A year ago (almost exactly) I wrote an entry taking to task a paper analyzing protein kinases in the draft chimpanzee genome. After writing that entry, I felt it proper to leave a comment at the journal (BMC Genomics). Instead of publishing the comment, the editor invited me to formalize my criticisms and perhaps give positive suggestions of how to do such an analysis. Between Codon dissolving, my interlude of consulting and starting Infinity this got pushed to late May, it went out for review & a round of revision & then the original authors were invited to write a rebuttal. By the time their rebuttal came back (late fall), I decided I was getting a bit worn on the whole thing and just tweaked my submission to underline a few things rather than go hammer-and-tongs for a counter-rebuttal.
Anyhow, my criticism and the authors' response is now up on the BMC Genomics website & indexed in Medline (hooray!). I won't go hammer-and-tongs here either. But, whereas sometimes two parties in an argument agree to disagree, having established consensus on what they are arguing about, I would characterize this with this post's title: the authors' pretty much argue that all of my points are based on misunderstandings and misinterpretations of what they wrote. I of course don't agree on that point.
In the end, one key point is that they are arguing they did the best with the dataset they chose to use as a source and I argue that they should have been more skeptical of the source. In the end, what I believe is that many of their unusual results will go away if the chimp genome is finished or if the chimp mRNAs under dispute are questioned.
So, this ends up as another project for my "Proposal to sequence genomes KR thinks deserve sequencing" grant. Ha! It would be fun to have a slush fund to pursue these sorts of things. $10K and access to chimp poly-A RNA is all this problem would need. But, I'm not independently wealthy so it will remain a pipe dream. Of course, there is a bonobo sequencing project and that would be somewhat useful. But if you go looking for such, make sure you google "Bonobo ensembl" not "Bonobo ensemble" as my smartphone helped me do -- you get some bizarre links but nothing to do with great ape sequencing.