Author: Mike White

Genomes, Books, and Science Fiction

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”

Kuhn book club rescheduled to Tuesday

For those of you who were missing the Structure of Scientific Revolutions book club yesterday, we’ll have to reschedule for Tuesday. Business intervened, including paper proofs and a Washington University Inaugural Symposium of the Center for Biological Systems Engineering at which I saw a video of a Pavlovian locust (yes, old grasshoppers learn new tricks – locusts can learn to associate new odors with food). And of course the ENCODE stuff came out.

So take the extra time to finish Kuhn’s book, and we’ll talk about chapters IX – XIII on Tuesday.

Quote of the day: Doolittle and Sapienza on selfish DNA

From “Selfish genes, the phenotype paradigm, and genome evolution,” W. Ford Doolittle & Carmen Sapiena, Nature 284:601-3 (1980), here is one of the original definitions of selfish DNA:

Non-phenotypic selection

What we propose here is that there are classes of DNA for which a ‘different kind of explanation’ may well be required. Natural selection does not operate on DNA only through organismal phenotype. Cells themselves are environments in which DNA sequences can replicate, mutate, and so evolve. Although DNA sequences which contribute to organismal phenotypic fitness or evolutionary adaptability indirectly increase their own chances of preservation, and may be maintained by classical phenotypic selection, the only selection pressure which DNAs experience directly is the pressure to survive within cells. If there are ways in which mutation can increase the probability of survival within these cells without effect on the organismal phenotype, then sequences whose only ‘function’ is self-preservation will inevitably arise and be maintained by what we call ‘non-phenotypic selection’. Furthermore, if it can be shown that a given gene (region of DNA) or class of genes (regions) has evolved a strategy which increases its probability of survival within cells, then no additional (phenotypic) explanation for its origin or continued existence is required.

The truly provocative and disturbing stuff in ENCODE

… at least from my perspective. I’ll now stop ranting about the hype and media coverage of ENOCDE, and extend my compliments to the consortium for an amazingly well-coordinated effort to achieve an impressive level of consistency and quality for such a large consortium. Whatever else you might want to say about the idea of ENCODE, you cannot say that ENCODE was poorly executed.

It’s time to get into the interesting stuff – what’s actually in the papers. Among the results I’ve been most eagerly awaiting to see in print are the DNase hypersensitivity results now published in Thurman et al. (Nature 489, 75–82 (06 September 2012) doi:10.1038/nature11232)

Why is this interesting? Because it raises provocative and possibly disturbing questions regarding how transcription factors navigate and read out information from the genome. Continue reading “The truly provocative and disturbing stuff in ENCODE”

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”