Simulating Organisms

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Computers have been simulating specific cellular processes for years, but now a complete organism has been modeled thanks to the work of those at Stanford University and the J. Craig Venter Institute. Although only a single cell bacterium, a 128 cluster of computers take 10 hours to simulate a single division of the cell. Half a gigabyte of data is also generated during the division, raising the possibility of quantifying how much information a living thing contains.

The information on this bacterium was gleaned from over 900 scientific papers and is modeled down to the molecular level, including DNA. However the information describing the interactions between molecules is the primary focus and the most challenging to model.

Although the biological process itself represents a self-organizing system, humans imbue an intentional organizing structure on the biological system when defining it for a particular domain. In this case, simulating the system requires organizing its data in such a way that a computer can operate on the system in an efficient manner. This was accomplished by an insight to “break up the functionality of the cell into subgroups, which we could model individually, each with its own mathematics, and then to integrate these submodels together into a whole.”

By breaking down the complex system interactions into individual manageable resources, scientists formulated a model that accomplishes accurate results in a relatively short amount of time. Observations from this process have already generated new insights and biological discoveries. With new organizational models and faster computers, larger organisms are sure to be next.