I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
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
Oh, good idea. Let's search for treasure!
Posted by: Terrance | October 21, 2008 2:05 PM
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....
Posted by: Gerardo Camilo | October 21, 2008 2:18 PM
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...
Posted by: Jared | October 21, 2008 2:19 PM
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.
Posted by: Renee | October 21, 2008 2:29 PM
Comings 1972 (first use of "junk DNA" in print, and a much broader review than Ohno's official coining of that term):
Orgel and Crick (1980) (first detailed discussion of 'selfish DNA'):
Posted by: TR Gregory | October 21, 2008 2:41 PM
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.
Posted by: Larry Moran | October 21, 2008 4:06 PM
If Chinese detectives investigating a murder found incriminating DNA on a boat, wouldn't that be junk DNA which had a use?
Posted by: Ian | October 21, 2008 5:05 PM
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.
Posted by: Paul Lundgren | October 21, 2008 5:12 PM
Paul,
That Village People vision in my head is too funny!!! You made my day with that one!! Thanks, I needed that.
Posted by: inthelab365 | October 21, 2008 6:16 PM
@9:
If that lame joke makes you laugh, you need to get outthelab more often.
Posted by: Paul Lundgren | October 21, 2008 8:43 PM
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.
Posted by: thisisfunny | October 22, 2008 7:37 AM
While Paul's suggestion is amusing, I'm not up for the photoshoppery:
Posted by: Sili | October 22, 2008 4:10 PM
I phail ...
Posted by: Sili | October 22, 2008 4:13 PM
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.
Posted by: Jason | October 22, 2008 5:47 PM
Jason: Can you provide any details?
Posted by: Pasta Apotheosis | October 22, 2008 9:34 PM
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.
Posted by: Jason | October 23, 2008 2:46 PM
I know all those guys - the picture of John was taken by K. Mar -- our administrative assistant.
Posted by: Jason | October 23, 2008 2:49 PM
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
Posted by: crunkcar | November 3, 2008 11:02 PM