Michael Eisen has also weighed in on the ENCODE media blitz, but it’s interesting that he criticizes the hype for a very different reason:
The issues all stem, ultimately, from the press releases issued by the ENCODE team, one of which begins:
The hundreds of researchers working on the ENCODE project have revealed that much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work – and mutations in these regions might lead to human disease. The new information delivered by ENCODE is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.
The problems start before the first line ends. As the authors undoubtedly know, nobody actually thinks that non-coding DNA is ‘junk’ any more. It’s an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it. Which is fairly often. And has been for at least the past decade. So it is more than just intellectually lazy to start the story of ENCODE this way. It is dishonest – nobody can credibly claim this to be a finding of ENCODE. Indeed it was a clear sense of the importance of non-coding DNA that led to the ENCODE project in the first place. And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn’t need to be overturned.
Let’s parse this statement, because there are some pretty significant differences here between what Dr. Eisen is saying and what I have said.
1. As the authors undoubtedly know, nobody actually thinks that non-coding DNA is ‘junk’ any more.
I’m not sure, but I think he may be suggesting that everyone already knows that 100% of the genome is functional. If so, then this claim is definitely false — I certainly don’t think it’s all functional and I know many colleagues who would be very unlikely to ascribe function to millions of copies of transposable elements, thousands of pseudogenes, and various other non-coding sequences. Again, onion test.
Update: Michael says “I was not saying that everybody knows that 100% of the genome is functional! I was saying that nobody thinks that 100% of non-coding DNA is non-functional. My point was that it’s dishonest to pretend like they’re the first people to debunk the junk DNA meme.”
2. It’s an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it.
Not true. I see the same “long dismissed as junk…” trope in peer-reviewed research papers all the time.
3. Which is fairly often. And has been for at least the past decade.
More than that. Stories about the supposed demise of junk DNA have been appearing in major media since the 1990s (New York Times, Science, Nature) and there were plenty of reports about potential functions of non-coding DNA throughout the 1980s.
4. So it is more than just intellectually lazy to start the story of ENCODE this way.
Agreed. But it’s pretty much the standard introduction to papers and media stories on non-coding DNA nowadays.
5. It is dishonest – nobody can credibly claim this to be a finding of ENCODE.
Well, nobody can claim to have refuted the long-held notion that all non-coding DNA is non-functional because there was never any period during which scientists ignored possible functions of non-coding DNA. Functions were contemplated for every new type of non-coding DNA elements upon their discovery, and both the “junk DNA” and “selfish DNA” ideas were met with significant resistance. ENCODE’s specific claim that 80% of the genome is functional is new, though. (As is their definition of “function”).
6. Indeed it was a clear sense of the importance of non-coding DNA that led to the ENCODE project in the first place. And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn’t need to be overturned.
It’s important to distinguish between the different views that one can have on function of non-coding DNA. The notion that “all non-coding DNA is functionless junk” is a straw man position that no one has ever seriously held. So, yes, there was already an expectation that some non-coding DNA would turn out to have function — and plenty of examples were already well known. This extreme “it’s all junk” idea did not need to be overturned, because no one claimed it and, as noted, other examples that refute it were already known. However, there is another claim that is coming out in these media reports and in quotes from the ENCODE authors — that the evidence indicates that 80% or more of the genome is functional. This is a claim that is based on the flimsiest of definitions of “functional” and is not one that likely to be unconvincing to many experts. So, the claim that “there is little or no non-functional DNA at all” is somewhat unique to ENCODE (John Mattick thinks so too). But it is a problematic claim because the evidence for this assertion is very tenuous.
Somewhere in the middle is what I believe to be the most reasonable view: a significant percentage of the non-coding DNA in the human genome is functional in the sense of being biologically meaningful, but most of it probably is not. This is certainly the view that is most consistent with the evidence, and it is, in fact, the one that the early proponents of the “junk DNA” concept actually held. As I noted in a previous post, the ENCODE authors have to work pretty hard to even get the 80% figure, which would still leave an awful lot of non-functional nucleotides in the genome.