A hypothesis for the origins and evolution of protein complexes. Gene duplication with conservation of protein interactions is frequent . Self-interactions (homomeric interactions) have special structural properties (see text for details) that are conserved into the duplicated interaction between paralogous proteins (light-dark interaction). Interactions between paralogous proteins are more versatile functionally and structurally, and are systematically selected for in evolution. These interactions are central in the establishment and evolution of clusters in PINs and protein complexes.