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Junk in the Media

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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:

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.

Comments

  1. #1 Ian
    April 26, 2007

    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:

    “Genetic material derisively called “junk” DNA because it does not contain the instructions for protein-coding genes and appears to have little or no function is actually critically important to an organism’s evolutionary survival, according to a study conducted by a biologist at UCSD.”

    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:

    “Parasite Or Partner? Study Suggests New Role For Junk DNA” — 2002-05-15

    “Rodent Social Behavior Encoded In Junk DNA” — 2005-07-12

    “Jewels That May Help Explain Behavioral Disorders Found Among “Junk” DNA” –2002-12-09

    “Essential Cell Division “Zipper” Anchors To So-Called Junk DNA” — 2002-08-30

    (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:

    ” belying the notion that heterochromatin is simply a passive recipient of “junk DNA” in eukaryotic genomes.” (PLoS Genet. 2005 Jul;1(1):e9. Epub 2005 Jul 25)

    “We are therefore getting further and further from the original idea that this DNA was simply “junk DNA” … ” (Cytogenet Genome Res. 2005;110(1-4):25-34)

    ” We also apply the method to the analysis of coding and noncoding DNA sequences and find that the latter have higher multiscale entropy, consistent with the emerging view that so-called “junk DNA” sequences contain important biological information.” (Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021906. Epub 2005 Feb 18.)

    “LINE-1 elements and X chromosome inactivation: a function for “junk” DNA?” ( Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6248-9.)

    “Active genes in junk DNA? Characterization of DUX genes embedded within 3.3 kb repeated elements.” (Gene. 2001 Feb 7;264(1):51-7.)

    So if everyone is busy refuting the term, who is actually using it in the first place? Who’s being refuted here?

  2. #2 RPM
    April 26, 2007

    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.

  3. #3 RPM
    April 26, 2007

    John Timmer has weighed in on the actual article, which appears to be forthcoming in PNAS, but currently embargoed.

  4. #4 TR Gregory
    April 26, 2007

    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.

  5. #5 TR Gregory
    April 26, 2007

    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?

  6. #6 RPM
    April 26, 2007

    I was intentionally playing fast and loose, or something of the sort. But I fixed the post Doctor Gregory.

  7. #7 TR Gregory
    April 26, 2007

    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. ;-)

  8. #8 RPM
    April 26, 2007

    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?

  9. #9 TR Gregory
    April 26, 2007

    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. :-)

  10. #10 Ian
    April 27, 2007

    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.

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