In the search for principles of pattern generation in complex biological systems, an operational approach is presented that embraces both theory and experiment. The central mathematical concepts of self-organization in nonequilibrium systems (including order parameter dynamics, stability, fluctuations, and time scales) are used to show how a large number of empirically observed features of temporal patterns can be mapped onto simple low-dimensional (stochastic, nonlinear) dynamical laws that are derivable from lower levels of description. The theoretical framework provides a language and a strategy, accompanied by new observables, that may afford an understanding of dynamic patterns at several scales of analysis (including behavioral patterns, neural networks, and individual neurons) and the linkage among them.