Starting from Rothstein's analysis of the EPR paradox, the logical incompleteness of quantum mechanics and non-separability which implies "the death of atomism" (Primas) are discussed from both physical and logico-epistemological points of view. Indeed, the indeterminacy of the microphysical, simple-elementary entities as fundamental ground of physis involves the breakdown of any kind of reductionism. Reductionism presupposes the possibility of such a determinacy, and so it is nothing else than a particular form of "determinism". The indeterminate universe of physical processes is non-separable and a physics of the universe as a whole seems to be needed. Furthermore, from a historical and philosophical point of view the principle of separability is shown to be related to the meta-physical project of the technical dominion over nature and the emergence of non-separability in physical theories is analysed.