Well, break is over so of course I have a bad cold. But back to blogging.
If you haven’t seen it yet, there is an in-depth article in the NYT Magazine about Sebastian Seung and his plan to map the…a…well, some connectome:
What the field needed, Tank said, was a computer program that could trace them automatically — a way to map the brain’s connections by the millions, opening a new area of scientific discovery. For Seung to tackle the problem, though, it would mean abandoning the work that had propelled him to the top of his discipline in favor of a highly speculative engineering project.
Back in Cambridge, Seung spoke with two of his graduate students, who, like everyone else in the lab, thought the idea was terrible. Over the next few weeks, as the three of them talked and argued, Seung became convinced that the Heidelberg project was bound to be more interesting, and ultimately less risky, than continuing with the theoretical work he had lost faith in. “Make sure your passports are ready,” he said finally. “We are going to Germany next month.”
…At the end of a long day, Seung and I sat on a pair of blue bar stools, sharing some peanuts and sipping on beers at Janelia’s in-house watering hole. Seung was feeling daunted. Even at Janelia, which plans to spend roughly $50 million and has some of the best tool-builders on the planet, the connectome of a fruit fly looks to be a decade away. A fruit fly! Will he live to see the first human connectome? “It could be possible,” he said, “if we assume that I exercise and eat right.”
And then there’s this fact about the C. elegans connectome that I did not know:
Brenner settled on the worm C. elegans for simplicity’s sake; it is small and prospers in a laboratory dish. The results were published in 1986 at book length, taking over the entirety of Philosophical Transactions of the Royal Society of London, science’s oldest journal, the outlet for a young Isaac Newton. Biologists were electrified and still sometimes refer to that 340-page edition of the journal as “the book.”
I would love to see a copy of that issue. As a worm researcher I’ll agree with Eve Marder: “If we want to understand the brain,” Marder says, “the connectome is absolutely necessary and completely insufficient.”
The big stumbling block here is probably not the technology but the manpower required to stitch together images and do the tracing. I get the impression that a lot of people thought that Sebastian Seung would be able to figure out the machine vision and really automate the tracing. It’s not at all a knock on him that he couldn’t, in the end: the problem is just too hard. But it’s not clear to me how this scales up without it.