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The Informatics Axon News - Headlines

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Bradley Monk
24 October 2009

G Protein-Coupled Receptors (GPCRs) are my favorite receptors in the whole wide world. Their versatility allows them to modulate a remarkable number of signaling pathways; environmental stimuli such as light, neurotransmission signals like acetylcholine, and hormonal stimuli such as adrenaline, all utilize GPCRs.

GPCRs are localized on plasma membranes and activated by extracellular ligands. However, recent studies have opened the door to the possibility that GPCRs exist and function INSIDE the cell -- HOW THE! -- is exactly what a group from Washington University in St. Louis (a.k.a. Wash-U) has been exploring...

Flu Season
Jeremy Biane
2 April 2010

The common cold can strike at any time. But there are certain periods throughout the year where the prevalence of illness goes way up. These peak times usually come during the cold winter months, which over the years has led to much popular speculation about flu transmission. Probably the most repeated adage is that the cold weather somehow makes us susceptible to catching a cold (I mean, it is called a cold, after all). Braving the weather without the proper clothing??? Boy, you’ll get sick. Going outside with wet hair??? You’re done for. But with just a little knowledge of microbiology and physiology, the logic of these beliefs start to break down. Sure, protecting yourself from the elements is sound general advice, but just how the heck does exposure to the cold stir up those flu virons within?

Jeremy Biane
Published: 11 October 2009

BDNF - Waaay cooler than you

If there were a competition to determine the current biological “wonder molecule,” brain-derived neurotrophic factor, or BDNF, would have to be among the finalists. Found in the central nervous system, BDNF is important for neuronal growth and differentiation, and has been shown to stave off neurodegeneration in animal models of Alzheimers [1]. Additionally, BDNF appears to play a vital role in LTP and memory.

Back in 2007, Bekinschtein et al published an article in Neuron showing that maintenance of a recently acquired associative-learning task required BDNF synthesis 12 hours after learning [2]. That is, BDNF appeared to be necessary for consolidation of the memory, though not for its initial formation. But as the title of this post would indicate, this story can't all be about our hot little BDNF molecule. Dopamine has got to enter the picture somewhere, right?


Jeremy Biane
29 October 2009

One of the central predictions of the Hebbian theory of learning is that memories are stored by the same neurons that were engaged during learning. Although Hebb published his famous postulate, “neurons that fire together, wire together” (paraphrasing, of course) over 50 years ago, actual evidence that both learning and memory activate the same population of neurons has largely been absent. However, new research out of the Hausser lab lends experimental support to this long-standing assumption, and also indicates that reactivation of just a fraction of these “memory neurons” is enough to conjure up full blown recall.

Relocating the Engram
Jeremy Biane
Published: 7 August 2009

Over 50 years ago, the scientific community was introduced to the fascinating case of Henry Molaison. Better known to neuroscientists by the initials HM, Molaison lost function of his hippocampus following surgery for intractable seizures, rendering him unable to form any new (conscious) memories. But HM was not completely devoid of all memory. In fact, his memory for childhood events was rather keen, suggesting that this hippocampus structure may be necessary for forming new memories, but may not be where memories are ultimately stored. And thus began a massive effort to understand the role of the hippocampus
in memory formation and consolidation. Since then, a vast number of studies have strengthened the hypothesis of a time-limited role for the hippocampus in memory formation. The latest entry to this continuing saga comes from a study published in The Journal of Neuroscience

Advance Publication
Jeremy Biane
Published: 27 July 2009

There is an advertisement on the Science homepage that sometimes catches my eye. The little sliver of an ad features a couple of gummy-looking dudes all running to some elusive goal, with the caption underneath, “It’s not just what you know, but when you know it.” Hard to argue with that. In science, if you’re second, well you’re just replicating someone else’s work, and good luck getting that published. It doesn’t matter if your path was independent of that other guy, he’ll still get all the credit (just ask Alfred Russel Wallace). And it’s not just in science, but in business, medicine, and even mate selection (sorry gals, taken). So it seems that in this world there’s not just a premium on knowing, but knowing as soon as possible. And apparently this holds for monkeys staring at strange shapes while strapped to a chair.

Jeremy Biane
Published: 22 October 2009

The Morris Water Maze - Nightmare for rodent and graduate student alike

Love it or hate it, the Morris Water Maze is a staple of most memory labs. If you’re a PI, you probably love it. If you’re a graduate student, undergrad, technician, or any other poor soul that actually has to run the damn thing, it’s very likely that you hate it. And for how widespread its use is, it certainly has many, many limitations. Don’t tell me that plunking a rat into a pool of milky water, with an invisible platform as his only means for escape, is a pure measurement of spatial memory. The stress alone is enough to confound your measurement. But as the saying goes, it’s the worst test for spatial memory we have, except for every other test in existence…

A New Role For Vitamin P
Jeremy Biane
Published: 19 May 2009

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.

(Purge articles)
Mot Juste - Opinions

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On the existence of god
Jeremy Biane
Published: 24 March 2010

As a neuroscientist, I'm always a bit surprised when a colleague believes in god. I mean, our pursuit as neuroscientists is to uncover the rigid physical laws that govern biological processes and behavior, which doesn't leave much room for things like free will. Of course, the absence of free will doesn't preclude the existence of god, but it certainly challenges the commonly held view of a Judaea-Christian God. And while I don't feel it's my place to dissuade others from their beliefs, I am always receptive to a good debate.

Bradley Monk
6 December 2009

The following article is featured on the NPR news website, along with a nice little video.

Harald Wolf of the University of Ulm and his assistant Matthias Whittlinger proposed that ants have "pedometer-like" cells in their brains that count the steps they take.

How Do Ants Get Home?

Most ants get around by leaving smell trails on the forest floor that show other ants how to get home or to food. They squeeze the glands that cover their bodies; those glands release a scent, and the scents in combination create trails the other ants can follow.

That works in the forest, but it doesn't work in a desert. Deserts are sandy and when the wind blows, smells scatter.

So how do desert ants find their way home?

Is Free Will and Illusion?"

Published: July 5, 2009

A response evoked by (not directed at) this essay published in Nature <imagemap> Image:Freewilldoors.png|Click on a path!|thumb|110px|Choose a Path|

poly 68 296 72 303 145 287 72 262 44 256 51 271 39 267 21 257 32 256 44 256 LeftRoad poly 158 283 226 299 234 277 248 267 259 264 273 260 259 256 RightRoad

</imagemap> 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.

Joey Jo-Jo jr. Shabbadu
5 November 2009

One of the most prevalent assumptions we make as neuroscientists is that the brain communicates using a binary code. That is, either a neuron fires and action potential and passes along information (1), or it doesn’t (0). Presumably, information is stored and conveyed by the pattern of neurons that are active at any particular time. For example, let’s say we have 10 neurons. Neurons 2,4,6 and 8 represent an apple, while neurons 3,5,6 and 9 represent a banana. If 2,4,6,and 8 are active at one time point, we identify an apple. If only neurons 2,4 and 8 fire, we would probably still identify an apple due to activation of the entire network via pattern completion. But the point is a neuron has to fire an action potential in order to convey information. Right?

The Future of Science Publishing
Jeremy Biane
Published: 15 August 2009

Cell Press is currently showing off what it's calling "the article of the future" on it's website. By segregating out different parts of the "traditional" manuscript, linking them together in novel ways, and adding some promising new content, the publishing giant aspires to "take full advantage of online capabilities, allowing readers individualized entry points and routes through the content, while using the latest advances in visualization techniques." Does it work?

Four Color Theorem
Bradley Monk
Published: 5 October 2009

There are no borders of the same color!

Say that you’re asked to draw a map of the United States, but are only given four different colored crayons. There is only one rule, you can’t use the same color on two states that share a border. Think you could do it?

The truth is, three colors are adequate for most maps; with an additional fourth color, we can satisfy our rule for anything drawn onto a piece of paper. I didn’t believe it at first, so I tried to crack the theorem. Now I have no more crayons, and lots of abstract artwork.

Presendential Lecture - Origins of abstract knowledge: number and geometry
Jeremy Biane
17 October, 2009

How can you not be intrigued by the subject matter of this talk? Ok, I can see why some may not be, as even the mention of math sends many running for the aisles. But, I find it very intriguing. I mean, this is one of our uniquely human* characteristics that encompasses consciousness, logic, reason and a set of rules that appears be applicable to the entire physical (and perhaps metaphysical) world! So where the hell does one begin to study such a phenomenon as mathematical reasoning???

Computation for everyone!
Jeremy Biane
Published: 18 Oct. 2009

How do we learn to perfect our aim?

Let’s see…10am on a Sunday...5 hours sleep...Computational lecture...Presenter is British...

Hmmm, lots of factors were adding up to predict a very drab presentation (sorry, Brits. Although that accent sounds quite erudite and impressive, you can be a bit dry). But, holy crap, this lecture rocked! Daniel Wolpert does an excellent job of translating his very technical work to the masses, and gave probably the best synopsis of Baysian theory that I’ve ever heard (though I’m no statistician and can’t comment on it’s accuracy).

His conviction: brains evolved to enable interaction with the environment. Therefore, by understanding movement and how it is controlled, we can basically understand the brain.

(Purge articles)
Behavioral Conditioning via Channel Rhodopsin

Published: June 1, 2009

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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