Links post

• The Slaughterhouse Problem: is a resolution in sight? (Food Politics): Overview of the slaughterhouse problem by Marion Nestle, author of Food Politics and Safe Food. “The slaughterhouse problem is what small, local meat producers have to contend with when their animals are ready to be killed. The USDA licenses so few slaughterhouses, and the rules for establishing them are so onerous, that humanely raised (if that is the correct term) animals have to be trucked hundreds of miles to considerably less humane commercial facilities to be killed... Furthermore, appointments for slaughter must be made many months or years in advance — whether the animals are ready or not.”
  
• A Movable Beast: Four-legged mobile slaughter (cows, goats, sheep) comes to the northeast! There is now a mobile unit in New York state which can travel to farms to provide slaughter services (and helps mitigate the problem described by Nestle in the post I mentioned above). Until now, the only mobile units in the northeast were mobile poultry processors. The arrival of mobile four-legged slaughter units is a good thing — trucking animals long distances to slaughter is unpleasant for them. This also allows farmers more oversight over how their animals are treated on that important last day. Four-legged slaughter is more highly regulated than poultry slaughter; it is also technically more complicated because of chilling requirements. So this was a long time in coming.
• A good week for UK science journalism (despite one big fail) (Not Exactly Rocket Science). A bunch of links to interesting new ideas in science journalism.
• Seals do it with whiskers, sharks do it with noses – tracking fish with supersenses. Seals can sense the passage of fish in the water with their sensitive whiskers up to 35 seconds after the fish have swum by. I think this sort of insight into alternative senses is so interesting — what is it like to be able to perceive these sorts of things? How do their brains interpret it? Is it like sight is to us?
• fight club soap: Nature Publishing Group proposed a 400% price hike of the licensing fee paid to them by the University of California library system. The UC schools proposed boycotting NPG. Boycotting NPG would be a big deal; they publish some very important journals. This post, by a librarian, summarizes the situation well and has some interesting ideas about the broader impact it may have on academic journal pricing.
• Nutritional inadequacy: Is it what your pet’s having for dinner? (PetConnection): “So, ‘holistic’ pet food companies, don’t you have trade or industry groups? Create your own third-party-verified feeding trials the way the organic food industry created its own certification programs. That would be something to brag about.” Hear, hear.
• The Switches That Can Turn Mental Illness On and Off: Review of current state of research on how epigenetics affects stress. (Epigenetics is a set of mechanisms that affect how your DNA is accessed and read, and therefore how it is used. I have posted about it before.)

SICP: Scientific Information Communication Protocol

A researcher does a study. Based on the results, he comes to a conclusion about a small part of the nature of the universe. He writes up this conclusion and sends it to a journal. His peers review it and conclude that he did a good job in designing, implementing, and interpreting his study. In due time, his paper is published. The researcher receives non-monetary rewards.

Then, one day, he realizes he was wrong. He was wrong in a small way; he doesn't have to do another study to disprove his results, but he realizes he leapt to his conclusions. His interpretation was faulty. His data would have appeared different under very slightly changed study design. He considers letting his colleagues know. But how? He can't amend his paper. It is out there, as unrecallable as toothpaste from a tube. Does he write a letter to the journal? Post a note on his web page? Perhaps blog? None of these things will reach the audience that his original paper did.

It struck me, recently, how clumsy the communication protocol is that researchers use. They publish in papers. For a paper to change after publication, a slow, complicated machinery must be put in motion. A subsequent paper can show conflicting results. The paper can be found to be based on fraudulent data and recalled. Or the results can simply be gradually forgotten as science moves in a different direction. In any of these situations, change is slow.

I said as much in my bioethics class today. The professor asked, "How would you change things?" I suggested a world in which peer reviewed papers still existed, but another, non-peer-reviewed channel existed as well. We'd all know to take this channel's contents with a grain of salt, as they would be offered without the cautious filter of peer review. We would be much less likely to reference data from this channel in our papers. But we'd keep abreast of the conversations in it before completely trusting information we found in the more respectable peer-reviewed channel. It would be a place for back-and-forth, for something closer to a true conversation. (I've seen conversations in journals: two labs publishing an alternating series of articles that reference and refute each other, a dialog conducted over the course of years. It's rare and somewhat awestriking to observe.)

One of my classmates replied that I was idealistic. Well, sure. But this second channel is technologically very possible today. It might even currently be in the midst of developing out of the medium of science blogging. What would it take to start building mechanisms for allowing people to search it as easily as they currently use PubMed and Google Scholar to search the primary channel? I can't yet think where to start. Maybe all I need to do is sit back and wait, and watch the scientific information communication protocol evolve on its own, from its current clumsy elephantine form to something more nuanced and potentially graceful.