Actually, in the case that was described in the Panda’s Thumb article, function was restored, where part of the gene that had that previous function was present: “The rescue of E. coli ΔguaB represents a partial self-rescue; it was rescued by the hybrid YdjO257/GuaB283, a combination of 257 amino acids of YdjO and 283 amino acids of GuaB. The full length GuaB is 488 amino acids, meaning that ~60% of GuaB, fused to an almost full length YdjO (267 amino acids), seemingly performed the function of GuaB.” So this is not a new function.
Now you also need to demonstrate that gene fusion is the normal type of mutation that natural selection has to operate on, I think it’s actually rare, and changes in residues within a gene is the usual form of mutation.
Yes, he did, and he explains why, did you in fact read his explanation? He makes several points in reply, none of which you have addressed. Here is an excerpt: “Evidently we have made a mistake, because mutants that ought to be readable according to our calculation clearly aren’t readable. As you may have guessed, the mistake is that the 2-in-7 typo rate was tolerable only because it was restricted to a narrow section of seven positions. The fact that the remaining 35 positions were without error compensated in large measure for the errors in the mutated section.”
“The remedy is to use a different starting sequence. Specifically, we need the starting sequence to be of the same quality that we intend to require of mutant sequences in order for them to be accepted. Otherwise the mismatch in quality will skew our results.” This is under the heading “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.”.This was your point, now you need to reply to Axe’s extended reply to this.
By the way, where is Art, the author of the article that set out to refute Axe’s paper? Why does he seem to have vanished? So that someone else needs to take up the task of defending this…