To Model the Simplest Microbe in the World, You Need 128 Computers

More

What a pathbreaking computer simulation tells us about the future of biotechnology.

cellmodules.jpg


Mycoplasma genitalium
has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes. M. genitalium's diminutive genome made it the first target for Stanford and J. Craig Venter Institute researchers who wanted to simulate an organism in software.

The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.

This has a direct bearing on one of the big questions about technology over the next 50 years: how successful will biotechnologies be? On the one hand, we've made tremendous strides in describing the molecular processes that power life. I'm not just talking about genomics, but  whole sets of other molecules and interactions (see: proteomics, metabolomics, epigenomics, transcriptomics). The new work stands as a testament to how far we've come. We can now simulate most known interactions within the cell: how the code of its DNA becomes proteins, how those proteins interact, and how the cell uses energy.

On the other hand, the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.

"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," lead scientist Covert told the New York Times. "I find this fact completely fascinating, because I don't know that anyone has ever asked how much data a living thing truly holds."

One cell. One division. Half a gig of data. Now figure that millions of bacteria could fit on the head of a pin and that many of them are an order of magnitude more complex than M. genitalium. Or ponder the idea that the human body is made up of 10 trillion (big, complex) human cells, plus about 90 or 100 trillion bacterial cells. That's about 100,000,000,000,000 cells in total. That'd take a lot of computers to model, eh?  If it were possible, that is.

It's not that I think this level of biological complexity makes it impervious to human engineering. Clearly, that's not the case. But, it does seem that it is very difficult to manipulate or optimize living systems without causing major, unintended consequences. We can only simulate one of the simplest cells in the world through years of research, but we change trillions of trillions of cells with ease.

Jump to comments
Presented by

Alexis C. Madrigal

Alexis Madrigal is a senior editor at The Atlantic, where he oversees the Technology Channel. He's the author of Powering the Dream: The History and Promise of Green Technology. More

The New York Observer calls Madrigal "for all intents and purposes, the perfect modern reporter." He co-founded Longshot magazine, a high-speed media experiment that garnered attention from The New York Times, The Wall Street Journal, and the BBC. While at Wired.com, he built Wired Science into one of the most popular blogs in the world. The site was nominated for best magazine blog by the MPA and best science Web site in the 2009 Webby Awards. He also co-founded Haiti ReWired, a groundbreaking community dedicated to the discussion of technology, infrastructure, and the future of Haiti.

He's spoken at Stanford, CalTech, Berkeley, SXSW, E3, and the National Renewable Energy Laboratory, and his writing was anthologized in Best Technology Writing 2010 (Yale University Press).

Madrigal is a visiting scholar at the University of California at Berkeley's Office for the History of Science and Technology. Born in Mexico City, he grew up in the exurbs north of Portland, Oregon, and now lives in Oakland.

Get Today's Top Stories in Your Inbox (preview)

'Stop Telling Women to Smile'

An artist's campaign to end sexual harassment on the streets of NYC.


Elsewhere on the web

Join the Discussion

After you comment, click Post. If you’re not already logged in you will be asked to log in or register. blog comments powered by Disqus

Video

Where Time Comes From

The clocks that coordinate your cellphone, GPS, and more

Video

Computer Vision Syndrome and You

Save your eyes. Take breaks.

Video

What Happens in 60 Seconds

Quantifying human activity around the world

Writers

Up
Down

More in Technology

Just In