alife-commons

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." trit: 0

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