Three principles guide natural pattern formation in both biological and non-living systems: (1) patterns form from interactions of numerous individual particles, or agents, such as sand grains, molecules, cells or organisms; (2) assemblages of agents can adopt combinatorially large numbers of different configurations; (3) observed patterns emerge through the selection of highly functional configurations. These three principles apply to numerous natural processes, including the origin of life and its subsequent evolution. The formalism of functional information, which relates the information content of a complex system to its degree of function, provides a quantitative approach to modeling the origin and evolution of patterning in living and nonliving systems.