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The thesis of this paper is that the "rational fool" syndrome can be applied to mainstream public sector agricultural research that is conducted in a way that is rational in the short term, but acts against its own long-term viability. Historically, a main concern of such research has been to maximize high levels of food production together with low prices to consumers. As a result, mainstream agricultural science has ignored negative impacts or externalities, which has contributed to a crisis of credibility with the general public and politically sensitive decision makers. A long-term strategic research agenda for the public sector is being defined that is new and relevant to present efforts to integrate natural resource management and sustainable agricultural production. Such an agenda must be understood as a way of managing natural resources for the production of food and environmental services essential to human well-being. If agricultural systems are viewed and managed as parts of whole ecosystems, the key properties of complex systems that need to be taken into account will force researchers to consider long-term effects and environmental externalities. Research products will then be increasingly strategic in nature, and the research process will be "democratized" as it involves and gains the support of a broad set of stakeholders. Private sector research cannot be expected to meet this need because strategic studies of resource management are required that cannot be made exclusive or proprietary and are, in other words, public goods. Several innovative research initiatives are under way that signal opportunities for change. This paper first elaborates on this argument and then illustrates key elements of the integrated natural resource management approach, with examples of approaches that show promise as alternatives to mainstream agricultural science. Although numerous and diverse, integrated approaches manifest several properties that can be defined as the keystones of a new paradigm.