MackinawiteFeS
Reduced-iron sulfide surface that binds dissolved metals and hosts early thioester-forming chemistry.
abiogenesis-chemical-evolution
by
Leo Wierny
Leo WiernyBUILD AN EMERGENT ORIGIN-OF-LIFE SIMULATION Build a complete, interactive, scientifically grounded simulation of abiogenesis and chemical evolution. This must NOT be a traditional artificial-life simulation where organisms, metabolism, reproduction, DNA, food, predators, fitness, or species are manually scripted. The central rule is: SCRIPT THE LAWS. DO NOT SCRIPT LIFE. Begin with chemistry, matter, energy and environmental gradients. If organized systems emerge, they must emerge because the underlying physical and chemical rules make them possible. The ultimate experiment is: 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? There must never be a command equivalent to: spawnLife() There must never be: if molecule == RNA then reproduce There must never be: organism.health += energy There must never be a manually assigned evolutionary fitness score. Instead: physics → chemistry → reaction networks → self-organization → compartments → replication → variation → differential persistence → evolution if the simulated conditions allow those things to occur. ⸻ 1. FUNDAMENTAL PHILOSOPHY Treat life as a special organizational state of ordinary matter. The simulation begins with no distinction between “living” and “nonliving.” Everything consists of chemicals interacting according to the same rules. A structure only becomes organism-like 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 * consequently undergoes natural selection Do not give any of those properties to a structure merely because it has been labeled an organism. ⸻ 2. DO NOT ATTEMPT TO ENUMERATE ALL POSSIBLE CHEMICALS A literal database containing every possible chemical is impossible. Instead create an extensible chemical grammar. Each molecular species should contain properties such as: * 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 Allow previously unseen molecular species to be constructed dynamically from valid chemical transformations. The initial library below is therefore the starting chemistry, not the universe of possible chemistry. ⸻ 3. INITIAL EARLY-EARTH CHEMICAL INVENTORY Include at minimum the following species or chemically equivalent protonation states. Solvent and acid/base chemistry H₂O H⁺ / H₃O⁺ OH⁻ Model water explicitly as the bulk solvent at the continuum level rather than rendering every water molecule. Local pH must emerge from acid/base concentrations. ⸻ Major dissolved ions Na⁺ K⁺ Mg²⁺ Ca²⁺ Fe²⁺ Fe³⁺ Ni²⁺ Zn²⁺ Mn²⁺ Cl⁻ HS⁻ S²⁻ SO₃²⁻ SO₄²⁻ HCO₃⁻ CO₃²⁻ H₂PO₄⁻ HPO₄²⁻ PO₄³⁻ Their concentrations must influence ionic strength, membrane stability, polymer folding, precipitation and reaction rates. ⸻ Atmospheric/geochemical feedstock H₂ N₂ CO₂ CO CH₄ NH₃ NH₄⁺ H₂S SO₂ Allow gas exchange between atmosphere and water according to solubility and partial pressure. ⸻ Important prebiotic carbon/nitrogen compounds HCN — hydrogen cyanide HNC — hydrogen isocyanide where appropriate NH₂CN — cyanamide HC₃N — cyanoacetylene HCONH₂ — formamide HCHO — formaldehyde CH₃CHO — acetaldehyde CH₃OH — methanol HOCH₂CHO — glycolaldehyde glyceraldehyde dihydroxyacetone glyoxal Do not treat these merely as collectible resources. They participate in kinetic reaction networks. ⸻ 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 Allow additional carboxylic acids to emerge. ⸻ Amino acids At minimum: glycine alanine serine aspartic acid glutamic acid valine leucine isoleucine proline threonine cysteine methionine phenylalanine Do not assume modern protein synthesis. 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 Include instability and degradation. Do not make ribose artificially immortal. ⸻ Nucleobases and precursors adenine guanine cytosine uracil purine pyrimidine 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 Allow activated versions where chemically justified. ADP and ATP should be possible products of chemistry but should NOT simply be 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 Include phosphate adsorption to minerals and realistic difficulty of phosphorylation. ⸻ 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 Include 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 simple amphiphilic esters Amphiphilic properties must arise from molecular structure. Above appropriate concentrations, amphiphiles should spontaneously: form micelles form sheets form droplets form vesicles exchange molecules grow shrink fuse rupture Do not script a “cell membrane object” first. A membrane should originate from amphiphile self-assembly. For computational scalability, it is acceptable to replace fully atomistic membrane simulation with a validated coarse-grained membrane model. ⸻ 4. MINERAL WORLD Include mineral surfaces because early-Earth chemistry did not occur in an empty beaker. Include: FeS / mackinawite FeS₂ / pyrite Fe₃S₄ / greigite NiS magnetite silica serpentine minerals olivine-related minerals brucite carbonate minerals iron oxides clay minerals such as montmorillonite phosphate-bearing minerals It is watching something appear that we did not explicitly tell the program to make. I’m not gonna get to detailed but start
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Evolving chemistry · inspection surface
Inspect the inventory, not the outcome
Every species below is a chemical actor in the same kinetic network. Select a class to filter, select a species to read its concentration history and its contribution to the local pH and ionic strength.
Molecular classes
Species concentration
| Species | Class | Concentration | M g mol⁻¹ | Δ mol L⁻¹ h⁻¹ | Inspect |
|---|---|---|---|---|---|
| H₂O | ClassSolvent and acid/base chemistry | Concentration55.40 M | Molar mass18.015 | Δ per hour+0.00 nM | |
| Cl⁻ | ClassMajor dissolved ions | Concentration550.00 mM | Molar mass35.450 | Δ per hour+0.00 nM | |
| Na⁺ | ClassMajor dissolved ions | Concentration420.00 mM | Molar mass22.990 | Δ per hour+0.00 nM | |
| Mg²⁺ | ClassMajor dissolved ions | Concentration53.00 mM | Molar mass24.305 | Δ per hour−1.06 mM | |
| CO₂ | ClassAtmospheric / geochemical feedstock | Concentration33.00 mM | Molar mass44.009 | Δ per hour+2.31 mM | |
| SO₄²⁻ | ClassMajor dissolved ions | Concentration29.00 mM | Molar mass96.060 | Δ per hour+0.00 nM | |
| HCO₃⁻ | ClassMajor dissolved ions | Concentration24.00 mM | Molar mass61.017 | Δ per hour−480.00 µM | |
| K⁺ | ClassMajor dissolved ions | Concentration18.00 mM | Molar mass39.098 | Δ per hour+180.00 µM | |
| H₂S | ClassAtmospheric / geochemical feedstock | Concentration14.00 mM | Molar mass34.080 | Δ per hour+840.00 µM | |
| hydrogen sulfide | ClassSulfur chemistry and energetic intermediates | Concentration14.00 mM | Molar mass34.080 | Δ per hour+840.00 µM | |
| Ca²⁺ | ClassMajor dissolved ions | Concentration11.00 mM | Molar mass40.078 | Δ per hour+0.00 nM | |
| NH₄⁺ | ClassAtmospheric / geochemical feedstock | Concentration5.60 mM | Molar mass18.039 | Δ per hour−168.00 µM | |
| formic / formate | ClassSimple organic acids | Concentration3.40 mM | Molar mass46.025 | Δ per hour+136.00 µM | |
| HS⁻ | ClassMajor dissolved ions | Concentration2.70 mM | Molar mass33.070 | Δ per hour+135.00 µM | |
| acetic / acetate | ClassSimple organic acids | Concentration2.70 mM | Molar mass60.052 | Δ per hour+162.00 µM | |
| bisulfide | ClassSulfur chemistry and energetic intermediates | Concentration2.70 mM | Molar mass33.070 | Δ per hour+135.00 µM | |
| HCHO | ClassPrebiotic carbon/nitrogen compounds | Concentration2.30 mM | Molar mass30.026 | Δ per hour+368.00 µM | |
| formaldehyde | ClassSugars and sugar precursors | Concentration2.10 mM | Molar mass30.026 | Δ per hour+315.00 µM | |
| glycine | ClassAmino acids | Concentration1.90 mM | Molar mass75.067 | Δ per hour+171.00 µM | |
| CH₃OH | ClassPrebiotic carbon/nitrogen compounds | Concentration1.60 mM | Molar mass32.042 | Δ per hour−32.00 µM | |
| alanine | ClassAmino acids | Concentration1.40 mM | Molar mass89.094 | Δ per hour+112.00 µM | |
| HCN | ClassPrebiotic carbon/nitrogen compounds | Concentration1.10 mM | Molar mass27.026 | Δ per hour+132.00 µM | |
| H₂ | ClassAtmospheric / geochemical feedstock | Concentration870.00 µM | Molar mass2.016 | Δ per hour−8.70 µM | |
| Fe²⁺ | ClassMajor dissolved ions | Concentration840.00 µM | Molar mass55.845 | Δ per hour+50.40 µM | |
| HCONH₂ | ClassPrebiotic carbon/nitrogen compounds | Concentration820.00 µM | Molar mass45.041 | Δ per hour+41.00 µM | |
| glycolic | ClassSimple organic acids | Concentration680.00 µM | Molar mass76.051 | Δ per hour+20.40 µM | |
| N₂ | ClassAtmospheric / geochemical feedstock | Concentration640.00 µM | Molar mass28.014 | Δ per hour+0.00 nM | |
| serine | ClassAmino acids | Concentration620.00 µM | Molar mass105.093 | Δ per hour+37.20 µM | |
| HOCH₂CHO | ClassPrebiotic carbon/nitrogen compounds | Concentration590.00 µM | Molar mass60.052 | Δ per hour+76.70 µM | |
| glycolaldehyde | ClassSugars and sugar precursors | Concentration570.00 µM | Molar mass60.052 | Δ per hour+68.40 µM | |
| orthophosphate | ClassPhosphorus chemistry | Concentration540.00 µM | Molar mass94.971 | Δ per hour+37.80 µM | |
| NH₃ | ClassAtmospheric / geochemical feedstock | Concentration480.00 µM | Molar mass17.031 | Δ per hour−9.60 µM | |
| CH₃CHO | ClassPrebiotic carbon/nitrogen compounds | Concentration470.00 µM | Molar mass44.053 | Δ per hour+51.70 µM | |
| valine | ClassAmino acids | Concentration440.00 µM | Molar mass117.148 | Δ per hour+17.60 µM | |
| lactic / lactate | ClassSimple organic acids | Concentration390.00 µM | Molar mass90.078 | Δ per hour+19.50 µM | |
| glycerol | ClassAmphiphiles | Concentration390.00 µM | Molar mass92.094 | Δ per hour+15.60 µM | |
| thiols | ClassSulfur chemistry and energetic intermediates | Concentration380.00 µM | Molar mass— | Δ per hour+30.40 µM | |
| leucine | ClassAmino acids | Concentration360.00 µM | Molar mass131.175 | Δ per hour+14.40 µM | |
| H₂PO₄⁻ | ClassMajor dissolved ions | Concentration320.00 µM | Molar mass96.987 | Δ per hour+12.80 µM | |
| aspartic acid | ClassAmino acids | Concentration310.00 µM | Molar mass133.103 | Δ per hour+15.50 µM | |
| NH₂CN | ClassPrebiotic carbon/nitrogen compounds | Concentration280.00 µM | Molar mass42.040 | Δ per hour+39.20 µM | |
| glutamic acid | ClassAmino acids | Concentration280.00 µM | Molar mass147.130 | Δ per hour+14.00 µM | |
| pyruvic / pyruvate | ClassSimple organic acids | Concentration260.00 µM | Molar mass88.062 | Δ per hour+26.00 µM | |
| threonine | ClassAmino acids | Concentration250.00 µM | Molar mass119.120 | Δ per hour+10.00 µM | |
| octanoic acid | ClassAmphiphiles | Concentration240.00 µM | Molar mass144.210 | Δ per hour+12.00 µM | |
| glyoxal | ClassPrebiotic carbon/nitrogen compounds | Concentration220.00 µM | Molar mass58.036 | Δ per hour+19.80 µM | |
| isoleucine | ClassAmino acids | Concentration220.00 µM | Molar mass131.175 | Δ per hour+6.60 µM | |
| HPO₄²⁻ | ClassMajor dissolved ions | Concentration190.00 µM | Molar mass95.979 | Δ per hour+5.70 µM | |
| proline | ClassAmino acids | Concentration180.00 µM | Molar mass115.132 | Δ per hour+5.40 µM | |
| oxalic / oxalate | ClassSimple organic acids | Concentration170.00 µM | Molar mass90.034 | Δ per hour+3.40 µM | |
| CO₃²⁻ | ClassMajor dissolved ions | Concentration160.00 µM | Molar mass60.009 | Δ per hour+1.60 µM | |
| cysteine | ClassAmino acids | Concentration130.00 µM | Molar mass121.158 | Δ per hour+9.10 µM | |
| succinic / succinate | ClassSimple organic acids | Concentration120.00 µM | Molar mass118.088 | Δ per hour+4.80 µM | |
| decanoic acid | ClassAmphiphiles | Concentration110.00 µM | Molar mass172.260 | Δ per hour+6.60 µM | |
| malonic | ClassSimple organic acids | Concentration94.00 µM | Molar mass104.061 | Δ per hour+2.82 µM | |
| glyceraldehyde | ClassSugars and sugar precursors | Concentration89.00 µM | Molar mass90.078 | Δ per hour+5.34 µM | |
| glyceraldehyde | ClassPrebiotic carbon/nitrogen compounds | Concentration86.00 µM | Molar mass90.078 | Δ per hour+6.02 µM | |
| malic / malate | ClassSimple organic acids | Concentration83.00 µM | Molar mass134.087 | Δ per hour+3.32 µM | |
| methionine | ClassAmino acids | Concentration76.00 µM | Molar mass149.211 | Δ per hour+3.80 µM | |
| SO₂ | ClassAtmospheric / geochemical feedstock | Concentration72.00 µM | Molar mass64.066 | Δ per hour+1.44 µM | |
| methanethiol | ClassSulfur chemistry and energetic intermediates | Concentration69.00 µM | Molar mass48.107 | Δ per hour+4.83 µM | |
| SO₃²⁻ | ClassMajor dissolved ions | Concentration61.00 µM | Molar mass80.060 | Δ per hour+610.00 nM | |
| fumaric / fumarate | ClassSimple organic acids | Concentration61.00 µM | Molar mass116.072 | Δ per hour+1.83 µM | |
| prebiotic heterocycles | ClassNucleobases and precursors | Concentration55.00 µM | Molar mass— | Δ per hour+1.65 µM | |
| phenylalanine | ClassAmino acids | Concentration54.00 µM | Molar mass165.190 | Δ per hour+1.62 µM | |
| erythrose | ClassSugars and sugar precursors | Concentration46.00 µM | Molar mass120.104 | Δ per hour+1.38 µM | |
| S²⁻ | ClassMajor dissolved ions | Concentration44.00 µM | Molar mass32.060 | Δ per hour−1.32 µM | |
| sulfide | ClassSulfur chemistry and energetic intermediates | Concentration44.00 µM | Molar mass32.060 | Δ per hour+1.32 µM | |
| dihydroxyacetone | ClassPrebiotic carbon/nitrogen compounds | Concentration41.00 µM | Molar mass90.078 | Δ per hour+2.05 µM | |
| purine | ClassNucleobases and precursors | Concentration41.00 µM | Molar mass120.112 | Δ per hour+2.05 µM | |
| pyrimidine | ClassNucleobases and precursors | Concentration37.00 µM | Molar mass80.088 | Δ per hour+1.48 µM | |
| lauric acid | ClassAmphiphiles | Concentration36.00 µM | Molar mass200.320 | Δ per hour+1.44 µM | |
| HC₃N | ClassPrebiotic carbon/nitrogen compounds | Concentration31.00 µM | Molar mass51.048 | Δ per hour+3.10 µM | |
| adenine | ClassNucleobases and precursors | Concentration28.00 µM | Molar mass135.130 | Δ per hour+1.68 µM | |
| CO | ClassAtmospheric / geochemical feedstock | Concentration19.00 µM | Molar mass28.010 | Δ per hour+1.52 µM | |
| simple fatty alcohols | ClassAmphiphiles | Concentration16.00 µM | Molar mass— | Δ per hour+480.00 nM | |
| guanine | ClassNucleobases and precursors | Concentration14.00 µM | Molar mass151.130 | Δ per hour+700.00 nM | |
| Fe³⁺ | ClassMajor dissolved ions | Concentration12.00 µM | Molar mass55.845 | Δ per hour−480.00 nM | |
| elemental sulfur | ClassSulfur chemistry and energetic intermediates | Concentration12.00 µM | Molar mass32.060 | Δ per hour+240.00 nM | |
| myristic acid | ClassAmphiphiles | Concentration9.80 µM | Molar mass228.370 | Δ per hour+294.00 nM | |
| cytosine | ClassNucleobases and precursors | Concentration9.60 µM | Molar mass111.102 | Δ per hour+384.00 nM | |
| simple thioesters | ClassSulfur chemistry and energetic intermediates | Concentration8.40 µM | Molar mass— | Δ per hour+1.09 µM | |
| monoacylglycerols | ClassAmphiphiles | Concentration7.40 µM | Molar mass— | Δ per hour+370.00 nM | |
| HNC | ClassPrebiotic carbon/nitrogen compounds | Concentration6.40 µM | Molar mass27.026 | Δ per hour+576.00 nM | |
| uracil | ClassNucleobases and precursors | Concentration6.30 µM | Molar mass112.087 | Δ per hour+252.00 nM | |
| acetyl phosphate | ClassPhosphorus chemistry | Concentration4.20 µM | Molar mass140.030 | Δ per hour+462.00 nM | |
| palmitic acid | ClassAmphiphiles | Concentration4.10 µM | Molar mass256.430 | Δ per hour+82.00 nM | |
| Mn²⁺ | ClassMajor dissolved ions | Concentration3.60 µM | Molar mass54.938 | Δ per hour+72.00 nM | |
| ribose | ClassSugars and sugar precursors | Concentration3.40 µM | Molar mass150.130 | Δ per hour+68.00 nM | |
| adenosine | ClassNucleosides and nucleotides | Concentration3.20 µM | Molar mass267.240 | Δ per hour+96.00 nM | |
| simple amphiphilic esters | ClassAmphiphiles | Concentration2.90 µM | Molar mass— | Δ per hour+116.00 nM | |
| pyrophosphate | ClassPhosphorus chemistry | Concentration2.80 µM | Molar mass173.940 | Δ per hour+140.00 nM | |
| CH₄ | ClassAtmospheric / geochemical feedstock | Concentration2.60 µM | Molar mass16.043 | Δ per hour+130.00 nM | |
| ribulose | ClassSugars and sugar precursors | Concentration2.60 µM | Molar mass150.130 | Δ per hour+26.00 nM | |
| acetyl thioesters | ClassSulfur chemistry and energetic intermediates | Concentration2.60 µM | Molar mass— | Δ per hour+468.00 nM | |
| PO₄³⁻ | ClassMajor dissolved ions | Concentration2.30 µM | Molar mass94.971 | Δ per hour+0.00 nM | |
| Ni²⁺ | ClassMajor dissolved ions | Concentration2.10 µM | Molar mass58.693 | Δ per hour+63.00 nM | |
| arabinose | ClassSugars and sugar precursors | Concentration2.10 µM | Molar mass150.130 | Δ per hour+21.00 nM | |
| condensed phosphates | ClassPhosphorus chemistry | Concentration1.90 µM | Molar mass— | Δ per hour+76.00 nM | |
| xylose | ClassSugars and sugar precursors | Concentration1.80 µM | Molar mass150.130 | Δ per hour+18.00 nM | |
| guanosine | ClassNucleosides and nucleotides | Concentration1.70 µM | Molar mass283.240 | Δ per hour+34.00 nM | |
| Zn²⁺ | ClassMajor dissolved ions | Concentration1.40 µM | Molar mass65.380 | Δ per hour+0.00 nM | |
| cytidine | ClassNucleosides and nucleotides | Concentration1.10 µM | Molar mass243.220 | Δ per hour+22.00 nM | |
| uridine | ClassNucleosides and nucleotides | Concentration940.00 nM | Molar mass244.200 | Δ per hour+18.80 nM | |
| trimetaphosphate | ClassPhosphorus chemistry | Concentration870.00 nM | Molar mass236.890 | Δ per hour+34.80 nM | |
| simple hexoses | ClassSugars and sugar precursors | Concentration720.00 nM | Molar mass180.156 | Δ per hour+7.20 nM | |
| AMP | ClassNucleosides and nucleotides | Concentration680.00 nM | Molar mass347.220 | Δ per hour+20.40 nM | |
| H⁺ / H₃O⁺ | ClassSolvent and acid/base chemistry | Concentration398.00 nM | Molar mass19.023 | Δ per hour+7.96 nM | |
| GMP | ClassNucleosides and nucleotides | Concentration390.00 nM | Molar mass363.220 | Δ per hour+7.80 nM | |
| OH⁻ | ClassSolvent and acid/base chemistry | Concentration251.00 nM | Molar mass17.007 | Δ per hour−2.51 nM | |
| CMP | ClassNucleosides and nucleotides | Concentration240.00 nM | Molar mass323.200 | Δ per hour+4.80 nM | |
| UMP | ClassNucleosides and nucleotides | Concentration210.00 nM | Molar mass324.180 | Δ per hour+4.20 nM |
Local state
pH
8.10
acidicbasicpH emerges from the acid/base concentrations; the value above is the negative logarithm of the summed proton activity.
Ionic strength
1.542 MI = ½ Σcᵢzᵢ²
freshsalineDerived from every charged species present; it modulates membrane stability and reaction rates.
Concentration over time
H₂OSolvent and acid/base chemistry‑ basis: Alkaline vent interface — 4.3 Gyr · 41.7 h simulated
Reaction Networks
Every filament is a rule, not a script.
Each edge below is a valid chemical transformation permitted by the current state — concentrations, pH, temperature, ionic strength and mineral surfaces set which pathways carry flux and how fast. No pathway is scripted; the network is read back from the chemistry, not written into it.
Pathways & rates
static list
- Atmosphericcarbon4.2nM s⁻¹
- AtmosphericSimple organic acids1.1nM s⁻¹
- Solvent and acidMajor dissolved ions2.4nM s⁻¹
- Solvent and acidcarbon5.4nM s⁻¹
- Major dissolved ionsMineral world0.6nM s⁻¹
- Mineral worldSulfur chemistry and energetic intermediates0.9nM s⁻¹
- Sulfur chemistry and energetic intermediatescarbon1.8nM s⁻¹
- Sulfur chemistry and energetic intermediatesAmino acids1.4nM s⁻¹
- carbonSugars and sugar3.1nM s⁻¹
- Simple organic acidsSugars and sugar2.2nM s⁻¹
- Sugars and sugarNucleobases and1.3nM s⁻¹
- carbonNucleobases and2.6nM s⁻¹
- Nucleobases andNucleosides and nucleotides1.1nM s⁻¹
- PhosphorusNucleosides and nucleotides0.4nM s⁻¹
- Mineral worldPhosphorus0.5nM s⁻¹
- Amino acidsAmphiphiles0.8nM s⁻¹
- Simple organic acidsAmphiphiles1.7nM s⁻¹
- Sulfur chemistry and energetic intermediatesAmphiphiles0.7nM s⁻¹
- AtmosphericSimple organic acids0.9nM s⁻¹
Trace a node to read the rate-weighted pathways leaving it. Node hue is assigned by molecular class, so the palette you see is generated by the chemistry itself.
Pathways & rates
hover to trace · click to open in Molecules
| Reactant | Product | Class | Rate | Weight |
|---|---|---|---|---|
| AtmosphericProductcarbonClassReactiveWeight78% | carbon | Reactive | 4.2nM s⁻¹ | 78% |
| AtmosphericProductSimple organic acidsClassReactiveWeight20% | Simple organic acids | Reactive | 1.1nM s⁻¹ | 20% |
| Solvent and acidProductMajor dissolved ionsClassEnergyWeight44% | Major dissolved ions | Energy | 2.4nM s⁻¹ | 44% |
| Solvent and acidProductcarbonClassEnergyWeight100% | carbon | Energy | 5.4nM s⁻¹ | 100% |
| Major dissolved ionsProductMineral worldClassSaltWeight11% | Mineral world | Salt | 0.6nM s⁻¹ | 11% |
| Mineral worldProductSulfur chemistry and energetic intermediatesClassMineralWeight17% | Sulfur chemistry and energetic intermediates | Mineral | 0.9nM s⁻¹ | 17% |
| Sulfur chemistry and energetic intermediatesProductcarbonClassReactiveWeight33% | carbon | Reactive | 1.8nM s⁻¹ | 33% |
| Sulfur chemistry and energetic intermediatesProductAmino acidsClassReactiveWeight26% | Amino acids | Reactive | 1.4nM s⁻¹ | 26% |
| carbonProductSugars and sugarClassReactiveWeight57% | Sugars and sugar | Reactive | 3.1nM s⁻¹ | 57% |
| Simple organic acidsProductSugars and sugarClassReactiveWeight41% | Sugars and sugar | Reactive | 2.2nM s⁻¹ | 41% |
| Sugars and sugarProductNucleobases andClassEnergyWeight24% | Nucleobases and | Energy | 1.3nM s⁻¹ | 24% |
| carbonProductNucleobases andClassReactiveWeight48% | Nucleobases and | Reactive | 2.6nM s⁻¹ | 48% |
| Nucleobases andProductNucleosides and nucleotidesClassNucleotideWeight20% | Nucleosides and nucleotides | Nucleotide | 1.1nM s⁻¹ | 20% |
| PhosphorusProductNucleosides and nucleotidesClassReactiveWeight7% | Nucleosides and nucleotides | Reactive | 0.4nM s⁻¹ | 7% |
| Mineral worldProductPhosphorusClassMineralWeight9% | Phosphorus | Mineral | 0.5nM s⁻¹ | 9% |
| Amino acidsProductAmphiphilesClassEnergyWeight15% | Amphiphiles | Energy | 0.8nM s⁻¹ | 15% |
| Simple organic acidsProductAmphiphilesClassReactiveWeight31% | Amphiphiles | Reactive | 1.7nM s⁻¹ | 31% |
| Sulfur chemistry and energetic intermediatesProductAmphiphilesClassReactiveWeight13% | Amphiphiles | Reactive | 0.7nM s⁻¹ | 13% |
| AtmosphericProductSimple organic acidsClassReactiveWeight17% | Simple organic acids | Reactive | 0.9nM s⁻¹ | 17% |
Run context
Hydrothermal vent field — 4.2 Gyr
Temperature72°C
pH6.4
Redox-0.21V
Energy flux0.84W m⁻²
Thermal gradient 42 °C across the vent field; proton gradient at the alkaline interface.
Instrument
Abiogenesis & chemical evolution
SCRIPT THE LAWS.NOT THE LIFE.
Begin with chemistry, matter, energy and environmental gradients. Organized systems appear only if the underlying physical and chemical rules make them possible.
Begin the experimentH₂OH₃O⁺OH⁻HCNNH₂CNHCHOHC₃NHCONH₂CO₂H₂CH₄H₂SHS⁻FeSFeS₂Fe₃S₄NiSMg²⁺Ca²⁺Fe²⁺Zn²⁺HPO₄²⁻PO₄³⁻pyrophosphateacetyl phosphateacetyl thioesterglycinealanineserinecysteineriboseglycolaldehydeglyceraldehydeadenineuracilAMPUMPoctanoic aciddecanoic acidlauric acidpalmitic acidglycerolmontmorillonitemackinawitegreigitemagnetite
The Ultimate Experiment
Can an initially nonliving chemical environmentcontinuously driven away from thermodynamic equilibrium by external energyspontaneously produce persistent autocatalytic systems, compartments, heredity, competition, evolution and increasingly organism-like entities?
Built for the people who ask it. A laboratory instrument for
- synthetic biologists
- origin-of-life researchers
- computational chemists
- science-curious learners
- museum-grade exhibition visitors
It begins with chemistry, matter, energy, and environmental gradients — and nothing else. No outcome is authored ahead of the run. The central rule governs everything downstream: Script the laws. Do not script life. A single instruction is deliberately missing from the source — spawnLife() does not exist.
Causal chain
Physics becomes chemistry. Chemistry becomes a network.
This is the sequence the simulation is permitted to traverse. Each stage is a consequence of the one before it, computed from the rules rather than issued as an instruction.
Conditional
The chain proceeds only if the simulated conditions allow those things to occur. No stage is scheduled, guaranteed, or triggered by a named life event.
- 01Stage
physics
lawMatter, energy and environmental gradients set the arena; no outcome beyond these laws is prescribed.
- 02Stage
chemistry
lawBond formation and acid/base equilibria proceed from energetics and rates alone.
- 03Stage
reaction networks
lawCoupling between reactions yields networks whose structure was never enumerated in advance.
- 04Stage
self-organization
conditionalLocal order appears where flux, catalysis and surface chemistry make it favourable.
- 05Stage
compartments
conditionalAmphiphile self-assembly produces boundaries that concentrate their own contents.
- 06Stage
replication
conditionalProducts that catalyse further product formation can propagate when kinetics allow.
- 07Stage
variation
conditionalImperfect copying and side reactions generate a spread of descendant compositions.
- 08Stage
differential persistence
conditionalWhatever persists longest and multiplies fastest dominates the population by physics, not by scoring.
- 09Stage
evolution
conditionalComposition drifts and accumulates across generations; nothing is directed toward a target form.
Physics → chemistry → reaction networks → self-organization → compartments → replication → variation → differential persistence → evolution.
Every stage after the first is written as conditional, because the laws decide.
Initial Inventory
The starting chemistry of an early-Earth vessel.
Every species below enters the same kinetic reaction network. None of them is a collectible resource, a label for life, or a privileged ancestor — they are simply matter and energy under the same rules as everything that follows.
13 classes126 species
Solvent and acid/base chemistry
H2O / H+- H₂O
- H⁺ / H₃O⁺
- OH⁻
Water is modelled as the bulk solvent at the continuum level; local pH emerges from acid/base concentrations. Individual water molecules are not rendered.
Major dissolved ions
CHARGE- Na⁺
- K⁺
- Mg²⁺
- Ca²⁺
- Fe²⁺
- Fe³⁺
- Ni²⁺
- Zn²⁺
- Mn²⁺
- Cl⁻
- HS⁻
- S²⁻
- SO₃²⁻
- SO₄²⁻
- HCO₃⁻
- CO₃²⁻
- H₂PO₄⁻
- HPO₄²⁻
- PO₄³⁻
Concentrations feed ionic strength, membrane stability, polymer folding, precipitation and reaction rates.
Atmospheric / geochemical feedstock
P(gas)- H₂
- N₂
- CO₂
- CO
- CH₄
- NH₃
- NH₄⁺
- H₂S
- SO₂
Gas exchange between atmosphere and water follows solubility and partial pressure.
Prebiotic carbon/nitrogen compounds
C/N- HCN
- HNC
- NH₂CN
- HC₃N
- HCONH₂
- HCHO
- CH₃CHO
- CH₃OH
- HOCH₂CHO
- glyceraldehyde
- dihydroxyacetone
- glyoxal
Kinetic network participants, not collectible resources.
Simple organic acids
R-COOH- 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 from valid transformations.
Amino acids
NH2-CHR- glycine
- alanine
- serine
- aspartic acid
- glutamic acid
- valine
- leucine
- isoleucine
- proline
- threonine
- cysteine
- methionine
- phenylalanine
Condensation into short peptides only — no modern protein synthesis is assumed.
Sugars and sugar precursors
CnH2nOn- formaldehyde
- glycolaldehyde
- glyceraldehyde
- ribose
- arabinose
- xylose
- erythrose
- ribulose
- simple hexoses
Instability and degradation are included; ribose is not immortal.
Nucleobases and precursors
HETERO- adenine
- guanine
- cytosine
- uracil
- purine
- pyrimidine
- related prebiotic heterocycles
Thymine may arise later but need not dominate primordial chemistry.
Nucleosides and nucleotides
NTP- adenosine
- guanosine
- cytidine
- uridine
- AMP
- GMP
- CMP
- UMP
- activated nucleotides
ADP and ATP are possible products of chemistry, never supplied as a universal primordial energy currency.
Phosphorus chemistry
P-O-P- orthophosphate
- pyrophosphate
- trimetaphosphate
- other condensed phosphates
- acetyl phosphate
Phosphate adsorption to minerals and the realistic difficulty of phosphorylation are modelled.
Sulfur chemistry and energetic intermediates
S / SH- hydrogen sulfide
- bisulfide
- sulfide
- elemental sulfur
- thiols
- methanethiol
- simple thioesters
- acetyl thioesters
Thioester chemistry couples energetically favourable and unfavourable reactions.
Amphiphiles
C6-C18- octanoic acid
- decanoic acid
- lauric acid
- myristic acid
- palmitic acid
- simple fatty alcohols
- glycerol
- monoacylglycerols
- simple amphiphilic esters
Amphiphilic behaviour arises from molecular structure — above threshold concentration these species self-assemble.
Mineral world
SURFACE- FeS / mackinawite
- FeS₂ / pyrite
- Fe₃S₄ / greigite
- NiS
- magnetite
- silica
- serpentine minerals
- olivine-related minerals
- brucite
- carbonate minerals
- iron oxides
- clay minerals such as montmorillonite
- phosphate-bearing minerals
Surfaces enter here as inventory only; adsorption, catalysis and phosphate binding are treated in the mineral band.
Starting chemistry, not the universe
This library is the starting chemistry, not the universe of possible chemistry. Species that were never listed are constructed dynamically from valid chemical transformations, each new molecule carrying the same grammar of properties as the ones above.
- molecular graph / bond topology
- molecular mass / formal charge
- oxidation state / acid-base groups
- polarity / hydrophobicity / solubility
- diffusion coefficient / absorption spectrum
- bond energies / activation-energy estimates
- membrane permeability / surface adsorption affinity
- catalytic groups / degradation pathways
- polymerization sites / stereochemistry
The mineral world13 surfaces
Early-Earth chemistry did not occur in an empty beaker.
Every reaction below runs against a mineral interface. Each surface contributes a distinct physical role — adsorption, catalysis, phosphate retention, redox mediation — and the same ledger governs both the dissolved species and the surfaces they touch.
PyriteFeS₂
Persistent sulfide mineral whose surface couples electron transfer and drives reductive carbon fixation.
GreigiteFe₃S₄
Mixed-valence sulfide offering both electron donors and acceptors at the same interface.
MilleriteNiS
Nickel sulfide surface that adsorbs cyanide species and catalyses their condensation.
MagnetiteFe₃O₄
Mixed ferrous–ferric oxide that adsorbs organics and mediates redox gradients.
SilicaSiO₂
Mineral framework providing high-surface-area scaffolding for concentrating dilute organics.
SerpentineMg₃Si₂O₅(OH)₄
Hydration product of olivine; its formation releases hydrogen and drives alkaline vent chemistry.
Olivine(Mg,Fe)₂SiO₄
Primary mantle silicate whose aqueous alteration supplies the reducing power of serpentinizing systems.
BruciteMg(OH)₂
Alkaline hydroxide layer that buffers local pH and stabilises anionic intermediates.
Carbonate mineralsCaCO₃ / MgCO₃
Precipitating carbonate phases that fix dissolved CO₂ and regulate alkalinity.
Iron oxidesFe₂O₃ / FeOOH
Ferric oxide phases that adsorb phosphate and anionic species onto their surfaces.
Montmorilloniteclay mineral
Swelling clay whose interlayer cations adsorb nucleotides and template polymer condensation.
Phosphate mineralsapatite group
Phosphate-bearing surfaces that adsorb orthophosphate and make phosphorylation energetically reachable.
Boundary condition
No mineral surface here is granted behaviour the chemistry does not give it — the surfaces are laws, not actors.
Adsorption affinities, catalytic groups and phosphate binding are properties of the mineral, evaluated per collision like every dissolved species. Nothing is placed by hand at the interface.
- adsorption
- catalysis
- phosphate adsorption
- redox mediation
No boundary is drawn. Boundaries close themselves.
Above the concentration where packing beats dissolution, amphiphiles assemble the same way the bulk solvent pushes them to — into micelles, sheets, droplets and vesicles. No cell membrane object is scripted first: a membrane is a consequence of molecular structure and local concentration, and it keeps changing for as long as the chemistry around it does.
Micelle
C8–C18 amphiphile aggregate
Above the critical aggregate concentration, amphiphile tails sequester from water and heads face the bulk solvent, closing into a spherical aggregate with no interior volume.
spherical aggregateSheet
planar bilayer lamella
At lower curvature the same molecules pack into extended lamellae. Sheets stack, slide against one another and expose mineral surfaces to a two-dimensional reaction field.
extended bilayerDroplet
surfactant-stabilised organic phase
A sparingly soluble organic phase is stabilised by an adsorbed amphiphile monolayer, creating a bounded interior without any pre-declared boundary object.
soft interfaceVesicle
closed bilayer compartment
When a sheet closes on itself it encloses a volume of bulk solution. The boundary is a thin refractive shell a few nanometres thick, assembled entirely by the packing of its amphiphiles.
closed aqueous compartmentStructure lifecycle
Every boundary is re-weighted by the next molecule that arrives or leaves.
- 01
Growth
Amphiphiles exchange from solution into an existing boundary faster than they leave it, so the structure gains area.
- 02
Shrinkage
When the local amphiphile concentration falls below equilibrium, the reverse flux dominates and the structure loses molecules.
- 03
Fusion
Two boundaries that meet can merge into a single larger structure, combining their enclosed volumes and contents.
- 04
Rupture
A destabilised boundary fails, releases its contents to the bulk solution, and its amphiphiles return to the free pool.
Not scripted
There is no cell membrane object in the model. No compartment is declared, labelled, or given a lifetime by the program — a boundary exists only while amphiphile flux keeps it closed.
Emerged
A membrane originates from amphiphile self-assembly. Compartments appear only where the simulated concentration, temperature and ionic conditions make closure favourable, and they persist only while that remains true.
Five things that may appear — and what makes them persist
Each category below is an outcome the model is permitted to reach, never an instruction it is given. Nothing was explicitly told the program to make. Every marker on this axis is a chemical consequence of the laws set upstream, not a run history. Outcomes can be inspected in the Emergence and Structures surfaces.
Emergence categoryScroll down the spine
Autocatalytic systemsautocatalytic set
Possible outcome
conditional on chemistry
Autocatalytic networks may persist
Persistence · 01
reaction cycles sustained while the gradient holds
Compartmentsvesicle
Possible outcome
conditional on chemistry
Compartments may self-assemble
Persistence · 02
boundaries persist while amphiphile supply continues
Replicationtemplate copying
Possible outcome
conditional on chemistry
Templated copying appears
Persistence · 03
copy lineages persist only as long as their chemistry is resupplied
Variationcopy error
Possible outcome
conditional on chemistry
Imperfect descendants accumulate
Persistence · 04
variant populations persist where their kinetics permit
Differential persistenceselection
Possible outcome
conditional on chemistry
Some lineages outlast others
Persistence · 05
persisting lineages outlast non-persisting ones
Nothing was told to appear
There is no spawn command in this model, and no branch that rewards one molecule over another. A structure held together here because its chemistry let it hold together — a marker on the axis is a consequence, not an event trigger.
Where to watch it happen
The same quantities tracked along this axis resolve into the Emergence surface, where autocatalytic sets and compartments can be tracked if they form, and into the Structures surface, which holds the assembled forms and their persistence over simulated time.
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