The importance of underlying fundamental entities in theoretical sciences, which in most cases are hypothetical, unobservable, or even speculative in nature, such as quarks and gluons in QCD, from the realist perspective, and also from the hypothetic-deductive methodology, is clear and understandable. It has deep roots in human desire for explanation. However, it might be argued that the stress on the importance of underlying entities, which ground a reductive analysis of science, is in direct opposition to the holistic stance of structuralism. According to this stance, the empirical content of a scientific theory lies in the global correspondence between the theory and the phenomena in the domain under investigations at the structural level, which is cashed out with mathematical structures without any reference to the nature of the phenomena, either in terms of their intrinsic properties, or in terms of the underlying unobservable entities. Thus for structuralists no ontological interpretation of structure would be possible or even desirable. A structuralist, such as Bas van Fraassen (1997), would argue that if you insist to interpret the mathematical structure anyway, then different ontological interpretations would make no difference to science. That is, no ontological interpretation should be taken seriously.