I don’t think so. Axe’s response was more to other criticisms, and do not address the key point that I reiterate here. Specifically, the flaw in Axe’s argument is that he equates the bases of the hills I illustrate in Figures 1 and 2 of my post.
The points Axe responds to are:
Objection 1: Axe’s paper doesn’t claim to support intelligent design or challenge Darwinism, so it’s a mistake to use it for those purposes.
This is completely unrelated to my argument.
Objection 2: Although Axe makes a case that functional sequences are rare in sequence space, this has no bearing on whether new protein folds can evolve. The evolution of new protein folds simply requires that functional sequences not be isolated in sequence space, which has nothing to do with how rare functional sequences are.
This is also completely unrelated to my criticism.
Objection 3: Because Axe measured mutational sensitivity from a weakly functional starting sequence rather than the fully functional natural enzyme, the mutants he generated were inappropriately disadvantaged, and this is why he arrived at such a low value for the prevalence of functional sequences.
The Objection is either a misunderstanding or misrepresentation of my criticism. I do mention that he used a weakly-functional starting sequence, and I illustrate (in Fig. 2 of my post here on PS) what this means for Axe’s conclusions. But my remarks have nothing to do with a mutant being disadvantaged (whatever that means). Furthermore, as @Rumraket has stated, Axe’s word games do absolutely nothing to rescue the 2004 study from my criticism. The main point remains unaddressed.
Objection 4: Axe’s experiment doesn’t reflect how evolution really works. He mutated amino acids in groups of ten, whereas evolution sifts mutations one at a time. Consequently, Axe’s results tell us nothing about whether protein folds can or cannot evolve.
This has nothing to do with my critique.
So, @BenKissling, as can be seen, Axe really has not addressed the fundamental weakness in his study, or, more precisely, the conclusions he and other ID proponents draw from it. He does not accurately represent my argument, and his attempted response is not relevant to the matter of proteins, activity, and sequence space.
I would remind you that two DI scientists - @Agauger and @bjmiller - have both chosen to avoid this issue completely, even when given ample opportunity to discuss this matter. That speaks volumes to me and should give you pause as well.