Ultra-consvered pseudo-junk DNA?

Here‘s why I’m dreaming of one day becoming a developmental biologist and/or geneticist. Stanford researchers identified a group of DNA regions which are extremely conserved (80-100 million years of mammalian evolution and going strong) in macaque monkeys, mice, dogs and humans. They could call this DNA “junk” because it’s redundant, at least on the short scale.

Junk DNA on its own is a fascinating phenomenon. It’s curious that some regions are in fact called “junk” and by the same token, extent the metaphor in the respect that even junk can be useful, and if not to its original owner, then to someone else. You can call ERV’s junk, but I bet the original viruses didn’t think so, and you can call a hypothetical stretch of DNA with an apparently invisible or completely redundant function that serves nothing but aiding commensal organisms junk, and, again, I bet they wouldn’t think so.

It’s also important to define junk DNA on the basis that the removal of junk DNA affects no physiological function in the organism, even more undoubtedly when there are copies of DNA that are partially removed, leaving other copies intact.

Since having an excess is in fact having too much (I can get a copy or two of a seemingly meaningless strand of DNA, but hundreds and thousands? Improbable and effectively ridiculous) – these DNA regions are appropriately called junk.

But, see, here’s the thing: because junk DNA is classically known to be neutral and its removal or modification are observed to be undamaging, I think this particular research shows rather clearly that it is NOT, in fact, junk DNA.

In case some creationist twerp decides to quote-mine this, I do not mean that this research shows evidence of a divine plan in our nucleic acids. The evidence obviously shows that this DNA is important, but nobody can figure out why, and more interestingly, to whom.

The researchers suggested that it could be a special “immunity” bank, to be deployed should a particular disease or bacterial infection comes about.

I find this suggestion curious and I think I can stretch it even further: it is possible that mammalian evolution allowed for certain mechanisms to stay relatively dormant to allow greater response to a selection pressure that comes regularly to a species, or even to the entire mammalian class.
It is unlikely, however, that such special genetic equipment stays precisely the same for 100 million years. Even if a series of great extinctions bottlenecked the entire mammalian population in the near past, that is, the past 65 million years, it is laughably improbable that complete regions remain ultra-conserved for ANY reason, even, perhaps, “anti-extinction genes”.

There has to be a more likely, simpler (and probably harder to detect) explanation to the conservation of pseudo-junk regions. If the reason for the conservation is elusive enough to escape detection after being pulled out of the genome without harming the organism, it is possible that the only reason that this DNA is conserved is because it serves its own purpose as a “hijacker DNA strand”. This is a phenomenon called “drive” by geneticists, and there’s already a huge repository of documented cases for drive, even in whole chromosomes. Perhaps the only thing unique about these stretches of DNA is that they somehow inhibit their own mutative nature. Should ANY region be able to do just that, you could say that it’s got the most positive selection pressure thinkable.

I’m only surprised this doesn’t happen more often. Then again, it is possible that other regions of DNA would benefit just as much by producing qualities that inhibit the inhibition of these selfish DNA regions to mutate.

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