Obvious issue with the paper. . . From the Conclusion section:
Yes, that’s an obvious objection. His response is to remove from the paper any utility for comparing common descent with ID. What he has chosen to do is compare two models, neither of which corresponds to the expectations of biological evolution. Which of the two non-relevant models fits better might of interest to, well, I can’t think off-hand of anyone, but somebody, but it is not a test of the superiority of evolution or ID for explaining biological data.
If this were an actual scientific effort, an appropriate step would have been to simulate gene family evolution under a fairly realistic model of evolution – including missing data, since these genomes are neither perfectly sequenced nor perfectly annotated – and run the same test. I think it likely that the dependency model would be a better fit for that dataset than the simple tree model he’s been using.
Another obvious sanity check would be to take some of the gene families that are missing in scattered species and (a) do a BLAST search on those species, to see if the gene family is actually present but incorrectly annotated, and (b) see if there is sequencing coverage in the appropriate regions of the appropriate genomes.
These kinds of tests are essential. A study like this, which depends critically on the absence of data in public databases assembled from many different analytical approaches, can very easily reach completely incorrect conclusions if assumptions about data completeness and uniformity are not checked.