The epigenetics miracle?


Jerry Coyne is mildly incensed — once again, there’s a lot of recent hype about epigenetics, and he doesn’t believe it’s at all revolutionary. Well, I’ve written about epigenetics before, I think it’s an extremely important subject central to our understanding of development, and…I agree with him completely. It’s important, we ought to spend more time discussing it in our classes, but it’s all about the process of gene expression, not about radically changing our concepts of evolution. I like to argue that what multigenerational epigenetic effects do is blur out or modulate the effects of genetic change over time, and it might mask out or highlight allelic variation, but ultimately, it’s all about the underlying genetic differences.

Coyne mentions one journalist who claims that new discoveries in epigenetics would “make Darwin swoon,” which is a bizarre standard. Darwin knew next-to-nothing about genetics — he had his own weird version of Lamarckian inheritance — and wasn’t even equipped to imagine molecular biology, so yes, just about anything in this field would dazzle him. My freshman introductory biology course would blow Charles Darwin away — he’d have to struggle to keep up with the products of American public education.

(Also on Sb)

Comments

  1. Prof.Pedant says

    Darwin might have to struggle for a while, but I expect that he would be a very attentive and inquiring student – you would get lots and lots of questions from him!

  2. says

    Variation that was seen and not accounted for by genes alone is now explainable via epigenetics. Rapid adaptation to temporary (a few generations at most) conditions appears quite possible, and useful to organisms.

    But in many ways it’s sort of a snoozer. Fine, some genes are expressed, others aren’t (or aren’t much), and we always knew that, we just weren’t sure what the causes were. A gap in our knowledge is filled, yet it doesn’t really change our previous understandings all that much.

    Glen Davidson

  3. says

    Rapid adaptation to temporary (a few generations at most) conditions appears quite possible

    The (ongoing) change and conditions causing them might last a lot longer than a few generations, but a specific epigenetic change occurring at a given time doesn’t seem to last for many generations, and would presumably have to be renewed to continue.

    Glen Davidson

  4. Matt Penfold says

    I have long wished it was possible to bring back Darwin, so he could be shown what has been done with his theory.

    I rather suspect he would be taken aback at the progress we have made in genetics but also rather pleased his theory has stood the test of time.

  5. says

    Well, “revolutionary” is a matter of degree. Our understanding of epigenetics and gene regulation more broadly hasn’t changed suddenly, in a catastrophic breakthrough; but if you compare our understanding today to what it was when I was in graduate school it’s a very large difference. It’s not surprising that it seems revolutionary to people who are just catching up with it. Agreed, it doesn’t fundamentally undermine the basic Darwinian idea, although the recognition that environmental influences can indeed influence gene expression in subsequent generations is at the very least a pretty big gloss on the original. And BTW it has important social implications – we really need to be even more concerned about maternal and child health than a one-generation perspective would inspire.

  6. says

    As some here have noted, and as Coyne sees, the relevant property of epigenetic modifications is that they revert after several generations. So it is very hard to see how they could cause change that lasted for thousands or millions of generations. Not unless there was genetic change accompanying them (or immediately following them). And in that case it is the genetic change that is the long-term effect.

    So as interesting (and dramatic) as epigenetic modifications are, Coyne is right — they do not serve as the mechanism of major long-term change, at least not by themselves.

  7. bjoern s. says

    most of the overemphasis on epigenetics is strongly related to a fundamental misunderstanding based on the dna=blueprint analogy

  8. colluvial says

    @Matt Penfold: “I rather suspect he (Darwin) would be taken aback at the progress we have made in genetics . . .”

    And also quite likely taken aback at the persistence yet utter lack of progress made by evolution opponents.

  9. says

    In other words, scientifically illiterate morons are reporting stories to the scientifically ignorant masses, and spreading hyperbole? Sounds like any news outlet if you ask me. Most don’t even recognize science, let alone have the ability to report on it…

  10. devogene says

    I agree with both Prof.Myers and Coyne, but I am not sure if prof.Myers accepts the gene centred view of evolution that Prof.coyne accepts? I don’t btw.

  11. says

    One of the funnier invocations of epigenetics I’ve ever heard was this “Teeth are affected by epigentic factors too. Duh. Ever heard of wear?”

  12. strange gods before me says

    If you told Darwin that every organism on Earth has exactly the same DNA and all variation is epigenetic, he wouldn’t have any reason to think you were lying.

  13. hyoid says

    Is it accurate that the sperm can be affected by the male inhaling tobacco smoke? Thus increasing the probability of a clef pallet or some defect in the offspring?
    I guess I’m asking if smoking can damage the gene? And if so, can that damage be propagated to the next generation and so forth.
    If not so, then sorry for commandeering your mental processes for my own selfish Eugene’s benefit.

  14. Old Rockin' Dave says

    I suspect that Darwin would not only be dazzled by what we know about genetics, he would be delighted. I don’t think it would take that powerful and supple mind very long to catch up.

  15. Toiletman says

    Epigenetics has been a great discovery that filled some gaps in detail understanding of evolution but these IDiots are of course using it in the usual way “DARWIN IS WRONG!!!!!11111″ and also refer to evolution as “darwinism” and always imply that it is a kind of ideology that solely bases on the teachings of one person but they are, as we all know (atleast I hope so), completely wrong. Darwin was one of the greatest scientists of the 19th century but he was just a human scientist and wrote a book about a new biological theory (back then it was really just a theory) and gave lots of evidence for it. However, despite having a sharp mind, he simply could not know things about molecular biology and especially genetics because it was not known back then. They IDiots think that evolution, like their religion, is something monolithic that does not change and thus fundamentally misunderstanding sciences. Darwin’s and Wallace’s theories have been gradually expanded with new biological knowledge and the more we have found out, the more evidence spoke for evolution. It’s a process in which we find out more and more and epigenetics is one of the newest discoveries in evolutionary biology. It’s fascinating and fills detail questions we could not answer properly so far but absolutely nothing in epigenetics speaks against evolution. That notion is absolutely bizarre since there wouldn’t be any epigenetics without evolution.

    Viva la evolution! :D

  16. DLC says

    Personally, I think Darwin would be astounded by the developments since his day. He would then proceed to make an attempt to catch up, probably succeeding in time.

  17. uncle frogy says

    depending on what age Darwin is brought now from then he would be diagnosed and treated for I believe was some kind of tropical parasite. I suspect it would take a little time but that he would learn the details of what has been learned since then and would not be surprised but enthralled like any good scientist. maybe not do research but he was creative so maybe with his experience and the new information since then who is to say

    uncle frogy

  18. M says

    Oh, I think Darwin would be a VERY interested student. I think he’d love modern biology.

    Oddly Darwin would probably even fit in pretty well with our time, he seemed to be ahead of his own considerably, when reading his diaries and such.

    I mean the fundies always say he’s racist and unfortunately some atheists bought it, but he actually was very much a non-racist in an era full of racists. (In fact in quite a few writings pointing out the hypocracy of the racists of his time.) Darwin often admired the people his contemporaries considered ‘savages’.

  19. Antiochus Epiphanes says

    While anyone can respond to this, if you are still lingering around, Joe Felsenstein*, I would love to read your perspective.

    The discussion of the importance of epigenetic phenomena in evolution seems in some ways parallel to the discussion of the importance of group selection. I don’t think that these discussions are of much use, unless one can demonstrate under what conditions these phenomena may have a stronger role in evolution than selection does.

    This has been a focus of those interested in group selection theory, but I haven’t run across any serious work on epigenetics. It’s one thing to say that epigenetics will not provide the revolution that overthrows Darwin, but quite another to add it to the evolutionary model(as has been done with other mechanisms of evolution, e.g. drift, sexual selection, etc.).

    Anyway, it seems intuitive to me**, that epigenetic effects decrease heritability (in the same way that environmental variance does), which would temporarily weaken the ability of selection to act on a trait. Because the effect is sporadic, it may have a negligible effect on a single locus over many generations, but may result in the preservation of slightly greater allelic diversity averaged over the genome…thus a greater opportunity for genetic interactions, and variability that selection could act on.

    IDK…if this is true, epigenetic effects may increase the genetic robustness of populations.

    *I am not worthy.
    **And therefore utterly incorrect.

  20. Antiochus Epiphanes says

    Michael S: ?

    Darwin predates Einstein. Is the name “Darwin” widely associated with credibility outside of his work in biology?

  21. pfooti says

    Words are pretty funny things. As a cognitive scientist, I use “epigenetic” to mean an entirely different thing, deriving from Jean Piaget’s use of the term in describing the creation/derivation of knowledge from inborn understandings (or not).

  22. says

    Antiochus Epiphanes asked for comments on:

    The discussion of the importance of epigenetic phenomena in evolution seems in some ways parallel to the discussion of the importance of group selection. I don’t think that these discussions are of much use, unless one can demonstrate under what conditions these phenomena may have a stronger role in evolution than selection does.

    Epigenetic inheritance is a kind of inheritance so it affects the outcome of selection but is not directly opposed to it.

    This has been a focus of those interested in group selection theory, but I haven’t run across any serious work on epigenetics. It’s one thing to say that epigenetics will not provide the revolution that overthrows Darwin, but quite another to add it to the evolutionary model(as has been done with other mechanisms of evolution, e.g. drift, sexual selection, etc.).

    Three papers I know of are:

    # Slatkin, M. 2009. Epigenetic inheritance and the missing heritability problem. Genetics 182 (3): 845-850.

    # Tal, O., E. Kisdi and E. Jablonka. 2010. Epigenetic contribution to covariances between relatives. Genetics 184 (4): 1037-1050.

    # Carja, O. and M. W. Feldman. 2011. An equilibrium for phenotypic variance in fluctuating environments owing to epigenetics. Journal of the Royal Society Interface Published online before print August 17, 2011, doi: 10.1098/​rsif.2011.0390.

    Anyway, it seems intuitive to me, that epigenetic effects decrease heritability (in the same way that environmental variance does), which would temporarily weaken the ability of selection to act on a trait. Because the effect is sporadic, it may have a negligible effect on a single locus over many generations, but may result in the preservation of slightly greater allelic diversity averaged over the genome…thus a greater opportunity for genetic interactions, and variability that selection could act on.

    Dunno. Epigenetic effects are also (temporarily) heritable.

    I think the publication of papers on long-term evolutionary effects of epigenetics has been impeded by the (correct) feeling that there won’t be many. The literature has mostly concentrated on the ways epigenetic phenomena may confound heritability estimation.

    IDK…if this is true, epigenetic effects may increase the genetic robustness of populations.

    I am not sure what is meant by that but it sounds as if the Carja and Feldman paper may be relevant.

  23. says

    Every time I see talk of a new revolution in science, I wonder if the person using the phrase has read The Structure Of Scientific Revolutions, and if so, how they’ve managed to ignore what Kuhn was on about. It might make for provocative reading and enforce the provisional nature of scientific knowledge, but damn is it frustrating. I can only imagine how scientists in the field feel about it…

  24. Antiochus Epiphanes says

    Joe Felsenstein: Domo arigato!

    Kel: I personally found Kuhn impenetrably dull to read. The SoSR IMHO could have been written as a longish essay. I may be wrong, but I imagine that Kuhn isn’t on the bookshelf of many scientists.

  25. ichthyic says

    Darwin is the new Einstein.

    damn! time reversal!

    so, uh, is Galileo now the new Sagan?

  26. ichthyic says

    I think the publication of papers on long-term evolutionary effects of epigenetics has been impeded by the (correct) feeling that there won’t be many.

    moreover, unless an epigenetic effect is somehow connected to a trait with huge selective effect on it, or one linked genetically to such a trait, and occurs in a small population, you still would expect whatever equilibrium conditions occurred before the localized epigenetic effect happened to reassert.

    IOW, unless there was basically a fixation event in one or two generations (pretty unlikely), then you would not expect to see a localized epigenetic effect override the effects of long term selection, or even drift for that matter.

    Still, I could think of some hypotheses that would be fun to test.

    FWIW, there is already work showing that the areas that control methylation, for example, are conserved and maintained by selection.

    http://www.sciencedirect.com/science/article/pii/S009286741100482X

  27. ChasCPeterson says

    Smoking has been shown to affect DNA methylation of tumour suppressor genes,

    In, if I read the press release correctly, cells derived from cervical smears? Is smoking really a risk factor for cervical cancer? And if so, what’s the mechanism between smoke in the lungs and methylation someplace entirely else?

    can’t see why it couldn’t affect spermatozoa

    Well, whatever the mechanism is, it has to involve delivery of a chemical in the blood, and there’s the blood-testis barrier in the way there.

    I imagine that Kuhn isn’t on the bookshelf of many scientists.

    And I know for a fact that it’s on more scientists’ shelves than have read it.
    *sheepishly raises hand*

  28. Antiochus Epiphanes says

    Ick: Muchos nachos for the link.

    ChasCPeterson: I fought like hell to get through that slim little book, and I’m not sure that I learned much more than I would have by consulting the Pfft.

  29. Antiochus Epiphanes says

    This is also a good primer:

    Richards, C.L., O. Bossdorf, and M. Pigliucci. 2010. What role does heritable epigenetic variation play in phenotypic evolution? Integrative Biology Faculty Publications. Paper 34.

    Some of the speculation is similar to my own.

    Another major research question concerning the consequences
    of epigenetic inheritance systems on evolution is
    related to their connection, if any, with the issue of evolvability
    (Pigliucci 2008). The latter is often understood as a property
    of biological systems that facilitates the exploration of
    phenotypic space, and hence the evolutionary process itself.
    Epigenetic modifications have been linked with examples of
    “evolutionary capacitors” such as the Hsp90 stress-response system (Sollars et al. 2003) and prions (Brookfield 2001),
    themselves often invoked as candidate mechanisms for
    increased evolvability. More generally, however, the higher
    mutation levels of epigenetic markers can be seen—despite
    their lower long-term stability—as a factor accelerating the
    exploration of phenotypic space and augmenting the searching
    capability of natural selection, perhaps in a manner
    directly analogous to a similar role hypothesized for phenotypic
    plasticity, the feasibility of which has been confirmed
    by mathematical models (Borenstein et al. 2006).

    Anyway, the Slatkin paper also appears to be interesting in that it proposes a means of incorporating this kind of iheritance into a standard evolutionary model…I hope I can get to it tonight. The semester starts tomorrow and I have a bunch of unrelated (and boring) shit to do.

  30. says

    I personally found Kuhn impenetrably dull to read. The SoSR IMHO could have been written as a longish essay. I may be wrong, but I imagine that Kuhn isn’t on the bookshelf of many scientists.

    I think I was helped by reading it as an audiobook. And not being a scientist probably helped too, though there were a few moments in the book where what he said was completely baffling – like that there are no observations independent of theory. That was wrong even within the examples he gave!

    Still, even a casual glance should show the difference between a scientific revolution, and an extension of an existing paradigm.