Coupled transitions and temporary stages of non-equilibrium in the persistence of encoded tokens

This record contains the English version of record of the essay “Coupled transitions and temporary stages of non-equilibrium in the persistence of encoded tokens: A relational material ontology for science”, revised following technical comments by Stergios Pellis in May 2026. The Portuguese version will be published separately under its own DOI. This essay develops a second formulation of the ontology proposed in the Law of the Obligatory Stage of Non-Equilibrium in the historical persistence of material codes. The first formulation distinguished code-token, code-lineage, and the obligatory stage of non-equilibrium, arguing that the historical persistence of material codes depends on maintenance, repair, copying, and retransmission within local flow regimes. The present version does not abandon that formulation; it reanchors it at a more fundamental level: before the organism, before the token, and before the very notion of “life,” there are finite material configurations, harnessable differences, coupled transitions, relaxation, and reinscription. The central thesis defended here is that no material entity should be taken as a stable foundation. What presents itself as stability is, more rigorously, a chain of coupled transitions between finite material configurations. In this framework, “useful energy” is not a substance, but a local material difference not yet relaxed, capable of generating couplable flux; “time” is not an independent entity, but the operational relation between configurations that form, persist, relax, or are reinscribed; and “non-equilibrium” is not a state, but the finite duration of material differences continually replenished before relaxation. From this basis, encoded tokens, such as deoxyribonucleic acid, ribonucleic acid, and virions, are defined not as autonomous entities, but as encoded material configurations, produced by prior coupled transitions, temporarily preservable, and capable of operating only when reinserted into new material transitions of flux, repair, copying, or reinscription. Organisms, in turn, are not fundamental units; they are temporary chains of non-equilibrium material transitions through which encoded tokens are maintained, recombined, and reinscribed before functional decay. In this revised version, a minimal formalization of the coupled transition is added as an operator between configurations under the relaxation of harnessable differences. The distinction between multiscale form and condition of persistence is also made explicit: form describes structures of invariance, recursion, or scale; persistence describes the temporal viability of a configuration under dissipative dynamics. Thus, form may be necessary for certain modalities of persistence, but it is not sufficient to guarantee it. Finally, the essay applies this ontology to the critique of the post-Neolithic consensus. By starting its reading from the human organism, this consensus converts a local chain of non-equilibrium into the interpretive center of matter, reducing earth, sea, air, microbes, plants, animals, minerals, climate, and other material chains to “environment,” “resource,” or “mere background.” The proposal defended here inverts this order: one does not start from the human to explain matter; one starts from finite material configurations to relocate the human as merely a late, local, and transient case among countless material chains.