Scientific Search Depends on Its Substrate: Constructing and Auditing Exploration Representations

Scientific search depends on decisions made before the first experiment: which alternatives remain distinguishable and which transitions a policy can take. We formalize this organization as a scientific exploration substrate and introduce CASES (Constructing and Auditing Scientific Exploration Substrates), a protocol for constructing, auditing, and activating substrates. A task policy records scientific, semantic, structural, and executable requirements; the audit authorizes the states and operations those requirements support. Controlled comparisons show that changing the substrate can alter search outcomes even when the policy remains fixed. Across scientific settings, the effects vary with task structure and consumer capability, shaping both which solutions can be reached and how evidence can be reused. Together, these results establish scientific search organization as an explicit experimental variable, separable from the policy that explores it.