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Mar. 28th, 2006

11:16 am - First simulation of a life form.

In the journal Structure (doi:10.1016/j.str.2005.11.014) five researchers from the University of Illinois, Urbana-Champaigne report "the first all atom simulation of an entire life form, satellite tobacco mosaic virus, albeit an extremely primitive one with an artificial nucleotide sequence." This is an exciting announcement; my own simulations, however, predict this story will undergo rapid inflation when exposed to journalism.

Tobacco mosaic virus is the reason many gardeners who smoke do not smoke in their garden. Humans, even smokers, cannot 'get' tobacco mosaic virus, but in smoking and handling tobacco products, they can 'give' tobacco mosaic virus to their plants -- particularly to tomato plants (tobacco and tomato are both in the Solanaceae or nightshade family.) One reason many researchers study the virus is the big plus that the virus poses no threat to researchers (tomato gardens aside). Another is that it is really easy for researchers to make more of it, whenever they want, from some infected plants. It is an extremely simple 'life form', apparently made up of 61 proteins and a pamphlet-sized string of RNA.

It appears that what they simulated was the structural properties of the viral body in water under different temperature conditions. You can think of it as being akin to a computational reconstruction of the collapse of the World Trade Center, that takes no account of the interactions of the people or stuff inside. Of course, this *is* a virus. Presumably there isn't a bunch of stuff inside, the virus's protein coat and RNA payload are pretty much all it has got. (There are illusions in the article to a single 'mystery protein', though; hopefully some reader expert in virology can tell us more about that.) And anything that helps us learn more about viruses is a good deal, because it certainly seems that most viruses are not on our side.

Still it should be recognized that the simulation of the internal workings of any whole organism -- all the activities and interactions of proteins and metabolites; all the internal work and signalling -- is still quite far off. According to one of the team members, Klaus Schulten, "it could still be a long time before scientists can simulate a digital dog wagging its tail." (quote from LiveScience.com) Understated humor. It will still be a long time before scientists can deeply simulate a protozoon wagging its flagellum...

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