Consciousness and how it got to be that way

Sunday, May 2, 2010

Junk DNA and Cancer

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.


  1. Mike, here are a few armchair guesses from the peanut gallery:

    1. If we reproduce before the junk DNA cancer kills us, we free up resources for the next generation. There's little selection pressure to clean up the DNA mess.

    2. Junk DNA might act as a nice random number generator for mutations. It might be more evolutionarily fit to have the junk and have some variation than to mutate more slowly and avoid cancer.

    3. Space. How much of your blog post is blank space? How many of the words that you use are just used to put the important nouns and verbs into the right place in the sentence?

    4. Looking at your last sentence, try turning it around: What's the disadvantage to carrying so much junk DNA? Possibly cancer, right? Now, ask what the advantage would be to having an error checker running constantly to clean it up? Imagine the resource hit from Norton Antivirus running on your genome.

    Again, this is just a guess from a guy who hasn't had any formal biology since high school. I have, however, reproduced twice so chalk up a few points for the fitness of my junk DNA, right?

  2. Speculating #1 (no selection pressure because junk DNA, specifically LTR cancer doesn't kill organisms prior to reproduction): point is, the fitness cost is still nonzero, so there should be slow but steady downward pressure on LTR expansion. RE #2, it's always a hard sell to argue for a mechanism that enhances mutation, because such mechanisms innately tend to erase themselves. You can make an argument for diminishing returns (at a certain point the energy cost of perfectionist proofreading outweighs the fitness cost of mutations) but that's different than selecting for mutability.