Dance Your Ph.D Contest Accepting Entries

It's summertime, which means the call has gone out for submissions to the annual "Dance Your Ph.D." Contest. Eagle-eyed readers of Science may have noticed an oddly titled article in this weeks edition: Calling All Dancing Scientists (Bohannon J. Science (2010) 328(5983):1226). Not a treatise on scientists with lucrative alternative careers as breakdancers, this article was rather a call for submissions to the 2010 "Dance Your Ph.D" Contest.

This contest promotes the use of the human body in motion as a medium for communicating science, asking graduate students to compose interpretive dances that capture the spirit (and content) of their Ph.D research.

Researchers may submit their dances in categories defined by scientific field: Biology, Chemistry, Physics, and Social Sciences. Finalists will be chosen by an independent panel of judges, and screened at the Imagine Science Film Festival (NYC, Oct 15-24), when winners will be chosen. Winners of each category will be awarded a $500 cash prize; winning dances in each category will compete for the title of Best Ph.D Dance of All (and an additional $500).

To enter the contest, you need to:

1) Choreograph and film an interpretive dance depicting your Ph.D research

2) Post the video on Vimeo.com

3) Follow the directions for entering the contest at www.gonzolabs.org/dance

The submission deadline is September 1st.

Contestants and winners from 2009 can be viewed by searching Youtube.

Of special interest to Stanford students will be recent grad Jennifer Shieh's entry, entitled Adhesion and Endocytosis in Neuronal Migration.

Tom Südhof, 2 others win Kavli Prize in Neuroscience

Today the Norwegian Academy of Science and Letters announced the winners of the Kavli Prize, a 1 million dollar award given out every other year. All told, 3 prizes are awarded, one each for astrophysics, nanoscience, and neuroscience (for a total of $3 million dollars). An official description of the Kavli Prizes states that they "were set up to recognise outstanding scientific research, honour highly creative scientists, promote public understanding of scientists and their work and to encourage international scientific coop eration." The Kavli Prize in Neuroscience is specifically geared towards awarding "outstanding achievement in advancing our knowledge and understanding of the brain and nervous system, including molecular neuroscience, cellular neuroscience, systems neuroscience, neurogenetics, developmental neuroscience, cognitive neuroscience, computational neuroscience, and related facets of the brain and nervous system."

The Kavli Prize in Neuroscience was awarded to Stanford's Tom Südhof, as well as Richard H. Scheller (Genentech) and James E. Rothman (Yale) for their combined work on neurotransmission, in particular the molecular mechanisms of vesicle release.

The nanoscience prize will be shared by Donald M. Eigler (IBM's Almaden Research Center) and Nadrian C. Seeman (NYU). The astrophysics prize goes to Jerry Nelson (UC Santa Cruz), J. Roger P. Angel (U. Arizona) and Raymond N. Wilson (formerly of European Southern Observatory, Germany).

NY Times coverage of the announcement, as well as brief overviews of the awardees research.

The Kavli Prize Website.

DarWIN, not DarLOSE

Back in the early days of this blog, I wrote about an upcoming (at the time) movie about the writing and publication of Origin of the Species, by Charles Darwin. That movie, called Creation (discussed back in January), has since aired in theaters. This blog post is not about that movie.

It's about a fake movie, or more accurately a trailer for a fake movie, that presents a reinterpretation of the voyage of the Beagle and Darwin's struggle to publish his theories in the same vein as the recent re-imagining of Sherlock Holmes. Fans of both that film and of Darwin, will probably appreciate the trailer, which includes scenes where Darwin narrates a fight scene a la Robert Downey Jr. ("First use handkerchief to distract.... second, force feed Dodo egg.")

The best exchange prize is currently being vied for between two gems:

"How can a monkey turn into a man?" "The same way a hand can turn into a fist."

"My name is DarWIN, not DarLOSE!"

DARWIN at FunnyorDie.com [Warning, some lines regarding "natural selection" and the "rise of man" are probably not meant for the ears of children.]

[Also, thanks to @AdamRutherford and @ScienceHsu for the tweet and re-tweet, respectively.]

Snakes. On a Plane. In Free-fall.

At this point in my blogging career, my love of wacky research has become increasingly well documented (see previous posts The Best of Pubmed Part 1 and Part 2). So I'm sure no one will be surprised to learn of my excitement when I learned about the following study via the lovely bloggers over at ScienceBlogs. The research in question was published in April 2005 in the journal Zoology under the title of "The Behavioral Responses of Amphibians and Reptiles to Microgravity on Parabolic Flights". Translation: Snakes. On a plane. In freefall.

In honor of the course in the Neurobiology of Behavior that so many Neuroscience students are currently working hard to survive, below is a synopsis of this most epic paper. I highly encourage rampant discussion in the comments section regarding the scientific merit of this paper, as well as proposed projects to expand upon its findings.

Note: It turns out there is a rich literature regarding the behavioral consequences of exposure to altered gravity. My favorite segment of this literature? The one concerned with the "Gravitational Neurobiology of Fish".

1) What was the main question asked in the paper?

How do various reptiles and amphibians react when abruptly exposed to microgravity? Specifically, what behavioral patterns can be observed, and how do these patterns compare to behavior observed in normal gravity? Really, the question is how various species perceive "weightlessness".

2) What (novel) techniques were used?

Researchers collected 53 animals from 23 species of amphibians and reptiles. They were loaded onto a large plane (a Falcon 20), and taken on a parabolic flight. Researchers filmed the behavior of the animals, presumably which simultaneously quoting prolifically from Samuel L. Jackson.

3) What results were reported?

Depending on the animal, the researchers report different behavioral responses to sudden weightlessness. Some animals didn't move much, others attempted to righten themselves, producing large whole-body motions as if they were trying to grab at something to stabilize themselves. Still other animals displayed a behavior described in the paper as "a skydiving posture". As for the snakes, several species moved around until they'd knotted their tails around their bodies, at which point they settled down.

4) What conclusions did the authors draw from their results, and were these conclusions justified?

The researchers seemed most interested in the behavior exhibited by the snake species that knotted their tails around their bodies. To paraphrase the paper, the fact that these snakes became quiescent after successfully knotting themselves up suggests that the snakes brains gives higher priority to proprioceptive input from their body over the vestibular input. The authors suggest that the proprioceptive input was being interpreted by the snake as stable physical contact, and not as a self-embrace occurring during free-fall. Which is interesting, as it suggests a hierarchy for the interpretation of competing information from sensory modalities. However, being not an expert in the responses of animals to microgravity, I can't really comment on the validity of the results - but I highly encourage any experts in snake-chucking that we have in the audience to leave comments.

The best part of this paper is inevitably the figures, which include pictures and 10 fantastic videos of animals in the middle of their free-fall behavior, most notably the self-embracing snake (see video below).

Wassersug et al. The Behavioral Responses of Amphibians and Reptiles to Microgravity on Parabolic Flights. Zoology (Jena). 2005: 108(2): 107-20.

The hysterical original post on Science Blogs, by Jason G. Goldman, who makes all the required Indian Jones and Snakes on a Plane jokes.

Rapping about Evolution

It's hard to find good music about science. I imagine a distinct lack of successful songwriters interested in creating music discussing high level scientific ideas. When someone does attempt a composition, the science is usually a shallow shadow of a lecture half remembered from high school biology class. Either that, or the composition and lyricism of the song leaves listeners with memories of camp songs in elementary school ("Bats eat bugs, they don't eat people!"), and so will never make it to any playlist in your ipod*. Baba Brinkman is a glorious exception. Mr. Brinkman, who hails from Vancouver, is a hip-hop/rap artist (a self-described "rap troubadour"), who has composed some truly amazing songs about evolution. Mr. Brinkman's music excels on two fronts. His songs are well written, and would not sound out of place in a hip-hop playlist. Which is to say that these are no campfire songs. And his songs' science has been peer-reviewed by Mark Pallen, an evolutionary biologist and rap enthusiast at the University of Birmingham, so they are scientifically accurate.

Mr. Brinkman's website, Babasword, provides the following description of Mr. Brinkman's collection of evolutionary-themed music, which he performs during a show entitled The Rap Guide to Evolution.

“The Rap Guide to Evolution” explores the history and current understanding of Darwin’s theory, combining remixes of popular rap songs with storytelling rap/poems that cover Natural Selection, Artificial Selection, Sexual Selection, Group Selection, Unity of Common Descent, and Evolutionary Psychology. Dr. Pallen has vetted the entire script for scientific and historical accuracy, making it a powerful teaching tool as well as a laugh-out-loud entertainment experience. The show also engages directly with challenging questions about cultural evolution, asking the audience to imagine themselves as the environment and the performer as an organism undergoing a form of live adaptation.

Mr. Brinkman's show was recently reviewed by Olivia Judson over at the NYTimes, who describes The Rap Guide to Evolution as "a set of mini-lectures disguised as rap songs", containing lyrics that "are, for the most part, witty, sophisticated and scientifically accurate; and they lack the earnest defensiveness that sometimes haunts lectures on evolution."

Some examples, which along with Mr. Brinkman's other songs can be listened to online at CBC Radio:

A song entitled Natural Selection includes the following lyrics, set against a pulsing beat.

It's survival of the fittest but fitness is a tricky thing

It changes from place to place, from winter to spring

But the real question in this social scientific simile is heredity,

Whether we inherit our techniques from our predecessors, or invent them separately

But then we’re talking memes, and that’s a different thing,

Richard Dawkins can I get a proper definition please.

Later in the song,

See everybody’s always talking about “Do you believe in evolution” “Do you believe in creation”

No body believes in evolution.

You either understand evolution, or you don’t.

There’s nothing to believe.

Something to perceieve, feel, experience.

Do you believe in gravity?

Come on.

You can see it with your own eyes.

You just got to look.

And in another song, this one called DNA, Mr. Brinkman sings:

Yeah, this goes out to Watson and Crick.

Who discovered the twist.

Human genome project

And those who speed up the process

Like digital PCR

record a gene faster than a VCR

This is the future so you’d better get used to it.

This is what we are.

And in one of my favorite songs, Performance Feedback Revision, Mr. Brinkman describes how his songs are created, further expanding his lyrical description to describe the concept of descent-with-modification.

And sometimes people ask me: How does your show get written.

Like this: Performance. Feedback. Revision

…

And how do human’s beings ever learn to do anything

Like this: Performance. Feedback. Revision

And evolution is really just kind of an algorithm that goes

Like this: Performance. Feedback. Revision

So the genetic code of every living thing was written

Like this: Performance. Feedback. Revision

So the genes are like a text with a thousand pages

And revisions occur in the random changes that come from mutations.

And when they see the light, well that’s the performance, that’s the phenotype.

After spending some quality time listening to Mr. Brinkman's songs while analyzing patch-clamp recordings this Friday, I am, as Olivia Judson predicted "amused by the in-jokes and amazed by the erudition". Furthermore, I am astounded by the quality of the music, which will soon be making its debut in my iTunes playlist, because the best part about Mr. Brinkman's songs is that they are available for purchase, from both Amazon and the iTunes store.

*Or another other MP3 player.

[This post has been brought to you in honor of the Stanford Graduate Formal, from which I am recovering this morning, and which featured prodigious amounts of hip-hop/rap music, none of which mentioned descent-with-modification.]

A Brief Primer on Optogenetics

There's a joke running around the Stanford Neuroscience graduate program regarding the popularity of optogenetics. During the many seminars I have attended while at Stanford, I've noticed that the Neuroscience researchers are involved in a steamy love affair with optogenetics. In the current issue of NatureNews, a news feature explores the history of optogenetics, explains the bases of the technique, and generally serves as one big love letter from systems neuroscientists to the inventors of the technique, Stanford Professor Karl Deisseroth and now-MIT Professor Ed Boyden.

For those non-neuroscientists out there, optogenetics is a technique that uses light to activate or silence neurons with an intense level of specificity. In more scientific terms, optogenetics involves infecting target neurons with protein channels that open following illumination with particular wavelengths of light. Optogenetics was pioneered by Deisseroth and Boyden back in 2005, when they first inserted a light-sensitive channel from green algae, called channelrhodopsin-2 (ChR2), into cultured neurons. Since then, Deisseroth and Boyden have provided opto-tools to over 750 labs all over the world, and have created multiple light-sensitive channels that allow highly sophisticated activation and suppression of neuronal populations.

The Nature article includes an excellent description of the basic optogenetics technique that is perfectly suited as an introduction for both non-molecular biologists and non-neuroscientists. In addition, it interviews several eminent systems neuroscientists (including the highly-likable* UCSF Professor Loren Frank, and Stanford Professor Krishna Shenoy) who have utilized optogenetics to make significant advances in their research. All in all, well worth a read.

Neuroscience: Illuminating the Brain. by Lizzie Buchen:  NatureNews, Published online 5 May 2010 | Nature 465, 26-28 (2010) | doi:10.1038/465026a.

*Note: "Highly-likable" is based on my personal experience - arguably the funnest grad school interview I had was with Loren Frank.

The Best of PubMed (Part II)

Spring has finally arrived in Northern California, and with it course assignments that require me to spend an inordinate amount of time searching for literature on PubMed. As a reminder for readers not constantly reminded of the glories of this website, PubMed is a catalogue of papers published by most of the worlds biomedical journals. For those of you with long memories, back in February I wrote a post highlighting some of the more unusual papers included in the 19 million scientific citations listed by PubMed. Since that first post, I've been keeping my eyes peeling for more epic examples of odd research that has, by one way or another, seen the light of publication.

Without further ado, here are just a few of the papers I've found with subjects that range from humorous, awkward, to just plain weird. Some of these papers were discovered (and shared) by members of my Twitter community, some I actively searched for, and some I came across in the course of a legitimate literature search. As with Part 1, some of these papers are not suitable for work, children, or those with weak stomachs and vivid imaginations - these I have marked: consider yourself warned.

In the category of Additions, Fun Times and Feelings:

The Effects of Smoking and Abstinence on Experience of Happiness and Sadness in Response to Positively Valence, Negatively Valence, and Neutral Film Clips. Dawkins L, Acaster S and Powell JH. Addict Behav. 2007 Feb;32(2):425-31. Epub 2006 Jul 7.

Addition to indoor tanning: relation to anxiety, depression and substance use. Mosher CE, Danoff-Burg S. Arch Dermatol. 2010 Apr;146(4):412-7.

In the category of One Step Closer to Cylon-Human Relationships:

Can machines think? Interaction and perspective taking with robots investigated via fMRI. Krach S et al. PLoS One. 2008 Jul 9;3(7):e2597.

Social behavior of dogs enountering AIBO, an animal-like robot in a neutral and in a feeding situation. Kubinyi E et al. Behav Processes. 2004 Mar 31;65(3):231-9.

In the category of This Title Can't Accurately Reflect The Paper's Actual Subject, Right?

The half-tico, half-gringo robot. Finklea L. Pharos Alpha Omega Alpha Honor Med Soc. 2009 Spring;72(2):32-4.

In the category of Research that Should Totally be Used to Explain Human Behavior:

Social bonds between unrelated females increase reproductive success in feral horses. Cameron EZ, Setsaas TH, and Linklater WL. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13850-3. Epub 2009 Aug 10.

In the category of Unexpected, but in Retrospect Very Logical

The photic sneeze reflec as a risk factor to combat pilots. Breitenbach RA et al. Mil Med. 1993 Dec;158(12):806-9.

In the category of I Was Searching For Optic Flow Papers, And This is What Your Give Me?

Interactions of airflow oscillation, trachela inclination, and mucus elasticity significantly improve simulated cough clearance. Ragavan AJ, Evrensel CA, Krumpe P. Chest. 2010 Feb;137(2):355-61. Epub 2009 Sep 17.

In the category of You Can Read Minds? Okay, Prove It.

Telepathy in mental illness: deluge or delusion? Greyson B. J Nerv Ment Dis. 1977 Sep;165(3):184-200.

NOTE: This last paper may be disturbing to people. But its a perfect example of the mind-boggling research that corporations fund for publication, and has also received quite a bit of press in the last month. I would be remiss if I didn't include it.

Effect of an electronic control device exposure on a methamphetamine-intoxicated animal model. Dawes DM et al. Acad Emerg Med. 2010 Apr;17(4):436-43. [Also known as that study where people payed by TASER International gave sheep meth and then tased them]

And that's all for now. Until next time, happy PubMed-ing!

The Brain in the News

Over the past couple of weeks neuroscience has produced a couple of public-interest research stories. Normally, I'd be tempted to write blog posts about each one, however a combination of research and coursework has been severely constraining my time. So, here's a roundup of some of the culturally-relevant neuroscience research/stories that have appeared recently. To start us off, the NYTimes this week featured an article written by Olivia Judson (an evolutionary biologist and author of "Dr. Tatiana's Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex."). Dr. Judson writes about recent research which suggests that being overweight can cause damage to your brain. Specifically cited are two studies on the role of fat in increasing dementia risk (Whitmer et al 2008) and cognitive decline (Dahl et al 2009). Not mentioned in the article, but well worth reading and comtemplating is a recent Nature study by Paul Johnson and Paul Kenny that examined the possibility that obesity can induce addition-like dysfunction of reward systems (Dopamine D2 receptors in addition-like reward dysfuction and compulsive eating in obsese rats.)

Research published in Nature casts doubt on the efficacy of "brain-training" to increase cognitive function. Discussion of the findings and potential flaws in the study is ongoing. Read the article at Nature, and get a sense for the main complaints about the experimental design at NatureNews. A video segment on the research is also available from Nature - more writing/video on the research and its implications is probably provided by various news media groups (such as TIME).

MIT Physicists have modeled the ability of improvised explosive devices to generate electric fields in the skull. Their research suggests that the shock waves from explosions will interact with the skull bone to produce electric fields. The exact consequences of exposing the brain to such extraneous electricity are not known, though it seems likely that those effects would be detrimental if enough electricity was generated (and if the effects weren't overshadowed by the direct effect of the shockwave itself on the brain). The model is written up by MSNBC, and the research will be presented on April 20 at a Baltimore meeting of the Acoustical Society of America.

Over the the blogosphere, two excellent posts:

Over at LabSpaces, a discussion (and review of a recently published PLoS ONE article) over whether the pressures to publish are pushing researchers to produce positive, publishable results, thus decreasing the overall quality of scientific research. Do Pressures to Publish Increase Scientists' Bias?

Also, the always fantastic NeuroPhilosophy presents a blog post on how bodily motions influence memory and emotions. The post reviews research recently published in the journal Cognition, which "provides evidence of a causal link between motion and emotion, by showing that bodily movements influence the recollection of emotional memories, as well as the speed with which they are recalled." Bodily Motions Influence Memory and Emotions

Neuroscience 2010 Abstract Submission Opens

In case you haven't received one of many emails from the Society for Neuroscience, here's a reminder that abstract submission opened today. Submission will remain open thru May 5th. Submission of your abstract can be done online at the Neuroscience 2010 website. See the call for abstracts for submission information and guidelines.

Neuroscience 2010 will be held in San Diego from November 13-17, with more than 30,000 attendees expected. Special lectures will include talks by Martin Chalfie, Helen Mayberg, Okihide Hikosaka, Pawan Sinha, Hank Greely (on Neuroethics) and Glenn Close (regarding dialogues between neuroscience and society).

Cortical Stoke Alters Physiology of Reticular Thalamic Nucleus

An article published today in the Journal of Neuroscience describes the effect of focal cortical lesions on the reticular thalamic nucleus. The research, conducted by Stanford's Jeanne Paz (with help from Catherine Christian and Isabel Parada from the Huguenard and Prince labs) shows that focal cortical injuries significantly alter the intrinsic properties and synaptic excitability of inhibitory neurons in the reticular thalamus. Focal cortical injury (as will occur following a cortical stroke) causes significant damage or death to the thalamocortical relay neurons that project to the affected cortical area. Neurons of the inhibitory reticular thalamic nucleus general survive, although many of their corticothalamic and thalamocortical inputs are destroyed. The physiological properties of the survivng reticular neurons would determine recovery of the thalamocortical circuit after injury, however, these properties were not known.

The research by Jeanne and company looked at the physiology of inhibitory reticular thalamic neurons in a focal cortical stroke model. Their main findings are that:

1. Changes to reticular thalamic neuron physiology occur by the end of the first week after injury.
2. Reticular neurons have:
   • decreased membrane input resistance
   • reduced low-threshold calcium burst responses
   • weaker evoked excitatory synaptic responses.

Jeanne and company conclude that such alterations in excitability of the inhibitory neuronal population could lead to loss of inhibition of surviving relay nuclei, which would in turn increase the output of those surviving thalamocortical relay neurons, enhancing thalamocortical excitation and potentially facilitate recovery of thalamic and cortical sensory circuits. Of course, these enhancements in excitability could (and often do) go too far, inducing a hyper-excitable thalamocortical circuit. These results are therefore notable, in that they provide clues as to the pathophysiology of post-stroke epilepsy.

Focal Cortical Infarcts Alter Intrinsic Excitability and Synaptic Excitation in the Reticular Thalamic Nucleus. Jeanne T Paz, Catherine A Christian, Isabel Parada, David Prince and John Huguenard. J. Neuroscience. April 14, 2010, 30(15): 5465-5479.