Reconstructing Scientific Knowledge: A Multidimensional Framework for Understanding Evidence, Causality, and Observable Phenomena in Objective Reality

This record contains the complete supplementary materials associated with the scientific framework paper Reconstructing Scientific Knowledge. The materials provide full transparency for all methodological processes, scoring systems, datasets, and computational workflows used in the development and demonstration of the Evidence Reliability Score (ERS). The supplementary package is designed to support reproducibility, open scientific practice, and independent verification of all analyses. The contents include the ERS scoring manual, extraction sheets, preregistration documents, sensitivity analyses, simulation plans, case study datasets, and all code and reproducible notebooks used for scoring, modelling, and figure generation. These materials accompany the main paper and allow readers to examine the operational definitions, scoring rules, and analytical decisions in detail. The supplementary materials cover the following components: Overview of all supplementary content Evidence Reliability Score manual with scoring rubric, subscores, weighting options, and worked examples Structured extraction sheets for all case studies and simulations Full preregistration protocol including search strategy, screening rules, inclusion criteria, and analysis plan Code and reproducible notebooks for ERS scoring, simulations, sensitivity analyses, and figure generation Sensitivity analyses across alternative weighting schemes, confounding strength, publication bias, measurement precision, and mechanistic coherence Case study datasets for nutrition science, epilepsy dietary interventions, psychedelic research, cannabis pharmacology, and anabolic steroid literature Supplementary figures and tables including flowcharts, correlation matrices, simulation outputs, and evidence reordering tables Supplementary notes on epistemic uncertainty, mechanistic reasoning, reproducibility, and domains where ideal evidence is impossible Data and code availability statements Versioning and update policy All materials are openly accessible and intended to support researchers, reviewers, and readers who wish to examine or extend the ERS framework. This Zenodo record will be updated as new case studies are added or methodological refinements are made.