Just wanted to let everyone know that Ann Gauger has replied to Dennis Venema.
Whether or not the nylonase enzyme was generated by a frameshift mutation and resulted in a new protein fold, the fact of the matter is that mutation directed a completely new enzymatic activity!
As I understand their argument, Axe and Gauger claim that new protein folds are exceedingly rare. But this is really part of their long-standing argument that “sure, evolution can work on small scales, but show me something brand new that mutation and selection have done!” I would say that mutations leading to the development and honing of an enzyme (with or without frameshift and protein folds) that breaks down a newly-introduced synthetic product is a pretty good example of evolution doing something new.
I also have a problem with the way she threw the word “nonsense” into the discussion, especially since she misapplied the term (a nonsense mutation is a nucleotide substitution that makes a premature stop codon). It really seems like this is a desperate attempt to divert attention away from something that doesn’t fit their narrative.
Thanks, @pevaquark, I’ll check out the actual article later (and not Gauger’s interpretation of it) to see if there is more to add.
(nice photoshop skills, by the way!)
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The first thing to pay attention to is the use of the words homologous and analogous. When Negoro et al. (2005) say that the enzyme has structure analogous to B-lactamase folds they are not saying that it was previously a B-lactamase. However, they do put forth the idea that the nylonase enzyme did evolve from a pre-existing esterase that had B-lactamase like folds.
At the end of the day, Negoro et al. were able to point to specific amino acid changes that allowed the esterase to evolve into a nylonase. If this isn’t “new information” in the ID sense, then their definition is irrelevant to the process of evolution. Evolving new activity and substrate specificity is the hallmark of evolution.
However, it is probably unfair to claim that this is an example of de novo production of new protein folds from random sequence since it did evolve from a protein with folds already in place. At the same time, the nylonase enzyme only has 10-20% amino acid identity shared with other esterases and B-lactamases, so there is obviously not a lot of specificity for these types of folds.
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