I am not interested in getting into a battle with any of my fellow bloggers on this issue, especially since I actually read all of the blogs involved and appreciate what each one of them has to say. But I do have to point out that sometimes the blogosphere overreacts, and things get blown out of proportion. Also, the sun rises in the morning and snow is cold.
On his new powerblog (seriously, Seed must have told him he has to post something every 15 minutes), Greg Laden made the following statement:
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.
What I actually said was, I think, pretty innocuous and mostly accurate:
Over on his blog, Greg Laden points to some new work by John Mattick’s group on non-coding RNA expression in mouse brains. It’s interesting stuff, and worth a look. Please bear in mind as you do, however, that non-protein-coding but functional RNA is nothing new. Ribosomes are made of non-coding RNA, for one thing. Sadly, Greg seems to have bought into the distortions (several promoted by Mattick) about what people have said about non-coding DNA.
That was the extent of my discussion of Greg in particular. I then provided a list of examples of functions that have been suggested, and concluded by giving my opinion about how the results of this quite interesting paper should be interpreted realistically.
Larry says I have “already tried to teach Greg some real science about junk DNA”. RPM says I “put Greg in his place”. Genome Technology Online says I “blasted” Greg. And SF Matheson says Greg is “being spanked a little too hard” (he could be referring to commenters, but this follows a line about what Larry and I wrote).
In his reaction and in the comments to others, Greg decides to:
1) School me on why genome size is relevant, with special reference to birds and flying. Since this is based partly on my own work, I find this curious.
2) Insinuate that objection to claims of function for all eukaryotic DNA are cultish, and that those who agree with Larry Moran and me are “disciples”.
3) Say (to RPM) “…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 get a qualifier, but am listed).
Again, here is what Greg claimed:
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.
And yet again, here is what I actually said about Greg’s statement — no more, no less:
Sadly, Greg seems to have bought into the distortions (several promoted by Mattick) about what people have said about non-coding DNA.
I think they are distortions. And I think Greg’s statement shows he agrees with them. Judge for yourself if the blogosphere got this one right with regard to what I, myself, actually wrote.
___________
Update:
I feel I should provide some clarification, so let me address the statements that Greg made and explain why they are inaccurate.
(1) The “Junk DNA” story is largely a myth.
This is false. There is good reason to expect that much or most of the genome is non-functional, and it takes evidence to show otherwise.
(2) 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…
Yes, we do. We know that about half of the genome in humans is made of inactive transposable elements. We know that many mechanisms can add or subtract DNA without being related to function. We know the patterns of diversity in genome size for 10,000 species of eukaryotes.
(3)… or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.”
This implies that there is a role and we just don’t have the details about it, but the premise is not something you can assume as a given.
(4) It does really seem that scientists assumed for too long that there was no function in the DNA.
This is not true, but it is the claim made by Mattick and others (usually non-scientists). People assumed function from the very beginning, either for all DNA or simply a lot of it. This is true right back to the very first use of the term “junk DNA”, and it was true when people had to explicitly challenge the assumption of function, and it has continued up to the present. Some people, mostly sequencers, may have ignored the rest of the genome and focused on genes, but that does not reflect the range of views that have always been expressed.
