The blogosphere overreacts!

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.



3 comments to The blogosphere overreacts!

  • greg laden

    TRG: I really do want to get past the discussion of who said and meant what when they said this or that thing, as soon as possible.

    I probably made two mistakes, but I do not want to belabor them any more than anyone else wants to admit they were rude. I probably over characterized or at least poorly stated the argument. As I have stated in a number of places, including on your site, I do not think that most DNA has a directly relevant function (as “code” as it were?) … it does not code for anything or regulate coding. I think there is a broad “significance” to DNA’s total amount (genome size) and here I defer to you to specify, as you are an expert on this area. I am NOT prepared to make the distinction between “function” “adaptive function” and “significance” or to link or unlink any of these concepts without a great deal further discussion and consideration. All these terms are moving target (or at least, individuals may have their own pet definitions and they will not all be the same).

    I also think that you have not been particularly impolite or offensive, but I may have made the second mistake of putting you in the same boat as some other bloggers. Sorry about that. And yes, I cannot shake the feeling that geneticists as a group (not necessarily all geneticists) have some communication or socialization problems! Can you possibly understand, when there is a long list of posts essentially saying that Greg Laden is stupid, or lacks reasoning powers, etc, that I would feel a bit ganged up on? Is it really the case that no matter how many time I state the contrary, that you and other blogging genetics experts are immutably convinced, and are inclined to go through great lengths to prove, that I believe in widespread function (as in coding or regulation, etc.) of the genome? Why would that be? I do not understand it at all.

    The conversation going on at Sandwalk about junk DNA, which you are participating in, is very interesting. One gets the impression that “junk DNA” is pretty darn important, yet at the same time, irrelevant. I would suggest that this is not a complexity or strangeness of the DNA, but rather, the theoretical context in which we consider the DNA.

    Let’s all try to start acting like scholars talking about an interesting topic!

      (Quote)

  • TR Gregory

    Greg,

    Thanks, I appreciate the comments. But, in closing, I have to say that 1) I was not rude and what I said was appropriate based on your claims (whether they reflect what you actually think or not is a different issue, and 2) I am totally in favour of a scholarly discussion, but your reaction, including what you said about me, does not meet those criteria.

      (Quote)

  • SFMatheson

    TRG–
    Your comments here, and on Greg’s blog, have been generally flawless. I was indeed referring to Larry’s demolition when I said that the corporal punishment of our hyperprolific fellow blogger was a bit too severe. And I agree that Laden overreacted. My interest in this conversation is based in part on my ongoing project to debunk the creationist folk science to which you have occasionally referred, and so I am eager for this conversation to devolve into the scholarly discussion that Greg is seeking. And you can call me Steve.

    Greg–
    Though you’re right that Larry likes to pick fights, regular readers of your blog might be thinking of pots and kettles right now. I say enough of the whining about your punishment; spin it as peer review! (That’s what I do on my blog.)

      (Quote)

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