Molecular systems engineering attempts to capture the complexity and emergent properties prevalent in biology. The uniqueness of this initiative relies on the combination of both chemical- and biological modules. In this approach, complex dynamic phenomena emerge as the result of the integration of molecular modules (molecular- or biological prosthetics) designed to interact in a programmed way with their complex environment. In this manner, it should be possible to create molecular factories and cellular systems whose properties are more than sum of the attributes of the individual modules.