Education is a goal-oriented field. But if we want to treat education scientifically so we can accumulate, evaluate, and refine what we learn, then we must develop a theoretical framework that is strongly rooted in objective observations and through which different theoretical models of student thinking can be compared. Much that is known in the behavioral sciences is robust and observationally based. In this paper, I draw from a variety of fields ranging from neuroscience to sociolinguistics to propose an over-arching theoretical framework that allows us to both make sense of what we see in the classroom and to compare a variety of specific theoretical approaches. My synthesis is organized around an analysis of the individual’s cognition and how it interacts with the environment. This leads to a two level system, a knowledge-structure level where associational patterns dominate, and a control-structure level where one can describe expectations and epistemology. For each level, I sketch some plausible starting models for student thinking and learning in physics and give examples of how a theoretical orientation can affect instruction and research.