tag:blogger.com,1999:blog-137103362012-01-20T16:51:45.144-05:00Enjoy a steamy dollop of neuroscience blogEric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.comBlogger571100tag:blogger.com,1999:blog-13710336.post-61628650251950863592012-01-20T16:46:00.002-05:002012-01-20T16:51:45.262-05:00

Given image stored in matrix M:%build the filter to convolve with the imageimFilt=fspecial('gaussian',10,10); %convolve themsmoothed=imfilter(K,imFilt,'symmetric','conv');

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-66909376865704622602011-11-07T22:29:00.002-05:002011-11-07T22:29:47.976-05:00

Alone in Bryan Research Building. Surprised there aren't more people here furiously getting their posters ready...

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-42150792021764825062011-07-25T10:57:00.004-04:002011-07-25T11:01:15.471-04:00

I haven't read it yet, so have no comments, just wanted to get the abstract here so I don't forget to take a closer look.ReferencePayandeh, Scheuer, Zheng, Catterall (2011) The crystal structure of a voltage-gated sodium channel. Nature 475: 353-358.Pubmed linkAbstractVoltage-gated sodium (NaV) channels initiate electrical signalling in excitable cells and are the molecular targets for drugs and

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-58128016775233111162011-04-19T11:15:00.010-04:002011-04-19T11:58:35.046-04:00

This post is for people who get the following error in Matlab when using the data acquisition toolbox:Warning: Port is not line configurable. All line directions on the port have been setIt took a long time for me to find an online discussion of this problem.This is a bit of a bummer, no independent control of lines allowed by drivers for most of the newer National Instruments data acquisition

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-16533362241188493742010-06-03T00:14:00.012-04:002010-08-12T15:08:24.526-04:00

Table of Contents of posts on consciousness.-------------------------------------Below you'll find a series of quotations that highlight the topics we have been discussing in the last nine posts. I chose them for their exceptional eloquence, clarity, and influence. They are not in chronological order, but are roughly in ascending order of specificity of the claims. This will be the final post in

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-37486946919923512022010-05-28T23:23:00.014-04:002010-05-29T17:40:04.699-04:00

Number fourteen in my series of posts on consciousness. Table of Contents is here.-------------------------------------The perception-as-interpretation view, summarized in the previous post, is useful as an informal ordinary-language hypothesis about consciousness. However, it is obviously a long shot from a final literal scientific theory. While it seems to be a useful way of speaking, I think

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-89209458378415150992010-05-07T16:54:00.015-04:002011-08-20T08:38:08.595-04:00

R (site here) is a great open-source environment for statistical analysis. But I'm a Matlab user. Luckily, it is pretty easy to run R code from Matlab. Since I just set it up in my Matlab environment, I thought I'd write out the recipe I followed. I have only done the following in Windows XP, and I used Matlab version 7.8. I think it will only work in Windows. It assumes you already have R and

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com13tag:blogger.com,1999:blog-13710336.post-40081435997319342002010-05-06T01:08:00.014-04:002010-08-18T11:09:37.374-04:00

Number thirteen in my series of posts on consciousness. Table of Contents is here.---------------------------While elaborating on the parallels between perception and language interpretation, we have unpacked many features of the nature of visual perception that should hold up even if we end up finding the view of perception-as-interpretation wanting. In this post I’ll briefly integrate the data

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com25tag:blogger.com,1999:blog-13710336.post-69915543019125709262010-04-25T22:32:00.019-04:002010-04-26T09:54:28.400-04:00

Number twelve in my series of posts on consciousness. Table of Contents is here.---------------------------In this continuation of the previous two posts, let’s finish examining the parallels between linguistic interpretation and visual perception. Recall the first three similarities were: 1) applicability of the content/vehicle distinction, 2) the possibility of ambiguity, and 3) sensitivity

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2tag:blogger.com,1999:blog-13710336.post-21072899841287226752010-04-01T22:58:00.014-04:002010-04-19T09:26:25.628-04:00

Eleventh in my series of posts on consciousness. Table of Contents is here.--------------------------------------------------In this sequel to the previous post, we continue to examine the similarities between linguistic interpretation and perception, and explore the hypothesis that perception is stimulus interpretation.2. BistabilityJust as we can experience bistable visual percepts, sentences

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-85258644508830995712010-03-16T23:10:00.019-04:002010-04-19T09:15:33.408-04:00

Number ten in my series of posts on consciousness. Table of Contents is here.------------------------------------There is a natural tendency to describe bistable perception as the experience of competing interpretations of a stimulus. This tendency can be partly explained by the many similarities between linguistic interpretation and visual perception. Let’s consider three such similarities in

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2tag:blogger.com,1999:blog-13710336.post-1476858564388321442010-03-07T21:52:00.016-05:002010-03-08T12:51:33.767-05:00

Number nine in my series of posts on consciousness. All the posts are indexed here.---------------------We are examining the popular view that visual perception is a form of interpretation, specifically the interpretation of a stimulus. We should start by determining what, exactly, is a stimulus?So as not to keep you waiting, the answer is roughly that a visual stimulus is visible light that is

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-20670230028319042002010-02-17T09:49:00.003-05:002010-02-17T09:59:46.095-05:00

I haven't forgotten that I owe further posts in the consciousness series. I've been working at them, but have so far held off on posting until their organization was clear in my mind. The material is finally coming together in a way I like. Upshot? I have at least six posts in the queue, but am still organizing them and polishing them. I expect to have the first out next week and then they will

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag: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-10678749511030342852009-08-16T16:30:00.019-04:002010-06-03T00:50:43.990-04:00

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.com8tag: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.com4tag: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.com0tag:blogger.com,1999:blog-13710336.post-9736317773154393392008-01-09T17:57:00.001-05:002008-01-10T17:16:29.104-05:00

A new neuroscience journal, Frontiers in Neuroscience, recently published its inaugural issue. It has a big-name editorial board including Larry Abbot,Henry Markram, and my postdoctoral advisor Miguel Nicolelis.They are taking a big risk with this journal, as it flouts the traditional business model of the big journals like Nature (expensive, for profit journals with access only to paid

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com4tag:blogger.com,1999:blog-13710336.post-69317110974688791132007-12-18T23:47:00.002-05:002008-08-01T10:46:56.737-04:00

Developing Intelligence provided a helpful summary of a fun and thought provoking paper by Douglas and Martin that addresses the question, "What is the basic cortical computation?" with special emphasis on the traditional answer: whatever it is that a column does.The paper points out that the traditional functional columns (as seen in rat whisker barrels and ocular dominance columns in V1) don't

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2tag:blogger.com,1999:blog-13710336.post-28497500601694450702007-11-27T19:33:00.000-05:002007-11-28T16:40:46.814-05:00

It's been a few weeks since SFN. It was exceptionally well organized, San Diego was beautiful, and the scientific content overwhelming as always. Sebastian Seung's entertaining Presidential Lecture, The Once and Future Science of Neural Networks, generated more chatter and emotion than any I've seen at SFN.There were two main neuroscience topics in Seung's talk, the hedonistic synapse and

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com3tag:blogger.com,1999:blog-13710336.post-34475897654982830132007-11-15T15:40:00.000-05:002007-11-15T15:44:18.936-05:00

Grants are done, things are manageable so I'm firing this thing up again. I notice there are lots of new neuro-themed blogs out there so I'll have to update my sidebar over the next couple of weeks.As for the blog, my initial experiment gave a negative result: a blog isn't a good place to simply provide dry and detailed summaries of a technical work such as Hille's. My plan with that is to finish

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1162051312592185402006-10-28T12:01:00.000-04:002007-09-22T17:38:23.597-04:00

Mid-November 2007, this blog restarts in earnest.Still working on Boltzmann (well, experiments, really, but the Boltzmann is on my mind, and almost bloody done). Once I'm done with that, I'm gonna drastically change things here. Not sure how, yet!

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1157505125676763322006-09-05T21:04:00.000-04:002006-09-05T21:12:06.026-04:00

A new primer on combinatorics that I wrote can be found here. I first cover basic stuff like permutations and combinations. The rest focuses on a more complicated counting problem, which leads to a derivation of the multinomial coefficient. The multinomial coefficient is used in a lot of fields. For instance, it comes up in the derivation of the Boltzmann Distribution in statistical mechanics.As

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2tag:blogger.com,1999:blog-13710336.post-1156823259456939252006-08-28T23:38:00.000-04:002006-08-28T23:47:39.840-04:00

A PDF of my newly revised probability theory refresher can be downloaded here. It is a quick and informal review of concepts from elementary probability theory. If you want to refresh your memory about what a prior probability is, what marginal probabilities are, or what Bayes' Theorem is, it provides such information. As always, I am on the lookout for comments that will help me to improve

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1139180306803100522006-07-19T17:56:00.000-04:002006-07-19T15:58:56.703-04:00

I expect to kick-start this puppy in August. I've been working on a grant, which I will send out next week.As for the Boltzmann distribution post I keep promising, I luckily found a good text, Statistical Mechanics: A Survival Guide. It has an amazingly clear description of its derivation, and answers exactly the questions I was getting confused about (and this was after consulting a few

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com7tag:blogger.com,1999:blog-13710336.post-1129228235791083302005-10-13T14:30:00.000-04:002006-01-06T15:32:21.493-05:00

Those of us who got our neuroscience education recently are raised from our undergraduate days to think that electric currents across the membrane are generated from ion flow through pores in channels. While true, it is easy to lose appreciation for the fact that this was hard-fought knowledge and things could have turned out quite differently. There are multiple lines of converging evidence for

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com5tag:blogger.com,1999:blog-13710336.post-1126555352860493542005-09-28T15:54:00.000-04:002005-10-13T15:58:32.383-04:00

Chapter 2 outlined the HH theory of the action potential: when they wrote their papers, nobody yet knew the mechanism of current flow. From p 61:A variety of mechanisms were considered possible. These included permeation in a homogeneous membrane, binding and migration along charged sites, passage on carriers, and flow through pores...The pathways might be formed from phospholipid or from protein

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1126554837880010902005-09-21T03:50:00.000-04:002006-07-19T04:05:53.380-04:00

Hille discusses gating currents at greater length in later chapters (e.g., Chapters 9, 12, 18, and 19), and explicitly draws on the material on the topic in Chapter 2, so the topic deserves a few bits of bandwidth.In the HH model of voltage-gated Na and K channels, there exist gating particles that respond to changes in voltage and thereby switch between the permissive and nonpermissive state (

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1125431186267380802005-08-30T15:45:00.000-04:002005-09-11T10:28:57.716-04:00

The previous post summarized, in somewhat qualitative terms, the HH model of the action potential. Since then, I've written up a supplement to Hille's description of their quantitative model. It is available online as HH_Conduct.pdf. It goes into a little more detail than Hille about their model. For instance, it motivates and describes the equation they actually used to fit their gk data, thus

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1124139014858234522005-08-29T16:46:00.000-04:002005-09-05T16:01:46.003-04:00

Last updated 9/01/05 In Chapter 2, Hille provides an excellent summary of the classical period in biophysics that culminated in the Hodgkin-Huxley papers of 1952. This work on the squid giant axon laid the foundation for thinking about the electrical properties of neurons that has persisted to this day.Bernstein's membrane hypothesisBernstein was the first physiologist to hypothesize that

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1124762174984707232005-08-22T21:42:00.000-04:002005-08-27T12:04:31.030-04:00

Since first-order differential equations come up fairly frequently in Hille (and in any quantitative treatment of anything in science, for that matter), I have spent the past week writing up a primer on first-order differential equations for neuroscientists. You can download it here: Diff_Eq.pdf. Here is the introductory section of the manuscript: Ordinary first-order differential equations

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1123793192846577622005-08-11T16:39:00.001-04:002008-03-31T11:35:21.729-04:00

I am presently writing a summary of Chapter 2 of ICEM. I'll be on vacation the next few days, but it should be done sometime next week. While I am happy to continue providing summaries, I'd be even happier if anybody out there wants to contribute one! If interested, please email me to let me know what chapter and we'll discuss the details.

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com0tag:blogger.com,1999:blog-13710336.post-1123594018386441932005-08-09T08:53:00.000-04:002005-08-09T10:20:02.533-04:00

David Touretzky and others at CMU have written a great program called HHsim: Graphical Hodgkin-Huxley Simulator. If you want to actually tinker with the variables discussed in Chapters 1 and 2 of ICEM, it provides a great platform. It is a stand-alone implementation of the HH model of the squid giant axon (Chapter 2 of ICEM), and lets you play around with current clamp, voltage clamp, and tweak

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1122588387896061462005-08-08T18:04:00.000-04:002006-12-02T15:14:35.800-05:00

In this introductory chapter Hille provides general background that should serve as a useful reference for the rest of the book. Even in this chapter, the density of the book, and its sometimes frustrating tendency to quickly make arcane technical points as if they were part of the average neuroscientist's working knowledge, is exhibited in full force (see pages 14-15 for his derivation of the

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com3tag:blogger.com,1999:blog-13710336.post-1122589005523110402005-07-28T18:06:00.000-04:002005-10-13T15:48:38.826-04:00

Here is the Table of Contents of Ion Channels of Excitable Membranes. As we progress through the book, to each chapter title below will be added a link to the first post on that chapter. Chapter 1: IntroductionPart I: Description of ChannelsChapter 2: Classical biophysics of the squid giant axonChapter 3: The superfamily of voltage-gated channelsChapter 4: Voltage-gated calcium channels Chapter 5

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com1tag:blogger.com,1999:blog-13710336.post-1118891444863860702005-06-15T23:10:00.000-04:002005-07-28T17:59:48.923-04:00

Welcome to Neurochannels, a blog where we will discuss a series of neuroscience books. The idea of starting a blog was suggested, with ambiguous seriousness, by Serapio Baca. The first book will be the third edition of Bertil Hille's classic Ion Channels of Excitable Membranes. In fact, that book was the inspiration for the name of the blog. Expect the first post in early August.

Eric Thomsonhttp://www.blogger.com/profile/06847717704454032165noreply@blogger.com2