Midden DNA

Some people don’t like the term “junk DNA”, because they assume all that extra DNA in the human genome must be doing something. Some of those people are tenured faculty, members of the ENCODE project, and have trouble penning reasonable definitions of biological function.

Other people have experimental data to show that random sequences of DNA can be biochemically active without physiological effect, understand that the genome’s complexity resists easy classification, and can, simultaneously, understand that these swathes of non-functional DNA are valuable because they contain the history of our evolution.

In that light, I am going to propose that we abandon the misleading phrase “junk DNA” and adopt a word from archaeology used to describe piles of informative waste: midden*.

A midden…is an old dump for domestic waste which may consist of animal bone, human excrement, botanical material, vermin, shells, sherds, lithics (especially debitage), and other artifacts and ecofacts associated with past human occupation. The word is of Scandinavian via Middle English derivation, but is used by archaeologists worldwide to describe any kind of feature containing waste products relating to day-to-day human life. – Wikipedia

Now, if you want to call it midden DNA or the DNA midden, that I am happy to leave up to personal taste and style.

*A potential confusion might arise when researchers sequence DNA from biological samples in an actual midden heap – a risk with which I am willing to live.

Keeping genomes small

We read this paper in my Eukaryotic Genomes class (more than 10 years ago…sigh). The paper suggests that you need to be proactive about getting rid of pseudogenes and transposable elements if you want to keep your genome small:

High intrinsic rate of DNA loss in Drosophila


Nature 384, 346 – 349 (28 November 1996)

Differences in deletion rate may also contribute to the divergence in genome size among taxa, the so-called ‘C-value paradox’. Two reports find a positive correlation between genome size and intron size in a variety of taxa. In addition, the reduction in the intron size in birds, whose genome size is smaller than that of other tetrapods, has been inferred to be due to multiple separate deletions scattered along the introns. It is noteworthy that pseudogenes are much rarer in birds than in mammals. These results argue that differences in genome size among related organisms may be determined primarily by the variation in the genome-wide deletion rate, and not, for instance, by different rates of insertion of transposable elements.

An ode to junk

It is an unfortunate circumstance that ENCODE publicity decided to declare “junk DNA” dead, again. It’s not a totally unique position. Creationists and John Mattick have argued that there is no useless DNA for ages.

The demise of “junk DNA” is a fait accompli of the way “functional” is defined. It is not a definition of “functional” most of us would recognize. Ewan Birney, who should know, explains that when ENCODE says “functional” they mean “not biochemically inert in at least one of our many assays*”. As Mike has noted from his own research experience, many totally random DNA sequences synthesized in a tube are “not biochemically inert” nor are they biologically “functional”.

The fact is, if you only think of “junk DNA” as a problem, you aren’t seeing the forest for the trees – and you certainly are lacking a touch of poetry in your bleak soul. Continue reading “An ode to junk”

Sometimes you wanna go…

…where everybody knows their genomics. Bum bum bum.

Which is as far as I’m taking that, because I have the bad feeling that y’all would suggest that I’m the Cliff Clavin around here (I’m so the Carla).

Technology willing (let’s all take a long, suggestive look at Mike for a moment), we will be doing a live Google Hangout to talk about the ENCODE project tonight (Tuesday, 11 September) at 9PM Eastern. We’ll chat about what it means for science, “junk DNA”, and who (if anyone) actually knows what they are talking about.

Oh yeah, it is BYOB until we get that whole virtual liquor license thing sorted out.

*Leave a comment here or tweet @joshwitten or @finchandpea if you are interested and need a hangout invite.

Polling junk DNA

I missed this poll by Chris Gunter yesterday, asking “If you are a non-genomicist, can you tell us if you thought/were taught much of the genome was “junk”?

Well, I’m 1) a day late and 2) not a non-genomicist, but I’ll reply anyway, because we need a little history review.

In my Eukaryotic Genomes course in grad school (in the year the draft Human Genome sequence came out), I was taught by Tom Eickbush, not so much about ‘junk DNA’, but about ‘selfish DNA’. The point is largely the same regardless of what we call it. Among the first papers we read in Eickbush’s class were the classic Doolittle and Sapienza and Orgel and Crick papers on selfish DNA.

The key argument of these papers was this: parasitic DNA that can replicate itself within the genome requires no other explanation for its existence other than is ability to replicate, period. It does not need to be functional, from the perspective of the organism. It may acquire a useful function. But in general, absent evidence of such a useful function, we don’t need to ask the question, ‘what is the function of this DNA?’ There’s no mystery why it’s there – because it can replicate. Continue reading “Polling junk DNA”

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