Okay, I’ve spent more time with the paper (and supplementary material) I first mentioned in my blog post three days ago (blog post “Coding in the Brain, Paper Bloat, and the Need to Change the Way Papers are Published“). The authors’ conclusion was that the “cortex is likely to use primarily a rate code.”

Note: The paper is titled “Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex” and was published July 1, 2010 in Nature. Be sure to also look at the 42 pages of supplementary material available here!

On my initial reading of the paper I thought I must have missed the new empirical and/or theoretical evidence that led to their conclusion. As it happens there is none. Their conclusion, which they hedge at several points, is based on a circular argument.

A perturbation was elicited by the researchers, consisting of a single extra spike in one neuron, that produced approximately 28 additional spikes in its postsynaptic targets. The spike produced a detectable increase in firing rate in the local network. The observed amplification was characterized by intrinsic variations in membrane potential on the order of 2.2 to 4.5 millivolts.

The authors concluded that since the additional spike resulted in stimulus independent variations in membrane potential, the variations in membrane potential “are pure noise, and so carry no information at all.” First note that the variations in membrane potential are stimulus independent because the perturbation – the spike elicited by the research team – is stimulus independent.

So really the argument comes down to the following:

• a) Neurons and neuronal circuits are exquisitely sensitive to signals.
• b) The brain, or at least the neocortex, is a noisy system.
• Therefore c) the brain, or neocortex, must be using rate coding.

This adds nothing to the question of what kind or kinds of coding are being used by the cerebral cortex. The same data could be used to make the following argument:

• a) Neurons and neuronal circuits are exquisitely sensitive to signals.
• b) The brain, or at least the neocortex, responds in a spatially and temporally precise manor to a single presynaptic spike.
• Therefore c) the brain, or neocortex, must be using temporal coding.

I’ll conclude with just one more point about the 42 pages of supplementary material and the fact that they did not publish their computational models or data to open online repositories.

The team investigated the relationship between postsynaptic currents and the probability of eliciting an extra spike by constructing a biophysically realistic model of a layer 5 pyramidal cell based on the existing model Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995) published in the SenseLab ModelDB repository. (The model and its associated paper are briefly reviewed in my blog post “Standard Neocortical Pyramidal Neuron Model.”) The authors made three changes to the existing model:

• The temperature was increased from 23 degrees centigrade to 37 degrees centigrade.
• All membrane conductance values were multiplied by 3.
• The passive reversal potential was set to -75 millivolts rather than -70 millivolts.

These changes are easy enough for the reader to make in the original model by Mainen and colleagues. However, the authors specified in the supplementary material that the way they mimicked neuron activity as it would be while the neuron was part of the brain in a living animal “by bombarding the model neuron with synaptic input sufficiently large to generate voltage fluctuations on the order of 3 millivolts at the soma and a firing rate of 2.6 Hertz.” How, exactly, did they set this up so that the reader may replicate their results?


Other related blog posts:

Coding in the Brain, Paper Bloat, and the Need to Change the Way Papers are Published

Standard Neocortical Pyramidal Neuron Model