The development of complexity theory in the natural sciences is described, and summarized in six principles of complex emergent wholes. It is suggested that complexity theory is leading biology toward a science of qualities based on participation and intuition. It is argued on metaphorical and epistemological grounds that these principles which describe the emergence of complex wholes can be applied to social and organizational life. The six principles are then applied to qualitative and action research practice, with a particular reference to co-operative inquiry, in order to provide principles for good practice and theoretical support for the nature of valid inquiry processes.