Why is Jerry Coyne blocking scientific discussion?

This is a guest blog by Ben Allen of the Plektix blog. I don’t agree entirely with it; Jerry Coyne has the right to police his blog in any way he chooses, and I also don’t find Nowak’s critique of inclusive fitness theory at all convincing — so I’m actually more on Coyne’s side on this issue! But Ben works with Nowak, has some expertise on this subject, and was not allowed to express himself on Coyne’s blog, so I offered him an opportunity to say his piece here.

Posting it here is not an endorsement of Ben’s position, but he has reasonable arguments that I’m willing to give an airing.

PZ Myers

I imagine most readers of this blog are familiar with Jerry Coyne.  If not, he’s a prominent biologist and atheist who maintains the blog Why Evolution is True.   And apparently, he has taken to blocking commenters who disagree with him, even over substantive scientific issues. 

First, some background: A conflict has been brewing over how to model the evolution of social behavior.  At issue is a method called inclusive fitness theory, which emphasizes the role of genetic relatedness between interacting organisms.  In 2011, Martin Nowak, Corina Tarnita, and EO Wilson (hereafter, NTW) published an article arguing that inclusive fitness is a mathematically limited method, and that the role of relatedness has been overemphasized in the evolution of worker castes in social insects. 

NTW’s article generated a strong response—most famously, a letter signed by 137 prominent researchers (also some talking bears).  I happen to agree with Nowak, and have collaborated with him and Wilson on follow-up work.  However, intelligent people can disagree on this issue, and I trust that science will sort it out.

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Icelanders are awesome

seljalandsfoss

It’s not just because they are lucky enough to live in one of the most spectacular landscapes on the planet. It’s also because they’re great model organisms, guinea pigs — the zebrafish of humanity. They represent a small, isolated population with a well-documented history and excellent medical records, so they’re just the people you might want to do in-depth genetic studies on.

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Does this cause cancer?

Broccoli

I get asked that question so often. My usual answer is, “I don’t know, probably.” (It’s also a good answer if they ask, “does this prevent cancer?”) That’s safe to say, because just about anything can be found associated with cancer, if you look hard enough. I’ve read enough papers to know that if you can find a study accusing a food to be of the devil, you can find another one saying it’s angelic. And there will probably be some feckless mass media organ screaming CAUSE or CURE.

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Public Service Announcement: Don’t experiment on your own eyeballs

chlorine6

Photosensitizers are chemicals that absorb photons and use that energy to promote electrons to higher energy states, and typically those activated electrons produce free radicals that react with other substances in the cell. That’s not particularly scary: your eyes contain proteins, opsins, and a chemical, retinal, that also absorb photons and use the energy to cause a conformational change in retinal. But photosensitizers are also used in cancer therapy. Load up a tumor with photosensitizers, then shine a laser on it, and all the free radicals do a bang-up job of destroying the cells, exactly as you want.

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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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