arXiv subjects

Amahury J. López-Díaz

Publications and source records attributed to Amahury J. López-Díaz.

3 recordsLinked to original sources

arXiv2026

A Matter of Time: Towards a General Theory of Agency

Agency is widely invoked in biology, cognitive science, artificial intelligence, and philosophy, yet its organizational basis, its empirical thresholds, and the operational criteria that distinguish it from other teleonomic terminology remain unsettled. Building on temporally parametrized (F, A)-systems, we propose a multidimensional theory of biological agency grounded in relational biology, physical biosemiotics, and process ontology. Our central claim is that the precarious physical realization of self-reference is necessarily diachronic; constitutive constraints act, decay, and are regenerated over distinct characteristic timescales. By temporalizing organizational diagrams ordered by specified relation deletion, we obtain a structural partial order, rather than an evolutionary ladder, that distinguishes four defeasible conditions: autonomy as internal regeneration of constitutive constraints under material openness; goal-directedness as viability-biased maintenance; agency as endogenous anticipatory modulation of organism--environment coupling; and open-endedness as reconstruction of the variables, measurement relations, effectors, and norms through which future viability is defined. We translate these distinctions into a closure-sensitive mechanistic workflow and a provisional profile of operational signatures for semantic closure, measurement--control complementarity, anticipatory modulation, affordance reconstruction, syntactic open-endedness, and viability-corrected skill acquisition. Markov blankets and active inference are treated as derived modeling tools, while Bickhard's interactivism clarifies anticipatory error and normativity. Across chemical, cellular, multicellular, and artificial systems, our framework turns agency from an all-or-none attribution into a falsifiable, scale-explicit research program.

cs.AI↗

arXiv2026

Characterizing Open-Ended Evolution Through Undecidability Mechanisms in Random Boolean Networks

Discrete dynamical models underpin systems biology, but we still lack substrate-agnostic diagnostics for identifying finite-horizon dynamical signatures that may be relevant to open-ended evolution (OEE), such as the recurrent production of novel phenotypic states rather than rapid settling or unstructured noise. We introduce a simple, model-independent metric, Ω, that summarizes the residence-time-weighted contribution of attractor cycle lengths across the sequence of recurrent episodes realized within a finite observation window. Ω is zero for single-attractor dynamics and also vanishes for pure novelty without recurrence, while increasing when trajectories repeatedly enter multiple persistent cyclic phenotypes. Using Random Boolean Networks (RBNs) as a controlled testbed, we compare classical Boolean dynamics with biologically motivated non-classical mechanisms (probabilistic context switching, annealed rule mutation, paraconsistent logic, modal necessary/possible gating, and quantum-inspired superposition/paired-state coupling) under homogeneous and heterogeneous updating schemes. Our results support the view that undecidability-adjacent, state-dependent mechanisms -- implemented as probabilistic context switching, modal necessity/possibility gating, paraconsistent logic, or quantum-inspired correlated branching -- are enabling conditions for sustained novelty. At the end of our manuscript we outline a practical extension of Ω to continuous/hybrid state spaces, positioning Ω as a portable proxy for OEE in biological modeling and a guide for engineering evolvable synthetic circuits.

q-bio.PE↗

arXiv2025

Closing the Loop: How Semantic Closure Enables Open-Ended Evolution?

This manuscript explores the evolutionary emergence of semantic closure -- the self-referential mechanism through which symbols actively construct and interpret their own functional contexts -- by integrating concepts from relational biology, physical biosemiotics, and ecological psychology into a unified computational enactivist framework. By extending Hofmeyr's (Fabrication, Assembly)-systems -- a continuation of Rosen's (Metabolism, Repair)-systems -- with a temporal parametrization, we develop a model capable of capturing critical properties of life, including autopoiesis, anticipation, and adaptation. Our stepwise model traces the evolution of semantic closure from simple reaction networks that recognize regular languages to self-constructing chemical systems with anticipatory capabilities, identifying self-reference as necessary for robust self-replication and open-ended evolution. Such a computational enactivist perspective underscores the essential necessity of implementing syntax-pragmatic transformations into realizations of life, providing a cohesive theoretical basis for a recently proposed trialectic between autopoiesis, anticipation, and adaptation to solve the problem of relevance realization. Thus, our work opens avenues for new models of computation that can better capture the dynamics of life, naturalize agency and cognition, and provide fundamental principles underlying biological information processing.

physics.bio-ph↗