1. Eck, R. V. & Dayhoff, M. O. Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences. Science 152, 363–366 (1966).

2. Hartman, H. Speculations on the origin and evolution of metabolism. J. Mol. Evol. 4, 359–370 (1975).

3. Hartman, H. Conjectures and reveries. Photosynth. Res. 33, 171–176 (1992).

4. de Duve, C. Blueprint for a Cell: The Nature and Origin of Life (Neil Patterson Publishers, 1991).

5. Morowitz, H. J., Kostelnik, J. D., Yang, J. & Cody, G. D. The origin of intermediary metabolism. Proc. Natl Acad. Sci. USA 97, 7704–7708 (2000).

6. Smith, E. & Morowitz, H. J. The Origin and Nature of Life On Earth (Cambridge Univ. Press, 2016).

7. Smith, E. & Morowitz, H. J. Universality in intermediary metabolism. Proc. Natl Acad. Sci. USA 101, 13168–13173 (2004).

8. Sousa, F. L. et al. Early bioenergetic evolution. Phil. Trans. R. Soc. Lond. B 368, 20130088 (2013).

9. Lazcano, A. & Miller, S. L. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85, 793–798 (1996).

10. Deamer, D. & Weber, A. L. Bioenergetics and life’s origins. Cold Spring Harb. Perspect. Biol. 2, a004929 (2010).

11. Martin, W. & Russell, M. J. On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans. R. Soc. Lond. B 362, 1887–1926 (2007).

12. Martin, W., Baross, J., Kelley, D. & Russell, M. J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 6, 805–814 (2008).

13. Weiss, M. C. et al. The physiology and habitat of the last universal common ancestor. Nat. Microbiol. 1, 16116 (2016).

14. Russell, M. J., Hall, A. J. & Martin, W. Serpentinization as a source of energy at the origin of life. Geobiology 8, 355–371 (2010).

15. McDermott, J. M., Seewald, J. S., German, C. R. & Sylva, S. P. Pathways for abiotic organic synthesis at submarine hydrothermal fields. Proc. Natl Acad. Sci. USA 112, 7668–7672 (2015).

16. Parker, E. T. et al. Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proc. Natl Acad. Sci. USA 108, 5526–5531 (2011).

17. Heinen, W. & Lauwers, A. M. Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment. Orig. Life Evol. Biosph. 26, 131–150 (1996).

18. Cody, G. D. Primordial carbonylated iron–sulfur compounds and the synthesis of pyruvate. Science 289, 1337–1340 (2000).

19. Varma, S. J., Muchowska, K. B., Chatelain, P. & Moran, J. Native iron reduces CO 2 to intermediates and end-products of the acetyl-CoA pathway. Nat. Ecol. Evol. 2, 1019–1024 (2018).

20. Huber, C. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science 276, 245–247 (1997).

21. Wachtershauser, G. Evolution of the first metabolic cycles. Proc. Natl Acad. Sci. USA 87, 200–204 (1990).

22. Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).

23. Dörr, M. et al. A possible prebiotic formation of ammonia from dinitrogen on iron sulfide surfaces. Angew. Chem. Int. Ed. 42, 1540–1543 (2003).

24. Navarro-González, R., McKay, C. P. & Mvondo, D. N. A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning. Nature 412, 61–64 (2001).

25. Martin, W. F. & Thauer, R. K. Energy in ancient metabolism. Cell 168, 953–955 (2017).

26. Sousa, F. L., Preiner, M. & Martin, W. F. Native metals, electron bifurcation, and CO 2 reduction in early biochemical evolution. Curr. Opin. Microbiol. 43, 77–83 (2018).

27. Halmann, M. in The Origin of Life and Evolutionary Biochemistry (eds Dose, K. et al.) 169–182 (Springer, 1974).

28. Schwartz, A. W. Phosphorus in prebiotic chemistry. Phil. Trans. R. Soc. Lond. B 361, 1743–1749 (2006).

29. Keefe, A. D. & Miller, S. L. Are polyphosphates or phosphate esters prebiotic reagents? J. Mol. Evol. 41, 693–702 (1995).

30. Goldford, J. E., Hartman, H., Smith, T. F. & Segrè, D. Remnants of an ancient metabolism without phosphate. Cell 168, 1126–1134 (2017).

31. Goldford, J. E. & Segrè, D. Modern views of ancient metabolic networks. Curr. Opin. Syst. Biol. 8, 117–124 (2018).

32. Ebenhöh, O., Handorf, T. & Heinrich, R. Structural analysis of expanding metabolic networks. Genome Inform. 15, 35–45 (2004).

33. Handorf, T., Ebenhöh, O. & Heinrich, R. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 61, 498–512 (2005).

34. Raymond, J. & Segrè, D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 311, 1764–1767 (2006).

35. Petrov, A. S. et al. History of the ribosome and the origin of translation. Proc. Natl Acad. Sci. USA 112, 15396–15401 (2015).

36. Aziz, M. F., Caetano-Anollés, K. & Caetano-Anollés, G. The early history and emergence of molecular functions and modular scale-free network behavior. Sci. Rep. 6, 25058 (2016).

37. Barve, A. & Wagner, A. A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature 500, 203–206 (2013).

38. Szappanos, B. et al. Adaptive evolution of complex innovations through stepwise metabolic niche expansion. Nat. Commun. 7, 11607 (2016).

39. Pál, C. & Papp, B. Evolution of complex adaptations in molecular systems. Nat. Ecol. Evol. 1, 1084–1092 (2017).

40. Lipmann, F. Attempts to map a process evolution of peptide biosynthesis. Science 173, 875–884 (1971).

41. Muchowska, K. B. et al. Metals promote sequences of the reverse Krebs cycle. Nat. Ecol. Evol. 1, 1716–1721 (2017).

42. Muchowska, K. B., Varma, S. J. & Moran, J. Synthesis and breakdown of universal metabolic precursors promoted by iron. Nature 569, 104–107 (2019).

43. Meringer, M. & Cleaves, H. J. Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents. Sci. Rep. 7, 17540 (2017).

44. Zubarev, D. Y., Rappoport, D. & Aspuru-Guzik, A. Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle. Sci. Rep. 5, 8009 (2015).

45. Vetsigian, K., Woese, C. & Goldenfeld, N. Collective evolution and the genetic code. Proc. Natl Acad. Sci. USA 103, 10696–10701 (2006).

46. David, L. A. & Alm, E. J. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469, 93–96 (2011).

47. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).

48. Keller, M. A., Kampjut, D., Harrison, S. A. & Ralser, M. Sulfate radicals enable a non-enzymatic Krebs cycle precursor. Nat. Ecol. Evol. 1, 0083 (2017).

49. Keller, M. A., Turchyn, A. V. & Ralser, M. Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol. Syst. Biol. 10, 725 (2014).

50. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).

51. Dellomonaco, C., Clomburg, J. M., Miller, E. N. & Gonzalez, R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355–359 (2011).

52. Orth, J. D., Thiele, I. & Palsson, B. Ø. What is flux balance analysis? Nat. Biotechnol. 28, 245 (2010).

53. Henry, C. S., Broadbelt, L. J. & Hatzimanikatis, V. Thermodynamics-based metabolic flux analysis. Biophys. J. 92, 1792–1805 (2007).

54. Chandru, K. et al. Simple prebiotic synthesis of high diversity dynamic combinatorial polyester libraries. Commun. Chem. 1, 30 (2018).

55. Forsythe, J. G. et al. Ester-mediated amide bond formation driven by wet-dry cycles: a possible path to polypeptides on the prebiotic earth. Angew. Chem. Int. Ed. 54, 9871–9875 (2015).

56. Wächtershäuser, G. Groundworks for an evolutionary biochemistry: the iron–sulphur world. Prog. Biophys. Mol. Biol. 58, 85–201 (1992).

57. Bar-Even, A. Does acetogenesis really require especially low reduction potential? Biochim. Biophys. Acta 1827, 395–400 (2013).

58. Poudel, S. et al. Origin and evolution of flavin-based electron bifurcating enzymes. Front. Microbiol. 9, 1–26 (2018).

59. Duval, S. et al. Electron transfer precedes ATP hydrolysis during nitrogenase catalysis. Proc. Natl Acad. Sci. USA 110, 16414–16419 (2013).

60. Gogarten, J. P. & Deamer, D. Is LUCA a thermophilic progenote? Nat. Microbiol. 1, 16229 (2016).

61. Segré, D., Ben-Eli, D., Deamer, D. W. & Lancet, D. The lipid world. Orig. Life Evol. Biosph. 31, 119–145 (2001).

62. Großkopf, T. et al. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evol. Biol. 16, 163 (2016).

63. Ibarra, R. U., Edwards, J. S. & Palsson, B. O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186–189 (2002).

64. Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F. A Software Package for Chemically Inspired Graph Transformation (Springer, 2016).

65. Banzhaf, W. & Yamamoto, L. Artificial Chemistries (MIT Press, 2015).

66. Flamholz, A., Noor, E., Bar-Even, A. & Milo, R. eQuilibrator – the biochemical thermodynamics calculator. Nucleic Acids Res. 40, 770–775 (2012).

67. Noor, E., Haraldsdóttir, H. S., Milo, R. & Fleming, R. M. T. Consistent estimation of Gibbs energy using component contributions. PLoS Comput. Biol. 9, e1003098 (2013).

68. Halevy, I. & Bachan, A. The geologic history of seawater pH. Science 355, 1069–1071 (2017).

69. Bar-Even, A., Flamholz, A., Noor, E. & Milo, R. Thermodynamic constraints shape the structure of carbon fixation pathways. Biochim. Biophys. Acta 1817, 1646–1659 (2012).

70. Milo, R., Jorgensen, P., Moran, U., Weber, G. & Springer, M. BioNumbers – the database of key numbers in molecular and cell biology. Nucleic Acids Res. 38, D750–D753 (2010).

71. Schellenberger, J. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2.0. Nat. Protoc. 6, 1290–1307 (2011).

72. Ribeiro, A. J. M. et al. Mechanism and catalytic site atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Res. 46, D618–D623 (2018).

73. Mall, A. et al. Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium. Science 359, 563–567 (2018).