The Triple Helix of university–industry–government relations is compared with alternative models for explaining the current research system in its social contexts. Communications and negotiations between institutional partners generate an overlay that increasingly reorganizes the underlying arrangements. The institutional layer can be considered as the retention mechanism of a developing system. For example, the national organization of the system of innovation has historically been important in determining competition. Reorganizations across industrial sectors and nation states, however, are induced by new technologies (biotechnology, ICT). The consequent transformations can be analyzed in terms of (neo-)evolutionary mechanisms. University research may function increasingly as a locus in the “laboratory” of such knowledge-intensive network transitions.