More dumb claims that environmental epigenetics will completely revise our view of evolution

There’s an interesting new paper out on the genetic basis of eye loss in cave fish, reported in a manuscript in biorxiv (not yet peer reviewed) by Aniket Gore et al. (reference and free download at bottom. ) It’s also summarized by New Scientist in the online article below (click on screenshot to go to article), as well as in a copy of the magazine’s paper issue, which I saw in Cambridge.  I’ll briefly summarize the paper, but what interested me at first was how New Scientist dealt with it.

The original title in the paper journal was “Blind cavefish’s strange evolution”, but now it’s this online (click on screenshot to go there):

That’s not much of a difference. What is different is how they sell the result in the paper version versus the online version, which I suspect came later (or was revised).  The paper version says this (h/t to Andrew Berry for the screenshot):

So that makes you think that the researchers found something that may lead to revising the “standard view of evolution.” But the first paragraph of the online version is nowhere near as strong:

We’ve found out why a Mexican cavefish has no eyes – and the surprising answer is likely to be seized upon by those who think the standard view of evolution needs revising.

To me that’s a big difference, for the striking result is now one that “some people who already think the standard view of evolution needs revising” will “seize upon.” And that online version is more correct, for there’s simply nothing in the paper that would lead us to call for a revision—or even a reexamination” of the standard Darwinian theory. The paragraph has changed from touting the result as a potential kink in evolutionary theory to a finding that those who already don’t like that theory could use as ammunition against it. But those people are, as we’ll see, wrong.

So what was found? We know that Mexican tetra, Astyanax mexicanus, has some blind forms that have lost their eyes after invading caves. In the blind tetras, eye development starts normally, but then the incipient eyes start to regress (that’s evidence for evolution, by the way), and they’re left with eyes of variable size—or none at all. There are some three dozen different blind forms in different caves, and many of these developed independently from the normally-eyed surface-dwelling form. The blind versus sighted forms aren’t regarded as two species because they can all mate with each other, and because the blind forms are no more closely related to each other than to some sighted forms. They’re better regarded as “ecotypes” or “morphs” then species.

Here are the two forms, sighted on top and blind at bottom:

Why did these fish, as do many animals that invade and evolve in caves, lose their eyes? We’re not sure, but there are several theories. If you have eyes that you don’t need, because it’s dark (these fish get around using their lateral lines), then you might get a reproductive advantage by diverting the metabolic energy needed to produce eyes into other features that enhance reproduction, like gonads or eggs. Or, eye loss may be advantageous because besides eyes being useless in caves, they’re easily damaged or infected, and thus losing them may enhance your survival and reproduction. Alternatively, mutations that lead to eye loss, normally weeded out in surface populations, might accumulate over time in caves, so that the eyes would eventually disappear over generations. Or several of these factors, and others I haven’t mentioned, could operate together. We don’t know for sure, but one can think of ways to test these ideas.

What these researchers found, and what got the editors all excited about revising evolution, was that the genes that normally form eyes appear to have been inactivated not by changes in their own DNA sequence by mutation, but by “methylation”: epigenetic changes in which methyl groups are stuck on the DNA bases of eye-making genes, presumably inactivating them. As the authors note, ““Although a central role for DNA methylation in development and disease has been well-documented, our results suggest that epigenetic processes can play an equally important role in adaptive evolution.”

Well, we already know that epigenetic processes have played a role in adaptive evolution, for the way development proceeds—the way cells become different from one another as they develop from a single fertilized egg—is largely through the acquisition of methylated groups that can be inherited within a body as a cell divides. That is, the position of and influences on a cell can cause it to acquire methylation marks that turn it into difference courses of development: a liver cell, a kidney cell, a bone cell, and so on. But these changes, all inherited among cells in a single body, have resulted from natural selection: they’re adaptive because having different kinds of cells and tissues is adaptive.  What has happened is that the DNA program itself, within the egg, contains information that says “methylate cell X at genes Y and Z if it experiences condition C”, and so on. Although development involves more than simply differential turning on and off of genes by methylation, this is an important way that development proceeds in multicellular organisms.

The thing is, this is not a violation of evolutionary theory in any sense. The commands for methylation under certain conditions, and the results of a gene being methylated, have evolved by changes in regular DNA sequences that control the methylation of other DNA sequences. It’s just an evolved way to regulate genes.

What has likely happened in these cave fish, then, is that other, “regulatory” genes have changed in the cave forms that provide instructions sort of like this: “hey, gene Y: at a certain point, you attach methyl groups to other genes for eye formation, shutting down those genes and causing the eyes to degenerate.” That could easily evolve by conventional natural selection.

(Since there appear to be no changes in the DNA sequences of eye-forming genes themselves, it’s not likely that they themselves have evolved direct sensitivity to environmental conditions and so can turn themselves off in the dark. Blind cave fish raised in the light, as many hobbyists do, don’t develop eyes. There is some evolved change somewhere in the cave fish genome that simply turns the eyes off regardless of the environment, and it does so by methylation.)

Thus we have no challenge here to conventional evolutionary theory. In fact, the New Scientist piece, to its credit, quotes scientists who say that:

“This is a most interesting paper,” says evolutionary biologist Douglas Futuyma of Stony Brook University in New York. But he doesn’t think it poses any challenge to standard evolutionary theory as the epigenetic change is itself most likely a result of a genetic change.

Gore’s team shows that the silencing of the eye genes is due to the increased activity of a specific gene involved in methylation, Futuyma points out. So the question then is, what is making this gene more active?

“I think it likely that there has been an alteration in DNA sequence of that gene,” he says.

I agree. Yet Eva Jablonka, always a big proponent of “neo-Darwinism is wrong”, thinks that something more is going on: that the cue to methylate the genes producing eyelessness doesn’t come from other genes, but from the environment itself! That is, somehow the presence of darkness is an environmental effect that methylates the eye-forming genes in adaptive ways, making the eyes disappear.

That would be the kind of environmental epigenetics that truly is non-Darwinian, for it would be “Lamarckian” inheritance in which an environmentally acquired change somehow becomes adaptively incorporated into the DNA and is inherited from then on. As I’ve said repeatedly, we have no examples of such acquired methylation lasting more than two or three generations, so there’s no evidence that it could serve as a stable basis of inheritance, much less of adaptation.

Nevertheless, Jablonka persists:

However, Jablonka thinks that heritable epigenetic changes alone could explain the loss of eyes. What is more, she even thinks it possible that the epigenetic changes were somehow triggered by the cave environment in the first place. That would be a form of Lamarckian evolution: the idea that characteristics acquired during an individual’s lifetime can be passed on to descendants.

Absent any evidence that such acquired methylations are stable over generations, this is not credible. (Note that the paper’s authors make no such claim.) And that’s why the more rational evolutionists aren’t going to accept such Lamarckian evolution until we find some good cases.

The article concludes with more doubts:

David Shuker at the University of Edinburgh, UK, is unconvinced by this or any of the other proposed examples of evolution via epigenetic mechanisms.

There is no doubt that some animals respond to the environment via epigenetic mechanisms, he says, but these mechanisms have evolved via genetic changes. “It goes through genetically built systems,” Shuker says.

So, like Futuyma, he thinks standard evolutionary processes such as mutation and natural selection still explain all we have discovered.

“We are always finding new ways in which these processes manifest themselves,” says Shuker. “We have found lots of amazing things.” But the basic principles remain valid, he says.

Shuker is suspicious of some efforts to promote the idea of an “extended evolutionary synthesis”. He thinks some people are trying sneak religious ideas back into evolutionary theory.

“They are trying to allow organisms to have agency not controlled by genes,” he says.

I don’t know Dr. Shuker (Futuyma is my pal), but I like him already! At any rate, the editors’ realization that only Jablonka (and perhaps a few other outlier evolutionists) push this kind of inheritance as something requiring us to revise evolutionary theory, may be one reason why New Scientist dialed back the enthusiasm of its first paragraph. It’s interesting enough to find out that fish’s “eye genes” have lost their expression via methylation induced by other genes; we don’t need to go hog wild and start postulating new theories of evolution.

________

A. V. Gore et al. 2017. An epigenetic mechanism for cavefish eye degeneration. Biorxiv, online.

22 Comments

  1. Brian salkas
    Posted October 27, 2017 at 1:39 pm | Permalink

    Fascinating! I still don’t 100% understand it, but this article certainly helped me grasp some basic things about epigenetics that I was unsure about.
    Thanks for yet another great article.

  2. Charles Sawicki
    Posted October 27, 2017 at 1:42 pm | Permalink

    Keep up the bioscience posts! I didn’t know that cell differentiation during development involved changes in methylation but it’s a nice mechanism.

  3. Jorge Rojas
    Posted October 27, 2017 at 2:00 pm | Permalink

    I´ve always avoid reading something about the biologist who propose the EES, but would you recomended any book of them? I was interesting in Laland’s latest book latesthttps://www.amazon.com/dp/B01M34K5VV/_encoding=UTF8?coliid=I2QKOXN6MHBPP3&colid=3CYIP0RNOMN7R, but I’m not sure it is worth

    • Posted October 27, 2017 at 2:03 pm | Permalink

      That’s a trade book, I think, which means it’s not meant for scientists, which would be good if you’re not an evolutionist. On the other hand, I haven’t read it, and can’t pass judgment one way or the other. But it won’t give you an overview of the challenges mounted against “conventional” evolutionary theory. To get a summary of those you’d have to read a scientific symposium volume, and there are some of those if you need a recommendation.

      • Jorge Rojas
        Posted October 27, 2017 at 3:07 pm | Permalink

        Thanks for your reply! Actually I’m not a biologist nor a biologist student.
        I’m only very interested about evolution and more than once I have heard that “Darwinism has been overcome” (I think refering to EES) so I’m looking for something that explain the discoveries that have take to some biologists to propose EES, but without any bias.

  4. Posted October 27, 2017 at 2:35 pm | Permalink

    Reblogged this on The Logical Place.

  5. YF
    Posted October 27, 2017 at 2:47 pm | Permalink

    Nice analysis Jerry. Somewhat similarly, the process of learning (nurture) is genetically guided (nature).

  6. Mark R.
    Posted October 27, 2017 at 3:12 pm | Permalink

    Thanks for breaking this down for us, very interesting indeed.

    What is Jablonka’s motivation for trying to push Lamarckian evolution? Fame for debunking neo-Darwinism? Do you think she really believes in Lamarckism? Maybe trying to get a Templeton grant? Strange.

    • infiniteimprobabilit
      Posted October 27, 2017 at 7:10 pm | Permalink

      Well, Lamarckism would be vastly quicker and more efficient than the incredibly wasteful, indirect, cruel, subject-to-noise feedback mechanism that is Darwinian evolution.

      If I were a deist God (of the set-it-up-and-let-it-run variety) I’d make sure evolution ran on Lamarckian lines. (Not sure how to do that – it would require a fundamental change in the mechanisms of DNA – but I guess as G*d I’d figure out something).

      Now if G*d could have done that – but G*d chose not to – that doesn’t say much for the benevolent-G*d school of thought, does it? The old theodicy problem again. Sorry, Templeton.

      cr

  7. Simon Hayward
    Posted October 27, 2017 at 3:33 pm | Permalink

    “That is, somehow the presence of darkness is an environmental effect that methylates the eye-forming genes in adaptive ways, making the eyes disappear”

    We’re all permeated by dark energy dude 🙂

    On another flippant note, my Geordie wife might say “why aye” to this.

    Since I had no choice about the previous bad jokes, I’ll ask a question. We are talking about an evolved mechanism to actually avoid making eyes. Intuitively, I would have thought that these animals were more likely to accumulate mutations (nonsense or missense) that disrupt pathways critical to making eyes leading to a bunch of pseudogenes. Just as there are pseudogenes for (for example) olfactory receptors in whales.So, a lack of positive selection for the ability of a whale to act as a bloodhound leads to a gradual loss of receptor function by random attrition. It seems perhaps that there is little price for making the receptors.

    However, here we have a new active process. This would seem to suggest that a useless eye carries a huge reproductive price, while a useful eye is incredibly valuable (in the land of the blind….). So does this represent a different class of active vs passive gene switching based upon cost/benefit ratios imposed by the specific structures under consideration, and if so are there other examples in nature that you know of?

    I know that there are many species in which this phenomenon of eye loss in caves has been observed but I have no data on the mechanisms, any thoughts?

  8. Desnes Diev
    Posted October 27, 2017 at 3:40 pm | Permalink

    “Yet Eva Jablonka, always a big proponent of “neo-Darwinism is wrong”, thinks that something more is going on: that the cue to methylate the genes producing eyelessness doesn’t come from other genes, but from the environment itself! That is, somehow the presence of darkness is an environmental effect that methylates the eye-forming genes in adaptive ways, making the eyes disappear.”

    Am I too naive to think that, if blind Astyanax raised in captivity under light condition do not recover their eyes (over 4-5 generations), this idea would be invalidated?

    • jjcar40
      Posted October 27, 2017 at 4:07 pm | Permalink

      Desnes, I was wondering something similar, but I believe Jablonka et al would be validated if sight did not return. That is, if the environment created an enduring change to the DNA.

      Jerry, could you please enlighten us here? I agree with Desnes that the simple test of taking the blind fish out of darkness for several generations would seem to bring clarity. Are we missing something?

      Great post, in any event.

    • Posted October 27, 2017 at 4:09 pm | Permalink

      Well, it has to be reversible in light, but you more or less have the right idea. Or, put eyed fish in darkness. If the environment does this, they should lose their eyes in just a couple of generations. Neither will happen. People regularly rear blind cavefish in the light for decades and they never get their eyes back.

  9. Posted October 27, 2017 at 3:55 pm | Permalink

    The “seized upon” version reminds me of Trump’s favorite excuses to cover his untruths — “someone told me” or “people are saying”. It is cowardice, pure and simple. So what does the New Scientist editorial staff really believe?

  10. Paul S
    Posted October 27, 2017 at 4:11 pm | Permalink

    I’m probably over simplifying or plain wrong, but isn’t it possible that some open sea fish are born blind or sight impaired and the reason they are only found in caves is because the ones in the open sea get eaten and can’t reproduce?
    I’m not saying it’s common, but I’d think if your born with a trait that causes immediate death, you can’t pass that trait on very well.

    • Paul S
      Posted October 27, 2017 at 4:12 pm | Permalink

      I hate when I mess up “you’re”

    • Posted October 27, 2017 at 10:46 pm | Permalink

      Since it looks to be a trait acquired several times in these blind cave fish, it might be possible, at least in some of them.
      The way to check is to see if the target sequences that are methylated are identical in the different populations.

  11. Posted October 27, 2017 at 8:57 pm | Permalink

    I recall a certain freshman biology teacher writing an article on this in a now defunct sciencey online magazine. He went all neo-lamarckian, too.

    Didn’t Jablonka — who’s a full-out classic lamarkian — get caught fudging at one point?

  12. Posted October 27, 2017 at 10:44 pm | Permalink

    Very interesting. I had not really thought about methylation being used to shut down genes in an evo devo process, but of course that is a pretty common way to inactivate genes in general so it should not be surprising to see it in evo devo.

    Odd that the targeted genes have not accumulated mutations, though.

  13. Mike
    Posted October 28, 2017 at 5:45 am | Permalink

    I seem to recall some involvement of PAX6? So that the there was trade off in eye loss versus jaw size.

    I can’t seem to find it now

  14. Posted October 30, 2017 at 11:28 am | Permalink

    Jablonka has a book _Evolution in Four Dimensions_ that got by the MIT Press review process that talks about some of this stuff. I wonder how that happened.


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