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Non-Mendelian Inheritance Undermines Neo-Darwinism

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Photo: Galápagos finch, by Mike's Birds from Riverside, CA, US, CC BY-SA 2.0 , via Wikimedia Commons.

Few beside historians know about the crisis of evolution in the late 19th century continuing into the early 20th century. At the time, most intellectuals had been convinced of evolution in some form, but critics of Darwin’s natural selection were many. Neil Thomas writes about that period in his new book, Taking Leave of Darwin. Even before Darwin died in 1882, he was feeling the pressure of critics against his theory and was relying more on the Lamarckian notions he had tried to supplant. Doubts about natural selection increased well after the rediscovery of Mendel’s laws of heredity. Finally in the 1930s the “Neo-Darwinists” breathed a sigh of relief when they found a way to incorporate Mendelism. Their relief led to strong confidence in Darwinian evolution that roared into overconfidence at the Darwin Centennial and still reigns today. New findings are unraveling that confidence. 

More scientists are realizing that organisms have other ways to inherit traits. In 2017, some of those methods were introduced here. Last month, Emily Reeves categorized some of the sources of genetic change. In her table, “random copy errors” and “chemically induced mutagenesis” were only two of them. At the CELS conference in June, engineers and biologists mooted some cutting-edge ideas of internal reprogramming by organisms enabling them to adapt to changing environments. That almost sounds Lamarckian: if an organism can “learn” adaptations and pass them on, is that “inheritance of acquired characteristics” due to “use and disuse”? Whatever it is, it is not unguided variation in the sense Darwin taught. Any process that shares existing information is also anti-Darwinian. That includes horizontal gene transfer (HGT), hybridization and introgression.

Flinch at Beak Evolution

Of all things, Darwin’s finches are coming up for debate again. Lifetime finchologists Peter and Rosemary Grant just published a paper in PNAS that conjures up “Morphological ghosts of introgression in Darwin’s finch populations.” The ghosts spooked them.

We discovered a surprisingly large reduction in average beak size from samples of G. fortis collected roughly 30 y apart in the period after the disappearance of mega-magnirostris. Reduction was expected in the absence of gene flow, but was not expected to be restricted to the beak depth dimension, nor was the magnitude expected. Without observations or measurements of living birds from that time, it is not possible to do more than speculate on the causes. Unlike the situation with G. fortis in response to mega-magnirostris, we have no a priori hypothesis and no basis for invoking a bias in the collecting of samples. Selection alone is not likely to be a viable post hoc explanation for a major trait-specific change in fewer than 10 generations, in view of the strong positive genetic correlations between beak depth and the other two beak dimensions in the related G. fortis population on Daphne Island (28). A possible explanation is hybridization with the smaller G. fuliginosa…. However, there is no negative skew in the distribution of the late G. fortis sample … that would indicate introgressive hybridization. Genetic data from specimens in museums may help to resolve the question of whether the morphological ghost of introgression from mega-magnirostris in the early sample was almost completely exorcised by selection, replaced by a different ghost of hybridization with G. fuliginosaor both. [Emphasis added.]

The ghost of hybridization is scaring them into changing their view of finch evolution by natural selection. The information on beak size from an extinct species apparently is showing up in some living species. This can only be due to information-sharing between the islands. If this happens in one of the most famous icons of evolution, where else is it occurring?

Resistance Is Futile

Nature reports that “Massive DNA ‘Borg’ structures perplex scientists.” These unexpected structures appear to be a library of information accessible to microbes.

The Borg have landed — or, at least, researchers have discovered their counterparts here on Earth. Scientists analysing samples from muddy sites in the western United States have found novel DNA structures that seem to scavenge and ‘assimilate’ genes from microorganisms in their environment, much like the fictional Star Trek ‘Borg’ aliens who assimilate the knowledge and technology of other species.

It’s one of the largest extrachromosomal elements (ECEs) ever found. 

These extra-long DNA strands, which the scientists named in honour of the aliens, join a diverse collection of genetic structures — circular plasmids, for example — known as extrachromosomal elements (ECEs). Most microbes have one or two chromosomes that encode their primary genetic blueprint. But they can host, and often share between them, many distinct ECEs. These carry non-essential but useful genes, such as those for antibiotic resistance.

These large ECEs can have a million DNA base pairs and can be as large as a third of the main chromosome in microbes. Do they function as collections of genetic information available to microbes?

Borgs seem to house many genes needed for entire metabolic processes, including digesting methane, says Banfield. She describes these collections as “a toolbox” that might super-charge the abilities of Methanoperedens.

Claire Ainsworth at New Scientist says that the Borgs have “huge potential for new information” that could be shared between organisms.

The large number of protein-coding genes that Borgs contain is also remarkable. While the majority of these are unknown, about a fifth resemble genes found in archaea — particularly those of a methane-consuming genus called Methanoperedens in which the Borgs replicate. As well as assimilating host genes, there are signs that different kinds of Borg can swap DNA with each other and possibly move between hosts, potentially allowing Methanoperedens to acquire new genes from elsewhere.

Banfield found some examples of this “novel form of giant, extrachromosomal DNA” in mud on her own property, says The Scientist. Imagine discovering a new form of genetic information- sharing right under one’s feet! Lamarck, Darwin, and early geneticists knew nothing about this.

In one mud sample, recovered from Banfield’s own property, they discovered a colossal linear stretch of DNA: nearly 1 million base pairs long and carrying mostly genes previously unreported in the literature. The sequence had unique characteristics, including distinct base pair patterns on both ends and sites for DNA replication, leading the authors to conclude the genetic behemoth might be playing some sort of functional role.

In addition to genetic information for genes, the Borgs may also contain tools like CRISPR for inserting the information into hosts. Banfield considers this find an example of “new mechanisms for processes that as yet, we don’t even know exist.”

Internal Reprogramming

Here’s another report that sounds downright Lamarckian. The University of Copenhagen reports that “Exercise improves health through changes on DNA.” Previously it was thought that exercise strengthened only the tissues and organs. This finding extends the benefits to the genetic code itself.

Now scientists at the University of Copenhagen have discovered that the beneficial effects of physical exercise may in part result from changes to the structure of our DNA. These changes are referred as ‘epigenetic’.

The news does not say that the resulting DNA changes are heritable, but who knows? If exercise can cause changes in the body distant from muscle, what else might be going on?

The scientists found that exercise benefited organs that are distant from muscle, like the brain. They speculate that these benefits might result from signals released by muscles into the bloodstream. In particular, they found that exercise remodels enhancer activity in skeletal muscle that are [sic] linked to cognitive abilities, which opens for the identification of exercise training-induced secreted muscle factors targeting the brain.

Their work was published in Molecular Metabolism by Williams et al., “Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health.” Can epigenetic signals also reach the gametes? It is too early to tell, but what a thought.

Have scientists been overlooking obvious facts about inheritance? When watching a cell divide under a microscope, clearly much more goes into each daughter cell than just the chromosomes. Organelles that may have been modified or adapted by epigenetic mechanisms also enter the daughter cells. This occurs in gametes, too; sperm cells, for instance, deliver more than DNA. They bring proteins and transcription factors that play a role in fitting the genetic information to the zygote. Offspring inherit not just the genome. They get the epigenome, too.

Widespread Information Sharing

A team of 33 scientists reports in bioRxiv about “Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae.” HGT may explain instances of so-called “convergence” by sharing of information instead of chance. Wasn’t it dubious to think that “distantly related” organisms could converge on the same solutions by chance anyway? The possibilities for rethinking convergence are at hand: if organisms can reprogram their genetic networks in response to a changing environment, they can quickly spread this information to other species through shared libraries which may include toolkits for incorporating the information into the genome or epigenome.

It is becoming increasingly apparent that large amounts of genetic information can be shared in previously undiscovered ways. A scientific revolution about inheritance may be afoot. Neo-Darwinism will be seen as antiquated and simplistic. Darwin’s picture of vertical inheritance of accidental variations did not consider ways that information can be swapped and shared, as is coming to light now. Design scientists have an opportunity to consider the functional implications of widespread hybridization and introgression, epigenetic modifications of DNA, “Borg” libraries, and even perhaps viruses and retrotransposons. What about those nasty secretion systems like the TTSS in bacteria that inject material into target cells? Could the disease-causing ones be examples of information-sharing machines gone rogue?

Exciting days may be ahead for design science. Long-standing questions about adaptation — the precise fit of organisms to their habitats — would be seen as internalized, engineered responses, not caused or “driven” by the environment. That would presuppose foresight, and foresight would presuppose intelligent design.