Scientists, on the other hand, have been exploring other possibilities and testing various models. They have shown that the molecular data is not consistent with sudden origins. Instead it shows that all of the major animal phyla are related and that their common ancestors probably lived millions of years before the Cambrian explosion. Thus, the evidence indicates deep divergence and the lack of transitional fossils does not prove the non-existence of these ancestral forms.
In order to support his creationist view, Meyer has to discredit the molecular evidence. We've already seen that he has five arguments against the data [Darwin's Doubt: The Genes Tell the Story?]. The first three were: (1) there are no transitional fossils [The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes]; (2) different molecular phylogenies do not agree in all detail [Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]; and (3) different genes evolve at different rates [Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates].
None of those arguments are correct and one of them (#3) is just plain silly.
His fourth arguments is that IDiots are allowed to ignore the molecular evidence because mutation rates are not constant.
Other problems run even deeper, having to do with the assumptions that make comparative analyses possible in the first place. These comparisons assume the accuracy of molecular clocks—that mutation rates of organisms have remained relatively constant throughout geological time. ...Theme
Even if we assume that mutation and natural selection can account for the emergence of novel proteins and body plans, we cannot also assume that the protein molecular clock ticks at a constant rate.
MutationI'm not sure if Stephen Meyer understands what causes the molecular clock. It's a combination of mutation rate and the rate of fixation of nearly neutral alleles by random genetic drift [The Modern Molecular Clock, Random Genetic Drift and Population Size]. Modern population genetics shows us that the overall rate of change should be the same as the mutation rate. Since mutation rates are relatively constant, there will be a stochastic molecular clock.
Meyer quotes from a 1999 paper by Valentine, Jablonski, and Erwin.
Valentine, Jablonski, and Erwin note, "Different genes in different clades evolve at different rates, different parts of genes evolve at different rates and, most importantly, rates within clades have changed over time.This is an accurate quote. Valentine et al. were critical of the exact dating of the splits between various animal phyla although they noted that there was general consensus on deep divergence. They also noted that, regardless of rates, the overall pattern does not suggest rapid radiation. They said,
The new data, primarily from 18S rRNA but more recently from additional molecules, indicate a very different configuration (Fig. 5). Although resolution of the branching pattern within the major groups has been a challenge (though this difficulty is not in itself convincing evidence for a rapid evolutionary burst; see Abouheif et al., 1998), the new basic framework appears robust. Some changes should be expected in the placement of groups within the framework, especially groups wherein relatively few taxa have been sampled.The observation that different genes evolve at different rates and different parts of the same gene evolve at different rates is trivial. I fault Valentine et al. for mixing up several different observations in their 1999 paper and even in the 2013 book by Erwin and Valentine.
Molecular clocks are based on the rate of substitution at neutral sites. Some genes have more neutral sites than others and some parts of genes have more neutral sites than other parts that are more highly conserved. The rate of change is measured as the number of changes at these sites and not the rate of change over all amino acids in the protein.
Valentine et al. also discuss the calibration of the molecular clock—that is the rate of change per year as calibrated against known divergences based on the fossil record. This calibration is difficult but Valentine et al don't distinguish between those calibrated rates and the mutation rates that underlie the molecular clock. In those cases where we have reliable dates (e.g. hominid evolution) we now know that the rates over millions of years are very close to the known mutation rates in extant species [see Mutation].
Valentine et al. do seem to imply that mutation rates are different in different lineages and not just that the calibration of rates can be a problem in some lineages.
I don't believe they are correct. All the evidence we have suggests that the overall mutation rate due to errors in DNA replication are pretty constant in different lineages and, presumably, over time. Thus, our theoretical understanding of molecular evolution suggests that there should be an approximate molecular clock and that's what the data overwhelmingly shows in almost all cases.
But even if I'm wrong it would be an extraordinary coincidence if all the changes in mutation rate just happened to completely obscure the fact the all the modern animal phyla sprang into existence at the same time about 520 million years ago as Stephen Meyer believes.
Meyer also quotes a paper by Ho et al. (2005) where the opening sentence of their introduction says, "The rate of molecular evolution can vary considerably among different organisms, challenging the concept of the 'molecular clock.'" The authors don't offer any evidence to support this statement. The paper is about constructing trees from simulated data where some of the algorithms allowed for rate changes in different lineages. This is not very good support for the idea that mutation rates can vary considerably in different lineages thus invalidating one of the key assumptions of the molecular clock.
Keep in mind too that molecular clocks are calibrated based on the estimated age of presumably ancient fossils. If, however, such estimates are incorrect by even a few million years, of if the fossil used to calibrate the mutation rate does not lie at the actual divergence point on the tree of life, the estimated mutation rate may be badly skewed.Myer is confused about the difference between calculating the actual mutation rate in changes per year and whether the mutation rate is relatively constant over time. We all agree that calibrating the rate of molecular change is difficult—although we are reaching a consensus on values that clearly place the divergence of major animal phyla in the Precambrian. On the other hand, there is widespread consensus that the underlying mutation rates are pretty much the same and that means there IS a molecular clock as predicted by population genetics.
It's true that calibrating the molecular clock is difficult, though not as difficult as Meyer claims. It's not true that the underlying theory is wrong and mutation rates vary considerably from lineage to lineage thus invalidating molecular phylogeny.
Ho, S. Y., Phillips, M. J., Drummond, A. J. & Cooper, A. (2005) Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution 22:1355-1363. [doi: 10.1093/molbev/msi125]
Dunn et al. (2005) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749 [doi: 10.1038/nature06614]
Valentine, J. W., Jablonski, D. & Erwin, D. H. (1999) Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126:851-859. [PDF]