neurodudes

Some surprising and important news from Nature Biotechnology about a common technique in cellular imagining, fluorescence resonance energy transfer, or FRET. Specifically, it looks like ATP/Mg can significantly alter the FRET signal, which has commonly been used for looking at Ca, voltage, and various other binding interactions in neurons:

Given these findings, we predict that fluctuations in free or Mg2+-bound ATP will affect the signal output of most—if not all—CFP-YFP–based FRET indicators.

(more…)

Is science just about facts, or are theories and conceptualizations important too? Should we worry about having good theories, or do the facts pretty much give us everything we need to know. This article, entitled “Facts, concepts, and theories: The shape of psychology’s epistemic triangle“, discusses this issue for the field of Psychology, though its contents are also applicable to Neuroscience and AI.

If anyone has any additional questions that they think would be good to address at the workshop, leave it as a comment below.

NIPS 2006 Workshop Announcement and Call for Abstracts
Decoding the Neural Code

There is great interest in sensory coding. Studies of sensory coding typically involve recording from sensory neurons during stimulus presentation, and the investigators determine which aspects of the neuronal response are most informative about the stimulus. These studies are left with a decoding problem: are the discovered codes, sometimes quite exotic, ultimately used by the nervous system to guide behavior? In our one-day workshop, researchers with many different backgrounds will evaluate what we know about neuronal decoders and suggest new strategies, both experimental and computational, for addressing the decoding problem.

Each hour, five to six researchers will address a particular question for five minutes, followed by a half-hour discussion. We will also set aside time for a poster session.

We tentatively plan to include the following questions, and are soliciting additional questions from our speakers:
1. Which variables that encode stimuli are actually used to guide behavior?
2. What mechanisms do nervous systems use to decode encoded information?
3. Are motor systems better than sensory systems for experimentally addressing decoding?
4. What computational and experimental techniques are needed to address decoding? For instance, should information theory be used to address decoding as well as encoding?

For information on abstract submission, go to the workshop web site at http://science.ethomson.net/NIPS_workshop.html.

Netflix is offering $1 million dollars to anyone who can improve the accuracy of its recommender system by 10%. If no one wins, then whoever gets closest each year gets $50,000 (there are various additional rules of course). They are also providing a 100 million ratings from their service (anonymized) as a dataset.

Details here:

http://www.netflixprize.com/

Here is a paper showing that “whisker stimulation evokes increases in astrocytic cytosolic calcium (Ca2+) within the barrel cortex of adult mice”.

Wang X, Lou N, Xu Q, Tian GF, Peng WG, Han X, Kang J, Takano T, Nedergaard M.
Astrocytic Ca2+ signaling evoked by sensory stimulation in vivo.
Nat Neurosci. 2006 Jun;9(6):816-23.

As a psychology instructor who often teaches a course on cognitive psychology, I am intrigued with the whole nature/nurture debate and how it relates to neuropsychology. It seems like we look to nature when we want to control the universe, when we want to follow the rules of:

Predictability
words and music by Dr. BLT (c)2006

http://www.drblt.net/music/predict.mp3

and we turn to the supernatural when we are comfortable with the idea of not having to predict and control everything.

A New Psychology resource, community built by psychologists and trainees, to unify the body of psychology information in one place:

http://psychology.wikia.com/wiki/Main_Page

Check it out, and if it interests you, please contribute, or review it on your blog.

Tom Michael, Mostly Zen – site admin

Interesting developments — although, hard to know precisely how serious any of this is. Any thoughts from students, postdocs, others in the trenches at MIT (and willing to give perspective to the outside world)?

Boston Globe, July 15

“The professors, in a letter to MIT’s president, Susan Hockfield , accuse professor Susumu Tonegawa of intimidating Alla Karpova , “a brilliant young scientist,” saying that he would not mentor, interact, or collaborate with her if she took the job and that members of his research group would not work with her.”

Boston Globe, July 19

“In a letter responding to professors who wanted MIT to investigate the senior professor’s treatment of the job recruit, Hockfield said there are “ongoing tensions among MIT’s neuroscience entities” and suggested that the current situation “threatens ongoing disruption of the collegiality of our academic enterprise.” The letter, dated Monday, was obtained by the Globe.”

The Journal of Physiology announced in the editorial in their recent issue that they have completed digitizing their archive all the way back to 1878, and that it’s now open-accessible from PubMed Central here. (Though I note that the PMC archive, contrary to the statements of the editorial, only goes back to 1904 at the moment.

This is great news, as a lot of classic neuroscience papers were published J Physiol in the 50s and 60s, and previously their online archive had only gone back to 1997 or so. See for example, the Hodgkin and Huxley 1952 papers (1, 2, 3, 4) and Hubel and Wiesel 1962.

-John O’Leary

PLoS Biology: Scientific Illiteracy and the Partisan Takeover of Biology

On evolution:

One-third of Americans think evolution is “definitely false”; over half lean one way or another or aren’t sure. Only 14% expressed unequivocal support for evolution—a result Miller calls “shocking.”

On literacy:

“When I first started asking about DNA,” he says, “I used an open-ended question that asks, ‘If you saw the term DNA in a newspaper, would you have a clear understanding of what that means, a general sense of what it means, or not much idea?’” If respondents said they had a clear understanding, they would be asked to define DNA in their own words. “I got things like the ‘Dow Jones News Association,’” Miller says, laughing. “If you don’t know what DNA is, you can’t follow the stem-cell debate.”

And perhaps most important:

The era of nonpartisan science is gone, says Miller, who urges scientists and science educators to learn the rules of this new game and get behind moderate Republicans as well as Democrats to protect the practice and teaching of sound science. Given the partisan attack on evolution and stem-cell research, he thinks scientists need to learn more about how the political process works. They need to be willing to run for the school board, write $500 or even $5,000 checks to support moderate candidates, and defeat Christian right-wing candidates. “Scientists need to become involved in partisan politics and to oppose candidates who reject evolution or attack scientific research,” he says. “It takes time, money, and paying attention to the issues.”