Junk DNA debate: Critics of the ENCODE project cite humped bladderwort.

Is Junk DNA Really Junky? A Fish-Eating Plant Weighs In.

Is Junk DNA Really Junky? A Fish-Eating Plant Weighs In.

What Have We Learned?
Oct. 3 2013 8:31 AM

Is Junk DNA Really Junky?

The delicious, religious debate over what most of our genome is good for.

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These high expectations for noncoding DNA peaked last fall thanks to an ambitious project known as ENCODE. It set out to catalogue every last bit of noncoding DNA in the human genome. It cost $288 million and produced a supernova burst of 30 scientific papers last September, including an overview article in Nature with 442 co-authors. Given its size and scope, ENCODE covered a lot. But its leaders trumpeted one main finding above all: that 80 percent of noncoding DNA had some sort of biological function. This was like Columbus discovering five new continents at once—whole new worlds of unexpected genetic activity and potential therapeutic targets to exploit. If the Human Genome Project deflated hopes about genetic medicine, ENCODE pumped them right back up.

All the while, however, a few scientists were grumbling about ENCODE, and in a slew of papers from earlier this year, they argued that ENCODE was vastly overselling itself. In particular, they disputed the claim that 80 percent of the genome was somehow “active” or “functional.” For instance, cells sometimes transcribe DNA into RNA only to turn around and destroy that RNA moments later. It’s Sisyphean work that doesn’t benefit the organism at all—but ENCODE nevertheless counted that DNA as functional. (One ENCODE leader even admitted that, in trying to determine what percentage of DNA they should count as “functional,” his team had played around with different definitions, resulting in a range between 20 and 80 percent. They ultimately decided to push the 80 percent because “the bigger number ... brings home the impact of this work to a much wider audience.”)

In other words, critics complained, ENCODE had defined “functional DNA” so broadly that the term lost all meaning. No biologist really disputes ENCODE’s goal: Some junk DNA does have a function, and we need to understand it. But in saving the baby, ENCODE may have saved a lot of scummy bathwater, too.


The scientific backlash was harsh enough, but critics really worked themselves into a lather over ENCODE’s marketing campaign, which included scores of interviews, an iPad app, and a promotional cartoon. One critic equated the media push with “sleight-of-hand.” Another announced that he was “ready to drink [him]self into a stupor.” One especially vitriolic paper chided the ENCODE scientists’ “absurd conclusions” and “self-serving” behavior; even the acknowledgments section contains snide comments. The paper concluded, less than magnanimously, that “the ENCODE results were predicted by one of its 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.”

If all this wasn’t enough, the intelligent design crowd soon jumped into the fray, making the debate even more acrimonious. In short, proponents of intelligent design—a branch of creationism that uses scientific language but not scientific ideas or standards of evidence—strongly backed ENCODE. Why? Because the sheer bulk of junk DNA inside us doesn’t reflect well on God’s engineering skills. Why not eliminate the waste, Big Guy? But if most noncoding DNA does have an essential purpose, then perhaps God crafted us molecule by molecule after all. And if that’s the case, well, then evolution is bunk and Jesus Christ died for our sins (or something like that—their reasoning’s a bit fuzzy). To be clear, no one claims that ENCODE scientists support intelligent design. But critics worried that, in addition to producing flawed science, ENCODE also provided ammunition for the enemy.

Now, finally, the poor humped bladderwort has been dragged into the contretemps. Millions upon millions of years ago, the bladderwort had a normal complement of junk DNA. (We know this because it shares an ancestor with grapes and tomatoes, both of which are pretty bloated with junk.) For whatever reason, though, it began to shed that extraneous DNA generation by generation, until it arrived at the svelte genome of today. At the same time—and here’s the key—the bladderwort has been evolving a lot, even picking up new traits. Indeed, the water traps it evolved to catch bugs and tadpoles are one of the marvels of the plant kingdom, capable of snapping shut in less than a millisecond, hundreds of time faster than you can blink your eye. In other words, even while the bladderwort’s genome got vastly simpler, its body got more complex—which undermines the idea that 80 percent of junk DNA does something vital. And sure enough, the scientists who decoded the bladderwort genome took a swipe at ENCODE in their paper.

Of course, you could now argue that it’s the ENCODE critics who are stretching things. After all, how much can the genome of the bladderwort, a plant, really tell us about the genome of Homo sapiens, an animal? But even within the animal kingdom there’s basically no correlation between genome size and sophistication. The lungfish, for instance, has an enormous genome, some 133 billion letters long, 40 times bigger than the human genome. Meanwhile certain species of Takifugu puffer fish—(in)famous as an occasionally poisonous delicacy in Japan—have a wee genome, just 365 million letters. And neither fish is obviously more complex or well-adapted. Some creatures load up on junk, others slim down, but both can thrive.

In an unsettled area of science, it’s easy to whip between two extremes. Junk DNA is completely necessary! No, no, wait. It’s completely unnecessary! Take a breath: The answer almost certainly lies somewhere in between. But no one knows which end of the spectrum is closer to the truth. Will the epithet junk DNA prove more accurate than we realize, or will it go down as the greatest misnomer in science? Part of the answer lies within, and it will become clearer as we sequence more and more human beings. But we also need to keep sequencing sponges and worms and elephant sharks, to give us a wider perspective. Those organisms may seem a little obscure or dull, it’s true. But then again, so too did the humped bladderwort.