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”

Whitehorse’s Achilles’ Desire

Husband and wife duo Whitehorse pack an emotional punch with the first single from their new album The Fate of the World Depends on this Kiss. (I promise I’m not wallowing in clichés here, the punch is literal. Watch the video.) Luke Doucet and Melissa McClelland, major talents in their own right, have continued their musical partnership that began last year with the release of their self-titled debut. Continue reading “Whitehorse’s Achilles’ Desire”

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.

Random Genome, Naked Genome

On Saturday, my former Center for Genome Sciences colleague Sean Eddy brought up the idea of a Random Genome Project: let’s create a random genome to serve as a null model of genome function. With this random genome, we can determine how much supposedly functional biochemical activity do we expect to see just by chance, and, among other things, we might use a random genome to explore how new functions evolve by “repurposing” (Eddy’s great term) non-functional DNA. In the comments to that post, you can read some discussion of how you might go about making a random genome.

An easier task would be to implement the random genome computationally, an idea I’ve been exploring recently, using a genome-wide binding model along the lines of the one by Wasson and Hartemink.

Why do this? Because we could explore two kinds of null models – the random genome described by Sean Eddy, and the naked genome. Continue reading “Random Genome, Naked Genome”

Sunday Science Poem: Reality and The Snow Man

For this week’s poem, we’re coming back to Wallace Stevens, with one his most famous poems, “The Snow Man”. If you’ve read any Wallace Stevens, it’s probably this early poem.

John Serio writes that Stevens’ “most distinctive achievement” is this:

In an age of disbelief or, what might be worse, one of indifference to questions of belief, Stevens adds a metaphysical dimension. In doing so, he does not imply anything religious, yet goes beyond humanism. “The chief defect of humanism,” he writes, “is that it concerns human beings. Between humanism and something else, it might be possible to create an acceptable fiction.”… Poetry is supreme because it shifts our orientation from a traditional subject of belief, such as God, to its source – the creative, ever changing, infinitely renewable process of constructing a credible truth.1

The “renewable process of constructing a credible truth” sounds much like Thomas Kuhn’s description of the scientific process. Much of Stevens’ poetry tackles questions about how we construct our mental representations of reality. Continue reading “Sunday Science Poem: Reality and The Snow Man”