A Kimura Age to the Kern-Hahn Era: neutrality & selection

I’m pretty jaded about a lot of journalism, mostly due to the incentives in the industry driven by consumers and clicks. But Quanta Magazine has a really good piece out, Theorists Debate How ‘Neutral’ Evolution Really Is. It hits all the right notes (you can listen to one of the researchers quoted, Matt Hahn, on an episode of my podcast from last spring).

As someone who is old enough to remember reading about the ‘controversy’ more than 20 years ago, it’s interesting to see how things have changed and how they haven’t. We have so much more data today, so the arguments are really concrete and substantive, instead of shadow-boxing with strawmen. And yet still so much of the disagreement seems to hinge on semantic shadings and understandings even now.

But, as Richard McElreath suggested on Twitter part of the issue is that ultimately Neutral Theory might not even be wrong. It simply tries to shoehorn too many different things into a simple and seductively elegant null model when real biology is probably more complicated than that. With more data (well, exponentially more data) and computational power biologists don’t need to collapse all the complexity of evolutionary process across the tree of life into one general model, so they aren’t.

Let me finish with a quote from Ambrose, Bishop of Milan, commenting on the suffocation of the Classical religious rites of Late Antiquity:

It is undoubtedly true that no age is too late to learn. Let that old age blush which cannot amend itself. Not the old age of years is worthy of praise but that of character. There is no shame in passing to better things.

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7 thoughts on “A Kimura Age to the Kern-Hahn Era: neutrality & selection

  1. From the paper:

    “Up to 80-85 percent of the human genome is probably affected by background selection,” the authors wrote.

    “they concluded that less than 5 percent of the human genome evolved by chance alone.”

    What about the onion test and c-value enigma/paradox? Do they have any explanation for that or just want to have their papers published?

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  2. I always wonder how it is possible that in a certain intellectual, or better ideological framework people and ideas can be successful in “science” by making up an hypothesis which makes absolutely no sense, but can be dressed up with a fancy slogan and an elegant mathematical model.
    No serious biologist and observer on the ground could have ever believed that crap if it was not preached from the pulpit. You must stay in the ivory tower or preach to it. I mean there are some highly intelligent people,some even honest ones, which create models which the majority cant fully understand, but what does it help if the premises are wrong?
    Like in most economic models which only work in a theoretical construct of reality which ignores to much of reality itself.

    Its time neutral theory gets buried. Its overdue.

    Reminds me a lot of “pots not people”, just somewhat less obvious at first glance.
    But all fits together and into the ideological turn of the 1960s. Its no coincidence all those flawed concepts were created or became successful at that period of time, there was a political demand. Unfortunataly such concepts are hard to overturn once established.

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  3. From my reading of the article, I gather that the latest findings can be summarized: genetic draft is a bigger deal than genetic drift.

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  4. Also, I don’t much like how the selectionist vs. adaptationist graph is presented.

    There may be vastly more mutations, which, considered on their own, are neutral in their effects than there are mutations which are positive in their effects. Nonetheless, these neutral sites may show signs of selection merely because they are close to loci which do have positive effects.

    The graph tends to confuse rather than clarify this point.

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  5. As I see it, the real issue is not that most small mutations are neutral or that you could create nice mathematical models from the neutral null hypothesis, as long as the models and data available aren’t sufficient for much more complex models than such comparatively simple mindgames. No, thats not the real issue.
    That would have been ok, as long as you see the neutral aspect of mutations and variation as what it is, a second or probably even third tier player for the greater game of evolution. Contributing something significant at times, rarely, but really not that important at all in comparison to the forces of selection.
    The insanity of the neutral hypothesis is that they made pure chance such a major player in the evolutionary game and the differentation of populations and species, even on the highest functional level, what it is not under normal circumstances. Analogous evolution of so many species throughout the animal kingdom is probably one of the most primitive examples for the opposite, but still: Selection finds a way to create a functional similarity even from vastly different original forms, as long as the selective pressures are just strong and lasting enough. Considering how the smallest deviations can be the cause of death, or more or less offspring throughout an organisms life time in nature, the idea of major genetic and even significant functional changes being primarily the result of random processes is blatantly absurd.
    The large scale work on polygenic and linked traits is just the last nail in the coffin of this overblown neutrality concept. It finally proves that even the truly neutral parts of the genome, of which there might be much less than originally thought anyway, being under constant, even if indirect, selective pressures.
    From the birth of the idea and its first popular spread, the original hypothesis had always to fight an unreasonable rearguard action, even with all that power and prestige behind it. Because a false concept needs much more energy and protection by authority to stay alive, while a correct one can win by just being on the table again.
    That explains a lot of paradigm changes in recent years. The concepts were always crap, but they were kept alive with huge efforts, because some people needed it and some others were so involved in it, that they couldn’t think out of the box any more. They must hit the wall of unequivocal data and (preventable?) catastrophes to (hopefully) wake up again. Looking at economic sciences, only a few truly learned their lesson, but in genetics things are more straightforward in the end, and that makes it so satisfying these days.

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  6. I have zero qualification to opine, but I did find “minas s” comment, pasted below, from the Quanta article, to be stimulating. “Unknown spatial factors”!? That’s stitching with some mighty fine thread, but given angstrom scale, intuitively sounds very probable. Wild times in evodevo, is why I keep hanging around GNXP. Come for the science, stay for the freethinking–or is it the other way around. Gratitude! :
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    ” minas s • 4 days ago

    Cancer cell adaptation is complex. Mutations act through the downstream biochemical pathways they affect. Mutations interact with each other and depending on the signals of the microenvironment, the fittest clones survive. Also sometimes they show some endocrinology type adaptation. Also epigenetic factors or complex post-translational modification factors help cancer cells to adapt to a specific microenvironment. Unknown spatial factors might also play a role.
    My opinion is that a survival of the fittest biochemical pathways is what better describes what happens at the end of the day, instead of giving a strict genomic explanation.”

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