A first: Scientists simulate entire organism

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A first: Scientists simulate entire organism

Article by: JOHN MARKOFF , New York Times
Updated: July 20, 2012 - 9:01 PM

Experts said the Stanford software simulation is a giant step toward developing computerized laboratories.

This undated handout image provided by the J. Craig Venter Institute shows negatively stained transmission electron micrographs of aggregated M. mycoides. Scientists announced a bold step Thursday in the enduring quest to create artificial life. They've produced a living cell powered by manmade DNA.

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PALO ALTO, CALIF. -- Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts.

The scientists and other experts said the work was a giant step toward developing computerized laboratories that could carry out complete experiments without the need for traditional instruments.

For medical researchers and drug designers, cellular models will be able to supplant experiments during the early stages of screening for new compounds. And for molecular biologists, models that are of sufficient accuracy will yield new understanding of basic biological principles.

The simulation of the complete life cycle of the pathogen, Mycoplasma genitalium, was presented Friday in the journal Cell. The scientists called it a "first draft" but added that the effort was the first time an entire organism had been modeled in such detail -- in this case, all of its 525 genes.

"Where I think our work is different is that we explicitly include all of the genes and every known gene function," team leader Markus W. Covert, assistant Stanford professor of bioengineering, wrote in an e-mail. "There's no one else out there who has been able to include more than a handful of functions or more than, say, one-third of the genes."

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 that are generated by cell processes.

M. genitalium, with its 525 genes, is far less complex, for example, than another more traditional bacterium used in traditional laboratory experiments, E. coli, which contains 4,288 genes. The researchers said that more complex cells would present significant challenges. Currently it takes about nine to 10 hours of computer time to simulate a single division of the smallest cell -- about the same time the cell takes to divide in its natural environment.

"The real question on our minds is: What happens when we bring this to a bigger organism, like E. coli, yeast or even eventually a human cell?" Covert said.

He noted that E. coli divides every 20 to 30 minutes and that the number of molecular interactions in E. coli is a much higher multiple, which would significantly extend the time required to run the simulation.