plurigrid/asi
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Chemical Organization Theory
**Category:** Phase 3 Core - Autopoietic Systems **Status:** Skeleton Implementation **Dependencies:** `categorical-composition` (reaction networks as categories)
SKILL.md
Full skill instructions
Chemical Organization Theory
Category: Phase 3 Core - Autopoietic Systems
Status: Skeleton Implementation
Dependencies: categorical-composition (reaction networks as categories)
Overview
Implements Chemical Organization Theory (COT) for modeling self-maintaining autopoietic systems through reaction-diffusion dynamics, organizational closure detection, and self-maintenance verification.
Capabilities
- Reaction Networks: Define chemical reaction systems
- Organizational Closure: Detect self-maintaining organizations
- Reaction-Diffusion: Spatial dynamics simulation
- Autopoiesis: Verify self-production and boundary maintenance
Core Components
-
Reaction Network Builder (
reaction_network.jl)- Define species and reactions
- Stoichiometric matrices
- Mass-action kinetics
-
Organization Detection (
organization_detection.jl)- Closure detection (no external inputs required)
- Self-maintenance verification
- Organizational hierarchy
-
Reaction-Diffusion Simulator (
reaction_diffusion.jl)- Spatial PDE integration
- Pattern formation
- Turing instabilities
-
Autopoietic Analysis (
autopoiesis.jl)- Boundary formation detection
- Self-production metrics
- Organizational resilience
Integration Points
- Input from:
categorical-composition(reaction networks as categories) - Output to:
emergent-role-assignment(role stability as organizations) - Coordinates with:
formal-verification-ai(verify closure properties)
Usage
using ChemicalOrganizationTheory
# Define reaction network
network = ReactionNetwork()
add_species!(network, [:A, :B, :C])
add_reaction!(network, [:A, :B] => [:C], rate=0.1)
add_reaction!(network, [:C] => [:A, :B], rate=0.05)
# Detect organizations
orgs = find_organizations(network)
# Simulate reaction-diffusion
grid = Grid2D(100, 100)
state = initialize_state(grid, network)
trajectory = simulate_rd(network, state, time=100.0)
# Check autopoiesis
is_autopoietic = check_autopoiesis(network, orgs[1])
References
- Dittrich & Speroni di Fenizio "Chemical Organization Theory" (2007)
- Fontana & Buss "The Barrier of Objects" (1996)
- Varela et al. "Autopoiesis: The Organization of Living Systems" (1974)
Implementation Status
- Basic reaction network structures
- Stoichiometric analysis
- Full organization detection algorithm
- Reaction-diffusion solver
- Autopoiesis verification metrics
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