Biocurious is a weblog about biology, quantified.

Worm Art

by Andre on 30 September 2014

worm tracks on a agar plate


Bill Bialek on theory in the age of Big Data

by Andre on 29 September 2014

One of the most talked about Big Data projects in the last year or so has been the BRAIN initiative in the US. It was prompted by the incredible advances that are being made in technologies to image and manipulate neural activity optically. In its early incarnation, the goal was to record the activity of every neuron in a brain over time. With Billions and Billions of neurons, that would most assuredly lead to a big pile of data.

In this context, Bill Bialek was invited to give some opening remarks on the second day of the Kavli/NSF symposium on the BRAIN initiative. Thankfully, they’ve made the video available, and it’s one of the most lucid expositions of the essential role that theory still plays in the age of Big Data that I’ve seen. He focusses on the brain and behaviour, but you could substitute cell biology and ‘omics without changing the message much.

Highlights from the talk:

Data mining [is] popular. But miners know gold when the see it. Theory is the source of explicit, testable hypotheses about what is golden in your data.

He goes on to make an important related point: even the algorithms you choose to apply represent implicit hypotheses about the data and strongly shape what you will find and how you will be able to interpret it.

If the goal is to explain behaviour in terms of neurons, synapses, molecules… we run the risk that the ingredients of explanation will outstrip the phenomena we are trying to explain.

So we need better quantitative characterisations of behaviour and better theories of what brains do.

Suppose I showed you a movie of what 10 000 water molecules are doing as the wander around in that liquid. I do not believe that by staring at hours of that movie you would ever induce the concept of wet. You can’t just look! It doesn’t work.

Bigger data will never solve this.


Mapping the mind of a worm, one synapse at a time

by Andre on 25 June 2014

John White is a legendary scientist who, with Eileen Southgate, mapped the wiring diagram of the entire nervous system of C. elegans. This is still the only complete wiring diagram, or connectome, that we have for any animal, a feat that’s all the more impressive given that it was started in the early ’70s. And you can now read a first-person description of how it happened in the history section of WormBook:

Getting into the mind of a worm—a personal view

Check it out and read about the atmosphere at the LMB and the joys of working with early computers. The basic procedure for reconstructing the mind of a worm was to cut it into very thin sections, image them with an electron microscope, and then find the cells, processes, and synapses in consecutive sections to figure out what’s connected to what. Here’s an example of a series of images from Dan Bumbarger who works on worm connectomics today:

Reconstructing all the connections is not an easy task even if you don’t have to write your own graphics software, but in 1970, it was, shall we say, an ambitious PhD project. Which brings me to my favourite quote from the piece:

Sydney [Brenner] seemed a bit like the Pied Piper of Hamelin on speed—leading all who followed into the unknown.

This is the first worm history entry that’s actually written for and hosted on the WormBook site. I hope it’s the first of many.


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