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The virtual cell that simulates life - possible applications for bioremediation clean up

Computer viruses are old news, but virtual bacteria might just be the future of biology. 

Because on processors at Stanford University a simulation of the entire bacterium Mycoplasma genitalium, its DNA, and the constituents of its single cell is allowing biologists to tease apart the way life works.

 "The public hear about a new 'cancer gene' being discovered, or a new 'Alzheimer's gene'. You hear about these all the time and you might wonder, with all these discoveries, where are the cures to those complex diseases?," explains co-author Prof Markus Covert, speaking to BBC Radio 4's Material World.

"The answer is that cancer is not a one-gene problem. There are thousands of factors interacting in very complicated ways and for us to understand a disease like that, we really need to start going back and trying to see if we can understand the whole cell," continues Prof Covert.

It was the complexity of the cell, the drive to understand how DNA leads to interactions with other molecules, and gaining the ability to explain how things can go wrong, that led the Stanford researchers to recreate M. genitalium's whole life-cycle digitally.

"We've done a lot at the single gene level, but if we really want to take discovery to the next level, we're going to need to consider systems: biological networks and pathways, and to do that we need a computational framework."

Prof Covert and his colleagues have been experimenting with live M. genitalium bacteria for many years, but the simulation they have developed now allows them to see whether their virtual bacterium behaves in the same way as the living organisms, highlighting where gaps in the understanding of biological processes lie.

"When we see something wrong, it's basically pointing us to those little nooks and crannies that we don't really understand," Prof Covert said.

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