Molecules as Primary Archaeological Evidence: An Epistemic Framework for Multi-Omics Archaeology and Heritage Science

Biomolecular and multi-omics approaches have transformed archaeology and heritage science, yet they are still widely conceptualized as ancillary techniques that refine narratives built on artifacts, architecture, and texts. This Perspective argues instead for treating molecules as primary archaeological evidence with their own epistemic status, temporalities, and bias structure. Drawing on a corpus of multi-omics case studies from the central and eastern Mediterranean (chiefly Sicily, Malta, and Egypt), together with comparative material from the lower Danube, Polynesia, and the Andes, and engaging directly with the philosophy of science, we adopt a critical entity realism grounded in the practice of physical intervention on molecular entities, and we develop evidential reasoning chains that connect instrumental data to historical phenomena. From this grounding, we propose a six-dimensional epistemic framework: (1) redefinition of archaeological evidence; (2) molecular counter-archive against preservation bias; (3) polytemporality of molecular signals; (4) ethics and conservation as internal epistemic variables; (5) identity, boundaries, and connectivity in a molecular key; and (6) methodological pluralism and interpretive convergence. The framework has concrete implications for curatorial policies, sampling strategy, and data governance, and opens a productive dialogue between biomolecular heritage science and archaeological theory.