Some links on "ortholog conjecture" paper and critiques of it

Recently a paper by Matt Hahn was published in PLoS Computational Biology entitled "Testing the ortholog conjecture with comparative functional genomic data from mammals."  The paper created a bit of a stir as some aspects of it call into question some of the standard assumptions made in comparative genomic analysis.

I alas do not have time to go into all the details but fortunately others have tackled this and I am posting some links here:

Will try to post my own comments soon.  I note - I am skeptical of their conclusions but still going through the paper to understand everything before commenting in more detail.