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Asi chemical-organization-theory

Chemical Organization Theory

install
source · Clone the upstream repo
git clone https://github.com/plurigrid/asi
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/plurigrid/asi "$T" && mkdir -p ~/.claude/skills && cp -r "$T/ies/music-topos/.codex/skills/chemical-organization-theory" ~/.claude/skills/plurigrid-asi-chemical-organization-theory && rm -rf "$T"
manifest: ies/music-topos/.codex/skills/chemical-organization-theory/SKILL.md
source content

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

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