The recent drastic development of agriculture, together with the growing societal interest in agricultural practices and their consequences, pose a challenge to agricultural science. There is a need for rethinking the general methodology of agricultural research. This paper takes some steps towards developing a systemic research methodology that can meet this challenge – a general self-reflexive methodology that forms a basis for doing holistic or (with a better term) wholeness-oriented research and provides appropriate criteria of scientific quality.From a philosophy of (...) research perspective,science is seen as an interactive learning process with both a cognitive and a social communicative aspect. This means, first of all,that science plays a role in the world that it studies. A science that influences its own subject area, such as agricultural science, is named a systemic science. From this perspective, there is a need to reconsider the role of values in science. Science is not objective in the sense of being value-free.Values play, and ought to play, an important role in science – not only in form of constitutive values such as the norms of good science, but also in the form of contextual values that enter into the very process of science. This goes against the traditional criterion of objectivity. Therefore, reflexive objectivity is suggested as a new criterion for doing good science, along with the criterion of relevance. Reflexive objectivity implies that the communication of science must include the cognitive context, which comprises the societal,intentional, and observational context. Ina ccordance with this, the learning process of systemic research is shown as a self-reflexive cycle that incorporates both an involved actor stance and a detached observer stance. The observer stance forms the basis for scientific communication.To this point, a unitary view of science as a learning process is employed. A second important perspective for a systemic research methodology is the relation between the actual,different, and often quite separate kinds of science. Cross-disciplinary research is hampered by the idea that reductive science is more objective, and hence more scientific, than the less reductive sciences of complex subject areas – and by the opposite idea that reductive science is necessarily reductionistic. Taking reflexive objectivity as a demarcator of good science, an inclusive framework of science can be established. The framework does not take the established division between natural, social, and human science as a primary distinction of science.The major distinction is made between the empirical and normative aspects of science,corresponding to two key cognitive interests.Two general methodological dimensions, the degree of reduction of the research world and the degree of involvement in the research world, are shown to span this framework. The framework can form a basis for transdisciplinary work by way of showing the relation between more and less reductive kinds of science and between more detached and more involved kinds of science and exposing the abilities and limitations attendant on these methodological differences. (shrink)