C. Elegans: The Worm That No Computer Scientist Can Crack

Summary

The Santa Ana winds were already blowing hard when I ran the first worm simulation. I’m no hacker, but it was easy enough: Open a Terminal shell, paste some commands from GitHub, watch characters cascade down the screen. Just like in the movies. I was scanning the passing code for recognizable words—neuron, synapse—when a friend came to pick me up for dinner. “One sec,” I yelled from my office. “I’m just running a worm on my computer.”At the Korean restaurant, the energy was manic; the wind was bending palm trees at the waist and sending shopping carts skating across the parking lot. The atmosphere felt heightened and unreal, like a podcast at double speed. You’re doing, what, a cybercrime? my friend asked. Over the din, I tried to explain: No, not a worm like Stuxnet. A worm like Richard Scarry.By the time I got home it was dark, and the first sparks had already landed in Altadena. On my laptop, waiting for me in a volumetric pixel box, was the worm. Pointed at each end, it floated in a mist of particles, eerily stick-straight and motionless. It was, of course, not alive. Still, it looked deader than dead to me. “Bravo,” said Stephen Larson, when I reached him later that night. “You have achieved the ‘hello world’ state of the simulation.”Larson is a cofounder of OpenWorm, an open source software effort that has been trying, since 2011, to build a computer simulation of a microscopic nematode called Caenorhabditis elegans. His goal is nothing less than a digital twin of the real worm, accurate down to the molecule. If OpenWorm can manage this, it would be the first virtual animal—and an embodiment of all our knowledge not only about C. elegans, which is one of the most-studied animals in science, but about how brains interact with the world to produce behavior: the “holy grail,” as OpenWorm puts it, of systems biology.Unfortunately, they haven’t managed it. The simulation on my laptop takes data culled from experiments done with living worms and translates it into ...