So, I can’t spend a lot more time on this today but I am rediscovering the nylonase story and I think it’s pretty complicated. The JBC paper I have been discussing, linked above, argues persuasively, as near as I can tell, that the new enzyme arose by conventional modes of duplication and mutation. The authors of that paper describe the sequences that explain (for the most part) the new activity (breakdown of nylon). And they note that the new enzyme has the same overall structure (fold) as the ancestral enzyme. A straightforward frameshift, to a new protein sequence, is not the likely explanation. If that’s what Ann Gauger wrote, then she’s right.
In my post last year, I noted that the original idea by Ohno was not really a frameshift at all, but a very interesting phenomenon called overprinting. Linked in post above.
However, if ID needs de novo gene birth to be a fiction, then ID is dead. Nylonase may not be a good example (or a valid example at all), but new protein sequences are known to be birthed from non-coding sequence, and de novo gene birth is probably more common and likely than we once thought. I’ve written semi-recently about a new gene (protein) coming about by a frameshift, and there are whole excellent review articles on de novo gene birth. Links below.
https://royalsocietypublishing.org/doi/full/10.1098/rstb.2014.0332