Gauger: Answering Art Hunt on Real Time Evolution

[T_aquaticus]

@swamidass

Internal Genetics. the genetic manipulations are merely so that the researchers could better measure and study the evolutionary process, but they do not actually altering the mechanism. A good analogy might be tagging a wild animal with a radio transmitter, and then releasing him back into the wild to track his movements. Yes, there is an immense amount of designed technology in the transmitter, but this just helps us observe what the wild animal does on its own, without directing him. It does not appear the manipulations alter or direct the course of the evolutionary mechanism, so why is this a valid objection?

Just to be clear, here are the specific genetic manipulations:

The expression of the his operon (including hisA) is regulated by an attenuation mechanism that regulates the amount of read-through of a transcriptional terminator before the first structural gene of the operon according to the availability of charged histidinyl-tRNA (28). As this results in very low expression of hisA in medium containing histidine, we included a mutation (hisO1242) (29) which removes the transcriptional terminator, thereby leading to derepressed transcription of the his operon even in the presence of histidine. This selection resulted in very few mutants (an estimated mutation frequency of less than 10-11 / cfu).
http://science.sciencemag.org/content/sci/suppl/2012/10/17/338.6105.384.DC1/1226521.Nasvall.SM.pdf

All they did was remove a section of DNA upstream of the gene so that it would be expressed even in the presence of histidine. If the gene is not expressed then there can’t be selection for beneficial mutations in that gene. In other words, they simply made it possible to select for and detect mutations that changed the activity from his+ to trp+. The genetic manipulations themselves did not cause those mutations. The mutations that did occur in the hisA gene are entirely natural.

Let’s compare the methods used by Nasvall et al. to the methods used by Gauger and Axe:

For each of the fifteen candidate positions identified by sequence alignment, we constructed a mutant bioF gene specifying the Kbl amino acid at the candidate site. Plasmids carrying these mutant genes were introduced into an engineered strain of E. coli lacking the chromosomal bioF gene (see Methods) in order to test for biotin auxotrophy. Interestingly, of these fifteen single amino-acid substitutions, the only one disruptive enough to produce the Bio– phenotype is the replacement of histidine 152 with asparagine (see Table 1).
Gauger

What did Gauger and Axe conclude from this work?

The finding that functional conversions within fold families are much harder to achieve in the laboratory than was expected raises the question of their evolutionary feasibility.
[ibid.]

Gauger and Axe used designed site directed mutagenesis to change amino acid residues, and they concluded that this was a fair test for evolution. For those who may not be familiar with this process, it involves the purposeful targeting of a base or several bases to produce a specific change in sequence. Gauger and Axe also had the manipulated gene on an engineered plasmid that guaranteed its expression in all conditions, just as was the result of the manipulations Nasvall et al. introduced. Gauger and Axe also grew the bacteria in an artificial environment where they added or subtracted biotin.

In comparison, Nasvall et al. allowed the gene to be mutated naturally by the mechanisms already present in the bacteria. @Agauger is now saying that allowing the gene to be mutated naturally is not valid for testing evolution, but is already an author on a paper where there were designed and targeted mutations, artificial promoters, and artificial environments. Even with all of these conditions, the experiments in the Gauger and Axe paper were considered a valid test of evolution. These positions don’t square up.