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. Life as a Phase Transition — Series Overview Foundational framework A. An Architectural Origin of Organismal UnityFoundational Paperhttps://doi.org/10.5281/zenodo.18305134 B. Life as a Phase TransitionFoundational Paperhttps://doi.org/10.5281/zenodo.18176157→ Defines life as a maintained, non-equilibrium basin governed by regulation and boundary constraints. Heredity constraint and theory closure C. The Analogue Heredity Ceiling and the Basin Digitisation TransitionHeredity constraint frameworkhttps://doi.org/10.5281/zenodo.18250555→ Formalises the limit of compositional (analogue) heredity and explains why replayable archives (digitisation) become unavoidable within the life-as-a-phase-transition framework. Companion papers — Mechanisms and consequences 2. The Basin of Identity: microRNA as a Kinetic Anchor in Multicellular Dynamics https://doi.org/10.5281/zenodo.18181118 → Explores how kinetic anchoring mechanisms stabilise basin identity in multicellular systems, now interpretable as local management of identity dimensionality and heritability stress. 3.Boundary Shedding as Basin MaintenanceA Control-Theoretic Extension of Life as a Phase Transitionhttps://doi.org/10.5281/zenodo.18215113→ Describes boundary shedding as a regulatory strategy for maintaining basin coherence under stress. 4.Cohesive Membranes and the Emergence of Multicellular Basin IdentityWhen Many Compartments Become One Organismhttps://doi.org/10.5281/zenodo.18215283→ Examines how multicellular organisation emerges from coupled boundary systems and shared basin identity. 5. From Control to ReplayArchives, Development, and Sexual Reproduction in Boundary-Defined Lifehttps://doi.org/10.5281/zenodo.18215367→ Investigates replay, development, and sexual reproduction as stabilising mechanisms, now unified by the Basin Digitisation Transition. 6. Boundary Architecture and Failure in Living SystemsA regulation-first classification of biological formhttps://doi.org/10.5281/zenodo.18226987→ Classifies biological form and failure modes through boundary architecture and regulatory breakdown. 7.The Boundary Renewal Principle:An Architectural Account of Heredity and Evolutionhttps://doi.org/10.5281/zenodo.18335521