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 by far the most complete topological alignments of biological networks to date. We 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.