Scaffold shedding as a network dynamical model for the origin of minimal cells

Abstract

Origin-of-life research often asks how prebiotic chemistry assembled the components required for a minimal cell. This paper proposes a complementary network-dynamical model: minimal cells may arise not only by acquiring functions, but by shedding the environmental scaffolds that first supplied them. I model prebiotic organisation as a heterogeneous scaffold network of mineral, physical, geochemical, and proto-biochemical supports. Such systems may initially require generative overshoot: more organising constraints than a later minimal cell requires. Mineral surfaces, pores, convection, redox gradients, wet-dry cycles, lipid films, templating effects, and concentration mechanisms may each contribute functions that later become internalised. Thermodynamic pruning then removes unstable, weakly coupled, redundant, costly, or context-bound supports. Most trajectories remain within a default non-living cycle of scaffold-rich organisation, overshoot, redundancy correction, pruning, and inert relaxation. In favourable trajectories, however, pruning can induce an off-ramp when four operator-classes become mutually coupled: Individuation, Memory, Transformation, and Recursion. I term this coupling IMTR closure. These operators correspond biologically to boundary formation, heritable information, metabolism, and replication-construction, but are treated here as abstract functional requirements for minimal cellular organisation. The model is formalised as a dynamic heterogeneous hypergraph in which scaffold nodes and coupling hyperedges are progressively weakened or removed by a pruning operator. Minimal-cell emergence occurs when an IMTR sub-hypergraph becomes self-maintaining under further pruning. On this view, the minimal cell is not the first assembled package of living parts, but the self-maintaining subnetwork that survives scaffold loss. Minimal-cell emergence is therefore interpreted as thermodynamic pruning arrested at self-renewing closure.