Agent-Skills.md

Agent Skills: alife-commons

Artificial Life atlas covering open-ended evolution, chemical reaction networks, morphogenesis, self-replication, and programmable chemistry. Use when picking a simulation framework, wiring ALife models into the skill graph, or onboarding contributors to the ALife cluster.

UncategorizedID: plurigrid/asi/alife-commons

Repository

plurigrid/asi
plurigridLicense: MIT
6712

Install this agent skill to your local

pnpm dlx add-skill https://github.com/plurigrid/asi/tree/HEAD/skills/alife-commons

Skill Files

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skills/alife-commons/SKILL.md

Skill Metadata

Name
alife-commons
Description
"Artificial Life atlas covering open-ended evolution, chemical reaction networks, morphogenesis, self-replication, and programmable chemistry. Use when picking a simulation framework, wiring ALife models into the skill graph, or onboarding contributors to the ALife cluster."

alife-commons

A single entry point that intermixes every ALife-primary skill in the repo. Edges emitted below make each family member depth-1 from this hub.

Tree decomposition of the ALIFE 2025 theme graph yields 7 bags, tree-width 2. evolution is the universal adhesion vertex (appears in 6/7 bags).

Families

open-ended-evolution

alife · alife2025 · truealife · true-alife · jaxlife-open-ended · skill-evolution

Comprehensive index: alife (256+ repos). Proceedings: alife2025 (337 pages, 80+ papers). JAX simulator: jaxlife-open-ended. Self-indexing automata: true-alife. Skill-level evolution patterns: skill-evolution. Energy tracking: truealife.

chemical-reaction-networks

catalyst-chemical · chemical-abstract-machine · chemical-organization-theory · crn-topology · turing-chemputer

Catalyst.jl ODE modeling: catalyst-chemical. Berry-Boudol CHAM: chemical-abstract-machine. Org theory / closure: chemical-organization-theory. Reaction graph topology: crn-topology. Programmable synthesis (XDL): turing-chemputer.

morphogenesis-and-growth

lindenmayer-systems · phyllotaxis

L-systems for fractal/plant generation: lindenmayer-systems. Golden-angle succulent growth as propagator network: phyllotaxis.

self-organization

autopoiesis · social-emergence-protocol

Varela-inspired self-modifying agents: autopoiesis. Stigmergic bootstrapping of complex social behaviors: social-emergence-protocol.

complexity-measurement

assembly-index

Cronin's Assembly Theory for molecular complexity and life detection.

protocol-evolution

protocol-evolution-markets

Prediction markets for protocol standard survival/fork/merge dynamics.

Cross-family threading

  • CRN <-> Evolution: catalyst-chemical models reaction dynamics that alife2025 papers analyze for open-endedness (Bags 1,2 in tree decomposition).
  • Morphogenesis <-> Evolution: lindenmayer-systems + phyllotaxis produce phenotypes that jaxlife-open-ended evaluates for fitness.
  • Self-org <-> CRN: autopoiesis closure conditions map to chemical-organization-theory organizational closure.
  • Complexity <-> Evolution: assembly-index provides the fitness landscape metric for skill-evolution and protocol-evolution-markets.
  • All <-> ALIFE 2025: alife2025 proceedings cover all families above; its 7-theme classification is the canonical reference.

Cross-hub edges

  • para-mensch-commons: autopoiesis bridges via cybernetic self-reference.
  • open-games: protocol-evolution-markets uses open game semantics for market dynamics.
  • dynamic-sufficiency: chemical-organization-theory closure maps to causal state gating.
  • acsets: crn-topology and catalyst-chemical model reactions as attributed C-sets.
  • interaction-nets: chemical-abstract-machine CHAM rules are interaction net reductions.
  • narya-proofs: assembly-index complexity bounds admit formal verification.

GF(3) theme balance

From the tree decomposition (7 bags, tree-width 2):

| Bag | Vertices | Trit sum | Status | |-----|----------|----------|--------| | 1 | evolution, emergence, CRN | +1+0-1 = 0 | balanced | | 2 | evolution, CRN, morphogenesis | +1-1+0 = 0 | balanced | | 3 | evolution, morphogenesis, self-replication | +1+0-1 = 0 | balanced | | 4 | evolution, self-replication, complexity | +1-1+0 = 0 | balanced | | 5 | evolution, complexity, cognition | +1+0-1 = 0 | balanced | | 6 | evolution, cognition, emergence | +1-1+0 = 0 | balanced | | 7 | emergence, CRN | +0-1 = -1 | rebalance via hub trit 0 |

Hub trit assignment: 0 (ERGODIC) — coordinator role in the triadic system.

Use when

  • Picking a simulator or formalism for artificial life research
  • Wiring a new ALife skill into the hub mesh
  • Onboarding a contributor to the ALife cluster
  • Cross-referencing ALIFE 2025 proceedings themes with existing skills
  • Computing tree decompositions of theme graphs for GF(3) rebalancing