Saturday, December 13, 2008

Epigenetics at SEED

 
Epigenetics is one of the latest fads in biology. It arises out of evo-devo and its proponents tell us that epigenetics will transform the way we think about evolution. I've been trying to understand this phenomenon starting with some simple questions about what, exactly, is so new. I'd be happy if someone could just explain what they mean by "epigenetics" [Epigenetics in New Scientist, Epigenetics Revisited, Epigenetics, Epigenetics Again].

Eva Jablonka is a Professor at the Cohn Institute for the History and Philosophy of Science and Ideas at Tel-Aviv University (Israel). Jablonka was one of the 16 people who met in Alterberg, Austria last summer to discuss the faults in modern evolutionary biology. She writes an article entitled "Extending Darwinism" in the latest issue of SEED magazine.
I and several other biologists believe the MS [Modern Synthesis1] is in need of serious revision. Growing evidence indicated that there is more to heredity than DNA, that heritable non-DNA variations can take place during development, sometimes in response to an organism's environment. The notion of soft inheritance is returning to reputable scientific inquiry. Moreover, there seem to be cellular mechanisms activated during periods of extreme stress that trigger bursts of genetic and non-genetic heritable variations, inducing rapid evolutionary change. These realizations promise to profoundly alter our view of evolutionary dynamics.
Nothing new here, folks. It's just the same old gibberish that we've been hearing for the past several years.

If there is as much natural variation induced by environmental factors as lab studies suggest, then rapid evolutionary change could occur without any genetic change at all.

Eva Jablonka
But there is one thing that's worth noting. Eva Jablonka has done what few of her fellow epigeneticists have attempted. She defines what she means by epigenetics!
Epigenetics is a term that includes all the processes underlying developmental flexibility and stability, and epigenetic inheritance is part of this. Epigenetic inheritance is the transmission of developmental variations that have nothing to do with changes in the DNA base sequences. In its broad sense, it covers the transmission of any differences that do not depend on gene differences, so it encompasses the cultural inheritance of different religious beliefs in humans and song dialects in birds. It even includes the developmental legacies that a young mammal may receive from its mother through her placenta or milk—transmitted antibodies, for example, or chemical traces that tell the youngsters what the mother has been eating and, therefore, what they should eat.
Yes, but does it include the kitchen sink?

The good thing about incorporating these things into evolutionary theory is that it solves the problem of creationism. As long as creationism is passed on from parent to child then it becomes part of evolution. Isn't that cool?


1. Her version of the Modern Synthesis only includes natural selection.

24 comments:

  1. I always thought that epigenetics just referred to stuff like methylation of DNA sequences like we learned in BIO250.

    It sounds like this is just a specialized form of memetics (mainly, parent to offspring memetics) and should be viewed separately from biological evolution.

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  2. I was following all that quite comfortably until you pulled "creationism" out of the hat and I thought "Hello! Larry has found another creationist under his bed!"

    Trivially speaking given that creationism resiliently propagates from one moment to the next in our great cosmos it is, by definition, all part of a more generalized notion of 'evolutionary' change.

    So yeah, I agree, creationism must be related to bed bugs.

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  3. Esaul from what's being said I think it's more specific traits and tendencies that the parents or older kin pass on to the child biologically/physically via methods other than the transmission of DNA.

    It's much better if you ignore her broad definition that would include the cultural transmission of humans which would complicate things and just narrow it down to traits that biologically prime the offspring for the environment.

    PS the above isn't necessarily perfect; just an improvement.

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  4. There has recently been an article in Nature trying to clarify and define a series of concepts that are more or less use loosely in the scientific community, in terms of their real meaning.
    One of this terms in precisely 'Epigenetics'.
    The article ends with a quote from Mark Ptashne, which reflects its loose use : "epigenetics is a useful word if you don't know what's going on - if you do, you use something else".

    I invite you to read the article the October 23rd issue of Nature, page 1023.

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  5. I don't see how evo-devo gave birth, in a matter of speaking, to epigenetics.

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  6. As long as creationism is passed on from parent to child then it becomes part of evolution. Isn't that cool?

    I don't know if it's cool, but it's certainly obvious. We inherit a lot more than DNA sequence from our parents, from the molecular to the cultural. The fact that biologists like Larry still insist on looking at everything through their DNA sequence blinders is a big problem. DNA mutation and the underlying mechanisms happen to be easily studied in the lab. As a results we've learned some cool stuff over the past hundred years of molecular biology. Now it's time to embrace the wider picture of inheritance and move on to bigger things.

    I think that's what the "epigeneticists" are trying to say.

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  7. PZ and Abbie recently discussed epigenetics - check these links:

    http://scienceblogs.com/pharyngula/2008/07/abbie_and_pz_on_tv.php

    http://scienceblogs.com/pharyngula/2008/07/epigenetics.php

    http://scienceblogs.com/erv/2008/07/erv_on_epigenetics.php

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  8. Art,

    I suspect Larry will be thinking of PEV (Position Effect Variegation) in Drosophila—? There is a long-established broader use of the term outside of molecular biology per se, too.

    To me, it's not there that are no definitions of epigenetics, it's that at first blush there are too many and that they can (seemingly) be rather divergent.

    Molecular epigenetics (i.e. leaving aside the wider uses of the term, which I only have an amateur understanding of) does have reasonably long roots. I also believe that it's roots are not just in evo-devo (or rather it's predecessor), although that it one area that strongly supported it. The "new" fad about epigenetics reminds me of how bioinformatics was "discovered" by those outside the field and suddenly it was this "new field". Basically, they had suddenly realised that an existing thing was relevant to them! A similar thing seems to be happening for molecular epigenetics.

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  9. The Modern Synthesis needs revision, but such revision should come from paleontology and evo-devo, not epigenetics.

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  10. Larry is just trying to poke his finger into eyes, as usual. Pretty boring...
    No, Larry, Jablonkas defintion does not include the kitchen sink. She says: 1) inheritable changes 2) Not in the primary sequence of DNA. She gives an example: cultural evolution of song in birds.

    Other examples are persistent dna methylation, for instance...which is very interesting, regardless of what dumb ole Larry may say

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  11. What's the difference, epigenetically, between heritable and taught?

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  12. I agree this was a poor article. It said little and explained nothing, as did several others in the same issue. I am becoming more and more disappointed in SEED for the superficiality of its articles and for its not allowing feedback (no letters to editors, or other way for readers to respond).

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  13. A. Vargas says,

    Other examples are persistent dna methylation, for instance...which is very interesting, regardless of what dumb ole Larry may say

    Dumb ole Larry agrees that DNA methylation is interesting. That's why it's covered in my textbook and that's why I've blogged about it several times.

    The best understood example is the restriction modification system in bacteria; Restriction, Modification, and Epigenetics.

    We've known about restriction/modification enzymes for almost fifty years. Surprisingly, in all that time there weren't any evolutionary biologists who thought that our understanding of evolution was in need of revision because of the existence of restriction/modification genes in the bacteria genome.

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  14. Joseph Knight says,

    The Modern Synthesis needs revision, but such revision should come from paleontology and evo-devo, not epigenetics.

    I agree with you about paleontology but I'm not convinced that evo-devo has anything new to contribute to a general evolutionary theory.

    But in addition to paleontology, the hardened version of the Modern Synthesis could do with a new injection of facts from population genetics and molecular evolution.

    It's pretty clear from her article that Eva Jablonka has not assimilated the concept of random genetic drift and does not think it's part of the Modern Synthesis.

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  15. "I'm not convinced that evo-devo has anything new to contribute to a general evolutionary theory"

    larry is part of a bunch of gene-happy fools who are happy to think development is not an importnat issue for understanding evolution. They think they can jump form genotype to phenotype to evolution without considering exactly how the genotype relates to the phenotype.

    Coincidentally, Larry knows dick about embryology andthe role of ev-devo in the discussion of convergence and homology.

    Is that restriction enzyme thing all you care about in methylation, Larry?

    Maybe some day you will read up some more and include the freakin' ENVIRONMENT into the picture.

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  16. lol We quoted the same parts.

    I am not pleased with that article. It whished right by my kook-threshold, rendering any of its positive points useless.

    Not helpful for communicating science to laypeople. Not. Helpful.

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  17. The article ends with a quote from Mark Ptashne, which reflects its loose use : "epigenetics is a useful word if you don't know what's going on - if you do, you use something else".

    The quote is from Adrian Bird.

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  18. Larry,

    Upcoming paper in Science:

    Mihola, O. et al. (2008) A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase. Science, DOI: 10.1126/science.1163601.

    Speciation genes restrict gene flow between the incipient species and related taxa. Three decades ago, we mapped a mammalian speciation gene, hybrid sterility 1 (Hst1), in the intersubspecific hybrids of house mouse. Here we identify this gene as Prdm9, encoding a histone H3 lysine-4 trimethyltransferase. We rescued infertility in male hybrids with bacterial artificial chromosomes carrying Prdm9 from a strain with the "fertility" Hst1f allele. Sterile hybrids display down-regulated microrchidia 2B (Morc2b) and fail to compartmentalize {gamma}H2AX into the pachynema sex (XY) body. These defects, seen also in Prdm9 null mutants, are rescued by the Prdm9 transgene. Identification of a vertebrate hybrid sterility gene reveals a role for epigenetics in speciation, and opens a window to a hybrid sterility gene network.

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  19. SteveF says,

    Larry,

    Upcoming paper in Science:

    Mihola, O. et al. (2008) A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase. Science, DOI: 10.1126/science.1163601.

    Speciation genes restrict gene flow between the incipient species and related taxa. Three decades ago, we mapped a mammalian speciation gene, hybrid sterility 1 (Hst1), in the intersubspecific hybrids of house mouse. Here we identify this gene as Prdm9, encoding a histone H3 lysine-4 trimethyltransferase. We rescued infertility in male hybrids with bacterial artificial chromosomes carrying Prdm9 from a strain with the "fertility" Hst1f allele. Sterile hybrids display down-regulated microrchidia 2B (Morc2b) and fail to compartmentalize {gamma}H2AX into the pachynema sex (XY) body. These defects, seen also in Prdm9 null mutants, are rescued by the Prdm9 transgene. Identification of a vertebrate hybrid sterility gene reveals a role for epigenetics in speciation, and opens a window to a hybrid sterility gene network.


    The authors identified a gene with different alleles in different mouse populations. Those alleles produce different phenotypes that lead to hybrid sterility when individuals from the two populations interbreed.

    In this case the phenotype is histone methylation patterns.

    Since histone methylation patterns are part of the broad category of epigenetics, the study reveals a connection between one form of epigenetics and speciation genes. We can add that to a long list of phenotypes, both behavioral and physical, that contribute to speciation.

    What's the big deal? The epigenetic phenotype is caused by a typical gene and mutations in that gene affect the phenotype.

    Does this mean we have to re-think our understanding of evolution?

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  20. Does this mean we have to re-think our understanding of evolution?

    No, I just thought you might find it interesting!

    There's another paper on genes and speciation from H Allen Orr upcoming as well:

    A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

    http://www.sciencemag.org/cgi/content/abstract/1163934

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  21. I think the interesting thing about epigenetics is that it provides evidence that "mind" or self-organization mechanisms can give the illusion of "evolution" in the field. For example, if a creature were to generate a new trait epigenetically and pass it on to its progeny, then it may in fact fool scientists into believing the population "evolved." The changes in the field/fossil record may be, in fact, be a history of changes in epigenetics/junk DNA. Put differently, changes in the field may just be a result of changes in mind.

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  22. Hi supersport!

    (this may seem rather cryptic - I strongly suspect that the above anonymous commenter is "supersport", a fairly notorious and utterly cretinous troll on evolution/creation messageboards)

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  23. This comment has been removed by the author.

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  24. pposition to silly "gene-happiness" has always existed within the more knowledgeable biologist. epigenetics has given molecular resolution to many phenomena previously known (but traditionally ignored by the thoughtless masses) such as parent-of origin effects, "assymetric" hybrid crosses, and genetic assimilation (Larry seems to think its all about restriction enzymes in bacteria...).

    Some fools tend to think that all that exists is what they can explain and understand. Rather than seeing unexplained phenomena as a challenge, they ignore it. That is why the current surge of epigenetics is beautiful, and a slap to the face of cynics. They don't like it. They insist there is still nothing to it.

    Ideologically, a big problem is that some people (specially triumphalist biochemists-molecular biologists) think that the primary sequence of DNa is like a code that contains "the information" for everything that goes on in the organism . But, of course, none of that is going on in the cell (well, unless you are an ID creationist, in which case you are welcome to think of the metaphor as a literal truth: DNA, plain and simple, is "the language of god", like Collins would have it)

    These light-headed DNA worshippers are not happy with the facts that show how much of the phenotype, and of inheritance, can change without any change in the primary sequence of DNA (their precious "program")

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