ENCODE debate revived online

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In the social-media age, scientific disagreements can quickly become public — and vitriolic. A report from the ENCODE (Encyclopedia of DNA Elements) Project consortium proposes a framework for quantifying the functional parts of the human genome. It follows a controversial 2012 Nature paper by the same group that concluded that 80% of the genome is biochemically functional (Nature 489, 5774; 2012). Dan Graur, who studies molecular evolutionary bioinformatics at the University of Houston in Texas and is a vocal ENCODE critic, weighed in on this latest report. ENCODE's “stupid claims” from 2012 have finally come to back to “bite them in the proverbial junk”, Graur wrote on his blog. The targets noticed. “Some people seek attention through hyperbole and mockery,” says the report's first author Manolis Kellis, a computer scientist at the Massachusetts Institute of Technology in Cambridge. “We should stay focused on the issues.”

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This is just the latest skirmish in an ongoing battle. In a scathing 2013 article, Graur and co-authors argued that the ENCODE researchers had essentially ignored evolutionary evidence that suggests that only 2–15% of the genome was under pressure from natural selection (D. Graur et al. Genome Biol. Evol. 5, 578590; 2013). Graur's paper ended with a bang: “The ENCODE results were predicted by one of its lead authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.”

The latest ENCODE report drew wide attention on Twitter. The paper didn't provide any estimates about the proportion of the human genome that is functional; instead, it laid out the case that any accurate inventory of the functional parts of the genome must include evolutionary, genetic and biochemical data.

Given the history, some Twitter users wondered how Graur would respond. He soon ended the suspense with a series of tweets blasting ENCODE's statistics and methodology. In one, he wrote that “the recent half-hearted recantation of #ENCODE was published without a press release.” In his blog post, he wondered why the ENCODE consortium seemed so eager to back away from its “80%” claim. Through it all, he admittedly showed very little tact. “I believe science is a search for the truth, not a lesson in manners,” he says. “I don't do politeness.”

Kellis says that ENCODE isn't backing away from anything. The 80% claim, he says, was misunderstood and misreported. Roughly that proportion of the genome might be biochemically active, he explains, but some of that activity is undoubtedly meaningless, leaving unanswered the question of how much of it is really 'functional'. Kellis also argues that focusing on the portion of the genome that is shaped by natural selection can be misleading. For example, he says, genes that cause Alzheimer's disease or other late-in-life disorders may be largely immune to evolutionary pressure, but they are still definitely functional.

Kellis, M. et al. Proc. Natl Acad. Sci. USA 111, 61316138 (2014)

Elsewhere on Twitter: in a preemptive strike to prevent at least some future conflicts between scientists, a group of researchers has published a much-discussed ten-step guide for the 'care and feeding of scientific data'. It is intended to make data more meaningful, accessible and reproducible. Step one — “cherish, document, and publish your data”— may seem like a colossal task, but the authors note that it is getting easier than ever to manage and store data. Once it hit social media, the guide prompted self-reflection and a little bit of boasting. “Glad we do all 10,” tweeted Theresa Hahn, associate professor of oncology at the Roswell Park Cancer Institute in Buffalo, New York.

Goodman, A. et al. PLoS Comput. Biol. 10, e1003542 (2014)

The ongoing discussion about women in science revved up again online after an editorial in Nature Materials highlighted that, whereas intentional gender discrimination is largely a thing of the past, accidental bias against women is still common. Whether trying to get a postdoc position or a spot on a conference panel, women still have to fight against stereotypes. The editorial notes that “no matter how self-reflective we are, our thinking has been shaped by exposure to the gender roles in our culture. On average, we consider women more likeable but less competent in areas such as mathematics and physics that are characterized as being male.” The Institute of Chemical Research of Catalonia in Spain showed solidarity by tweeting the editorial's tag line: “Unconscious biases are a roadblock for gender equality in science.” Two days later, the institute tweeted that “women are strongly encouraged to apply” for two of its recent job openings.

Nature Mater. 13, 427 (2014)

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