Comments

1. #1 apalazzo

   January 16, 2008

   RPM,

   I think that journalists think that they can cover “junk DNA” and treat it as if we just discovered something profound – but if you take all this data out of the context of how a cell operates, you just end up spewing crap. As for them not covering other topics, they can’t even begin to write about these ideas because they don’t understand how it fits in to the bigger picture of biological activity.

   I guess what I’m saying is that with “junk DNA” journalists are lulled into a false sense of security … (I can imagine them saying – “wow this is big, it has major implications for evolution, it’s a paradigm shift”) and missing the boat. When they look at RNA export they can’t link it up to their naive notions of biology and just don’t cover it.

2. #2 sparc

   January 16, 2008

   Alex’s paper is really cool. And the experiments are on a technical level that even many non-molecular biology biologists won’t understand.

3. #3 razib

   January 16, 2008

   I think that journalists think that they can cover “junk DNA” and treat it as if we just discovered something profound – but if you take all this data out of the context of how a cell operates, you just end up spewing crap. As for them not covering other topics, they can’t even begin to write about these ideas because they don’t understand how it fits in to the bigger picture of biological activity.

   journalism has a bias toward descriptive non-contingent science because it’s easy to write about. they mess up evolutionary genetics more than vertebrate paleontology because the latter is not as contingent.

4. #4 Greg Laden

   January 17, 2008

   I certainly did not mean to imply that I have the opinion that non-coding DNA is by and large doing something special in the way of specific function. I do think Genome size matters and since “junk” is most of the genome size, then junk matters. We all have slightly (or more than slightly) different ideas of terms like “function” and “adaptatin” and “it matters” and I do not know that anyone in particular has been anointed as the keepr of those definitions.

   I probably overstated the point of the paper I was reviewing. My position is not that most (or even a lot) of what you seem to think of as Junk is “not Junk” by most definitions. My position is, rather, here is an interesting paper that makes the claim that something that really seems like sawdust on the floor … a small percentage of it … is something else. And, I did not write the paper, I just “blogged it.”

   Over on my site, where as you now there is a certain amount of discussion on this, the question of what “ad hominem” has been brought up.

   The phrasing: “Ouch! Now, Greg is no geneticist. Thankfully, T. Ryan Gregory puts Greg in his place.” might well be ad hominem or it might not be. But it is at the very least mean spirited and not very helpful. I do not need Gregory, or you, or Moran, to “put me in my place” thank you very much.

   I know that your opinion/knowledge about this issue is anything less then very well formed, sophisticated, and an interesting read. I have nothing but respect for your command of this field. For example, the post (Your Bones Got a Little Genome) you pointed people to earlier from my site is a must read in this area (though I quickly add it leaves open the very strong possibility that the sheer amount of DNA … which is mainly controlled by the volume of junk … is incredibly important despite efforts to falsify that hypothesis).

   But I have to say that this post of yours, Moran’s writing on this, and to a much lesser extent T.R. Gregory’s work, is sufficiently impolite and tending sometimes to the obnoxious that it makes it hard for people to engage in learning, as opposed to debate.

   I am not innocent. I need to tone down the rhetoric and address the essential debates … the science … more directly and usefully.

   Flogging each other is good for business, but I’m not sure it is worth it.

5. #5 Larry Moran

   January 17, 2008

   Greg,

   I’ve been learning about genome organization and junk DNA for almost 35 years. I’ve taught courses in this field and I’ve written textbooks that address the topic. I’ve posted dozens of articles on my blog explaining the concept of junk DNA and why scientists think that much of our genome serves no function. I’ve presented the evidence that backs up that conclusion.

   On your blog you posted an article that said,

   The “Junk DNA” story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don’t know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.” It does really seem that scientists assumed for too long that there was no function in the DNA.

   I’m one of those scientists you are criticizing. You claim that I believe in a “myth” and that I have “assumed” something that’s obviously wrong (to you). What you did was to dismiss everything that I’ve said about junk DNA and the scientific evidence for it. You did this on reading a single paper by John Mattick who clearly has an agenda that’s not scientific by any standard that I recognize.

   Are you surprised that I took offense?

6. #6 Jim Thomerson

   January 17, 2008

   Isn’t a statement like.”Junk DNA has no function.” the kind of negative statement which is logically very difficult to prove?

7. #7 Greg Laden

   January 17, 2008

   Larry,

   My belief is that most non coding DNA has not been shown to have a function other than its role in genome size, which is interesting, potentially important, and worthy of further research.

   For you to think that I had you in mind at all, or that I was somehow negating, ignoring, or disagreeing with your career-long writing on the topic, is not an accurate representation of my point of view, my intentions, or my actions. This is not about you.

   I have nothing but respect and admiration for your writing and your research.

   Larry, your curmudgeon demeanor is sometimes cute and endearing. But it can wear thin. Very thin.

8. #8 TR Gregory

   January 18, 2008

   Greg,

   I can understand your reaction, but please restrict your comments about me to what I *actually* said, not what others have said I said.

9. #9 Greg Laden

   January 18, 2008

   TRG: I will do that.

10. #10 resonator

    January 18, 2008

    All that stuff about non-coding DNA is hype? What about the thousands of strongly conserved sequences, hundreds of which have been shown to function as enhancers? What about microRNAs? Also, more than twice as much DNA as protein-coding DNA consists of untranslated regions in mRNAs. Are we claiming that UTRs have no function?

    Much of the genome may not have a known function, but these categorical pronouncements are bizarre.

11. #11 peter nowack

    January 23, 2008

    In molecular biology, “junk” DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 80-90% of the human genome has been designated as “junk”, including most sequences within introns and most intergenic DNA. While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some is believed to function in ways that are not currently understood. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Some consider the “junk” label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term “noncoding DNA” (although junk DNA often includes transposons that encode proteins with no clear value to their host genome). However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be being expressed, which supports the view that the term “junk DNA” may be a misnomer.

12. #12 RPM

    January 23, 2008

    However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be being expressed, which supports the view that the term “junk DNA” may be a misnomer.

    I’d be willing to wager that a large fraction of the human genome that is transcribed (80% as you say, which I presume you’re basing on the ENCODE data) is non-functional. It’s transcribed in error. The hypothesis that the majority of the human genome is junk (or crap, or non-functional, or whatever) is not based on a lack of evidence for function. Rather, it is based on positive evidence that we know that most of the human genome is made up of dead transposable elements, pseudogenes, and other known non-functional elements.

13. #13 apalazzo

    January 26, 2008

    RPM,

    I agree that most of the transcribed stuff is non-functional in the sense that the sequence of the RNA does not matter, but the act of transcribing is probably very important. There are lots of hints from cell biology and molecular biology labs that local transcription has a profound effect on histone modification and genome packaging.

    Re: resonator. miRNAs are a big discovery – but what % of the genome do they account for? 0.001%? And as for enhancers and UTRs, we’ve known about these for quite a while. Perhaps we were a bit clueless on the % of the genome dedicated to these elements, but most people would have been in the right ballpark. This is not really new. All the hype is on this ncRNA. Some of it is surely functional, but the functional data indicates that these are low in number. To find ncRNAs we need to perform functional studies i.e. cell biology, biochemistry, molecular biology etc. There’s no shortcuts.