Thursday, 6 September 2012

ENCODE: highlighting the best and worst of science in the modern world

A massive ENCODE publication release was made yesterday, including 30 papers, an iPad App (downloaded and looking good) and a Virtual Machine full of data. I'm not going to give my opinions on the findings here because, frankly, there's too much to digest. Instead, I recommend reading Ed Yong's summary and the thoughts of Ewan Birney. [Image pinched from Ed Yong.]

ENCODE is an amazing example of what humanity can achieve it is puts time, effort and resources into a coordinated scientific endeavour - and also a reminder (should we need one) of how much more there is to learn about our genome. My mind is blown just thinking about reading all the papers and trying to make sense of them. (I wish I could clear my diary for a few days but deadlines loom!)

ENCODE is also a stark reminder of what it means to do science in the 21st Century world of bloggers, tweeter and general bitchers who just like to take quotes and soundbites out of context and then moan about them. The ability of some folk to digest 30 data-dense papers in a few hours (or minutes) and then have an informed opinion about them - and why they are wrong - is astounding.

So, my second recommendation is this: ignore the hype and all the nonsense flying around about what Ewan Birney meant by "functional" (he explains if you bother to read) and what this means for "junk" DNA. (Probably not much - I am sure it still exists, there just might be quite a lot more functional bits and long-range interactions than we thought - but let's let science and investigation answer that one.) Ignore all this and read the papers (if you're a scientist or committed lay person) or wait for the dust to settle for some reasoned, rational responses (if you are lacking the time/capacity/inclination to tackle 30 papers plus extras). Concentrate on the content and not the language. (I suspect a lot of it comes down to your definition of "junk" and "functional". I don't think I would choose the definitions that they have but, as the authors, it is their prerogative to define their terms and the serious reader's responsibility to make sense of the articles in that context.)

It's going to be years before we make sense of all this new data and work out how much of it is important. Years of wonderful, real science, not soundbites and speculations. As any ground-breaking study is likely to do, ENCODE has raised far more questions than answers - what (if anything) are all these DNA elements doing? Get excited by those questions and start thinking about how we can answer them. Keep your mind open to the possibilities and don't just shoot them down because they make you - or your future discourse with Creationists - uncomfortable.

So, could Ed and Ewan been more careful about the "80% functional" quote? Yes. Should they have been? I'm not so sure. Creationists are having a field day with it but so what? Whatever the finding, Creationists will try to twist it to their goals. That's one of their defining characteristics. If we change how we do or report science to pander to that particular bunch of deluded crackpots, we hand them victory. (Ewan explains his choice and, whether you agree or not, it was his choice to make. Our choice, is how we interpret the quote and whether we bother to find out what he actually meant before slagging it off.)

As a final footnote, I had the pleasure of meeting Ewan Birney once at a conference in Hinxton and the man is phenomenal. As with all great scientists, he is not going to be 100% right 100% of the time but ignore or scoff at him at your peril.

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