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

We’ve looked at some recent papers that take rate coding to task and argue that individual action potentials and their precise timing are important for signal processing in the brain. The recent paper “Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex” (published July 1, 2010 in Nature) provides support for rate coding in the cerebral cortex. In fact, it goes further and states that the evidence rules out the importance of individual spikes and their precise timing for signal processing in the cerebral cortex.

But what does that have to do with paper bloat? It just so happens that this six page paper has 42 pages of supplementary material associated with it. This is not unusual. At least not with the types of papers discussed in this blog. A six page paper discussed two days ago had 88 pages of supplementary material and a paper discussed last November had 177 pages of supplementary material. Each paper is becoming a book. How may we, with finite life spans, keep up?

The nature of the journal article must change. Supplementary material is a necessity but instead of each article sitting on top of a submerged mammoth sized text it will be linked (using Semantic Web technologies) with visualization, simulations, and other high-level methods for efficiently conveying large masses of information. Naturally, interested parties will be able to drill down into text and equations but they’ll be able to absorb a lot of the information by working with the products of the study rather than reading about them.

There is another reason to bring up the urgent need for a change in publishing practices in connection with this article. The authors base some of their work on an existing model that runs in NEURON and is available from the SenseLab ModelDB repository (Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995)). However, they did not publish their own models to an open repository. That’s the least they should have done to help readers evaluate their conclusions. They also should have published their physiological data to an open data repository.

Fundamentally, the team asked if small perturbations to spiking activity in cortical networks are amplified. Here’s what they found:

• A perturbation consisting of a single extra spike in one neuron produced approximately 28 additional spikes in its postsynaptic targets.
• A single spike in a neuron produced a detectable increase in firing rate in the local network.
• The observed amplification led to intrinsic, stimulus independent variations in membrane potential of the order of 2.2 to 4.5 millivolts.

Their conclusions hinge on the idea that a well defined perturbation resulted in stimulus independent variations in membrane potential. How can the one lead to the other but, on the other hand, be independent? The authors state that the variations in membrane potential “are pure noise, and so carry no information at all.” They go on to conclude “for the brain to perform reliable computations, it must either use a rate code, or generate very large, fast depolarizing events, such as those proposed by the theory of synfire chains.” They follow this up by recording activity from layer 5 pyramidal cells in somatosensory cortex. They state that their “findings are consistent with the idea that cortex is likely to use primarily a rate code.” They came to this conclusion because they found that large, fast depolarizing events were very rare.

The question of signal processing in the brain is fundamental so these conclusions warrant a careful look and deep consideration. Over the next couple of days I’ll post closer looks at the work reported in 48 pages of journal article and supplementary material.

Other related blog posts:

Neuronal Group Selection and Spike Timing Dependent Plasticity

A Taste of Neuroscience Papers in the Future

Spontaneously Formed Neuronal Groups Far Exceed the Number of Neurons