A Weird Little Plant is Nearly Free of Junk DNA. Big Contentions Underlie Seemingly Cute Story

Weird Plant, Weird Genome

A paper released in Nature this week had all the elements of a good science story. An odd little plant called a carnivorous bladderwort was found to have almost none of the so-called junk DNA that makes up the bulk of other organisms’ genomes. The human genome is more than 98% noncoding “junk.”   

This pretty little killer plant offered a nice hook for delving into what has become one of the more contentious debates in biology – what does all this noncoding DNA do, if anything?

I thought more people would pick up on the story, but the Nature press materials didn’t include it among the findings that got a blurb.  At LiveScience, Tia Ghose covered it, and her story got picked up on a number of other news sites, including NBCnews.com.

But the story is something of a carnivorous plant itself. The problem was with the way the results were being interpreted to imply that because this plant doesn’t need much non-coding DNA, we don’t either. Fall for that and you may get chewed on by scientists. Here’s what Ghose says:

The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans.

It’s an extrapolation that’s not justified by anything the scientists actually found. It reminds me of the cases where scientists find some critter that’s capable of asexual reproduction and headlines start running with the statement that “men aren’t necessary.” Well, the fact that some complex organisms can reproduce without sex doesn’t prove that sex has no evolutionary benefit and this bladderwort doesn’t prove that other organisms don’t need at least some of their junk DNA.

And so the LiveScience story caused a few scientists to become apoplectic.  It didn’t help that it ran under the misleading headline, Junk DNA Mystery Solved: It’s Not Needed.

The contentious nature of junk DNA became clear last fall when a sprawling sequencing effort known as ENCODE announced their results. In that case, ENCODE scientists made a claim that in human DNA, 80% of this noncoding “junk” had some function. Quite a few biologists begged to differ. On the Tracker, I took some reporters to task for uncritical reporting of those results here and here.

Some of the scientists seem to be fighting over a false dichotomy – either the “junk” is useful or it isn’t – when it may well turn out that some of ours has an essential role and some does not.

In the blog Not Exactly Rocket Science, Ed Yong also had the prescience to pick up on this finding, and unlike the superficial treatment at LiveScience, his effort led to a real story with depth, context and a variety of sources. It helped that he brought in background on the surprising variability of genome sizes across different organisms:

The onion, for example, has around five times more DNA than you do, with a genome that’s around 15 billion DNA letters long. The wheat genome is slightly bigger still. And even these genetic titans look positively svelte next to the record-breaking genome of the Japanese “canopy plant”—a pretty, white flower whose 150-billion-letter genome is the largest of any plant.

It’s a good story overall but a passage at the top still suggests the same misleading extrapolation to humans that led some scientists to whine about the LiveScience piece:

If you stripped all these “non-coding” sequences from the human genome, would you still get a normal, living person? This experiment will always be a fantasy for us, for reasons of impossibility and ethics, but it’s one that some living things have unwittingly carried out.

It’s fair enough to say that this plant may tell us something interesting about the nature of noncoding DNA in other organisms. That may be what the author meant, but I read this passage to imply that the bladderwort genome points to an answer – that we can cut off our junk and be none the worse for wear.

A quote from the lead researcher takes a swipe at ENCODE but at this stage I don't think either ENCODE hype or anti-ENCODE hype should be presented unchallenged: 

“If a plant can get rid of junk DNA, it is possible that the role of this junk, if any, can be achieved by other means,” says Herrera-Estrella. “Our study also generates some doubts as to whether junk DNA is as important for humans, as stated by the ENCODE initiative.”

One interesting bit of context I picked up during the ENCODE kerfuffle is that this issue has gotten mixed up with the intelligent design movement, and that mix-up may help explain why some scientists are getting so emotional. The ID people apparently made some sort of prediction that people would discover a purpose to some of the junk DNA. And indeed, there was some gloating among ID-ers after the ENCODE announcement, and some consternation among scientists over the gloating.

It’s annoying to watch pseudoscientists gloat and easy for me to sympathize with those who want to stick it to creationists. But junk DNA is not going to make any difference. Creationism isn’t a falsifiable hypothesis and creationists will always find excuses to gloat. This is on the same level as global warming deniers still gloating every time it snows somewhere. 

There’s nothing that scientists can find in junk DNA that would help creationists’ case short of perhaps discovering that someone embedded a very explicit message the way Craig Venter’s group has encoded messages into the synthetic DNA in some of their  organisms. But there's also nothing science can find that would shut the creationists up. 

That aside, understanding what the majority of our DNA does and how it evolved is a fascinating quest and one that’s well worth following. 

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