My school makes me proud

(Note: edited per helpful comments from AMW)

The genetics researchers at the University of Georgia, of which I am currently a graduate student (in a different department), have recently published some important research that’s gaining some attention among the scientific community. The length of the headline makes it clear how complex the research in question was: “New research shows how gene function drives natural selection in important class of genetic elements.” Here are a couple quotes that I understand the most and thus (rightly or wrongly) seem most salient.

Transposons are the Clark Kents of a genome. Apparently mild-mannered and inconsequential but with sudden bursts of activity, these free-floating bits of genetic material have for millions of years been sneaking into the genetic maps of plants and animals, dramatically increasing a genome’s size.

For years, researchers thought that most of this DNA was passive “junk” and knew little about it. New findings, however, are peeling back the odd and baffling world of transposons. Now, researchers at the University of Georgia have just found that natural selection on gene function is driving the evolution of one kind of transposable element called the LTR retrotransposon. (LTR refers to the “long terminal repeat”—a repetition of a recognizable sequence of nucleotides, the chemical bases that make up strands of DNA.)

A good theory has explanatory power.  A large part of the genomes of  both animals and plants is composed of genetic information that does not code for proteins, but are relics of earlier stages in which they did;  this left-over, non-coding DNA has been nicknamed “junk DNA”.  As Stephen Matheson at Quintessence of Dust points out (HT: AMW), scientists have never assumed it was completely useless and knew that it frequently takes on other roles within the genome, but it’s still somewhat remarkable that this relic data would comprise the vast majority of each genome.  Now it’s more understandable why this “junk” sticks around: the new research helps demonstrate that this non-coding, “junk” DNA can actually offer selective advantage, which is not just a “gee whiz” fact, but one that can be quite helpful:

Understanding the evolutionary pressures between host genome and transposable element will in the future be of interest to those studying retroviruses, which evolved from retrotransposons. There are a number of animal and human diseases caused by retroviruses including HIV/AIDS, avian leukosis and feline leukemia.

This is a cracking good quote: evolutionary science is useful in the real world. How many such developments can the ID crowd point to? Many of them still insist that “junk” DNA can’t exist because “God don’t make no junk.” Evolution says that it’s “junk” in the sense that it no longer serves its original purpose, but as this shows, apparently it can become useful in a different function later. The persistence of certain types of apparently junk DNA through reuse makes perfect sense of the data.

“In this study, we specifically wanted to assess the pattern of selection on these elements—a pattern that could derive from the effect of the elements on the host genome, or the effect of host silencing mechanisms on the elements,” Baucom said. “Our expectation was that if the elements are adapting to the host genome, we should see evidence of positive selection in the genes involved in transposition.”

Another feature of a good, useful theory: it makes predictions.

“Overwhelmingly, we found that LTR retrotransposons are under significant evolutionary constraint, by finding strong purifying selection on genes involved in their replication and life-cycle, regardless of the family that any the LTR retrotransposon sequences might belong,” says Baucom.

An even better feature of a theory: it makes predictions that turn out to be correct.

What the scientists found helps explain why these elements can, while lying quiet for millions of years, suddenly amplify within genomes while not causing more long-term harm than to take up space. And yet the observation that a tiny percentage of the elements actually become active parts of genomes provides an intriguing glimpse into how these twin evolutionary pressures can, in rare cases, “sign an armistice.”

Now, I’m the first to tell you that I don’t know all that’s going on in this research. So be sure to read the full article here and let me know if I’m misinterpreting anything.

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