chemart / autopoiesis-vmu

hub:
  repo_type: generator
  builtin: autopoiesis-vmu
  tags:
  - banzhaf-yamamoto
chemistries:
- id: autopoiesis-vmu
  name: Varela-Maturana-Uribe autopoiesis model
  intuition: 'The model that named computational autopoiesis. A lattice holds substrate, a catalyst and
    links. The catalyst turns two neighbouring substrates into a link; links bond to adjacent links into
    chains; and links spontaneously decay back to substrate. Nothing tells the system to build a membrane,
    yet a closed chain forms around the catalyst - and because the catalyst keeps producing links, the
    boundary repairs itself as its parts decay. Substrate crosses it while the enclosed catalyst cannot
    escape. The interesting behaviour lives entirely in space, not in the reaction list.

    '
  aliases:
  - SCL
  - Substrate-Catalyst-Link model
  - computational autopoiesis
  origin: Varela, Maturana & Uribe, 1974
  book: 6.1.5
  refs:
  - '[881]'
  - '[557]'
  - '[559]'
  - doi:10.1016/0303-2647(74)90031-8
  family: origin-of-life
  kind: generator
  constructive: false
  S:
    repr: 'One particle per site of a 2D toroidal lattice: hole, substrate (O), catalyst (*) or link ([O]).
      A link carries up to two bonds to neighbouring links and may hold one absorbed substrate, so the
      species are S (substrate), C (catalyst) and L0/L1/L2 (a link with 0, 1 or 2 bonds), each link species
      also as L0S/L1S/L2S when it holds an absorbed substrate. A doubly bonded link (L2) is a chain link,
      a closed chain is a membrane, and a membrane enclosing a catalyst is a cell. Holes are empty space,
      not a species.

      '
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    - 3
    scheme: 'Production * + 2 O -> * + [O] (two substrates of the catalyst''s neighbourhood become a link
      and a hole) ; bonding of neighbouring links, at most two bonds per link and one bond per adjacent
      pair, forbidden for a free link that has a chain link in its neighbourhood (chain-based bond inhibition)
      ; disintegration [O] -> O + O, which also drops the link''s bonds ; absorption [O] + O -> [O]O and
      emission [O]O -> [O] + O of one substrate by a link, which is how a membrane passes substrate.

      '
    notes: 'No rate law is published: the probabilities below are lattice-update parameters, not rate
      constants, so the reactions carry no rate.

      '
  A:
    reactor: lattice-2d
    dilution: none; the lattice is closed and every site always holds exactly one particle
    notes: 'Each time step every particle acts once, in random order: it swaps with one of its four von
      Neumann neighbours with probability sqrt(m_i m_j) of the two mobility factors (bonded links are
      immobile), and then acts by type. Interactions (catalysis, bonding, inhibition, absorption, emission)
      use the eight-cell Moore neighbourhood, so an 8-connected closed chain is impermeable to the 4-connected
      motion of all other particles.

      '
  params:
  - name: mode
    type: enum
    default: lattice
    choices:
    - lattice
    - reactions
    role: structural
    meaning: 'lattice: run the lattice and return the reactions that fired, with counts (status observed),
      the grid in extras.space and the membrane measurements in extras.analysis; reactions: the reactions
      the chemistry defines, as a complete network'
  - name: initial
    type: enum
    default: substrate
    choices:
    - substrate
    - cell
    role: structural
    meaning: 'substrate: the book''s figure 6.3 at t = 0, a catalyst surrounded by substrate; cell: start
      from a ready-made cell, the twelve-link closed membrane around the catalyst of Von Kamp (2002) figure
      2'
  - name: width
    type: int
    default: 30
    min: 5
    max: 400
    range: Von Kamp (2002) figure 2 uses a 30 x 30 world
    role: spatial
    meaning: lattice width (toroidal)
  - name: height
    type: int
    default: 30
    min: 5
    max: 400
    range: Von Kamp (2002) figure 2 uses a 30 x 30 world
    role: spatial
    meaning: lattice height (toroidal)
  - name: steps
    type: int
    default: 120
    min: 0
    max: 1000000
    range: spontaneous formation of a cell from a bare catalyst takes thousands of steps; Von Kamp's runs
      go to 50,000
    role: population
    meaning: time steps; in each one every particle moves and acts once
  - name: n_catalysts
    type: int
    default: 1
    min: 0
    max: 1000
    range: the book's figure 6.3 starts from a single catalyst
    role: population
    meaning: catalysts; the first is placed at the centre of the lattice, any others at random
  - name: substrate_density
    type: float
    default: 1.0
    min: 0.0
    max: 1.0
    role: population
    meaning: fraction of the non-catalyst sites that start as substrate; the rest start as holes. Holes
      are also produced by the catalysis reaction
  - name: production_probability
    type: float
    default: 1.0
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: 'probability per time step that a catalyst turns two neighbouring substrates into a link
      and a hole (Von Kamp 2002, table 1: 1.0)'
  - name: disintegration_probability
    type: float
    default: 0.01
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: 'probability per time step that a link spontaneously disintegrates (Von Kamp 2002, table
      1: 0.01)'
  - name: bond_probability
    type: float
    default: 1.0
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: probability that an admissible bond between two neighbouring links is formed; not published,
      see decisions
  - name: absorption_probability
    type: float
    default: 0.5
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: 'probability per time step that a link tries to absorb a neighbouring substrate (Von Kamp
      2002, table 1: 0.5)'
  - name: emission_probability
    type: float
    default: 0.5
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: 'probability per time step that a link tries to emit its absorbed substrate into a neighbouring
      hole (Von Kamp 2002, table 1: 0.5)'
  - name: bond_inhibition
    type: bool
    default: true
    role: structural
    meaning: 'chain-based bond inhibition: a free link may not bond while chain links are in its neighbourhood.
      This is the rule omitted from the 1974 publication and restored by McMullin & Varela (1997); false
      reproduces the failure of the published algorithm'
  - name: chain_inhibit_count
    type: int
    default: 1
    min: 1
    max: 8
    range: 'Von Kamp (2002) table 1: chainInhibitBondCount = 1, turned off at the neighbourhood size'
    role: structural
    meaning: how many chain links in the neighbourhood of a free link suppress bond formation
  - name: mobility
    type: dict
    default:
      substrate: 0.5
      catalyst: 0.1
      link: 0.1
      hole: 0.5
    role: spatial
    meaning: mobility factor per particle type (Von Kamp 2002, table 1); two neighbours swap with probability
      sqrt(m_i m_j), and a link with one or two bonds is immobile whatever its factor
  provides:
  - topology
  - stoichiometry
  - catalysts
  - space
  - initial-state
  fidelity: reconstructed
  sources:
  - 'Varela, F. J., Maturana, H. R. & Uribe, R. (1974). Autopoiesis: the organization of living systems,
    its characterization and a model. BioSystems 5(4):187-196 (book ref [881]). doi:10.1016/0303-2647(74)90031-8.
    The model and its phenomena are taken from the book''s account of it (6.1.5 and figure 6.3); the paper
    itself could not be retrieved, see decisions.'
  - 'McMullin, B. & Varela, F. J. (1997). Rediscovering Computational Autopoiesis. Santa Fe Institute
    Working Paper 97-02-012; Proc. 4th European Conference on Artificial Life (ECAL 97). Abstract used:
    the re-implementation found that ''chain-based bond inhibition'' was essential to the autopoietic
    phenomenology and undocumented in the original work. https://econpapers.repec.org/paper/wopsafiwp/97-02-012.htm'
  - 'McMullin, B. (2000). Some remarks on autocatalysis and autopoiesis. Annals of the New York Academy
    of Sciences 901:163-174, section 6.4 (SCL: the re-implementation ''specifically corrected a defect
    in the original published description of the model, establishing that a previously undocumented interaction
    (chain inhibition) was in fact essential to the autopoietic phenomenology''). doi:10.1111/j.1749-6632.2000.tb06276.x.
    https://doras.dcu.ie/28135/7/bmcm9901.pdf'
  - 'Von Kamp, A. W. (2002). Self-reproducing entities in an artificial chemistry: implications of autopoietic
    and other organisations. PhD thesis, Dublin City University (McMullin''s group; the work extends McMullin''s
    SCL 0.05.11). Section 2.2 (the qualitative SCL chemistry: particle types, absorption and emission,
    bonds and chains, immobility of bonded links, chain-based bond inhibition, the catalysis reaction,
    spontaneous disintegration), section 2.3.3 (self-maintenance by repair and the role of chain-based
    bond inhibition), section 4.8 (what the extended system changes relative to original SCL), figure
    2 (a 30 x 30 world with a twelve-link membrane) and table 1 (the standard parameter values used here).
    https://doras.dcu.ie/18260/1/A_W_Von_Kamp.pdf'
  - 'McMullin, B. (1997). Computational Autopoiesis: The Original Algorithm. Santa Fe Institute Working
    Paper 97-01-001. The reference documentation of the algorithm; not retrievable (see decisions), so
    its content is used only as reported by Von Kamp (2002).'
  decisions:
  - 'The book (6.1.5 and figure 6.3) gives the three reactions and the phenomena but no algorithm, so
    the lattice model is McMullin''s SCL reconstruction. Variant implemented: the *original* SCL (self-maintenance
    by repair with spontaneously disintegrating links), not the later SCL-DIV of Von Kamp (2002) (lifetime
    units, membrane growth by displacement, catalyst autocatalysis, fission) and not SCL-GRO (McMullin
    & Gross 2001).'
  - 'Neither McMullin (1997) nor McMullin & Varela (1997) could be retrieved: elm.eeng.dcu.ie and www.eeng.dcu.ie
    are offline or have an invalid certificate, the Santa Fe Institute working-paper files 404, and the
    CiteSeerX and Internet Archive mirrors are unreachable from here. The rule set and every published
    number therefore come from Von Kamp (2002), a DCU thesis built on McMullin''s SCL 0.05.11 that documents
    the original system, together with the abstract of McMullin & Varela (1997) and section 6.4 of McMullin
    (2000) for chain-based bond inhibition. The 1974 paper itself is open only at repositorio.uchile.cl,
    behind a proof-of-work wall.'
  - 'Published parameter values (Von Kamp 2002, table 1): mobility factors substrate 0.5, hole 0.5, catalyst
    0.1, link 0.1; productionProbability 1.0; disintegrationProbability 0.01; absorptionProbability 0.5;
    emissionProbability 0.5; chainInhibitBondCount 1; inhibitOnlyFreeLinks true (only free links are inhibited,
    which is what lets a free link close a gap between two singly bonded chain ends). The bonding probability
    of original SCL is not published (SCL-DIV bonds with probability one after scanning the neighbourhood),
    so bond_probability defaults to 1.0 for the single randomly chosen neighbour of the original scheme
    and is flagged here rather than presented as published.'
  - 'Neighbourhoods: the sources do not state them for the square lattice of original SCL. Interactions
    use the 8-cell Moore neighbourhood and motion the 4 von Neumann neighbours, so an 8-connected closed
    chain of links separates the lattice for 4-connected motion and a membrane is genuinely closed. Von
    Kamp (2002, section 4.2) moved to a hexagonal lattice precisely because the rectangular one makes
    such choices ambiguous.'
  - 'Disintegration stoichiometry: the book writes the decay as [O] -> O, but production consumes two
    substrates and leaves a link plus a hole, and the caption of Von Kamp (2002) figure 2 (a 30 x 30 world
    with a twelve-link membrane and one catalyst, ''591 substrates in total ... if all links and catalysts
    disintegrated, there would be 619 substrates'', i.e. 2 x 12 + 4) implies a link disintegrates into
    two substrates. A disintegrating link therefore becomes a substrate and puts a second substrate (and
    its absorbed one, if any) into an adjacent hole when there is one; both L -> 2 S and L -> S appear
    among the observed reactions.'
  - Only chain-based bond inhibition is implemented. The catalyst-based bond inhibition that Von Kamp
    (2002, section 4.8) parameterises as catInhibitBondCount, bond decay (present in McMullin's SCL, absent
    in Varela et al. 1974) and all SCL-DIV mechanisms are not implemented; no probability is published
    for the first two.
  - 'Network: status observed. Species carry the bond state (L0, L1, L2) and the absorbed substrate (L0S,
    L1S, L2S), because both change what a link can do; holes are empty space and not a species, so production
    reads C + 2 S -> C + L0 as in the book. Reactions carry no rate: the probabilities are per-particle
    update probabilities of the lattice algorithm, not rate constants, and no rate law is published. Motion
    is not a reaction. Mode ''reactions'' returns the same species with the reactions the chemistry defines,
    status complete.'
  - 'Dropped v1 parameters: grid (a matrix type) becomes width, height, substrate_density and initial;
    p_bond and p_decay become bond_probability and disintegration_probability, joined by the other published
    probabilities and the mobility factors. Defaults are small: a 30 x 30 world (Von Kamp''s figure 2)
    for 120 steps, which shows the elementary reactions; spontaneous closure around a bare catalyst needs
    thousands of steps, and initial=cell starts from a formed cell instead.'
  reference_impl: McMullin's SCL and Von Kamp's SCL-DIV (Objective-C on Swarm), formerly at http://www.eeng.dcu.ie/~alife/src/scl-div/
    (host offline)
  phenomena:
  - 'spontaneous formation of a closed, substrate-permeable boundary around a catalyst (book figure 6.3:
    links formed at t = 2 bond into a closed boundary by t = 6)'
  - the boundary is permeable to substrate, which crosses by being absorbed and re-emitted by a membrane
    link, and impermeable to links and catalysts, because bonded links are immobile
  - 'regeneration of the boundary after the decay of one of its constituents: a free link inside the cell
    moves into the gap and bonds, re-closing the membrane (Varela et al. 1974)'
  - without chain-based bond inhibition, the rule omitted from the 1974 publication, the free links inside
    a cell bond to each other and to the membrane instead of staying mobile, and ruptures are not repaired
    (McMullin & Varela 1997)
  notes: 'The model that named computational autopoiesis, and the standard example of a chemistry whose
    interesting behaviour lives in space rather than in stoichiometry: the reaction set is three lines,
    and everything depends on who is next to whom. It satisfies the six conditions for an autopoietic
    unit listed in the book; McMullin (2000, section 6.4) argues it still fails a stricter test, because
    two adjacent cells tend to merge rather than keep their individuality.

    '