PFUSRC-055-FD From Darwin to Topology: A Mind-Matter Integrated Reconstruction of Evolutionary Theory — Intelligent Refinement Theory and Its Integration with PFUSRC Topological Ontology

Classical Darwinism and its modern synthetic synthesis rely on three core premises: undirected random mutation, natural selection as the sole creative evolutionary driver, and genes as the exclusive carrier of heredity. A large body of frontier molecular biology, epigenetics and developmental biology data from 2024 to 2026 has revealed systematic contradictions against these foundational assumptions. This paper proposes Intelligent Refinement Theory, arguing that biological evolution is an active directional optimization process driven by hierarchical nested topological intelligence, rather than blind random trial and error. The theory is intrinsically self-consistent with the PFUSRC primordial flow-ultimate stillness coaxial biconical ontology, forming a cross-scale closed explanatory system covering cosmology, quantum mechanics, biological evolution and artificial intelligence. Evolution is redefined as the continuous self-manifestation of intelligent entities searching for low-impedance projection channels within the cosmic topological substrate. This paper provides complete logical reasoning, cross-disciplinary empirical evidence, preliminary mathematical modeling frameworks and multiple testable biological predictions, realizing a paradigm shift from external environmental selection to integrated mind-matter topological self-optimization.