The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links:
- ERV linked with a tone of disgust.
- I restated my frustration with the term junk DNA.
- JR Minkel, the author of the Scientific American article, responded to my criticisms.
- Ryan Gregory replied to Minkel's SciAm blog post, introducing the term "junctional DNA" to
replace junk DNAdescribe sequences with unknown function. Gregory alsotells us how a genome is like an onion (let me count the ways), or something of the sortwonders why onions have really big genomes. - If you have any further questions about junk DNA, Ryan Gregory is also collecting questions about junk DNA. Word on the street is he may even answer some of them.
What do I think about junk DNA? Should we replace it with another term (ie, junctional DNA, funk DNA)? I'd rather just see the whole thing scrapped. Abandoned. Junked.
Update: At Gregory's request, I changed his bullet point. I've been accused of "sloppy reporting", but I prefer to think of it as playing fast and loose. I shoot from the hip. I'm a hip shooter. And I thought the sarcasm irony intentional-douchebaggery was clear. Also, John Timmer writes about the actual paper.
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I've been complaining about the term "junk DNA" for a long time now, though my complaints have been in pretty low-impact fora (Usenet, for the most part). My most recent complaint was a letter I wrote to Science Daily News, in 2005. My complaint then was that the term "junk DNA" is almost entirely one used by journalists, not scientists -- and almost the only time journalists use it, is to then smarmily tell scientists not to call it that.
I never got an answer to my letter, but I amplified my complaint in my blog. Here's what I wrote then:
An article in today's Science Daily News punched one of my hot buttons. It opens:
I call bullshit. If you look up the phrase "junk DNA" on PubMed (or for that matter, in Science Daily News' own archives) what you'll find is article after article demonstrating function after function for quote quote, so-called junk DNA, unquote unquote. And every one of the articles raises that same claim, that this DNA is called ("so-called") "junk".
It's NOT called junk. The only people who call it "junk" are lazy journalists who then smugly think they're fighting dogma, when in fact they're just parroting dogma. Time after time there's the claim that this DNA is "termed" or "called" or "so-called" "junk", but that's all it is, I can't find any evidence that it really is called junk.
So for years the only use of "junk DNA" has been to refute the term "junk DNA", and yet Science Daily News is still acting as if this is some kind of bold struggle against orthodox persecution.
Here's Science Daily News' own parroting. Notice that the only time they use the term is to refute it:
(Probably more, but Science Daily News' search engine is buggy; I had to manually edit URLS it screwed up to find this many.)
Representative quotes from the research literature show the same pattern -- almost the only times "junk DNA" is used, it's in (literal or figurative) quotes, and the context is that the term is a misnomer: Examples:
So if everyone is busy refuting the term, who is actually using it in the first place? Who's being refuted here?
But, Ian, the majority of the human genome (and many other eukaryotic genomes) is junk. There isn't any known function, and I doubt any function will ever be discovered. Each of those references you point to provides "function" for a small fraction of junk DNA.
I'm not against using the term junk DNA because it's not descriptive, but because journalists don't know how to use it.
John Timmer has weighed in on the actual article, which appears to be forthcoming in PNAS, but currently embargoed.
If I may make a small clarification, I introduced "junctional DNA" to apply to a very specific category of non-coding DNA, namely regions with a presumed by currently unknown function. Otherwise, I argue that it should be labeled accurately as non-coding DNA, or by sequence type (e.g., transposable element or pseudogene) or function (e.g., regulatory DNA or structural DNA). Let's keep things precise; loose usage of terms is the basis of the problem.
Also, I did not say genomes are like onions. I introduced a logical way of assessing any claims about universal functions for noncoding portions of eukaryote genomes. Isn't this kind of sloppy reporting for the sake of a catchy line what you rail against?
I was intentionally playing fast and loose, or something of the sort. But I fixed the post Doctor Gregory.
Thanks (I think). I will make a mental note that your posts are meant to be shots from the hip rather than accurate scientific discussions so that I don't misinterpret you in the future. ;-)
TR, the misunderstanding is, well, understandable. Hell, I don't even understand half the things that come out of my mouth . . . er, that I type. Sometimes I'm truthful; othertimes I'm full of a heaping pile of bullshit. And, sometimes, reality lies somewhere in between.
And if you check back in the comments, do you go by TR, Ryan, T Ryan, Zinglebert Bambledack, T, Dr Gregory, or something else?
Only my mom calls me Zinglebert Bambledack. TRG seems simple enough for blog purposes. :-)
But, Ian, the majority of the human genome (and many other eukaryotic genomes) is junk. There isn't any known function, and I doubt any function will ever be discovered. Each of those references you point to provides "function" for a small fraction of junk DNA.
I'm not against using the term junk DNA because it's not descriptive, but because journalists don't know how to use it.
That wasn't the argument I was trying to make.
The point I was trying to make is that the term "junk DNA" is in fact hardly used at all in the primary literature, so when journalists sneer at scientists for using the term, they're wrong in the most basic sense.
When a journalist puts "junk DNA" in quotes, who is she quoting? Her implication is that she's quoting the scientists who use the tmer, but she's not; she's merely quoting herself (or at least, her field). When a journalist smirks about "so-called" Junk DNA, who calls it so? The implication is that it's scientists, but it's mainly journalists.
That being the case, journalists should stop acting as if they're scoring points off scientists by pointing at the term whenever a new function for junk DNA is identified.
The term isn't a bad one. It's just not a term that is particularly common in the primary literature.