Still, Covert’s approach shows one way forward – the dawn of virtual biology. You could sequence a genome, construct a model or simulation, compare that to the real organism, work out the flaws in the model, and rectify those flaws with further experiments. Rinse and repeat. Eventually, you would have a zoo of models. If you have a new genome, start by comparing it to one of the existing simulations and work from there. It’s not quite the black box we envisaged, but it’s something.
If scientists are trying to find fungi or bacteria that can perform a specific job – say, clean up hazardous waste, to produce certain nutrients – it would be valuable to identify such organisms from their genomes alone. “We can use the sequencing to look for phenotypes that are relevant for our objective,” says Jens Nielsen from the Chalmers University of Technology in Sweden. And if that objective is to artificially design new life-forms, as folks like Craig Venter are trying to do, then prediction becomes essential, rather than wishful. “You’d worry about side effects and you’d want computational tools that can avoid them,” says Covert. “When we talk about rationally designing a new organism, you’d want to predict a phenotype.”
“I doubt we’d ever get to 100% prediction because biology is so variable,” says Nielsen. But Kruglyak adds, “I don’t think that in principle, there are any showstoppers that would make it impossible. It would just take a whole lot more work and continued technological development beyond what we can do today.”