The Autopoietic Threshold: The Emergence of Cellular Individuality from Kinetically-Driven Replicative Landscapes

Previous models in this series have established a unified framework where thermodynamic selection in energy gradients generates landscapes of proto-replicators, and kinetic selection drives their differential optimization. This work addresses the subsequent major transition: the emergence of individuality and autopoiesis. We argue that the success of the kinetic-replicative engine generates inherent internal conflicts—specifically molecular parasitism and the dilution of public goods—that threaten its long-term sustainability in an open medium. We demonstrate that physical compartmentalization emerges as the inevitable solution to these conflicts. Compartments that, by stochastic contingency, enclose cooperative sets of replicators and catalysts, and where an active coupling is established between internal processes and boundary maintenance, will obtain a decisive robustness advantage. This creates a new unit of selection: the autopoietic protocell. Therefore, autopoiesis—the self-production and maintenance of a delimited system—is not an axiomatic starting point, but an evolutionary innovation that stabilizes and potentiates the pre-existing replicative-thermodynamic engine. This transition marks the shift from selection acting solely on molecules (governed by the kinetic constant *k*) to selection acting on supramolecular systems (governed by a systemic fitness, Φ), laying the physical foundations for the Darwinian evolution of complexity.