Evolution of Metabolism in a Graph-based Toy-Universe

The graphs for metabolites have the atoms ofthe chemical molecule as vertices and chemicalbonds are represented by edges. The vertex la-bels indicate the atom-type (H,O,N,C), edge la-bels stand for the bond types ( , =, #).Since enzymes are modeled as graph rewrit-ing rules (consisting of a left rule and a rightrule), enzyme graphs are superimpositions oftwo graphs (substrate and product). Conse-quently, two labels for each edge are used.The connectivities between metabolites and en-zymes and therefor the metabolic network aremodeled in a bipartite labeled graph.