Philosophy observes the sciences. But it has also played a role in the formation of the sciences. And this is especially true in the case of the social sciences.
The idea here is an elusive one. It is that the founders of the social sciences – perhaps similar to all intellectual or creative founders – possessed framing assumptions, presuppositions, or intuitions about what their eventual product ought to look like. Various ideas capture some of this: presupposition, paradigm, guiding framework, tacit knowledge, or “style”. A style of technology or architecture is a “mindset” that guides the creator into affirming one set of choices and denying another; ruling out certain solutions to a problem while favoring others. And many of these ideas derived from philosophy -- for example, empiricism, rationalism, deductivism, atomism, or reductionism.
The nineteenth- and twentieth-century founders of the social sciences had a set of intellectual interests that led them to ask questions about the way that society works. They were led to engage in careful, disciplined study of social phenomena. But how to proceed? What should the results look like? What modes of explanation should be pursued? What should they expect to find? None of the founders proceeded with a “blank slate”. Instead, they were guided by specific intellectual hunches and presuppositions about what a scientific treatment of a subject ought to involve. The histories of physics, chemistry, and biology were very well known to the founders, and the chief logical characteristics of the science of these domains were also well understood. The “stylized facts” about what a domain of inquiry is and what a scientific study of a domain involves were fairly specific. It turns out that these facts were misleading in deep and broad ways when applied to the social world. And contemporary sociology continues to bear the imprint of these early presuppositions.
We might be tempted to call these assumptions about domain, method, and theory a “paradigm”, but it is better to think of them as constituting a “proto-paradigm”. “Paradigm” describes a more advanced stage of the formation of a field of knowledge. The framing ideas that guided the founders were less specific; they represented high-level, abstract presuppositions about the nature of science and the nature of any subject matter that is amenable to scientific study and explanation. They constitute a framework of advanced commonsense about the subject matter. We might describe this framework as a “folk philosophy of knowledge” that is to some extent unexamined but that guides the pursuit of knowledge, the form that it takes, and the ways in which it is evaluated.
Given these historical circumstances, naturalism as a "proto-paradigm" for the social sciences is unsurprising—even though it is profoundly misleading. The strongest — really, the only — examples of scientific achievement in the nineteenth century were in the fields of chemistry, physics, medicine, and biology. There was a developed “proto-theory” of nature that was the object of scientific study (the characteristics and metaphysics of law-governed natural phenomena). The natural world was conceived of as a system of law-governed events and processes. And the logical characteristics of natural science theory were reasonably well understood as well: induction, discovery of laws and regularities, explanation through assimilation within a set of natural laws, confirmation.
There is a fundamental problem with this set of "naturalistic" presuppositions: social phenomena are constituted by a fundamentally different ontology. "Agents in structures" are the fundamental "molecules" of social life -- and this ontology should not be expected to give rise to strong regularities. Instead, we should expect a substantial amount of heterogeneity and plasticity among social entities and processes, and we should expect contingency and path-dependency in the unfolding of social phenomena.