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6Sep 2012

Did ENCODE Results Get the Junk out of Our Genomic Trunk?

Faye Flam

The big front page science story today was the raft of papers from Science and Nature on the first fruits of a multi-year, 440-scientist effort to examine our DNA – in particular that vast majority of the genome that isn’t part of any gene and doesn’t hold the code for a protein.  Among the exciting findings to drop from this effort, dubbed ENCODE, was the realization that many disease-relevant DNA variants occurred in this non-gene DNA.

This was a challenging story to make clear and exciting for general readers with only the dimmest understanding of DNA, genes and their relationship to each other.

Some of the news coverage reminded me of those commercials that show before and after pictures, where the before picture is made to look fatter or more out of shape or uglier than seems plausible in order to make the after picture more impressive.
In this case, the implausible before pictures painted the scientific community as convinced that 99% of our DNA was useless “junk”, and thus they were totally shocked and awed to hear that some of it actually did something. That raises the question of why they would spend $288 million dollars studying this DNA if they’d so thoroughly written it off.

Biologists haven’t used the term “junk” DNA for years, and many never liked it. They knew long before this project that the non-coding portion of DNA contained some “regulatory” regions that controlled the activation of genes. What’s exciting about these new papers is that the scientists were able to locate many of these regulatory regions.  And they found many held variations that other studies had linked to cancer, autoimmune disease and other serious illnesses.   

The project scientists said they found 4 million “switches”, and I would have liked a better explanation of what these switches consist of and how they do their thing. Some of the news stories referred to the switches as genes and others just as DNA. This issue called out for some of that nitty-gritty science writing that helps readers form a mental image.

Another hazard of this story is that there’s still a raging disagreement among scientists about how much of the genome is made up of these regulatory elements and how much is unemployed and possibly unemployable. Experiments that were part of the project showed that 80 percent of the non-coding DNA was functional, which led to much grousing over the meaning of functional.

Skeptics are saying those experiments merely show this DNA is potentially active but that doesn’t mean it’s essential. U of Washington researcher Josh Akey said much of this “functional” DNA could still be filled with mutations that would have no effect on you or your health. He posits that as little as 2-3 percent of this non-coding stuff is essential. Others are convinced that all 80% is functional and essential, and they will soon find 100% of our genome is doing important work.

At his Discover Blog, Not Exactly Rocket Science, Ed Yong caught onto the disagreement early and is promising continued coverage. He also gave some nice examples of how regulatory DNA might work.  

Gina Kolata covered the story for the New York Times. Her lede started with several questions, including why identical twins don’t always get sick with the same things. My first thought was that even lay readers would be able to tell you it’s the environment. And wouldn’t the regulatory stretches of DNA be the same in identical twins? She eventually says environmental exposures can slightly alter these switches – but did she mean alter the DNA or cause an epigenetic change? She doesn’t say. The twin thing may have come out of the press conference or one of the news releases since multiple reporters described it in very similar language.   

Kolata’s story did have some interesting elements – including an interview with a prostate cancer researcher who sees the new data as important to his work. And she quotes someone posing the intriguing question of why we’d need 4 million switches to control our 21,000 genes.

Rob Stein wrote about the news for His lede played off the junk DNA angle but he explained further down that nobody really believed it was all junk anyway:

Scientists unveiled the results of a massive international project Wednesday that they say debunks the notion that most of our genetic code is made up of so-called junk DNA.

Stein offered a reasonably clear explanation of the scientists’ pet metaphor - comparing this project to Google Maps. In isolation the sound bite is sexy as hell but not that helpful to lay readers who have no idea where we’re trying to go and how we got lost in the first place. Stein does a big service by pinning the scientists down and asking them to explain.   

Dan Vergano’s USA Today story also started with the Junk DNA angle: International research teams have junked the notion of "junk" DNA, reporting that at least 80% of the human genetic blueprint contains gene switches, once thought useless, that control the genes that make us healthy or sick.

David Brown and Hristio Boytchev covered the story for the Washington Post. Here’s their lede:  Most of a person’s genetic risk for common diseases such as diabetes, asthma and hardening of the arteries appears to lie in the shadowy part of the human genome once disparaged as “junk DNA.”

Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades.

This is pretty good, since it gets at the medical significance fast, and by using the phrase “once thought useless” he doesn’t imply that this project shifted the paradigm.

At Reuters, Sharon Begley describes the news as “the largest single batch of discoveries about human DNA since the completion of the human genome project in 2003”

Specific examples are always helpful in a story like this, and she quickly jumps to one that could advance cancer research:
 The discoveries, representing what the journal Nature calls the "guidebook to the human genome," range from the esoteric - what is a gene? - to the practical - that just 20 gene switches may underlie 17 seemingly unrelated cancers, giving companies a workable number of drug targets.

There's also some mind-bogglingly idiotic stuff popping up from the Discovery Institute that could make good fodder for anyone with a blog aimed at mocking creationists. They've convinced themselves that if all the DNA has a function, it must have been hand-designed by God.


Congratulations on the attention to the ENCODE announcement Wednesday. To me, it probably was the biggest in genomics since the ‘finished’ human sequence was posted on the web in 2003 and analyzed extensively in Nature late in 2004. By then it was becoming painfully clear how little we knew about how the genome actually functions in health and disease.  The shock led to ENCODE, a pilot phase with DNA chips and from 2007 a “production phase” with sequencing. The five-year sequencing-based inquiry into vast stretches of non-coding DNA showed that disease-related mutations seem concentrated there -- often far from their associated protein blueprints. And clusters of such control-room changes show up in clusters of common diseases (hinting at some simplicity among the exploding complexity).

As Faye Flam notes, this was a daunting story.  In the time available, none of the reporters could hope to tackle all 30 of the papers simultaneously published in four journals. Yes, there was the now-common conference call, an important institution in science journalism that merits closer study.  But reporters also were bombarded by press releases from two funders, the National Human Genome Research Institute and the NIH Common Fund; three institutes, Broad, Cold Spring Harbor, and Sanger; and six universities, Penn State, Wayne State, Washington, Yale, MIT, and UC Santa Cruz. They also got detailed background pieces by Brendan Maher of Nature and Elizabeth Pennisi of Science, lengthy commentaries in Nature, Science, and Genome Research, and a detailed AAAS podcast interview by Sarah Crespi of one ENCODE first author, Matthew Maurano of the University of Washington.

The resulting coverage was a blizzard – most showing evidence of following the genome story that we will be covering for decades. In London alone, near the highly articulate ENCODE straw boss Ewen Birney (who put out a brightly-written blog of his own), there was independent coverage by the Times, Guardian, Independent, Daily Mail, Daily Telegraph, the Economist, New Scientist, BBC News, and even the Sun (promising babies to order).  Also doing their own stories were the Scotsman in Edinburgh, the Irish Times in Dublin, Le Monde (noting the absence of French participation), the Frankfurter Rundschau, and Die Welt.

The range in the U.S. was amazing: Malcolm Ritter of the Associated Press called the findings “the first comprehensive look at how our DNA works.” Gautam Naik and Robert Lee Hotz of the Wall Street Journal wrote, “The deepest look into the human genome so far shows it to be a richer, messier and more intriguing place than was believed just a decade ago.” Delthia Ricks at Newsday wrote of “a radical overhaul” of ideas. Robert Bazell and Maggy Fox at NBC News said that, in the search for what makes us human, “our scientists have been looking in the wrong place for a very long time.” Steve Hall at Scientific American referred to “a stunning inventory of previously hidden switches, signals and sign posts embedded like runes throughout the entire length of human DNA.” Brandon Keim at Wired obtained a strong skeptical quote from Aravinda Chakrabarty at Johns Hopkins: “These are initial steps, necessary but not complete.” Also covering were CBC News, CNN, the LA Times, and Time Magazine.

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I realize that "introns" in my comment is too narrow a term, and should be "introns and other non-coding DNA."

This post made my day, Faye. Before I came to the Tracker today--I was hoping ENCODE would covered here--I sent an email to a colleague who asked if we could set up an editorial session to discuss coverage of the ENCODE papers:


Sure, we can meet, but only if everyone promises they won't use the term "junk DNA" in any stories. :)

Seriously, my problem with "junk DNA" is that it's a concept that really only exists in journalists' minds at this point, and they only keep using it because it's an eyecatching piece of slang, not because it reflects anything about genomics. No scientist has thought that intronic DNA is "junk" for a long, long, long time. And every time the term is used, it's used as a straw man, followed in the next sentence or graf by "but it isn't," which has gotten really ridiculous at this point. It's perfectly possible, and a lot more informative, to make the point that introns are *different* from exons without resorting to the J word. </rant>

Watch TR Gregory - he's blogging a storm about this:

and I bet Larry Moran is not yet finished with this:


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