Michael Eisen on epigenetics

May 11, 2016 • 11:15 am

Micheal Eisen, a well known geneticist at UC Berkeley, has weighed in on genetics and l’affaire Mukherjee on his website It is Not Junk. As you’ll see from his post (click on the screenshot below to go there), he thinks that Mukherjee way overrated the significance of epigenetics in his New Yorker piece. I like the title of his post, and love the subtitle, which you’ll recognize as a variant of Arthur Clarke’s Third Law.


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Just a few excerpts (indented) and my comments:

Biologists now invoke epigenetics to explain all manner of observations that lie outside their current ken. Epigenetics pops up frequently among non-scientists in all manner of discussions about heredity. And all manner of crackpots slap “epigenetics” on their fringy ideas to give them a veneer of credibility. But epigenetics has achieved buzzword status far faster and to a far larger extent than current science justifies, earning the disdain of scientists (like me) who study how information is encoded, transferred and read out across cellular and organismal generations.

True, and I’m not quite sure why it’s become a buzzword. One explanation is that it somewhat circumvents genetic determinism by suggesting that the environment, your behavior, or even (à la Chopra) your will can change your genes, perhaps in a heritable way. That makes it appeal to those Leftists who don’t like genetic determinism. Also, epigenetics has been construed as eroding the modern theory of evolution by suggesting (wrongly) that evolution can occur in a Lamarckian way—through the inheritance of environmentally acquired “DNA marks. People always love the notion that “Darwin was wrong”—although in this case it wouldn’t hold, as Darwin himself had a Lamarckian view of inheritance. But “epigenetics” is a buzzword among geneticists, too, and I’m not quite sure why.

Eisen on Mukherjee and the science he conveys in the New Yorker piece:

In one way this debate is incredibly important because it is ultimately about getting the science right. Mukherjee’s piece contained several inaccurate statements and, by focusing on one aspect of Allis’s work, gave an woefully incomplete picture of our current understanding of gene regulation.

Any system for conveying information about the genome – which is what Mukherjee is writing about – has to have some way to achieve genomic specificity so that the expression of genes can be tuned up or down in a non-random manner. Transcription factors, which bind on to specific DNA sequences, provide a link between the specific sequence of DNA and the cellular machines responsible for turning information in DNA into proteins and other biomolecules. Small RNAs, which can bind to complementary sequences in DNA, also have this capacity.

But there is scant evidence for sequence specificity in the activities of the proteins that modify DNA and the nucleosomes around which it is wrapped. Rather they get their specificity from transcription factors and small RNAs. That doesn’t render this biochemistry unimportant – the broad conservation of proteins involved in modifying histones shows they play important roles – but ascribing regulatory primacy to DNA methylation and histone modifications is not consistent with our current understanding of gene regulation.

Yes, and count on a scientist, rather than a journalist (unless he’s Carl Zimmer) to report the science accurately. It is the specificity of gene action that Mukherjee is interested in: after all, he began his piece with a discussion of cellular differences—between identical twins and, later in the piece, between cells within a body, all of which start with a single undifferentiated cell, the egg. And we know that specificity of gene action is conferred by small RNAs and transcription factors. We don’t know the same for histones or epigenetic markers.

But I digress. I see there are now a lot more articles on the Internet about this argument, which in the end IS about getting the science right (although it seems to also be about not looking bad if you’re famous). But I can’t be arsed to talk about every piece. Just Google “Mukherjee epigenetics” if you’re interested.

h/t: Charleen

19 thoughts on “Michael Eisen on epigenetics

  1. When you add a prefix to a word, that word becomes ultraspecial (see what I did there?) SO… epigenetics is the penultimate in genetics!

    1. But quantum really never had it this bad.

      Quantum systems are conservative and reversible and rigorously. mathematically solvable. [Quantum Chaos is a misnomer and one can still write out an equation for N-particle systems even if there is no idempotent solution.]

      Epigenetics appears to have a bag full of ambiguity attached to it that is not going to be cleaned up anytime soon.

      1. They both attract crackpots, but the resemblance ends there. Quantum theory is extraordinarily precise and central to understanding the physical world.

    2. Damn, beat me to it. I was going to write a piece extolling the virtues of the new field of ‘quantum epigenetics’ and explain how different epigenetic versions of yourself could be entangled in variant multiverses. But, oh well.

      I note that other responders point out that quantum mechanics is a coherent model with rigorous mathematics that makes elegantly testable predictions about the real world. Yes, indeed. Epigenetics, while less well understood (and we probably won’t ever have a readily comprehensible mathematical model of epigenetic mechanisms), certainly has a rational scientific basis. What is know about epigenetic modification of DNA, histones and, particularly, inheritance do not, in any way, support the wilder fantasies of the pseudo-epigenetic dreckmongers. Similarly, purveyors of ‘quantum’ woo, use words associated with quantum phenomena (‘uncertainty’, ‘entanglement’, ‘duality’) to peddle all manner of silliness.

      BTW, is a surgeon who attempts and fails to remove her own gall-bladder an idempotent operator?

  2. “But I can’t be arsed to talk about every piece.”

    Every piece of arse is too much to ask.

  3. My feelings toward Carl Zimmer go from huge fanboy to total envy of someone who has so much writing talent. But Carl was finally shown up by his brother Ben, also a writer specializing in linguistics. Ben wrote a piece about the musical Hamilton (opening in Chicago in September!), titled “Hamilton Through the Lens of Language.”

    He sent out a tweet about the piece which was retweeted by Lin-Manuel Miranda, the creator and star of the play which just received a few thousand or so Tony nominations.

    Poor Carl – all he could do was tweet this –

  4. For some people, the only thing they want to know about epigenetics is that is makes Richard Dawkins wrong. Please somebody just give them some information, any information, that makes Richard Dawkins wrong.

    1. Depressingly, I run across exactly that, a lot. Even more depressingly, mostly on a science website that is so strictly science oriented that you can earn a warning or even suspension for merely commenting about anything not accepted by mainstream science.

  5. Hi Jerry,

    I’m starting to think some of the underlying end all be all jumps to epigenetics that Michael noted in his piece there is the ‘generational curse’ referenced in the Bible:

    “or I the Lord your God am a jealous God, visiting the iniquity of the fathers on the children to the third and the fourth generation of those who hate me”

  6. I stand chastised.
    I thought that epigenetics included everything that influenced gene expression, including transcription factors in the first place.
    Epigenetics appears now to be reduced to DNA methylation and histone acetylation (among others) and hence only small part of what epigenetics should be : interesting, nay essential (particularly if we include transcription factors and RNA’s) part of the scientific genetic edifice…
    In my defence, I always found the ‘Lamarckian inheritance’ -indeed proposed by some- to be completely unwarranted and nearly absurd.
    Sadly, because of these unwarranted ‘Lamarckian’ and even ‘Lysenkonian’ connotations epigenetics has become a kind of swear word.
    Environment, including other genes, is pervasive, you cannot have a functional airplane if there’s no air. But it is not the aileron that makes the plane fly.

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