Beyond Substrate Independent Computation

What if biological continuity is not adequately described by information alone, but by the persistence, transformation, and re-instantiation of organized processes across scales? Beyond Substrate-Independent Computation develops the MasterMito framework as a testable, implementation-oriented approach to multiscale biological self-continuity. Rather than assuming that identity, computation, or biological organization can be separated cleanly from their physical substrates, the book examines how continuity may depend on coupled processes spanning molecular, cellular, energetic, informational, and system-level organization. The monograph develops explicit concepts, operators, transition rules, and computational formulations intended to turn an abstract question into a research program that can be implemented, simulated, challenged, and refined. MasterMito is presented not as a completed theory of life or consciousness, but as a framework for investigating when an or ganized biological process remains meaningfully continuous as its components, states, and scales change. Bringing together biological organization, computation, complex systems, and operator-based modeling, the book asks a deeper methodological question: if continuity is a process rather than a static property, what must remain invariant-and what may change-for a system to remain itself?