Junk DNA

After seeing the articles on the human genome project, I was obliged to do a little speculating. It turns out that instead of some 100,000 genes that we expected to find along our lengthy strands of DNA, there are instead only 30,000 to 40,000 genes instead. Here is an article about the overall project and some of its amazing conclusions.

This means that we have many stretches of “junk” DNA along the old double helix. What occurred to me is that this could be a useful survival feature in a number of ways.[ul][li]Instead of having compact genetic material that would be more susceptible to damage by cosmic rays or other ionizing radiation, there are enormous “buffer” regions between critically encoded zones. This makes a lot of sense. There might have been an earlier hominid that had more densely encoded DNA and was thus eliminated by exposure to the harsher conditions of prehistoric times.[/li]
Yet, this may not entirely be the case since critical gene groups manifest in “clusters” in certain specific areas. There is speculation that this centralizing of critical functions, like the mapping of how an embryo develops, makes that region less subject to interference from junk DNA inserting itself. Obviously, there are just as many questions raised as answered, as you can see from this article.

[li]Overproduction of genetic material keeps the DNA engines running at a healthier clip. If small quantities were all that was needed, there might be a greater chance of atrophy or impaired function. To have lots of material necessary for correct genetic expression there is an assurance of more robust functioning.[/li]
[li]With increased DNA length there would be more sites for matching sequences to “fit” themselves to. This maximizes the opportunity for “jumping” genes. As a potential source of relatively benign mutations, this would also contribute to survival.[/ul][/li]What implications do you see in this work? Do you think that there will be just as many curses as boons in this biomedical Pandora’s box. I’m particularly interested in the opinions of any genetic researchers who may haunt these boards.

My own take on this is that once the ethical dilemmas are solved, this will prove to be one of the greatest scientific advances in the history of human existence.

I don’t believe this would be the case. If cosmic rays (or whatever) cause 1 mutation per 100 base-pairs (bad numbers I know, but this is just an example) and we had 100 base-pairs, all of which were coding, we’d get 1 mutation. If we had 200 base-pairs, 100 coding and 100 junk, we’d get 2 mutations, 1 in the coding and 1 in the junk that would likely have no affect. Same thing. It doesn’t seem that extra DNA would protect the rest in any way.

Many proteins are present in cells in incredibly tiny amounts. Some are only used at very infrequent intervals. These proteins do not “atrophy” due to disuse (they DO have a half-life, but that’s not really the same thing, and is due to the structure of the protein, not how often it is forced to work), but can remain inert until they are needed. We can take the “DNA engines” (i.e. polymerases and such), store 'em in a bottle, add 'em to a DNA solution much later, and they’ll happilly chug away replicating the DNA. It is not necessary to keep them busy.

Also, just because we do not know the function of much of the DNA in the human genome does not mean that said DNA is necessarilly “junk”. There are regulatory sequences which allow inhibitory or promoting proteins to bind, places for transcription factors to bind, long repeated sections that cap the ends and prevent chromosome degradation, ancestral genes that have ceased to function, et cetera. There are likely regulatory sequences of types and functions that haven’t been figured out yet. And yes, some of it is almost surely “junk” that just got into the works during millions of replications. But there is not necessarilly any advantage to this non-coding DNA. It may just sit there largely innert and get replicated from generation to generation.

Junk from our point of view. From its point of view, it’s getting a free ride, replicated by the robots that we are pleased to call “human beings”.

Remember that there is only one life form on Earth: DNA. Everything else is just the machinery that DNA uses to make more copies of itself.

Brian covered this excellently. I just want to emphasize that altho the LA article referred to all the rest as “junk,” most of it is probably not junk. It was once thought, back in the stoneage time of DNA knowledge (about ten years ago), that there was a lot of junk DNA, only to discover that what they called junk had essential functions, as Brian stated: regulation, etc. Thus, that undermines the very foundation of the tenets of buffer areas.

First of all, let me point out that this is not a new discovery - it’s been common knowledge for years. What has not been known (and still isn’t, really) is how much junk we have. It’s clear that there is quite a bit, but the exact percentage keeps shrinking due to scientists figuring out new functions for stuff we thought was useless.

And, actually, the junk does seem to provide some protection from mutagens. It’s a surface area-to-volume type thing.

As for the clusters that were mentioned, often related genes in clusters arose through gene duplication. Through various processes you can get two copies of the same gene placed end-to-end. Over time, they diverge, taking on slightly different roles. The hemoglobin gene family is the classic example of this.

Lessee, what else? Oh, yeah. The idea that there may have been a proto-hominid with less junk probably doesn’t hold much water. Most organisms, if not all, have a pretty significant amount of junk floating around. There are salamanders (or was it frogs? Amphibians, anyway) with something like 8 times as much DNA as we have. For large organisms, anyway, carrying all that extra DNA doesn’t seem to be much of a problem, so it tends to accumulate.

I think the selective pressure that acts on us (eukaryotes) to eliminate redundant DNA sequences must be relatively small. In other words, if you have in your genome a couple of mega-base-pairs of ancient retroviruses and tandem repeats that I don’t, it doesn’t give me much of an advantage over you.

But it seems to be pretty easy for new “junk” DNA to come into being. For example, recombination errors can cause big segments of DNA to be duplicated. If the segment that’s duplicated is bad for you (like the small part of chromosome 21 that causes Down Syndrome when repeated) it will be eliminated pretty soon by natural selection. But if the duplicated section has a neutral (or approximately neutral) effect on your fitness, new mutations should become fixed in the population at a rate that’s equal to the rate of mutation (a theorem proved by Motoo Kimura).

The problem with this idea is, of course, that neutral reductions in the size of your genome (which can also be caused by recombination errors)should also be fixed in the population at a rate that’s equal to the rate of mutation.

So either increases in genome size are more likely to happen randomly or be neutral than reductions, or extra DNA is beneficial for certain organisms (maybe because it reacts with and dilutes the effect of mutagens like free radicals).

I would be surprised if someone hasn’t already done experiments to address these issues with fruit flies. It should be possible to give a fruit fly a bunch of extra DNA to see how that affects its fitness (and resistance to mutagens), or to remove a lot of “junk” DNA from a fruit fly to see how that affects its fitness. (I’m pretty sure that redundant DNA in bacteria has a bad effect on fitness, but that doesn’t necessarily apply to eukaryotes.)

Stephen Jay Gould has a co-ed column in today’s NY Times re the paucity of genes in humans. Of particular importance to this thread is the following:

“Second, the unique contingencies of history, not the laws of physics, set many properties of complex biological systems. Our 30,000 genes make up only 1 percent or so of our total genome. The rest — including bacterial immigrants and other pieces that can replicate and move — originate more as accidents of history than as predictable necessities of physical laws. Moreover, these noncoding regions, disrespectfully called “junk DNA,” also build a pool of potential for future use that, more than any other factor, may establish any lineage’s capacity for further evolutionary increase in complexity.”