Life depends on the capacity of individual cells to respond effectively to cues about their changing internal and external environments. Cellular decision making and responses are orchestrated by complex molecular networks consisting of entities such as proteins or RNAs connected by interactions such as activation or synthesis. One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterization of the molecular components and interactions. Then, the cellular “task” of the network—its function—should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles.