Algorithmic Systems Biology

Throughout the history of computer science, leading researchers—including Turing, von Neumann, and Minsky—have looked to nature. This inspiration has often led to extraordinary results, some of which acknowledged biology even in their names: cellular automata, neural networks, and genetic algorithms, for example. Computing and biology have been converging ever more closely for the past two decades, but with a vision of computing as a resource for biology. The resulting field of bioinformatics addresses structural aspects of biology, and it has produced databases, pattern manipulation and comparison methods, search tools, and data-mining techniques.47, 48 Bioinformatics’ most notable and successful application so far has been the Human Genome Project, which was made possible by the selection of the correct abstraction for representing DNA (a language with a four-character alphabet). But things are now proceeding in the reverse direction as well. Biology is experiencing a heightening of interest in system dynamics by interpreting living organisms as information manipulators. It is thus moving toward “systems biology.”