ENCODE reactions The ENCODE project has definitely dominated the news this week. I’ve had various reactions to my mega-post from “one of your best” to “you blew it”. I do want to note, as in this set of tweets, that getting in all the nuances and caveats, capturing both the enthusiasm and scepticism about the project, and making it all make sense for both a general and scientific audience, to a deadline, was not easy. It was more like the opposite of easy. I’ve mulled over the post in the ensuing days. I knew not to use the “long dismissed as junk” trope. I mentioned that the types of elements that were identified were not a surprise, and ENCODE’s value was as a comprehensive catalogue. I tried to point out where the 80% figure came from, the uncertainty around it, and what “functional” meant. One of the hardest things about a story like this is that even if you have a mental list of points and caveats to tick off, and even if you think you get them in the piece, you never know if readers will pick up on them, or what message they’ll end up taking away. Are those points visible, or just there? Anyway, I eventually decided that what was in the post was reasonable, but it needed more. I still think it’s important to get across what the ENCODE researchers think about their work, it is an exciting project, and it’s a lot more than junk-or-no-junk. But given the widespread commentary – critical, sceptical and thoughtful – it needed an update. You’ll find that update in the main post itself, time- and date-stamped, and an explanation about why I decided to edit rather than post a follow-up. I’ve also been collecting links to other commentary, specifically about the science of the project. They’re there in the post itself, but repeated here to draw attention to them. The list in the post will continue to be updated. This list will not.
[If you read one thing, read this] The best summary of the reactions yet: Fighting about ENCODE and junk by Brendan Maher. Graceful, measured stuff.
ENCODE: the human encyclopedia, a long-read feature also by Brendan Maher, laying out more of the results beyond the junk DNA angle.
This 100,000 word post on the ENCODE media bonanza will cure cancer, by Michael Eisen, heavily critical of the PR, and some of the claims (but see also: Michael Eisen’s take on ENCODE by T. Ryan Gregory).
Mike White at The Finch and Pea is one of the few to delve into the papers for interesting angles not covered by the media coverage. Some interesting stuff here.
Michael Eisen again on the neutral theory of molecular function.
The ENCODE project: lessons for scientific publication, by Daniel Macarthur
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