Nice to see you @billcole!
Yes @Cornelius_Hunter claims this all the time.
I’ve been at this at length with him in the past. He has yet to produce any actual evidence of this. I’ve ready his blog extensively and have yet to see any actual evidence against common descent. I think part of the reason he is so convinced is that he uses an entirely different type of thinking, logic, and methodology as we do in mainstream science. Using his idiosyncratic methodology it is not surprising he comes to different conclusions.
@vjtorley took @Cornelius_Hunter to task on his logic here Baker’s dozen: Thirteen questions for Dr. Hunter | Uncommon Descent, and he has yet to respond to these questions. In particular, @Cornelius_Hunter really needs to answer question #4 before any rational conversation is possible:
Do you accept that if hypothesis A readily explains an empirical fact F and hypothesis B does not, then F (taken by itself) constitutes scientific evidence for A over B? Or putting it another way, if a fact F is predicted by hypothesis A, and compatible with hypothesis B but not predicted by B, then do you agree that F constitutes scientific evidence for A over B? If not, why not?
In all cases by him and others I have seen, the “evidence” that they thinks counts against common descent only works this is way if we adopt an incorrect understanding of evolution. So, they are really just arguments against strawmen understandings of common descent. For example, the recognition horizontal gene transfer complicates the simplified “Tree of Life” is not the evidence against common descent that Hunter thinks it is: Darwin's God: The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared. Biology is just a much complicated than our simple models. We can explain somethings with a simple model, but we have to move more complicated models to explain other more things. And in some cases, we do not yet know the complexities necessary to explain what we see. This ignorance though, does not proof that it is impossible to have evolved, just that we have reached the limits of our current understanding.
Alongside these really flawed arguments is a resolute refusal to provide alternate explanations for the wide range of patterns we see that are explained by common descent, but not common design. If we are to reject common descent we need to (1) explain all the patterns explained by common descent AND (2) explain more than common descent can. Just pointing to something that is not fully explained by common descent (which is not even what is happening here) is not enough to reject common descent. We need a more powerful alternate theory.
I do grant that some patterns are explained by common design too (without contradicting common descent), however a larger number of patterns are only explained by common descent. For example, no known design principle explains why human/chimps have one tenth the differences than those between mice/rats. Why are we more similar to chimps than rats are to mice? Common descent explains this quantitatively, theoretically, and_experimentally_, but no design principle does. Likewise, why does synonymous divergence approximately equal intron substitution divergence, and are greater than nonsynonymous divergence? Why does this same pattern (synonymous vs. nonsynonymous, vs. intron) appear in variation and mutation rates too? Why does species divergence closely correlate with mutation rates across the genome? I could go on and on.
Common descent + neutral theory explains and predicts all these patterns and many many more with a solid quantitative framework. There is just so many different and independent patterns that are clearly modeled by neutral theory and common descent that it is impossible to even summarize them here. I could go on and on.
This gets to question #4 above. Common descent predicts so much that common design alone does not. This is certainly not an argument against design, but is a very strong argument for common descent. I’ve asked @Cornelius_Hunter and other anti-common-descent “theorists” to explain these patterns with design principles. There are no takers. I think the reason is obvious; there is no known design explanation for these patterns but common descent. This is why common descent is nearly universally accepted in biology.
There is no debate in mainstream science now, and one has to change the rules entirely (as does @Cornelius_Hunter) to make even a weak case against it.
@Billcole, if not common descent, what do you think explains these patterns?
