Biology as Rules of Interaction

Magazine article, 2009

Interaction is characteristic of life, whether between an organism and its environment, or between different subsystems of an organism, and so on all the way down to molecular interactions. One computational abstraction of a biological system is a set of rules saying how each kind of molecule (or other agent) interacts with others; the states the system can reach via interactions can then be worked out. The number of states will be enormous in general, but because not all interactions are possible in every state, some rule sets give a limited state space and interesting behavior. States-and-interactions can model all of computation and concurrency. We note some ideas from computer science that enable our computational view of biology, and some areas to be studied.