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 just going to leave this here…

It’s the Foodbabe opining on body chemistry.

For several years, I’ve started my day with warm lemon water and cayenne pepper. Lemon water is very alkaline and can stimulate the liver. It can change your taste buds so you don’t crave sugary foods, and instead crave alkaline ones like fruits and vegetables. The cayenne pepper has been proven to boost your metabolism. But both of those ingredients together strengthen the immune system. I’ve gotten fewer colds because of following this habit. An acidic body promotes disease and inflammation. I try to make my diet mostly alkaline. And with water, you want to make sure it’s not contaminated. Unfortunately, our water is contaminated with everything from chlorine to fluoride.

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Maybe there aren’t any serious scientists questioning junk DNA?

The NY Times has a response to responses to Carl Zimmer’s article on junk DNA, and there I am, the first citation. One thing that’s interesting is that it mentions that there were mixed reactions from readers, with some pushback to the idea…but all the scientists they quote on the subject have no problem at all with the concept of junk in our genome. I looked hard for a link to someone levying a solid criticism, and it ain’t there.

Maybe they don’t exist?