System Requirements Document for abiogenesis-chemical-evolution

1. Introduction

abiogenesis-chemical-evolution is a complete, interactive, scientifically grounded simulation of abiogenesis and chemical evolution. Its product intent is to test one question: can an initially nonliving chemical environment, continuously driven away from thermodynamic equilibrium by external energy, spontaneously produce persistent autocatalytic systems, compartments, heredity, competition, evolution, and increasingly organism-like entities?

The governing rule of the product is "Script the laws. Do not script life." The simulation begins with chemistry, matter, energy, and environmental gradients. If organized systems emerge, they emerge only because the underlying physical and chemical rules make them possible. The intended causal chain is:

physics → chemistry → reaction networks → self-organization → compartments → replication → variation → differential persistence → evolution

— and only if the simulated conditions allow those things to occur.

The audience is synthetic biologists, origin-of-life researchers, computational chemists, science-curious learners, and museum-grade exhibition visitors. The product is a laboratory instrument with the gravitas of a gallery piece: the data is the aesthetic, and the emotional register is awe, contemplative wonder, and intellectual rigour — the feeling of watching something appear that was never told to appear.

2. System Overview

The system is a web-delivered, backend-executed simulation environment. Users configure an early-Earth chemical world — starting chemical inventory, concentrations, protonation states, environmental gradients, external energy inputs, and mineral surfaces — then start, pause, and advance the simulation over time. The backend performs the actual physical and chemical computation: reaction kinetics, acid/base equilibria, diffusion, gas exchange, mineral surface interactions, amphiphile self-assembly, and the longitudinal tracking of emergent structures. The frontend renders the evolving state as a full-bleed generative visualization and provides instrument-panel inspection surfaces.

Actors. Three accepted human personas operate the product: the Simulation Operator (configures and runs the experiment), the Chemistry Inspector (examines emergent chemistry in detail), and the Emergence Observer (tracks self-organized and increasingly organism-like structures). The simulation engine itself is a non-persona system actor.

Accepted behavior. The system must model water as an explicit bulk continuum solvent; derive local pH from acid/base concentrations; carry a defined initial early-Earth chemical inventory; allow gas exchange between atmosphere and water by solubility and partial pressure; support an extensible chemical grammar that constructs previously unseen species from valid chemical transformations; model mineral surfaces and their adsorption/catalytic roles; and allow amphiphiles to self-assemble into micelles, sheets, droplets, and vesicles that exchange molecules, grow, shrink, fuse, and rupture.

Ownership. Application-owned identity governs access to durable simulation configurations, runs, observations, and inspection history. Configuration and execution surfaces are restricted to the Simulation Operator; inspection surfaces are restricted to the Chemistry Inspector and Emergence Observer respectively.

Narrow exclusions. This is explicitly not a traditional artificial-life simulation. Organisms, metabolism, reproduction, DNA, food, predators, fitness, and species are never manually scripted. There is no spawnLife() equivalent, no if molecule == RNA then reproduce logic, no organism.health += energy logic, and no manually assigned evolutionary fitness score. No organism-like property is ever granted to a structure merely because it has been labeled an organism.

2a. Product Interpretation and Delivery Boundary

The product is delivered as a first-party web application with a backend simulation engine. Identity is application-owned: users establish access through self-service enrollment and return through verification, because durable simulation configurations, run history, observations, and inspection state must remain bound to the correct participant and be resumable across sessions. The anonymous entry surface (Landing) explains the simulation and its law-driven purpose before identity is established; protected configuration, execution, and inspection surfaces remain unavailable until identity is established.

Everything described in this document is current scope. The simulation's emergent outcomes — autocatalytic sets, compartments, heredity, competition, evolution — are not features to be built; they are possible results of the scripted laws and are tracked and observed when they occur. No capability in this document may be implemented by scripting a life outcome.

2b. Source Content Inventory

The authoritative source defines a required initial early-Earth chemical inventory. This inventory is the starting chemistry, not the universe of possible chemistry; additional species are constructed dynamically from valid chemical transformations.

Solvent and acid/base chemistry: H₂O; H\xe2\x81\xba / H\xe2\x82\x83O\xe2\x81\xba; OH⁻. Water is modeled explicitly as the bulk solvent at the continuum level rather than rendering every water molecule. Local pH emerges from acid/base concentrations.

Major dissolved ions: Na\xe2\x81\xba, K\xe2\x81\xba, Mg²\xe2\x81\xba, Ca²\xe2\x81\xba, Fe²\xe2\x81\xba, Fe³\xe2\x81\xba, Ni²\xe2\x81\xba, Zn²\xe2\x81\xba, Mn²\xe2\x81\xba, Cl⁻, HS⁻, S²⁻, SO\xe2\x82\x83²⁻, SO\xe2\x82\x84²⁻, HCO\xe2\x82\x83⁻, CO\xe2\x82\x83²⁻, H₂PO\xe2\x82\x84⁻, HPO\xe2\x82\x84²⁻, PO\xe2\x82\x84³⁻. Their concentrations must influence ionic strength, membrane stability, polymer folding, precipitation, and reaction rates.

Atmospheric / geochemical feedstock: H₂, N₂, CO₂, CO, CH\xe2\x82\x84, NH\xe2\x82\x83, NH\xe2\x82\x84\xe2\x81\xba, H₂S, SO₂. Gas exchange between atmosphere and water occurs according to solubility and partial pressure.

Important prebiotic carbon/nitrogen compounds: HCN (hydrogen cyanide); HNC (hydrogen isocyanide, where appropriate); NH₂CN (cyanamide); HC\xe2\x82\x83N (cyanoacetylene); HCONH₂ (formamide); HCHO (formaldehyde); CH\xe2\x82\x83CHO (acetaldehyde); CH\xe2\x82\x83OH (methanol); HOCH₂CHO (glycolaldehyde); glyceraldehyde; dihydroxyacetone; glyoxal. These participate in kinetic reaction networks and are not merely collectible resources.

Simple organic acids: formic acid / formate; acetic acid / acetate; glycolic acid; lactic acid / lactate; pyruvic acid / pyruvate; oxalic acid / oxalate; malonic acid; succinic acid / succinate; fumaric acid / fumarate; malic acid / malate. Additional carboxylic acids may emerge.

Amino acids (at minimum): glycine, alanine, serine, aspartic acid, glutamic acid, valine, leucine, isoleucine, proline, threonine, cysteine, methionine, phenylalanine. Modern protein synthesis is not assumed; these are simply molecules capable of reactions including condensation into short peptides. Additional amino acids and non-biological amino-acid analogues may form.

Sugars and sugar precursors: formaldehyde; glycolaldehyde; glyceraldehyde; ribose; arabinose; xylose; erythrose; ribulose; simple hexoses when reaction pathways permit. Instability and degradation are included; ribose is not artificially immortal.

Nucleobases and precursors: adenine, guanine, cytosine, uracil, purine, pyrimidine, and related prebiotic heterocycles. Thymine can arise later but does not need to dominate primordial chemistry.

Nucleosides and nucleotides: adenosine, guanosine, cytidine, uridine; AMP, GMP, CMP, UMP. Activated versions are allowed where chemically justified. ADP and ATP should be possible products of chemistry but are not supplied as the universal primordial energy currency; primitive systems should initially be capable of using other energetic chemistry.

Phosphorus chemistry: orthophosphate; pyrophosphate; trimetaphosphate; other condensed phosphates; acetyl phosphate. Phosphate adsorption to minerals and the realistic difficulty of phosphorylation are included.

Sulfur chemistry and energetic intermediates: hydrogen sulfide; bisulfide; sulfide; elemental sulfur where relevant; thiols; methanethiol; simple thioesters; acetyl thioesters. Thioester chemistry should be capable of coupling energetically favorable and unfavorable reactions.

Amphiphiles (families, not a single magic lipid): fatty acids approximately C6–C18 (octanoic acid, decanoic acid, lauric acid, myristic acid, palmitic acid); simple fatty alcohols; glycerol; monoacylglycerols; simple amphiphilic esters. Amphiphilic properties must arise from molecular structure.

Mineral world: FeS / mackinawite; FeS₂ / pyrite; Fe\xe2\x82\x83S\xe2\x82\x84 / greigite; NiS; magnetite; silica; serpentine minerals; olivine-related minerals; brucite; carbonate minerals; iron oxides; clay minerals such as montmorillonite; phosphate-bearing minerals.

2c. Page Content and Component Coverage

Landing

• Information / state: Anonymous public entry. Explains the origin-of-life simulation, its intended users, and its law-driven scientific purpose before identity establishment. Communicates the central rule "Script the laws. Do not script life." and the ultimate experiment question.
• Primary action: Begin the experiment (entry into identity establishment).
• Supporting actions: Navigate to Login for returning users; navigate to Sign Up for new users.
• Domain entities: Simulation premise; the causal chain physics → chemistry → reaction networks → self-organization → compartments → replication → variation → differential persistence → evolution.
• Component responsibilities: Full-viewport generative canvas as the hero (the simulation's own data rendered as generative art); oversized headline overlaid at lower-left; thin amber rule above the headline; one-line subhead; minimal HUD at top-right showing elapsed simulated time and a live count of emergent structures; vertical instrument-control rail at top-left; single text-link CTA "Begin the experiment →" beneath the headline.
• States: Loading — canvas initializes the particle field; Empty — no run context yet, canvas shows ambient primordial inventory; Success — hero renders and CTA is available; Error — canvas fails to initialize, static fallback frame with headline and CTA remains usable; Recovery — retry canvas initialization without losing the entry path.

Login

• Information / state: Returning verification surface. Accepts credentials to resume access to durable simulation configurations, runs, observations, and inspection history.
• Primary action: Verify identity and resume.
• Supporting actions: Navigate to Sign Up; return to Landing.
• Domain entities: User identity; session continuity.
• Component responsibilities: Credential input; submit control; error region; link to enrollment.
• States: Loading — verification in progress; Empty — no credentials entered; Success — identity verified, redirect to the appropriate protected surface; Error — invalid credentials, inline message, inputs preserved; Recovery — retry without re-entering identity.

Sign Up

• Information / state: Self-service enrollment for independently starting users. Establishes a first-use identity that owns durable simulation configurations, runs, and observations.
• Primary action: Create identity and enter the product.
• Supporting actions: Navigate to Login; return to Landing.
• Domain entities: User identity; role assignment (Simulation Operator, Chemistry Inspector, Emergence Observer).
• Component responsibilities: Enrollment inputs; submit control; validation region; link to verification.
• States: Loading — enrollment submission in progress; Empty — no inputs entered; Success — identity created, redirect to the appropriate protected surface; Error — invalid or incomplete input, inline validation, inputs preserved; Recovery — correct and resubmit.

Chemistry Setup

• Information / state: Configures the starting chemical inventory, concentrations, and protonation states drawn from the extensible chemical grammar. Presents the initial early-Earth inventory by class (solvent/acid-base, dissolved ions, atmospheric feedstock, prebiotic carbon/nitrogen compounds, organic acids, amino acids, sugars, nucleobases, nucleosides/nucleotides, phosphorus chemistry, sulfur chemistry, amphiphiles).
• Primary action: Commit the starting chemical configuration.
• Supporting actions: Adjust concentrations; select protonation states; add species from the grammar; remove species; reset to the initial inventory.
• Domain entities: Molecular species; elemental formula; molecular graph; bond topology; molecular mass; formal charge; acid/base groups; oxidation state; polarity; hydrophobicity; solubility; diffusion coefficient; absorption spectrum; approximate heat capacity; bond energies; activation-energy estimates; membrane permeability; adsorption affinity for mineral surfaces; catalytic groups; degradation pathways; polymerization sites; stereochemistry where relevant.
• Component responsibilities: Inventory class panels; concentration dials (circular gauges / radial readouts); protonation-state selectors; species property readouts in tabular numerals; commit control.
• States: Loading — inventory and grammar load; Empty — no species selected, prompt to begin from the initial inventory; Success — configuration committed and available to the run; Error — invalid concentration or incompatible protonation state, inline message; Recovery — correct the offending entry and recommit.

Energy Setup

• Information / state: Configures environmental gradients and external energy inputs that drive the chemical environment away from thermodynamic equilibrium.
• Primary action: Commit the energy and gradient configuration.
• Supporting actions: Set gradient magnitudes and directions; set external energy input levels; reset to defaults.
• Domain entities: Environmental gradients; external energy inputs; thermodynamic disequilibrium parameters.
• Component responsibilities: Gradient controls; energy-input controls; live readout of configured disequilibrium; commit control.
• States: Loading — parameter schema loads; Empty — no gradients configured, prompt to set at least one driving input; Success — configuration committed; Error — out-of-range or inconsistent input, inline message; Recovery — correct and recommit.

Minerals

• Information / state: Configures mineral surfaces and their adsorption and catalytic roles in the early-Earth chemical environment. Presents the mineral world: FeS / mackinawite, FeS₂ / pyrite, Fe\xe2\x82\x83S\xe2\x82\x84 / greigite, NiS, magnetite, silica, serpentine minerals, olivine-related minerals, brucite, carbonate minerals, iron oxides, clay minerals such as montmorillonite, and phosphate-bearing minerals.
• Primary action: Commit the mineral surface configuration.
• Supporting actions: Select mineral species; set surface abundance; set adsorption affinity; set catalytic role; reset.
• Domain entities: Mineral species; surface abundance; adsorption affinity; catalytic role; phosphate adsorption.
• Component responsibilities: Mineral selection panels; abundance controls; adsorption/catalytic readouts; commit control.
• States: Loading — mineral catalog loads; Empty — no minerals selected, prompt to select surfaces; Success — configuration committed; Error — invalid abundance or unsupported combination, inline message; Recovery — correct and recommit.

Simulation

• Information / state: The revisitable execution workspace for starting, pausing, and advancing the simulation over time. Shows current run state, elapsed simulated time, and the live emergent-systems census.
• Primary action: Start, pause, and advance the simulation.
• Supporting actions: Reset the run; adjust time scale; revisit a prior run; observe the live census (vesicle count, autocatalytic set count, polymer length distribution).
• Domain entities: Run; elapsed simulated time; time scale; emergent-systems census; environmental parameters (temperature, pH, redox, energy flux).
• Component responsibilities: Fixed left-edge vertical rail (64px desktop, 48px bottom bar on mobile) holding run/pause/reset controls and time-scale; top-left HUD for environmental parameters; top-right HUD for the emergent-systems census; bottom-left molecular inventory ticker; full-bleed simulation canvas.
• States: Loading — run state and canvas initialize; Empty — no run started, prompt to begin; Success — run advancing, census updating; Error — run fails to advance, inline message with the failing condition; Recovery — pause, correct configuration, resume or restart without losing the run record.

Chemistry

• Information / state: Presents the evolving molecular species, concentrations, local pH, ionic strength, and reaction networks for inspection.
• Primary action: Inspect the current chemical state.
• Supporting actions: Filter by species class; inspect reaction networks; read local pH and ionic strength; follow concentration over time.
• Domain entities: Molecular species; concentration; local pH; ionic strength; reaction networks; reaction rates.
• Component responsibilities: Species concentration views; pH and ionic-strength readouts; reaction-network diagrams; tabular numerals in IBM Plex Mono.
• States: Loading — chemical state loads; Empty — no run data yet, prompt to start a run; Success — state rendered; Error — state unavailable, inline message; Recovery — retry load.

Molecules

• Information / state: Focused inspection of individual and dynamically constructed molecular species and their chemical properties.
• Primary action: Inspect a selected molecule.
• Supporting actions: Browse dynamically constructed species; read the full property set; trace the valid chemical transformations that produced the species.
• Domain entities: Molecular species; elemental formula; molecular graph; bond topology; molecular mass; formal charge; acid/base groups; oxidation state; polarity; hydrophobicity; solubility; diffusion coefficient; absorption spectrum; approximate heat capacity; bond energies; activation-energy estimates; membrane permeability; adsorption affinity for mineral surfaces; catalytic groups; degradation pathways; polymerization sites; stereochemistry.
• Component responsibilities: Species list; property panel; transformation provenance view.
• States: Loading — species index loads; Empty — no species match the current filter; Success — species and properties rendered; Error — species unavailable, inline message; Recovery — retry or clear filter.

Structures

• Information / state: Tracks emergent micelles, sheets, droplets, and vesicles through growth, shrinkage, fusion, and rupture.
• Primary action: Inspect an emergent structure.
• Supporting actions: Follow a structure's lifecycle; observe molecule exchange; observe growth, shrinkage, fusion, and rupture events.
• Domain entities: Micelle; sheet; droplet; vesicle; molecule exchange; growth; shrinkage; fusion; rupture.
• Component responsibilities: Structure list; lifecycle timeline; event markers; translucent vesicle membrane rendering as thin refractive shells.
• States: Loading — structure index loads; Empty — no structures have formed yet, prompt to continue the run; Success — structures and lifecycles rendered; Error — structure data unavailable, inline message; Recovery — retry load.

Emergence

• Information / state: Tracks the appearance and persistence of autocatalytic systems, compartments, replication, variation, and differential persistence.
• Primary action: Inspect emergence events.
• Supporting actions: Follow persistence over time; inspect autocatalytic sets; inspect compartments; inspect replication and variation events; inspect differential persistence.
• Domain entities: Autocatalytic system; compartment; replication; variation; differential persistence; persistence duration.
• Component responsibilities: Emergence timeline; autocatalytic-set census; persistence tracking; emergence bloom markers on the canvas.
• States: Loading — emergence index loads; Empty — nothing has emerged yet, prompt to continue the run; Success — emergence events and persistence rendered; Error — emergence data unavailable, inline message; Recovery — retry load.

3. Functional Requirements

FR-1 — Build the simulation. As a Simulation Operator, I should have a complete, interactive, scientifically grounded simulation of abiogenesis and chemical evolution, so that I can run the origin-of-life experiment. (explicit)

• Trigger/input: Operator opens the product and starts a run.
• Observable result: A running simulation whose state advances according to physical and chemical rules.
• Access state: Protected; requires established identity.
• Failure/recovery: If the run fails to advance, the failing condition is surfaced and the run can be paused, corrected, and resumed.
• Continuation: Operator proceeds to configure or observe the run.

FR-2 — No traditional artificial-life scripting. As a Simulation Operator, I should have a simulation in which organisms, metabolism, reproduction, DNA, food, predators, fitness, and species are never manually scripted, so that any organized system that appears is genuinely emergent. (explicit)

• Trigger/input: Any run.
• Observable result: No scripted organism, metabolism, reproduction, DNA, food, predator, fitness, or species behavior exists in the simulation.
• Access state: Not applicable.
• Failure/recovery: Not applicable — this is a binding constraint on implementation.
• Continuation: All behavior proceeds from the scripted laws.

FR-3 — Script the laws, not life. As a Simulation Operator, I should have the simulation begin with chemistry, matter, energy, and environmental gradients, so that organized systems emerge only because the underlying physical and chemical rules make them possible. (explicit)

• Trigger/input: Run initialization.
• Observable result: The initial state contains only chemistry, matter, energy, and gradients.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: The causal chain proceeds only if conditions allow.

FR-4 — The ultimate experiment. As a Simulation Operator, I should be able to determine whether an initially nonliving chemical environment, continuously driven away from thermodynamic equilibrium by external energy, spontaneously produces persistent autocatalytic systems, compartments, heredity, competition, evolution, and increasingly organism-like entities. (explicit)

• Trigger/input: A configured run with external energy driving the environment away from equilibrium.
• Observable result: The run either produces these outcomes or does not; the outcome is observable in the Emergence and Structures surfaces.
• Access state: Protected.
• Failure/recovery: If no emergence occurs, the run continues and the conditions can be adjusted.
• Continuation: Operator inspects and iterates.

FR-5 — No spawnLife() equivalent. As a Simulation Operator, I should never encounter a command equivalent to spawnLife(), so that life is never directly created. (explicit)

• Trigger/input: Any interaction.
• Observable result: No such command exists.
• Access state: Not applicable.
• Failure/recovery: Not applicable — binding constraint.
• Continuation: Not applicable.

FR-6 — No if molecule == RNA then reproduce logic. As a Simulation Operator, I should never encounter logic equivalent to if molecule == RNA then reproduce, so that replication is never triggered by a molecule label. (explicit)

• Trigger/input: Any run.
• Observable result: No such logic exists.
• Access state: Not applicable.
• Failure/recovery: Not applicable — binding constraint.
• Continuation: Not applicable.

FR-7 — No organism.health += energy logic. As a Simulation Operator, I should never encounter logic equivalent to organism.health += energy, so that organism health is never directly incremented. (explicit)

• Trigger/input: Any run.
• Observable result: No such logic exists.
• Access state: Not applicable.
• Failure/recovery: Not applicable — binding constraint.
• Continuation: Not applicable.

FR-8 — No manually assigned evolutionary fitness score. As a Simulation Operator, I should never encounter a manually assigned evolutionary fitness score, so that differential persistence arises only from the chemistry. (explicit)

• Trigger/input: Any run.
• Observable result: No fitness score is assigned.
• Access state: Not applicable.
• Failure/recovery: Not applicable — binding constraint.
• Continuation: Not applicable.

FR-9 — Intended causal chain. As a Simulation Operator, I should observe the causal chain physics → chemistry → reaction networks → self-organization → compartments → replication → variation → differential persistence → evolution, if the simulated conditions allow those things to occur. (explicit)

• Trigger/input: A run with conditions that permit the chain.
• Observable result: The chain proceeds or halts according to the conditions.
• Access state: Protected.
• Failure/recovery: If the chain halts, the run continues and conditions can be adjusted.
• Continuation: Operator inspects the chain's progress.

FR-10 — Life as a special organizational state of ordinary matter. As a Simulation Operator, I should have the simulation begin with no distinction between "living" and "nonliving," with everything consisting of chemicals interacting according to the same rules. (explicit)

• Trigger/input: Run initialization.
• Observable result: No living/nonliving distinction exists in the initial state.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: All structures are treated as chemicals.

FR-11 — Organism-like properties are earned, not labeled. As a Simulation Operator, I should have a structure become organism-like only because it maintains chemical disequilibria, captures usable free energy, acquires raw materials, catalyzes reactions, repairs or replaces components, preserves internal conditions, contains reaction networks, creates copies or descendants, transmits chemically encoded information, produces imperfect descendants, competes for limited resources, and consequently undergoes natural selection. (explicit)

• Trigger/input: A structure's actual behavior in the run.
• Observable result: Organism-like properties are observed only where the structure actually exhibits them.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Observer tracks the structure's persistence.

FR-12 — No organism-like properties by label. As a Simulation Operator, I should never see organism-like properties given to a structure merely because it has been labeled an organism. (explicit)

• Trigger/input: Any run.
• Observable result: No label grants properties.
• Access state: Not applicable.
• Failure/recovery: Not applicable — binding constraint.
• Continuation: Not applicable.

FR-13 — Extensible chemical grammar. As a Simulation Operator, I should have an extensible chemical grammar rather than an attempt to enumerate all possible chemicals, so that previously unseen molecular species can be constructed dynamically from valid chemical transformations. (explicit)

• Trigger/input: A valid chemical transformation occurs in the run.
• Observable result: A previously unseen molecular species is constructed and becomes inspectable.
• Access state: Protected.
• Failure/recovery: If a transformation is invalid, no species is constructed.
• Continuation: The new species participates in the reaction network.

FR-14 — Molecular species properties. As a Chemistry Inspector, I should be able to inspect each molecular species' elemental formula, molecular graph, bond topology, molecular mass, formal charge, acid/base groups, oxidation state, polarity, hydrophobicity, solubility, diffusion coefficient, absorption spectrum, approximate heat capacity, bond energies, activation-energy estimates, membrane permeability, adsorption affinity for mineral surfaces, catalytic groups, degradation pathways, polymerization sites, and stereochemistry where relevant. (explicit)

• Trigger/input: Inspector selects a species.
• Observable result: The full property set is displayed.
• Access state: Protected; Chemistry Inspector.
• Failure/recovery: If a property is unavailable, the panel indicates it.
• Continuation: Inspector inspects another species.

FR-15 — Initial library is starting chemistry. As a Simulation Operator, I should have the initial chemical library treated as the starting chemistry, not the universe of possible chemistry. (explicit)

• Trigger/input: Run initialization.
• Observable result: The initial inventory is present; new species can still be constructed.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: The run proceeds.

FR-16 — Solvent and acid/base chemistry. As a Simulation Operator, I should have H₂O, H\xe2\x81\xba / H\xe2\x82\x83O\xe2\x81\xba, and OH⁻ present, with water modeled explicitly as the bulk solvent at the continuum level rather than rendering every water molecule, and local pH emerging from acid/base concentrations. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: Local pH is derived from acid/base concentrations and is inspectable.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: pH influences the ongoing chemistry.

FR-17 — Major dissolved ions. As a Simulation Operator, I should have Na\xe2\x81\xba, K\xe2\x81\xba, Mg²\xe2\x81\xba, Ca²\xe2\x81\xba, Fe²\xe2\x81\xba, Fe³\xe2\x81\xba, Ni²\xe2\x81\xba, Zn²\xe2\x81\xba, Mn²\xe2\x81\xba, Cl⁻, HS⁻, S²⁻, SO\xe2\x82\x83²⁻, SO\xe2\x82\x84²⁻, HCO\xe2\x82\x83⁻, CO\xe2\x82\x83²⁻, H₂PO\xe2\x82\x84⁻, HPO\xe2\x82\x84²⁻, and PO\xe2\x82\x84³⁻ present, with their concentrations influencing ionic strength, membrane stability, polymer folding, precipitation, and reaction rates. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: Ionic strength, membrane stability, polymer folding, precipitation, and reaction rates respond to ion concentrations.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Ion chemistry continues.

FR-18 — Atmospheric / geochemical feedstock and gas exchange. As a Simulation Operator, I should have H₂, N₂, CO₂, CO, CH\xe2\x82\x84, NH\xe2\x82\x83, NH\xe2\x82\x84\xe2\x81\xba, H₂S, and SO₂ present, with gas exchange between atmosphere and water according to solubility and partial pressure. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: Gases exchange between atmosphere and water according to solubility and partial pressure.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Gas exchange continues.

FR-19 — Prebiotic carbon/nitrogen compounds in kinetic networks. As a Simulation Operator, I should have HCN, HNC where appropriate, NH₂CN (cyanamide), HC\xe2\x82\x83N (cyanoacetylene), HCONH₂ (formamide), HCHO (formaldehyde), CH\xe2\x82\x83CHO (acetaldehyde), CH\xe2\x82\x83OH (methanol), HOCH₂CHO (glycolaldehyde), glyceraldehyde, dihydroxyacetone, and glyoxal present and participating in kinetic reaction networks rather than being treated merely as collectible resources. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These compounds participate in kinetic reaction networks.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Network chemistry continues.

FR-20 — Simple organic acids. As a Simulation Operator, I should have formic acid / formate, acetic acid / acetate, glycolic acid, lactic acid / lactate, pyruvic acid / pyruvate, oxalic acid / oxalate, malonic acid, succinic acid / succinate, fumaric acid / fumarate, and malic acid / malate present, and additional carboxylic acids should be able to emerge. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These acids are present; additional carboxylic acids emerge when pathways permit.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Acid chemistry continues.

FR-21 — Amino acids. As a Simulation Operator, I should have at minimum glycine, alanine, serine, aspartic acid, glutamic acid, valine, leucine, isoleucine, proline, threonine, cysteine, methionine, and phenylalanine present as molecules capable of reactions including condensation into short peptides, without assuming modern protein synthesis, and additional amino acids and non-biological amino-acid analogues may form. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These amino acids are present and can condense into short peptides; additional amino acids and analogues may form.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Peptide chemistry continues.

FR-22 — Sugars and sugar precursors with instability. As a Simulation Operator, I should have formaldehyde, glycolaldehyde, glyceraldehyde, ribose, arabinose, xylose, erythrose, ribulose, and simple hexoses when reaction pathways permit, including instability and degradation, and ribose must not be artificially immortal. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These sugars are present, degrade realistically, and ribose is not artificially immortal.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Sugar chemistry continues.

FR-23 — Nucleobases and precursors. As a Simulation Operator, I should have adenine, guanine, cytosine, uracil, purine, pyrimidine, and related prebiotic heterocycles present, with thymine able to arise later without dominating primordial chemistry. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These nucleobases are present; thymine may arise later.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Nucleobase chemistry continues.

FR-24 — Nucleosides and nucleotides. As a Simulation Operator, I should have adenosine, guanosine, cytidine, uridine, AMP, GMP, CMP, and UMP present, with activated versions allowed where chemically justified, and ADP and ATP should be possible products of chemistry but not supplied as the universal primordial energy currency, with primitive systems initially capable of using other energetic chemistry. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These nucleosides and nucleotides are present; ADP and ATP arise as products; other energetic chemistry is usable.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Nucleotide chemistry continues.

FR-25 — Phosphorus chemistry. As a Simulation Operator, I should have orthophosphate, pyrophosphate, trimetaphosphate, other condensed phosphates, and acetyl phosphate present, including phosphate adsorption to minerals and the realistic difficulty of phosphorylation. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These phosphorus species are present; phosphate adsorbs to minerals; phosphorylation is realistically difficult.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Phosphorus chemistry continues.

FR-26 — Sulfur chemistry and energetic intermediates. As a Simulation Operator, I should have hydrogen sulfide, bisulfide, sulfide, elemental sulfur where relevant, thiols, methanethiol, simple thioesters, and acetyl thioesters present, with thioester chemistry capable of coupling energetically favorable and unfavorable reactions. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These sulfur species are present; thioester chemistry couples favorable and unfavorable reactions.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Sulfur chemistry continues.

FR-27 — Amphiphile families. As a Simulation Operator, I should have amphiphiles as families rather than a single magic lipid — fatty acids approximately C6–C18 (octanoic acid, decanoic acid, lauric acid, myristic acid, palmitic acid), simple fatty alcohols, glycerol, monoacylglycerols, and simple amphiphilic esters — with amphiphilic properties arising from molecular structure. (explicit)

• Trigger/input: Run initialization and ongoing chemistry.
• Observable result: These amphiphile families are present; amphiphilic properties arise from structure.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Amphiphile chemistry continues.

FR-28 — Spontaneous amphiphile self-assembly. As an Emergence Observer, I should see amphiphiles above appropriate concentrations spontaneously form micelles, sheets, droplets, and vesicles, and exchange molecules, grow, shrink, fuse, and rupture, with no "cell membrane object" scripted first — a membrane originates from amphiphile self-assembly. (explicit)

• Trigger/input: Amphiphile concentration exceeds the appropriate threshold.
• Observable result: Micelles, sheets, droplets, and vesicles form; they exchange molecules, grow, shrink, fuse, and rupture.
• Access state: Protected; Emergence Observer.
• Failure/recovery: If no self-assembly occurs, the run continues and conditions can be adjusted.
• Continuation: Observer tracks the structures in the Structures surface.

FR-29 — Coarse-grained membrane model permitted. As a Simulation Operator, I should have the option for fully atomistic membrane simulation to be replaced with a validated coarse-grained membrane model for computational scalability. (explicit)

• Trigger/input: Computational scalability requirement.
• Observable result: A validated coarse-grained membrane model may be used.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Membrane behavior continues to be simulated.

FR-30 — Mineral world. As a Simulation Operator, I should have mineral surfaces present — FeS / mackinawite, FeS₂ / pyrite, Fe\xe2\x82\x83S\xe2\x82\x84 / greigite, NiS, magnetite, silica, serpentine minerals, olivine-related minerals, brucite, carbonate minerals, iron oxides, clay minerals such as montmorillonite, and phosphate-bearing minerals — because early-Earth chemistry did not occur in an empty beaker. (explicit)

• Trigger/input: Run initialization.
• Observable result: These mineral surfaces are present and participate in the chemistry.
• Access state: Protected.
• Failure/recovery: Not applicable.
• Continuation: Mineral chemistry continues.

FR-31 — Self-service enrollment. As a new user, I should be able to enroll myself so that I can independently start using the simulation. (required_inference)

• Trigger/input: New user opens Sign Up.
• Observable result: An identity is created and the user enters the product.
• Access state: Anonymous entry.
• Failure/recovery: Invalid or incomplete input is reported inline and inputs are preserved.
• Continuation: User proceeds to configure or observe.

FR-32 — Returning verification. As a returning user, I should be able to verify my identity so that I can resume access to durable simulation configurations, runs, observations, and inspection history. (required_inference)

• Trigger/input: Returning user opens Login.
• Observable result: Identity is verified and the user resumes access.
• Access state: Anonymous entry.
• Failure/recovery: Invalid credentials are reported inline and inputs are preserved.
• Continuation: User proceeds to the appropriate protected surface.

FR-33 — Role-aware authorization. As a Simulation Operator, I should have configuration and execution access, and as a Chemistry Inspector or Emergence Observer, I should have observational inspection access, so that the correct participant reaches the correct surface. (required_inference)

• Trigger/input: Authenticated user navigates to a protected surface.
• Observable result: Access is granted or denied according to role.
• Access state: Protected.
• Failure/recovery: Denied access is reported and the user is returned to an allowed surface.
• Continuation: User proceeds within their allowed surfaces.

FR-34 — Backend execution. As a Simulation Operator, I should have durable simulation state, chemical transformations, emergent structures, and longitudinal tracking executed on the backend, so that runs persist and can be resumed. (required_inference)

• Trigger/input: A run is started or resumed.
• Observable result: Simulation state persists and advances on the backend.
• Access state: Protected.
• Failure/recovery: If backend execution fails, the run is paused and the failure is surfaced.
• Continuation: Operator resumes or restarts.

4. User Personas

Simulation Operator

Product context. The Simulation Operator is the person who sets up and runs the origin-of-life experiment. They work at the configuration and execution layer: they define the starting chemical inventory, the environmental gradients and external energy inputs, and the mineral surfaces, then start, pause, and advance the simulation over time.

Primary goal. To observe whether persistent autocatalytic systems, compartments, heredity, and evolution emerge from the scripted physical and chemical rules without any scripted life, and to inspect the resulting chemical and organizational state.

Distinct accepted responsibilities. The Operator owns the configuration surfaces (Chemistry Setup, Energy Setup, Minerals) and the execution surface (Simulation). They commit the starting chemical inventory, concentrations, and protonation states from the extensible chemical grammar; they commit the environmental gradients and external energy inputs that drive the environment away from equilibrium; they commit the mineral surface configuration; and they start, pause, advance, and reset the run.

Relevant inputs or decisions. Which species and concentrations to start from; which protonation states to use; which gradients and energy inputs to apply; which mineral surfaces to include and at what abundance; when to start, pause, advance, or reset.

Interactions with other accepted participants. The Operator's configuration and execution produce the state that the Chemistry Inspector and Emergence Observer inspect. The Operator does not perform the inspection work; they produce the run that makes it possible.

Observable success. A run that advances according to the scripted laws, with the configured chemistry, gradients, and minerals in effect, and with the emergent-systems census updating.

Chemistry Inspector

Product context. The Chemistry Inspector examines the emergent chemistry in detail. They work at the inspection layer: molecular species, reaction networks, concentrations, pH, ionic strength, and the properties of dynamically constructed molecules.

Primary goal. To verify that observed structures and reaction pathways arise from valid chemical transformations and the underlying rules rather than from scripted outcomes.

Distinct accepted responsibilities. The Inspector owns the Chemistry and Molecules surfaces. They inspect the evolving molecular species, concentrations, local pH, ionic strength, and reaction networks; they inspect individual and dynamically constructed molecular species and their full property set; and they trace the valid chemical transformations that produced a species.

Relevant inputs or decisions. Which species or reaction network to inspect; which dynamically constructed molecule to examine; which property to verify.

Interactions with other accepted participants. The Inspector depends on the Simulation Operator's run for the state they inspect. Their verification work is distinct from the Emergence Observer's structural tracking.

Observable success. A verified chain of valid chemical transformations behind every observed species and pathway, with no scripted outcome.

Emergence Observer

Product context. The Emergence Observer watches for and tracks the appearance of self-organized structures such as micelles, sheets, droplets, and vesicles, and any autocatalytic or replicating systems that arise.

Primary goal. To detect and follow the emergence of increasingly organism-like entities and differential persistence over time, confirming that nothing was explicitly told to the program to make.

Distinct accepted responsibilities. The Observer owns the Structures and Emergence surfaces. They track emergent micelles, sheets, droplets, and vesicles through growth, shrinkage, fusion, and rupture; they track the appearance and persistence of autocatalytic systems, compartments, replication, variation, and differential persistence; and they follow persistence over time.

Relevant inputs or decisions. Which structure or emergence event to follow; how long to track persistence; which autocatalytic set or compartment to inspect.

Interactions with other accepted participants. The Observer depends on the Simulation Operator's run for the state they track. Their structural and emergence tracking is distinct from the Chemistry Inspector's molecular verification.

Observable success. A tracked record of emergence events and persistence that confirms the structures arose from the scripted laws rather than from any explicit instruction.

5. Core User Flows

Flow 1 — Simulation Operator: First use and run configuration

1. The Operator arrives at Landing anonymously and reads the simulation's purpose and the central rule "Script the laws. Do not script life."
2. The Operator selects "Begin the experiment →" and proceeds to Sign Up.
3. On Sign Up, the Operator enters enrollment details and submits. The system creates the identity and assigns the Simulation Operator role.
4. The Operator lands on Chemistry Setup and configures the starting chemical inventory, concentrations, and protonation states from the extensible chemical grammar, drawing on the initial early-Earth inventory by class.
5. The Operator commits the chemical configuration. If a concentration or protonation state is invalid, an inline message appears and the Operator corrects it and recommits.
6. The Operator proceeds to Energy Setup and configures the environmental gradients and external energy inputs that drive the environment away from equilibrium, then commits.
7. The Operator proceeds to Minerals and selects the mineral surfaces and their adsorption and catalytic roles, then commits.
8. The Operator proceeds to Simulation and starts the run. The run advances on the backend, the elapsed simulated time and emergent-systems census update, and the canvas renders the evolving state.
9. The Operator pauses, adjusts the time scale, or resets as needed. If the run fails to advance, the failing condition is surfaced, and the Operator pauses, corrects the configuration, and resumes or restarts without losing the run record.
10. The Operator continues to observe the run and may hand off inspection to the Chemistry Inspector and Emergence Observer.

Flow 2 — Simulation Operator: Returning to resume a run

1. The Operator arrives at Landing and selects Login.
2. On Login, the Operator enters credentials and submits. If credentials are invalid, an inline message appears and the inputs are preserved; the Operator retries.
3. On successful verification, the Operator resumes access to their durable simulation configurations, runs, observations, and inspection history.
4. The Operator proceeds to Simulation, revisits a prior run, and resumes advancing it.
5. The Operator continues to observe and may adjust configuration as needed.

Flow 3 — Chemistry Inspector: Verifying emergent chemistry

1. The Chemistry Inspector arrives at Landing and proceeds through Login (or Sign Up on first use) to establish access.
2. The Inspector opens Chemistry and inspects the evolving molecular species, concentrations, local pH, ionic strength, and reaction networks. If no run data exists yet, the surface prompts them to start a run.
3. The Inspector filters by species class and follows concentration over time.
4. The Inspector opens Molecules and selects a species — including a dynamically constructed one — to inspect its full property set and trace the valid chemical transformations that produced it.
5. If a species is unavailable or a filter returns nothing, the surface indicates it and the Inspector retries or clears the filter.
6. The Inspector verifies that the observed structures and reaction pathways arise from valid chemical transformations and the underlying rules rather than from scripted outcomes, and continues inspecting.

Flow 4 — Emergence Observer: Tracking self-organization and emergence

1. The Emergence Observer arrives at Landing and proceeds through Login (or Sign Up on first use) to establish access.
2. The Observer opens Structures and tracks emergent micelles, sheets, droplets, and vesicles through growth, shrinkage, fusion, and rupture. If no structures have formed yet, the surface prompts them to continue the run.
3. The Observer follows a structure's lifecycle and observes molecule exchange and the growth, shrinkage, fusion, and rupture events.
4. The Observer opens Emergence and tracks the appearance and persistence of autocatalytic systems, compartments, replication, variation, and differential persistence. If nothing has emerged yet, the surface prompts them to continue the run.
5. When a new autocatalytic set or vesicle forms, the canvas announces it with a luminous bloom that settles into the ambient flow.
6. The Observer follows persistence over time and confirms that nothing was explicitly told to the program to make, then continues tracking.

Flow 5 — System: Backend simulation execution

1. The Simulation Operator starts or resumes a run on Simulation.
2. The backend executes the physical and chemical computation: reaction kinetics, acid/base equilibria, diffusion, gas exchange, mineral surface interactions, amphiphile self-assembly, and longitudinal tracking of emergent structures.
3. The backend persists durable simulation state so the run can be resumed.
4. The frontend renders the evolving state on the canvas and updates the environmental-parameter HUD, the emergent-systems census, and the molecular inventory ticker.
5. If backend execution fails, the run is paused and the failure is surfaced to the Operator, who resumes or restarts.

6. Visuals, Colors, and Theme

The creative direction is authoritative: Data made physical — an origin-of-life simulation rendered as a living generative artwork, after the muse Refik Anadol. The headline is "SCRIPT THE LAWS. NOT THE LIFE." The data is the aesthetic; every visual element is derived from simulation state.

Mode. Dark mode only.

Palette (dark mode).

Data-driven color alphabet (procedural, not fixed UI colors). Molecular classes are assigned hues procedurally so the palette itself evolves with the chemistry: violet #8B5CF6 for nucleotides; coral #E8635A for reactive intermediates; sage #7A9E6B for mineral surfaces; amber #C8A24E for energy; teal #3DD6C8 for amphiphiles.

Typography. Headings: Space Grotesk at 300–500 weight, wide, geometric, slightly technical, with generous tracking (+0.02em) on display sizes and tight leading (0.95–1.05) on large headlines. Uppercase micro-labels in Space Grotesk 500 at 11px with +0.15em tracking for data readouts and section markers. Body: IBM Plex Sans 400 at 15–16px, 1.6 line-height, for its scientific-instrument character and excellent numeral legibility. Numbers and chemical formulas: IBM Plex Mono 400 for tabular alignment.

Type scale. 1.25 modular, fluid: display clamp(48px, 8vw, 128px); h1 clamp(32px, 5vw, 64px); h2 clamp(24px, 3vw, 40px); h3 24px; body 16px; small 13px; micro-label 11px. Display type uses clamp() so the headline scales from 48px on mobile to 128px on desktop without ever cropping or overflowing.

Shape language. Full-bleed generative canvas as the dominant surface — no card chrome, no rounded rectangles floating on gradients. Thin luminous strokes (1px, 40–60% opacity) for data overlays and HUD elements. Circular gauges and radial readouts for concentration dials. Section boundaries are soft horizontal light-washes rather than hard rules. The only rectangles are data panels with 0px radius and 1px hairline borders at 15% opacity — instrument-panel austerity, not SaaS softness.

Spacing rhythm. A 12-column grid with a fixed 64px left-edge vertical rail on desktop (collapsed to a 48px bottom bar on mobile). HUD panels float at the canvas corners. Generous vertical rhythm between editorial sections below the fold.

Imagery style. The simulation's own data rendered as generative art: particle fields colored by molecular class, fluid-dynamic flows showing concentration gradients, luminous filament networks showing reaction pathways, translucent vesicle membranes rendered as thin refractive shells. Mineral surfaces appear as textured planes with subtle topographic displacement. No stock photography, no 3D product renders, no illustration.

Forbidden. Centered headline + subtext + blue button + gradient blob hero; white or near-white background with blue/indigo accent; Inter, Roboto, Arial, Helvetica, Open Sans, Lato, Poppins, or system-ui for headings or body; grid of identical hover-lift cards; stock photography, 3D product renders, or flat clip-art illustration; any UI element that implies scripted life (organism icons, health bars, fitness scores, species labels); rounded-rectangle glassmorphism panels with soft shadows; decorative motion that does not correspond to simulation state.

7. Signature Design Concept

The public entry is a full-viewport (100vh) generative canvas on a #05060A void. The dominant element is a slow-churning 3D particle field — 40,000 points at 60fps — representing the primordial chemical inventory, colored by molecular class (amber for energy carriers, teal for amphiphiles, violet for nucleotides, coral for reactive intermediates). Particles drift with curl-noise advection, occasionally clustering into transient luminous structures that bloom and dissolve.

Overlaid at the lower-left, spanning 8 of 12 columns, is a single oversized headline in Space Grotesk 300 at clamp(48px, 8vw, 128px), reading "SCRIPT THE LAWS. NOT THE LIFE." in warm off-white (#E8E4DC), with a thin amber rule above it and a one-line subhead in IBM Plex Sans 16px at 70% opacity. At the top-right corner, a minimal HUD shows elapsed simulated time and a live count of emergent structures. At the top-left, a vertical rail of instrument controls. The composition is asymmetric, the canvas bleeds to all edges, and no gradient blob, no centered stack, and no blue button appears anywhere. The CTA is a single text link "Begin the experiment →" in amber at 14px, positioned beneath the headline.

The signature moves are: the full-bleed generative particle canvas as the hero (never a static image); the emergence bloom — when a new autocatalytic set or vesicle forms, a luminous pulse expands from its location and settles into the ambient flow, announcing emergence without any scripted "life" event; the instrument-panel HUD with hairline borders at 15% opacity, tabular numerals in IBM Plex Mono, and a live molecular inventory ticker scrolling along the bottom edge; the scroll-linked scale morph — as the user scrolls from hero into narrative, the camera pulls back from molecular to planetary scale, the particle field resolving into a globe-like distribution; and the data-driven color alphabet assigned procedurally by molecular class, so the palette itself evolves as new species emerge.

8. Interaction Model & Motion Direction

Interaction Model: Animated Motion Tempo: cinematic Hero Dimensionality: webgl

Landing Hero Motion Brief. The focal subject is the primordial chemical inventory rendered as a slow-churning 3D particle field of 40,000 points, colored by molecular class. The input→transformation→outcome thesis: ambient curl-noise advection (input) causes particles to cluster into transient luminous structures that bloom and dissolve (transformation), so the viewer sees order appearing from simple laws without any scripted life event (outcome). The motion vocabulary is continuous slow generative flow — the canvas never freezes, even when the simulation is paused, because the visualization breathes at 0.1Hz to signal that the system is alive; particle fields drift with curl-noise advection; when a new autocatalytic set emerges, a brief luminous bloom pulses outward from its location and then settles into the ambient flow; scroll-linked morphing pulls the camera back from molecular to planetary scale as the user scrolls from hero to narrative, the particle field resolving into a globe-like distribution. The composed first frame is the full-viewport canvas on #05060A with the particle field already drifting, the headline at lower-left, the amber rule above it, the subhead beneath, the top-right HUD showing elapsed simulated time and a live emergent-structure count, the top-left instrument rail, and the amber CTA text link beneath the headline. The reduced-motion state falls back to a static frame with a subtle CSS opacity pulse on emerging structures, and all data panels become scrollable lists.

Landing Hero 3D Scene Brief — DIRECTION-DERIVED. One crafted real-time scene: a 40,000-point particle field advected by curl noise on a #05060A void, with points colored by molecular class (amber energy, teal amphiphile, violet nucleotide, coral reactive intermediate, sage mineral). The scene shows the product's defining state — a primordial chemical inventory in continuous motion, occasionally clustering into transient luminous structures that bloom and dissolve — so the viewer sees emergence as a visual fact rather than a claim. The scene is asymmetric, bleeds to all edges, and never freezes.

9. Non-Functional Requirements

NFR-1 — No scripted life. The simulation must never contain a command equivalent to spawnLife(), logic equivalent to if molecule == RNA then reproduce, logic equivalent to organism.health += energy, or a manually assigned evolutionary fitness score. (explicit) — Rationale: the central rule "Script the laws. Do not script life."

NFR-2 — No scripted artificial-life constructs. Organisms, metabolism, reproduction, DNA, food, predators, fitness, and species must never be manually scripted. (explicit) — Rationale: the product is explicitly not a traditional artificial-life simulation.

NFR-3 — No organism-like properties by label. No organism-like property may be granted to a structure merely because it has been labeled an organism. (explicit) — Rationale: life is a special organizational state of ordinary matter.

NFR-4 — Extensible chemical grammar. The system must not attempt to enumerate all possible chemicals; it must use an extensible chemical grammar that constructs previously unseen species from valid chemical transformations. (explicit) — Rationale: a literal database of every possible chemical is impossible.

NFR-5 — Water as continuum bulk solvent. Water must be modeled explicitly as the bulk solvent at the continuum level rather than rendering every water molecule. (explicit) — Rationale: computational scalability without losing explicit solvent chemistry.

NFR-6 — Coarse-grained membrane model permitted. Fully atomistic membrane simulation may be replaced with a validated coarse-grained membrane model for computational scalability. (explicit) — Rationale: computational scalability.

NFR-7 — Kinetic networks, not collectible resources. Prebiotic carbon/nitrogen compounds must participate in kinetic reaction networks and must not be treated merely as collectible resources. (explicit) — Rationale: the chemistry must be real, not a resource game.

NFR-8 — No assumed modern protein synthesis. The simulation must not assume modern protein synthesis. (explicit) — Rationale: amino acids are simply molecules capable of reactions including condensation into short peptides.

NFR-9 — Ribose is not artificially immortal. Ribose must degrade realistically. (explicit) — Rationale: instability and degradation are part of the chemistry.

NFR-10 — ATP is not the universal primordial energy currency. ADP and ATP must be possible products of chemistry but must not be supplied as the universal primordial energy currency; primitive systems must initially be capable of using other energetic chemistry. (explicit) — Rationale: primordial energetics must not be assumed modern.

NFR-11 — No scripted cell membrane object. A "cell membrane object" must not be scripted first; a membrane must originate from amphiphile self-assembly. (explicit) — Rationale: self-assembly must be emergent.

NFR-12 — Backend execution for durable state. Durable simulation state, chemical transformations, emergent structures, and longitudinal tracking must be executed on the backend. (required_inference) — Rationale: runs must persist and be resumable across sessions.

NFR-13 — Readable text and controls stay whole. Headlines, wordmarks, labels, numbers, cards' text, and controls must stay entirely inside the viewport and their container at 375px, 768px, and 1280px, wrapping or scaling (for example font-size: clamp(...) with its mobile size) to fit, and no other element may cover any part of them. (explicit) — Rationale: accessibility and legibility across viewports.

NFR-14 — Reduced-motion fallback. All motion must respect prefers-reduced-motion: the hero falls back to a static frame with a subtle CSS opacity pulse on emerging structures, and all data panels become scrollable lists. (explicit) — Rationale: accessibility.

NFR-15 — Data-driven motion only. Every animation must correspond to simulation state; decorative motion that does not correspond to simulation state is forbidden. (explicit) — Rationale: the data is the aesthetic.

10. Tech Stack

• Frontend: React (web application).
• 3D / generative rendering: WebGL / React Three Fiber for the full-bleed generative canvas and the 40,000-point particle field.
• Backend: Python / FastAPI for the simulation engine and API.
• Storage: Appropriate persistent storage for durable simulation configurations, runs, observations, and inspection history.
• Containerization: Docker / docker-compose for local and deployment packaging.
• Orchestration: Kubernetes only if deployment requires it.

11. Assumptions and Constraints

Assumptions.

• A-1 [Assumption — not specified by user]: The simulation runs as a web-delivered application with a backend engine; the source does not specify a delivery platform, so the default web delivery is assumed.
• A-2 [Assumption — not specified by user]: Identity is application-owned because durable simulation configurations, runs, observations, and inspection history must remain bound to the correct participant and be resumable.
• A-3 [Assumption — not specified by user]: The three accepted personas (Simulation Operator, Chemistry Inspector, Emergence Observer) are the closed active-human catalog; no additional personas are introduced.
• A-4 [Assumption — not specified by user]: The initial early-Earth chemical inventory is the starting chemistry; additional species are constructed dynamically from valid chemical transformations.

Constraints.

• C-1 (explicit): This must NOT be a traditional artificial-life simulation where organisms, metabolism, reproduction, DNA, food, predators, fitness, or species are manually scripted.
• C-2 (explicit): There must never be a command equivalent to spawnLife().
• C-3 (explicit): There must never be logic equivalent to if molecule == RNA then reproduce.
• C-4 (explicit): There must never be logic equivalent to organism.health += energy.
• C-5 (explicit): There must never be a manually assigned evolutionary fitness score.
• C-6 (explicit): Do not give organism-like properties to a structure merely because it has been labeled an organism.
• C-7 (explicit): Do not attempt to enumerate all possible chemicals; use an extensible chemical grammar instead.
• C-8 (explicit): Do not treat prebiotic carbon/nitrogen compounds merely as collectible resources; they must participate in kinetic reaction networks.
• C-9 (explicit): Do not assume modern protein synthesis.
• C-10 (explicit): Do not make ribose artificially immortal.
• C-11 (explicit): ADP and ATP should NOT simply be supplied as the universal primordial energy currency.
• C-12 (explicit): Do not script a "cell membrane object" first; a membrane should originate from amphiphile self-assembly.
• C-13 (explicit): Water must be modeled explicitly as the bulk solvent at the continuum level rather than rendering every water molecule.
• C-14 (explicit): For computational scalability, it is acceptable to replace fully atomistic membrane simulation with a validated coarse-grained membrane model.

12. Glossary

• Abiogenesis: The emergence of life from nonliving chemistry; the subject of the simulation.
• Autocatalytic system: A set of reactions whose products catalyze the reactions that produce them, capable of persisting when conditions allow.
• Chemical grammar: The extensible rule system that constructs previously unseen molecular species from valid chemical transformations, rather than enumerating all possible chemicals.
• Coarse-grained membrane model: A validated simplification of fully atomistic membrane simulation used for computational scalability.
• Compartment: A bounded region — such as a vesicle — that separates internal chemistry from the surrounding environment.
• Differential persistence: The observable outcome in which some systems persist longer than others because of their chemistry, without any manually assigned fitness score.
• Emergence: The appearance of organized systems — autocatalytic sets, compartments, heredity, competition, evolution — arising only because the underlying physical and chemical rules make them possible.
• Emergence bloom: The luminous pulse that expands from the location of a newly formed autocatalytic set or vesicle and settles into the ambient flow.
• Extensible chemical grammar: See Chemical grammar.
• Micelle: A spontaneous amphiphile aggregate above the appropriate concentration.
• Mineral surface: A mineral phase — such as mackinawite, pyrite, or montmorillonite — that participates in adsorption and catalysis.
• Molecular species: A chemical entity defined by its elemental formula, molecular graph, bond topology, and the full property set.
• Primordial void: The deep near-black ground (#05060A) of the visual design.
• Script the laws, do not script life: The central rule of the product — only physical and chemical laws are scripted; life outcomes are never scripted.
• Self-assembly: The spontaneous formation of micelles, sheets, droplets, and vesicles from amphiphiles above the appropriate concentration.
• Vesicle: A compartment bounded by an amphiphile membrane that can exchange molecules, grow, shrink, fuse, and rupture.