ew… epigenetics in SEED…

*sigh*

My swooning over Venter on the cover of the latest edition of SEED was rudely interrupted by Larry Moran. Evidently he really does get SEED ‘for the articles’. heh.

Epigenetics at SEED

Yeah, um, this SEED article… this article is not helpful. For you, or me, or the scientific literacy we are fighting for.

If someone held a gun to my head and screamed “DEFINE EPIGENETICS!!!!”, this is what I would say:

Histone and DNA modifications that alter chromatin structure–> gene expression. Some people also include siRNA.

I think that is kinda an idiomatic definition of ‘epigenetics’, at least in my scientific circles. For instance, if someone published a paper vaguely titled ‘Herpes Simplex Virus-1 induces epigenetic modifications upon infection’, I would guess that their paper is about some histone acetylation or DNA methylation, and a subsequent change in gene expression, or something like that.

I would not give the scientifically curious gunman this response:

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.

What the hell? Antibodies in a mothers breast milk are epigenetics now? A baby knows what it should eat because of epigenetics?? Songs birds singing is epigenetics?

What??

*rubs temples*

Look, Ive started to notice a pattern in science.

There are some people who are convinced that they are leading a revolution. Paradigm shifters, if you will. In reality, these people are just kinda… kooky…

There is another group of people. Theyre just doing their science thing, stumble upon something cool, fight (with science) to move the scientific community. They dont realize they are leading a revolution, they just do. These people win Nobels.

As someone who just dabbles in epigenetic research as a ‘hobby’, I am not pleased with this SEED article. Dr. Jablonka… the tone of her article… the content of her article… makes me wince. It puts her in ‘category 1′.

I and several other biologists believe the MS [modern evolutionary synthesis] 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 organisms 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.

… Doesnt that sound familiar?

… Doesnt that sound like the comments we hear from… other… groups?

*blech*

Comments

  1. #1 Austin
    December 15, 2008

    Glad to see someone else was less than satisfied by that article. I wasn’t sure if Dr. Jablonka was just trying to use as many words as she thought the public might seize upon, or if she really does have such a fast and loose definition of epigenetics.

    Then again, this is science, and Dr. Jablonka is a scientist. I’ve never read any of her papers, but if she can prove one or more of her hypotheses of epigenetic heritability (and the results can be replicated) we can work on changing how we view evolution. Otherwise, we continue with what we do know.

  2. #2 ERV
    December 15, 2008

    Austin– thats one of the many problems with this article. There is evidence of inheritable epigenetic ‘flags’ (methylate me, not me. ubiquitinate here, but not here.) and understanding this could help us grow transplant organs ex vivo, or increase fertility/in vitro fertilization, and so on. All of her claims arent garbage.

    But she tarnished the ‘real’ science with ‘religion is epigenetics’ and ‘antibodies are epigenetics’ and other bullshit.

    How is a normal SEED reader supposed to know which parts are science, and which parts are the delusions of a paradigm shifter?

  3. #3 Becca
    December 15, 2008

    I don’t personally care a great deal for the “culture is part of biology” stuff, though sometimes there are legitimate grey areas when defintions get too broad they loose something essential. So the quote from the Seed article strikes me as slightly annoying.

    That said, sorry erv, but you’re wrong about the fundamental nature of “epigenetics”.
    Literally, it would mean “above genetics” and a defintion addressing “heritable changes that aren’t encoded by DNA base pair order” is a perfectly legit way to put it.
    Not that “histone acetylation and methylation” isn’t part of the story… but it’s a bit like defining genetics as “replication and transcription”. Key biochemical mechanisms are not the same as the whole discipline.

    As for the last paragraph, I think somebody needs to figure out how to calculate the derivitive of evolution. We don’t really understand all the factors driving the rate of evolutionary change, but if anyone ever gets to a useful mathematical treatment of it, it probably will revolutionize what we can apply evolution toward.

  4. #4 Tyler DiPietro
    December 15, 2008

    “Literally, it would mean “above genetics” and a defintion addressing “heritable changes that aren’t encoded by DNA base pair order” is a perfectly legit way to put it.”

    Well, she did disclaim the fact that her definition was idiomatic, not literal.

  5. #5 Johnny Vector
    December 15, 2008

    Blech. Sounds to me a lot like the proponents of “chaos theory” in the 80s. Cause that sure changed our paradigms, huh? Just like you say about this, there’s real science there, and then it gets all whipped up into a great creamy froth by the paradigm shifters and booksellers, and pretty soon the public is all “oh that, that is soooo 10 years ago.”

    Besides, the real paradigm shifters have 4 on the floor, and this stuff sounds pretty 3 on the tree to me.

  6. #6 MattK
    December 15, 2008

    I would like to see a tie in between some of that stuff (even the kitchen sink) and speciation. Whether one includes cultural transmission under epigenetics or not, I would be very interested in ways in which it can feed back into evolution. I’m thinking dialects in songbirds and Orcas. Orcas, specifically, have apparently very little gene flow between parapatric groups with different dialects and other cultural traits. Are culturally inherited traits leading to reproductive isolation, or is it mostly a matter of isolation leading to cultural differences? I suspect that being difficult to study organisms with long lifespans and small population sizes mean that Orcas are not a great model organism for this type of question. I wonder what the ornithologists have done…

  7. #7 Puzzled
    December 15, 2008

    One thing the article (suspiciously) glossed over is the generational staying power of her claimed Lamarckian mechanisms. I mean, Neo-Darwinism has DNA, and we know that some of the things stored in it have lasted over a billion years of generations. The mechanism she proposes are lucky to last a few generations. How can that be a serious challenge to Neo-Darwinism as an explanation? Even if her mechanisms are real, they’re at best a minor adjunct to the force that is neo-darwinism.

    I tried to give her a fair chance, but she seemed kooky and unconvincing. I’d be glad if anyone knows better.

  8. #8 llewelly
    December 15, 2008

    hey folks. epi is just another prefix meaning cool and trendy.

  9. #9 RobC
    December 16, 2008

    Why is it the kookier the article, the more meaningless abbreviations are used? Would it kill the author to write out “modern synthesis?” MS means Multiple Sclerosis to me.

    And are cancer patients loosing their culture and religion because of therapeutic HDAC and DNMT inhibitors?

    Maybe its “scienceish”, like Colbert’s truthiness, but not science. Its almost like the Star Trek universe-take grains of truth from physics and run with them. But there’s a different between fun in sci-fi and scientists running wild and suggesting culture, religion and song birds are due to DNA methylation and the histone code.

    My favorite example:
    “CHAOS THEORY AND THE EVOLUTION OF CONSCIOUSNESS AND MIND: A THERMODYNAMIC-HOLOGRAPHIC RESOLUTION TO THE MIND-BODY PROBLEM”
    New ideas in psychology 1995, vol. 13, no2, pp. 107-127

  10. #10 Puzzled
    December 16, 2008

    “CHAOS THEORY AND THE EVOLUTION OF CONSCIOUSNESS AND MIND: A THERMODYNAMIC-HOLOGRAPHIC RESOLUTION TO THE MIND-BODY PROBLEM”

    That sounds like something Alan Sokal would make fun of.

  11. #11 MattK
    December 16, 2008

    But there’s a different between fun in sci-fi and scientists running wild and suggesting culture, religion and song birds are due to DNA methylation and the histone code.

    Hmm, scientists gone wild… I like.

    I haven’t read the article, but I’m going to hazard a guess and say that culture etc are discussed as examples of epigenetic phenomena conceptually similar to DNA methylation etc rather than being caused by it (although the reason why song bird songs can be products of DNA but not DNA methylation escapes me).

    I get that people (myself included) find the idea of epigenetics as defined in the quote from the article to be frustratingly all-encompassing. Ok fine. And yes, it may be hyperbole to suggest that epigenetics (whatever it is) represents a paradigm shift (didn’t this win a most overused phrase award at some point like five years ago?). Nevertheless, if people want to put a stop to this everything-is-epigenetics business then they need to come up with a clear conceptual boundary between things that modify phenotypic expression (like methylation) that are heritable and things that modify phenotypic expression (like cultural transmission of bird song dialects) that are also heritable. For all I know someone has already done this. If so, maybe I could be pointed in the right direction.

  12. #12 Bob O'H
    December 16, 2008

    Becca @3 – I’m not sure what you mean about a mathematical treatment of evolution. Isn’t that what Fisher gave us? The rate of evolution is given by the Breeder’s equation, for example.

    hey folks. epi is just another prefix meaning cool and trendy.

    So it’s really just an epiphenomenon.

  13. #13 John S. Wilkins
    December 16, 2008

    In a mild defence of Eva’s work – the term “epigenetics” has a history that is well before the genetic revolution, and refers to the notion that fetuses are developed through a process of construction, as opposed to the idea that the fetus is preformed. Modern genetics is a mix of both ideas. The generality of the term is contextual and while it may be that molecular biologists have a particular sense of the term, that doesn’t thereby make it the sole legitimate one. See the Stanford article.

    Eva’s ideas are somewhat polemic, yes, but she does know the science pretty well, and while I think she uses words to overstress the originality of her view, that is hardly unique to her. In particular I think she’s not proposing anything at all like Lamarckism.

  14. #14 Savva
    December 16, 2008

    A strange discussion. The epigenetic control system of the organism is totally based on the genetically encoded information. Here is what I postulated in my article in the book published in 2007, see http://www.misaha.com

    The Epigenetic Biofield Control System (BCS) is the operative control system of the organism. In BCS, the genetic information is re-encoded on some other than biochemical physical carrier. It evolves in ontogenesis into a hierarchy of subordinate BCS of the whole organism, organs, tissues and cells. At all levels it holds four fundamental programs of life: development, maintenance, reproduction, and death. The mind is an essential part of the BCS at the whole organism level, serving behavioral aspects of all fundamental programs (in addition to the physiological aspect´┐Żsee Fig.1)

    BCS participates in biological evolution which brings the ideological discussion between IDs and Darwinists into the realm of science.

  15. #15 Lorax
    December 16, 2008

    I think the vitriol directed at the SEED article in somewhat overblown. Epigenetics has been around far longer than modern evo-devo or understanding the function of histones. Yeast geneticists were studying non-mendelian inheritance patterns as epigenetic problems back in the 40s and 50s. One problem is that young scientists often lack historical perspectives outside their particular field. If you only know about epigenetics from the human genetics literature, you may indeed have the sense that epigenetics is a histone modification specific event with the potential to include siRNA. This perspective is inaccurate even though these perspectives may be endemic in a particular field.

    That said, religion is not epigenetic.

  16. #16 Joshua
    December 16, 2008

    One of these days, I have to read The Structure of Scientific Revolutions just to figure out once and for all whether it’s Kuhn who was full of crap or whether he was totally reasonable and just got co-opted by generations of egomaniacs searching for validation.

  17. #17 Tatarize
    December 16, 2008

    ERV, stop being Persnickity Patty (Correction Courtney?). “it covers the transmission of any differences that do not depend on gene differences” — I knew growing up partly outside of Chicago and partly in Southern California was epigenetic. The fact that I say “dude” isn’t my fault, it’s my epigenetics. Nothing you can say can fix my now warped view of science. Did you know circumcision in Jewish families was epigenetic? The new fight isn’t nature v. nurture, it’s genetic v. epigenetic.

    In reality I think I have a pretty good grasp of epigenetics, having read this and other science related blogs. I am not a biologist but my understanding is that genes are regulated by themselves and the environment and sometimes those regulations get passed on to the next generation whose expression of genes are partially influenced by the environment of the parent, independent of the genes themselves or the environment of the children. — If that’s largely wrong, you’ve done a horrible job relaying epigenetics to the public. If accurate, thank you.

  18. #18 ERV
    December 16, 2008

    Savva is on automatic junk from his constant spamming, but I let #14 through for the lulz.

  19. #19 Becca
    December 16, 2008

    +1 to Lorax (minus the subtle criticism directed at ‘young scientists’, which would be bizarre coming from me).

    “Becca @3 – I’m not sure what you mean about a mathematical treatment of evolution. Isn’t that what Fisher gave us? “
    Fisher gave us mathematical equations for the part of genetics following from homologous recombination in sexually reproducing species, not evolution broadly.
    Obviously the levels of recombination are major drivers of easy-to-analyze traits in animals and plants.
    Beyond Fisher, epigenetics is telling us that we also need to consider the non-DNA code mechanisms (like parental imprinting) in keeping track of interesting heritable traits.

    Furthermore, there are also the rates of horizontal gene transfer (yay retroviruses!) to consider. In microbes, these may be more important than sheer mutational rate assumed to be a main mechanism of change for assexually reproducing organisms.

    But what I was trying to get at is actually the next level. How did mutational controls evolve (polymerases and their error rates, substrate specificity, cell cycle checkpoints… a lot of things fall under this umbrella)? Can we quantitate that? Can we quantitate the rate of change of horizontal gene transfer?
    Do we even know the conditions which favor rapid “evolvability” (could we set up an equation for it if we wanted to)?

  20. #20 rrt
    December 16, 2008

    It sounds to me like she’s being careless with her terms, whatever else she may be thinking. And while I haven’t read it, isn’t this basically what Dawkins was toying with when he wrote about extended phenotypes?

  21. #21 Blake Stacey
    December 16, 2008

    Joshua:

    It’s been said that there were in fact two Thomas Kuhns, the rational one and his insane twin brother. Some of his views apparently changed over time, as well, which complicates the issue. I rather enjoyed the perspectives in Alan Sokal’s Beyond the Hoax (2008) on this whole muddle.

  22. #22 SC
    December 16, 2008

    Thank you for posting about this! This issue is the first one I’ve ever read (picked it up at the airport last month), and I was perplexed by that piece.

    they loose something essential

    cancer patients loosing their culture

    Why is this such a common mistake? I see it so often (most amusingly, when during Crackergate someone sent a letter to the president of the U. of Minnesota in support of PZ Myers arguing that it would “be a mistake for the university to loose him”), and I honestly don’t get it.

  23. #23 David Welsh
    December 16, 2008

    What is your collective opinions of Bruce Lipton’s writings?

  24. #24 Jason
    December 17, 2008

    Abbie – ouch! That post by savva made you laugh but made my inner biologist shriek! wtf is he on?

  25. #25 Martin
    December 20, 2008

    George Johnson does not like this post – or your thoughts on science journalism that you expressed in your BHtv diavlog with Ed Yong -
    http://brainwaveweb.com/diavlogs/16633?in=00:46:39&out=00:51:05

  26. #26 Matt Heath
    December 20, 2008

    @Martin: He was kind of a dick about it too, assuming Abbie’s attitude came from some bad experience with a hick paper.

  27. #27 Eric Saveau
    December 20, 2008

    Wow. George Johnson doesn’t come across as a committed journalist, but a pompous boorish git who adores the sound of his own voice.

  28. #28 MattK
    December 20, 2008

    Oh man, the dude is an ass. He doesn’t get what ERV is about, and he ignored everything that Ed Yong said (that addressed the asshat’s issues better than the asshat did). He mentioned a few science journalists that he thinks are good. Fine, I’m sure there’s a couple of those. In my experience, almost every science article in the popular press that I come across is oversimplified, misdirected, and factually inaccurate (why can’t they ever seem to find an informed person to proof their work?). And he seems to suggest that scientists don’t like journalists ’cause the don’t just swallow the press release. FAIL. The thing that I hate about most science journalism is that most of what it does is regurgitate the press release (including all the self serving hype therein). When they do try to cover ‘both sides’ a lot of the time it is with an issue that does not have two legitimate sides. So they fail in the journalism part and in the science part. Two wrongs don’t make a right.

  29. #29 Eric Saveau
    December 20, 2008

    He also objects to Abbie’s informal style of writing, ignoring the importance of actual content. That’s creotard logic.

  30. #30 Coturnix
    December 20, 2008

    DNA modification/histones/methylation stuff is just a small (but currently fashionable) subset of epigenetics. The term originates with Waddington and incorporates all inheritance not reliant on the DNA sequence, including stuff like learning. Waddington took the term from ‘epigenesis’ which was the opposing view to ‘preformationism’ earlier on. Wikipedia article is actually very good on this topic.

  31. #31 Robert Gagnon
    December 21, 2008

    ERV & Co,

    If you really want to communicate, like tell us folk, about your scientific enthusiams et al, it might work better if you used English more like Sean Carroll & Co. We unwashed few may actually get your message!

    Or you could choose to whine and moan in your “creotard logic” and language. If that’s your preference enjoy yourselves!!!

    I like George J and John H and appreciate their welcome incrementing our knowledge of science and life.

    Take Care!

  32. #32 Coturnix
    December 21, 2008

    Insisting on “proper” language is a sign of insecurity, an attempt to keep the power hierarchies as they are, keeping the Barbarians out of the Gate, protecting one’s ass in a power structure in which one learned how to get ahead without being secure in one’s own qualities. It is a fear of meritocracy. Forcing people to use a particular language style also forces them onto your turf where you have formal power over them. Of course you are threatened when someone uses other types of rhetoric, because you will have to, again, build your reputation the hard way and you know deep inside that you cannot and will lose.

  33. #33 SciPhu
    December 21, 2008

    Just thought I’d mention that the very last part of the last quote in this post refers to HsP90 and some very interesting research into how this chaperone “masks” mutations by folding proteins that would otherwise be folded incorrectly. It has nothing to do with “other groups” (creationists ?), but rather some very intriguing research from Dr. Susan Lindquist at the Whitehead institute (among others).

  34. #34 Lorax
    December 22, 2008

    @SciPhu. The Hsp90 research is fascinating and has direct implications on anti-fungal drug resistance in the opportunistic pathogen Candida albicans (see The evolution of fungal drug resistance: modulating the trajectory from genotype to phenotype. Cowen LE. Nat Rev Microbiol. 2008 Mar;6(3):187-98). However, much of this research is done in yeast and plants and probably never shows up in the search cues of mammalian researchers or virologists (This might come off a little insulting, but no worse than the “other group” allusion made in the post.)

    BTW Becca, you may be the first to have used the term “subtle” in context to me. ;-)

  35. #35 MarkH
    December 24, 2008

    What is shocking to me in the clip is how he reads your article like he’s retarded. He doesn’t know what siRNA is? How an arrow denotes “leads to” or “results in”? And how did he pronounce chromatin?

    I start to doubt the status of this guy as some kind of science journalism expert when he isn’t even familiar with some basic scientific terms and concepts. And blogs are replacing science journalism, especially if you consider CNN’s elimination of their science wing telling, or the fact we’re now linked from NYT science. We’re legit, we’re experts and in aggregate have a broader expertise than a single journalist could ever provide, we have something to contribute, get over it.

  36. #36 martinj
    December 26, 2008

    I guess it’s a matter of naming your field more than anything else, but still: Aren’t there phenomena among for birds (behavioural responses to environmental stresses) and mammals (hormonal environmental effects in the uterus), that could legitimately be filed under epigenetics, even if they had no direct connection with histone modification and methylation?