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This study examines how social and natural scientists converged on a new ontological approach to science. Three distinguishing features comprise this new approach. They include: (1) an integration of the social and ecological into a fully coupled social-ecological systems perspective, (2) a holistic view of scientific phenomena requiring a transdisciplinary approach to its study, and (3) the refutation of a purely equilibrium-based understanding of systems. We explore this by first introducing complex adaptive systems science and reconsidering systems theory. We next look at the application of complex adaptive systems in institutional analyses conducted by political economists. Following this, we show how ecologists used the concept of resilience to apply a similar approach to the study of ecosystems. Finally, we show how a growing community of social and natural scientists have united to utilize a social-ecological systems framework to take a more holistic and transdisciplinary approach to science.