sunflowers
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Since the Scopes Trial of 1925 and the Darwin Centennial of 1959, neo-Darwinism has used intimidation and groupthink to maintain its status of "accepted truth" beyond need of further evidence. Critical papers have appeared, but usually outside the leading biology journals. Indeed, merely expressing doubts about Darwin has been a career-limiting move for many (see Free Science). Look at these recent papers, though, and see if it appears to be getting safer to question the explanatory omnipotence of random mutations and natural selection.

How Powerful Is Natural Selection, Really? How powerful is natural selection if it can stall out? This team ran mutation experiments on E. coli's translation machinery and found that "cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations." Darwin's mechanism is not omnipotent. Natural selection, being blind, can stop improving one module and skip to another, leaving the first module below optimum. The authors are not quitting their subscription to natural selection, but they are losing faith in its ability to explain molecular machines by a simple mechanism.
Overall, our results highlight the fact that it is impossible to fully understand the evolution of a cellular module in isolation from the genome where it is encoded and the population-level processes that govern evolution. The ability of natural selection to improve any one module depends on the population size, the rate of recombination, the supply, and the fitness effects of all beneficial mutations in the genome and on how these quantities change as populations adapt. Further theoretical work and empirical measurements integrated across multiple levels of biological organization are required for us to understand adaptive evolution of modular biological systems. [Emphasis added.]
This team resurrected an old criticism levied against Darwin: "a longstanding evolutionary question — dating to criticisms of Darwin's theories by his contemporaries — concerns how such ecological divergence can occur when challenged by hybridization with non-adapted populations." In their studies of sunflowers, the researchers found adaptation occurring not through traditional neo-Darwinian mechanisms, but by information sharing: hybridization and introgression. They explain this non-Darwinian "borrowing" of supergenes, which are "Massive blocks of genes — inherited together 'plug and play' style." Where do you remember the term "plug and play" from? Was it not in intelligently designed peripheral devices able to operate in a computer without user intervention?
"Initially, evolutionary biologists believed that geographic isolation between populations was required for them to differentiate into ecological races or separate species," says UBC evolutionary biologist Loren Rieseberg. "But recent research shows that populations that exist side by side can, and do, differentiate."

"The traits that govern such differentiation often appear to be inherited together as supergenes despite genetic exchange with non-adapted populations that are nearby. In many cases, plants are able to adapt to a new environment by borrowing a supergene or two from a related species that is already adapted."
Such mechanisms of supergene sharing "play a larger role in evolution than previously thought," the headline says. Within one supergene, which can be as long as several million base pairs of DNA, multiple adaptive traits can be passed along from one plant to another. These may include traits for "seed size, timing of flowering, as well as the ability to withstand environmental stresses such as drought or limited nutrient availability, among many others." Here was their reaction to observing a pervasive, non-Darwinian process:
"We were quite surprised," says University of British Columbia (UBC) geneticist Marco Todesco. "Cases in which individual supergenes controlled adaptive traits had been reported before, but it wasn't clear if they were the rule or just a small number of odd exceptions. What found [sic] is that supergenes have a pervasive role in adaptation, and can be truly massive."
Non-Darwinian Thinking Among Biologists This paper and the next one are preprints (not yet certified by peer review), but they reveal additional non-Darwinian thinking among biologists willing to stick their necks out. These authors studied a trait that had an on-off switch. That's pretty cool in design thinking. Why would natural selection keep a useless trait for 200 million years? Maybe the organism was programmed with foresight to know the trait could be useful again some day if the environment were to change.
Dollo's law of irreversibility states that once a complex adaptation has been lost in evolution, it will not be regained. Recently, various violations of this principle have been described. Here, we argue that the logic underlying Dollo's law only applies to traits that are constitutively expressed, while it fails in case of 'plastic' traits that are up- or downregulated according to needs. We tested this hypothesis for an archetypal violation of Dollo's law, the loss and regain of fat synthesis in parasitic wasps. Wasps from lineages that supposedly had lost lipogenic ability more than 200 million years ago were grown under various conditions. In line with our hypothesis, it turned out that fat synthesis had not been lost but was only switched on in low-fat environments. Such plasticity cannot only explain supposed violations of Dollo's law, but also the maintenance of adaptations to rarely occurring extreme events.
Punk Eek, Back in Vogue? Eugene Koonin, the occasional gadfly to Darwinian conformism, contributed to this paper, arguing that punctuated equilibrium is the "default mode of evolution" in certain conditions, and that stasis is the norm. The opening lines recall Stephen Jay Gould's bold affronts to standard neo-Darwinism back in the 1980s:
Punctuated equilibrium is a mode of evolution in which phenetic change occurs in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but no major phenotypic change occurs. Punctuated equilibrium has been originally proposed within the framework of paleobiology, to explain the lack of transitional forms that is typical of the fossil record.
The import of this Darwin-free paper is clear from the title of the news release from the University of Southern California, "Design redundancy is in our DNA." Design? Can you say that in a scientific paper? Oliver Bell is smiling in the accompanying photo, apparently not fearing censorship by the Darwin mandarins. "Design redundancy is not only an invention of engineers for building machines, but also a principle of nature for designing organisms," writes Cristy Lytal in the first sentence. Yikes! Where did the censors go?

While the paper itself does not mention design (as in intelligent design), it does mention "redundancy" 17 times, e.g., "these findings... demonstrate that PRC2/cPRC1 and vPRC1 act redundantly to silence lineage-specific genes and ensure robust maintenance of mESC self-renewal." Surely natural selection must be responsible for this excellent performance. What? No mention of Darwin, selection or evolution?
The redundancy is that there are two separate groups of PRCs [polycomb repressive complexes), and both groups independently and simultaneously work to silence the same lineage-specific genes. If PRC group one stops working, then group two can handle the job. If PRC group two fails, then group one is a capable backup.
Redundancy sounds like a principle an engineer would design into a robot or software program for critical fail-safe functions. Why would natural selection do that? The earlier paper by Venkataram et al. already found that "cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations." If one PRC would be unlikely to evolve to be optimized through natural selection, why would a second one emerge and also be optimized? This is undoubtedly one of many backup plans in the living world.

The scientists observed how stem cells maintain their identity during development. Bell adds,
"Thus, the PRCs coordinate redundant mechanisms that ensure robust repression of key lineage-specification genes not only for differentiation, but also for maintaining the identity of mouse embryonic stem cells."
Design, clearly, is "written in our DNA." What a concept. It might lead to a movement.