Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012

Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].

I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?

The short answer is "yes," as you can see from the summary box below. The person who wrote the article says that "the functional portion of the genome" is 80% of the total. He/she emphasizes this in the text ...

ENCODE researchers took an intensive look not just at genes but at all of the DNA in between. Their results drive home that much of the genome that at one time was dismissed as "junk DNA" actually seems to play an essential role, often by helping to turn genes on or off. They pinpointed hundreds of thousands of landing spots for proteins that influence gene activity, many thousands of stretches of DNA that code for different types of RNA, and lots of places where chemical modifications serve to silence stretches of our chromosomes, concluding that 80% of the genome was biochemically active.

This is, as we now know, very misleading. Just because DNA binding proteins are found on DNA does not mean that the binding site has a function. Just because a region of DNA is transcribed on occasion does not mean that the RNA is functional. You do not overthrow 40 years of evidence that most of our genome is junk on the basis of spurious binding sites and aberrant transcription.

Besides, we already knew about all these results years ago so the September papers do not count as a real "breakthrough" by any stretch of the imagination. But Science justifies the "breakthrough" status by pointing out that major newspapers were fooled ...

When these papers were published in September, the media went wild. ENCODE was hailed in The New York Times as a "stunning resource" and "a major medical and scientific breakthrough" with enormous and immediate implications for human health. The Guardian called it "the most significant shift in scientists' understanding of the way our DNA operates since the sequencing of the human genome."

This is a cop-out. Science is published by a scientific organization and we expect a more serious appraisal than what you might see in newspapers. What do the editors of Science think? Do they also believe that the ENCODE results represent a "significant shift in scientists' understanding of the way our DNA operates"? 'Cause if they do, they are as wrong as the journalists who wrote for The Guardian.

In fairness, someone at Science decided that it would be a good idea to mention the controversy, so they added

But several scientists in the blogosphere called the coverage overhyped and blamed the journals and ENCODE leaders for overplaying the significance of the results. For example, ENCODE reported that 76% of DNA is transcribed to RNA, most of which does not go on to help make proteins. Various RNAs home in on different cell compartments, as if they have fixed addresses where they operate, suggesting that they play a role in the cell. Critics argue, however, that it was already known that a lot of RNA was made, and that many of these RNAs may be spurious genome products that serve no purpose. Likewise, one ENCODE researcher found 3.9 million regions across 349 types of cells where proteins called transcription factors bind to the genome—but again, it's unclear how much of that binding is functional.

I suppose we have to give them credit for recognizing that there's a problem but it's clear that the person who wrote the article doesn't really believe the critics otherwise he/she would never have led off with this statement ...

Their results drive home that much of the genome that at one time was dismissed as "junk DNA" actually seems to play an essential role, often by helping to turn genes on or off.

All in all, this is just another example of bad science journalism. Science magazine is shirking its responsibility as a leading science magazine. Either the ENCODE publicists are correct or the scientists in the blogosphere are correct. They can't both be right. The editors of Science owe it to their readers to get to the bottom of this controversy.

Is it, or is it not, true that most of the human genome is functional? It still looks to me like the editors have chosen the wrong side of the controversy.

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