In Nature Lamprecht et al provide evidence that the presence of long terminal repeats (LTRs, a form of junk DNA) increases the risk of humans' developing certain cancers, especially lymphomas. [Added later: in 2007 the ENCODE study was supposed to show evidence that intragenic regions are pervasively transcribed but there's a large segment that believes this to be an artifact.]
Initially the discovery that our genomes were to a first approximation entirely composed of non-coding garbage characters was a surprise. But on further evolutionary reflection, it made sense: DNA is about copying itself, and it sometimes codes for proteins in networks with other pieces of DNA as a replication strategy. Consequently we should expect that most DNA is passively or selfishly just along for the ride, except in highly fecundity-dependent species where the extra time and energy make a fitness difference (like bacteria). Before you make the effort to back-of-the-envelope calculate the daily cost of replicating the 97% extra noncoding portion of our genome, realize that I have doubtless expended more calories typing this blog post than I will expend from all the DNA replication and proofreading I do during the entire day.
But even if the energy expended is not a problem, this paper revives the debate, because it shows that there still is a fitness cost for junk DNA in multicellular organisms - but it's paid in terms of cancer risk rather than energy cost. It's a little harder to write this off as fitness noise. We're back to the old question of what the advantage is for multicellular organisms to carry so much junk DNA.
Annals of targeted advertising
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