Continuing the discussion from Series reviewing Douglas Axe's Undeniable:
Axe’s reply to Venema contains the following statement:
[Venema] sees “strong evidence” that “new genes that code for novel, functional proteins can pop into existence from sequences that did not previously encode a protein.” The authors of the paper he cites in support of this are more cautious. Like all authors, they want to think the evidence they provide is strong, but considering the number of assumption involved, they are compelled to be more tentative: “These results suggest that BSC4 may be a newly evolved gene” (emphasis added).
Wanting to find the context for this statement, I decided to read the 2017 article Venema referenced:
“Foldability of a Natural De Novo Evolved Protein” (links here and here)
Here are the statements I did find:
Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. [emphasis mine]
We have demonstrated for the first time that a young, naturally functional protein, encoded by a gene that evolved recently de novo from noncoding DNA, folds to a structure with some properties found in native globular proteins. [original emphasis]
Even if the native form of Bsc4 differs from the structures studied here, however, the results still demonstrate for the first time the rudimentary foldability of a natural de novo evolved sequence.[original emphasis]
These statements do not contain even a hint of the caution that Axe thought necessary. In fact, the statement Axe quotes is not even in the paper.
So what gives?
I had to go back to Venema’s essay to find an answer. What I saw was that Venema had cited two different papers on BSC4; an earlier one from 2008, and a more recent one from just a few months ago (the one I had read). Axe’s quotation was from the paper 10 years ago–a very long time in a fast-moving scientific field.
Axe completely ignores the paper published just 4 months ago, which undoubtedly contains a better representation of what is known about BSC4 than the 2008 paper. And that 2017 paper does not contain the slightest hint of caution or suggestion. Venema’s statements about BSC4 have the same degree of confidence as the statements by the authors of the 2017 paper. Thus Axe’s accusation that Venema was too confident seems to be misleading.
As a non-biologist, I am in no position to discern whether the authors of the 2017 paper were overly confident in their statements. At a minimum, though, Axe would have to explain to his readers why the authors of the 2017 paper were incorrect; and he would have to identify those authors as the source of the error, rather than Venema.
Best,
Chris Falter
P.S. The 2008 paper is hardly a source of support for Axe’s position. For example, it contains the following statement:
Comparative genomic study supports the notion that novel protein genes derive from preexisting genes or parts of them. For example, exon shuffling, gene duplication, retroposition, and gene fusion and fission all contribute to the origin of new genes (Long et al. 2003).
