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12Sep 2012

Skeptical Takes on Elevation of Junk DNA and Other Claims from ENCODE Project

Faye Flam
John Timmer, author of skeptical and scathing arstechnica piece

Over the last few days, several interesting blog posts and pieces have cast doubt on those front-page claims that our so-called junk DNA is not so junky after all. The first wave of news stories, which broke last Wednesday, came as the result of a raft of 30 journal articles and a big media blitz promoting the latest results of a project called ENCODE. The purpose of the project was to better understand the 98% of our DNA that isn’t officially part of any gene.

The critics in the blogosphere are peeved at the ENCODE scientists and the journals for allegedly hyping the news, and at journalists for taking the bait.

Some scientists are annoyed with the way the results were spun to imply that everyone previously assumed 98% of our DNA was junk and therefore useless to us. Others are complaining that journalists uncritically repeated claims that ENCODE proved 80% of our genome was not junk. (This interpretation is widely disputed). I covered some concerns about the coverage in this Tracker post last week.

(I also touched on the ENCODE news in my weekly evolution column, noting that more than a year ago scientists announced that, far from being junk, a piece of non-coding DNA may have a profound influence on your junk - if you happen to be a male mammal, that is.)

This blog post by biologist Sean Eddy – who overlapped with me at Caltech - gave a clear and helpful explanation of the concerns of the skeptics. He cites several blog posts by other biologists who are unhappy with the way the ENCODE results were spun.

“So when you read a Mike Eisen saying “those damn ENCODE people, we already knew noncoding DNA was functional”, and a Larry Moran saying “those damn ENCODE people, there is too a lot of junk DNA”, they aren’t contradicting each other. They’re talking about different (sometimes overlapping) fractions of human DNA. About 1% of it is coding. Something like 1-4% is currently expected to be regulatory noncoding DNA given what we know (and our knowledge about regulatory sites is especially incomplete). About 40-50% of it is derived from transposable elements, and thus affirmatively already annotated as “junk” in the colloquial sense that transposons have their own purpose (and their own own biochemical functions and replicative mechanisms), like the spam in your email. And there’s some overlap: some mobile-element DNA has been co-opted as coding or regulatory DNA, for example.”

I found this breakdown to be quite helpful. Biologist T. Ryan Gregory is also writing some interesting blog posts on the matter.

A provocative contrarian piece appeared this week in arstechnica, written by biologist-turned-journalist John Timmer, under the headline, “Most of What You Read was Wrong: How Press Releases Rewrote Scientific History”.  Those are fighting words. Timmer does an excellent job of articulating the nature of the skepticism. He explains in clear detail how “activity” measured by the ENCODE tests doesn’t necessarily imply this DNA is doing anything for us. And he tries to detangle some of the confusion surrounding the meaning of the term junk DNA.

“Many press reports that resulted painted an entirely fictitious history of biology's past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can't entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work—and, in some cases, the scientists themselves.”

Timmer admits that he thinks ENCODE is a great project, which was the bottom line of the press coverage, after all. So really, not everything you read in the papers was wrong.  

“ENCODE remains a phenomenally successful effort, one that will continue to pay dividends by accelerating basic science research for decades to come.”

And for all the bombast in the headline, Timmer’s piece doesn’t indicate that he ever confronted the sources of the original ENCODE claims. He should have. I wanted to know how they would respond.

I decided that if Timmer wouldn’t do it, I would go back to ENCODE biologist John Stamatoyannopoulos, who was quoted in the first wave of news. He said he thought the skeptics hadn’t fully understood the papers, and that some of the activity measured in their tests does involve human genes and contributes something to our human physiology. He did admit that the press conference mislead people by claiming that 80% of our genome was essential and useful. He puts that number at 40%. Otherwise he stands by all the ENCODE claims:  

“What the ENCODE papers (not the main paper in Nature, but the other length papers that accompanied it) have to say about transposons is incredibly interesting.  Essentially, large numbers of these elements come alive in an incredibly cell-specific fashion, and this activity is closely synchronized with cohorts of nearby regulatory DNA regions that are not in transposons, and with the activity of the genes that those regulatory elements control.  All of which points squarely to the conclusion that such transposons have been co-opted for the regulation of human genes -- that they have become regulatory DNA.  This is the rule, not the exception....”

The plot thickens. It’s clear now that a number of credible scientists think aspects of the ENCODE claims to the press were crap. Whether any of it is actually crap is yet to be determined, but stories that didn’t include any skeptics were missing an essential element. At the same time, those reporting on the skepticism would have produced great stories had they taken the criticism back to the original sources and pinpointed the nature of the disagreement.

While many journalists found original ways to extol the virtues of the ENCODE project - and I missed a few in my original post - cheering on science is not really our role. One thing we can bring to the table is a story that includes context, history, and multiple perspectives. It’s a difficult task that requires listening to and understanding people on different sides of a debate. But it might be worth doing here. - Faye Flam


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