A friend writes to draw attention to research papers in the Biologic Institute’s journal (as opposed to review papers). This might provide a start for those interested:
At the very end of 2014, BIO-Complexity published a paper by Reeves, Gauger, and Axe, “Enzyme Families–Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family” which reported experimental results attempting convert various proteins to perform the function of a closely related proteins. They showed that this enzyme conversion would require more mutations than would be feasible over the history of life.
Yesterday on ENV Ann Gauger reviewed their latest research paper in BIO-Complexity, co-published with Doug Axe, “Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only if Preceded by Invention — Selection Itself Is Not Inventive.” I recommend Ann’s post explaining the paper. This is also an original research paper that reports both experimental and theoretical research.
In their 2014 paper. they had tried to convert proteins to perform the functions of other proteins. But those proteins didn’t already have the functions of the target. We often hear of a “promiscuity” hypothesis where a protein has a primary function but might also have a side activity with some weakly selectable function. In time, that side-activity might be refined and optimized to perform some new function very well. This new paper tested the promiscuity hypothesis through both experimental lab-work and theoretical simulations.
Experimental Work: The new study started with “a junk protein with weak activity against the antibiotic ampicillin, but without a properly folded enzymatic structure. It could not be improved by three rounds of random mutation and selection. In contrast, a weakly functional protein with a destabilized but properly folded structure could rapidly be optimized to wild-type levels and beyond.”
So their research suggests the promiscuity hypothesis only works if you’ve already got the right kind of functional protein fold.
Theoretical Work: They also tested this same question using Stylus, a computer model co-developed by Doug Axe that simulates Darwinian evolution in realistic manner. Here’s how Ann explains what they did:
Using a random sequence whose product has very weak similarity to the target character as a starting point, Doug asked whether it could be evolved by random mutation and selection to produce a character that resembles the archetype that was its goal. Short answer — it could not. For details see the new paper describing the work. Next he tested whether an already existing character with some weak similarity to the target could be evolved by mutation and selection to a proficient version of the target character. Once again, the answer was no. However, if the starting character was only six mutations away from optimization, it improved rapidly upon mutation and selection.
The BIO-Complexity paper presented both experimental research and theoretical research (i.e., computer simulations) that converge on a common conclusion: Selection and mutation can refine things that already have a well-honed function (i.e., as Ann puts it, “the starting protein already exists as a functional fold of the right design”). But the mechanism can’t generate new functions. In other words, it can’t generate new folds or novel functions.
See also: This is embarrassing: “Darwin’s Doubt” debunker is 14 years behind the times
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