The Junk DNA Preservation Society

Futurepundit has an interesting post based on a new paper about so-called junk DNA. Only 2% or so of the human genome actually encodes protein sequences. The rest is a grab-bag of broken genes and virus-like sequences called mobile elements that hijack the cell's DNA copying-machinery from time to time and insert new copies of themselves back into the genome. A pair of scientists have come up with some ideas about why organisms like us have junk-rich genomes, while bacteria have barely any. I was going to post on it until pre-Thanksgiving business overwhelmed me.

After summarizing this research, Futurepundit then predicts that people will use genetic engineering to strip junk DNA from their genomes. The appeal is obvious--why slow ourselves down with all that seemingly useless DNA? Why not use some of that space for new and improved genes that let us live for centuries or become smart enough to read the new Medicare bill over breakfast? There are also arguments for getting rid of junk DNA that Futurepundit doesn't mention. When mobile elements jump around to new homes, they can trigger diseases as they mutate the genome.

Junk-free genomes may indeed become possible in the future, but they're probably not a wise idea. Even if junk DNA doesn't benefit us in any obvious way, that doesn't mean that we can do without it. Many stretches of DNA encode RNA which never become proteins, but that doesn't make the RNA useless--instead, it regulates the production of other proteins. Some broken genes (known as "pseudogenes") may no longer be able to encode for proteins, but they can still help other genes produce more of their proteins. (Scientists can't yet say how these particular pseudogenes do this, but the evidence is clear that they do.) Junk DNA can serve other functions as well--such as bulking up cells to a suitable size. And there are doubtless going to be many other discoveries coming in future years about important benefits from the mysterious 98% of our genome that doesn't fit a 1950s conception of useful DNA. (For more on this, you can read an essay I wrote for Natural History.)

None of this is meant to dispute the fact that much of junk DNA acts selfishly on evolutionary time-scales. There's plenty of astonishingly selfish behavior among these stretches of genetic material, like the mobile elements that have to get other mobile elements to make copies of them. It's just that we have to recognize that evolution works on different levels--on the levels of genes, genomes, cells, organisms, groups, and maybe even species and related groups of species. And something that's selfish at one level can become selfless at another level. Recently, for example, scientists found evidence that many mobile elements include sequences that can shut down their own spread. This is a feature of many successful parasites--they can thrive in their host without killing them too quickly.

It's on this evolutionary scale where purging junk DNA makes the least sense. The pasting and copying of junk DNA is a major source of new genetic variation. Instead of changing a nucleotide here or there, mobile elements can shuffle big stretches of DNA into new arrangements, taking regulatory switches and other genetic components and attaching them to different genes. While some of this variation may lead to diseases, it also prepares our species to adapt to new environmental challenges. (Similarly, pseudogenes that are truly broken still have the potential to become working genes again. Some scientists have proposed calling them "potogenes." )

If we turn ourselves into a genetically modified monoculture, we'll have to rely solely on our own genetic engineering, while abandoning a natural system of genetic engineering that's been finely honed over billions of years. We may be clever, but I just don't think we're quite so smart yet to take such a step.

Recently Jurgen Brosius at the University of Munster wrote an eloquent paper in Bioessays that made some similar points (although not on junk DNA). It's entitled, "From Eden to a hell of uniformity? Directed evolution in humans." Here's part of the abstract:

"The first major concern is that the genome will never be a completely reliable crystal ball for predicting human phenotypes. This is especially true for predictions concerning the performance of alleles in future generations whose populations might be subjected to different environmental and social challenges. The second, and perhaps more important, concern is that the end result of germline intervention and genetic enhancement will likely lead to the impoverishment of gene variants in the human population and deprive us of one of our most valued assets for survival in the future, our genetic diversity."

To fend off threats to the mysterious wilderness that is our junk DNA, I propose the establishment of the Junk DNA Preservation Society.


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I don't have the book to hand, but isn't "junk DNA" one of the scientific hooks in Greg Bear's _Darwin's Radio_? If I recall correctly, Bear treats the junk DNA as the engine of something like punctuated equilibrium, or, at any rate, extraordinarily high-speed evolutionary change. In the novel, this turns out to be both necessary [i.e., triggered by environmental pressures] and terrifying [because the process kills most mothers of the new species].