Following up on @Rumraket’s remarks:
Nasvall et al. developed and set out to test a model for the evolution of new genes that they call the “innovation-amplification-divergence (IAD)” model:
We propose the innovation-amplification-divergence (IAD) model (Fig. 1A), which allows the evolution of new genes to be completed under continuous selection that favors maintenance of the functional duplicate copies and divergence of the extra copy from the parental allele (5). The IAD model proposes that the ancestral gene has a weak secondary activity (innovation) (6, 7), and when a change in conditions makes this activity useful, selection favors increased gene dosage (amplification), resulting in two or more copies of the parent allele. The increased copy number pro- vides multiple targets for beneficial mutations and buffers any negative effects a new mutation may have on the original activity. During continuous growth under conditions that select for both the original activity and the new activity, beneficial mutations will accumulate (divergence) in the copies. Any improved copy can be further amplified, whereas less functional copies, including the parental gene, can be lost. Ultimately, this results in a gene duplication in which one gene copy encodes the parent activity and another copy provides an improved, new activity.
To test this model, they broke it down into its three components and evaluated each step separately. For this, they focused on two enzymes that catalyze chemically-related reactions, but that are in pathways for histidine or tryptophan biosynthesis, respectively.
To experimentally test the IAD model, we examined a histidine biosynthetic enzyme (HisA), and through continuous selection we created, by duplication and divergence, a new gene that catalyzes a step in tryptophan synthesis. The original HisA and TrpF enzymes both catalyze isomerization of a phosphoribosyl compound, but each acts on different substrates in the biosynthesis of the amino acids histidine and tryptophan (Fig. 1B). HisA and TrpF enzyme activities are selectable by growth in minimal media lacking histidine and tryptophan. In addition, the enzymes are structurally related and evolved from a common ancestor (8).
Thus, briefly, they first asked whether they could identify a HisA variant that could catalyze the TrpF reaction; this was simple, accomplished by screening trpF mutants that could grow on media lacking tryptophan (and, obviously, histidine). They isolated bacteria able to do this and confirmed that they had indeed isolated strains in which HisA had acquired TrpF activity (and was thus bifunctional). This is a positive experimental confirmation for the “innovation” part of their model. (Note that, other than conduct the experiment with a mutant strain, these researchers did nothing to promote or guide the outcome.)
The researchers then set out to test the second step of the model, and specifically to ask if gene amplification could improve the growth of cells that carry the bifunctional gene. I won’t describe the set-up, other than to say that they placed the bifunctional gene into a genetic context that allowed for easy generation and assay of gene amplification, and then performed selections in strains in which the bifunctional strain was the only source of HisA and TrpF activity. They identified variants that indeed grew better, and confirmed that the improved growth was due to gene amplification. This outcome is positive experimental support for the second part of their model.
To test the third step of the model, they then allowed lineages to continue to evolve under the same selection (no his or trp) for thousands of generations. They succeeded in isolating many better-growing variants. Different of these had bifunctional enzymes with further alterations; collectively, these alterations define many (most?) of the different mechanisms by which evolution might improve the enzyme:
As predicted from the IAD model, we observed the appearance of a diverged gene copy with improved activity, relaxed selection for maintenance of the unimproved copies in the amplified array, loss of the unimproved copies, and, in some cases, reduction in the total gene copy number.
Compare what Nasvall did with Ann’s description:
The story: Näsvall et al. created a gene that encoded an enzyme that was able to carry out two functions, but very poorly.
No, they did not “create” a bifunctional gene. Random mutation and natural selection was the mechanism, not design.
They placed that gene in a strain of Salmonella that lacked the genes for those functions. Then they cultured the bacteria under conditions where they needed to carry out those functions to grow. Guess what? The bacteria duplicated the genes so as to make more of the poorly functioning enzymes.
Which was the exact point of the assay – to test the hypothesis that duplication can contribute to enzyme evolution. The answer, it turns out, is yes. (It seems to me that Ann’s objection here is quite akin to claiming that enzyme assays are not valid because the biochemist first makes extracts (and purified enzymes) and then conducts tests with non-natural substrates. In other words, the objection fails.)
Over time, the genes acquired mutations (remember, we are talking about a lot of bacteria) and the ones that helped the most gave the best growth rate, and… after thousands of generations they had evolved separate enzymes for each function — meaning not that they had evolved new enzymes, but that they had divided up the pre-existing dual-functional gene into two genes.
Again, not correct. Nasvall et al. noted:
The evolved genes fell into three classes: (i) specialized genes with strongly improved HisA activity and loss of TrpF activity, (ii) specialized genes with strongly improved TrpF activity and loss of HisA activity, and (iii) generalist genes whose encoded enzyme showed a moderate increase in both activities …
Note that, among the classes of enzymes are ones in which HisA has now become TrpF (for all intents and purposes). This is a transition that Gauger and Axe say cannot occur (from the abstract):
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.
Note that the only “tools” Nasvall et al. used were random mutation and natural selection - exactly what Gauger and Axe claim are not tenable means for generating new functions.
The bottom line - Ann, @Wayne_Rossiter, Behe, and others object to Nasvall et al. for reasons that are completely baseless.
(Sorry this is so long - the words are needed to clear up the confusion sown by Ann and others.)