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.

Science Caturday: I’m a cil? No. Uracil.

Continue reading “Science Caturday: I’m a cil? No. Uracil.”

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”

For Sale; 1 Vote, Price: “Science” or Best Offer

This was originally a guest post at Sheril Kirshenbaum’s Culture of Science. In light of Romney’s “defeat” of Obama in the Science Debate, I thought it was worth revisiting, as some of the points may help explain why Obama’s responses seemed to reflect minimal time, effort, and concern with the debate.

Perhaps my earliest political memory came from presidential election coverage in, let’s call it 1988. I distinctly recall a portion of a news segment on voting experiences in which a Catholic priest described the ghosts of his ancestors compelling him to vote a straight Democratic ticket.

I think about that priest when I hear the “why is the Republican party anti-science?” discussion and I wonder. While we can debate whether Republicans are more anti-science than Democrats[1], the rhetoric of Republican politicians is certainly more hostile toward science and the scientific establishment. When confronted with such statements about your colleagues, yourself, and your field of work, it is natural to wonder “why?”. Continue reading “For Sale; 1 Vote, Price: “Science” or Best Offer”