What explains the remarkable regularities in distribution and abundance of species, in size distributions of organisms, or in patterns of nutrient use? How does the biosphere maintain exactly the right conditions necessary for life as we know it? Gaia theory postulates that the biota regulates conditions at levels it needs for survival, but evolutionary biologists reject this explanation because it lacks a mechanistic basis. Similarly, the notion of self-organized criticality fails to recognize the importance of the heterogeneity and modularity of ecological systems. Ecosystems and the biosphere are complex adaptive systems, in which pattern emerges from, and feeds back to affect, the actions of adaptive individual agents, and in which cooperation and multicellularity can develop and provide the regulation of local environments, and indeed impose regularity at higher levels. The history of the biosphere is a history of coevolution between organisms and their environments, across multiple scales of space, time, and complexity.