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If evolution is unpredictable and irreversible, …

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As some researchers using a computational model claim, according to ScienceDaily:

Evolutionary theorist Stephen Jay Gould is famous for describing the evolution of humans and other conscious beings as a chance accident of history. If we could go back millions of years and “run the tape of life again,” he mused, evolution would follow a different path.

A study by University of Pennsylvania biologists now provides evidence Gould was correct, at the molecular level: Evolution is both unpredictable and irreversible. Using simulations of an evolving protein, they show that the genetic mutations that are accepted by evolution are typically dependent on mutations that came before, and the mutations that are accepted become increasingly difficult to reverse as time goes on.

The study focuses exclusively on the type of evolution known as purifying selection, which favors mutations that have no or only a small effect in a fixed environment. This is in contrast to adaptation, in which mutations are selected if they increase an organism’s fitness in a new environment. Purifying selection is by far the more common type of selection. More.

Although the media release says boo about it, doesn’t this mean that Darwinian natural selection, as usually described is a minor factor in evolution? “[a]daptation, in which mutations are selected if they increase an organism’s fitness in a new environment” sounds a lot like “natural selection acting on random mutation.”

Gould and Dawkins, recall, were famously at loggerheads, so some clarity about siding with Gould would be welcome. But maybe it’s not easy these days to be clear about that?

Also, is not the “irreversibility” thesis support for Dollo’s law (not accepted in many quarters today)?

See also: Remember Dollo’s Law?: Once a trait was lost through evolution, it could not be regained.

Well, no one told the life forms about it, and frogs, snapdragons, and snakes, among other, apparently broke it with impunity, so that the “law” is in the process of being retired.

Here’s the abstract:

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background. (paywall) – Premal Shah, David M. McCandlish, and Joshua B. Plotkin. Contingency and entrenchment in protein evolution under purifying selection. PNAS, June 2015 DOI: 10.1073/pnas.1412933112

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6 Replies to “If evolution is unpredictable and irreversible, …

  1. 1
    Mung says:

    Speaking of evolving proteins, don’t miss this article at ENV and the accompanying video.

  2. 2
    bornagain77 says:

    as to:

    “Using simulations of an evolving protein, they show that the genetic mutations that are accepted by evolution are typically dependent on mutations that came before, and the mutations that are accepted become increasingly difficult to reverse as time goes on.”

    Behe, referring to empirical evidence, pointed this ‘Dollo’s Law’ principle out a few years ago. Moreover, besides the past, Behe pointed out that the principle holds for the future as well:

    Dollo’s law, the symmetry of time, and the edge of evolution –
    Excerpt: We predict that future investigations, like ours, will support a molecular version of Dollo’s law:,,, Dr. Behe comments on the finding of the study, “The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future.

    Evolutionary Adaptations Can Be Reversed, but Rarely – May 2011
    Excerpt: They found that a very small percentage of evolutionary adaptations in a drug-resistance gene can be reversed, but only if the adaptations involve fewer than four discrete genetic mutations.

    From Thornton’s Lab, More Strong Experimental Support for a Limit to Darwinian Evolution – Michael Behe – June 23, 2014
    Excerpt: In prior comments on Thornton’s work I proposed something I dubbed a “Time-Symmetric Dollo’s Law” (TSDL).3, 8 Briefly that means, because natural selection hones a protein to its present job (not to some putative future or past function), it will be very difficult to change a protein’s current function to another one by random mutation plus natural selection.
    But there was an unexamined factor that might have complicated Thornton’s work and called the TSDL into question. What if there were a great many potential neutral mutations that could have led to the second protein? The modern protein that occurs in land vertebrates has very particular neutral changes that allowed it to acquire its present function, but perhaps that was an historical accident. Perhaps any of a large number of evolutionary alterations could have done the same job, and the particular changes that occurred historically weren’t all that special.
    That’s the question Thornton’s group examined in their current paper. Using clever experimental techniques they tested thousands of possible alternative mutations. The bottom line is that none of them could take the place of the actual, historical, neutral mutations. The paper’s conclusion is that, of the very large number of paths that random evolution could have taken, at best only extremely rare ones could lead to the functional modern protein.

    Further notes on Dollo’s law: The loss of morphological traits over time, for all organisms found in the fossil record, was/is so consistent that it was made into a ‘scientific law’:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.”

    A general rule of thumb for the genetic deterioration implied by Dollo’s Law, as it applies to the fossil record, is found here:

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;

    Of related note:

    No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes – November 2011
    Excerpt: Hughes now proposes a model he refers to as the plasticity-relaxation-mutation (PRM) model. PRM suggests that adaptive phenotypes arise as follows: (1) there exists a phenotypically plastic trait (i.e., one that changes with the environment, such as sweating in the summer heat); (2) the environment becomes constant, such that the trait assumes only one of its states for a lengthened period of time; and (3) during that time, deleterious mutations accumulate in the unused state of the trait, such that its genetic basis is subsequently lost.
    ,,, But if most adaptations result from the loss of genetic specifications, how did the traits initially arise? One letter (Chevin & Beckerman 2011) of response to Hughes noted that the PRM “does not explain why the ancestral state should be phenotypically plastic, or why this plasticity should be adaptive in the first place.”

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.

  3. 3
    Mung says:

    OT: There’s something unnatural going on with “Recent Comments.” It doesn’t always display the recent comments.

  4. 4
    Axel says:

    Sometimes, Refresh, solves it, mung. But perhaps you’ve tried it.

  5. 5
    Mung says:

    Thanks Axel, yes, tried that. I think I’ll try restarting the browser or using a different browser just to see what happens.

  6. 6
    wd400 says:

    Although the media release says boo about it, doesn’t this mean that Darwinian natural selection, as usually described is a minor factor in evolution?

    No? Why do you think this?

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