Thanks Josh. As a matter of fact, I find the module idea very interesting. And I was pleased to see that Dr. Ewert acknowledged what I see as the main objection to the conclusions. He writes:
“…the dependency graph model has an advantage over common descent in fitting the data because it can postulate modules to explain otherwise inexplicably distributed gene families…This is why we must also take into account the parsimony or complexity of the model.”
I find that to be a very honest statement of the problem in comparing the two models. But I am philosophically not in agreement with the solution using parsimony. My general attitude toward parsimony in biology is negative, since Occam’s Razor is violated at almost every turn in biochemistry and physiology.
What I think would be fascinating would be an incorporation of the gene module approach in an explanation of convergence within the evolutionary framework.