Major criticisms of Darwin’s Doubt by informed critics:
1. Meyer’s book, which is supposed to be about the Cambrian Explosion, gets the Cambrian Explosion fossil record wrong.
2. Meyer says that transitional fossils for the Cambrian groups don’t exist, but fossils with morphology transitional between the crown phyla do exist, oodles of them.
3. Meyer claims that phylogenetic methods are worthless, but doesn’t know that phylogenetic hypotheses are statistical statements and are statistically testable through standard methods – methods which themselves are testable and well-tested.
4. Meyer claims that the evolution of new genetic information is virtually impossible, a claim he is able to sustain mostly because he doesn’t understand the phylogenetic methods (see above) that are necessary for inferring the history of the origin of genes.
5. Meyer’s claim that “massive amounts” of new genetic information was required for the Cambrian Explosion is belied by the fact that gene number, and most of the key developmental patterning genes are shared broadly across the phyla, and even outside of bilaterians, rather than looking like they originated in the midst of the divergence of the phyla.
6. Meyer claims that the “junk DNA” hypothesis has been refuted, and that therefore the 90+ percent of large animal genomes that doesn’t code for genes or gene regulation is actually a massive additional amount of new information, but Meyer doesn’t rebut or even acknowledge the massive, basic, evidential problems with this idea.
6a. Simple calculations show that if most of the DNA in large-genomed organisms like humans was essential, given known mutation rates, we would die from fatal mutations each generation. This was Ohno’s original argument for junk DNA, and it has not been rebutted by ENCODE, the creationists, or anyone else.
6b. Genome sizes in complex animals and plants vary by orders of magnitude within many specific groups (tetrapods, onions, ferns, salamanders, arthropods, whatever), but despite this, within each group they all have about the same number of genes, and approximately the same organs and developmental complexity.
6c. When you actually look at the sequences in the variable fraction of the genome, most of it looks like the product of mutational processes with no selective filtering – transposon remnants, fossil viruses, duplications and other mutational errors, etc. Furthermore, unlike genes and important regulatory regions, which are well-conserved between closely related species, the apparent junk DNA looks like it has no constraint.the same organs and developmental complexity.
Edited to fix 6c.