plurigrid/ies/music-topos/.codex/skills/chemical-organization-theory

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

1. Reaction Network Builder (reaction_network.jl)

   • Define species and reactions
   • Stoichiometric matrices
   • Mass-action kinetics

2. Organization Detection (organization_detection.jl)

   • Closure detection (no external inputs required)
   • Self-maintenance verification
   • Organizational hierarchy

3. Reaction-Diffusion Simulator (reaction_diffusion.jl)

   • Spatial PDE integration
   • Pattern formation
   • Turing instabilities

4. 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

• [x] Basic reaction network structures
• [x] Stoichiometric analysis
• [ ] Full organization detection algorithm
• [ ] Reaction-diffusion solver
• [ ] Autopoiesis verification metrics