Abstract The energetic basis of molecular complementarity is presented. In biological systems requiring both homeostasis and non-equilibrium state maintenance, molecular complementarity provides a framework for the co-existence of these states within an organism. Smoothly changing homeostatic and thermodynamic systems, such as regulation of pH or an ensemble of asynchronous muscle crossbridges, are modeled using Liapunov functions. When biological systems undergo discontinuous state changes, such as the initiation of the heartbeat, life/death transition or the detachment of molecules, alternative analytical systems such as catastrophe theory provide information that continuous analytical methods cannot, Catastrophe theory produces a model of biology in which death can occur by two distinct mechanisms: loss of homeostatic control or loss of sufficient free energy. Molecular complementarity buffers molecules from temporal and physical changes. The usefulness of molecular complementarity is limited to association energies near the ambient energy, kT. Within this range, complementarity will alter molecular functions and will convert scalar biochemical reactions into vectorial physiological processes. Both thermodynamic and catastrophic models can be used to link energetic and homeostatic processes: the former providing quantitative information from continuous systems; the latter providing qualitative information from discontinuous systems involving state changes.