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 NPR.org. 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.