Max Libbrecht on ENCODE’s results regarding junk DNA.

Max Libbrecht is a PhD student at the University of Washington, and was one of the several hundred researchers involved in the ENCODE project. I have already mentioned Max because of his important comments on ENCODE and junk DNA elsewhere on the interwebs. I mentioned that he would be welcome to write a guest post on my blog, but he has done one better and started his own blog. Max’s inaugural post is entitled “On ENCODE’s results regarding junk DNA“. It’s an important, unambiguous statement coming from an ENCODE team member, so I am reproducing it in its entirety here. That’s it, though — I’m not re-posting all his future blog posts, so you’ll just have to head over there and subscribe yourself.

After I took part in an AMA (“Ask Me Anything”) on reddit, there has been some discussion elsewhere (such as by Ryan Gregory and in the comments of Ewan Birney’s blog) of what I and the other ENCODE scientists meant.  In response, I’d like to echo what many others have said regarding the significance of ENCODE on the fraction of the genome that is “junk” (or nonfunctional, or unimportant to phenotype, or evolutionarily unconserved).

In its press releases, ENCODE reported finding 80% of the genome with “specific biochemical activity”, which turned into (through some combination of poor presentation on the part of ENCODE and poor interpretation on the part of the media) reports that 80% of the genome is functional.  This claim is unlikely given what we know about the genome (here is a good explanation of why), so this created some amount of controversy.

I think very few members of ENCODE believe that the consortium proved that 80% of the genome is functional; no one claimed as much on the reddit AMA, and Ewan Birney has made it clear on his blog that he would not make this claim either.  In fact, I think importance of ENCODE’s results on the question of what fraction of DNA is functional is very small, and that question is much better answered with other analysis, like that of evolutionary conservation.  Lacking proof either way from ENCODE, there was some disagreement on the AMA regarding what the most likely true fraction is, but I think this stemmed from disagreements about definitions and willingness to hypothesize about undiscovered function, not misinterpretation of the significance of ENCODE’s results.

I think many members of the consortium (including Ewan Birney) regret the choice of terminology that led to the misinterpretations of the 80% number.  Unfortunately, such misinterpretations are always a danger in scientific communication (both among the scientific community and to the public).  Whether the consortium could have done a better job explaining the results, and whether we should expect the media to more accurately represent scientific results, is hard to say.

I think the contribution of ENCODE lies not in determining what DNA is functional but rather in determining what the functional DNA actually does.  This was the focus of the integration paper and the companion papers, and I would have preferred for this to be the focus of the media coverage.


2 comments to Max Libbrecht on ENCODE’s results regarding junk DNA.

  • gillt

    So this wasn’t an arsenic sized media debacle and the scientists in the consortium didn’t make a huge mistake interpreting their own data? 

      (Quote)

  • Galt

    In Nature mag. 6-sept-2012 (ENCODE articles), on pg 52, Joseph R. Ecker author of ENCODE Explained writes:
    “One of the more remarkable findings described int he consortium”s entree paper (page 57) is that 80% of the genomeic elemens linked to bichemical functions, dispatching the widely held view that the human genome is mostly ‘junk DNA.’”
    On page 57, Ewan Birney writes in the abstract on the main ENCODE article:
    “These data allow us to assign biochemical functions for 80% of the genome, in particular outside of the  well-studied protein-coding regions.”
    Further down in the bottom of the page it says:
    “The vast majority (80.4%) of the human genome participates in at least one biochemical RNA-and/or chromatin-associated event in at least one cell type.”
    Ewan’s own blog finally explains that 60% of this is from trivial fact that introns get transcribed.
    If the best of the press, one of Nature’s own writers and in the very same issue 5 pages earlier, can’t get it right, then what hope is there for the rest of the media?  I do not think the media is to blame.  It looks like they were deliberately misled.
    (Despite this unfortunate misleading of facts, the ENCODE project has produced good data.)
     

      (Quote)

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