tag:blogger.com,1999:blog-137103362009-12-01T11:15:59.207-05:00Enjoy a steamy dollop of neuroscience blogEric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-13710336.post-46214975647535801212009-12-01T11:15:00.003-05:002009-12-01T11:15:59.329-05:00

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-69806635680284523792009-11-12T16:31:00.002-05:002009-11-12T16:32:50.158-05:00

In the rat thalamus, each whisker is represented by a chunk of tissue known as a 'barreloid'. The following image is Figure 12c from Haidarliu and Ahissar (2001) Size Gradients of Barreloids in the Rat Thalamus. It is a drawing of a large chunk of a rat's brain, with the location of the barreloids indicated by the cuboid shape:Where, exactly, are the barreloids? Perceptually the cube is bistable,

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-31195795555137983402009-11-09T14:23:00.003-05:002009-11-09T14:35:15.319-05:00

The barrel cortex roughly corresponds to the primary somatosensory cortex of rodents. It has become a standard model system for the study of cortical structure, function, and development. It's the system where I spend most of my life as a postdoc.Fox's book Barrel Cortex is the best overview that I have seen. It is unfortunately much too costly for out-of-pocket purchase (140 bucks), but your

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-23218452288358082992009-09-23T13:08:00.010-04:002009-09-23T21:59:55.098-04:00

Number eight in my series of posts on consciousness. All the posts are indexed here.----------------------------The previous two posts were a tour of ambiguous visual stimuli. Let's use these data to generate ideas about consciousness. Ideally, these ideas will lead to prediction-generating hypotheses about consciousness and clarify the explanatory target for neuroscience.Interpreting NeckerLet's

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com3tag:blogger.com,1999:blog-13710336.post-11626226364833323782009-09-10T22:21:00.053-04:002009-09-13T11:20:47.145-04:00

The seventh in my series of posts on consciousness. All the posts are indexed here.--------------------------------In this post we'll finish the tour, started in the previous post, of ambiguous figures.MotionSome of the most compelling illusions include things that move. Indeed, every time we watch a movie we succumb to the illusion of apparent motion. As we saw in the previous post, a rotating

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com7tag:blogger.com,1999:blog-13710336.post-75979732041213527892009-09-05T00:00:00.089-04:002009-09-07T22:41:59.808-04:00

The sixth in my series of posts on consciousness. All the posts are indexed here.Background: Why do we need psychology?Instead of just diving into the neural data, let's take some time to examine our target, consciousness. Clarifying the features of conscious awareness will provide a more precise target for our neuronal theories.The ultimate goal is to develop an understanding of consciousness at

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com11tag:blogger.com,1999:blog-13710336.post-14080497364566305572009-08-28T15:22:00.012-04:002009-08-30T17:39:18.999-04:00

To prepare the next installment in my series on consciousness research, I've been studying the Necker Cube. Little did I know that the cube was actually a prism that displays the main threads of perception research since 1833. An entire book could easily be written about this simple little line drawing. Despite all the research, there are still basic questions about the cube that haven't been

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-10678749511030342852009-08-16T16:30:00.011-04:002009-09-23T14:24:26.359-04:00

This post will be a permanent placeholder for links to all of my consciousness posts. It will expand until I finish posting on the topic.(1) Creationists take aim at consciousness: It begins by mentioning that the Creationists have finally discovered consciousness, but mostly focuses on why real scientists should take consciousness seriously as an object of (scientific) study.(2) Introducing Mr B

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1934698979822983282009-08-06T21:40:00.015-04:002009-08-07T14:19:08.489-04:00

An intermezzo in my series of consciousness posts. It's been a while since I posted, so I needed to oil the chain.In conversations about consciousness, the voice of the garden-variety biologist (Mr B) often gets drowned out. This is typically due to blithely confident philosopher-types who act as if the armchair provides just as much authority as the lab bench when it comes to consciousness.

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com3tag:blogger.com,1999:blog-13710336.post-68907822917271216082009-02-25T17:46:00.013-05:002009-02-27T10:02:47.033-05:00

A big day for systems neuroscience in Nature yesterday: three papers! Each paper investigates a different question about synaptic organization in the cortex. Not one paper created a new word ending in '-omics,' an auspicious sign.I superficially describe the main results from each paper below, with some figures.First, Brown and Hestrin bring us Intracortical circuits of pyramidal neurons reflect

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com4tag:blogger.com,1999:blog-13710336.post-17048565640903482392009-02-13T16:21:00.006-05:002009-02-14T09:29:51.396-05:00

Why not read something cool about evolutionary biology in honor of one of our greatest naturalists?Some good online reading:*Darwin: an online exhibit from the American Museum of Natural History.*15 Evolution Gems: beautiful piece put together by Nature discussing 15 papers published in their journals that provide striking examples of evolutionary thinking. Unfortunately no figures.*Evolution 101

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-11119060125019910202009-01-23T14:38:00.037-05:002009-08-16T16:30:07.786-04:00

Mr B has hypothesized that the brain is necessary and sufficient for conscious experience in humans (and probably other animals). The brain, unfortunately for Mr B, is an incredibly complex object. It consists of multiple interdependent processes that operate across different spatial and temporal scales.Spatial scales in the brainThe left-hand side of the figure below lists neuronal processes

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com5tag:blogger.com,1999:blog-13710336.post-64293209338691423262008-12-17T19:36:00.020-05:002009-03-31T17:00:56.808-04:00

Now we'll look at how your garden-variety biologist (Mr B) approaches the phenomenon of consciousness. For now, we'll have him treat it as he would any other biological phenomenon.Recall that Mr B takes a naturalistic, empirical approach to things. His first order of business is to determine what variables are correlated with conscious states (just as he did with action potential generation).

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com6tag:blogger.com,1999:blog-13710336.post-63814871383953332102008-12-09T13:10:00.008-05:002009-01-30T14:49:19.597-05:00

This is the second of my ongoing discussion of biological approaches to consciousness and creationists' recent attacks on such approaches. In this post I sketch a portrait of a fictional character, a garden-variety biologist we'll call 'Mr B.'Let's assume Mr B doesn't understand how neurons fire action potentials. In the rest of this post we'll examine his general approach to the problem. In a

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com7tag:blogger.com,1999:blog-13710336.post-4033347736863981132008-12-03T12:00:00.018-05:002008-12-17T20:46:22.418-05:00

A recent opinion piece in New Scientist, Creationists declare war over the brain, discusses the natural alignment between antievolutionists and those that think the human mind (in particular consciousness) is forever outside the explanatory reach of neuroscience. The topic of consciousness tends to bring out the nutballs, and creationism ties people's knickers in knots, so the article has

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com15tag:blogger.com,1999:blog-13710336.post-64436412333480812762008-10-28T13:34:00.006-04:002009-10-14T15:37:35.399-04:00

Gilles Laurent makes an excellent point in 23 Problems in Systems Neuroscience:Integrative neuroscience is an odd biological science. Whereas most biologists would now agree that living organisms share a common evolutionary heritage and that, as a consequence, much can be learned about complex systems by studying simpler ones, systems neuroscientists seem generally quite resistant to this

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com9tag:blogger.com,1999:blog-13710336.post-41681842967521391882008-08-12T14:01:00.024-04:002008-08-19T14:34:59.835-04:00

Cruising the web, I ran into the official Application for Enrollment in Scientology Religious Services. Surprisingly, it reads much more like a legal contract than a standard application. I found the paragraph that discusses psychiatry quite interesting. It certainly helps explain some of Tom Cruise's behavior. Below is the full paragraph, with comments on the main points.Scientology is

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-46736897398555783582008-07-23T13:06:00.009-04:002008-08-01T10:57:00.671-04:00

As shown below in EEG traces recorded during different stages of sleep, when we record neuronal activity on a large scale (either local field potentials or EEG signals) things do not typically look 'flat.' Since the signals recorded at these electrodes are basically the linear sum of the voltage fields generated by dendritic activation in a little sphere around the electrode, if the voltages from

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2tag:blogger.com,1999:blog-13710336.post-77443374636183407152008-07-02T16:28:00.008-04:002008-07-05T10:36:33.741-04:00

Anscombe's Quartet is a group of four data sets that provide a useful caution against blindly applying statistical methods to data. Each data set consists of ten x- and y-values such that the mean and variance of x and y, the correlation coefficient, regression line, and error of fit using the line are the same. But as you can see, they are clearly quite different data sets:The x- and y-values

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com4tag:blogger.com,1999:blog-13710336.post-25883153595299094452008-04-06T17:46:00.003-04:002008-04-15T12:45:29.953-04:00

Neurodudes, one of the first neuroscience blogs I ever saw, seems to have gone 404. Hopefully it is just temporary.Note added 4/14/08: it seems to be back up, with a sleek new look.

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-75432563806433143962008-03-31T23:35:00.010-04:002008-04-01T16:41:52.232-04:00

In the previous post, I briefly discussed the background and methods behind this paper by Ritt et al.. In this post I summarize and discuss the main results. I just noticed that Neuron added the apt banner, "What the rat's vibrissa tell the rat's brain" to the article.Ex vivo whiskersAs I discussed in the previous post, the resonance hypothesis is the claim that the resonance frequencies of

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-81463720955311709842008-03-07T17:50:00.025-05:002008-03-15T15:11:17.484-04:00

This is the first of a two-part post on the recent Neuron paper Embodied information processing: vibrissa mechanics and texture features shape micromotions in actively sensing rats by Jason Ritt and others in Christopher Moore's group. They provide a much-needed high-resolution look at the the movement of whiskers in freely-moving rats as they perform a discrimination task.Where's the

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-58021270797601465832008-02-25T15:20:00.013-05:002008-02-26T11:23:10.925-05:00

While the Blue Brain folk want to construct an incredibly detailed model of a single cortical column, a recent paper by Izhikevich and Edelman (Large-scale model of mammalian thalamocortical systems) reports on a less detailed model of the entire human thalamocortical system. Some of the details of their model (roughly from large-scale to lower scale) include:1. The cortical sheet's geometry was

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-8123429206245616802008-02-18T13:14:00.030-05:002008-03-12T14:51:40.628-04:00

Warning: this post isn't directly about neuroscience, but a mathematical tool that is used quite a bit by researchers.One of the most important operations in linear algebra is the singular value decomposition (SVD) of a matrix. Gilbert Strang calls the SVD the climax of his linear algebra course, while Andy Long says, "If you understand SVD, you understand linear algebra!" Indeed, it ties about a

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-69181136964235176602008-01-29T15:11:00.000-05:002008-01-29T15:22:39.523-05:00

Over at Nature's neuroscience group, I wrote up a summary and discussion of the excellent paper Spatiotemporal Dynamics of Cortical Sensorimotor Integration in Behaving Mice by by Ferezou et al.. You can find the original paper here, and my summary is here.Here is the conclusion paragraph of my summary:Ferezou et al. showed that subthreshold responses to whisker stimulation can be quite broadly

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0