Epigenetics, a confused muddle in the media

By Grant Jacobs 22/03/2010 12

Guardian features writer Oliver Burkeman leads the on-line science section with a piece titled ’Why everything you’ve been told about evolution is wrong.’

DNA (unmethylated). Source: wikipedia.

It’s caused something of a fuss amongst some in science writing circles, with replies by Adam Rutherford and Jerry Coyne.

Reading these replies and the comments below them you’d be forgiven for thinking that some think it ought to be titled Why everything you’ve been told about evolution by Oliver Burkeman is wrong.

Personally I find his article well meant, but muddled and approached the wrong way.

There’s the title, which is not ’provocative’, but wrong. At the time of NewScientist’s ’Why Darwin was wrong about the tree of life’ cover title debacle, I ruminated that titles that seek attention through stating falsehoods, are best immediately corrected in the initial portion of the article. If they are not corrected immediately and firmly, they mislead.

In Burkeman’s case, I feel the title rather than serving as a teaser has readers falling back to it thinking ’that must be want he means’ when confused. Burkeman didn’t write the title, but it sets a position for unclear statements that don’t do him any favours.

His article draws from several popular science books, in particular Fodor and Piattelli-Palmarini’s What Darwin Got Wrong.

Burkeman’s biggest mistake, I think, is that he speaks for himself rather than representing the views of others, as it more usually the case in newspaper articles.

He indicates that he lacks scientific background on this topic and I think he would have been wiser to acknowledge this to himself better and not present his reading of what these authors mean but instead interviewed accepted specialists in evolutionary theory and epigenetics and present what they say.

So, a general thought: in order to judge a book proposing a particular interpretation of science, wouldn’t you need to have a deep knowledge of that area of science in order to know where it fell with respect to the evidence?

For example, Burkeman writes:

Unfortunately, that also makes it embarrassingly awkward to ask a question that seems, in the light of recent studies and several popular books, to be growing ever more pertinent.

Did it not occur to him that if he acknowledges that he is one of ’those of us who aren’t professional scientists,’ he is not in a good position to judge if the views of these books are ’ever more pertinent’?

He goes on:

What if Darwin’s theory of evolution — or, at least, Darwin’s theory of evolution as most of us learned it at school and believe we understand it — is, in crucial respects, not entirely accurate?

Such talk, naturally, is liable to drive evolutionary biologists into a rage, or, in the case of Richard Dawkins, into even more of a rage than usual.

Why would it enrage biologists?

If evidence backs it solidly it’d be very interesting and every biologist knows aspects of Darwin’s theory are ’not entirely correct’. Darwin wrote before the development of genetics, molecular biology and microbiology, which gave evolution a molecular basis it never had in his day. (It’s not that Darwin was wrong, as that he would have had more to add to what he did say.)

Burkeman seems to want to imply that the public are catching up with something scientists have been hiding from the ’culture at large’ about how ’most of us think about how life came to be the way it is’ in case it might be ’ammunition to the proponents of creationism or “intelligent design”.’

Far from being hidden, it has been one of the ’trendiest’ topics in molecular biology over the past 5-6 years. You couldn’t miss it if you tried. It is delayed in getting into textbooks, but that is how it always has been and how it should be. It takes time for new things to be explored and the initial incorrect paths to be corrected.

To put the bubris aside, those interested in the philosophy should read Ned Block & Philip Kitcher’s polite, but rounded, criticicism of Fodor and Piattelli-Palmarini’s book What Darwin Got Wrong, e.g.:

Fodor and Piattelli-Palmarini are not biologists. Fodor is a leading philosopher of mind and cognitive scientist, best known for his ideas about the modularity of mind and language of thought; Piattelli-Palmarini is a cognitive scientist. They do not have new data, new theory, close acquaintance with the everyday practice of evolutionary investigations, or any interest in supplying alternative explanations of evolutionary phenomena. Instead, they wield philosophical tools to locate a ’conceptual fault line’ in contemporary Darwinism. Apparently unshaken by withering criticism of Fodor’s earlier writings about evolutionary theory, they write with complete assurance, confident that their limited understanding of biology suffices for their critical purpose. The resulting argument is doubly flawed: it is biologically irrelevant and philosophically confused. We start with the biology.

I prefer to simply look at what observations show us. So, let’s briefly look at epigenetics.1

Burkeman gives a number of examples of epigenetic effects that I hope to address later in a series of articles. A key point is are the changes able to be passed on repeatedly, generation after generation, as genes are.

The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF(Source: molecularstructure.org)
The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF. (Source: molecularstructure.org)

I am not aware of an example of epigenetic ’inheritance’ that does this. All those I have read are limited to one or two generations. Trans-generational effects have been observed, but there isn’t evidence of this being inherited in the on-going fashion that genes are.

Note that I am distinguishing between transgeneration effects and inheritance: altering the regulation of a gene is not the same as inheritance of the gene itself.

Epigenetics confuses some because this form of modifying the expression of a gene involves changing the DNA by adding a methyl group–a carbon with it’s bound hydrogens–to some DNA bases. (Biologists say that a gene is ’expressed’ or ’active’ when it is used and that genes that not used are ’repressed’.)

This modification of the DNA base doesn’t change what the gene codes for; what is altered is how the genes are regulated.

One of the reason that biologists expect these ’epigenetic marks’ to not be passed on in a simple hereditary fashion is that DNA methylation is removed in the early stages of a growing embryo and then laid down again anew.

One way of looking at epigenetic effects on offspring is that they may provide a short-term response to (severe) environment pressure by evoking temporary choices of what genes to use for a generation or two, over and above the longer-term genetic inheritance.

Furthermore, observations that imply offspring are changed through the parent’s experiences does not make epigenetics replace conventional genetics or ’Darwinian’ evolution.

Like most new additions in science, it adds to the previous work, not replaces them.

The shame of it is that Burkeman gets it more-or-less right, only to contradict himself, giving the impression that he so doesn’t understand when he has it right or wrong. He gets this more-or-less right:

The epigenome plays a crucial role in determining which genes actually express themselves in [determining] a creature’s traits: in effect, it switches certain genes on or off, or turns them up or down in intensity.

Later he writes contradicting this, ’it seems that the environment plays a role in creating those traits in future generations’ (my emphasis added).

In the second, he has the epigenetic effects creating new traits. They don’t, they alter how the existing genes are used. It’s a subtle difference, but an important one.

Epigenetics doesn’t ’influence heredity,’ it influences how genes are expressed. The hereditary units – genes – are still passed on as they always are, but how they are used may be altered through epigenetic effects.

Finally, although much of the fuss about epigenetics in the general media and popular books have been with epigenetics affecting offspring, the more common example of epigenetic effects is during the development of the body or long-term changes in gene expression. It’s a good example of popular thought latching on to the exceptional cases and conflating them.


1 Epigenetics has been my main research interest over the last 6+ years. I became interested in it because I believed it signaled a change to finally (as in ’about damn time’) moving from a linear view of genomes in computational biology and mainstream molecular biologyto viewing them as structures. This is a spiel I can leave for another time. My own interests are with how organising chromatin structure affects gene expression.

2 Burkeman’s footnotes note that the original claimed that genes caused random mutations, rather than undergo them. This would indicate to me that he is far out of his depth in trying to access the science himself.


I’ve corrected a few broken links and a too many silly rewriting-on-the-fly errors. My apologies.

Other articles on this issue are at Culturing Science, Genomicron,  tbo’s posterous, Slightly foxing and others.

I should have made clear I’m writing about epigenetics in mammals. I couldn’t speak for epigenetics in plants, for example.

Other genetics articles on Code for life:

The inheritance of face recognition, or should you blame your parents if you can’t recognise faces?

Tracking disease and human migration through genetics

Deleting a gene can turn an ovary into a testis in adult mammals

Genetic tests and personalised medicine

Metagenomics-finding organisms from their genomes

12 Responses to “Epigenetics, a confused muddle in the media”

  • “…the possibility remains that multigenerational epigenetics could be another aspect to evolution and adaptation” (Wikipedia)

    Research has also revealed that retroviruses have contributed to evolutionary change.

    These scientific revelations don’t mean that we should throw away the theory of evolution but they make statements like:
    “All organisms on Earth are descended from a common ancestral gene pool” (Wikipedia) somewhat redundant. It was recently changed to “All living organisms on Earth are descended from a common ancestor or ancestral gene pool”.

    Science keeps (surreptitiously) changing its mind about evolution.

    D J Wray
    Packaged Evolution: The Intelligent Universe

  • Hi Grant, I confess that this is not my field either. However, I refer you to a review article of epigentic phenomena which suggests that some phenotypic epigenetic characteristics can be inherited up to 13 generations after the original enviromental stimuli altered the ancestor’s gene (admittedly it was a fly). Not really sure what this all means but would like your opinion as it seems to contradict what you said in your blog.

    Jablonka, E., & Raz, G. (2009). Transgenerational epigenetic inheritance: Prevalence, mechanisms, and implications for the study of heredity and evolution. Quarterly Review of Biology, 84(2), 131-176. doi: 10.1086/598822


  • Bruce,

    I didn’t mean to imply this never occurs in other species, just remarking more casually that I wasn’t familiar with any examples in mammals. Looking back on it, it might have been clearer if I’d left it out. What I really was trying to lead to was distinguishing “true” inheritance and what is essentially environmental control of gene expression (that can be confused as being inherited) and that the underlying DNA sequence of the genes haven‘t been altered.

    Thanks for pointing to the review. I can’t promise much as I’m swamped with work and I look at the molecular steps that occur later in “higher” animals (somewhere in between DNA methylation and chomatin-level control of gene expression, if you like; the latter is the thing I’m really interested, not DNA methylation), rather than the organism-level story in different species. Drosophila biology isn’t something I know as well as I‘d like to.

  • Grant,

    For examples of transgenerational epigentic effects in mammals see:

    Waterland, R. A., & Jirtle, R. L. (2003). Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation. Mol. Cell. Biol., 23(15), 5293-5300. doi: 10.1128/mcb.23.15.5293-5300.2003


    Anway, M. D., Cupp, A. S., Uzumcu, M., & Skinner, M. K. (2005). Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility. Science, 308(5727), 1466-1469. doi: 10.1126/science.1108190


  • Bruce,

    I’m too busy to deal with this right now, I have a lot of deadlines to meet. I may not find time, as it would likely take days to track each individual story forward in time to the latest papers and read around to fully understand them and I simply haven’t that sort of time right now.

    I would suggest Youngson & Whitelaw Ann. Rev. Genet. Genomics. 2008.

    Quick snippets for you,

    From the end of the abstract:

    There is a trend for those outside the field of molecular biology to assume that most cases of transgenerational epigenetic effects are the result of transgenerational epigenetic inheritance, in part because of a misunderstanding of the terms. Unfortunately, this is likely to be far from the truth.

    Final paragraph of review:

    In animals, both adaptive and nonadaptive transgenerational epigenetic effects do occur. Many, perhaps most, of these effects are not the result of the direct transfer of information via the gametes. The advantage of epigenetically preadapting offspring to their future environment via the gametes appears to have been mostly outweighed by the desire to prevent inherited epimutations and safeguard the pluripotency of the epigenetic program of early development. The observations of trans-generational effects of nutritional availability, chemical exposure, and inherited epimutations are generally limited to one generation. […]

    Please note I am not saying that multi-generational examples that do not involve the gametes do not exist, I tried to point out earlier, as these are not inheritance in the sense I am referring to. I’m wary of non-adaptive examples, or examples that involve “breaking” the system, for other reasons.

    I’m also not much a fan of trying to take a few exceptions to the general rule to propose a new “rule”. By its nature, evolution will always have exceptions to the general rule (in fact I like to say that the only “rule” at that level of biology is that there are no universal rules [i.e. there are no laws]). This isn’t me making excuses (!), its my view on the nature of biology. I sometimes think that the philosophers who get involved in this don’t seem to appreciate this point.

  • Thank you for an informative and pleasant Saturday morning read. I found your site while browsing through a Google employee’s profile, of all places! He really liked this article, and so did I. I appreciate your inclusion of images, by the way

    The closing resonated the most, however:

    Finally, although much of the fuss about epigenetics in the general media and popular books have been with epigenetics affecting offspring, the more common example of epigenetic effects is during the development of the body or long-term changes in gene expression. It’s a good example of popular thought latching on to the exceptional cases and conflating them.

    Ellie a.k.a. Demeter of CiteUlike.org
    Postscript: apologies if html for style not allowed by Sciblogs.

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