The Discovery Institute has a new article out on what they claim is another example of “devolution”.
There are a few other topics in that article, but I thought we could focus on the evolution of DNA repair in irradiated E. coli for the purposes of this thread.
From my initial reading, the Discovery Institute is trying to redefine mutations as a “latent ability” in order to make the evidence go away.
It would probably be best to read the source material to see what actually happened.
Yes, we have seen this. However, how do they propose to demonstrate that this is the case? If active genes are so fragile that they fall apart with mutations, how are latent genes preserved?
I think they’d quote Emerson:
A foolish consistency is the hobgoblin of little minds. A great person does not have to think consistently from one day to the next. 
From the abstract of the peer reviewed paper:
It’s pretty obvious from the abstract that irradiation resistance was due to mutations that happened during the experiment and were not pre-existing mutations. If someone has access to the full paper perhaps they could give us some specifics about these mutations and how they affected the genes they are found in.
This is correct. All replicate populations were started from the same initial strain. I’m reading the paper now and will report back with some more info in a bit.
I believe the following section from the Discussion provides the relevant info regarding the DNA repair mutations:
Modified DNA repair proteins and RNA polymerase enhance IR resistance.Eachpopulation has traversed unique evolutionary paths to reach the same goal (Fig. 8AtoD). Despite varied levels of clonal interference in each population, significant geneticparallelismin these populations allow us to identify at least some of the contributorsto extreme IRresistance. In one isolate from population IR9-50, IR9-50-1, mutationsinrecD,recN, andrpoB/rpoCincrease IR resistance of the Founder Δe14 parentderivative. However, these variants—singly or together—do not account entirelyfor the IR resistance phenotype of IR9-50-1 at a dose of 1,000 Gy (Fig. 9AandB).Noneof these genes have been previously implicated as mutational targets con-tributing to IR resistance (45–47).
The effects of mutations in these genes reveal complex interactions. When presentin an otherwise wild-type background, the mutations inrecDandrpoBexhibit a clearcontribution to IR resistance, although results with therecNmutation were variable. TherecDandrpoBeffects were not additive, and combining them demonstrated diminish-ing returns epistasis. When therpoBmutation was reverted to wild type in the IR9-50-1mutant background, the IR resistance phenotype was reduced little or not at all.However, reverting therecDandrecNmutation to wild type resulted in a considerableloss of IR resistance. It appears likely that a complete genetic deciphering of the IRresistance of IR9-50-1 and other isolates will require a more systematic consideration ofrelationships between mutations and genetic backgrounds.
Although additional contributions are clearly present, the alterations in RecD, RecN,and RpoB/RpoC (Fig. 9) provide the clearest evidence for phenotypic contributions in the current work. RecD is part of the RecBCD heterotrimer responsible for preparingssDNA required for RecA loading, initiating homologous recombination. The RecD A90Evariant is likely a loss of function mutation, as a RecD deletion in the Founder Δe14background increases IR resistance as much as the A90E variant in this background.RecD inactivation produces a hyperrecombination phenotype (59–62). Increased ho-mologousrecombination could be of significant use to repair highly fragmented DNApost-IR, with approximately 15 DSBs generated at 1,000 Gy (1).
RecNis a cohesin-like protein which is involved in RecA-mediated double-strandbreak repair (63–66). There is little known about the precise function of RecN, thoughithas been implicated in maintaining proximity of broken dsDNA ends to an activeRecA filament. The function of the K429Q variant is unknown, but the K429 residue ispositioned in a RecN domain highly conserved among bacteria. The K429Q variant isunlikely to be a loss of function, sincerecNdeletion greatly enhances IR sensitivity (46,67). Further work on these RecN variants may shed new light on the function of theRecNprotein.
RpoB and RpoC are the beta and beta-prime subunits of RNA polymerase, respec-tively. Stringent mutations of RNAP, which mimic the effects of ppGpp binding andtherefore the stringent response, are located primarily in RpoB and RpoC (68). Some ofthesestringent mutants are capable of rescuing UV sensitivity ofruvABCmutants ofE.coli, potentially due to decreased stability of contacts of RNAP with DNA (69,70). Similartothese previous observations, the mutations in RpoB that are prevalent in our evolvedpopulations do not locate to a single region of RpoB and therefore may affect DNAinteraction throughout the DNA channel formed by RpoB/RpoC. Previously describedstringent mutations L571Q and H1244Q mutants (69,70) affect residues near thoseaffectedin the present study. These mutations likely decrease stability of RNAP on DNAand may allow for easier removal of RNAP that has stalled at a DNA lesion. Removal ofstalled RNAP may be crucial for efficient DNA repair due to RNAP occluding the lesionfrom repair machinery or providing a major obstacle to DNA replication (71). Inaddition,many stringent mutants of RNAP also confer resistance to the antibioticRifampicin. Mutated variants of RNAP at P535 (72) and S574 (73–75) (which have alsobeenisolated in this study) have previously been isolated using selection for rifampinresistance. Although these are the first RNA polymerase mutations detected inE. colievolved for IR resistance, similar mutants have been generated during experimentalevolution ofE. colifor trimethoprim and doxycycline resistance (58), heat tolerance (76,77), growth in nutrient-limited conditions (78,79), and acid resistance (80,81). Modi-ficationsin RNA polymerase may confer enhanced fitness throughout serial passaging,a common feature of experimental evolution studies. This advantage, combined with apotential ability to enhance DNA repair, may explain the rapid appearance ofrpoBorrpoCalleles in each evolving lineage (except IR10).
It looks like I will have to wait 6 months, unless I can talk @davecarlson into email a copy to me 
This is pretty interesting. The study actually directly contradicts the Polar Bear ApoB case they are making. They have staked their claim saying most missense mutations must be “damaging”, but in this case we know for a fact that the missense mutations increased biomolecular function.
@BJB, can you test these mutations in Polyphen? That will be an entertaining detail to throw into the conversation.
I’m happy to email a copy of the paper to anybody who PM’s me their address.
The mutations were novel, but the DI has latched onto the first author calling this new resistance a “latent ability”. The first sentence of the paper’s discussion reads:
“It is clear that latent within the E. coli genome is a capacity for resistance to extreme doses of ionizing radiation.”
The DI takes this to mean that it was a designed feature - the bacteria were designed in such a way to be able to mutate “easily” to become radiation resistant.
The bacterial genes involved either lack homologues in humans, or have diverged far too much. None of the relevant ancestral E. coli sites are conserved in humans, so polyphen can’t do anything with them.
The second example of “devolution” in the article (the gut microbiome) has nothing to do with Behe’s thesis - it’s just documenting the nearly neutral theory of molecular evolution. It has nothing to do with adaptive mutations being “damaging”, it’s about most fitness-affecting mutations being non-adaptive! The quote even says that these non-adaptive mutations are purified in the long run, so it has little to do with long-term evolution.
The EN article quotes this part of the primer (not the original paper):
The observed patterns of between-host polymorphism reject the predictions of a simple neutral model of molecular evolution for several human gut bacteria. Synonymous site polymorphism (i.e., that does not lead to changes in the protein sequence) exhibits a variance clearly inconsistent with a model, in which neutral mutations arise in each host and a single lineage transmits between hosts. However, the pattern of polymorphism at synonymous and nonsynonymous sites is consistent with the slightly deleterious theory of molecular evolution [16], in which widespread purifying selection may keep a microbial ecosystem functional, at long time scales, for all hosts. Much of the variation observed can be explained by postulating the recurrence of a high fraction (90%) of mutations whose effects decrease fitness by a very modest amount (approximately 0.01%) but still strong enough to be purified in the long run.
But for some reason leaves off the very next paragraph, when Gordo begins to talk about adaptive mutations. Surely this is the part that might actually be relevant to Behe’s thesis?
When looking for signs of evolution (identity by descent with modification) within hosts, significant changes in SNV frequency could be detected on a time scale of six months (occurring in 12% of the time comparisons). This was possible even under the strong criteria imposed for low false-positive rates (frequency changes above 60%), which can greatly limit power to detect true events that may occur but remain undetected with this type of data. Of the identified events, approximately three-fourths involved a handful of SNVs rising to high frequency on a time scale of hundreds of generations. Such an observation is highly unlikely under neutral evolution (in which mutations would take a much longer time to change in frequency) but fully consistent with natural selection increasing the frequency of mutation and/or recombination created alleles having fitness effects of a few percent. The remaining one-fourth of the detected changes involved thousands of SNVs, compatible with the replacement of a dominant strain by a newcomer invader strain or with a rapid spread of another resident strain, which was colonizing that host at low frequency [14]. Furthermore, albeit under the strong filtering criteria imposed to avoid false negatives and/or positives, gene content differences could also be inferred. These involved gene losses (caused by mutation [deletions] or recombination) and gene gains, potentially recombination derived, which tended to change the accessory (noncore) genome.
Neither this primer that EN article quotes nor the original paper provide any evidence in favour of Behe’s thesis. The paper doesn’t do any kind of characterisation of the adaptive (or non-adaptive) mutations to see if they’re “damaging” or not.
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The 3rd example in the EN article (staying afloat) is even worse.
It quotes this press release about this paper.
The study looked at how robust protein interaction networks (interactomes) were to breakdown.
However, the subject of the paper is completely irrelevant, because the only point the EN author seizes on is a throwaway line from the press release about one way the breakdown of networks could happen: mutations.
Hold the presses! Mutations can break down networks of interactions! Wait, what does this have to do with Behe’s thesis again? Absolutely nothing. The EN article’s takeaway is simply:
Mutations do not construct new complex machines. This study says that they “gum up the works.”
The original paper is interesting though - worth a read.
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I also took a look at the 6 “short stories” mentioned at the end of the article:
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A paper in PNAS by Milner et al. shows that fungi can gain new functions! Yes, but the method is by horizontal gene transfer (HGT) — i.e., by borrowing existing genes. Scientists found that fungi can gain transporter-encoded genes by HGT, giving them a “distinct competitive advantage in a given environment,” they say. “This has wide implications for understanding how acquisition of single genes by HGT can drastically influence the environments fungi can colonize.” How many other claimed instances of gain-of-function mutations are really cases of HGT?
It’s a paper about beneficial fitness effects of HGT in fungi. How is this supposed to support Behe’s thesis that beneficial “non-damaging” mutations are rare? The last sentence reads as though the paper investigated cases of fitness increase that they presumed to represent a gain-of-function mutation but then were surprised to discover that they were actually HGT after all, but that isn’t what happened. The authors set out to identify cases of HGT and then examine their fitness effects.
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Darwin is devolving in beehives. Here is the honeybee version of the children’s story, “The Town Mouse and the Country Mouse.” Phys.org says that the “waggle dance” method of communication is disappearing in urban settings. “One possible reason may be human-induced habitat change,” which led to the loss of this complex, informative behavior.
Oh finally, an actual case of “loss”. At least, that’s what the EN article’s phrasing and chopped-up quotes would have you believe. In fact, if you actually read the Phys article and the original paper it turns out there’s no mention of the “waggle dance” behaviour disappearing in urban settings. The paper is basically about the effectiveness of the waggle dance in different circumstances. Through experiments, they found that the bees were able to learn whether or not it was worth their time to pay attention to the waggle dance or just go off and find food on their own. They found that in “disoriented” experimental conditions (where the dance was meaningless), the bees learned after a few days to not bother paying attention because it was a waste of time. The authors relate these experimental results to real environments, and conclude that in some environments, at some times, the waggle dance might not improve foraging success. They say:
”If there is no benefit of dance communication in temperate climates, then why do bees dance? First, the dance might still be beneficial to foraging success in our study area during other time periods, e.g., in spring. Bee colonies may gain weight during only a few weeks per year. For this reason, it is critically important that the colony can exploit the high-quality resources available while there are good foraging conditions; the dance is likely to play an important role in maximizing foraging efficiency during such periods. Second, encoded spatial information is only one part of the dance. For example, forage odor plays an important role in honeybee foraging, and incoming dancers will distribute this information to followers during their dance displays ( 19 , 28 , 36 ). Dancers can also reactivate foraging at a patch by stimulating experienced foragers to revisit foraging sites ( 8 ). Thus, while the spatial information contained in the dance will likely have a fluctuating value over the seasons, the other cues may mean that dancing remains an important feature of the honeybee’s foraging success.”
In other words, there’s no reason to think that the waggle dance behaviour is “disappearing” anywhere. Even if it was, what do you expect? If the behaviour provides no fitness advantage, why shouldn’t it be lost? Is that how low the bar for Behe’s “devolution” thesis is? If a bird evolves a long beak to get at nectar in deep flowers, then later the deep flowers die out and are replaced by shallow flowers, would Behe cry “devolution!” if the birds evolved shorter beaks again?
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Another Phys.org article says that antibiotic resistance genes “spread faster than so far thought.” The reason? It’s not the emergence of novel genes by mutation. Instead, “resistance genes hop around the genome.” Methods of gene sharing include viruses, phages, and transposons. An international team was surprised to find that “mobile genetic elements induce a fast distribution of resistance genes among genomes of different organisms.” One said, “The finding that resistance is also extensively transferred between bacteria without the involvement of plasmids is really quite surprising.”
Again, nothing to do with Behe’s thesis. Observing instances of HGT doesn’t mean that adaptive gain-of-function mutations are rare. I’ll add that from reading this paragraph from EN, I got the impression that the study in question represented some kind of huge, landmark study on the spread of antibiotic resistance from a large number of cases. In fact, it’s a quite small study, exposing fish to an antibiotic for a month and then looking at the gut microbiome for how the resistance genes spread. Also, contrary to what the EN authors writes, the paper does mention that several of the horizontally-transferred genes were mutated to confer resistance.
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Scientists found a plant genome with “among the most GC-biased genomes observed to date.” The parasitic plant uses only six amino acids, and is 95 percent composed of AT base pairs. “Darwin help us!” exclaims the exasperated author David Roy Smith in Current Biology . Apparently these two parasitic plants have forsaken richer genomes because they are able to get by with less.
Several issues here. For a start it should be made clear that David Roy Smith is the author of the Current Biology article commenting on the original study in PNAS, he’s not the author of the study itself. Second, look at how the EN author managed to twist his words. In the comment piece, Smith says:
”I thought I had seen it all. However, the recent sequencing and characterization of two plastid DNAs (ptDNAs) from the holoparasitic plant genus Balanophora (Figure 1) has proved me wrong and raised the bar of what defines an extreme genome [1]. With AT compositions of 88.4% and 87.8%, the B. reflexa and B. laxiflora plastomes have a smaller proportion of GC base pairs than any other ptDNA explored to date. Even more remarkable, the AT bias is most prominent in the true heart and soul of these genomes: the protein-coding genes. It stands to reason that coding DNA should contain at least some guanine and cytosine in order to encode the correct cohort of amino acids needed for making functional proteins. I guess the Balanophora ptDNAs did not get this memo. Darwin help us, the ycf2 gene from both species is 98% AT! Or, put differently: across the 750 nt that make up this plastid gene, there are fewer than eighteen sites containing a G or C.”
Ok, that’s the exclamation in context, does Smith sound in any way “exasperated” there? He’s excited, for goodness’ sake, not irritated!
The EN author says “the parasitic plant uses only 6 amino acids, and is 95 percent composed of AT base pairs.” This is just a basic failure of reading comprehension. The paper isn’t about the plant’s whole genome, it’s specifically talking about the plastid DNA. The original paper and Smith’s comment piece both make it clear that about 80% (not 100%) of the proteins encoded in the plastids consist of only 6 different amino acids, and that “several genes” in the plastid have an AT content in excess of 95%, not all of the genes or the entire plastid genome.
All these errors aside, does this study really support Behe’s thesis? I suppose it’s a case of adaptation via loss, so perhaps it does, but then again it’s also exactly what is expected by natural evolution. Parasitic organisms becoming more streamlined has been known about forever, this case is just an extreme example.
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Let’s all evolve like the birds evolve. How do birds adapt their songs? With “preexisting genetic variation.” Lai et al., writing in PNAS , seemed to want to hear their favorite Darwin tune, but found that parrotbills in Taiwan select “standing genetic variation” instead of de novo mutations. They found that “the evolutionary potential of a population depends significantly on its preexisting genetic diversity.” Selection of existing genetic variation is likely to swamp new beneficial mutations, because “ a high level of standing variation may allow a faster response to environmental changes than waiting for appropriate mutations to arise. ” Understandably so.
What…? Does the author of this EN article think that all/most adaptation should occur via mutations that appear de novo after the selection pressure appears? It’s completely uncontroversial that standing genetic variation is a huge source of variation for natural selection to act upon. Also, where does the author think this standing variation originally comes from if not mutations? This is baffling, and again has nothing to do with Behe’s thesis.
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Are humans evolving new beneficial mutations? Analysis of the human genome at the University of Barcelona identified 2,859 genes that apparently have been under selective pressure. Further reading shows that some of these result from “ hybridisation of the human species with the Neanderthals and other hominid species,” which implies sharing of existing genetic information. Other genetic changes aiding survival in certain environments, such as for lactose tolerance or ability to endure high altitudes (hypoxia), may result from relaxation or breaking of controls of existing genes. Overall, the research is revealing “how the introgression of archaic genomes have modelled our current genomes.”
Another completely irrelevant study to any of Behe’s ideas. The EN author doesn’t even attempt to write a “gotcha” sentence or two about these results. Some beneficial variants came from introgression, yes, the point being…?
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Conclusion
Honestly this is one of the worst EN articles I’ve ever read. Of the 9 studies they cited that supposedly supported Behe’s “devolution” thesis, literally none of them came close to doing so.
Exactly zero of their sycophants will do the same sort of analysis though. They’ll see lots of words and references. Therefore, the DI must be right!
Dennis Venema’s critique is still dead on:
Citing cases of devolution really doesn’t cut it if you ignore all of the constructive mutations.
For me, this why I think Behe’s ideas about IC and “devolutionary positive mutations” makes the front-loading design scheme unlikely. In fact, were I working on refining ID theory and given those two conditions I’d suspect that changes were introduced fairly often and in discrete stages, not pre-loaded. And with that refinement, I’d begin examining what that model would predict, compared with what we’ve observed. I wouldn’t just “wave my hands” about the implications of a particular set of design hypotheses. I’d want to create tests to rule out possible models. You know, “do science”.
The meaning of “devolve” has devolved.
We are Devo. I’d post a meme but…