WARNING: This post is just a rant against a review article Im too impatient to deal with today. Its really just a rant. heh.

Hey, you know whats even better than having ‘science reporters’ use the term ‘junk DNA’ in their pop-science articles?

A ‘real’ scientist using the term ‘junk DNA’ in their review on LINES/SINES/ERVs.
Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites

Following the discovery of transposons in plants and bacteria, the presence of mobile DNA in eukaryotic species gained widespread acceptance. However, the concept of “controlling elements” gave way to disparaging terms such as selfish DNA and “junk DNA.” Nevertheless, the notion of transposable elements as merely molecular parasites, benign at best and powerful mutagens at worst, that hijack cellular mechanisms for their own selfish propagation, seemed incomplete to some biologists. Given that evolution tends to dispose of that which is useless and harmful for a species, it was curious that the genome should be cluttered with so much “junk.” Now we understand that genomes have coevolved with their transposable elements, devising strategies to prevent them from running amok while coopting function from their presence. Repetitive DNA, and retrotransposons in particular, can drive genome evolution and alter gene expression. Evolution has been adept at turning some “junk” into treasure.

Really?

Really??

DUH! 1972, man, 1972. 1972 scientist figured that ‘junk DNA’ could be co-opted for ‘treasure’. Shit!

And the fact that we have evolved ways of co-opting (Im sorry, ‘restraining’ and ‘rehabilitating’) genomic parasites doesnt mean they arent genomic parasites. Dude, if I totally stripped all epigenetic modifications from your cells right now, any mobile element that retained the ability to replicate would. Its selfish DNA.

And whats up with conflating ‘useless’ and ‘harmful’?? Its called ‘drift’, man! Doesnt he read Genomicron or Sandwalk?? UGH!

The rest of the review is fine… its just like every other review of LINES/SINES/ERVs, going over pros/cons, evolutionary significance, etc. Other reviews also written by Kazazian 4.5 years ago.

*sigh* The review is fine. Its fine. I just dont have patience to deal with this intro this morning.

Comments

  1. #1 Terrance
    October 21, 2008

    Oh, good idea. Let’s search for treasure!

  2. #2 Gerardo Camilo
    October 21, 2008

    Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA,Junk DNA….

  3. #3 Jared
    October 21, 2008

    Calm down, Abbie, it seems like a review targeted to a very broad audience. As far as I can tell, while it gets technical, it leaves lots of specific research out. Breathe…

  4. #4 Renee
    October 21, 2008

    Yeah, that’s pretty infuriating… and misleading. Sorry, it doesn’t matter if it’s written for a popular audience, there’s no justification for saying that evolution will “dispose of that which is useless and harmful for a species.” That’s just wrong. There’s no evolutionary process which works for the good of the species. None. It is only ever a byproduct.

  5. #5 TR Gregory
    October 21, 2008

    Comings 1972 (first use of “junk DNA” in print, and a much broader review than Ohno’s official coining of that term):

    These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

    Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.

    Orgel and Crick (1980) (first detailed discussion of ‘selfish DNA’):

    It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another.

    Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.

  6. #6 Larry Moran
    October 21, 2008

    The modern definition of “junk DNA” is: DNA that does not have a function.

    That’s what we mean when we say that >90% of our genome is probably junk.

    One of the things we’ve learned in the past few decades is that evolution does not lead to perfection. There are lots of useless things that persist. They do not seem to be particularly harmful.

    Small hind limbs in whales are a classic example, but so are pseudogenes. This includes defective transposons.

    Any biologist who has not grasped this essential point should not be writing reviews in Cell.

  7. #7 Ian
    October 21, 2008

    If Chinese detectives investigating a murder found incriminating DNA on a boat, wouldn’t that be junk DNA which had a use?

  8. #8 Paul Lundgren
    October 21, 2008

    Sing it with the Village People:

    Junk D-N-A!
    It’s fun to play with the
    Junk D-N-A!

    You’re right, the arm motions aren’t as easy as the original.

  9. #9 inthelab365
    October 21, 2008

    Paul,

    That Village People vision in my head is too funny!!! You made my day with that one!! Thanks, I needed that.

  10. #10 Paul Lundgren
    October 21, 2008

    @9:

    If that lame joke makes you laugh, you need to get outthelab more often.

  11. #11 thisisfunny
    October 22, 2008

    You no what the said: “Ooh, ooh look at all this junk, how can anyone believe someone designed all this junk. Dem silly cretinists.” These days its not evidence for “bad design” it is just: Look, behold, the magic “power of natural selection”. It can do everything.

  12. #12 Sili
    October 22, 2008

    While Paul’s suggestion is amusing, I’m not up for the photoshoppery:

  13. #13 Sili
    October 22, 2008

    I phail

  14. #14 Jason
    October 22, 2008

    This is a pet pieve of mine, too, Abbie.

    But not in regards to viruses; I think DNA is far, far, far more functional than previously estimated (if you’re curious I can send you a manuscript of a paper that my buddy just got accepted in nature) — basically, I don’t believe junk DNA is a fair term. At all.

  15. #15 Pasta Apotheosis
    October 22, 2008

    Jason: Can you provide any details?

  16. #16 Jason
    October 23, 2008

    http://www.nature.com/news/2008/080827/full/4541042a.html

    Even know I know the manuscript was accepted, I don’t want to provide more info than this – but this is the paper that’s being alluded to.

  17. #17 Jason
    October 23, 2008

    I know all those guys – the picture of John was taken by K. Mar — our administrative assistant.

  18. #18 crunkcar
    November 3, 2008

    Interspersed repetitive DNA functions to block gene conversion, thereby allowing new genes to evolve. Please see
    http://www.repetitive-dna.org
    http://en.wikipedia.org/wiki/Interspersed_repeat

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