Regulation, Metabolism, and the Tape: A Semiotic and Dynamic Energy Budget Framework for Minimal Agency

===============================================================================MINIMAL AUTOPOIETIC AGENT: IN SILICO ARCHITECTURE AND BENCHMARK=============================================================================== DESCRIPTION:This package provides a zero-dependency reference Python implementation of theautopoietic, semiotic, and dynamic energy budget control architecture described in the preprint: "Regulation, Metabolism, and the Tape: A Semiotic and Dynamic Energy Budget Framework for Minimal Agency" The system formalizes Howard Pattee's physical biosemiotics, dynamic energy budget (DEB) theory, and biological autopoiesis. It demonstrates zero-shot survival, autonomous spatial evasion, structural self-repair, and continuous mitotic division in an adversarial, non-stationary environment without gradient-based learning or external reward signals. -------------------------------------------------------------------------------1. CORE ARCHITECTURAL COMPONENTS------------------------------------------------------------------------------- The agent couples a rate-independent genetic tape to rate-dependent metabolic dynamics through a state-conditioned regulatory pipeline: * ENERGY RESERVE (c >= 0): Obeys the first-law dynamic energy balance equation: dc/dt = f - a - u - r - d Where: f = Food intake rate from the environment a = Anabolic expenditure allocated to structural self-generation u = Somatic mechanical/kinematic action cost r = Obligatory baseline Landauer and metabolic maintenance dissipation d = Thermodynamic structural decay and localized hazard damage * METABOLIC AUTOPOIESIS (M): Coordinates catabolism and anabolism. Crucially, anabolism does not merely accumulate biomass; it acts as the endogenous autopoietic engine that synthesizes, maintains, and repairs the physical body (integrity I in [0, 1]). Structural self-repair takes absolute priority over growth. Only surplus anabolic flux is channeled into synthesizing the daughter tape (T'). * SENSORY HOLLAND TAG (tau): Evaluates environmental surface conditions using normalized Hamming string matching with wildcard (#) support. * HERITABLE TAPE (T) AND EPIGENETIC MARKS: Contains discrete instruction sequence (s), directional evolutionary priors (sign of w), and continuous epigenetic marks (mu). Epigenetic marks are dynamically up- or down-regulated across cycles in response to physiological stress and local hazard signals. * COMPILATION PIPELINE (Tag -> G -> G' -> G''): - G: Addresses environmental tag gated by energy surplus. - G': Integrates the tag with internal reserve (c) and somatic integrity (I) sampled strictly prior to reading the tape. - G'': Evaluates the tape through internal context G', resolving action selection and metabolic partitioning. * ACTION SPACE (A): - forage: Gathers environmental nutrients to replenish reserve c. - move: Expends kinetic work (u) to relocate between spatial patches, evading 80% of localized hazard damage and locating food. - shield: Hardens physical boundaries, absorbing 75% of incoming damage. - repair: Directs extra metabolic reserves into anabolic healing. * AUTOPOIETIC DIVISION (T -> T + T'): Once daughter tape T' is fully synthesized and reserve c exceeds the mitotic threshold, the agent executes cell fission, transferring a portion of its reserve to daughter lineages and resetting the lineage tag. -------------------------------------------------------------------------------2. IMPLEMENTED THEORETICAL EQUATIONS------------------------------------------------------------------------------- 1. Critical Food Intake Threshold: f* = r0 + d0 + delta / (kappa * (1 - I_min)) Below this threshold, structural integrity collapses in finite time, proving that a positive reserve (c > 0) is a physical necessity to buffer environmental famine. 2. Finite Starvation Buffer: L_safe = c(t0) / (f* - f0) + (I(t0) - I_min) / gamma Quantifies the maximum duration an organism can survive acute famine before lethal structural collapse. -------------------------------------------------------------------------------3. EMPIRICAL BENCHMARK RESULTS (ZERO-SHOT ADVERSARIAL TEST)------------------------------------------------------------------------------- The agent was placed zero-shot into a 3-patch landscape (Nominal Patch 0, Depleted Wasteland Patch 1, Contested Oasis Patch 2) subject to periodic predator shock waves. Over a 35-cycle trial, the agent demonstrated: - Final Outcome: SURVIVED (100% viability) - Structural Integrity: 1.00 (Perfect somatic maintenance across all shocks) - Final Energy Reserve: 11.98 units (Healthy buffer maintained) - Total Offspring: 4 complete mitotic cell divisions - Evasive Relocation: Autonomous migration from wasteland (P1) into the nutrient-rich oasis (P2), using tactical moves to dodge predator shock waves. -------------------------------------------------------------------------------4. USAGE AND REQUIREMENTS------------------------------------------------------------------------------- * Requirements: Python 3.8 or higher. Standard library only (no external packages required). * Execution: Run the standalone simulation script: python agentic_system.py Included Files: - agent_simulation.py : Full Python simulation and verification runtime. - framework_for_minimal_agency_preprint.tex: LaTeX preprint containing formal proofs and theorems. - figure1.png : Architectural flow-network diagram. - framework_for_minimal_agency_preprint.pdf : the preprint