Biogenesis

Introduction When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me...

@book{doi105962bhltitle59991,
    author = "Darwin, Charles and Darwin, Charles and Remnants, Edmonds \\&",
    title = "On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life /",
    year = "1859",
    booktitle = "John Murray eBooks",
    abstract = "Introduction When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me...",
    url = "https://doi.org/10.5962/bhl.title.59991",
    doi = "10.5962/bhl.title.59991",
    openalex = "W2883512297"
}

@misc{valleryradot1922fermentations41,
    author = "Vallery-Radot, P",
    title = "Fermentations et Gnrations dites Spontanes",
    year = "1922",
    howpublished = "Paris, Masson et Cie, v. II",
    note = "talkorigins\_source = {true}; raw\_reference = {Vallery-Radot, P., 1922, Fermentations et Gnrations dites Spontanes: Paris, Masson et Cie, v. II.}"
}

@misc{haldane1929the8,
    author = "Haldane, J. B. S",
    title = "The Origin of Life, in Bernal, J. D., ed., The Origin of Life",
    year = "1929",
    howpublished = "London, Weidenfeld and Nicolson, p. 242-249; Originally published in The Rationalist Annual , 1929",
    note = "talkorigins\_source = {true}; raw\_reference = {Haldane, J. B. S., 1929, The Origin of Life, in Bernal, J. D., ed., The Origin of Life: London, Weidenfeld and Nicolson, p. 242-249; Originally published in The Rationalist Annual , 1929.}"
}

@article{doi1023072420646,
    author = "Just, Th. and Опарин, А. И. and Morgulis, Sergius",
    title = "The Origin of Life.",
    year = "1938",
    journal = "The American Midland Naturalist",
    url = "https://doi.org/10.2307/2420646",
    doi = "10.2307/2420646",
    openalex = "W2000676511"
}

@misc{herrera1942a9,
    author = "Herrera, A. L",
    title = "A new theory of the origin and nature of life",
    year = "1942",
    howpublished = "Science, v. 96, p. 2497",
    note = "talkorigins\_source = {true}; raw\_reference = {Herrera, A. L., 1942, A new theory of the origin and nature of life: Science, v. 96, p. 2497.}"
}

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.

@article{doi101073pnas384351,
    author = "Urey, Harold C.",
    title = "On the Early Chemical History of the Earth and the Origin of Life",
    year = "1952",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.",
    url = "https://doi.org/10.1073/pnas.38.4.351",
    doi = "10.1073/pnas.38.4.351",
    openalex = "W2081145627",
    references = "doi101126science1142964416"
}

@book{wigner1961the44,
    author = "Wigner, E",
    title = "The probability of the existance of a self-reproducing unit, in The Logic of Personal Knowledge",
    year = "1961",
    publisher = "Glencoe, Ill., The Free Press, p. 231-238",
    note = "talkorigins\_source = {true}; raw\_reference = {Wigner, E., 1961, The probability of the existance of a self-reproducing unit, in The Logic of Personal Knowledge: Glencoe, Ill., The Free Press, p. 231-238.}"
}

@incollection{vegotsky1962protein42,
    author = "Vegotsky, A. and Fox, S. W",
    editor = "Florkin, M. and Mason, H. S.",
    title = "Protein molecules: intraspecific and interspecific variations",
    year = "1962",
    booktitle = "Comparative Biochemistry",
    publisher = "New York, Academic Press, v. IV, p. 185-224",
    note = "talkorigins\_source = {true}; raw\_reference = {Vegotsky, A., and Fox, S. W., 1962, Protein molecules: intraspecific and interspecific variations, in Florkin, M., and Mason, H. S., eds., Comparative Biochemistry: New York, Academic Press, v. IV, p. 185-224.}"
}

The structure of present-day ferredoxin, with its simple, inorganic active site and its functions basic to photon-energy utilization, suggests the incorporation of its prototype into metabolism very early during biochemical evolution, even before complex proteins and the complete modern genetic code existed. The information in the amino acid sequence of ferredoxin enables us to propose a detailed reconstruction of its evolutionary history. Ferredoxin has evolved by doubling a shorter protein, which may have contained only eight of the simplest amino acids. This shorter ancestor in turn developed from a repeating sequence of the amino acids alanine, aspartic acid or proline, serine, and glycine. We explain the persistence of living relics of this primordial structure by invoking a conservative principle in evolutionary biochemistry: The processes of natural selection severely inhibit any change a well-adapted system on which several other essential components depend.

@article{doi101126science1523720363,
    author = "Eck, Richard V. and Dayhoff, M. O.",
    title = "Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences",
    year = "1966",
    journal = "Science",
    abstract = "The structure of present-day ferredoxin, with its simple, inorganic active site and its functions basic to photon-energy utilization, suggests the incorporation of its prototype into metabolism very early during biochemical evolution, even before complex proteins and the complete modern genetic code existed. The information in the amino acid sequence of ferredoxin enables us to propose a detailed reconstruction of its evolutionary history. Ferredoxin has evolved by doubling a shorter protein, which may have contained only eight of the simplest amino acids. This shorter ancestor in turn developed from a repeating sequence of the amino acids alanine, aspartic acid or proline, serine, and glycine. We explain the persistence of living relics of this primordial structure by invoking a conservative principle in evolutionary biochemistry: The processes of natural selection severely inhibit any change a well-adapted system on which several other essential components depend.",
    url = "https://doi.org/10.1126/science.152.3720.363",
    doi = "10.1126/science.152.3720.363",
    openalex = "W2030831143"
}

@misc{bernal1967the1,
    author = "Bernal, J. D",
    title = "The Origin of Life",
    year = "1967",
    howpublished = "London, Weidenfeld and Nicolson, 345 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Bernal, J. D., 1967, The Origin of Life: London, Weidenfeld and Nicolson, 345 p.}"
}

@misc{rohlfing1967the30,
    author = "Rohlfing, D. L",
    title = "The catalytic decarboxylation of oxaloacetic acid by thermally prepared poly--aminoacids",
    year = "1967",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 118, p. 468-474",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1967, The catalytic decarboxylation of oxaloacetic acid by thermally prepared poly--aminoacids: Archives of Biochemistry and Biophysiology, v. 118, p. 468-474.}"
}

@misc{rohlfing1967thermal29,
    author = "Rohlfing, D. L",
    title = "Thermal poly--amino acids containing low proportions of aspartic acid",
    year = "1967",
    howpublished = "Nature, v. 216, p. 657-659",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1967, Thermal poly--amino acids containing low proportions of aspartic acid: Nature, v. 216, p. 657-659.}"
}

@misc{usdin1967inhibition40,
    author = "Usdin, V. R. and Mitz, M. A. and Killos, P. J",
    title = "Inhibition and reactivation of the catalytic activity of a thermal -amino acid copolymer",
    year = "1967",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 122, p. 258-261",
    note = "talkorigins\_source = {true}; raw\_reference = {Usdin, V. R., Mitz, M. A., and Killos, P. J., 1967, Inhibition and reactivation of the catalytic activity of a thermal -amino acid copolymer: Archives of Biochemistry and Biophysiology, v. 122, p. 258-261.}"
}

@misc{karmpitz1968glutaminsureoxydoreductase11,
    author = "Karmpitz, G. and Haas, W. and Baars-Diehl, S",
    title = "Glutaminsure-Oxydoreductase- Aktivitt von Polyanhydro--Aminosuren (Proteinoiden)",
    year = "1968",
    howpublished = "Naturwissenschaften, v. 55, p. 345-346",
    note = "talkorigins\_source = {true}; raw\_reference = {Karmpitz, G., Haas, W., and Baars-Diehl, S., 1968, Glutaminsure-Oxydoreductase- Aktivitt von Polyanhydro--Aminosuren (Proteinoiden): Naturwissenschaften, v. 55, p. 345-346.}"
}

@book{oparin1968genesis24,
    author = "Oparin, A. I",
    title = "Genesis and Evolutionary Development of Life",
    year = "1968",
    publisher = "New York, Academic Press, 203 p.; Translated by E. Maass",
    note = "talkorigins\_source = {true}; raw\_reference = {Oparin, A. I., 1968, Genesis and Evolutionary Development of Life: New York, Academic Press, 203 p.; Translated by E. Maass.}"
}

@misc{oshima1968the25,
    author = "Oshima, T",
    title = "The catalytic hydrolysis of phosphate ester bonds by thermal polymers of amino acids",
    year = "1968",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 126, p. 478-485",
    note = "talkorigins\_source = {true}; raw\_reference = {Oshima, T., 1968, The catalytic hydrolysis of phosphate ester bonds by thermal polymers of amino acids: Archives of Biochemistry and Biophysiology, v. 126, p. 478-485.}"
}

@misc{rohlfing1969catalytic32,
    author = "Rohlfing, D. L. and Fox, S. W",
    title = "Catalytic activities of thermal polyanhydro--amino acids",
    year = "1969",
    howpublished = "Advances in Catalysis, v. 20, p. 373-418",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., and Fox, S. W., 1969, Catalytic activities of thermal polyanhydro--amino acids: Advances in Catalysis, v. 20, p. 373-418.}"
}

@article{doi101038228636a0,
    author = "Paecht‐Horowitz, Mella and Berger, Julius and Katchalsky, A.",
    title = "Prebiotic Synthesis of Polypeptides by Heterogeneous Polycondensation of Amino-acid Adenylates",
    year = "1970",
    journal = "Nature",
    url = "https://doi.org/10.1038/228636a0",
    doi = "10.1038/228636a0",
    openalex = "W2070032819",
    references = "doi101126science12933571221a"
}

@book{cairnssmith1971the2,
    author = "Cairns-Smith, A. G",
    title = "The Life Puzzle",
    year = "1971",
    publisher = "On Crystals and Organisms and on the Possibility of a Crystal As an Ancestor: Toronto, University of Toronto Press, 165 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Cairns-Smith, A. G., 1971, The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal As an Ancestor: Toronto, University of Toronto Press, 165 p.}"
}

@article{doi101038233136a0,
    author = "Hall, D.O. and Cammack, Richard and Rao, Krishna",
    title = "Role for Ferredoxins in the Origin of Life and Biological Evolution",
    year = "1971",
    journal = "Nature",
    url = "https://doi.org/10.1038/233136a0",
    doi = "10.1038/233136a0",
    openalex = "W2060939270",
    references = "lemmon1970chemical"
}

@misc{monod1971chance18,
    author = "Monod, J",
    title = "Chance and Necessity",
    year = "1971",
    howpublished = "New York, A.A. Knopf; Translated by A. Wainhouse",
    note = "talkorigins\_source = {true}; raw\_reference = {Monod, J., 1971, Chance and Necessity: New York, A.A. Knopf; Translated by A. Wainhouse.}"
}

@misc{mueller1972organic20,
    author = "Mueller, G",
    title = "Organic microspheres from the Precambrian of South-West Africa",
    year = "1972",
    howpublished = "Nature, v. 235, p. 90-95",
    note = "talkorigins\_source = {true}; raw\_reference = {Mueller, G., 1972, Organic microspheres from the Precambrian of South-West Africa: Nature, v. 235, p. 90-95.}"
}

@article{osterberg1972polyphosphate26,
    author = "Osterberg, R. and Orgel, L. E",
    title = "Polyphosphate and trimetaphosphate formation under potetially prebiotic conditions",
    year = "1972",
    journal = "Journal of Molecular Evolution, v. 1, p. 241-248",
    note = "talkorigins\_source = {true}; raw\_reference = {Osterberg, R., and Orgel, L. E., 1972, Polyphosphate and trimetaphosphate formation under potetially prebiotic conditions: Journal of Molecular Evolution, v. 1, p. 241-248.}"
}

@book{wood1972light46,
    author = "Wood, A. and Hardebeck, H. G",
    title = "Light enhanced decarboxylations by proteinoids, in Rohlfing, D. L., and Oparin, A. I., eds., Molecular Evolution",
    year = "1972",
    publisher = "New York, Plenum Press, p. 233-245",
    note = "talkorigins\_source = {true}; raw\_reference = {Wood, A., and Hardebeck, H. G., 1972, Light enhanced decarboxylations by proteinoids, in Rohlfing, D. L., and Oparin, A. I., eds., Molecular Evolution: New York, Plenum Press, p. 233-245.}"
}

@book{iben1973molecules10,
    author = "Iben, I. and Jr",
    title = "Molecules in the Galatic Environment",
    year = "1973",
    publisher = "New York, John Wiley",
    note = "talkorigins\_source = {true}; raw\_reference = {Iben, I., Jr., 1973, Molecules in the Galatic Environment: New York, John Wiley.}"
}

@misc{kenyon1973a12,
    author = "Kenyon, D. H",
    title = "A theory of biogenesis",
    year = "1973",
    howpublished = "Science, v. 179, p. 789",
    note = "talkorigins\_source = {true}; raw\_reference = {Kenyon, D. H., 1973, A theory of biogenesis: Science, v. 179, p. 789.}"
}

@misc{schopf1973the35,
    author = "Schopf, J. W",
    title = "The evolution of the earliest cells",
    year = "1973",
    howpublished = "Scientific American, v. 239, no. 3, p. 111-138",
    note = "talkorigins\_source = {true}; raw\_reference = {Schopf, J. W., 1973, The evolution of the earliest cells: Scientific American, v. 239, no. 3, p. 111-138.}"
}

@book{keosian1974lifes13,
    author = "Keosian, J",
    title = "Life's beginnings-origin or evolution?, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry",
    year = "1974",
    publisher = "New York, Plenum Press, p. 221-231",
    note = "talkorigins\_source = {true}; raw\_reference = {Keosian, J., 1974, Life's beginnings-origin or evolution?, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry: New York, Plenum Press, p. 221-231.}"
}

@phdthesis{price1974synthesis28,
    author = "Price, C. C",
    title = "Synthesis of Life",
    year = "1974",
    publisher = "Stroudsburg, Pa., Dowden, Hutchinson \& Ross",
    note = "talkorigins\_source = {true}; raw\_reference = {Price, C. C., 1974, Synthesis of Life: Stroudsburg, Pa., Dowden, Hutchinson \& Ross.}"
}

@misc{turcotte1974evolution39,
    author = "Turcotte, D. L. and Nordmann, J. C. and Cisne, J. L",
    title = "Evolution of the Moon's orbit and the origin of life",
    year = "1974",
    howpublished = "Nature, v. 251, p. 124-125",
    note = "talkorigins\_source = {true}; raw\_reference = {Turcotte, D. L., Nordmann, J. C., and Cisne, J. L., 1974, Evolution of the Moon's orbit and the origin of life: Nature, v. 251, p. 124-125.}"
}

@misc{snyder1975a37,
    author = "Snyder, W. D. and Fox, S",
    title = "A model for the origin of stable protocells in a primitive alkaline ocean",
    year = "1975",
    howpublished = "BioSystems, v. 7, p. 222-229",
    note = "talkorigins\_source = {true}; raw\_reference = {Snyder, W. D., and Fox, S., 1975, A model for the origin of stable protocells in a primitive alkaline ocean: BioSystems, v. 7, p. 222-229.}"
}

@phdthesis{rohlfing1976thermal31,
    author = "Rohlfing, D. L",
    title = "Thermal polyamino acids",
    year = "1976",
    publisher = "synthesis at less than 100° C: Science, v. 193, p. 68-70",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1976, Thermal polyamino acids: synthesis at less than 100° C: Science, v. 193, p. 68-70.}"
}

@article{temussi1976structural38,
    author = "Temussi, P. A. and Paolillo, L. and Ferrara, L. and Benedetti, E. and Andini, S",
    title = "Structural characterization of thermal prebiotic polypeptides",
    year = "1976",
    journal = "Journal of Molecular Evolution, v. 7, p. 105-110",
    note = "talkorigins\_source = {true}; raw\_reference = {Temussi, P. A., Paolillo, L., Ferrara, L., Benedetti, E., and Andini, S., 1976, Structural characterization of thermal prebiotic polypeptides: Journal of Molecular Evolution, v. 7, p. 105-110.}"
}

@misc{fox1977molecular6,
    author = "Fox, S. W. and Dose, K",
    title = "Molecular Evolution and the Origin of Life",
    year = "1977",
    howpublished = "New York and Basel, Marcel Dekker, Inc., 370 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Dose, K., 1977, Molecular Evolution and the Origin of Life: New York and Basel, Marcel Dekker, Inc., 370 p.}"
}

@article{nakashima1977a23,
    author = "Nakashima, T. and Jungck, J. R. and Fox, S. W. and Lederer, E. and Das, B. C",
    title = "A test for randomness in peptides isolated from a thermal polyamino acid",
    year = "1977",
    journal = "International Journal of Quantum Chemistry, v. QBS4, p. 65-72",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., Jungck, J. R., Fox, S. W., Lederer, E., and Das, B. C., 1977, A test for randomness in peptides isolated from a thermal polyamino acid: International Journal of Quantum Chemistry, v. QBS4, p. 65-72.}"
}

@article{doi101016s0047248478800529,
    author = "Fox, Sidney Walter and Dose, Klaus 1928-",
    title = "Molecular evolution and the origin of life",
    year = "1978",
    journal = "Journal of Human Evolution",
    url = "https://doi.org/10.1016/s0047-2484(78)80052-9",
    doi = "10.1016/s0047-2484(78)80052-9",
    openalex = "W1511390927"
}

@misc{morris1978thermodynamics19,
    author = "Morris, H. M",
    title = "Thermodynamics and the origin of life",
    year = "1978",
    howpublished = "ICR Impact Series, v. 57, p. i-iv",
    note = "talkorigins\_source = {true}; raw\_reference = {Morris, H. M., 1978, Thermodynamics and the origin of life: ICR Impact Series, v. 57, p. i-iv.}"
}

@misc{schopf1978the36,
    author = "Schopf, J. W",
    title = "The evolution of the earliest cells",
    year = "1978",
    howpublished = "Scientific American, v. 239, p. 110-135",
    note = "talkorigins\_source = {true}; raw\_reference = {Schopf, J. W., 1978, The evolution of the earliest cells: Scientific American, v. 239, p. 110-135.}"
}

@phdthesis{nakashima1980synthesis21,
    author = "Nakashima, T. and Fox, S. W",
    title = "Synthesis of peptides from amino acids and ATP with lysine-rich protenoid",
    year = "1980",
    publisher = "Journal of Molecular Evolution, v. 15, p. 161-168",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., and Fox, S. W., 1980, Synthesis of peptides from amino acids and ATP with lysine-rich protenoid: Journal of Molecular Evolution, v. 15, p. 161-168.}"
}

@misc{crick1981life4,
    author = "Crick, F. J",
    title = "Life Itself",
    year = "1981",
    howpublished = "Its Origin and Nature: New York, Simon and Schuster",
    note = "talkorigins\_source = {true}; raw\_reference = {Crick, F. J., 1981, Life Itself: Its Origin and Nature: New York, Simon and Schuster.}"
}

@misc{groves1981an7,
    author = "Groves, D. I. and Dunlop, J. S. R. and Buick, R",
    title = "An early habitat of life",
    year = "1981",
    howpublished = "Scientific American, v. 245, no. 4, p. 64-73",
    note = "talkorigins\_source = {true}; raw\_reference = {Groves, D. I., Dunlop, J. S. R., and Buick, R., 1981, An early habitat of life: Scientific American, v. 245, no. 4, p. 64-73.}"
}

@misc{kuhn1981model14,
    author = "Kuhn, H",
    title = "Model considerations for the origin of life",
    year = "1981",
    howpublished = "Naturwissenschaften, v. 63, p. 68-80",
    note = "talkorigins\_source = {true}; raw\_reference = {Kuhn, H., 1981, Model considerations for the origin of life: Naturwissenschaften, v. 63, p. 68-80.}"
}

@misc{kuhn1981molecular15,
    author = "Kuhn, H",
    title = "Molecular self-organization and the origin of life",
    year = "1981",
    howpublished = "Agnew. Chem. Internat. Ed. Engl., v. 20, p. 500-520",
    note = "talkorigins\_source = {true}; raw\_reference = {Kuhn, H., 1981, Molecular self-organization and the origin of life: Agnew. Chem. Internat. Ed. Engl., v. 20, p. 500-520.}"
}

@misc{matsuno1981material17,
    author = "Matsuno, K",
    title = "Material self-assembly as a physicochemical process",
    year = "1981",
    howpublished = "BioSystems, v. 13, p. 237-241",
    note = "talkorigins\_source = {true}; raw\_reference = {Matsuno, K., 1981, Material self-assembly as a physicochemical process: BioSystems, v. 13, p. 237-241.}"
}

@misc{nakashima1981formulation22,
    author = "Nakashima, T. and Fox, S. W",
    title = "Formulation of peptides by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles",
    year = "1981",
    howpublished = "BioSystems, v. 14, p. 151- 161",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., and Fox, S. W., 1981, Formulation of peptides by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles: BioSystems, v. 14, p. 151- 161.}"
}

@misc{pivcova1981nmr27,
    author = "Pivcova, H. and Saudek, V. and Drobnik, J. and Vlasak, J",
    title = "NMR study of poly (aspartic acid) I. - and -peptide bonds in poly (aspartic acid) prepared by thermal polycondensation",
    year = "1981",
    howpublished = "Biopolymers, v. 20, p. 1605-1614",
    note = "talkorigins\_source = {true}; raw\_reference = {Pivcova, H., Saudek, V., Drobnik, J., and Vlasak, J., 1981, NMR study of poly (aspartic acid) I. - and -peptide bonds in poly (aspartic acid) prepared by thermal polycondensation: Biopolymers, v. 20, p. 1605-1614.}"
}

@article{yockey1981self47,
    author = "Yockey, H. P",
    title = "Self organization origin of life scenarios and information theory",
    year = "1981",
    journal = "Journal of Theoretical Biology, v. 91, p. 13-31",
    note = "talkorigins\_source = {true}; raw\_reference = {Yockey, H. P., 1981, Self organization origin of life scenarios and information theory: Journal of Theoretical Biology, v. 91, p. 13-31.}"
}

@misc{crick1982life3,
    author = "Crick, F",
    title = "Life Itself",
    year = "1982",
    howpublished = "Its Origin and Nature: New York, W.W. Norton, 192 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Crick, F., 1982, Life Itself: Its Origin and Nature: New York, W.W. Norton, 192 p.}"
}

@misc{salthe1982original34,
    author = "Salthe, S",
    title = "Original Life",
    year = "1982",
    howpublished = "Nature, v. 295, p. 452",
    note = "talkorigins\_source = {true}; raw\_reference = {Salthe, S., 1982, Original Life: Nature, v. 295, p. 452.}"
}

@misc{doolittle1983probability5,
    author = "Doolittle, R. F",
    title = "Probability and the Origin of Life, in Godfrey, L. R., ed., Scientists Confront Creationists",
    year = "1983",
    howpublished = "New York, W.W. Norton \& Co., p. 85-97",
    note = "talkorigins\_source = {true}; raw\_reference = {Doolittle, R. F., 1983, Probability and the Origin of Life, in Godfrey, L. R., ed., Scientists Confront Creationists: New York, W.W. Norton \& Co., p. 85-97.}"
}

@article{doi101007bf01808177,
    author = "Baross, John A. and Hoffman, Sarah",
    title = "Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life",
    year = "1985",
    journal = "Origins of Life and Evolution of Biospheres",
    url = "https://doi.org/10.1007/bf01808177",
    doi = "10.1007/bf01808177",
    openalex = "W2082856886",
    references = "doi1010079781461262848, doi101007bf00425213, doi101029jb086ib04p02737, doi101126science1473658563, doi101126science20343851073, doi101126science20744381421, doi101126science2134505340, doi1023072403256, openalexw1759691579, openalexw2026796374"
}

This addresswas presented by Freeman J. Dyson as the NishinaMemorial Lecture at the University of Tokyo, on October 17, 1984, and at Yukawa Institute for Theoretical Physics, on October 23, 1984.

@book{openalexw1882072473,
    author = "Dyson, Freeman J.",
    title = "Origins of Life",
    year = "1985",
    abstract = "This addresswas presented by Freeman J. Dyson as the NishinaMemorial Lecture at the University of Tokyo, on October 17, 1984, and at Yukawa Institute for Theoretical Physics, on October 23, 1984.",
    openalex = "W1882072473"
}

@article{doi101038319618a0,
    author = "Gilbert, Walter",
    title = "Origin of life: The RNA world",
    year = "1986",
    journal = "Nature",
    url = "https://doi.org/10.1038/319618a0",
    doi = "10.1038/319618a0",
    openalex = "W2050110866",
    references = "doi101007bf01732468, doi1010160092867482904147, doi1010160092867483901174, doi1010160092867485900923, doi101016s0074769608613704, doi101038319534a0, doi101038scientificamerican048188, doi101126science3941911, doi101126science6199841"
}

@misc{lewin1986rna16,
    author = "Lewin, R",
    title = "RNA catalysis gives fresh perspective to the origin of life",
    year = "1986",
    howpublished = "Science, v. 231, p. 545-546",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1986, RNA catalysis gives fresh perspective to the origin of life: Science, v. 231, p. 545-546.}"
}

@article{doi101038334609a0,
    author = "Miller, Stanley L. and Bada, Jeffrey L.",
    title = "Submarine hot springs and the origin of life",
    year = "1988",
    journal = "Nature",
    url = "https://doi.org/10.1038/334609a0",
    doi = "10.1038/334609a0",
    openalex = "W2053209359",
    references = "doi101007bf01660244, doi1010160012821x80901636, doi1010160016003251909593, doi1010160026265x73901124, doi101016s0047248478800529, doi101038201335a0, doi101038297187a0, doi101038331612a0, doi101073pnas84134398, doi101146annurevbi55070186003123, doi101146annurevbiochem551599, openalexw3193853653"
}

@article{doi101038338217a0,
    author = "Joyce, Gerald F.",
    title = "RNA evolution and the origins of life",
    year = "1989",
    journal = "Nature",
    url = "https://doi.org/10.1038/338217a0",
    doi = "10.1038/338217a0",
    openalex = "W1976379862",
    references = "doi101007bf01733901, doi1010160022283668903938, doi101016s0022283667800378, doi101016s0022519386800479, doi101016s0047248478800529, doi101038331612a0, openalexw2983085323, openalexw3038835020"
}

@misc{sachs1990translational33,
    author = "Sachs, A. B. and Davis, R. W",
    title = "Translational initiation and ribosomal biogenesis",
    year = "1990",
    howpublished = "involvement of a putative rRNA helicase and RPL46: Science, v. 247, p. 1077",
    note = "talkorigins\_source = {true}; raw\_reference = {Sachs, A. B., and Davis, R. W., 1990, Translational initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46: Science, v. 247, p. 1077.}"
}

@inproceedings{waldrop1990spontaneous43,
    author = "Waldrop, M. M",
    title = "Spontaneous Order, Evolution, and Life",
    year = "1990",
    booktitle = "Science, v. 247, p. 1543-1545; [Workshop on Artificial Life II, Feb. 5-9, 1990, Santa Fe, New Mexico]",
    note = "talkorigins\_source = {true}; raw\_reference = {Waldrop, M. M., 1990, Spontaneous Order, Evolution, and Life: Science, v. 247, p. 1543-1545; [Workshop on Artificial Life II, Feb. 5-9, 1990, Santa Fe, New Mexico].}"
}

@misc{woese1990evolutionary45,
    author = "Woese, C. R",
    title = "Evolutionary questions",
    year = "1990",
    howpublished = {the "progenote" (letter): Science, v. 247, p. 789},
    note = {talkorigins\_source = {true}; raw\_reference = {Woese, C. R., 1990, Evolutionary questions: the "progenote" (letter): Science, v. 247, p. 789.}}
}

Biological polymers have a preferred chirality ond can replicate themselves. Physical arguments provide insight into which of these unique and apparently related properties evolved first, and by what mechanism.

@article{doi1010631881264,
    author = "Аветисов, В. А. and Кузьмин, В. В. and Goldanskii, V.I.",
    title = "Handedness, Origin of Life and Evolution",
    year = "1991",
    journal = "Physics Today",
    abstract = "Biological polymers have a preferred chirality ond can replicate themselves. Physical arguments provide insight into which of these unique and apparently related properties evolved first, and by what mechanism.",
    url = "https://doi.org/10.1063/1.881264",
    doi = "10.1063/1.881264",
    openalex = "W2049299235"
}

@article{doi101007bf01140180,
    author = "Hennet, Remy J.‐C. and Holm, Nils G. and Engel, Michael H.",
    title = "Abiotic synthesis of amino acids under hydrothermal conditions and the origin of life: A perpetual phenomenon?",
    year = "1992",
    journal = "Die Naturwissenschaften",
    url = "https://doi.org/10.1007/bf01140180",
    doi = "10.1007/bf01140180",
    openalex = "W2079800805",
    references = "doi1010079781489904027, doi101007bf01808115, doi101016c20130121083, doi101016s0040402001993159, doi101029jb091ib10p10309, doi101038190442a0, doi101038297187a0, doi101038334609a0, doi101126science20744381421"
}

Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependent RNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable "core" of housekeeping genes accompanied by a much more flexible "shell" consisting mostly of genes coding for virion components and various accessory proteins is discussed. Shuffling of the "shell" genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution. Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the RNA-dependent RNA polymerase, which is the only universally conserved protein of positive-strand RNA viruses, three large classes of viruses, each consisting of distinct smaller divisions, were delineated. A strong correlation was observed between this grouping and the tentative phylogenies for the other conserved proteins as well as the arrangement of genes encoding these proteins in the virus genome. A comparable correlation with the polymerase phylogeny was not found for genes encoding virion components or for genome expression strategies. It is surmised that several types of arrangement of the "shell" genes as well as basic mechanisms of expression could have evolved independently in different evolutionary lineages. The grouping revealed by phylogenetic analysis may provide the basis for revision of virus classification, and phylogenetic taxonomy of positive-strand RNA viruses is outlined. Some of the phylogenetically derived divisions of positive-strand RNA viruses also include double-stranded RNA viruses, indicating that in certain cases the type of genome nucleic acid may not be a reliable taxonomic criterion for viruses. Hypothetical evolutionary scenarios for positive-strand RNA viruses are proposed. It is hypothesized that all positive-strand RNA viruses and some related double-stranded RNA viruses could have evolved from a common ancestor virus that contained genes for RNA-dependent RNA polymerase, a chymotrypsin-related protease that also functioned as the capsid protein, and possibly an RNA helicase.

@article{doi10310910409239309078440,
    author = "Koonin, Eugene V. and Dolja, Valerian V. and Morris, T.J.",
    title = "Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences",
    year = "1993",
    journal = "Critical Reviews in Biochemistry and Molecular Biology",
    abstract = {Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependent RNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable "core" of housekeeping genes accompanied by a much more flexible "shell" consisting mostly of genes coding for virion components and various accessory proteins is discussed. Shuffling of the "shell" genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution. Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the RNA-dependent RNA polymerase, which is the only universally conserved protein of positive-strand RNA viruses, three large classes of viruses, each consisting of distinct smaller divisions, were delineated. A strong correlation was observed between this grouping and the tentative phylogenies for the other conserved proteins as well as the arrangement of genes encoding these proteins in the virus genome. A comparable correlation with the polymerase phylogeny was not found for genes encoding virion components or for genome expression strategies. It is surmised that several types of arrangement of the "shell" genes as well as basic mechanisms of expression could have evolved independently in different evolutionary lineages. The grouping revealed by phylogenetic analysis may provide the basis for revision of virus classification, and phylogenetic taxonomy of positive-strand RNA viruses is outlined. Some of the phylogenetically derived divisions of positive-strand RNA viruses also include double-stranded RNA viruses, indicating that in certain cases the type of genome nucleic acid may not be a reliable taxonomic criterion for viruses. Hypothetical evolutionary scenarios for positive-strand RNA viruses are proposed. It is hypothesized that all positive-strand RNA viruses and some related double-stranded RNA viruses could have evolved from a common ancestor virus that contained genes for RNA-dependent RNA polymerase, a chymotrypsin-related protease that also functioned as the capsid protein, and possibly an RNA helicase.},
    url = "https://doi.org/10.3109/10409239309078440",
    doi = "10.3109/10409239309078440",
    openalex = "W2065717236",
    references = "doi10100703064746897, doi101038319618a0, doi101093aesa383396"
}

Carbonatites are igneous rocks formed in the crust by fractional crystallization of carbonate-rich parental melts that are mostly mantle derived. They dominantly consist of carbonate minerals such as calcite, dolomite, and ankerite, as well as minor...Read More

@article{doi101146annurevea23050195001243,
    author = "Chyba, Christopher F. and McDonald, G. D.",
    title = "The Origin of Life in the Solar System: Current Issues",
    year = "1995",
    journal = "Annual Review of Earth and Planetary Sciences",
    abstract = "Carbonatites are igneous rocks formed in the crust by fractional crystallization of carbonate-rich parental melts that are mostly mantle derived. They dominantly consist of carbonate minerals such as calcite, dolomite, and ankerite, as well as minor...Read More",
    url = "https://doi.org/10.1146/annurev.ea.23.050195.001243",
    doi = "10.1146/annurev.ea.23.050195.001243",
    openalex = "W2154618142",
    references = "doi1010160016703793905425"
}

@article{fox1995thermal,
    author = "Fox, Sidney W.",
    title = "Thermal synthesis of amino acids and the origin of life",
    year = "1995",
    journal = "Geochimica et Cosmochimica Acta",
    url = "https://doi.org/10.1016/0016-7037(95)00037-z",
    doi = "10.1016/0016-7037(95)00037-z",
    number = "6",
    pages = "1213-1214",
    volume = "59"
}

In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism.

@article{doi101126science2815377670,
    author = "Huber, Claudia and Wächtershäuser, Günter",
    title = "Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life",
    year = "1998",
    journal = "Science",
    abstract = "In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism.",
    url = "https://doi.org/10.1126/science.281.5377.670",
    doi = "10.1126/science.281.5377.670",
    openalex = "W2166068250",
    references = "doi101016s0047248478800529"
}

@misc{crossref1999biogenesis,
    title = "Biogenesis",
    year = "1999",
    booktitle = "Mitochondria",
    url = "https://doi.org/10.1002/0471223891.ch4",
    doi = "10.1002/0471223891.ch4",
    pages = "48-140"
}

@article{doi101016s1359029499000126,
    author = "Luisi, Pier Luigi and Walde, Peter and Oberholzer, Thomas",
    title = "Lipid vesicles as possible intermediates in the origin of life",
    year = "1999",
    journal = "Current Opinion in Colloid \& Interface Science",
    url = "https://doi.org/10.1016/s1359-0294(99)00012-6",
    doi = "10.1016/s1359-0294(99)00012-6",
    openalex = "W1985820082",
    references = "doi101016s0047248478800529"
}

@article{doi101023a1012790523136,
    author = "Viedma, Cristóbal",
    title = "Enantiomeric Crystallization from DL-Aspartic and DL-Glutamic Acids: Implications for Biomolecular Chirality in the Origin of Life",
    year = "2001",
    journal = "Origins of Life and Evolution of Biospheres",
    url = "https://doi.org/10.1023/a:1012790523136",
    doi = "10.1023/a:1012790523136",
    openalex = "W229923164",
    references = "doi101007bf01809580, doi101038233136a0, doi101038314438a0, doi1010631881264, doi101093oso97801950447680010001, doi101126science1523720363, doi101126science2504983975, fox1995thermal, openalexw1512177901, openalexw3157327320"
}

@misc{crossref2004biogenesis,
    title = "Biogenesis",
    year = "2004",
    booktitle = "Encyclopedic Dictionary of Genetics, Genomics and Proteomics",
    url = "https://doi.org/10.1002/0471684228.egp01375",
    doi = "10.1002/0471684228.egp01375"
}

@article{doi101007s0072600401064,
    author = "Zaia, Dimas Augusto Morozin",
    title = "A review of adsorption of amino acids on minerals: Was it important for origin of life?",
    year = "2004",
    journal = "Amino Acids",
    url = "https://doi.org/10.1007/s00726-004-0106-4",
    doi = "10.1007/s00726-004-0106-4",
    openalex = "W1970454669",
    references = "doi101023a1012790523136"
}

Just as Darwinian evolution in nature has led to the development of many sophisticated enzymes, Darwinian evolution in vitro has proven to be a powerful approach for obtaining similar results in the laboratory. This review focuses on the development of nucleic acid enzymes starting from a population of random-sequence RNA or DNA molecules. In order to illustrate the principles and practice of in vitro evolution, two especially well-studied categories of catalytic nucleic acid are considered: RNA enzymes that catalyze the template-directed ligation of RNA and DNA enzymes that catalyze the cleavage of RNA. The former reaction, which involves attack of a 2'- or 3'-hydroxyl on the alpha-phosphate of a 5'-triphosphate, is more difficult. It requires a comparatively larger catalytic motif, containing more nucleotides than can be sampled exhaustively within a starting population of random-sequence RNAs. The latter reaction involves deprotonation of the 2'-hydroxyl adjacent to the cleavage site, resulting in cleaved products that bear a 2',3'-cyclic phosphate and 5'-hydroxyl. The difficulty of this reaction, and therefore the complexity of the corresponding DNA enzyme, depends on whether a catalytic cofactor, such as a divalent metal cation or small molecule, is present in the reaction mixture.

@article{doi101146annurevbiochem73011303073717,
    author = "Joyce, Gerald F.",
    title = "Directed Evolution of Nucleic Acid Enzymes",
    year = "2004",
    journal = "Annual Review of Biochemistry",
    abstract = "Just as Darwinian evolution in nature has led to the development of many sophisticated enzymes, Darwinian evolution in vitro has proven to be a powerful approach for obtaining similar results in the laboratory. This review focuses on the development of nucleic acid enzymes starting from a population of random-sequence RNA or DNA molecules. In order to illustrate the principles and practice of in vitro evolution, two especially well-studied categories of catalytic nucleic acid are considered: RNA enzymes that catalyze the template-directed ligation of RNA and DNA enzymes that catalyze the cleavage of RNA. The former reaction, which involves attack of a 2'- or 3'-hydroxyl on the alpha-phosphate of a 5'-triphosphate, is more difficult. It requires a comparatively larger catalytic motif, containing more nucleotides than can be sampled exhaustively within a starting population of random-sequence RNAs. The latter reaction involves deprotonation of the 2'-hydroxyl adjacent to the cleavage site, resulting in cleaved products that bear a 2',3'-cyclic phosphate and 5'-hydroxyl. The difficulty of this reaction, and therefore the complexity of the corresponding DNA enzyme, depends on whether a catalytic cofactor, such as a divalent metal cation or small molecule, is present in the reaction mixture.",
    url = "https://doi.org/10.1146/annurev.biochem.73.011303.073717",
    doi = "10.1146/annurev.biochem.73.011303.073717",
    openalex = "W2073775872",
    references = "doi101021ja990592p"
}

Syntheses and polymerizations of alpha-amino acid N-carboxyanhydrides (NCAs) were reported for the first time by Hermann Leuchs in 1906. Since that time, these cyclic and highly reactive amino acid derivatives were used for stepwise peptide syntheses but mainly for the formation of polypeptides by ring-opening polymerizations. This review summarizes the literature after 1985 and reports on new aspects of the polymerization processes, such as the formation of cyclic polypeptides or novel organometal catalysts. Polypeptides with various architectures, such as diblock, triblock, and multiblock sequences, and star-shaped or dendritic structures are also mentioned. Furthermore, lyotropic and thermotropic liquid-crystalline polypeptides will be discussed and the role of polypeptides as drugs or drug carriers are reviewed. Finally, the hypothetical role of NCAs in molecular evolution on the prebiotic Earth is discussed.

@article{doi101002anie200600693,
    author = "Kricheldorf, Hans R.",
    title = "Polypeptides and 100 Years of Chemistry of α‐Amino Acid N ‐Carboxyanhydrides",
    year = "2006",
    journal = "Angewandte Chemie International Edition",
    abstract = "Syntheses and polymerizations of alpha-amino acid N-carboxyanhydrides (NCAs) were reported for the first time by Hermann Leuchs in 1906. Since that time, these cyclic and highly reactive amino acid derivatives were used for stepwise peptide syntheses but mainly for the formation of polypeptides by ring-opening polymerizations. This review summarizes the literature after 1985 and reports on new aspects of the polymerization processes, such as the formation of cyclic polypeptides or novel organometal catalysts. Polypeptides with various architectures, such as diblock, triblock, and multiblock sequences, and star-shaped or dendritic structures are also mentioned. Furthermore, lyotropic and thermotropic liquid-crystalline polypeptides will be discussed and the role of polypeptides as drugs or drug carriers are reviewed. Finally, the hypothetical role of NCAs in molecular evolution on the prebiotic Earth is discussed.",
    url = "https://doi.org/10.1002/anie.200600693",
    doi = "10.1002/anie.200600693",
    openalex = "W2027401476",
    references = "doi101038381059a0"
}

Attempts to model the spontaneous chemistry which presumably preceded the origin of life on Earth commonly result in the production of intractably complex mixtures of organic compounds. It is, therefore, difficult to understand how any kind of evolutionary process might have begun. A number of potential solutions to this well-known and frustrating problem have been offered in the literature over the years. The present contribution briefly reviews and evaluates some of the more promising possibilities.

@article{doi101002cbdv200790056,
    author = "Schwartz, Alan W.",
    title = "Intractable Mixtures and the Origin of Life",
    year = "2007",
    journal = "Chemistry \& Biodiversity",
    abstract = "Attempts to model the spontaneous chemistry which presumably preceded the origin of life on Earth commonly result in the production of intractably complex mixtures of organic compounds. It is, therefore, difficult to understand how any kind of evolutionary process might have begun. A number of potential solutions to this well-known and frustrating problem have been offered in the literature over the years. The present contribution briefly reviews and evaluates some of the more promising possibilities.",
    url = "https://doi.org/10.1002/cbdv.200790056",
    doi = "10.1002/cbdv.200790056",
    openalex = "W2078314735",
    references = "doi101126science12933571221a"
}

@article{doi101016jtet200710012,
    author = "Eschenmoser, Albert",
    title = "The search for the chemistry of life's origin",
    year = "2007",
    journal = "Tetrahedron",
    url = "https://doi.org/10.1016/j.tet.2007.10.012",
    doi = "10.1016/j.tet.2007.10.012",
    openalex = "W2953350983",
    references = "doi101007bf00439699, doi101007pl00006565, doi101016s0040403901994870, doi10108803701298629301, doi101098rstb20061904, lemmon1970chemical, openalexw2983085323"
}

@incollection{crossref2008biogenesis,
    title = "Biogenesis",
    year = "2008",
    booktitle = "Encyclopedia of Genetics, Genomics, Proteomics and Informatics",
    url = "https://doi.org/10.1007/978-1-4020-6754-9\_1782",
    doi = "10.1007/978-1-4020-6754-9\_1782",
    pages = "212-212"
}

@article{doi101007s1108400891505,
    author = "Zaia, Dimas Augusto Morozin and Zaia, Cássia Thaïs Bussamra Vieira and de Santana, Henrique",
    title = "Which Amino Acids Should Be Used in Prebiotic Chemistry Studies?",
    year = "2008",
    journal = "Origins of Life and Evolution of Biospheres",
    url = "https://doi.org/10.1007/s11084-008-9150-5",
    doi = "10.1007/s11084-008-9150-5",
    openalex = "W1993490997",
    references = "doi101023a1006668322298, doi101038199219a0, doi102138am20062289"
}

The inexorable evolution of solid-phase single chirality is demonstrated for the first time for a proteinogenic amino acid. Enantioenrichment is observed both under attrition-enhanced conditions and without the aid of particle grinding. Differences in the form of the conversion profiles for the process under the two sets of conditions provide suggestions concerning the mechanism of the transformation.

@article{doi101021ja8074506,
    author = "Viedma, Cristóbal and Ortíz, José E. and de Torres, Trinidad and Izumi, Toshiko and Blackmond, Donna G.",
    title = "Evolution of Solid Phase Homochirality for a Proteinogenic Amino Acid",
    year = "2008",
    journal = "Journal of the American Chemical Society",
    abstract = "The inexorable evolution of solid-phase single chirality is demonstrated for the first time for a proteinogenic amino acid. Enantioenrichment is observed both under attrition-enhanced conditions and without the aid of particle grinding. Differences in the form of the conversion profiles for the process under the two sets of conditions provide suggestions concerning the mechanism of the transformation.",
    url = "https://doi.org/10.1021/ja8074506",
    doi = "10.1021/ja8074506",
    openalex = "W2025110978",
    references = "doi101007bf01809580, doi1010160006300253900821, doi101021ja7106349, doi101038378767a0, doi101038nature04780, doi101073pnas0308363101, doi101103physrevlett94065504, doi101126science1523720363, doi101126science2504983975, doi101146annurevaa09090171000245, fox1995thermal"
}

@article{doi101038nrmicro1991,
    author = "Martin, William and Baross, John A. and Kelley, Deborah S. and Russell, Michael J.",
    title = "Hydrothermal vents and the origin of life",
    year = "2008",
    journal = "Nature Reviews Microbiology",
    url = "https://doi.org/10.1038/nrmicro1991",
    doi = "10.1038/nrmicro1991",
    openalex = "W1993130196",
    references = "doi101007bf01808177, doi101038191144a0, doi101038319618a0, doi10103835036572, doi10103835084000, doi101038nature04617, doi101038nrmicro1931, doi10108010409230490460765, doi101098rstb20061881, doi101098rstb20061904, doi101111j157469762001tb00576x, doi101126science1102556, doi101126science1173046528, doi101126science20343851073, doi101144gsjgs15430377, miller1953a, openalexw3041019241"
}

Of the 20 amino acids used in proteins, 10 were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these 10 early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

@article{doi101089ast20080280,
    author = "Higgs, Paul G. and Pudritz, Ralph E.",
    title = "A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code",
    year = "2009",
    journal = "Astrobiology",
    abstract = "Of the 20 amino acids used in proteins, 10 were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these 10 early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.",
    url = "https://doi.org/10.1089/ast.2008.0280",
    doi = "10.1089/ast.2008.0280",
    openalex = "W2071801216",
    references = "doi101007bf01734482, doi1010160016703794902887, doi101038199219a0"
}

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.

@article{doi101002bies200900131,
    author = "Lane, Nick and Allen, John F. and Martin, William",
    title = "How did LUCA make a living? Chemiosmosis in the origin of life",
    year = "2010",
    journal = "BioEssays",
    abstract = "Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.",
    url = "https://doi.org/10.1002/bies.200900131",
    doi = "10.1002/bies.200900131",
    openalex = "W2158033739",
    references = "doi101007bf01140180, doi101016jbbapap200808012, doi101038191144a0, doi10103835084000, doi101038nature04546, doi101038nature08013, doi101038nrmicro1931, doi101074jbcr000005200, doi101098rstb20021183, doi101098rstb20061904, doi101126science1173046528, doi101128mr5244524841988"
}

For life to have emerged from CO₂, rocks, and water on the early Earth, a sustained source of chemically transducible energy was essential. The serpentinization process is emerging as an increasingly likely source of that energy. Serpentinization of ultramafic crust would have continuously supplied hydrogen, methane, minor formate, and ammonia, as well as calcium and traces of acetate, molybdenum and tungsten, to off-ridge alkaline hydrothermal springs that interfaced with the metal-rich carbonic Hadean Ocean. Silica and bisulfide were also delivered to these springs where cherts and sulfides were intersected by the alkaline solutions. The proton and redox gradients so generated represent a rich source of naturally produced chemiosmotic energy, stemming from geochemistry that merely had to be tapped, rather than induced, by the earliest biochemical systems. Hydrothermal mounds accumulating at similar sites in today's oceans offer conceptual and experimental models for the chemistry germane to the emergence of life, although the ubiquity of microbial communities at such sites in addition to our oxygenated atmosphere preclude an exact analogy.

@article{doi101111j14724669201000249x,
    author = "Russell, Michael J. and Hall, A. J. and Martin, William",
    title = "Serpentinization as a source of energy at the origin of life",
    year = "2010",
    journal = "Geobiology",
    abstract = "For life to have emerged from CO₂, rocks, and water on the early Earth, a sustained source of chemically transducible energy was essential. The serpentinization process is emerging as an increasingly likely source of that energy. Serpentinization of ultramafic crust would have continuously supplied hydrogen, methane, minor formate, and ammonia, as well as calcium and traces of acetate, molybdenum and tungsten, to off-ridge alkaline hydrothermal springs that interfaced with the metal-rich carbonic Hadean Ocean. Silica and bisulfide were also delivered to these springs where cherts and sulfides were intersected by the alkaline solutions. The proton and redox gradients so generated represent a rich source of naturally produced chemiosmotic energy, stemming from geochemistry that merely had to be tapped, rather than induced, by the earliest biochemical systems. Hydrothermal mounds accumulating at similar sites in today's oceans offer conceptual and experimental models for the chemistry germane to the emergence of life, although the ubiquity of microbial communities at such sites in addition to our oxygenated atmosphere preclude an exact analogy.",
    url = "https://doi.org/10.1111/j.1472-4669.2010.00249.x",
    doi = "10.1111/j.1472-4669.2010.00249.x",
    openalex = "W2169672447",
    references = "doi101002bies200900131, doi101007bf01808177, doi101038nrmicro1991, doi101098rstb20061881, doi101098rstb20061904"
}

Recent synthetic approaches to understanding the origin of life have yielded insights into plausible pathways for the emergence of the first cells. Here we review current experiments with implications for the origin of life, emphasizing the ability of unexpected physical processes to facilitate the self-assembly and self-replication of the first biological systems. These laboratory efforts have uncovered novel physical mechanisms for the emergence of homochirality; the concentration and purification of prebiotic building blocks; and the ability of the first cells to assemble, grow, divide, and acquire greater complexity. In the absence of evolved biochemical capabilities, such physical processes likely played an essential role in early biology.

@article{doi101146annurevbiophys050708133753,
    author = "Budin, Itay and Szostak, Jack W.",
    title = "Expanding Roles for Diverse Physical Phenomena During the Origin of Life",
    year = "2010",
    journal = "Annual Review of Biophysics",
    abstract = "Recent synthetic approaches to understanding the origin of life have yielded insights into plausible pathways for the emergence of the first cells. Here we review current experiments with implications for the origin of life, emphasizing the ability of unexpected physical processes to facilitate the self-assembly and self-replication of the first biological systems. These laboratory efforts have uncovered novel physical mechanisms for the emergence of homochirality; the concentration and purification of prebiotic building blocks; and the ability of the first cells to assemble, grow, divide, and acquire greater complexity. In the absence of evolved biochemical capabilities, such physical processes likely played an essential role in early biology.",
    url = "https://doi.org/10.1146/annurev.biophys.050708.133753",
    doi = "10.1146/annurev.biophys.050708.133753",
    openalex = "W2105284342",
    references = "doi101021ja8074506"
}

The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. In the extant biosphere the reductive pentose phosphate (Calvin-Benson) cycle is the predominant mechanism by which many prokaryotes and all plants fix CO(2) into biomass. However, the fact that five alternative autotrophic pathways exist in prokaryotes is often neglected. This bias may lead to serious misjudgments in models of the global carbon cycle, in hypotheses on the evolution of metabolism, and in interpretations of geological records. Here, I review these alternative pathways that differ fundamentally from the Calvin-Benson cycle. Revealingly, these five alternative pathways pivot on acetyl-coenzyme A, the turntable of metabolism, demanding a gluconeogenic pathway starting from acetyl-coenzyme A and CO(2). It appears that the formation of an activated acetic acid from inorganic carbon represents the initial step toward metabolism. Consequently, biosyntheses likely started from activated acetic acid and gluconeogenesis preceded glycolysis.

@article{doi101146annurevmicro090110102801,
    author = "Fuchs, Georg",
    title = "Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?",
    year = "2010",
    journal = "Annual Review of Microbiology",
    abstract = "The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. In the extant biosphere the reductive pentose phosphate (Calvin-Benson) cycle is the predominant mechanism by which many prokaryotes and all plants fix CO(2) into biomass. However, the fact that five alternative autotrophic pathways exist in prokaryotes is often neglected. This bias may lead to serious misjudgments in models of the global carbon cycle, in hypotheses on the evolution of metabolism, and in interpretations of geological records. Here, I review these alternative pathways that differ fundamentally from the Calvin-Benson cycle. Revealingly, these five alternative pathways pivot on acetyl-coenzyme A, the turntable of metabolism, demanding a gluconeogenic pathway starting from acetyl-coenzyme A and CO(2). It appears that the formation of an activated acetic acid from inorganic carbon represents the initial step toward metabolism. Consequently, biosyntheses likely started from activated acetic acid and gluconeogenesis preceded glycolysis.",
    url = "https://doi.org/10.1146/annurev-micro-090110-102801",
    doi = "10.1146/annurev-micro-090110-102801",
    openalex = "W2130107304",
    references = "doi101002bies200900131, doi101002cbdv200790052, doi101007bf00032643, doi101038nrmicro1852, doi101038nrmicro1991, doi10108010409230490460765"
}

@article{doi101016jplrev201112002,
    author = "Saladino, Raffaele and Crestini, Claudia and Pino, Samanta and Costanzo, Giovanna and Mauro, Ernesto Di",
    title = "Formamide and the origin of life",
    year = "2011",
    journal = "Physics of Life Reviews",
    url = "https://doi.org/10.1016/j.plrev.2011.12.002",
    doi = "10.1016/j.plrev.2011.12.002",
    openalex = "W2095429191",
    references = "doi101002bies200900131, doi101007s1108400791132, doi101016jresmic200905004, doi101073pnas591110, openalexw2983085323"
}

Synthetic life: the origin of life on the early Earth, and the ex novo transition of non-living matter to artificial living systems are deep scientific challenges that provide a context for the development of new chemistries with unknown technological consequences. This Essay attempts to re-frame some of the epistemological difficulties associated with these questions into an integrative framework of proto-life science. Chemistry is at the heart of this endeavour.

@article{doi101002anie201204968,
    author = "Mann, Stephen",
    title = "The Origins of Life: Old Problems, New Chemistries",
    year = "2012",
    journal = "Angewandte Chemie International Edition",
    abstract = "Synthetic life: the origin of life on the early Earth, and the ex novo transition of non-living matter to artificial living systems are deep scientific challenges that provide a context for the development of new chemistries with unknown technological consequences. This Essay attempts to re-frame some of the epistemological difficulties associated with these questions into an integrative framework of proto-life science. Chemistry is at the heart of this endeavour.",
    url = "https://doi.org/10.1002/anie.201204968",
    doi = "10.1002/anie.201204968",
    openalex = "W2061543242",
    references = "doi101021ar200281t, doi10103835053176, doi101038nature07018, doi101038nature08013, doi101038nchem1110, doi101073pnas0408236101, doi10108010409230490460765, doi101098rstb20021183, doi101101cshperspecta002170, doi101126science1167856, doi101126science1217622, doi101146annurevbiophys37032807125817, doi1011861759220821, doi1011861759220832"
}

The process of delineating the origins of the chemistry of life starts with the consideration of the molecules that might have existed on prebiotic earth and extends to the discussion of potential mechanisms for assembly of these molecules into informational polymers capable of self-replication and transmittance of genetic information. At some point along this pathway, the property of single chirality emerges as the hallmark of the amino acids and sugars present in biological molecules. In the 20th century, researchers developed abstract mathematical theses for the origin of biomolecular homochirality from a presumably racemic collection of prebiotic molecules. Before the end of that century, experimental findings corroborated a number of basic features of these theoretical models, but these studies involved chemical systems without direct prebiotic relevance. Currently researchers are examining prebiotically plausible conditions that couple chemical and physical processes leading to single chirality of sugars and amino acids with subsequent chemical reactions that enhance molecular complexity. While these studies have been conducted for the most part in the context of the RNA World hypothesis, the experimental findings remain relevant to a "metabolism first" model for the origin of life. To many chemists interested in chembiogenesis, the synthesis of activated pyrimidine ribonucleotides under potentially prebiotic conditions by Sutherland's group provided a landmark demonstration of what Eschenmoser has described as "an intrinsic structural propinquity" between certain elementary chemical structures and modern biological molecules. Even while some synthetic issues for plausible prebiotic construction of RNA remain unsolved, our work has focused on coupling these synthetic advances with concepts for the evolution of biomlolecular homochirality. Drawing on our own findings as well as those from others, we present an intriguing "chicken or egg" scenario for the emergence of single chirality of sugars and amino acids. Our work incorporates both chemical and physical phenomena that allow for the amplification of a small initial imbalance of either sugars by amino acids or amino acid by sugars, suggesting that an enantioenriched chiral pool of one type of molecule could lead to a similarly enantioenriched pool of the other.

@article{doi101021ar200316n,
    author = "Hein, Jason E. and Blackmond, Donna G.",
    title = "On the Origin of Single Chirality of Amino Acids and Sugars in Biogenesis",
    year = "2012",
    journal = "Accounts of Chemical Research",
    abstract = {The process of delineating the origins of the chemistry of life starts with the consideration of the molecules that might have existed on prebiotic earth and extends to the discussion of potential mechanisms for assembly of these molecules into informational polymers capable of self-replication and transmittance of genetic information. At some point along this pathway, the property of single chirality emerges as the hallmark of the amino acids and sugars present in biological molecules. In the 20th century, researchers developed abstract mathematical theses for the origin of biomolecular homochirality from a presumably racemic collection of prebiotic molecules. Before the end of that century, experimental findings corroborated a number of basic features of these theoretical models, but these studies involved chemical systems without direct prebiotic relevance. Currently researchers are examining prebiotically plausible conditions that couple chemical and physical processes leading to single chirality of sugars and amino acids with subsequent chemical reactions that enhance molecular complexity. While these studies have been conducted for the most part in the context of the RNA World hypothesis, the experimental findings remain relevant to a "metabolism first" model for the origin of life. To many chemists interested in chembiogenesis, the synthesis of activated pyrimidine ribonucleotides under potentially prebiotic conditions by Sutherland's group provided a landmark demonstration of what Eschenmoser has described as "an intrinsic structural propinquity" between certain elementary chemical structures and modern biological molecules. Even while some synthetic issues for plausible prebiotic construction of RNA remain unsolved, our work has focused on coupling these synthetic advances with concepts for the evolution of biomlolecular homochirality. Drawing on our own findings as well as those from others, we present an intriguing "chicken or egg" scenario for the emergence of single chirality of sugars and amino acids. Our work incorporates both chemical and physical phenomena that allow for the amplification of a small initial imbalance of either sugars by amino acids or amino acid by sugars, suggesting that an enantioenriched chiral pool of one type of molecule could lead to a similarly enantioenriched pool of the other.},
    url = "https://doi.org/10.1021/ar200316n",
    doi = "10.1021/ar200316n",
    openalex = "W2334005130",
    references = "doi101021ja8074506"
}

The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic - as well as, arguably, evolutionary - perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of "which came first?" boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a 'top down' (or should it be 'present back'?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA - which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome - could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as 'proteins first', which holds that proteins either preceded RNA in evolution, or - at the very least - that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.

@article{doi10118617456150723,
    author = "Bernhardt, Harold S.",
    title = "The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a",
    year = "2012",
    journal = "Biology Direct",
    abstract = {The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic - as well as, arguably, evolutionary - perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of "which came first?" boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a 'top down' (or should it be 'present back'?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA - which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome - could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as 'proteins first', which holds that proteins either preceded RNA in evolution, or - at the very least - that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.},
    url = "https://doi.org/10.1186/1745-6150-7-23",
    doi = "10.1186/1745-6150-7-23",
    openalex = "W2117819109",
    references = "doi1011861745615071, doi1011861759220832"
}

@article{doi101021cr2004844,
    author = "Ruiz‐Mirazo, Kepa and Briones, Carlos and de la Escosura, Andrés",
    title = "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life",
    year = "2013",
    journal = "Chemical Reviews",
    url = "https://doi.org/10.1021/cr2004844",
    doi = "10.1021/cr2004844",
    openalex = "W2033873715",
    references = "doi1010023527607439, doi101002anie201204968, doi101006bbrc19990404, doi10100797836427811004, doi101007s1108400791132, doi1010160003269781902815, doi1010160006291x60901388, doi1010160022283668903926, doi1010160022283668903938, doi1010161074552195900314, doi101016s0022283675800830, doi101016s0022519386800479, doi101016s1389172301803224, doi101021cr020452p, doi101021ja8074506, doi101023a1006746807104, doi101038171737a0, doi101038225535b0, doi101038280445a0, doi101038343033a0, doi101038346818a0, doi101038355125a0, doi101038365566a0, doi101038381059a0, doi101038nature03959, doi101038nature04764, doi101038nature08013, doi101039c2cs35109a, doi101073pnas0912157107, doi101073pnas1106493108, doi101073pnas384351, doi101073pnas581217, doi101073pnas742560, doi101073pnas9784112, doi10108010409230490460765, doi101098rstb19520012, doi101126science1092464, doi101126science1161527, doi101126science2200121, doi101126science2705235467, doi101128mr5244524841988, doi1011861759220832, fox1958thermal"
}

@article{doi101038nrg3841,
    author = "Higgs, Paul G. and Lehman, Niles",
    title = "The RNA World: molecular cooperation at the origins of life",
    year = "2014",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3841",
    doi = "10.1038/nrg3841",
    openalex = "W1970977492",
    references = "doi101007bf00420631, doi101016jchembiol201303012, doi101016jplrev201206001, doi101038nature08013, doi101126science1092464, doi101126science1241888, doi101128mmbr6122392611997"
}

@article{doi101016jcub201506016,
    author = "Pressman, Abe and Blanco, Celia and Chen, Irene A.",
    title = "The RNA World as a Model System to Study the Origin of Life",
    year = "2015",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2015.06.016",
    doi = "10.1016/j.cub.2015.06.016",
    openalex = "W1879750355",
    references = "doi101007s1108400791132, doi101016jchembiol201303012, doi1011861759220832"
}

Over the last 70 years, prebiotic chemists have been very successful in synthesizing the molecules of life, from amino acids to nucleotides. Yet there is strikingly little resemblance between much of this chemistry and the metabolic pathways of cells, in terms of substrates, catalysts, and synthetic pathways. In contrast, alkaline hydrothermal vents offer conditions similar to those harnessed by modern autotrophs, but there has been limited experimental evidence that such conditions could drive prebiotic chemistry. In the Hadean, in the absence of oxygen, alkaline vents are proposed to have acted as electrochemical flow reactors, in which alkaline fluids saturated in H2 mixed with relatively acidic ocean waters rich in CO2, through a labyrinth of interconnected micropores with thin inorganic walls containing catalytic Fe(Ni)S minerals. The difference in pH across these thin barriers produced natural proton gradients with equivalent magnitude and polarity to the proton-motive force required for carbon fixation in extant bacteria and archaea. How such gradients could have powered carbon reduction or energy flux before the advent of organic protocells with genes and proteins is unknown. Work over the last decade suggests several possible hypotheses that are currently being tested in laboratory experiments, field observations, and phylogenetic reconstructions of ancestral metabolism. We analyze the perplexing differences in carbon and energy metabolism in methanogenic archaea and acetogenic bacteria to propose a possible ancestral mechanism of CO2 reduction in alkaline hydrothermal vents. Based on this mechanism, we show that the evolution of active ion pumping could have driven the deep divergence of bacteria and archaea.

@article{doi101089ast20151406,
    author = "Sojo, Víctor and Herschy, Barry and Whicher, Alexandra and Camprubí, Eloi and Lane, Nick",
    title = "The Origin of Life in Alkaline Hydrothermal Vents",
    year = "2016",
    journal = "Astrobiology",
    abstract = "Over the last 70 years, prebiotic chemists have been very successful in synthesizing the molecules of life, from amino acids to nucleotides. Yet there is strikingly little resemblance between much of this chemistry and the metabolic pathways of cells, in terms of substrates, catalysts, and synthetic pathways. In contrast, alkaline hydrothermal vents offer conditions similar to those harnessed by modern autotrophs, but there has been limited experimental evidence that such conditions could drive prebiotic chemistry. In the Hadean, in the absence of oxygen, alkaline vents are proposed to have acted as electrochemical flow reactors, in which alkaline fluids saturated in H2 mixed with relatively acidic ocean waters rich in CO2, through a labyrinth of interconnected micropores with thin inorganic walls containing catalytic Fe(Ni)S minerals. The difference in pH across these thin barriers produced natural proton gradients with equivalent magnitude and polarity to the proton-motive force required for carbon fixation in extant bacteria and archaea. How such gradients could have powered carbon reduction or energy flux before the advent of organic protocells with genes and proteins is unknown. Work over the last decade suggests several possible hypotheses that are currently being tested in laboratory experiments, field observations, and phylogenetic reconstructions of ancestral metabolism. We analyze the perplexing differences in carbon and energy metabolism in methanogenic archaea and acetogenic bacteria to propose a possible ancestral mechanism of CO2 reduction in alkaline hydrothermal vents. Based on this mechanism, we show that the evolution of active ion pumping could have driven the deep divergence of bacteria and archaea.",
    url = "https://doi.org/10.1089/ast.2015.1406",
    doi = "10.1089/ast.2015.1406",
    openalex = "W2267335000",
    references = "doi101002bies200900131, doi101007bf01140180"
}

Abstract How and where did life on Earth originate? To date, various environments have been proposed as plausible sites for the origin of life. However, discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. It remains unclear what geochemical situations could drive all the stages of chemical evolution, ranging from condensation of simple inorganic compounds to the emergence of self-sustaining systems that were evolvable into modern biological ones. In this review, we summarize reported experimental and theoretical findings for prebiotic chemistry relevant to this topic, including availability of biologically essential elements (N and P) on the Hadean Earth, abiotic synthesis of life's building blocks (amino acids, peptides, ribose, nucleobases, fatty acids, nucleotides, and oligonucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization. It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life's building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life's origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation. Future experimental research that mimics the conditions of the proposed model are expected to provide further constraints on the processes and mechanisms for the origin of life.

@article{doi101016jgsf201707007,
    author = "Kitadai, N. and Maruyama, S.",
    title = "Origins of building blocks of life: A review",
    year = "2017",
    journal = "Geoscience Frontiers",
    abstract = "Abstract How and where did life on Earth originate? To date, various environments have been proposed as plausible sites for the origin of life. However, discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. It remains unclear what geochemical situations could drive all the stages of chemical evolution, ranging from condensation of simple inorganic compounds to the emergence of self-sustaining systems that were evolvable into modern biological ones. In this review, we summarize reported experimental and theoretical findings for prebiotic chemistry relevant to this topic, including availability of biologically essential elements (N and P) on the Hadean Earth, abiotic synthesis of life's building blocks (amino acids, peptides, ribose, nucleobases, fatty acids, nucleotides, and oligonucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization. It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life's building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life's origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation. Future experimental research that mimics the conditions of the proposed model are expected to provide further constraints on the processes and mechanisms for the origin of life.",
    url = "https://doi.org/10.1016/j.gsf.2017.07.007",
    doi = "10.1016/J.GSF.2017.07.007",
    is_oa = "true",
    number = "4",
    pages = "1117-1153",
    semanticscholar_citation_count = "349",
    semanticscholar_id = "b0926c65e24d5418043226bdf1055eaf2178a79e",
    volume = "9"
}

This Perspective focuses on RNA in biological and nonbiological compartments resulting from liquid-liquid phase separation (LLPS), with an emphasis on origins of life. In extant cells, intracellular liquid condensates, many of which are rich in RNAs and intrinsically disordered proteins, provide spatial regulation of biomolecular interactions that can result in altered gene expression. Given the diversity of biogenic and abiogenic molecules that undergo LLPS, such membraneless compartments may have also played key roles in prebiotic chemistries relevant to the origins of life. The RNA World hypothesis posits that RNA may have served as both a genetic information carrier and a catalyst during the origin of life. Because of its polyanionic backbone, RNA can undergo LLPS by complex coacervation in the presence of polycations. Phase separation could provide a mechanism for concentrating monomers for RNA synthesis and selectively partition longer RNAs with enzymatic functions, thus driving prebiotic evolution. We introduce several types of LLPS that could lead to compartmentalization and discuss potential roles in template-mediated non-enzymatic polymerization of RNA and other related biomolecules, functions of ribozymes and aptamers, and benefits or penalties imparted by liquid demixing. We conclude that tiny liquid droplets may have concentrated precious biomolecules and acted as bioreactors in the RNA World.

@article{doi101021acsbiochem8b00081,
    author = "Poudyal, Raghav R. and Cakmak, Fatma Pir and Keating, Christine D. and Bevilacqua, Philip C.",
    title = "Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry",
    year = "2018",
    journal = "Biochemistry",
    abstract = "This Perspective focuses on RNA in biological and nonbiological compartments resulting from liquid-liquid phase separation (LLPS), with an emphasis on origins of life. In extant cells, intracellular liquid condensates, many of which are rich in RNAs and intrinsically disordered proteins, provide spatial regulation of biomolecular interactions that can result in altered gene expression. Given the diversity of biogenic and abiogenic molecules that undergo LLPS, such membraneless compartments may have also played key roles in prebiotic chemistries relevant to the origins of life. The RNA World hypothesis posits that RNA may have served as both a genetic information carrier and a catalyst during the origin of life. Because of its polyanionic backbone, RNA can undergo LLPS by complex coacervation in the presence of polycations. Phase separation could provide a mechanism for concentrating monomers for RNA synthesis and selectively partition longer RNAs with enzymatic functions, thus driving prebiotic evolution. We introduce several types of LLPS that could lead to compartmentalization and discuss potential roles in template-mediated non-enzymatic polymerization of RNA and other related biomolecules, functions of ribozymes and aptamers, and benefits or penalties imparted by liquid demixing. We conclude that tiny liquid droplets may have concentrated precious biomolecules and acted as bioreactors in the RNA World.",
    url = "https://doi.org/10.1021/acs.biochem.8b00081",
    doi = "10.1021/acs.biochem.8b00081",
    openalex = "W2791574316",
    references = "doi1011861759220832"
}

Significance Phosphate is crucial for the origin of life because it is ubiquitous in key biomolecules. A major issue is that prebiotic syntheses use concentrated phosphate to incorporate phosphate into biomolecules, whereas natural waters are generally phosphate-poor because phosphate reacts with calcium to form low-solubility apatite minerals. Here we show that carbonate-rich lakes can concentrate phosphate to >1 molal levels by locking up calcium in carbonate minerals, which prevents phosphate removal by apatite precipitation. Phosphate-rich lakes may have preferentially formed on the prebiotic Earth because of carbonic acid weathering under CO 2 -rich atmospheres and the absence of microbial phosphate consumption. This specifically points to an origin of life in carbonate-rich lakes, and so defines aqueous conditions that prebiotic chemists should consider.

@article{doi101073pnas1916109117,
    author = "Toner, J. D. and Catling, David C.",
    title = "A carbonate-rich lake solution to the phosphate problem of the origin of life",
    year = "2019",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Significance Phosphate is crucial for the origin of life because it is ubiquitous in key biomolecules. A major issue is that prebiotic syntheses use concentrated phosphate to incorporate phosphate into biomolecules, whereas natural waters are generally phosphate-poor because phosphate reacts with calcium to form low-solubility apatite minerals. Here we show that carbonate-rich lakes can concentrate phosphate to >1 molal levels by locking up calcium in carbonate minerals, which prevents phosphate removal by apatite precipitation. Phosphate-rich lakes may have preferentially formed on the prebiotic Earth because of carbonic acid weathering under CO 2 -rich atmospheres and the absence of microbial phosphate consumption. This specifically points to an origin of life in carbonate-rich lakes, and so defines aqueous conditions that prebiotic chemists should consider.",
    url = "https://doi.org/10.1073/pnas.1916109117",
    doi = "10.1073/pnas.1916109117",
    openalex = "W2996847227",
    references = "doi101002iroh19650500307, doi101038nature08013, doi101038nchem2202, doi101038nchem2878, doi101073pnas1117774109, doi101073pnas1721296115, doi101126science1092464, doi101126science2434996, doi1012019781439833544, doi102138rmg2002486, doi103133pp135, openalexw1509310308"
}

Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.

@article{doi101089ast20181979,
    author = "Deamer, David W. and Damer, Bruce and Kompanichenko, Vladimir",
    title = "Hydrothermal Chemistry and the Origin of Cellular Life",
    year = "2019",
    journal = "Astrobiology",
    abstract = "Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.",
    url = "https://doi.org/10.1089/ast.2018.1979",
    doi = "10.1089/ast.2018.1979",
    openalex = "W2979458459",
    references = "doi101126science12933571221a"
}

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.

@article{doi101089ast20192045,
    author = "Damer, Bruce and Deamer, David W.",
    title = "The Hot Spring Hypothesis for an Origin of Life",
    year = "2019",
    journal = "Astrobiology",
    abstract = {We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.},
    url = "https://doi.org/10.1089/ast.2019.2045",
    doi = "10.1089/ast.2019.2045",
    openalex = "W2996553307",
    references = "doi101007s1108400791132, doi101016jbioeng200703001, doi101023a1006746807104, doi101038nature08013, doi101038s415700160012, doi101073pnas1106493108, doi101073pnas1117774109, doi101098rstb20061881, doi101101cshperspecta034801, doi101126science1241888, doi101126scienceaax2747, fox1958thermal"
}

Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.

@article{doi103389fmicb201900780,
    author = "Merino, Nancy and Aronson, Heidi S. and Bojanova, Diana P. and Feyhl‐Buska, Jayme and Wong, Michael L. and Zhang, Shu and Giovannelli, Donato",
    title = "Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context",
    year = "2019",
    journal = "Frontiers in Microbiology",
    abstract = "Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.",
    url = "https://doi.org/10.3389/fmicb.2019.00780",
    doi = "10.3389/fmicb.2019.00780",
    openalex = "W2936282025",
    references = "colman2018geobiological, doi101002bies200900131, doi10100797894007648801, doi101007s0025300314487, doi1010160009254194001404, doi1010160016703771900196, doi1010160016703795000382, doi101016s016864960300028x, doi1010292006je002784, doi10103835059215, doi101038ismej201058, doi101038nmicrobiol201648, doi101073pnas0400522101, doi101073pnas0611525104, doi101126science1172466, doi101128aem0033509"
}

Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.

@article{doi101021acschemrev0c00191,
    author = "Muchowska, Kamila B. and Varma, Sreejith J. and Moran, Joseph",
    title = "Nonenzymatic Metabolic Reactions and Life’s Origins",
    year = "2020",
    journal = "Chemical Reviews",
    abstract = {Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.},
    url = "https://doi.org/10.1021/acs.chemrev.0c00191",
    doi = "10.1021/acs.chemrev.0c00191",
    openalex = "W3044573208",
    references = "branscomb2018frankenstein, doi101002bies201700179, doi101002bies201700182, doi101007pl00006565, doi1010160020711x94901198, doi1010160022283668903926, doi101016jgsf201707007, doi101016s0040403901994870, doi101038319618a0, doi101038nature08013, doi101038nature13068, doi101038s415590180644x, doi101038s415700160012, doi101073pnas591110, doi10108010409230490460765, doi101098rsob130156, doi101098rstb20061904, doi101101cshperspecta034801, doi101111brv12140, doi101126science1173046528, doi101126science1186120, doi101126scienceaax2747, doi101146annurevmi30100176002205, doi1011861745615071"
}

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

@article{doi101021acschemrev9b00664,
    author = "Frenkel‐Pinter, Moran and Samanta, Mousumi and Ashkenasy, Gonen and Leman, Luke J.",
    title = "Prebiotic Peptides: Molecular Hubs in the Origin of Life",
    year = "2020",
    journal = "Chemical Reviews",
    abstract = "The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.",
    url = "https://doi.org/10.1021/acs.chemrev.9b00664",
    doi = "10.1021/acs.chemrev.9b00664",
    openalex = "W3008483803",
    references = "doi101002anie201208397, doi101007pl00006565, doi101021cr2004844, doi101021ja01499a069, doi101038nchem2878, doi101038s415700160012, doi101073pnas9784112, doi101098rsob130156, doi101101cshperspecta034801, doi101126science1161527, doi1011861759220832, fox1958thermal"
}

@article{doi101016jearscirev2021103910,
    author = "Trolard, Fabienne and Duval, Simon and Nitschke, Wolfgang and Ménèz, Bénédicte and Pisapia, Céline and Nacib, Jihaine Ben and Andréani, M. and Bourrié, Guilhem",
    title = "Mineralogy, geochemistry and occurrences of fougerite in a modern hydrothermal system and its implications for the origin of life",
    year = "2021",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/j.earscirev.2021.103910",
    doi = "10.1016/j.earscirev.2021.103910",
    openalex = "W4200442220",
    references = "doi10100797836620364952, doi101016b9780126564464x50002, doi101016s0010854598002161, doi101016s0016703798002439, doi10103835084000, doi101126science1102556, doi101126science1151194, doi101180claymin19590042102, doi1015159781501508233, doi103390life11080777, openalexw599354073"
}

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid-liquid phase separation in water. The droplets underwent a steady growth-division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.

@article{doi101038s41467021255306,
    author = "Matsuo, Muneyuki and Kurihara, Kensuke",
    title = "Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life",
    year = "2021",
    journal = "Nature Communications",
    abstract = "The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid-liquid phase separation in water. The droplets underwent a steady growth-division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.",
    url = "https://doi.org/10.1038/s41467-021-25530-6",
    doi = "10.1038/s41467-021-25530-6",
    openalex = "W3201258865",
    references = "doi101126science12933571221a"
}

times higher than currently estimated. This suggests that seawater readily met the phosphorus requirements of emergent cellular systems and early microbial life, perhaps fueling primary production during the advent of oxygenic photosynthesis.

@article{doi101038s4146702232815x,
    author = "Brady, Matthew P. and Tostevin, Rosalie and Tosca, Nicholas J.",
    title = "Marine phosphate availability and the chemical origins of life on Earth",
    year = "2022",
    journal = "Nature Communications",
    abstract = "times higher than currently estimated. This suggests that seawater readily met the phosphorus requirements of emergent cellular systems and early microbial life, perhaps fueling primary production during the advent of oxygenic photosynthesis.",
    url = "https://doi.org/10.1038/s41467-022-32815-x",
    doi = "10.1038/s41467-022-32815-x",
    openalex = "W4294237906",
    references = "doi101073pnas1916109117"
}

@article{doi101038s4155702200999w,
    author = "Pulletikurti, Sunil and Yadav, Mahipal and Springsteen, Greg and Krishnamurthy, Ramanarayanan",
    title = "Prebiotic synthesis of α-amino acids and orotate from α-ketoacids potentiates transition to extant metabolic pathways",
    year = "2022",
    journal = "Nature Chemistry",
    url = "https://doi.org/10.1038/s41557-022-00999-w",
    doi = "10.1038/s41557-022-00999-w",
    openalex = "W4288447280",
    references = "doi101073pnas1916109117"
}

A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.

@article{doi101038s41598022212727,
    author = "Ter-Ovanessian, Louis M P and Lambert, Jean-François and Maurel, Marie-Christine",
    title = "Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid.",
    year = "2022",
    journal = "Scientific reports",
    abstract = {A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC9649776/",
    doi = "10.1038/s41598-022-21272-7",
    openalex = "W4309244441",
    pmcid = "PMC9649776",
    pmid = "36357418",
    references = "doi101007pl00006565, doi101021acschemrev0c00191, doi101021cm8001173, doi101021cr3003054, doi101021es3012854, doi101038nchem2878, doi101039b602051h, doi101073pnas1916109117, doi101093nargkr874, doi101371journalpcbi1003098"
}

Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.

@article{doi101098rsif20210641,
    author = "Fried, Stephen D. and Fujishima, Kosuke and Makarov, Mikhail and Cherepashuk, Ivan and Hlouchová, Klára",
    title = "Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids",
    year = "2022",
    journal = "Journal of The Royal Society Interface",
    abstract = "Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.",
    url = "https://doi.org/10.1098/rsif.2021.0641",
    doi = "10.1098/rsif.2021.0641",
    openalex = "W4210888723",
    references = "doi101016jsbi201711007, doi101021acschemrev0c00191"
}

Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.

@article{doi103390life12101508,
    author = "Root‐Bernstein, Robert and Brown, Adam W.",
    title = "Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems",
    year = "2022",
    journal = "Life",
    abstract = "Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.",
    url = "https://doi.org/10.3390/life12101508",
    doi = "10.3390/life12101508",
    openalex = "W4297477492",
    references = "doi103390life11080777"
}

Abstract. This is a comment on Michaelian and Simeonov (2015). Michaelian and Simeonov formulate the leading thought in their article: “The driving force behind the origin and evolution of life has been the thermodynamic imperative of increasing the entropy production of the biosphere through increasing the global solar photon dissipation rate”. I shall in the following try to provide some information that might help to clarify whether this is correct.

@article{doi105194bg1910132022,
    author = "Björn, Lars Olof",
    title = "Comment on “Fundamental molecules of life are pigments which arose and co-evolved as a response to the thermodynamic imperative of dissipating the prevailing solar spectrum” by K. Michaelian and A. Simeonov (2015)",
    year = "2022",
    journal = "Biogeosciences",
    abstract = "Abstract. This is a comment on Michaelian and Simeonov (2015). Michaelian and Simeonov formulate the leading thought in their article: “The driving force behind the origin and evolution of life has been the thermodynamic imperative of increasing the entropy production of the biosphere through increasing the global solar photon dissipation rate”. I shall in the following try to provide some information that might help to clarify whether this is correct.",
    url = "https://doi.org/10.5194/bg-19-1013-2022",
    doi = "10.5194/bg-19-1013-2022",
    openalex = "W4212908473",
    references = "doi103390life11080777"
}

Phosphorus (P) is critical to modern biochemical functions and can control ecosystem growth. It was presumably important as a reagent in prebiotic chemistry. However, on the early Earth, P sources may have consisted primarily of poorly soluble calcium phosphates, which may have rendered phosphate as a minimally available nutrient or reagent if these minerals were the sole source. Here, we review aqueous P availability on the early Earth (>2.5 Gyr ago), considering both mineral sources and geochemical sinks relevant to its solvation, and activation by abiotic and biological pathways. Phosphorus on Earth’s early surface would have been present as a mixture of phosphate minerals, as a minor element in silicate minerals, and in reactive, reduced phases from accreted dust, meteorites and asteroids. These P sources would have weathered and plausibly furnished the prebiotic Earth with abundant and potentially reactive P. After the origin of a biosphere, life evolved to draw on not just reactive available P sources, but also insoluble and unreactive sources. The rise of an ecosystem dependent on this element at some point forged a P-limited biosphere, with evolutionary stress forcing the efficient extraction and recycling of P from both abiotic and biotic sources and sinks. A review of aqueous phosphorus availability on the Earth’s early surface suggests a range of phosphorus sources supplied the prebiotic Earth, but that phosphorus availability declined as life evolved and altered geochemical cycling.

@article{doi101038s41561023011676,
    author = "Walton, Craig R. and Ewens, Sophia D. and Coates, John D. and Blake, Ruth E. and Planavsky, Noah J. and Reinhard, Christopher T. and Ju, Pengcheng and Hao, Jihua and Pasek, Matthew A.",
    title = "Phosphorus availability on the early Earth and the impacts of life",
    year = "2023",
    journal = "Nature Geoscience",
    abstract = "Phosphorus (P) is critical to modern biochemical functions and can control ecosystem growth. It was presumably important as a reagent in prebiotic chemistry. However, on the early Earth, P sources may have consisted primarily of poorly soluble calcium phosphates, which may have rendered phosphate as a minimally available nutrient or reagent if these minerals were the sole source. Here, we review aqueous P availability on the early Earth (>2.5 Gyr ago), considering both mineral sources and geochemical sinks relevant to its solvation, and activation by abiotic and biological pathways. Phosphorus on Earth’s early surface would have been present as a mixture of phosphate minerals, as a minor element in silicate minerals, and in reactive, reduced phases from accreted dust, meteorites and asteroids. These P sources would have weathered and plausibly furnished the prebiotic Earth with abundant and potentially reactive P. After the origin of a biosphere, life evolved to draw on not just reactive available P sources, but also insoluble and unreactive sources. The rise of an ecosystem dependent on this element at some point forged a P-limited biosphere, with evolutionary stress forcing the efficient extraction and recycling of P from both abiotic and biotic sources and sinks. A review of aqueous phosphorus availability on the Earth’s early surface suggests a range of phosphorus sources supplied the prebiotic Earth, but that phosphorus availability declined as life evolved and altered geochemical cycling.",
    url = "https://doi.org/10.1038/s41561-023-01167-6",
    doi = "10.1038/s41561-023-01167-6",
    openalex = "W4366086019",
    references = "doi101038s4158601914364, doi101073pnas1916109117"
}

@article{doi101038s42254022005503,
    author = "Ianeselli, Alan and Salditt, Annalena and Mast, Christof B. and Ercolano, Barbara and Kufner, Corinna L. and Scheu, Bettina and Braun, Dieter",
    title = "Physical non-equilibria for prebiotic nucleic acid chemistry",
    year = "2023",
    journal = "Nature Reviews Physics",
    url = "https://doi.org/10.1038/s42254-022-00550-3",
    doi = "10.1038/s42254-022-00550-3",
    openalex = "W4317234139",
    references = "doi103390life11080777"
}

Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H 2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO 2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H 2 reduces CO 2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO 2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H 2 -dependent CO 2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.

@article{doi103389fmicb20231257597,
    author = "Schwander, Loraine and Brabender, Max and Mrnjavac, Natalia and Wimmer, Jessica L. E. and Preiner, Martina and Martin, William",
    title = "Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life",
    year = "2023",
    journal = "Frontiers in Microbiology",
    abstract = "Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H 2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO 2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H 2 reduces CO 2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO 2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H 2 -dependent CO 2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.",
    url = "https://doi.org/10.3389/fmicb.2023.1257597",
    doi = "10.3389/fmicb.2023.1257597",
    openalex = "W4387305102",
    references = "doi101073pnas1916109117, doi101098rsta20180421, openalexw287848292"
}

@incollection{doi101016b9780443157509001105,
    author = "Prosdocimi, Francisco and de Farías, Sávio Torres",
    title = "From Myths to Molecules: A History for the Origins of Life in Earth",
    year = "2025",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-0-443-15750-9.00110-5",
    doi = "10.1016/b978-0-443-15750-9.00110-5",
    openalex = "W4410579837",
    references = "doi101016jpbiomolbio202407002"
}

Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, metabolism, and genetics, and they are mortal. The molecular structures and chemical reactions underlying these features are common to all, from the simplest bacteria to human beings. The origin of life is evolutionary with the emergence of a network of spontaneous biochemical reactions, and the evolution has taken place over a very long time. The evolution contains, however, some "landmarks" and bottlenecks, which in a revolutionary manner directed the evolution, and the article establishes an order of some of these events. Recent articles show that peptides in living organisms are long-time unstable with loss of their secondary homochiral conformations and with D-amino acids. Based on these observations and an extensive scientific literature on Abiogenesis, we argue that the first milestone in the prebiotic evolution is at the emergence of homochiral peptides in an aqueous solution with a high concentration of amino acids and a lower water activity than in the cytosol in living organisms. The homochiral peptides in cytosol are unstable, and the long-time aging of peptides in the cytosol causes mortality of living organisms. The metabolism and genetics are established in an environment with homochiral peptides in the Earth's crust for ≈ 4 Gyr ago at a lower water activity than in the cytosol in living organisms. Finally, the cells with cell division are established in the Hot Springs environment at the interface between the crust and the Hadean Ocean.

@article{doi101016jbiosystems2025105479,
    author = "Toxværd, Søren",
    title = "Origin of homochirality in peptides: The first milestone at the origin of life",
    year = "2025",
    journal = "Biosystems",
    abstract = {Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, metabolism, and genetics, and they are mortal. The molecular structures and chemical reactions underlying these features are common to all, from the simplest bacteria to human beings. The origin of life is evolutionary with the emergence of a network of spontaneous biochemical reactions, and the evolution has taken place over a very long time. The evolution contains, however, some "landmarks" and bottlenecks, which in a revolutionary manner directed the evolution, and the article establishes an order of some of these events. Recent articles show that peptides in living organisms are long-time unstable with loss of their secondary homochiral conformations and with D-amino acids. Based on these observations and an extensive scientific literature on Abiogenesis, we argue that the first milestone in the prebiotic evolution is at the emergence of homochiral peptides in an aqueous solution with a high concentration of amino acids and a lower water activity than in the cytosol in living organisms. The homochiral peptides in cytosol are unstable, and the long-time aging of peptides in the cytosol causes mortality of living organisms. The metabolism and genetics are established in an environment with homochiral peptides in the Earth's crust for ≈ 4 Gyr ago at a lower water activity than in the cytosol in living organisms. Finally, the cells with cell division are established in the Hot Springs environment at the interface between the crust and the Hadean Ocean.},
    url = "https://doi.org/10.1016/j.biosystems.2025.105479",
    doi = "10.1016/j.biosystems.2025.105479",
    openalex = "W4410496365",
    references = "doi101016jpbiomolbio202407002"
}

, the primary chemical driving force of aging. With all that, the energy benefits of aerobic metabolism have provided for the advent of multicellular organisms, in particular, those featuring massive extracellular matter and unrenewable cell populations, including those comprising the brain. Their functions are incompatible with complete renewal. This makes the role of oxygen in aging not limited to being the source of reactive oxygen species. Oxygen had been indispensable for the advent of both accumulators of chemical damage and ability to recognize it. In a sense, it was not a problem for nature to develop aging in the course of evolution towards humans, for whom being aware of aging is a problem. Its satisfactory solution cannot be chemical, physical, pharmacological, or otherwise technical. It can only be mental.

@article{doi101134s0006297925601674,
    author = "Golubev, Aleksei G.",
    title = "Chemistry of the Joint Origin and Evolution of Life, Death, and Aging",
    year = "2025",
    journal = "Biochemistry (Moscow)",
    abstract = ", the primary chemical driving force of aging. With all that, the energy benefits of aerobic metabolism have provided for the advent of multicellular organisms, in particular, those featuring massive extracellular matter and unrenewable cell populations, including those comprising the brain. Their functions are incompatible with complete renewal. This makes the role of oxygen in aging not limited to being the source of reactive oxygen species. Oxygen had been indispensable for the advent of both accumulators of chemical damage and ability to recognize it. In a sense, it was not a problem for nature to develop aging in the course of evolution towards humans, for whom being aware of aging is a problem. Its satisfactory solution cannot be chemical, physical, pharmacological, or otherwise technical. It can only be mental.",
    url = "https://doi.org/10.1134/s0006297925601674",
    doi = "10.1134/s0006297925601674",
    openalex = "W4414691491",
    references = "doi1010021873346814906, doi101016jpbiomolbio202407002"
}

The origin of life remains one of the most profound and enduring enigmas in the biological sciences. Despite substantial advances in prebiotic chemistry, fundamental uncertainties persist regarding the precise mechanisms that enabled the emergence of the first cellular entity and, subsequently, the foundational branches of the tree of life. After examining the core principles that define living systems, we propose that life emerged as a novel property of a prebiotically assembled system-formed through the integration of distinct molecular worlds, defined as sets of structurally and functionally related molecular entities that interact via catalytic, autocatalytic, and/or self-assembly processes. This emergence established a permanent system-process duality, wherein the system's organization and its dynamic processes became inseparable. Upon acquiring the capacity to replicate and mutate its genetic program, this primordial organism initiated the evolutionary process, ultimately driving the diversification of life under the influence of evolutionary forces and leading to the formation of ecosystems. The challenge of uncovering the origin of life and the emergence of biodiversity is not solely scientific, it requires the integration of empirical evidence, theoretical insight, and critical reflection. This work does not claim certainty but proposes a perspective on how life and biodiversity may have arisen on Earth. Ultimately, time and scientific inquiry will determine the validity of this view.

@article{doi103390life15111745,
    author = "Gómez‐Márquez, Jaime",
    title = "The Origin of Life and Cellular Systems: A Continuum from Prebiotic Chemistry to Biodiversity",
    year = "2025",
    journal = "Life",
    abstract = "The origin of life remains one of the most profound and enduring enigmas in the biological sciences. Despite substantial advances in prebiotic chemistry, fundamental uncertainties persist regarding the precise mechanisms that enabled the emergence of the first cellular entity and, subsequently, the foundational branches of the tree of life. After examining the core principles that define living systems, we propose that life emerged as a novel property of a prebiotically assembled system-formed through the integration of distinct molecular worlds, defined as sets of structurally and functionally related molecular entities that interact via catalytic, autocatalytic, and/or self-assembly processes. This emergence established a permanent system-process duality, wherein the system's organization and its dynamic processes became inseparable. Upon acquiring the capacity to replicate and mutate its genetic program, this primordial organism initiated the evolutionary process, ultimately driving the diversification of life under the influence of evolutionary forces and leading to the formation of ecosystems. The challenge of uncovering the origin of life and the emergence of biodiversity is not solely scientific, it requires the integration of empirical evidence, theoretical insight, and critical reflection. This work does not claim certainty but proposes a perspective on how life and biodiversity may have arisen on Earth. Ultimately, time and scientific inquiry will determine the validity of this view.",
    url = "https://doi.org/10.3390/life15111745",
    doi = "10.3390/life15111745",
    openalex = "W4416192137",
    references = "doi101016jpbiomolbio202407002, doi101017s1473550416000100, doi101038s42004024012646, doi101089ast20210162, doi103390life14050607"
}

The virus-first theory presents a model in which viral lineages emerged before cells. This proposal aims to give the theory greater relevance by offering a plausible evolutionary framework that explains both (i) the origin of viruses from prebiotic chemistry and (ii) how viruses contributed to the emergence of cells. Here, we propose that viruses should be understood as a distinct class of ribonucleoprotein (RNP) systems, some of which evolved directly from the RNP-world. In our model, simple progenotes produced capsid-like particles through the evolution of a single gene encoding a self-assembling peptide. This allowed the formation of icosahedral shells around RNA genomes, as observed today in certain viral families whose capsids consist of ~60 identical subunits derived from a single gene product. These early capsids enabled mobility and protection, representing key intermediates toward biological complexity. Over time, some of those populations acquired additional peptides and evolved more elaborate architectures. Finally, the incorporation of lipid-binding domains in those capsid-like peptides allowed the formation of proteolipidic membranes akin to those found in modern cells. This model provides a gradualistic and logically coherent evolutionary path from the RNP-world to the emergence of cellular life, emphasizing the foundational role of viruses in early evolution.

@article{doi103390microbiolres16070154,
    author = "Prosdocimi, Francisco and de Farías, Sávio Torres",
    title = "Virus-First Theory Revisited: Bridging RNP-World and Cellular Life",
    year = "2025",
    journal = "Microbiology Research",
    abstract = "The virus-first theory presents a model in which viral lineages emerged before cells. This proposal aims to give the theory greater relevance by offering a plausible evolutionary framework that explains both (i) the origin of viruses from prebiotic chemistry and (ii) how viruses contributed to the emergence of cells. Here, we propose that viruses should be understood as a distinct class of ribonucleoprotein (RNP) systems, some of which evolved directly from the RNP-world. In our model, simple progenotes produced capsid-like particles through the evolution of a single gene encoding a self-assembling peptide. This allowed the formation of icosahedral shells around RNA genomes, as observed today in certain viral families whose capsids consist of \textasciitilde 60 identical subunits derived from a single gene product. These early capsids enabled mobility and protection, representing key intermediates toward biological complexity. Over time, some of those populations acquired additional peptides and evolved more elaborate architectures. Finally, the incorporation of lipid-binding domains in those capsid-like peptides allowed the formation of proteolipidic membranes akin to those found in modern cells. This model provides a gradualistic and logically coherent evolutionary path from the RNP-world to the emergence of cellular life, emphasizing the foundational role of viruses in early evolution.",
    url = "https://doi.org/10.3390/microbiolres16070154",
    doi = "10.3390/microbiolres16070154",
    openalex = "W4412095934",
    references = "doi101016jpbiomolbio202407002"
}

Nucleic acid replication is a central process at the origin of life. On early Earth, replication is challenged by the dilution of molecular building blocks and the difficulty of separating daughter from parent strands, a necessity for exponential replication. While thermal gradient systems have been shown to address these problems, elevated temperatures lead to degradation. Also, compared to constant temperature environments, such systems are rare. The isothermal system studied here models an abundant geological environment of the prebiotic Earth, in which water is continuously evaporated at the point of contact with the gas flows, inducing up-concentration and circular flow patterns at the gas-water interface through momentum transfer. We show experimentally that this setting drives a 30-fold accumulation of nucleic acids and their periodic separation by a threefold reduction in salt and product concentration. Fluid dynamic simulations agree with observations from tracking fluorescent beads. In this isothermal system, we were able to drive exponential DNA replication with Taq polymerase. The results provide a model for a ubiquitous non-equilibrium system to host early Darwinian molecular evolution at constant temperature.

@article{doi107554elife100152,
    author = "Schwintek, Philipp and Eren, Emre and Mast, Christof Bernhard and Braun, Dieter",
    title = "Prebiotic gas flow environment enables isothermal nucleic acid replication.",
    year = "2025",
    journal = "eLife",
    abstract = "Nucleic acid replication is a central process at the origin of life. On early Earth, replication is challenged by the dilution of molecular building blocks and the difficulty of separating daughter from parent strands, a necessity for exponential replication. While thermal gradient systems have been shown to address these problems, elevated temperatures lead to degradation. Also, compared to constant temperature environments, such systems are rare. The isothermal system studied here models an abundant geological environment of the prebiotic Earth, in which water is continuously evaporated at the point of contact with the gas flows, inducing up-concentration and circular flow patterns at the gas-water interface through momentum transfer. We show experimentally that this setting drives a 30-fold accumulation of nucleic acids and their periodic separation by a threefold reduction in salt and product concentration. Fluid dynamic simulations agree with observations from tracking fluorescent beads. In this isothermal system, we were able to drive exponential DNA replication with Taq polymerase. The results provide a model for a ubiquitous non-equilibrium system to host early Darwinian molecular evolution at constant temperature.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12240584/",
    doi = "10.7554/eLife.100152",
    openalex = "W4402970773",
    pmcid = "PMC12240584",
    pmid = "40631871",
    references = "doi101002bies200900131, doi101002bip360030207, doi101007s1089501210598, doi1010160016703774901458, doi101021ja990592p, doi101038319618a0, doi101038381059a0, doi101038nature08013, doi101126science2835402674, doi1011861759220832"
}

OBJECTIVE: To investigate berberine (BBR) promotes mitochondrial biogenesis via the silent mating type information regulation 2 homolog 1/peroxisome proliferator-activated receptor gamma coactivator 1 alpha (SIRT1/PGC-1α) signaling pathway to exert its anti-atherosclerosis effects. METHODS: A total of 42 8-week-old AopE-/- mice were fed a high-fat diet for 12 weeks, and then randomly divided into 7 groups via a simple randomization method: the model group, the low-, medium- and high-dose BBR groups [BBRL 50 mg/(kg·d), BBRM 100 mg/(kg·d) and BBRH 150 mg/(kg·d), respectively], positive control group [atorvastatin, 3 mg/(kg·d)], BBR combined with nuclear respiratory factor 1 (Nrf1) inhibitor group (BBRH+EX527, 150 mg/kg BBR+10 mg/kg EX527), and Nrf1 inhibitor group [EX527, 10 mg/(kg·d)]. Six C57BL/6J mice fed with a normal diet were served as control. After 4 weeks of intragastric administration, samples were harvested, and serum, aorta, heart, and liver tissues were isolated for subsequent experiments. Biochemical kits were used to detect serum lipid content in mice. Hematoxylin-eosin, Oil Red O and Masson staining were used to assess lesion severity, lipid deposition, and fibrous cap thickness. Transmission electron microscopy and immunofluorescence were used to analyze mitochondrial morphology and function. Real time quantitative PCR assay and Western blot were utilized to measure the expression levels of SIRT1, PGC-1α, Nrf1, and mitochondrial transcription factor A (TFAM) at both the mRNA and protein levels, along with the quantification of mitochondrial DNA (mtDNA) copy-number in mouse aortas. RESULTS: After BBR intervention, BBRM and BBRH groups significantly reduced blood lipid levels in mice (P<0.01), alleviated aortic plaque deposition, and improved mitochondrial damage (P<0.05 or P<0.01). Additionally, BBR significantly upregulated the mRNA and protein expressions of SIRT1, PGC-1α, Nrf1, and TFAM (P<0.05 or P<0.01). And the relative copy number of mtDNA increased in a dose-dependent manner (P<0.01). In the BBRH+EX527 group, aortic lesions and mitochondrial damage were exacerbated, with concurrent decreases in mRNA and protein expression levels (P<0.05 or P<0.01). CONCLUSION: BBR promotes mitochondrial biogenesis, maintains mitochondrial function, and inhibits mitochondrial damage through the SIRT1/PGC-1α signaling pathway, thereby improving atherosclerosis.

@article{doi101007s1165502640378,
    author = "Wang, Si-Yu and Zheng, Jun-Meng and Han, Xin-Yi and Jin, Bo-Yuan and Hua, Cheng-Jun and Chen, Yu-Shan and Wang, Ting-Ting and Wang, Yun-Hao",
    title = "Berberine Ameliorates Atherosclerosis by Promoting Mitochondrial Biogenesis via SIRT1/PGC-1α Signaling Pathway.",
    year = "2026",
    journal = "Chinese journal of integrative medicine",
    abstract = "OBJECTIVE: To investigate berberine (BBR) promotes mitochondrial biogenesis via the silent mating type information regulation 2 homolog 1/peroxisome proliferator-activated receptor gamma coactivator 1 alpha (SIRT1/PGC-1α) signaling pathway to exert its anti-atherosclerosis effects. METHODS: A total of 42 8-week-old AopE-/- mice were fed a high-fat diet for 12 weeks, and then randomly divided into 7 groups via a simple randomization method: the model group, the low-, medium- and high-dose BBR groups [BBRL 50 mg/(kg·d), BBRM 100 mg/(kg·d) and BBRH 150 mg/(kg·d), respectively], positive control group [atorvastatin, 3 mg/(kg·d)], BBR combined with nuclear respiratory factor 1 (Nrf1) inhibitor group (BBRH+EX527, 150 mg/kg BBR+10 mg/kg EX527), and Nrf1 inhibitor group [EX527, 10 mg/(kg·d)]. Six C57BL/6J mice fed with a normal diet were served as control. After 4 weeks of intragastric administration, samples were harvested, and serum, aorta, heart, and liver tissues were isolated for subsequent experiments. Biochemical kits were used to detect serum lipid content in mice. Hematoxylin-eosin, Oil Red O and Masson staining were used to assess lesion severity, lipid deposition, and fibrous cap thickness. Transmission electron microscopy and immunofluorescence were used to analyze mitochondrial morphology and function. Real time quantitative PCR assay and Western blot were utilized to measure the expression levels of SIRT1, PGC-1α, Nrf1, and mitochondrial transcription factor A (TFAM) at both the mRNA and protein levels, along with the quantification of mitochondrial DNA (mtDNA) copy-number in mouse aortas. RESULTS: After BBR intervention, BBRM and BBRH groups significantly reduced blood lipid levels in mice (P<0.01), alleviated aortic plaque deposition, and improved mitochondrial damage (P<0.05 or P<0.01). Additionally, BBR significantly upregulated the mRNA and protein expressions of SIRT1, PGC-1α, Nrf1, and TFAM (P<0.05 or P<0.01). And the relative copy number of mtDNA increased in a dose-dependent manner (P<0.01). In the BBRH+EX527 group, aortic lesions and mitochondrial damage were exacerbated, with concurrent decreases in mRNA and protein expression levels (P<0.05 or P<0.01). CONCLUSION: BBR promotes mitochondrial biogenesis, maintains mitochondrial function, and inhibits mitochondrial damage through the SIRT1/PGC-1α signaling pathway, thereby improving atherosclerosis.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/10487483/",
    doi = "10.1007/s11655-026-4037-8",
    pmcid = "10487483",
    pmid = "42043671"
}

LncRNAs, defined as transcripts longer than 200 nucleotides with limited protein-coding potential, have emerged as important regulators of gene expression across multiple levels of cellular regulation. These molecules influence chromatin organization, transcriptional activity, and post-transcriptional processes through diverse interactions with DNA, RNA, and protein complexes. Although initially considered transcriptional byproducts, accumulating evidence now indicates that lncRNAs participate in a wide range of physiological processes and are implicated in numerous human diseases, including cancer, cardiovascular disorders, neurological diseases, and immune related conditions. However, the strength of mechanistic evidence varies substantially across the field, with robust functional validation currently limited to a relatively small number of well-characterized lncRNAs. In many cases, proposed regulatory roles remain supported primarily by expression correlations or limited perturbation studies, highlighting the need for careful evaluation of reproducibility, context dependence, and locus-specific effects. In addition, translating lncRNA discoveries into therapeutic strategies faces several practical challenges, including efficient tissue-specific delivery, subcellular localization constraints, isoform complexity, and potential off-target effects. This review provides an overview of current knowledge on lncRNA classification, biogenesis, and molecular mechanisms, evaluates their roles in human disease, and discusses emerging therapeutic approaches in the context of translational feasibility. By integrating mechanistic insights with current limitations and unresolved questions, we highlight priorities for future research aimed at harnessing lncRNAs for diagnostic and therapeutic applications in precision medicine.

@article{doi103390cimb48040414,
    author = "Dubey, Arvind Kumar and Kumar, Anil and Nurbekova, Zhadyrassyn and Kumar, Navin",
    title = "Long Non-Coding RNAs in Human Disease: An Overview of Biogenesis, Molecular Mechanism and Therapeutic Opportunities.",
    year = "2026",
    journal = "Current issues in molecular biology",
    abstract = "LncRNAs, defined as transcripts longer than 200 nucleotides with limited protein-coding potential, have emerged as important regulators of gene expression across multiple levels of cellular regulation. These molecules influence chromatin organization, transcriptional activity, and post-transcriptional processes through diverse interactions with DNA, RNA, and protein complexes. Although initially considered transcriptional byproducts, accumulating evidence now indicates that lncRNAs participate in a wide range of physiological processes and are implicated in numerous human diseases, including cancer, cardiovascular disorders, neurological diseases, and immune related conditions. However, the strength of mechanistic evidence varies substantially across the field, with robust functional validation currently limited to a relatively small number of well-characterized lncRNAs. In many cases, proposed regulatory roles remain supported primarily by expression correlations or limited perturbation studies, highlighting the need for careful evaluation of reproducibility, context dependence, and locus-specific effects. In addition, translating lncRNA discoveries into therapeutic strategies faces several practical challenges, including efficient tissue-specific delivery, subcellular localization constraints, isoform complexity, and potential off-target effects. This review provides an overview of current knowledge on lncRNA classification, biogenesis, and molecular mechanisms, evaluates their roles in human disease, and discusses emerging therapeutic approaches in the context of translational feasibility. By integrating mechanistic insights with current limitations and unresolved questions, we highlight priorities for future research aimed at harnessing lncRNAs for diagnostic and therapeutic applications in precision medicine.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42042074/",
    doi = "10.3390/cimb48040414",
    pmid = "42042074"
}

Peroxisomes are ubiquitous organelles that play vital roles in various physiological and biochemical processes, including fatty acid β-oxidation and reactive oxygen species (ROS) metabolism. These organelles have been implicated in the pathogenicity of many plant fungal pathogens. In this study, CaPex8, a homolog of Saccharomyces cerevisiae Pex8, was identified and characterized in Colletotrichum aenigma. CaPEX8 was found to localize to peroxisomes, and its deletion impaired the mutant's ability to utilize fatty acids as a carbon source. Using a green fluorescent protein (GFP) fused to the peroxisomal targeting signal PTS1, the import of peroxisomal matrix proteins was shown to be defective in ΔCapex8 mutants. Additionally, the mutants exhibited elevated conidiation, increased sensitivity to osmotic stress and oxidative stress, and impaired cell wall integrity. Peroxisome biogenesis was also disrupted in the absence of CaPEX8. Taken together, these results demonstrate that CaPex8 is essential for maintaining peroxisomal structure and function, and it significantly influences fungal growth, development, and pathogenicity in C. aenigma.

@article{doi103390jof12040241,
    author = "Lin, Yan-Xi and Cai, Ying-Ying and Yu, Shen-Dan and Wang, Jing and Wang, Xin-He and Hao, Zhong-Na and Zhang, Zhen and Qiu, Hai-Ping and Chai, Rong-Yao and Wang, Yan-Li and Liao, Qian-Sheng and Wang, Jiao-Yu",
    title = "Characterization of CaPEX8 in Peroxisome Biogenesis and Pathogenicity of Colletotrichum aenigma.",
    year = "2026",
    journal = "Journal of fungi (Basel, Switzerland)",
    abstract = "Peroxisomes are ubiquitous organelles that play vital roles in various physiological and biochemical processes, including fatty acid β-oxidation and reactive oxygen species (ROS) metabolism. These organelles have been implicated in the pathogenicity of many plant fungal pathogens. In this study, CaPex8, a homolog of Saccharomyces cerevisiae Pex8, was identified and characterized in Colletotrichum aenigma. CaPEX8 was found to localize to peroxisomes, and its deletion impaired the mutant's ability to utilize fatty acids as a carbon source. Using a green fluorescent protein (GFP) fused to the peroxisomal targeting signal PTS1, the import of peroxisomal matrix proteins was shown to be defective in ΔCapex8 mutants. Additionally, the mutants exhibited elevated conidiation, increased sensitivity to osmotic stress and oxidative stress, and impaired cell wall integrity. Peroxisome biogenesis was also disrupted in the absence of CaPEX8. Taken together, these results demonstrate that CaPex8 is essential for maintaining peroxisomal structure and function, and it significantly influences fungal growth, development, and pathogenicity in C. aenigma.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42042336/",
    doi = "10.3390/jof12040241",
    pmid = "42042336"
}

Peroxisomes are ubiquitous eukaryotic organelles that play critical roles in the infection processes of many plant pathogenic fungi. Peroxisome biogenesis depends on peroxins encoded by PEX genes. Pex8 is a fungus-specific peroxin present only in yeasts and filamentous fungi. In this study, we investigated the function of CoPEX8 in the cucumber anthracnose fungus Colletotrichum orbiculare using targeted gene deletion. Fluorescence microscopy using red fluorescent protein fused to peroxisomal targeting signal 1 (PTS1) showed that matrix protein import was abolished in the ΔCopex8 mutant. Compared with the wild-type strain, the ΔCopex8 mutant lacked detectable peroxisomes and exhibited severe defects in melanin production, fatty acid utilization, cell wall integrity, osmotic stress tolerance, and reactive oxygen species (ROS) scavenging. Deletion of CoPEX8 also reduced conidiation and impaired appressorium formation. Pathogenicity assays on cucumber leaves revealed that lesions produced by the ΔCopex8 mutant were significantly smaller than those caused by the wild-type strain. These results demonstrate that CoPEX8 is indispensable for peroxisome biogenesis and is essential for both development and virulence of C. orbiculare.

@article{doi103390jof12040248,
    author = "Wang, Xinhe and Wang, Jing and Yu, Shendan and Cai, Yingying and Lin, Yanxi and Zhang, Zhen and Noman, Muhammad and Qiu, Haiping and Hao, Zhongna and Chai, Rongyao and Wang, Yanli and Li, Lin and Li, Ling and Wang, Jiaoyu",
    title = "Pex8, a Fungal Specific Peroxin, Regulates Peroxisome Biogenesis and Pathogenicity in the Cucumber Anthracnose Fungus Colletotrichum orbiculare.",
    year = "2026",
    journal = "Journal of fungi (Basel, Switzerland)",
    abstract = "Peroxisomes are ubiquitous eukaryotic organelles that play critical roles in the infection processes of many plant pathogenic fungi. Peroxisome biogenesis depends on peroxins encoded by PEX genes. Pex8 is a fungus-specific peroxin present only in yeasts and filamentous fungi. In this study, we investigated the function of CoPEX8 in the cucumber anthracnose fungus Colletotrichum orbiculare using targeted gene deletion. Fluorescence microscopy using red fluorescent protein fused to peroxisomal targeting signal 1 (PTS1) showed that matrix protein import was abolished in the ΔCopex8 mutant. Compared with the wild-type strain, the ΔCopex8 mutant lacked detectable peroxisomes and exhibited severe defects in melanin production, fatty acid utilization, cell wall integrity, osmotic stress tolerance, and reactive oxygen species (ROS) scavenging. Deletion of CoPEX8 also reduced conidiation and impaired appressorium formation. Pathogenicity assays on cucumber leaves revealed that lesions produced by the ΔCopex8 mutant were significantly smaller than those caused by the wild-type strain. These results demonstrate that CoPEX8 is indispensable for peroxisome biogenesis and is essential for both development and virulence of C. orbiculare.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42042343/",
    doi = "10.3390/jof12040248",
    pmid = "42042343"
}

@incollection{drummondNonebiogenesis,
    author = "Drummond, Henry",
    title = "BIOGENESIS",
    year = "None",
    booktitle = "Natural Law in the Spritural World",
    url = "https://doi.org/10.1017/cbo9780511692703.003",
    doi = "10.1017/cbo9780511692703.003",
    pages = "59-94"
}