Google Base

Google has opened a new service called Google Base that allows you to upload, publish and index arbitrary data for free. Does this mean that scientists can now share their raw data simply by uploading it to Google Base, without bothering to store and webhost it themselves?

I checked out the site and it seems that Google explicitly invites all kinds of data, with no size restrictions. But I find it hard to believe that Google can really handle all the terrabytes of data that some labs generate; in fact, just a few days ago, I was thinking of uploading a few hundred gigs of imaging videos to Google Video; but do they really want that? On the other hand, maybe they can handle it; they are Google, after all.

So my opinion is that scientists should start submitting their data (all of it, including large raw data files) to Google Base until/unless Google says they changed their mind and they don’t want it.

Also, don’t forget about subject-specific databases like neurodatabase.org; until the bright future of ubiquitous cross-database integration arrives, it will be easier to search for things with the subject-specific databases, provided that enough people use the same ones.

See this news article in Nature for more commentary.

Web page tracking optical control of neural activity

A web page tracking work on the optical control of neural activity, “focusing on the applications of channelrhodopsin-2.”

Maintained by Edward Boyden (the first author on the September optical stimulation paper in Nature that we previously talked about).

The central role of expectation in cognition

I think we’re undergoing somewhat of a slow revolution in the cognitive sciences. The field is slowly coming to focus on the central role of prior expectation in cognition.

Evidence that prior expectation has a large effect on the interpretation of sensory input is by no means new, but it seems to me that people are focusing on prior expectation more and more when they theorize about the mind. For example:

* The recent post about hypnosis and the Stroop effect (the nytimes article focuses on this aspect of the work)
* The fact that most of the connections between lower-order sensory areas and higher-order areas are feedback connections from the higher to the lower
* The fact that imagining a visual image causes activation in (see [1], there’s a bunch of followup studies to that one too)
* This may be just a rumor, but I’ve heard that it’s been demonstrated that when you saccade, that near the end of the interim period when you cannot see, your primary visual cortical cells start firing in the patterns corresponding to what you expect to see at the new location. Does anyone have a source for that (I’ll ask the person who told me if they have a citation)?
* Jeff Hawkins’s effort to make theories of the mind centered on prediction
* The current fad in Bayesian analysis in theoretical cognitive science (which provides a mathematical framework for computing probabilities which take into account both prior expectation and evidence)

I don’t mean to imply that this potential paradigm shift is something that people are unaware of; indeed, Kosslyn, Hawkins and others have long been avid proponents of the view that sensory processing (as well as other aspects of cognition) is best understood as centered around prediction and prior expectation, not incoming sensory data.

[1] Kosslyn, S. M., Alpert, N. M., Thompson, W. L., Maljkovic, V., Weise, S. B., Chabris, C. F., Hamilton, S. E., Rauch, S. L., & Buonanno, F. S. (1993). Visual mental imagery activates topographically organized visual cortex: PET investigations. Journal of Cognitive Neuroscience, 5(3), 263–287.

Hypnosis can stop Stroop effect

This Is Your Brain Under Hypnosis – New York Times

Very interesting stuff. Subjects were hypnotized and told that days later they would see “gibberish” symbols printed in particular colors. They needed to report back the color that the word appeared in. (For those unfamiliar, the Stroop test presents color words, like “red”, in a different color, such as the word “red” written with green ink. People have difficulty reporting the color of the word because we have a strong need to “read” the written word.)

The highly hypnotizable subjects (grouped according to a predetermined measure) essentially showed no Stroop effect (ie. no reaction time difference with conflicting word and color). And, with fMRI, they saw that normally activated visual-reading areas were not activated in these subjects.

Timid Mice Made Daring by Removing One Gene

Timid Mice Made Daring by Removing One Gene – New York Times

Original article in Cell.

His Holiness's Message: Better living through chemicals (or electrodes)

His Holiness has spoken. He wants neuro-drugs to take and electrodes stuck in his brain so that he doesn’t have to spend hours meditating each day. (Enlightenment now!) If you want to do hot stuff, study physics or brain science. His interest in neuroscience stems from a long-standing interest in body hair. Yes, body hair. Americans need to figure their own way through this whole intelligent design business. Not all antidepressants are alike; for instance, the Dalai Lama is against tranquilizers. Definitely against tranquilizers. And, perhaps most surprisingly, His Holiness, approves of animal research — when it’s done right and with respect.

Minute-by-minute liveblog follows after the jump.

ok, we're in positon. bring on the lama!

We’ve made it through the abstruse and strangely ineffective security (in addition to the insane herd mentality of charging neuroscientists) and we’re ready to blog. Your spirtual enlightment will be forthcoming.

While you’re waiting, His Holiness has an op-ed piece in today’s NYT.

SfN 2005 Liveblogging!

In keeping with these fancy new Internet trends, I will attempt to do some live-blogging from the Society for Neuroscience 2005 Annual Meeting that starts on Saturday in DC. The big event is of course the Dalai Lama’s talk on Saturday afternoon. I give my poster presentation pretty early on (Sunday morning- D22, come say hi), so I should be able to find some time to blog.

I’ll be flying out tomorrow to DC but, until the real action kicks off, those curious can look at my itinerary. If you know of any cool posters/talks that I’ve missed, post it in the comments. My full itinerary after the jump…

Awesome new voltage-sensitive dye

New genetically encoded fluorescent voltage-sensitive dye.

Sensitivity: up to 34% change (delta F/F) per 100 mV.
Time constant: .5 ms.
Phototoxicity: You can expose the cells to light for up to 100 seconds without much effect; over 200 seconds is noticably damaging.
Location: specific to cell membranes.
Not ratiometric (if you don’t know what that is, don’t worry about it).

Excerpt from figure caption: “(c) Confocal section of HEK293 cells expressing eGFP-F shows very little fluorescence from internal membranes. Scale bar, 20 mum. (d) Fluorescence response (shown as colored increments) of hVOS on voltage pulses from -120 to +120 mV in steps of 20 mV from a holding potential of 0 mV in patch-clamped HEK293 cells.”

Baron Chanda, Rikard Blunck, Leonardo C Faria, Felix E Schweizer, Istvan Mody and Francisco Bezanilla. A hybrid approach to measuring electrical activity in genetically specified neurons. Nature Neuroscience 8, 1619 – 1626 (2005)

On the function of sleep

The nice NYT article on the function of sleep follows on a recent NIH-funded Nature insight series.

Some interesting facts from the NYT article:

• Sleep patterns vary greatly. Some bats sleep 20 hours, giraffes get 2 hours. (hmmm… grad students might be evolving toward giraffes…)
• Sleep has recently been found to occur in invertebrates too. Alternatively stated: Sleep is evolutionarily very old.
• Slow wave sleep is also found in fruit flies. (Divergence from fruit flies for us was 600 million years ago.)
• Some people don’t have any REM sleep. Behaviorally, these people are entirely normal, implying that it’s purpose might not be as obvious as one had thought (ie. required for the preservation of new memories, etc.)
• If you put a bunch of ducks in a row, the ones on the inside will sleep more often with both eyes closed. The ones on the outside will sleep with one eye open and it is (always?) the eye facing outward from the huddle. They are able to “sleep” one half of the brain at a time and, apparently, this sleeping with one eye open was lost in higher mammalian evolution. Fascinating.