The Informatics Axon News - Headlines
Behavioral Conditioning via Channel Rhodopsin
If you're in the field of neuroscience and for some crazy reason haven't heard of channel rhodopsin-2 (ChR2) yet, you will. It has got to be the sexiest contemporary technique available for the neuroscientist, and one that will probably earn Karl Deisseroth a trip to Stockholm in the future.
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A relatively new technique, ChR2 allows for tight temporal control of neuronal activation via photostimulation (optically mediated inhibition can be induced via the halorhodopsin channel).
The ability to express ChR2 in specific cell populations via genetic targeting make it far superior to previous methods of neuronal activation. Thus far, ChR2 has mainly been used to study synaptic plasticity and to map functional connections between neurons. However, a new paper in Science is the first to show that ChR2 activation can actually drive behavioral changes in adult mammals. While this result is not all that surprising, it's surely a milestone in the field and a harbinger for many, many studies to come.
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A New Role For Vitamin P
For many years, selective serotonin reuptake inhibitors (SSRIs) such as prozac have been a favorite pharmalogical treatment for depression. Interestingly, it is often weeks before the psychological effects of these drugs kick in, the cause of this lag period being largely unknown. As the drug is known to increase neurogenesis, some believe this upregulation of newborn cells - and the gradual time it takes for this process to occur - underlies the delayed impact of SSRIs.
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In a "recent" study published in Science magazine, Vetencourt et al throw another interpretation into the hat. Their study indicates that under the influence of fluoxetine (aka prozac), the adult rat visual cortex can undergo levels of reorganization typically restricted to developmental periods of life. This enhanced plasticity appears to be mediated by a decrease in inhibitory GABAergic signaling (an increase in which is known to coincide with the end of the critical period during development).
The authors ostensibly focus on how fluoxetine can be used as a treatment for amblyopia, a condition where signaling from one eye is impaired due to input deprivation during development. However, considering many systems-level plastic changes often take weeks to emerge in adult animals, one immediately wonders if reorganization of particular emotional areas of the brain might underlie the mood-enhancing effects of SSRIs (and, if so, why are such effects unipolar in their psychological consequence?). Or perhaps it is an overabundance of inhibitory signaling that SSRIs rectify?
Whatever the case, given what we already know about plasticity and sensory processing, you might consider increasing your vitamin p intake next time you take on a new language (I hear the side effects are pretty tolerable).
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Society for Neuroscience - Bonus Day!
Society for Neuroscience 2009 is holding it's annual conference in Chicago, IL on Oct. 17th - 21st. Attendees have three registration options...
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Advance
Members who renewed membership before Dec. 31, 2008 may register on Bonus Day, July 13. Advance member registration opens July 14 and advance non-member registration opens July 21. Advance registration closes Sept. 24. View registration fees.
Online Discount
SfN recommends online discount registration: Online registration includes a reduced fee and helps registrants avoid long lines at the annual meeting. Potential attendees can even register online at the convention center. Online discount registration opens Sept. 25 at midnight EDT and continues throughout the meeting. View registration fees.
In Line On-Site
Attendees can register on-site at the McCormick Place Campus. On-site, in-line registration opens Oct. 17 at 8 a.m. CDT. View registration fees.
Note: Once on-site, attendees can still take advantage of online discount registration.
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(Purge articles)
Is Free Will and Illusion?"
A response evoked by (not directed at) this essay published in Nature
Our editor for The Axon, Jeremy Biane had idea for an appropriate definition of free will, that I am going to expand upon. Let's call this theory the “everything being equal - test," which could be both the definition and the experiment. It’s my contention that it would prove humans, and probably most animals, have free will. But I can only imagine this two-option choice test that I have in mind, being anything other than theoretical. It would be one in which the test apparatus could adjust to balance the sum of the antecedent forces influencing the test-subject.
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Lets assume the test is measuring whether an entity can chose to go right or left. Suppose the apparatus is a round platform that slides along a track; a computer is used to control the movement of the platform. Say, a rock is released from 3 feet above the platform, at which point the computer calculates for the necessary adjustments, and a sliding mechanism puts the platform on the direct coordinates crunched by the computer. The rock should land on the sloped platform at end up in equilibrium.
At this point, it is likely that the rock is not going to make any further decision about which way it should go, so it is assumed that a rock does not have the ability to choose left over right, and thus does not have free will. If you could make a similar apparatus to test humans, one that takes into consideration a far greater number of antecedents beyond gravity, normal force, velocity, etc. - such as handedness, emotional state, hunger, tiredness, and every other minuscule physical property – then it might be possible to run an appropriate test. These factors could be entered into the computer controlling the round platform. The human participant jumps onto the platform from above but not before the computer slides the platform into place, at the exact point where all antecedent variables influencing a decision between left and right have been taken into consideration. This would create a sort of ultimate equilibrium between the participant and its two options. It is predicted that, if the human does not have the capacity of free will, it would be incapable of choosing left or right (much like the stone).
You can recognize this dilemma in home computers as a kernel error, followed by your operating system crashing. The human, I foresee, simply making a random choice. It is necessary that the choice be random, otherwise it would be predictable, and our computer program failed to consider every variable influencing the decision.
Things I’m left musing about:
We are affected by events that do not contact us physically. The manner by which a rock will tumble down a slope is determined by its shape; which was formed by forces of direct impact. Humans, however, have a shape that is formed by forces that I do not contend to be “direct impact.” A man gets stung by a bee (direct). A boy witnesses it (light), processes it (electrochemical), writes it down (symbolic), a friend reads it (light)(interpretive), and stores it (electrochemical). The bee sting took energy to directly impact the man, but that energy did not emit light, the light was simply available from other sources. Thus, the impact of the bee sting on the boy, was merely gleaned through symbolic interpretation – something uniquely intrinsic to this sole boy. The energy that went directly into the bee sting would not be useful for predicting future behavioral decisions of the boy (even though the boy is likely to have learned from the event, and to modulate his future behavior based on this information).
I think life, then consciousness, stems from the incalculable efficiency by which conscious organisms are able to transduce and manipulate energy. A complex understanding can be awakened by several photos borne before the human eye.
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It's Not the Ink!"
Do you want to post your Powerpoint lecture notes online? What about that colorful new figure from your most recently published article? If you post published material online, legally you must buy the copyright permissions; these run anywhere from $30 – $200 bucks per figure, graph, or table. It's somewhat ridiculous that we must buy back “our” own research after the publishing companies appropriate the rights to everything. Under this system, all the research and much of the funding eventually ends up in the hands of the publishing companies. Oh, and the $400/year price tag on some of these journals, it's not the ink.
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Over a month ago I was building a website to video-podcast the recorded lectures from the Research Society on Alcoholism's annual conference. While I was making the RSA Lecture Series website, my mentor/P.I. had me purchase the copyright permissions for the figures and graphs the presenters used on their Powerpoint slides so we could post them online. They weren't cheap; anywhere from $30 – $200 bucks a figure, graph, or table. I thought it was somewhat ridiculous that we were buying back “our” own research. I didn’t realize that publishing companies appropriate the rights to everything. My question is, why do we let them get away with this? Twenty years ago they provided a necessary service – the printing and distribution of research. Now we have the internet, and while they don’t have us in a strangle-hold anymore, we keep signing away the rights to our own research.
To fully grasp how senseless the current M.O. for publishing research is, I offer this useful analogy: We don’t mind paying taxes to build roads, because we need roads. The Tollway builds roads with their own money, and usually there is an incentive to use them instead of the ones that we’ve already purchased with our tax dollars. So we don’t mind paying the toll. It would be pretty crazy if we spent all this tax money building roads, have our state engineers inspect them for quality, and then just hand them over to the Tollway so they can collect a profit every time someone uses them. This is what we do with our research, though. We use grant money to pay for the subscriptions we need, and for journals that our university doesn’t subscribe to. Essentially, we conduct the research, write the articles, do the peer-review, and hand it all over to them...and then buy it back. It’s important to consider - under this system, much of the funding and all of the research eventually ends up in the hands of the publishing companies. Oh, and the 400 dollar a year price tag on some of these journals? It’s not the ink! TIME magazine costs around 15 dollars for 36 issues, and they actually pay their writers (unlike the Axon).
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(Purge articles)
Deus ex Machina - News Reel
The publishing process is broken. We aim to fix it.
“In this section, we discuss existing research into red-black trees, vacuum tubes, and courseware. On a similar note, recent work by Takahashi suggests a methodology for providing robust modalities, but does not offer an implementation...”
The above excerpt comes from a paper submitted by Philip Davis and Kent Anderson to The Open Information Science Journal. Confused by its meandering and seemingly bizarre prose? You should be. The entire paper was constructed using software that creates grammatically correct but nonsensical text. Surely such a paper would never be accepted for publication in a peer-reviewed journal, right? Wrong Read Full Article
Reconsidering the value of dopamine
Consult any introductory neuroscience text on the topic of dopamine, and you’re likely to be regaled with how dopaminergic neurons of the midbrain code for the rewarding value of a stimulus. According to this generally accepted theory, midbrain dopamine neurons increase their firing rate in response to a) an unexpected reward; or b) a stimulus that predicts delivery of reward. Conversely, firing rate decreases if reward is withheld following presentation of a reward-predicting stimulus. However, results regarding the response of dopamine neurons in response to adverse stimuli have been conflicting, with some experiments showing increased firing, and others depressed firing.
In this week’s edition of Nature, Matsumoto and Hikosaka recorded from distinct classes of dopaminergic neurons that differ based on their response to adverse stimuli – in essence showing that both response patterns exist in the same animal. Interestingly, these separate populations were largely confined to distinct regions of the midbrain, with neurons excited by adverse stimuli found mostly in the dorsolateral midbrain, while those inhibited by adverse stimuli located in ventromedial regions.
 While all recorded neurons showed the well-established excitatory response to rewarding stimuli, this study is the first concrete evidence that dopaminergic neurons of the midbrain may not be as homogenous as previously thought, with one population encoding the rewarding value of a stimulus (neurons excited by reward and inhibited by “punishment”), and the other seemingly encoding motivational salience (neurons excited by both rewarding and adverse stimuli).
The authors point out that, based on their location in the midbrain, these distinct populations of neurons can also be differentiated based on their primary target of axonal projection, which may account for the unique information carried by these different classes of neuron. It will also be interesting to see whether the type of dopamine receptors contacted differs by class.
Matsumoto and Hikosaka are quick to point out that their boundaries for classification are rather arbitrary, and in reality there probably exist many distinct categories based on more subtle criteria. Still, the study is a landmark in the reward signaling field, and provides fertile ground for reexamining our rather simple view of dopaminergic signaling.
Jeremy Biane 11 June 2009
| Expand to learn about major flaws in the current system for publishing research
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| Here's the gist
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| The first problem to understand about our current system for publishing research is that, in this system, all scientific discovery and most of the public tax dollars set-aside for research ends-up in the hands of the largest publishing companies.
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| The flow of information and tax dollars in scientific research looks like this (below). You see our current system, researchers are buying back their own published findings. This is why almost all information and public tax money quickly shifts to these companies who have created the journals of many research paradigms, practically flooding the market in order to accommodate as much free research as scientists are willing to give away.
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| The OneSci system (below) fixes this problem. Under the revised OneSci system, research funding gets recycled back into the research process because there is no need to subscribe to a pointless many journals. Published data is available for all types of research, making research publications easily searchable. This database should not simply include links to the article in some random journal, it should itself contain the actual research article. We should demand that it be mandatory for research funded by the tax dollars of citizens of the United States of American be published in an open-access repository that goes beyond PubMed linking, and it be free, forever!
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| Most journals owned by the largest publishing companies such as Wiley InterScience do give their authors the option of publishing their research under an open-access license. However, it cost around $3000 to do so (see picture below). This figure is not based on publishing costs; it is much higher. The figure is based on the approximate lost revenue generated by open-access publishing. Are you starting to understand how much money we are losing, and how much they are gaining?
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Dec 14 2011 10:28 am
for with low price for more