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Junk DNA in Scientific American

Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they’re at it again.

The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can’t find published anywhere (neither can ERV). Is Scientific American describing unpublished research on their website? Either way, they’re doing it poorly. The study described in the article identified non-coding sequences that were conserved across all sequenced mammalian genomes but missing from the chicken genome. Five percent of the sequences resemble known transposable elements, and the rest are of unknown origin. The Scientific American article said so much in nine paragraphs, and included the (unnecessary) word “junk” nine times (including twice in the headline and twice in a figure caption which is just a picture of a landfill).

Once again, I’ll say that I don’t mind the term “junk DNA” so long as it’s used appropriately. Throwing it around willy-nilly like every popular science writer seems to do is not the appropriate usage. Also, claiming that we have absolutely no freakin’ idea what non-coding DNA does is highly misleading. We know a fair bit about the function of non-protein coding DNA, including how it regulates transcription, how it encodes non-translated RNAs, and many studies have identified conserved non-coding elements. That said, a lot of it probably is junk. There are a ton of DNA sequences in any eukaryotic genome that serve absolutely no function, but they’re not deleterious enough to be purged from the population. So they’re just there, and that’s all there is to it.

Comments

  1. #1 Sandra Porter
    April 24, 2007

    I’ve read some of the papers that I think this work is based on. Here are some of the links:

    1. PLoS Genet. 2006 Oct 13;2(10):e168. Epub 2006 Aug 23.

    2. Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.

    or you can just do a PubMed search for David Haussler.

  2. #2 RPM
    April 24, 2007

    I know about Haussler’s work, but is there a new paper that they’re reporting on? It seems like the SA article is totally disconnected from any scientific publication.

  3. #3 ERV
    April 24, 2007

    Yeah I found those too– but neither of those publications contain the word ‘junk.’

    Almost all of the ID Creationist ‘quotes’ on scientists talking about ‘junk DNA’ have originated from bad science reporting, not actual journal articles.

  4. #4 Sandra Porter
    April 24, 2007

    It used to be that any DNA that didn’t code for a protein was considered “junk.” I don’t think the actual word is necessary.

    And I agree it would be nice if SA were to include references to the original articles.

  5. #5 ERV
    April 24, 2007

    Hey Genomicron is putting together a Q&A on ‘Junk DNA’– if you all have any questions or ideas, send them his way!

  6. #6 Andras Pellionisz
    April 24, 2007

    The is ample background on the misnomer “Junk” DNA (now formally abandoned by the International PostGenetics Society, http://www.postgenetics.org)

    The website is http://www.junkdna.com

    The Stanford press release (with the first author Craig Lowe at U.C. Santa Cruz…) is also featured there; and the comments are linked to their earlier work published last year in Nature.

    pellionisz_at_junkdna.com

  7. #7 ERV
    April 25, 2007

    HAHAHAHA! HI ANDRAS!

    Gee I cant help but wonder why he didnt say hello on my blog :( Im going to go cry now. ROFL!!

  8. #8 JR Minkel
    April 25, 2007

    Hi RPG and folks,

    I’m surprised my story elicited such a strong reaction. The photo was a bit weak, I grant you. And I forgot to cite the journal: PNAS online before print (doesn’t seem to be a public link yet). I have fixed that.

    As for the word/info ratio, I’m writing for a popular audience that may not have much science background, so a bit of hand holding is often warranted.

    Which of course leads to your primary objection–my use of “junk” to refer to noncoding but conserved DNA. According to one of your comments in an earlier post, “my problem with the term junk DNA is that it has been hijacked by the popular media to mean any non-coding DNA.”

    Fair enough. But your post implies that I got something wrong, as opposed to using terminology that might not pass muster in a thesis defense, which is not my venue. (Double standard on my part? You decide.)

    My story states that 95 percent of the genome has no obvious role, which is true as far as I know. As further context, I could have mentioned that only a third of the remainder is coding DNA, but that seemed like splitting hairs at the time.

    That said, I don’t like to give readers wrong impressions on weighty scientific subjects, given that I’m supposed to be telling them what’s what. I intend to move this discussion to our blog, where interested readers can benefit.

  9. #9 JR Minkel
    April 25, 2007

    Sorry, that should be RPM. I was thinking D&D, not vinyl.

  10. #10 RPM
    April 25, 2007

    JR, I wouldn’t take any of it as a personal attack on you, but you may have been the straw that broke the camel’s back. In my opinion, you could have written the entire article sans the term “junk DNA” and presented the story clearly to a lay-audience (of course, you’re the professional science writer, and I’m the scientist in training, so you may know better than I what works in popsci writing). I’m bothered by the overuse of the term in the popular science media, and I’d like to see the coverage of findings showing constraint/function of non-coding DNA reported without the words “junk DNA”.

  11. #11 JR Minkel
    April 25, 2007

    Hi, I hear what you’re saying. This is your subject and the way it’s portrayed to the outside world can be annoying. One physics blogger has complained that popular coverage of quantum computers essentially invalidates his life’s work. In cases like that, and this, it can mean there’s something we journalists aren’t getting. That might 1) be a story; and 2) have real consequences for the respect and funding a field gets.

    I like to think that I always try to find some happy medium of precision that satisfies researchers and readers alike, within reason, so in the end I’m glad to get the feedback.

  12. #12 ERV
    April 25, 2007

    I certainly dont mean this as an attack either, JR– I grew up on SciAm and Discover. But I would be happy as a clam if no one used the term ‘junk DNA’ again. I wouldnt use it in a publication any more than I would use ‘MT tropic HIV’– At one point in time it was a perfectly acceptable word, but today it is archaic. There are better words.

    Perhaps you can keep the excitement and readability with something like ‘stretches of sequenced genomes are still left unexplored’ ‘pioneers of this nucleotide landscape have discovered’ etc. (meh I cant write, you pretty it up! lol!)

    I admit I do have a personal stake in the death of ‘junk DNA’– I study ‘junk’ (endogenous retroviruses, ERVs). And Creationists and other anti-science communities never miss an opportunity to latch onto ‘junk’ for ‘evidence’ to ‘support’ their respective world views. (example) It gets obnoxious. :)

  13. #13 JR Minkel
    April 25, 2007

    Ha, I will ponder it. Here’s my post on the subject.

  14. #14 TR Gregory
    April 26, 2007

    In case you haven’t seen them, I have a couple of posts on “junk DNA” at Genomicron, part of a series I am working on:

    http://genomicron.blogspot.com/2007/04/word-about-junk-dna.html

    http://genomicron.blogspot.com/2007/04/junctional-dna.html

    http://genomicron.blogspot.com/2007/04/onion-test.html

    Junk DNA is a popular buzzword, and many of my colleagues continue to use it as such, but it no longer carries its original meaning and has lost all precision. It therefore is no longer useful as a scientific descriptor for noncoding DNA.

    Glad to see a journalist actually soliciting feedback on this, I must say.

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