Toward a Methodology of Foundational Inquiry: The Foundational Reconstruction Hypothesis

Abstract Scientific inquiry has developed sophisticated methodologies for constructing, evaluating, and revising explanatory theories across many disciplines. Less attention, however, has been devoted to a general methodology for investigating the foundational commitments upon which such theories depend. This paper proposes Foundational Inquiry as a domain-independent methodological discipline dedicated to the systematic investigation of scientific foundations. Rather than introducing a new scientific theory or alternative physical, mathematical, or biological foundations, it develops a methodological framework through which foundational commitments become explicit objects of scientific investigation. The central methodological principle of this framework is the Foundational Reconstruction Hypothesis, according to which every foundational commitment should be regarded as methodologically provisional until weaker reconstructions capable of preserving its explanatory role have been systematically investigated and either established or excluded. The paper argues that this reconstruction perspective applies independently of disciplinary boundaries. Through comparative analysis of physics, mathematics, and biology, it identifies a common methodological architecture underlying scientific explanation while remaining neutral regarding the specific theories in each discipline. To operationalize this perspective, the paper introduces the Reconstruction Protocol, a general procedure for identifying foundational commitments, defining their explanatory roles, constructing reconstruction candidates, evaluating explanatory preservation, and determining the methodological status of foundational concepts. Finally, the paper argues that scientific progress may be understood as possessing two complementary dimensions: the expansion of explanatory knowledge and the systematic reduction and justification of the foundational commitments upon which explanation depends. It proposes Foundational Inquiry not as a replacement for existing disciplines, but as a complementary methodological framework for the systematic investigation of scientific foundations.