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

By Alexis C. Madrigal

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

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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.

This article available online at:

http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/