A defense of ENCODE?

Dan Graur has snarled at the authors of a paper defending ENCODE. How could I then resist? I read the offending paper, and I have to say something that will weaken my own reputation as a snarling attack dog myself: it does make a few good points. But it’s mostly using some valid criticisms to defend an indefensible position.

Here’s the abstract.

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk.

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It’s money vs. principles

Museums (good museums, that is, not trashy sideshows like Ken Ham’s rubbish in Kentucky) have a real problem: they’re expensive to maintain. They aren’t dead piles of old bones, but are sites of active research, and they have to employ knowledgeable people to do the science that goes on there. It takes lots of money to keep one going.

But along comes a dilemma. Who has great big piles of money? Unfortunately, money tends to concentrate in the hands of assholes. And one thing many assholes would like to do is buy respectability and influence from more prestigious institutions…like museums. Some of the biggest, most assholish, ignorantest rich people are the Koch brothers, and the Koch brothers have been very generous in promoting their agenda by throwing money at museums.

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I’m happy to be a member of the “SJW Glittery hoo ha crowd”

Some guy named William Lehman has written an essay, Destroy the myth, destroy the culture, that starts off with a reasonable premise and then goes totally off the rails, in an entertainingly oblivious way, and as it’s crashing, invents a new label: the “SJW Glittery hoo ha crowd”. I love it, even though I don’t have a hoo ha, glittery or otherwise. I’m still happy to be associated with glittery hoo has fighting for social justice.

Anyway, the part I agree with is the importance of foundational myths to a culture — we need aspirational ideas, and something to give us a worthy cause. Where Lehman goes wrong is that he identifies with science fiction culture, and proceeds to regale us with a completely nonsensical vision of our foundational myths. Read and be astounded.

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Nerds are big business

This little fact surprised me.

Gen Con is currently Indianapolis Convention Center’s largest annual convention, bringing the city tens of millions of dollars in revenue. It was originally held in Lake Geneva, Wisconsin in the late 1960s and organized by none other than Gary Gygax, the father of modern role-playing games. Since then the event has morphed into a four-day event combining tabletop miniatures, board games, video games and live-action role-playing games. It regularly creates in excess of $50 million in revenue for the city of Indianapolis.

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Sometimes, the spam is kind of flattering

I just got sent a listing for a TWIN SCREW MOTOR YACHT WITH BOWTHRUSTER, only €185,000. It’s a little bit out of the price range of a college professor, even one who gets a little cash on the side from blogging, but it’s still nice that someone thinks I might be in the market for my very own personal yacht. If any of my readers is shopping for yachts right now, let me know and I can pass along the details.