Permutation City - Greg Egan

Paul Durham keeps making Copies of himself: software simulations of his own brain and body which can be run in virtual reality, albeit seventeen times more slowly than real time. He wants them to be his guinea pigs for a set of experiments about the nature of artificial intelligence, time, and causality, but they keep changing their mind and baling out on him, shutting themselves down.
Maria Deluca is an Autoverse addict; she's unemployed and running out of money, but she can't stop wasting her time playing around with the cellular automaton known as the Autoverse, a virtual world that follows a simple set of mathematical rules as its "laws of physics".
Paul makes Maria a very strange offer: he asks her to design a seed for an entire virtual biosphere able to exist inside the Autoverse, modelled right down to the molecular level. The job will pay well, and will allow her to indulge her obsession. There has to be a catch, though, because such a seed would be useless without a simulation of the Autoverse large enough to allow the resulting biosphere to grow and flourish — a feat far beyond the capacity of all the computers in the world.