Far from being harmful to evolution, these sorts of discoveries are a great boon. They show that scientists have been needlessly limiting themselves in the sorts of explanations open to them in explaining the evolutionary process.