Saturday, April 28, 2007

The Economist doesn't understand evolution   posted by the @ 4/28/2007 02:54:00 PM

"Evolution and religion: In the beginning" from The Economist

One time could be an accident:
In the second camp are those, including some high up in the Vatican bureaucracy, who feel that Catholic scientists like Father Coyne have gone too far in accepting the world-view of their secular colleagues. This camp stresses that Darwinian science should not seduce people into believing that man evolved purely as the result of a process of random selection. While rejecting American-style intelligent design, some authoritative Catholic thinkers claim to see God's hand in "convergence": the apparent fact that, as they put it, similar processes and structures are present in organisms that have evolved separately.

Twice is a serious error:
But Benedict XVI apparently wants to lay down an even stronger line on the status of man as a species produced by divine ordinance, not just random selection. "Man is the only creature on earth that God willed for his own sake," says a document issued under Pope John Paul II and approved by the then Cardinal Ratzinger.

Let's be clear, "random selection" is not a short-hand for "random mutation and natural selection". If anything, "random selection" is a description of neutral evolution.

Thus, as written, I have to join the camp that believes "that Darwinian science should not seduce people into believing that man evolved purely as the result of a process of random selection" and that "the status of man as a species [is] produced by ... not just random selection". Amen!

So WTF is wrong with the editorial staff at The Economist? They don't seem to actually understand evolution. You can send them an email and explain it to them.

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Tuesday, April 17, 2007

Macaques are not human   posted by p-ter @ 4/17/2007 07:11:00 AM

One of the more interesting parts of the paper reporting the sequencing of the rhesus macaque (also noted by Carl Zimmer) is that a number of mutations that cause Mendelian disease in humans are actually ancestral. That is, people with the disease have mutated to a sequence that's the same as the macaque one. Perhaps most notable are mutations in genes important in amino acid synthesis; one might expect these pathways to be well conserved. As the authors write:
In humans, these mutations greatly perturb the normal serum amino acid levels. Direct examination of macaque blood revealed lower concentrations of cystine and cysteine than in the human and slightly higher concentrations of glycine than in the human, but no increase in phenylalanine or ammonia, which might have been a predicted result of these changes. Although the effect of the observed alleles might be greatly influenced by compensatory mutations or other environmental factors, it remains a possibility that the basic metabolic machinery of the macaque may exhibit functionally important differences with respect to our own.
1. This is a strong argument for studying rare Mendelian diseases in humans. People sometimes bitch, "Who cares? Disease X affects 5 people in the entire world, why bother?". The answer, of course, is that those people are the human equivalents of knockout mice (to be horribly cold about it)-- people carrying rare recessive mutations are an important source of information about how those genes work in humans (see also this example), especially if those same genes are involved in different pathways in model organisms like the macaque or the mouse.

2. The ancestral disease alleles are also of prime interest for more detailed studies of selection. Deleterious mutations, of course, always have a probability of becoming fixed in a population; it takes more to show selection. But it's interesting ot note that the authors find a number of the mutations lead to mental retardation in humans. Could some of these genes be involved in human brain expansion and cognitive capabilities?

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Monday, March 12, 2007

An operational definition of the neutral theory?   posted by p-ter @ 3/12/2007 06:12:00 PM

I've often had the impression that debates about the neutral theory of molecular evolution are made confusing by people not defining their terms. Qualitative statements like "drift is more important than selection" tend to get tossed around. So this is from a recent paper:
This theory [the neutral theory] posits that the overall pattern of DNA evolution can be accounted for by mutation, genetic drift, and negative selection. It does not deny the operation of positive selection on some loci but only asserts that the overall pattern of genomic evolution can be explained without invoking adaptive evolution. Presumably, adaptive changes at any given time involve too small a fraction of the genome to be a statistically significant factor, despite their overwhelming biological significance.
I wonder if this is a generally accepted definition. If so, can the neutral theory officially be declared dead (at least for the protein-coding regions of the genome in Drosophila and human)?

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