A paper was published in which several pieces of DNA that do not encode proteins were reported to affect the faces of rodents. I did not find any mentioning of “junk DNA” in the paper, which made me very happy.
A press release was distributed by Lawrence Berkeley National Laboratory. In this press release there is no mentioning of “junk DNA.” Again, I was happy.
Sadly, however, “junk DNA” became the star and the headline in almost all the news reports. I wondered where the “junk DNA” came from, so I wrote Axel Visel, the corresponding author.
Axel Visel (a member of ENCODE) replied
I’m not sure about the sources of individual journalists (although I did speak to some of them), but generally speaking I think it’s a valid strategy for general media to use a provocative and widely recognized term in a title to capture the attention of their audience, as long as they set the record straight in the text.
When I talk to general audiences (or journalists) about my research, I generally explain that the function of most of the non-coding portion of the genome was initially unclear and many people thought of it as “junk DNA”, but that it has become clear by now that many parts of the non-coding genome are functional - as we know from the combined findings of comparative genomics, epigenomic studies, and functional studies (such as the mouse knockouts in our paper).
As far as I can tell, the majority of general news reports appropriately conveyed the point of this paper, i.e. that at least those non-coding sequences we looked at here are indeed not “junk”.
The answer was of course infuriating because of two errors. First, it equates noncoding DNA with junk DNA, which is wrong. Second, it assumes that discovering a few new binding sites whose total length is negligible in comparison with the total size of the genome tells us anything about the amount of junk DNA in the genome.
So I wrote back:
My problem is that junk DNA does not equal noncoding or nontranscribed DNA, and I am sort of sick to see junk DNA being buried, dismissed, rendered obsolete, eulogized, and killed twice a week. After all, your findings have no bearing on the vast majority of the genome, which as far as I am concerned is junk. Turning the genome into a well oiled efficient machine in which every last nucleotide has a function is the dream of every creationist and IDiot (intelligent designer), so the frequent killing of junk DNA serves no good purpose. Especially, since the evidence for function at present is at most 9% of the human genome. Why not call noncoding DNA noncoding DNA? After all, if a DNA segment has a function it is no junk.
To which he replied
…while I agree that equating every reproducible protein binding event with “function” is probably a too relaxed definition of the term “function” for most purposes, dismissing any sequence for which we cannot demonstrate evolutionary constraint at this point as “junk” doesn’t seem quite right either.
Visel’s answer was an additional reminder of the way different people use hypotheses in science. On the one hand, classically trained scientists (or scientists for short) use non-functionality as the null hypothesis. Nonfunctionality can be refuted if a function is found. On the other hand, there are ENCODE-ites, who assume that every nucleotide has a function unless proven otherwise. Thus, functionality is their null hypothesis. Unfortunately, functionality (much like the existence of God) can never be refuted.