Thank you for all the work you do to translate biological knowledge into a form that nonspecialists can comprehend. I have made use of your work in some of my blogging on evolution (e.g. https://letterstocreationists.wordpress.com/2014/04/02/realistic-expectations-for-transitional-fossils/ ).
I know this issue was discussed a bit in the comments on your earlier article on nylonase, but the treatment in Wikipedia indicates strongly no frameshift mutation was involved in the evolutionary development of the gene. The Wikipedia entry “Nylon-eating Bacteria” states:
”... Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or, for that matter, any other bacteria), and not effective on any material other than the manmade nylon byproducts...This discovery led geneticist Susumu Ohno in a paper published in April 1984 to speculate that the gene for one of the enzymes, 6-aminohexanoic acid hydrolase, had come about from the combination of a gene duplication event with a frameshift mutation. Ohno suggested that many unique new genes have evolved this way. A 2007 paper that described a series of studies by a team led by Seiji Negoro of the University of Hyogo, Japan, suggested that in fact no frameshift mutation was involved in the evolution of the 6-aminohexanoic acid hydrolase.”
The 2007 paper they cite here is Seiji Negoro, et al., Nylon-oligomer Degrading Enzyme/Substrate Complex: Catalytic Mechanism of 6-Aminohexanoate-dimer Hydrolase, Journal of Molecular Biology Volume 370, Issue 1, 29 June 2007, Pages 142–156. That 2007 Negoro paper seems to discuss mainly the mechanism of the hydrolase.
The 2005 Negoro paper you cited [Journal of Molecular Biology Volume 370, Issue 1, 29 June 2007, Pages 142–156] talks more about the genesis of the active EII gene from the barely-active EII’ gene. The abstract concludes, “...Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase.” That seems to be the basis of Wikipedia indicating in this “Nylon-eating Bacteria” article that no frameshift was involved.
The Wikipedia article “Frameshift Mutations” likewise claims that the frameshift concept is likely wrong:
“Frameshift mutations have been proposed as a source of biological novelty, as with the alleged creation of nylonase, however, this interpretation is controversial. A study by Negoro et al (2006) found that a frameshift mutation was unlikely to have been the cause and that rather a two amino acid substitution in the active site of an ancestral esterase resulted in nylonase.”
In this case the Wikipedia article cites the 2005 (not 2006) J. Molecular Biology article that I mentioned above.
In the comments on your earlier article, you stated that “As I understand it, confusion arises that there are duplications of the enzyme after the initial frameshift mutation that creates the first nylonase. These duplications undergo mutations that improve their specificity (recall that the first nylonase is a pretty poor nylonase). “ This implies that the Wikipedia interpretation is incorrect.
Would you mind elaborating more on what exactly the ancestral gene was and where the frameshift-causing mutation took place, how that affected the gene in terms of its original function, how Wikipedia erred, etc.? Hopefully you can address this in some detail in a separate article, with some of your nice illustrative figures. This nylonase gene is one of the clearer evidences for evolution, but the Wikipedia treatment can be used to dismiss it as just a trivial matter of a couple of point mutations. Thanks.....