"In 1980, two key papers — by Orgel and Crick, and by Sapienza and Doolittle — nicely laid out the argument that genomes contain “selfish” or “junk” DNA, largely transposon-derived, sometimes quite large amounts of it. These papers are quite beautiful and scholarly. They are careful to say, for example, that it would be surprising if evolution did not sometimes co-opt useful functions from this great amount of extra DNA sequence slopping around. Indeed, we are now finding many interesting examples of transposon-derived stuff being co-opted for organismal function (but these are the exception, not the rule). Without trying to be snide or pedantically academic, I’ll note that the main ENCODE paper cites neither Orgel/Crick or Sapienza/Doolittle; what this means is, regardless of what we read in the newspapers, ENCODE is not actually trying to interpret their data in light of the current thinking about junk DNA, at least in the actual paper.
Transposon-derived sequences are the poster child for “junk DNA” because we can positively identify transposon-derived sequences by computational analysis, and reconstruct the evolutionary history of transposon invasions of genomes. There’s likely to be other nonfunctional DNA “junk” too, in the DNA that we can’t currently put any annotation at all on, but the key point is that the dead bones of many transposons are something we can affirmatively identify...."
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