From Control to Replay: Archives, Development, and Sexual Reproduction in Boundary-Defined Life

The emergence of complex multicellular life requires not only stable biological identity but the capacity to reconstruct that identity across collapse, division, and generations. This paper addresses how such replayable biological organisation becomes possible within a regulation-first framework. We introduce an architectural separation between runtime control, which maintains viability within a boundary-defined basin, and inert reconstruction archives, which constrain how that basin can be rebuilt after disruption. DNA is treated not as an executive controller but as a chemically stable archive whose function is realised only through boundary-dependent execution. Within this framework, embryogenesis is reframed as staged basin replay rather than organismal construction. Early cleavage subdivides internal compartments without fragmenting identity, while subsequent development reflects context-dependent execution within a persistent, boundary-dominant basin. We further formalise boundary dominance as a necessary condition for stable integration and apply this principle to sexual reproduction, interpreting fertilisation as controlled archive transfer under resolved dominance rather than fusion of equal organisms. Differentiation is shown to require continuous stabilisation to prevent execution drift, dovetailing with kinetic anchoring mechanisms previously identified in multicellular systems. Together, these results unify development, sex, and inheritance under a single control-theoretic architecture grounded in boundary-defined identity. This paper completes a sequence of companion works developing a regulation-first, boundary-centric framework for biological identity, persistence, and complexity. This paper is Companion Paper 5 in a series developing a regulation-first, boundary-centric framework for biological identity. Foundational Paper: Life as a Phase Transition: https://doi.org/10.5281/zenodo.18176157 Companion Paper 2: The Basin of Identity: microRNA as a Kinetic Anchor in Multicellular Dynamics https://doi.org/10.5281/zenodo.18181118 Companion Paper 3: Boundary Shedding as Basin Maintenance A Control-Theoretic Extension of Life as a Phase Transition https://doi.org/10.5281/zenodo.18215113 Companion Paper 4: Cohesive Membranes and the Emergence of Multicellular Basin Identity When Many Compartments Become One Organism https://doi.org/10.5281/zenodo.18215283 Companion Paper 5: From Control to Replay: Archives, Development, and Sexual Reproduction in Boundary-Defined Life https://doi.org/10.5281/zenodo.18215367