Ann Gauger's Response to My Themelios Review

[T_aquaticus]

@Patrick

Are you asking her because she is a practicing scientist doing research in this area? Or because she is a paid staffer of DI?

Since most mutations come from the father the Y chromosome should have accumulated more substitution mutations since the split with the chimp lineage. This is what we find, as noted by Dr. Gauger:

The initial paper from the chimpanzee genome project reported that the Y-chromosome had diverged 1.9 percent, compared to 1.06 percent over the whole genome, and 0.8 percent on the X-chromosome. The authors acknowledged they had difficulty aligning and masking repetitive sequences, and had insufficient data for comparison, all of which would potentially affect their results.
Dr. Gaugers response

Then Dr. Gauger makes this strange statement:

Clearly, this was not predicted by the neutral theory. 30 percent change in 6 million years for the Y compared to <2 percent for autosomes is a big surprise. Logically, it cannot be used as an argument for common descent. Certainly, mechanisms can be proposed, and they have been. But that does not constitute an answer. The 30 percent divergence can be used to suggest a unique origin . Ultimately, we don’t know why the Y is so different in chimpanzees and humans, except that it is.

Without going too deeply into all of the issues within that statement, the one that really jumps out (at least to me) is why Dr. Gauger thinks that the rate of indel mutations and recombination events can be directly compared to the rate of substitution mutations. These involve very different mechanisms, so I am wondering if she has any reason for thinking that the number of bases affected by recombination, insertion, and deletion should be the same as the substitution rate, or that the indel and recombination rates should be predictable like the substitution rates are.