This article aims to show that fundamentality is construed differently in the two most prominent strategies of analysis we find in physical science and engineering today: (1) atomistic, reductive analysis and (2) Systems analysis. Correspondingly, atomism is the conception according to which the simplest (smallest) indivisible entity of a certain kind is most fundamental; while systemism, as will be articulated here, is the conception according to which the bonds that structure wholes are most fundamental, and scale and/or constituting entities are (...) of no significance whatsoever for fundamentality. Accordingly, atomists maintain that the basic entities—the atoms—are fundamental, and together with the “external” interactions among them, are sufficient for illuminating all the features and behaviors of the wholes they constitute; whereas systemists proclaim that it is instead structural qualities of systems, that flow from internal relations among their constituents and translate directly into behaviors, that are fundamental, and by themselves largely (if not entirely) sufficient for illuminating the features and behaviors of the wholes thereby structured. Systemism, as will be argued, is consistent with the nonexistence of a fundamental “level” of nondecomposable entities, just as it is consistent with the existence of such a level. Still, systemism is a conception of the fundamental in quite different, but still ontological terms. Systemism can serve the special sciences—the social sciences especially—better than the conception of fundamentality in terms of atoms. Systemism is, in fact, a conception of fundamentality that has rather different uses—and importantly, different resonances. This conception of fundamentality makes contact with questions pertaining to natural kinds and their situation in the metaphysics of the special sciences—their situation within an order of autonomous sciences. The controversy over fundamentality is evident in the social sciences too, albeit somewhat imperfectly, in the terms of debate between methodological individualists and functionalists/holists. This article will thus clarify the difference between systemism and holism. (shrink)