Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates

Stephen Meyer is promoting the idea that God made all the various types of animals over a short period of time about 530 million years ago. The molecular data refutes that speculation because it shows that the various phyla share common ancestors and many of those ancestors appear long before the Cambrian Explosion.

This data creates a serious problem for the IDiots so they have to discredit it in order to dismiss it. As we've seen in earlier posts, Meyer argues that the molecular data is wrong because: (a) there are no transitional fossils, and (b) different molecular phylogenies do not agree in all detail [see The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes and Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]. He has five anti-evolution arguments altogether [Darwin's Doubt: The Genes Tell the Story?]. The third one is that different genes evolve at different rates.

It's been known for decades that different genes evolve at different rates. The earliest comparisons were between the proteins; fibrinogen, globins, and cytochrome c. Those are the examples often shown in textbooks. Cytochrome c is well conserved. Most of the residues don't change very much because mutations would be lethal. The rate of change (evolution) is determined by substitutions that occur at neutral sites.

Globins are not as highly conserved so the sequences change more rapidly. The molecular clock ticks at a faster rate for globins because more neutral substitutions are allowed. Fibrinogens (fibrinopeptides) are not well-conserved. There are very few residues that can't be mutated. Fibrinogens are practically useless for constructing phylogenetic trees [The Modern Molecular Clock].

Some histones (H3 and H4) are highly conserved. Just about every amino acid is in contact with other histones in the nucleosome or with DNA and substitutions are lethal. H3 and H4 genes yield molecular clocks that tick so slowly that the genes can't be used to detect the relationships between animal phyla. Their sequences are almost identical.

The idea that different genes evolve at different rates has been around since 1970 and we have a good explanation. If you want to look at the relationships of the various animal phyla and you want to date their separation then you have to choose genes that evolve at the appropriate rates. Modern studies are not based on single genes: instead, it's common to use dozens or hundreds of concatenated genes in order to filter out stochastic noise and get accurate dates from calibrating the rate of evolution.

But here's how Stephen Meyer explains it ...

Reported Precambrian divergence times would vary even more dramatically were it not that evolutionary biologists and molecular taxonomists ignore certain molecules in their studies to avoid grossly contradictory results. Consider, for example histones—proteins found in all eukaryotes involved in packing DNA into chromosomes. Histones exhibit little variation from one species to the next. They are never used as molecular clocks. Why? Because the sequence differences between histones, assuming a molecular rate comparable to that of other proteins, [my emphasis LAM] would generate a divergence time at significant variance with those in studies of many other proteins. Specifically, the small differences between histones yield an extremely recent divergence, contrary to other studies. Evolutionary biologists typically exclude histones from consideration, because those times do not confirm preconceived ideas about what the Precambrian tree of life should look like.

Meyer wonders how scientists choose the appropriate genes and concludes that they pick the ones that conform to their preconceived notions of what the animal tree ought to look like.

... as one widely used textbook euphemistically puts it, evolutionary biologists must choose "phylogenetically informative" data. By this, they mean sequences that exhibit neither too little nor too much variation—where too much and too little are determined by preconceived consideration of evolutionary plausibility, rather than by reference to independent criteria for determining the accuracy of molecular methods.

The subjective quality of these considerations, where scientists "cherrypick" evidence that conforms to favored notions and discard the rest, casts further doubt on the extent to which molecular comparisons yield any clear historical signal.

This is so wrong. It's evidence that Meyer doesn't understand the science he criticizes but that's not a surprise. He is not an expert in biology or in evolution and we already have plenty of evidence of that.

What IS surprising is that a passage like this demonstrates that the book was not reviewed by anyone who is knowledgeable about the field. Any undergraduate who had completed a course in molecular evolution would easily spot the error. Even Jonathan McLatchie would have caught it!

David Klinghoffer might have reviewed the book before publication¹ so I'll let him have the last word from: The American Spectator Warmly Welcomes Darwin's Doubt.

You might not like what Stephen Meyer has to say in Darwin's Doubt, but a competent critic knows you need to react to what the author actually argues. By contrast, Meyer's critics have mostly refused to grapple with the main contentions of the book, the categories of evidence it advances. When you call them on this, they refuse to respond. Or in Farrell's case, they reply with name-calling.

Tells you something, doesn't it?

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1. A case of the blind leading the blind.