Scientists looked at the molecular data in order to test the hypothesis that the Cambrian animals appeared suddenly in a very rapid radiation. The molecular data did not show such a rapid radiation. The overall pattern was consistent with branching evolution spread out over many millions of years. The diagrams that Meyer shows in his book are similar to the figure shown below from Erwin et al. (2007).
Darwin's Doubt: The Genes Tell the Story? . I already covered the first one; namely, that the molecular data must be wrong because there are no transitional fossils [The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes].
Meyer refers to the molecular evidence as the "deep-divergence hypothesis" because the data indicates that the major animals forms diverged from a common ancestor long before the Cambrian Explosion.
According to Meyer ...
There is a second, more telling reason, to doubt the deep-divergence hypothesis,: the results of different molecular studies have generated widely divergent results. Yet presumably there was only one common ancestor of all the Metazoa and only one ultimate divergence point.Mayer is correct. It is very difficult to calibrate the molecular clock and arrive at a precise time for the divergence of the major phyla. The Erwin et al. study places many of the nodes in the Precambrian and the common ancestor at about 770 million years ago. Furthermore, there is some controversy over the exact branching order within the animal kingdom.
The dates shown above are common values in recent studies but there's a wide range of dates if you go back to the first papers from twenty years ago. Meyer quotes several scientists who challenge the calibration masurements, including the paper by Dan Graur and Bill Martin [Reading the Entrails of Chickens]. These are all valid criticisms but they don't affect the big picture. The data clearly shows a long fuse of evolution extending well into the Precambrian. The pattern does not show a rapid radiation condensed into a very short time frame and it certainly doesn't show that all of the major animal phyla sprang into existence without any obvious relationships.
His criticism is not relevant. You can't dismiss the form of the tree shown above just because the dates might be off by 100 million years or some of the branches might be misleading. That ain't gonna save him or his imaginary intelligent designer. The data is more than adequate to refute his hypothesis.
Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [doi: 10.1126/science.1206375]