Simulating life

I think this is a big deal: Stanford and Venter Institute Simulate an Entire Organism With Software (

Molecular biology has been running hot and cold in the headlines department. We decoded the human genome! BUT we don’t really understand it. Systems biology will lead to dramatic new treatments for diseases! BUT the diseases that most of us have, well we still don’t understand those well enough for systems biology to make one tiny tater tot’s worth of difference. Craig Venter synthesized a living organism! BUT actually he didn’t. It was more like xeroxing with style. Which is worth something, but it’s not exactly Frankensteiny.

But things are happening faster than ever in molecular biology (which is saying a lot), and some of it feels like a real turning point in our understanding of how life works. First of all, obtaining data is getting easier and easier. New sequencing technologies can (reportedly) sequence a human genome for less than $1000. And if you can sequence a healthy human cheaply, then you can sequence aberrant tumor cells just as cheaply. And this technique is, well and truly, leading to some remarkable success stories.

And now, with Venter’s latest announcement, we are at the beginnings of simulating life. As Richard Feynman said, “What I cannot create, I do not understand.” Biology up to this point has been mostly an exercise of poking at a black box: when I do X, then Y happens. But I have no idea why Y happens. And if I do Z instead of X, I have no real insight into what might happen. Simulation opens a new world of understanding living mechanism rather than living cause and effect. Again, it won’t lead quickly to miracle cures. But it is a big deal.

As the Times article reports,

The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules — including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.

“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds.”

This is as good an indication as any of how much room our computers have to improve. One tiny microbe can do what 128 computers are required to do, spewing 500 Mb along the way. To quote Feynman once again, “There’s plenty of room at the bottom.”