Well, it is a good thing that I have a thick skin and a good sense of humor, or I would be very put off by Larry Moran and probably T. Ryan Gregory as well.
Apparently, I stepped into an ongoing partially ad hominem debate over “Junk DNA” centering on the work of John Mattick and his research group. In this post, I’d like to provide a clarification of my “position” on Junk DNA, and I’ll spend a moment admonishing my colleagues for being dorks.
My offending post is here. This is a report on a recent paper by Mattick and others in which they provide evidence that non coding RNA does something … is not merely the stuff left over when “real genes” are getting transcribed and translated.
In my view, that paper is interesting and the evidence for ncRNA having some function is reasonable. It is clearly stated in the paper (but not emphasized in my post on the paper) that the magnitude of this possible function is very small … but it might be there.
There is a conception that I believe is generally held by the public, science teachers, interested parties, etc. that the genome can be classed into two categories: DNA sequences that ultimately code for proteins and DNA sequences that are “junk” … have no function whatsoever.
This is not true to a small extent and at many levels. By “a small extent” I mean that with one exception I’ll mention below, most of the DNA base pairs that do not directly relate to coding proteins have not been associated with any function. They may be parts of introns snipped out during coding, or they may be “pseudogenes” … sequences that may have been genes in the past but no longer function, or they may be other stuff that does not seem to do anything. Most of the non-Protein coding DNA is not known to have a function (again, see exception below).
Some of this DNA has a critically important function. It codes for molecules that are not proteins. One could argue that this does not count as Junk DNA. If one’s popular conception of Junk DNA is the DNA that does not code for proteins, then this counts. If not, it does not. But since we are speaking of popular conceptions, which are hard to define and rather slippery, we can certainly consider this type of DNA.
Then there are control regions. If you go back in time not too far, there were parts of the DNA that were known to not be “coding” because they were not part of the “code” for the molecules DNA specifies. Later in time, regions in this land of what would have to be counted as “Junk” were found to be critically important … they facilitate the coding process and the genetic system cannot do without them. It is possible that one could say that a formal definition of “Junk” would not include anything that is used in this manner, but that is backpedaling, and ignores the problem of popular conceptions being wrong.
A famous geneticist once said:
Some non-coding DNA is proving to be functional, to be sure. Gene regulation, structural maintenance of chromosomes, alternative splicing, etc., all involve sequences other than protein-coding exons. *
Genome size is a function of the total number of genes and the total amount of DNA that is not in genes (Junk, whatever). However, since the typical genome has only a small percentage of its total sequence in actual genes, that part of the equation cannot be very important, and it has been shown that the number of actual genes in a genome is not correlated to genome size.
However, it is also probably true that genome size matters. The metabolic rate of a cell, which is a very important variable, may correlate to genome size, for instance. Since genome size is primarily determined by the amount of “Junk” DNA, and genome size is important, I find it difficult go get out the words “So called Junk DNA is functionless.”
This does not seem to be a problem for people who work all the time at the genetic level, like T. Ryan Gregory. T (or shall I call him Ryan) studies genome size, but appears inclined to balk at any suggestion of function in Junk DNA, such as this. I am more of a whole organism guy, so to me, size matters. Body size variation across taxa is patterned in relation to a number of evolutionary and ecological factors, but size is acquired in a number of different ways. The way you get to be small or large is functional, not irrelevant. Size-factors are not “junk.”
It is also worth noting that “junk DNA” is linked to “genetic disease.” That might not be a “nice” function, but it matters. And it is interesting. To say that this is not a “function” is to have an inexcusably teleological view of “function.”
Here is how I would like to rephrase what I said in my original post:
“So called Junk DNA is many things to many people. The role of DNA that does not code for the usual proteins or other important molecules is interesting.”
What is also interesting is T Ryan Gregory’s and Larry Moran’s somewhat vitriolic or at least reactionary reaction to my post. Gregory reacted first, and I posted a comment on his site, and I will follow that up here with what I think is an important statement about the psychology of this issue. Since the discussion was getting interesting, I sent a link to my post and Gregory’s post to Moran saying I’d like his take on all of this. His reaction was to post “Greg Laden Gets Suckered by John Mattick,” which I will assume was meant in a tongue-in-cheek way, but I’m not sure everyone will see it that way. I’ll have to go over to his blog and kick his ass.
Here is what is behind all of this. Intelligent Design Proponents, Creation Scientists, Creationists, etc. have a hard time with Junk DNA. Indeed, truly junk DNA makes no sense in the context of an intelligent designer, and is in fact possibly evidence of a rather dumb designer. Natural selection is the dumb designer. For this reason, there is a link between seeking function in the junk and creationism.
You may have noticed that I am not a creationist.
Another (overlapping) issue is the teleological argument that has been made, that somehow, more DNA is better, and there is some kind of correlation between more, better, and “higher” organism … even to the extent that, say, dogs and humans are ranked on such as scale even though both are mammals (the human is generally ranked higher). Both Moran and Gregory have written quite a bit about these issues, and I strongly recommend Gregory’s post on the Onion Test.
Apparently, Mattick has been linked by Moran and Gregory to this kind of sloppy thinking. I did not know that. I have read Gregory’s critiques in the past, but I simply did not link this research team to Gregory’s critique to this paper. I was reading the paper as an isolated piece of research.
There are good things and bad things about my having done that. The bad thing is that one should be more familiar with the literature and thus able to look for aspects of the research that are not explicit. I can do that in numerous subfields of science, but not necessarily in this area of genetics. On the other hand, is it not the case that specific pieces of research should be taken at some point on their own, unless you know that a particular research team is likely to falsify data? Are Moran and Gregory acting inappropriately, derailing us all in the pursuit of knowledge because they overreact to this guy Mattick for, essentially, personal reasons, and because they see a creationist behind every implication of function among the junk? Or was I acting inappropriately because I deigned to review an article without actually being, or being a disciple of, Moran and Gregory?
Both. Neither. Scholarship is complex.