Well, the important restriction here is not gene families, but rather the presence/absence of genes. There is no sequence alignment at play here. So, no, this concern is is not applicable to Ewert’s paper. The paper uses standard model selection and nine genetic databases to demonstrate that the dependency graph model is superior to common descent, with respect to the presence/absence data. That’s it.
@Cornelius_Hunter, with all due respect, [you originally posted this] on @Winston_Ewert’s thread. We are not interested in your arguments on his behalf [on his thread]. He can make his own case. [We set up this] thread for your arguments. To be clear, you (or anyone else) can feel free to jump in to clarify and add important and relevant information [on the main thread]. We, however, are engaging @Winston_Ewert [there].
As I have pointed out before:
Your case is actually hurting his argument. Just let @Winston_Ewert do his thing. He is making progress. He doesn’t appear to need your help.
@Cornelius_Hunter Looks like you’ve been making your case on the BioLogos forum. That’s great. When I get some time later I’ll start reviewing where left things off last time, and clarifying your arguments. You are welcome to join in too. I’ll look forward too it.