Summaries and discussions of neuroscience texts
Model systems in systems neuroscience?
by noreply@blogger.com (Eric Thomson)28 Oct 2008 at 1:34 pm
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 simpelr ones, systems neuroscientists seem generally quite resistant to this ... read more
Scientology on psychiatry
by noreply@blogger.com (Eric Thomson)12 Aug 2008 at 2:01 pm
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 ... read more
What good is large-scale oscillatory activity?
by noreply@blogger.com (Eric Thomson)23 Jul 2008 at 1:06 pm
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 ... read more
Anscombe's Quartet
by noreply@blogger.com (Eric Thomson)2 Jul 2008 at 4:28 pm
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 ... read more
Dude, where's my 'dudes?
by noreply@blogger.com (Eric Thomson)6 Apr 2008 at 5:46 pm
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. ... read more
Getting intimate with rat whiskers (2): Ritt et al.
by noreply@blogger.com (Eric Thomson)31 Mar 2008 at 11:35 pm
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 whiskers As I discussed in the previous post, the resonance hypothesis is the claim that the resonance frequencies of ... read more
Getting intimate with rat whiskers (1): Ritt et al.
by noreply@blogger.com (Eric Thomson)7 Mar 2008 at 5:50 pm
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 ... read more
Large-scale thamamocortical model
by noreply@blogger.com (Eric Thomson)25 Feb 2008 at 3:20 pm
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 ... read more
Visualizing the SVD
by noreply@blogger.com (Eric Thomson)18 Feb 2008 at 1:14 pm
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 ... read more
Sensory processing in mouse motor cortex
by noreply@blogger.com (Eric Thomson)29 Jan 2008 at 3:11 pm
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 ... read more
Frontiers in Neuroscience
by noreply@blogger.com (Eric Thomson)9 Jan 2008 at 5:57 pm
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 ... read more
Cortical computation: some complications
by noreply@blogger.com (Eric Thomson)18 Dec 2007 at 11:47 pm
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) ... read more
Review of Seung's talk at SFN
by noreply@blogger.com (Eric Thomson)27 Nov 2007 at 7:33 pm
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 ... read more
Back in the swing
by noreply@blogger.com (Eric Thomson)15 Nov 2007 at 3:40 pm
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 ... read more
Update
by noreply@blogger.com (Eric Thomson)28 Oct 2006 at 12:01 pm
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! ... read more
How to count stuff
by noreply@blogger.com (Eric Thomson)5 Sep 2006 at 9:04 pm
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. ... read more
Probability refresher
by noreply@blogger.com (Eric Thomson)28 Aug 2006 at 11:38 pm
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 it. ... read more
I'm not dead, just writing a grant
by noreply@blogger.com (Eric Thomson)19 Jul 2006 at 5:56 pm
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 ... read more
Chapter 3 (2): Pore it on!
by noreply@blogger.com (Eric Thomson)13 Oct 2005 at 2:30 pm
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 ... read more
Chapter 3 (1): Toxins to the Rescue
by noreply@blogger.com (Eric Thomson)28 Sep 2005 at 3:54 pm
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 ... read more
Chapter 2 (3): Gating charges and gating currents
by noreply@blogger.com (Eric Thomson)21 Sep 2005 at 3:50 am
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 ( ... read more
Chapter 2 (2) : HH Conductance Model
by noreply@blogger.com (Eric Thomson)30 Aug 2005 at 3:45 pm
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 ... read more
Chapter 2 (1): Classical Biophysics of the Action Potential
by noreply@blogger.com (Eric Thomson)29 Aug 2005 at 4:46 pm
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 hypothesis Bernstein was the first physiologist to hypothesize that ... read more
Differential equations primer
by noreply@blogger.com (Eric Thomson)22 Aug 2005 at 9:42 pm
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 ... read more
Summaries update
by noreply@blogger.com (Eric Thomson)11 Aug 2005 at 4:39 pm
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. ... read more