Since the 1970s two fundamental shifts have occurred in health research funding: a reduction in the buying power of research dollars, and an increase in the competition for resources. Most fields have also seen a decrease in the dollars available for research. Pressures for justifying the relevance of research activities have become increasingly pragmatic. The thesis of this paper is that scientific creativity and innovation are compromised by the highly uncertain and competitive funding environment of contemporary health research. This is largely because criteria of scientific excellence predicated on an investigation's presumed future impact support the status quo of methods and subject matter in funded research. Extraordinary rationality among scientists seeking and allocating resources promotes the survival of the existing system over time, yet inhibits progressive development through the transformation of conceptual models. Therefore, despite a growing unrest about the way research on population health is conducted, new conceptions of the relationship between theory and methods have been slow to emerge. Amelioration of a disjunction between the institutionalized rules governing science and the culturally sanctioned goals of science requires commitment to a dialectic between orthodoxy and dissent.