(2017-11-30, 12:30 AM)malf Wrote: [ -> ]http://scienceblogs.com/dispatches/2007/...obability/
Some added depth in the comments too
For a research paper on problems with the neo-Darwinian evolution of new enzyme functions, see "The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway", at
http://bio-complexity.org/ojs/index.php/...O-C.2011.1:
Abstract
Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo.
We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.
Article on problems with the neo-Darwinian evolution of new enzyme functions: See
http://www.worldscientific.com/doi/pdf/1...08728_0022:
"First obstacle: Because gene expression is costly, it cannot be assumed that weakly converted enzyme functions isolated by laboratory selection would provide net selective benefit in wild populations.
...Second obstacle: Beneficial mutations appearing less than about once per generation in a global bacterial population may remain unfixed for a billion years or more.
...Third obstacle: Adaptations requiring duplication and modification of an existing gene should not be presumed feasible if they require more than two specific base substitutions, which seems to exclude most functional conversions. Enzymatic innovations requiring more than two specific mutations in a spare gene (provided by a duplication event) are implausible in neo-Darwinian terms."
Here is a 2010 review paper by Michael Behe in Quarterly Review of Biology which found that when bacteria and viruses undergo adaptations at the molecular level, they tend to lose or diminish molecular functions: Michael Behe, “Experimental Evolution, Loss-of-Function Mutations, and the “First Rule of Adaptive Evolution,” The Quarterly Review of Biology 85(4) (December, 2010).
An empirical study by Ann Gauger and Ralph Seelke found that when only two mutations along a stepwise pathway were required to restore function to a bacterial gene, even then the Darwinian mechanism failed (Ann Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” BIO-Complexity 2010 (2): 1-9).
I notice you haven't responded to the three challenges at the end of my post.