Biocurious is a weblog about biology, quantified.

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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At the MRC Clinical Sciences Centre, Imperial College London

by Andre on 22 June 2014

I’ve spent the last few years doing my best to switch fields from single molecule biophysics to single animal biophysics. It’s been a challenge and a lot of fun. What’s especially exciting is that I’ve found myself in what I think is an interesting niche with growing interest. You might call it physics of behaviour, quantitative phenotyping, or perhaps just measuring behaviour.

I haven’t been blogging, but I’ve published what I think are some cool papers on an unsupervised method for detecting behavioural motifs and using direct feature extraction to identify subtle phenotypes in a large database of worm behaviour. There was also a brief and very stimulating foray into modelling flu evolution.

The most significant change is that I’ve started my own group at the MRC Clinical Sciences Centre at Imperial College London. I’m finally getting around to setting up the group’s website, which should soon appear at http://behave.csc.mrc.ac.uk/ and that was actually the impetus for this post. I just couldn’t bring myself to remove the link to Biocurious and I couldn’t bear the thought of a link to a blog that hasn’t been active in four years.

To any readers who never deleted us from their RSS feeds, thank you! I’ll see what I can do about posting a bit of quantitative biology and behavioural goodness.

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Does the D stand for debt?

by PhilipJ on 11 February 2010

Hooray! Jorge Cham of PHD Comics fame is coming to Toronto to give a lecture in the Faculty of Medicine!

Wait, what’s that? It costs $10 to see Jorge Cham’s talk? The same Jorge Cham who has become grad-school famous for joking about the plight of graduate students, most of whom are pretty short on spare cash?

And his talk is in the Faculty of Medicine, a faculty known far and wide as being fairly flush with money?

You’ll have to excuse me if I don’t rush to buy a ticket.

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