Before revision:  In this paper, we present the first alignments of large networks based solely upon detailed network topology, and demonstrate that both species phylogeny (the ``tree of life'') and detailed biological function of individual proteins can be extracted from topological comparisons of biological networks.
After revision:  In this paper, we present the first alignments of large networks based solely upon detailed network topology, and demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from topological comparisons of biological networks.