This paper proposes to recover the topic of the philosophy of scientific method from its late nineteenth-century roots. The subject matter of scientific method sprouted from key inferential ingredients identified by Charles Peirce. In this paper, the historical path is traversed from the viewpoint of contemporary Cognitive Structural Realism (CSR). Peirce’s semiotic theory of methods and practices of scientific inquiry prefigured CSR’s reliance on embodied informational structures and experimentation upon forms of relations that model generic scientific domains. Three results are shown to follow from this convocation: (i) a naturalization of Peirce’s interconnected abductive, deductive and inductive stages of the logic of science, here characterized de novo in terms of CSR. (ii) a perspective to scientific modeling that incorporates processes of abstraction and generalization as originated from Peirce’s logic of science, and (iii) diagrammatic reasoning as a pivotal method in analyzing scientific reasoning in experimental practices.