I ran across an interesting Wired article discussing the merits of a new initiative: Open Notebook Science. This touches directly on the issue I brought up in a previous post.

So what happens to all the research that doesn’t yield a dramatic outcome — or, worse, the opposite of what researchers had hoped? It ends up stuffed in some lab drawer. The result is a vast body of squandered knowledge that represents a waste of resources and a drag on scientific progress. This information — call it dark data — must be set free.

It is a well written article, if a bit short, expressing why all research data should be open for public viewing. The “dark data”, results that didn’t see the limelight because they failed, were inconclusive or even contrary to the project, may be important to other research labs. Your trash may be my treasure.

In a similar vein, there is a movement called Open Notebook Science, championed by chemist Jean-Claude Bradley. This movement wants to make science completely open and transparent by having scientists post their notebooks. Complete access to notebooks, including the good, bad and ugly, would move science forward at a striking pace. I happen to agree with them. It is the next revolution in science. That said, it might take years to happen. There are a lot of politics and money tied up in the current system. Old habits die hard.

More links:

Jean-Claude Bradley’s blog
UsefulChem on Open Notebook Science
Science in the Open - blog on Open Science
Jeremiah Faith’s Open Notebook - Graduate student at Boston University
Jeremiah’s thoughts on Open Science

I like art. I almost went to an art school to become an artist instead of an engineering school. I was at first intrigued by what my school was doing, a “BioArt” exhibit. Sounds interesting, doesn’t it?

From Lab Work to Artwork: New Initiative Melds Biotechnology, Electronic Art
“Through ongoing art and research exhibitions open to the public, the BioArt program at Rensselaer will bridge the arts and sciences in a very real, very tangible way,” said Kathy High, head of the Arts Department and one of three faculty members leading the initiative. “I see the discipline as a way to allow all people to feel involved and participate in the advances made in biotechnology.”

I was walking through the Biotech building on my way to lab when a large poster caught my eye (it was new). Stopping to take a look, I saw a poster of artist Caitlin Berrigan inserting a butterfly needle into a vein in her arm. Another section of the poster showed her dripping the freshly removed blood over a terrarium of dandelions. The caption detailed how she ate dandelion root as a medicine for Hepatitis C, so she was “giving back” to the dandelions by giving them some of her own blood.

That’s something that makes you stop and go “hmm”. Not a good “this is enlightening me”-hmm. More like a “how did they convince the administration this was a good idea”-hmm.

More details after the jump.

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Deep brain stimulation has been all the rage lately, but not all is not well in Candy Land.

For those who suffer with the debilitating symptoms of Parkinson’s disease, Deep Brain Stimulation offers relief from the tremors and rigidity that can’t be controlled by medicine. A particularly troublesome downside, though, is that these patients often exhibit compulsive behaviors that healthy people, and even those taking medication for Parkinson’s, can easily manage.

DBS implants affect the region of the brain called the subthalamic nucleus (STN), which also modulates decision-making.

“This particular area of the brain is needed for what’s called a ‘hold-your-horses’ signal,” Frank said. “When you’re making a difficult choice, with a conflict between two or more options, an adaptive response for your system to do is to say ‘Hold on for a second. I need to take a little more time to figure out which is the best option.’”

You may have a sweet tooth but your brain doesn’t. More specifically, your neurons don’t especially enjoy storing glycogen. Accumulation of glycogen in neurons leads to cell death. It was widely supported that neurons don’t synthesize or store their own glycogen. Rather, they rely on their neighboring glial cells for nutrition.

A new study in Nature Neuroscience shows that, contrary to popular belief, neurons are capable of synthesizing glycogen. This glycogen synthesis pathway is inhibited by a redundant mechanism. Their research shows that if this mechanism fails, glycogen accumulates in neurons and leads to cell death, a key feature in several neurodegenerative diseases.

Details about the study after the jump.
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If the brain were so simple we could understand it, we would be so simple we couldn’t. - Lyall Watson

Welcome to the 34th edition of the bi-weekly neuroscience carnival - Encephalon. We have an excellent lineup of submissions, all waiting for your eager eyes to pour over.

To start, Jake Young gives us a great analysis of a study of human and macaque visual cortices. Researchers dissected and analyzed the brains of people who had lost vision in one eye, comparing the results to a controlled study of macaques who had been partially blinded. It’s a fascinating analysis that also demonstrates the limits of fMRI.

Even if your vision is perfectly fine, your perception of the world may be drastically different. Mo highlights a rare condition where afflicted individuals perceive their body parts being disproportionately large. Micro- and Macrosomatognosia are typically associated with migraine sufferers. Lewis Carol may have suffered from migraine headaches and Microsomatognosia, which is why this condition is often called Alice in Wonderland Syndrome.

Chris Chatham discusses research suggesting that differences in executive functions are 99 percent genetic. What’s executive function? Check out this post for more details.

More from Chatham: a report arguing that handedness is a by-product of language. Since language is produced primarily in one hemisphere, that hemisphere also evolved to become dominant in motor control.

Cognitive Daily discusses one of the few controlled studies to address the relationship between religious belief and prosocial behavior. Does thinking about God make you act more “virtuously”? What if you’re an atheist? While this is a small study, it does offer some answers to those and other questions.

The Primate Diaries has a nice discussion of “male menopause”. Of course, in this case, the $99 question is “Does male menopause exist.” The short answer is “no.” For the long answer, you’ll need to read the whole thing.

If male menopause isn’t sexy enough for you, how about lap dancing? The Primate Diaries takes a detailed look at a study that’s generated a lot of press interest, as well as coverage from several blogs.

When a patient is in a vegetative state, doctors are often powerless to return them to consciousness. Invasive surgery has met with some success, but The Cortical Column has found an example of a much less traumatic approach: deep pressure stimulation. Could this approach work for others, or is this just a one-shot anomaly? You’ll have to read the post to find out what Brian thinks.

Luckily, you aren’t in a vegetative state. But you should probably give your brain a little workout so it doesn’t become a vegetable. SharpBrains offers its list of the top 50 brain teasers and games for adults. There are some all-time classics here — maybe you’ll spot one you haven’t seen before.

You might be shy, but does that mean you are sick? Jeremy Burman reviews a new book -
Shyness: How Normal Behavior Became a Sickness. Due to changes in diagnostic technique, commonplace social anxiety (such as fear of public speaking) might be enough to label you with a mental disorder.

That wraps up this issue of Encephalon. Thanks for reading, I hope you enjoyed it. The next issue will be hosted at The Primate Diaries two weeks from today (November 5)

Special thanks to Dave from Cognitive Daily. Dave helped me get this issue together so I could spend more time working on BPR3’s code.

Straight from the “That’s pretty cool” department, scientists in England are growing neurons from fat cells.

The Manchester technique uses stem cells - immature cells which the body naturally uses to create different tissue types. So far, the team has extracted stem cells from fat tissue taken from rats, and managed to coax the cells into becoming neurons - nerve cells - in the laboratory.

Their next step is to repeat this in stem cells from human fat, and then create a full replacement nerve, using a biodegradable “sheath” to surround it. This nerve-filled tube could then be implanted to re-join the ends of a severed nerve virtually anywhere in the body, they claim.

Shelly at Retrospectacle posted an interesting article highlighting a phenomena well known to computer scientists - collaboration. This particular article highlights the “SuperHappyDevHouse”, an all-day event where coders and designers come together and work on projects. Shelly points out that this type of collaboration, as well as other more technologically oriented collaboration, is rarely exhibited by other science fields.

Coders are accustomed to communicating with each other must faster than their laboratory-bound counterparts. Some Google employees told me how they are barraged each day with a phalanx of email. Countless message boards, IRC channels, and other sites allow isolated programmers to share with each other.
[...]
By comparison, there are few chemistry message boards, and only the open access journals like chemistry central include a comments thread alongside every peer-reviewed research paper, and conferences are dry, twice-a-year poster and powerpoint affairs.

I couldn’t agree more. As a computer science major turned biology major, I have seen both worlds. For the most part, I learned all my computer science skills through the internet. I taught myself languages, databases, programming concepts through internet tutorials. If I had questions, I asked on forums and newsgroups. IRC was available for instant communication with experts.

When I first migrated to biology, I attempted the same thing when I had questions. I looked for biology forums, in particular neuroscience. I looked for IRC channels and newsgroups, tutorials and guides. I looked but found nothing. Science blogs were interesting and satiated my desire to become fully immersed in science but offered little to answer specific questions I had.

Why is this? My thoughts about why after the jump.
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Watson has done it again. Yep, the “Watson and Crick” Watson. He is again insinuating that those of African descent are less intelligent than Westerners, due to genetics. Bolding is mine.

James Watson [...] drew widespread condemnation for comments he made ahead of his arrival in Britain today for a speaking tour at venues including the Science Museum in London.

The 79-year-old geneticist reopened the explosive debate about race and science in a newspaper interview in which he said Western policies towards African countries were wrongly based on an assumption that black people were as clever as their white counterparts when “testing” suggested the contrary. He claimed genes responsible for creating differences in human intelligence could be found within a decade.

The newly formed Equality and Human Rights Commission, successor to the Commission for Racial Equality, saidit was studying Dr Watson’s remarks “in full”. Dr Watson told The Sunday Times that he was “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”. He said there was a natural desire that all human beings should be equal but “people who have to deal with black employees find this not true”.

I don’t care what Watson has done to advance science, he is an opportunist, chauvinistic prick. Or he is a drama whore looking for attention. Considering he has written another book, soon to be published, I would say this publicity prank fits both profiles. Fitting to his elitist attitude, the title of the new book is “Avoid Boring People: Lessons Learned from a Scientific Life”.

Others are already slamming Watson’s opinion and I’m sure more will follow soon. I expect the blogosphere to light up over this one.

“These comments serve as a reminder of the attitudes which can still exists at the highest professional levels.”

This is some incredible work done by DARPA on prosthetics. Once they get the mechanics worked out it appears they will be moving on to complete control over prosthetics via a brain or nerve interface. Very exciting.

*Note: The reporter is terrible, just try to tune him out.

I’ve been attending a Neuroscience Journal Club here at RPI since last year. I find they are very informative and enjoyable For those of you that don’t know what a journal club is, I’ll let you in on a disappointing secret: they aren’t held in treehouses

More thoughts and my experience with presenting after the jump.
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