Whenever an adequate theory is found in science, we will still be left with two questions: why this theory rather than some other theory, and how should this theory be interpreted? I argue that these questions can be answered by a theory of system relations. The basic idea is that fundamental characteristics of systems, viz. those arising from the general systemic nature of those systems, cannot be comprehended with the aid of discipline-specific methods. The systems theory required should commence with (...) an analysis of the qualitatively different relations possible between systems, because it is precisely the nature of those relations that determines the basic structures of systems. That the theory of the fundamental system relations and their ontological and epistemological implications is indeed able to provide the answers sought is demonstrated in theoretical physics and Plessner's analysis of the basic structures of plant, animal and human being. (shrink)