Junk DNA not all junk, but some still is

We  sometimes pick on media reporting here on Lost in Science – like just the other day – but it pains me to have to bring up criticism of what sounded like one the biggest science stories of the year. However, there has been a lot of hyperbole about the results of the ENCODE project and the claims that it ‘debunked’ the concept of junk DNA.

For those who missed the wall-to-wall media coverage, ENCODE stands for the ENCyclopedia Of DNA Elements. It’s an international collaboration of 442 scientists, who used 24 different tests on 147 human cell types and catalogued what each bit of DNA does.

In their press releases, ENCODE claimed to have found a function for 80% of DNA, including the non-coding parts, aka ‘junk’. But does this really overturn everything we thought we knew about DNA?

DNA, of course, is deoxyribonucleic acid. It’s a molecule found in the nucleus of each of our cells, and it’s the template for the construction of those cells and how they operate. Basically, it’s the blueprint to build a human being.

Some sections of DNA make up genes, which are codes for particular proteins. A related substance called ribonucleic acid (RNA) reads or transcribes the code and uses it to construct a protein, which then goes off and performs some sort of biological function.

The rest that isn’t a code for genes is the non-coding DNA. For years, it’s been known that some of this non-coding DNA contains switches that determine whether a gene gets read or not. But many have thought that the bulk of it is probably junk left over from evolution – things like old, mutated genes, and bits of viruses that have wormed their way into our DNA. This is the so-called ‘junk DNA’.

In 2003 the Human Genome Project – another big, international collaboration – successfully mapped all the genes in the human body. But they also found that only about 1.5% of our DNA is used to code genes.

ENCODE aims to to fill in the rest. Its members found plenty of those gene switches I mentioned earlier, but they also found some that weren’t genes but were still able transcribed by RNA, and some that only seem to work when the DNA molecule is curled up in a 3D shape.

These add up to the figure quoted before, of 80% of DNA with a biological function. But the key question, and the one that has generated most of the controversy about these claims, is what exactly do they mean by ‘function’?

For instance, you’d expect that those old viruses and broken copies of genes could be transcribed by RNA, even though they don’t do anything useful. All that’s really saying is that that bit of DNA can be copied. And although it’s true that ENCODE did find millions of switches, and we know they actually do something useful in cells, that’s not news because biologists already knew those switches existed.

If you restrict the definition of ‘functional’ only to genes and their switches, the estimate drops from the upper estimate of 80% to only around 20% having a function.

A Canadian biologist, T. Ryan Gregory, who has been one of the scientists most critical of the ENCODE hype, has pointed out that you can get an idea of the usefulness of the bulk of non-coding DNA by comparing humans with other species.

Pufferfish, for example, have more genes than us, but their DNA is 1/10 the size. So either the rest of it isn’t doing much, or they’ve found some way to get along without it. Then there are onions, which have about 5 times more DNA than humans. Assuming it’s not mostly junk, are onions really so complex to justify the difference?

Of course, this is one point of view – among many others – and it doesn’t mean that ENCODE is worthless. It is, after all, a huge project that has catalogued the various functions for future study. It’s also already provided some clues to diseases – sections of DNA that are associated with diseases were more likely to be non-coding – and it’s introduced lots of innovative tools for exploring the data.

But the real concern is the exaggerated claims and the way they were repeated unquestioningly by news outlets (helpfully, Gregory has catalogued the major reports).

Although we often blame inaccurate science reporting on the low priority it’s assigned in the media – The Australian dumping their science reporter Leigh Dayton being one example – in this case it was seen in internationally respected news organisations, including many dedicated science publications.

Nature and Science, two of the world’s most prestigious science journals, worked closely with ENCODE to publish special features and ensure maximum impact, with the simultaneous release of 30 papers (see www.nature.com/encode).

And that’s perhaps the problem. Scientific revolutions make very appealing stories, and the backing of such a powerful public relations machine means that even the best find them hard to resist.

Sometimes these stories are true, but generally it pays to be sceptical of the hype. In this case that’s justified, as ENCODE hasn’t completely revolutionised the way we understand DNA. We already knew it wasn’t all junk, and there’s still good reason to believe that much of it is.

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