We describe a process, Dual Phase Evolution (DPE), which is a widespread mechanism by which systems evolve. The process occurs in systems that switch between two phases: a balance phase and a variation phase. In DPE, processes drive systems to settle in a “balance” phase, but external stimuli can flip the system into a temporary “variation” phase, in which rapid change occurs on all scales. The system gradually returns to a new balance phase, often with different structure than formerly. We argue that the system occurs in many natural systems and show how it results from landscape connectivity in both evolution and long-term forest change. We describe how it underlies certain optimization algorithms, and can be implemented to improve the performance of existing optimization methods. Finally, we present simulation experiments that show how DPE may play a role in creating cliques, clusters, modules and other kinds of order within social networks.