Which is why I generally stay out of the biology discussions! 
Oh Garsh! 
If anomalous eukaryotic gene distributions cannot be explained by HGT, that raises the prior on the sort of picture Winston Ewert and Eric Holloway are developing.
Ewert’s approach is the best idea to come out of ID, ever (a testable hypothesis!). I had a discussion with Eric, and his approach is still very preliminary. I really think he ought to stick with accepted phylogenetic methods and not try to reinvent the wheel.