Cornelius Hunter: Arguments Against Common Descent

[Cornelius_Hunter]

@swamidass

Instead, I’m referring to, for example, synonymous mutations in proteins. It seems (though I could be wrong), you’ve restricted this to gene families. If that is the case, you are glossing over mutations more likely to be neutral. That seems to be a real problem. As this is actually where the nested clade evidence is stronger (at least from my assessment).

If I am right (and I may not be), it seems this is a direct falsification of the conceptual argument being put forward. It seems that “design modules” must be defined to be non-neutral, and you may have an explanation for why they almost fit in a nested tree. However, that does not explain why more neutral mutations (it is a relative term) might fit more tightly in a nested three than design modules. That seems to be a looming problem for your proposal. I don’t think you can make your case without dealing with this head one. It seems to be a direct falsification of your proposal, unless I’m missing something here.

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.