Here is another part of my paper, to be delivered at the annual meeting of the International Political Science Association this July in Montreal.
Almost nobody will nowadays dispute that: (i) living systems are organized in a radically different way than nonliving systems and (ii) living systems change in time in a radically different way than nonliving systems.
Without a strong idea of individual metabolic organization, it would be very difficult to provide a naturalized account of concepts like functionality, agency, unit of selection, etc., or to make a clear-cut distinction between organisms and other forms of cooperative or “ecological” networks.
We mean the property of a system that builds and actively maintains the rules that define itself, as well as the way it behaves in the world. So autonomy covers the main properties shown by any living system at the individual level: (i) self-construction (i.e., the fact that life is continuously building, through cellular metabolisms, the components which are directly responsible for its behavior) and (ii) functional action on and through the environment (i.e., the fact that organisms are agents, because they necessarily modify their boundary conditions in order to ensure their own maintenance as far from equilibrium, dissipative systems).
Apart from a particularly cohesive organization, organisms display a particularly marked impulse or urge to persist in their state of being (Spinoza’s conatus). It is, therefore, important to understand life at that individual level, and analyze carefully the implications of the emergence in the natural world of systems with that capacity to act for their own benefit, to constitute identities that distinguish themselves from the environment.
Originally used in the context of law and sociology (in the sense of self-government, from the Greek polis) or human cognition and rationality (in the sense of a cognitive agent that acts according to rationally self-generated rules, cf. Kant), for many it will sound like a high-level concept, with too many non-strictly-biological connotations. Broadly speaking, autonomy is understood as the capacity to act according to self-determined principles.