His main thesis is that all the animals appeared suddenly in the Cambrian and there's no evidence that they arose from ancestors living earlier in the Precambrian. Unfortunately for him, there IS plenty of evidence in the form of molecular evolution. By comparing genes and proteins we can show that all the animal groups are related to one another and that their common ancestors are spread out over a considerable period of time as shown in the phylogenetic tree below from a paper by Dunn et al. (2008).
Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"], by setting up a strawman [Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates], and by pointing out that molecular dating is not precise [Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]. His most ridiculous argument1 against molecular evolution is that the results must be wrong because there are no transitional fossils from before the Cambrian Explosion! [The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes]
None of those arguments stand up to close scrutiny but, as I warned you last week, there are actually five arguments against the validity of molecular evolution [Darwin's Doubt: The Genes Tell the Story?].
Are you ready for the final argument showing that molecular evidence must be discounted?
It's because all those phylogenetic trees are based on the assumption than the genes being compared are homologous. But "homologous" means that the genes share a common ancestor and that's exactly what the phylogenetic trees are supposed to show. Therefore, the entire enterprise is one big circular argument and none of the molecular evidence is valid. (In fact, the entire field of molecular evolution is based on a circular argument according to Stephen Meyer.)
Here's what he says on page 110.
The assumption (of universal common descent) raises the possibility that the ancestral entities represented by divergence points in these studies are artifacts of the assumptions by which molecular data are analyzed. Indeed, the computer programs that are used to compare molecular sequences have been written to produce trees showing common ancestors and branching relationships regardless of the extent to which the genes analyzed may or may not differ. Phylogenetic studies compare two or more gene sequences and then use degrees of difference to determine divergence points and nodes on a phylogenetic tree. Inherent in that procedure is the assumption that the nodes and divergence points existed in the past.According to Meyer, this flaw calls into question all trees constructed from genes and proteins but he's particularly concerned about those that challenge his view that God must have made the animals during the Cambrian explosion.
Thus, the deep divergence studies [molecular evidence] do not, in any rigorous sense, establish any Precambrian ancestral forms. Did a single, original metazoan or bilaterian ancestor of the Cambrian animals actually exist? The Precambrian-Cambrian fossil record taken on its face certainly doesn't document such an entity. But neither do deep-divergence studies. Instead, these studies assume the existence of such ancestors, and then merely attempt, given that assumption, to determine how long ago such ancestors might have lived. One could argue that the conflicting divergence points do at least show that some common ancestor existed in the Precambrian, since, despite their conflicting results, all divergence studies indicate at least that. But, again, to invoke molecular studies that assume the existence of a common ancestor as evidence for such an entity only begs the question. Certainly it provides no reason for using molecular evidence to trump fossil evidence. Perhaps the Precambrian rocks do not record ancestors for the Cambrian animals because none existed. To foreclose that possibility, and to resolve the mystery of the missing Precambrian ancestral fossils, evolutionary biologists cannot use studies that assume the existence of the very entity their studies are thought to establish.In order to see the flaw in Meyer's argument you have to imagine that you are a scientist back in the early 1960s. You have sequenced a bunch of cytochrome c proteins from a variety of difference species. You notice that they are very similar in sequence and you wonder whether these similarities arise because they evolved from a common ancestors. In other words, can you use sequence similarity to demonstrate homology?
You line up and compare the similar sequences. The first thing you notice is that some sequences are almost identical whereas others differ at many positions. For example, the sequences of the human and chimpanzee proteins are practically the same but they are both very different form the yeast sequence or the bacterial sequences of the same protein. You wonder whether these differences can be plotted as a tree of similar sequences not knowing in the beginning whether it will work or not. Maybe the relationships are not treelike, in which case they may not be due to descent from a common ancestors.
Remember that fifty years ago it wasn't clear that evolution by natural selection would yield a tree of sequence similarities because different lineages will adapt to different environments at different rates. It was also remotely possible that the cytochrome c proteins in different species arose by convergence and showed no trace of common ancestry.
The Modern Molecular Clock]. Thus, amino acid sequence similarity is a reliable indication of homology.
This conclusion is so well established that we often ignore its significance and we often forget to emphasize the difference between "similarity" and "homology." Phylogenetic trees are constructed from sequences that are similar and the fact that the relationship turns out to be treelike (it doesn't have to) means that the genes/proteins are homologous. Margoliash (1969) (and others) understood very well the difference between similarity and homology and that phylogenetic trees were constructed on evidene of similarity to reach a conclusion of homology [see Margoliash on "Homology" (1969)].
Meyer doesn't understand this. He exploits the sloppy use of "homology" by many modern molecular biologists to build a case for invalidating all molecular phylogenies that have ever been published. It's ridiculous to use an argument over semantics to rule out solid evidence of common descent.
But, that's exactly what Intelligent Design Creationists have to do because they don't have any scientific evidence to support their claims. Jonathan Wells tried the same trick back in 2000 when he wrote Icons of Evolution. Lots of people pointed out his error back then. It shows, once again, that IDiots don't learn from their mistakes.
1. It's a close call.
2. This tree is from Fitch and Margoloash (1967).
Dunn et al. (2005) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749 [doi: 10.1038/nature06614]
Fitch, W.M. and Margoliash, E. (1967) Construction of phylogenetic trees. Science 155:279–284.
Margoliash, E. (1963) Primary structure and evolution of cytochrome c. Proc. Natl. Acad. Sci. USA 50:672-679.
Margoliash, E. (1969) Homology: A Definition. Science 163:127