Andrew C has been examining the raw data in a highly technical field, and in terms of counting genomic changes was doing better than I was. There is nothing wrong with what he's been doing; it just so happens that one of the two human (and ape) proteins he's been looking at is on the y chromosome. Even you, surely, must appreciate that a functional gene for the most fundamental part of the protein synthetic apparatus cannot be on the y chromosome, since women make proteins the same way men do.
Have not been following the discussion all the way so I am not sure if andrewc made that claim. Neertheless, it does not vitiate from the central point of his argument - that the number of mutations between species does not agree with the evolutionary 'tree of life'. In fact, it makes his case stronger because evolutionists do not have the excuse of saying that it would destroy functioning to change the gene and thus mutations are restricted in such a gene. In fact, evolutionists often claim that the best places to find mutations is where there is no function (or no important function) for the genes involved. So I really do not see how this (if your assertion above is correct) in any way contradicts andrew's point.