The Humane metropolis is a rubric to summarize and promote environmental and social quality in contemporary urban mosaics. Because cities, suburbs, and exurbs, as spatially extensive and connected socio-ecological systems, exhibit many negative features, the humane metropolis identifies a strategy to combat the ills and instill more positive and sustainable features and processes in urban systems. Because the humane metropolis as a program has arisen primarily from social motivations, there is the opportunity to articulate more explicitly the role that science can play in addressing the humane metropolis program and evaluating its success. A humane metropolis can be summarized as one that 1) protects and restores ecological services in cities and suburbs, 2) promotes physical and mental health and safety of residents, 3) enhances efficiency by conserving energy, matter, water, and time, 4) facilitates equity by being inclusive, as well as socially and environmentally just, and 5) maintains a sense of community and a sense of place. We clarify the nature of science as a contributor to the social program, pointing out the social values motivating science, and the role that scientific knowledge and metaphor play in linking science with the social program of the humane metropolis. We further identify roles that socio-ecological research can play in meeting the goals of the humane metropolis. We use examples of environmental history, watershed function and restoration, and environmental justice