© Robin Davies, via University of Wisconsin-MadisonDid these three undergrads, working with postdoc Steven Bruckbauer, watch “evolution happen in real time”?
As Michael Behe has explained in these pages and in ID the Future podcasts, natural selection can appear to produce benefits to an organism, but at a cost. Most often, organisms carry on by breaking existing genes and proteins. This is the overriding message of his new book, Darwin Devolves. The tendency for existing complex functions to degrade in order to allow an organism to survive swamps any beneficial mutations that might arise de novo.

Occasionally, excited headline writers proclaim that scientists are watching evolution happen in real time. Let's scrutinize some of these claims to see what really happened. Did a new, innovative function arise by a beneficial mutation? Or did something break that provided a benefit in special circumstances?

News from the University of Wisconsin-Madison announces, "Radiation-resistant E. coli evolved in the lab give view into DNA repair." Accompanied by a photo of undergrads (above, with postdoc Steven Bruckbauer) who "are watching evolution happen in real time," the story appears ready to challenge Behe's principle.
In a recent study published online in the Journal of Bacteriology, biochemistry professor Michael Cox and his team describe blasting E. coli bacteria with ionizing radiation once a week, causing the bacteria to become radiation resistant. In doing so, they have uncovered genetic mutations and mechanisms underlying this resistance. [Emphasis added.]
Needless to say, high-energy ionizing radiation is not life's friend. It's a serious hazard for living things, including astronauts in the space station. If a microbe found a way to resist it, that's something! First, though, the article calls this another case of "directed evolution" (aka intelligent design), not Darwinian evolution.
Their experiment in "directed" evolution is simple. Lead author and postdoctoral researcher Steven Bruckbauer split a population of E. coli into four groups. Once a week, he and a team of undergraduate researchers use equipment in the Department of Medical Physics to hit each population with ionizing radiation until 99 percent of the cells are dead. They then grow the survivors - the one percent that best resisted the radiation - in culture. Most of the new bacteria that grow from these carry beneficial mutations for radiation resistance.
Maybe it bears looking closer at what actually happened in this case. Lo and behold, the genes for resistance were already present in all the bacteria.
While the overall mechanisms, such as enhanced DNA repair, are the same as in naturally resistant bacteria, many of the mutations that caused those changes have never been seen before. Bruckbauer adds that beyond DNA repair and changes to RNA polymerase, there are entirely new ways of being resistant that could arise.
Actual new functions were found! - but only in the imagination:
"These mechanisms for conferring resistance are just the ones we've seen," he says. "It's exciting to think about the novel possibilities we haven't identified or that haven't even evolved yet. There are some other mechanisms seen in nature that we expect to pop up eventually but then new ones might start evolving."
The team celebrated after 125 rounds of zapping the bacteria, but then admitted that they only uncovered a previously existing "latent ability to become highly radiation resistant with modifications to a few existing DNA repair proteins." It means that a stressful environment brought out something that was already present. Most likely, the "modifications to a few existing DNA repair proteins" broke regulatory controls on the repair system so that it became unleashed under this specific barrage of radiation. In any case, the bacteria survived, but nothing new evolved.

Gut Feelings

The human gut microbiome is a good place to test for innovative functions undergoing selection. Mutations happen so frequently, the microbiome could be evolving within our lifetimes. Isabel Gordo in PLOS Biology analyzes theoretical and experimental work on what kind of evolution is going on in those dark passageways. No surprise; it's Darwinism by devolution:
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, 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.
Staying Afloat

A study reported by Stanford University says that "Species evolve ways to backup life's machinery." Essentially, "A new analysis of biological data reveals that every species from bacteria to primates has developed ways to bypass breakdowns in the networks of proteins vital to sustaining life." As Behe would put it, are organisms removing car doors to improve gas mileage? Are they tossing cargo overboard to keep from sinking?
The scientists studied 1,840 species - from bacteria to primates - to understand how evolution built life forms that could survive in the face of natural adversities. What they discovered was profound yet intuitive: Every species has evolved backup plans that allow its protein machinery to find bypasses and workarounds when nature tries to gum up the works. No previous study has ever surveyed such a broad swath of species to find a survival strategy common to all life: Develop a versatile and robust molecular machinery.
The "interactome" of life - the set of gene regulatory networks and protein interactions - must survive perturbations to keep organisms alive. Mutations do not construct new complex machines. This study says that they "gum up the works." Unless species "from bacteria to primates" had pre-existing strategies to backup and survive degradation by mutations, life would quickly devolve to extinction.

Short Stories

Briefly, here are some other tests of Darwinism's ability to innovate:
  • 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?
  • 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.
  • 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."
  • 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.
  • 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 preexistinggenetic 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.
  • 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."
These examples show that all life, from cells to primates, do survive the onslaught of nature's attempts to "gum up the works" with mutations. They do this, though, not by innovation of complex new functions by chance. Instead, they go to desperate extremes to stay alive in spite of mutations. They can exchange pre-existing genetic information from other sources. They can rely on built-in mechanisms to fix and work around the mutations. In short, Behe is right: Darwin devolves, yet life goes on.