Abiogenesis

@article{doi101038216029a0,
    author = "Hodgson, G. W. and Baker, B.L.",
    title = "Porphyrin Abiogenesis from Pyrrole and Formaldehyde under Simulated Geochemical Conditions",
    year = "1967",
    journal = "Nature",
    url = "https://doi.org/10.1038/216029a0",
    doi = "10.1038/216029a0",
    openalex = "W2036775766",
    references = "doi101016c20130121083, doi101021ja01295a027, doi101021ja01614a001, doi101038199222a0, doi101038202125a0, doi101073pnas495737, doi101126science1173046528, doi101126science12833331214, doi101126science14736651572, openalexw331990907"
}

@book{rutten1971the2,
    author = "Rutten, M. G",
    title = "The Origin of Life by Natural Causes",
    year = "1971",
    publisher = "Amsterdam, London, New York, Elsevier",
    note = "talkorigins\_source = {true}; raw\_reference = {Rutten, M. G., 1971, The Origin of Life by Natural Causes: Amsterdam, London, New York, Elsevier.}"
}

@incollection{doi10100797814684900469,
    author = "Cole, Francis E. and Graf, E. R.",
    title = "Precambrian ELF and Abiogenesis",
    year = "1974",
    url = "https://doi.org/10.1007/978-1-4684-9004-6\_9",
    doi = "10.1007/978-1-4684-9004-6\_9",
    openalex = "W71035227",
    references = "doi1010160024320565903267, doi101016c20130121083, doi1010382151230a0, doi101038235109a0, doi101073pnas591110, doi101126science1173046528, doi101126science12833331214, doi101126science1303370245, doi101126science1683930470, doi1023072420646"
}

@book{oster1974irreversible1,
    author = "Oster, G. F. and Silver, I. L. and Tobais, C. A",
    title = "Irreversible Thermodynamics and the Origin of Life",
    year = "1974",
    publisher = "New York, London, Paris, Gordon and Breach Science Publications",
    note = "talkorigins\_source = {true}; raw\_reference = {Oster, G. F., Silver, I. L., and Tobais, C. A., 1974, Irreversible Thermodynamics and the Origin of Life: New York, London, Paris, Gordon and Breach Science Publications.}"
}

The observations of hydrothermal systems along midoceanic spreading centers by the deep‐diving submarine, Alvin, have led to numerous geological theories to explain phenomena ranging from heat flow to the formation of massive sulfide deposits. Unusual life in the forms of giant tube worms and mussels (Eos, Dec. 29, 1981) have been found to live along the submarine hot springs in chemically reducing and normally toxic sulfurous environments. Analyses of data over the past year or two have formed the basis of new life‐evolution schemes. J.B. Corliss, J.A. Baross, and S.E. Hoffman have outlined a process by which concentrations of methane, ammonia, hydrogen, and metals may have reacted, in several steps, to produce living organisms within or adjacent to submarine hydrothermal systems (Oceanol. Acta, 59–69, 1981).

@article{bell1982submarine,
    author = "Bell, Peter M.",
    title = "Submarine hot springs: Origin of life?",
    year = "1982",
    journal = "Eos, Transactions American Geophysical Union",
    abstract = "The observations of hydrothermal systems along midoceanic spreading centers by the deep‐diving submarine, Alvin, have led to numerous geological theories to explain phenomena ranging from heat flow to the formation of massive sulfide deposits. Unusual life in the forms of giant tube worms and mussels (Eos, Dec. 29, 1981) have been found to live along the submarine hot springs in chemically reducing and normally toxic sulfurous environments. Analyses of data over the past year or two have formed the basis of new life‐evolution schemes. J.B. Corliss, J.A. Baross, and S.E. Hoffman have outlined a process by which concentrations of methane, ammonia, hydrogen, and metals may have reacted, in several steps, to produce living organisms within or adjacent to submarine hydrothermal systems (Oceanol. Acta, 59–69, 1981).",
    url = "https://doi.org/10.1029/eo063i012p00201-04",
    doi = "10.1029/eo063i012p00201-04",
    number = "12",
    openalex = "W2022827068",
    pages = "201-201",
    volume = "63"
}

@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"
}

@article{doi101016009286749190082a,
    author = "Pace, Norman R.",
    title = "Origin of life-facing up to the physical setting",
    year = "1991",
    journal = "Cell",
    url = "https://doi.org/10.1016/0092-8674(91)90082-a",
    doi = "10.1016/0092-8674(91)90082-a",
    openalex = "W2019662242"
}

@article{doi101038355125a0,
    author = "Chyba, Christopher F. and Sagan, Carl",
    title = "Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life",
    year = "1992",
    journal = "Nature",
    url = "https://doi.org/10.1038/355125a0",
    doi = "10.1038/355125a0",
    openalex = "W2070744579",
    references = "doi1010079789400972223, doi1010160019103585901216, doi101038190389a0, doi101038331612a0, doi101038333313a0, doi101038338487a0, doi101038342139a0, doi101038343129a0, doi101126science11538074, doi101126science1303370245, doi101126science23247551225, doi101146annurevea13050185001051, schidlowski1988a, vidal1985earths"
}

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"
}

@article{doi101016s1389556702000394,
    author = "Emeline, Alexei V. and Otroshchenko, V. A. and Ryabchuk, V. K. and Serpone, Nick",
    title = "Abiogenesis and photostimulated heterogeneous reactions in the interstellar medium and on primitive earth",
    year = "2002",
    journal = "Journal of Photochemistry and Photobiology C Photochemistry Reviews",
    url = "https://doi.org/10.1016/s1389-5567(02)00039-4",
    doi = "10.1016/s1389-5567(02)00039-4",
    openalex = "W2950163835",
    references = "doi101016s1010603097001184, doi101016s1389556700000022, doi101021cr00017a016, doi101021cr00035a013, doi101021ja00464a015, doi101146annurevaa25090187000323, doi101146annurevastro381427, doi10114912425756, doi1015159780691220239, openalexw617322716"
}

A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood-Ljungdahl) pathway of CO2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood-Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood-Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH3 via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of alpha-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent-ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.

@article{doi101098rstb20061881,
    author = "Martin, William and Russell, Michael J.",
    title = "On the origin of biochemistry at an alkaline hydrothermal vent",
    year = "2006",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood-Ljungdahl) pathway of CO2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood-Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood-Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH3 via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of alpha-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent-ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.",
    url = "https://doi.org/10.1098/rstb.2006.1881",
    doi = "10.1098/rstb.2006.1881",
    openalex = "W2125611981",
    references = "doi101007bf01140180, doi101007bf01808177, doi1010160016703794902887, doi101038319618a0, doi10103832096, doi10103835084000, doi101073pnas316153, doi101093nargki012, doi101099002077135217, doi101111j157469762001tb00576x, doi101126science1092464, doi101126science1102556, doi101126science28454232124, doi101128br4111001801977, doi101128mmbr4111001801977, doi101128mmbr6122622801997, doi101128mr6046096401996, doi101144gsjgs15430377, openalexw3041019241"
}

@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"
}

@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"
}

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"
}

@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"
}

@incollection{doi10103713971010,
    author = "Huxley, Thomas Henry",
    title = "Biogenesis and abiogenesis.",
    year = "2012",
    booktitle = "Macmillan and Co eBooks",
    url = "https://doi.org/10.1037/13971-010",
    doi = "10.1037/13971-010",
    openalex = "W2480670981"
}

@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"
}

A sudden transition in a system from an inanimate state to the living state-defined on the basis of present day living organisms-would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages-dynamic kinetic stability (DKS)-which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred.

@article{doi101098rsob130156,
    author = "Pascal, Robert and Pross, Addy and Sutherland, John D.",
    title = "Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics",
    year = "2013",
    journal = "Open Biology",
    abstract = "A sudden transition in a system from an inanimate state to the living state-defined on the basis of present day living organisms-would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages-dynamic kinetic stability (DKS)-which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred.",
    url = "https://doi.org/10.1098/rsob.130156",
    doi = "10.1098/rsob.130156",
    openalex = "W2162557527",
    references = "doi101007bf00450633, doi101007bf00623322, doi1010160020711x94901198, doi101038171737a0, doi101038191144a0, doi101073pnas86147, doi101128mr5244524841988, doi1011861759220821, doi1023072298330, doi1023072965538, doi105860choice364495"
}

@article{doi101038nmeth2893,
    author = "Attwater, James and Holliger, Philipp",
    title = "A synthetic approach to abiogenesis",
    year = "2014",
    journal = "Nature Methods",
    url = "https://doi.org/10.1038/nmeth.2893",
    doi = "10.1038/nmeth.2893",
    openalex = "W2010389635",
    references = "doi10103835053176, doi101038nature02791, doi101038nature08013, doi101038nature12051, doi101038nchem1110, doi101073pnas95126854, doi101126science1060786, doi101126science1190719, doi101126science1217622, doi101126science1241459"
}

@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"
}

This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999).

@article{doi101089ast20131110,
    author = "Russell, Michael J. and Barge, Laura M. and Bhartia, R. and Bocanegra, Dylan and Bracher, Paul J. and Branscomb, Elbert and Kidd, Richard and McGlynn, Shawn E. and Meier, David H. and Nitschke, Wolfgang and Shibuya, Takazo and Vance, S. and White, Lauren M. and Kanik, I.",
    title = "The Drive to Life on Wet and Icy Worlds",
    year = "2014",
    journal = "Astrobiology",
    abstract = {This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999).},
    url = "https://doi.org/10.1089/ast.2013.1110",
    doi = "10.1089/ast.2013.1110",
    openalex = "W2081345082",
    references = "doi101002cbdv200790052, doi101016jastropartphys201303001, doi101016jepsl201110040, doi101098rsob130156, doi101128mmbr0001009"
}

Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.

@article{doi101002anie201506585,
    author = "Sutherland, John D.",
    title = "The Origin of Life—Out of the Blue",
    year = "2015",
    journal = "Angewandte Chemie International Edition",
    abstract = {Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.},
    url = "https://doi.org/10.1002/anie.201506585",
    doi = "10.1002/anie.201506585",
    openalex = "W1865631169",
    references = "doi101016s0040403901994870, doi101021cr2004844, doi101023a1006746807104, doi101098rsob130156, doi10247509201301, oró1961aminoacid"
}

@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"
}

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an "experiment" in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life.

@article{doi103390life5010872,
    author = "Damer, Bruce and Deamer, David W.",
    title = "Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life",
    year = "2015",
    journal = "Life",
    abstract = {Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an "experiment" in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life.},
    url = "https://doi.org/10.3390/life5010872",
    doi = "10.3390/life5010872",
    openalex = "W1993942594",
    references = "doi101007s1108400791132, doi101073pnas1117774109"
}

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"
}

The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.

@article{doi101017s0033583517000038,
    author = "Wachowius, Falk and Attwater, James and Holliger, Philipp",
    title = "Nucleic acids: function and potential for abiogenesis",
    year = "2017",
    journal = "Quarterly Reviews of Biophysics",
    abstract = "The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.",
    url = "https://doi.org/10.1017/s0033583517000038",
    doi = "10.1017/s0033583517000038",
    openalex = "W2599712977",
    references = "doi1010079781461251903, doi1010160092867482904147, doi1010160092867483901174, doi101016jcell200902009, doi101016jcell201403008, doi101038171737a0, doi101038319618a0, doi101038346818a0, doi101038nmeth2893, doi101126science2200121, doi101126science2895481905"
}

@article{doi101038s415700160012,
    author = "Sutherland, John D.",
    title = "Opinion: Studies on the origin of life — the end of the beginning",
    year = "2017",
    journal = "Nature Reviews Chemistry",
    url = "https://doi.org/10.1038/s41570-016-0012",
    doi = "10.1038/s41570-016-0012",
    openalex = "W2575357040",
    references = "doi101002anie201506585, doi101016009286749190082a, doi101016s0022283667800378, doi101038nchem2202, doi101038nmicrobiol2016116, doi101073pnas1019191108, doi101089ast20151406, doi101093acprofoso97801985072600010001, doi101098rsob130156, doi101126science1173046528, doi101126scienceaac6103"
}

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.

@article{doi103390life7010005,
    author = "Deamer, David W.",
    title = "The Role of Lipid Membranes in Life’s Origin",
    year = "2017",
    journal = "Life",
    abstract = "At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.",
    url = "https://doi.org/10.3390/life7010005",
    doi = "10.3390/life7010005",
    openalex = "W2573268563",
    references = "doi101073pnas1117774109, doi103390life5021239"
}

Origin of life models based on “energized assemblages of building blocks” are untenable in principle. This is fundamentally a consequence of the fact that any living system is in a physical state that is extremely far from equilibrium, a condition it must itself build and sustain. This in turn requires that it carries out all of its molecular transformations–obligatorily those that convert, and thereby create, disequilibria–using case‐specific mechanochemical macromolecular machines. Mass‐action solution chemistry is quite unable to do this. We argue in Part 2 of this series that this inherent dependence of life on disequilibria‐converting macromolecular machines is also an obligatory requirement for life at its emergence. Therefore, life must have been launched by the operation of abiotic macromolecular machines driven by abiotic, but specifically “life‐like”, disequilibria, coopted from mineral precipitates that are chemically and physically active. Models grounded in “chemistry‐in‐a‐bag” ideas, however energized, should not be considered.

@article{branscomb2018frankenstein,
    author = "Branscomb, Elbert and Russell, Michael J.",
    title = "Frankenstein or a Submarine Alkaline Vent: Who Is Responsible for Abiogenesis?",
    year = "2018",
    journal = "BioEssays",
    abstract = "Origin of life models based on “energized assemblages of building blocks” are untenable in principle. This is fundamentally a consequence of the fact that any living system is in a physical state that is extremely far from equilibrium, a condition it must itself build and sustain. This in turn requires that it carries out all of its molecular transformations–obligatorily those that convert, and thereby create, disequilibria–using case‐specific mechanochemical macromolecular machines. Mass‐action solution chemistry is quite unable to do this. We argue in Part 2 of this series that this inherent dependence of life on disequilibria‐converting macromolecular machines is also an obligatory requirement for life at its emergence. Therefore, life must have been launched by the operation of abiotic macromolecular machines driven by abiotic, but specifically “life‐like”, disequilibria, coopted from mineral precipitates that are chemically and physically active. Models grounded in “chemistry‐in‐a‐bag” ideas, however energized, should not be considered.",
    url = "https://doi.org/10.1002/bies.201700179",
    doi = "10.1002/bies.201700179",
    number = "7",
    openalex = "W2884939984",
    volume = "40",
    references = "doi101002bies200900131, doi101016jchembiol201303012, doi101016s000634950076615x, doi101016s000634959381035x, doi101016s0168644503000482, doi101021cr2004844, doi101038s415700160012, doi101073pnas1117774109, doi101088003448857512126001, doi101098rsob130156"
}

Origin of life models based on "energized assemblages of building blocks" are untenable in principle. This is fundamentally a consequence of the fact that any living system is in a physical state that is extremely far from equilibrium, a condition it must itself build and sustain. This in turn requires that it carries out all of its molecular transformations-obligatorily those that convert, and thereby create, disequilibria-using case-specific mechanochemical macromolecular machines. Mass-action solution chemistry is quite unable to do this. We argue in Part 2 of this series that this inherent dependence of life on disequilibria-converting macromolecular machines is also an obligatory requirement for life at its emergence. Therefore, life must have been launched by the operation of abiotic macromolecular machines driven by abiotic, but specifically "life-like", disequilibria, coopted from mineral precipitates that are chemically and physically active. Models grounded in "chemistry-in-a-bag" ideas, however energized, should not be considered.

@article{doi101002bies201700179,
    author = "Branscomb, Elbert and Russell, Michael J",
    title = "Frankenstein or a Submarine Alkaline Vent: Who Is Responsible for Abiogenesis?: Part 1: What is life-that it might create itself?",
    year = "2018",
    journal = "BioEssays: news and reviews in molecular, cellular and developmental biology",
    abstract = {Origin of life models based on "energized assemblages of building blocks" are untenable in principle. This is fundamentally a consequence of the fact that any living system is in a physical state that is extremely far from equilibrium, a condition it must itself build and sustain. This in turn requires that it carries out all of its molecular transformations-obligatorily those that convert, and thereby create, disequilibria-using case-specific mechanochemical macromolecular machines. Mass-action solution chemistry is quite unable to do this. We argue in Part 2 of this series that this inherent dependence of life on disequilibria-converting macromolecular machines is also an obligatory requirement for life at its emergence. Therefore, life must have been launched by the operation of abiotic macromolecular machines driven by abiotic, but specifically "life-like", disequilibria, coopted from mineral precipitates that are chemically and physically active. Models grounded in "chemistry-in-a-bag" ideas, however energized, should not be considered.},
    url = "https://pubmed.ncbi.nlm.nih.gov/29870581/",
    doi = "10.1002/bies.201700179",
    openalex = "W2884939984",
    pmid = "29870581",
    references = "doi101002bies200900131, doi101016jchembiol201303012, doi101016s000634950076615x, doi101016s000634959381035x, doi101016s0168644503000482, doi101021cr2004844, doi101038s415700160012, doi101073pnas1117774109, doi101088003448857512126001, doi101098rsob130156"
}

We argued in Part 1 of this series that because all living systems are extremely far-from-equilibrium dynamic confections of matter, they must necessarily be driven to that state by the conversion of chemically specific external disequilibria into specific internal disequilibria. Such conversions require task-specific macromolecular engines. We here argue that the same is not only true of life at its emergence; it is the enabling cause of that emergence; although here the external driving disequilibria, and the conversion engines needed must have been abiotic. We argue further that the initial step in life's emergence can only create an extremely simple non-equilibrium "seed" from which all the complexity of life must then develop. We assert that this complexity develops incrementally and progressively, each step tested for value added "in flight." And we make the case that only the submarine alkaline hydrothermal vent (AHV) model has the potential to satisfy these requirements.

@article{doi101002bies201700182,
    author = "Branscomb, Elbert and Russell, Michael J",
    title = "Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis?: Part 2: As life is now, so it must have been in the beginning.",
    year = "2018",
    journal = "BioEssays: news and reviews in molecular, cellular and developmental biology",
    abstract = {We argued in Part 1 of this series that because all living systems are extremely far-from-equilibrium dynamic confections of matter, they must necessarily be driven to that state by the conversion of chemically specific external disequilibria into specific internal disequilibria. Such conversions require task-specific macromolecular engines. We here argue that the same is not only true of life at its emergence; it is the enabling cause of that emergence; although here the external driving disequilibria, and the conversion engines needed must have been abiotic. We argue further that the initial step in life's emergence can only create an extremely simple non-equilibrium "seed" from which all the complexity of life must then develop. We assert that this complexity develops incrementally and progressively, each step tested for value added "in flight." And we make the case that only the submarine alkaline hydrothermal vent (AHV) model has the potential to satisfy these requirements.},
    url = "https://pubmed.ncbi.nlm.nih.gov/29974482/",
    doi = "10.1002/bies.201700182",
    openalex = "W2855186055",
    pmid = "29974482",
    references = "doi101016jgca200511008, doi101016s0010854598002161, doi10103835084000, doi10103835089509, doi10103846972, doi101038nature11871, doi101073pnas9083334, doi101098rstb20061881, doi101126science1102556, doi101144gsjgs15430377"
}

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

@article{doi101098rsif20180159,
    author = "Lancet, Doron and Zidovetzki, Raphael and Markovitch, Omer",
    title = "Systems protobiology: origin of life in lipid catalytic networks",
    year = "2018",
    journal = "Journal of The Royal Society Interface",
    abstract = "Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.",
    url = "https://doi.org/10.1098/rsif.2018.0159",
    doi = "10.1098/rsif.2018.0159",
    openalex = "W2884452513",
    references = "doi101016jchembiol201303012, doi101038s415700160012, doi105860choice462052"
}

Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence Fe II /Fe III oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.

@article{doi103390life8030035,
    author = "Russell, Michael J.",
    title = "Green Rust: The Simple Organizing ‘Seed’ of All Life?",
    year = "2018",
    journal = "Life",
    abstract = "Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: \textasciitilde 400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and \textasciitilde 120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence Fe II /Fe III oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.",
    url = "https://doi.org/10.3390/life8030035",
    doi = "10.3390/life8030035",
    openalex = "W2889035376",
    references = "branscomb2018frankenstein, doi101002bies201700179, doi101002bies201700182, doi101002j146020751982tb01276x, doi101016000926149500905j, doi101016jtim200411006, doi101021cr068037a, doi10103846972, doi101038nrmicro2415, doi101088003448857512126001, doi101126science1153213, doi101126science2434996, doi101126science2775326653"
}

@article{cartwright2019the,
    author = "Cartwright, Julyan H. E. and Russell, Michael J.",
    title = "The origin of life: the submarine alkaline vent theory at 30",
    year = "2019",
    journal = "Interface Focus",
    url = "https://doi.org/10.1098/rsfs.2019.0104",
    doi = "10.1098/rsfs.2019.0104",
    number = "6",
    openalex = "W2981187779",
    pages = "20190104",
    volume = "9",
    references = "doi101001archinte196103620040143016, doi101007bf00160147, doi101021acschemrev5b00014, doi101021acsinorgchem5b02157, doi101039b708995c, doi101144gsjgs15430377, doi1023072092944, doi103390life7020013, doi103390life8030035, doi107551mitpress110680010001"
}

Abstract The aim of this article is to provide the reader with an overview of the different possible scenarios for the emergence of life, to critically assess them and, according to the conclusions we reach, to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of directly proposing a concrete and unequivocal cradle of life on Earth, we focus on describing the different requirements that are arguably needed for the transition between non-life to life. We approach this topic from geological, biological, and chemical perspectives with the aim of providing answers in an integrative manner. We reflect upon the most prominent origins hypotheses and assess whether they match the aforementioned abiogenic requirements. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic icy moons.

@article{doi101007s1121401906248,
    author = "Camprubí, Eloi and de Leeuw, J.W. and House, Christopher H. and Raulin, F. and Russell, Michael J. and Spang, Anja and Tirumalai, Madhan R. and Westall, Francès",
    title = "The Emergence of Life",
    year = "2019",
    journal = "Space Science Reviews",
    abstract = "Abstract The aim of this article is to provide the reader with an overview of the different possible scenarios for the emergence of life, to critically assess them and, according to the conclusions we reach, to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of directly proposing a concrete and unequivocal cradle of life on Earth, we focus on describing the different requirements that are arguably needed for the transition between non-life to life. We approach this topic from geological, biological, and chemical perspectives with the aim of providing answers in an integrative manner. We reflect upon the most prominent origins hypotheses and assess whether they match the aforementioned abiogenic requirements. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic icy moons.",
    url = "https://doi.org/10.1007/s11214-019-0624-8",
    doi = "10.1007/s11214-019-0624-8",
    openalex = "W2996665395",
    references = "doi101002bies201700182, doi101007bf01734359, doi101016009286749390529y, doi101073pnas591110, doi101073pnas74115088, doi101073pnas87124576, doi101126science1173046528, doi101126science1962210, doi101126science2895481905, doi1023072103745, doi103390life8030035, doi105962bhltitle156765, doi105962bhltitle542"
}

The seminal Urey-Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the "RNA World" hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.

@article{doi101021acscentsci9b00520,
    author = "Das, Tamal and Ghule, Siddharth and Vanka, Kumar",
    title = "Insights Into the Origin of Life: Did It Begin from HCN and H 2 O?",
    year = "2019",
    journal = "ACS Central Science",
    abstract = {The seminal Urey-Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the "RNA World" hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.},
    url = "https://doi.org/10.1021/acscentsci.9b00520",
    doi = "10.1021/acscentsci.9b00520",
    openalex = "W2964526464",
    references = "doi1010382151230a0"
}

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"
}

There are two dominant and contrasting classes of origin of life scenarios: those predicting that life emerged in submarine hydrothermal systems, where chemical disequilibrium can provide an energy source for nascent life; and those predicting that life emerged within subaerial environments, where UV catalysis of reactions may occur to form the building blocks of life. Here, we describe a prebiotically plausible environment that draws on the strengths of both scenarios: surface hydrothermal vents. We show how key feedstock molecules for prebiotic chemistry can be produced in abundance in shallow and surficial hydrothermal systems. We calculate the chemistry of volcanic gases feeding these vents over a range of pressures and basalt C/N/O contents. If ultra-reducing carbon-rich nitrogen-rich gases interact with subsurface water at a volcanic vent they result in 10 - 3 ⁻ 1 M concentrations of diacetylene (C₄H₂), acetylene (C₂H₂), cyanoacetylene (HC₃N), hydrogen cyanide (HCN), bisulfite (likely in the form of salts containing HSO₃ -), hydrogen sulfide (HS -) and soluble iron in vent water. One key feedstock molecule, cyanamide (CH₂N₂), is not formed in significant quantities within this scenario, suggesting that it may need to be delivered exogenously, or formed from hydrogen cyanide either via organometallic compounds, or by some as yet-unknown chemical synthesis. Given the likely ubiquity of surface hydrothermal vents on young, hot, terrestrial planets, these results identify a prebiotically plausible local geochemical environment, which is also amenable to future lab-based simulation.

@article{doi103390life9010012,
    author = "Rimmer, Paul B. and Shorttle, Oliver",
    title = "Origin of Life’s Building Blocks in Carbon- and Nitrogen-Rich Surface Hydrothermal Vents",
    year = "2019",
    journal = "Life",
    abstract = "There are two dominant and contrasting classes of origin of life scenarios: those predicting that life emerged in submarine hydrothermal systems, where chemical disequilibrium can provide an energy source for nascent life; and those predicting that life emerged within subaerial environments, where UV catalysis of reactions may occur to form the building blocks of life. Here, we describe a prebiotically plausible environment that draws on the strengths of both scenarios: surface hydrothermal vents. We show how key feedstock molecules for prebiotic chemistry can be produced in abundance in shallow and surficial hydrothermal systems. We calculate the chemistry of volcanic gases feeding these vents over a range of pressures and basalt C/N/O contents. If ultra-reducing carbon-rich nitrogen-rich gases interact with subsurface water at a volcanic vent they result in 10 - 3 ⁻ 1 M concentrations of diacetylene (C₄H₂), acetylene (C₂H₂), cyanoacetylene (HC₃N), hydrogen cyanide (HCN), bisulfite (likely in the form of salts containing HSO₃ -), hydrogen sulfide (HS -) and soluble iron in vent water. One key feedstock molecule, cyanamide (CH₂N₂), is not formed in significant quantities within this scenario, suggesting that it may need to be delivered exogenously, or formed from hydrogen cyanide either via organometallic compounds, or by some as yet-unknown chemical synthesis. Given the likely ubiquity of surface hydrothermal vents on young, hot, terrestrial planets, these results identify a prebiotically plausible local geochemical environment, which is also amenable to future lab-based simulation.",
    url = "https://doi.org/10.3390/life9010012",
    doi = "10.3390/life9010012",
    openalex = "W2913129161",
    references = "doi103390life8030035"
}

Abiotic formation of n-alkane hydrocarbons has been postulated to occur within Earth's crust. Apparent evidence was primarily based on uncommon carbon and hydrogen isotope distribution patterns that set methane and its higher chain homologues apart from biotic isotopic compositions associated with microbial production and closed system thermal degradation of organic matter. Here, we present the first global investigation of the carbon and hydrogen isotopic compositions of n-alkanes in volcanic-hydrothermal fluids hosted by basaltic, andesitic, trachytic and rhyolitic rocks. We show that the bulk isotopic compositions of these gases follow trends that are characteristic of high temperature, open system degradation of organic matter. In sediment-free systems, organic matter is supplied by surface waters (seawater, meteoric water) circulating through the reservoir rocks. Our data set strongly implies that thermal degradation of organic matter is able to satisfy isotopic criteria previously classified as being indicative of abiogenesis. Further considering the ubiquitous presence of surface waters in Earth's crust, abiotic hydrocarbon occurrences might have been significantly overestimated.

@article{doi107185geochemlet1920,
    author = "Fiebig, Jens and Stefánsson, Andri and Ricci, Andrea and Tassi, Franco and Viveiros, Fátima and Silva, Catarina and Lopez, T. M. and Schreiber, Charlotte W. and Hofmann, Sven and Mountain, Bruce W.",
    title = "Abiogenesis not required to explain the origin of volcanic-hydrothermal hydrocarbons",
    year = "2019",
    journal = "Geochemical Perspectives Letters",
    abstract = "Abiotic formation of n-alkane hydrocarbons has been postulated to occur within Earth's crust. Apparent evidence was primarily based on uncommon carbon and hydrogen isotope distribution patterns that set methane and its higher chain homologues apart from biotic isotopic compositions associated with microbial production and closed system thermal degradation of organic matter. Here, we present the first global investigation of the carbon and hydrogen isotopic compositions of n-alkanes in volcanic-hydrothermal fluids hosted by basaltic, andesitic, trachytic and rhyolitic rocks. We show that the bulk isotopic compositions of these gases follow trends that are characteristic of high temperature, open system degradation of organic matter. In sediment-free systems, organic matter is supplied by surface waters (seawater, meteoric water) circulating through the reservoir rocks. Our data set strongly implies that thermal degradation of organic matter is able to satisfy isotopic criteria previously classified as being indicative of abiogenesis. Further considering the ubiquitous presence of surface waters in Earth's crust, abiotic hydrocarbon occurrences might have been significantly overestimated.",
    url = "https://doi.org/10.7185/geochemlet.1920",
    doi = "10.7185/geochemlet.1920",
    openalex = "W2964744142",
    references = "doi1010160009254188901015, doi1010160031920176900820, doi101016s0009254199000832, doi101016s0009254199000923, doi101016s001670370000377x, doi101016s096098220900431x, doi1010292001gb001807, doi10102992jc01511, doi101073pnas1004933107, doi101098rstb20061840"
}

Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the "error threshold," which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.

@article{doi101016jisci2020101756,
    author = "Jeancolas, Cyrille and Malaterre, Christophe and Nghe, Philippe",
    title = "Thresholds in Origin of Life Scenarios",
    year = "2020",
    journal = "iScience",
    abstract = {Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the "error threshold," which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.},
    url = "https://doi.org/10.1016/j.isci.2020.101756",
    doi = "10.1016/j.isci.2020.101756",
    openalex = "W3096560280",
    references = "doi101038nmeth2893, doi101098rsta20160346, doi103390life10030020"
}

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"
}

The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcanic arc) provides windows on subduction processes. Here, we present (1) the first observation of an extensive exposure of an undeformed Cretaceous seamount currently being subducted at the Mariana Trench inner slope; (2) vertical deformation of the forearc region related to subduction of Pacific Plate seamounts and thickened crust; (3) recovered Ocean Drilling Program and International Ocean Discovery Program cores of serpentinite mudflows that confirm exhumation of various Pacific Plate lithologies, including subducted reef limestone; (4) petrologic, geochemical and paleontological data from the cores that show that Pacific Plate seamount exhumation covers greater spatial and temporal extents; (5) the inference that microbial communities associated with serpentinite mud volcanism may also be exhumed from the subducted plate seafloor and/or seamounts; and (6) the implications for effects of these processes with regard to evolution of life. This article is part of a discussion meeting issue 'Serpentine in the Earth system'.

@article{doi101098rsta20180425,
    author = "Fryer, P. and Wheat, C.G. and Williams, Trevor and Kelley, Christopher and Johnson, K. and Ryan, Jeffrey G. and Kurz, Walter and Shervais, John W. and Albers, E. and Bekins, B. and Debret, B.P.R. and Deng, J. and Dong, Y. and Eickenbusch, P. and Frery, E.A. and Ichiyama, Yuji and Johnston, R.M. and Kevorkian, R.T. and Magalhães, V. and Mantovanelli, S.S. and Menapace, W. and Menzies, C.D. and Michibayashi, Katsuyoshi and Moyer, C.L. and Mullane, K.K. and Park, Jung‐Woo and Price, R.E. and Sissmann, O.J. and Suzuki, Shino and Takai, Ken and Walter, B. and Zhang, Rui and Amon, Diva J. and Glickson, D. and Pomponi, Shirley A.",
    title = "Mariana serpentinite mud volcanism exhumes subducted seamount materials: implications for the origin of life",
    year = "2020",
    journal = "Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences",
    abstract = "The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcanic arc) provides windows on subduction processes. Here, we present (1) the first observation of an extensive exposure of an undeformed Cretaceous seamount currently being subducted at the Mariana Trench inner slope; (2) vertical deformation of the forearc region related to subduction of Pacific Plate seamounts and thickened crust; (3) recovered Ocean Drilling Program and International Ocean Discovery Program cores of serpentinite mudflows that confirm exhumation of various Pacific Plate lithologies, including subducted reef limestone; (4) petrologic, geochemical and paleontological data from the cores that show that Pacific Plate seamount exhumation covers greater spatial and temporal extents; (5) the inference that microbial communities associated with serpentinite mud volcanism may also be exhumed from the subducted plate seafloor and/or seamounts; and (6) the implications for effects of these processes with regard to evolution of life. This article is part of a discussion meeting issue 'Serpentine in the Earth system'.",
    url = "https://doi.org/10.1098/rsta.2018.0425",
    doi = "10.1098/rsta.2018.0425",
    openalex = "W2998710986",
    references = "doi101098rsta20180421"
}

Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, have the potential to show us new fundamental science to explore, quantify, and understand nonequilibrium physicochemical systems, and shed light on the conditions for life's emergence. The physics and chemistry of these phenomena, due to the assembly of material architectures under a flux of ions, and their exploitation in applications, have recently been termed chemobrionics. Advances in understanding in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in complex systems and nonlinear and materials sciences, giving rise to this new synergistic discipline of chemobrionics.

@article{doi101162artla00323,
    author = "Cardoso, Silvana S. S. and Cartwright, Julyan H. E. and Čejková, Jitka and Cronin, Leroy and Wit, A. De and Giannerini, Simone and Horváth, Dezső and Rodrigues‬, Alírio E. and Russell, Michael J. and Sainz‐Díaz, C. Ignacio and Tóth, Ágota",
    title = "Chemobrionics: From Self-Assembled Material Architectures to the Origin of Life",
    year = "2020",
    journal = "Artificial Life",
    abstract = "Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, have the potential to show us new fundamental science to explore, quantify, and understand nonequilibrium physicochemical systems, and shed light on the conditions for life's emergence. The physics and chemistry of these phenomena, due to the assembly of material architectures under a flux of ions, and their exploitation in applications, have recently been termed chemobrionics. Advances in understanding in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in complex systems and nonlinear and materials sciences, giving rise to this new synergistic discipline of chemobrionics.",
    url = "https://doi.org/10.1162/artl\_a\_00323",
    doi = "10.1162/artl\_a\_00323",
    openalex = "W3044486488",
    references = "cartwright2019the, doi101007s1121401906248"
}

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.

@article{doi103390life10030020,
    author = "Preiner, Martina and Asche, Silke and Becker, Sidney and Betts, Holly C. and Boniface, Adrien and Camprubí, Eloi and Chandru, Kuhan and Erastova, Valentina and Garg, Sriram G. and Khawaja, Nozair and Kostyrka, Gladys and Machné, Rainer and Moggioli, Giacomo and Muchowska, Kamila B. and Neukirchen, Sinje and Peter, Benedikt and Pichlhöfer, Edith and Radványi, Ádám and Rossetto, Daniele and Salditt, Annalena and Schmelling, Nicolas and Sousa, Filipa L. and Tria, Fernando D. K. and Vörös, Dániel and Xavier, Joana C.",
    title = "The Future of Origin of Life Research: Bridging Decades-Old Divisions",
    year = "2020",
    journal = "Life",
    abstract = "Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.",
    url = "https://doi.org/10.3390/life10030020",
    doi = "10.3390/life10030020",
    openalex = "W3007934451",
    references = "branscomb2018frankenstein, doi101002bies201700179, doi101002bies201700182, doi101007bf00623322, doi101007s1108401909580x, doi1010160092867482904147, doi1010160092867483901174, doi101016jchembiol201303012, doi101016jgsf201707007, doi101038319618a0, doi101038nrmicro1931, doi101038nrmicro1991, doi101038s4158601914364, doi101093nargkw1092, doi101126science1173046528, doi101126science1303370245, doi101126science13434891501, doi101126scienceaax2747, doi1020944preprints2018060035v1, doi1020944preprints2018060035v2, doi103390life5021239"
}

The question of where life originated has been contentious for a very long time. Scientists have invoked many environments to address this question. Often, we find ourselves beholden to a location, especially if we think life originated once and then evolved into the myriad forms we now know today. In this brief commentary, we wish to lay out the following understanding: hydrothermal environments are energetically robust locations for the origins and early evolution of life as we know it. Two environments typify hydrothermal conditions, hydrothermal fields on dry land and submarine hydrothermal vents. If life originated only once, then we must choose between these two environments; however, there is no reason to assume life emerged only once. We conclude with the idea that rather than having an "either or" mind set about the origin of life a "yes and" mind set might be a better paradigm with which to problem solve within this field. Finally, we shall discuss further research with regards to both environments.

@article{doi103390life10040036,
    author = "Omran, Arthur and Pasek, Matthew A.",
    title = "A Constructive Way to Think about Different Hydrothermal Environments for the Origins of Life",
    year = "2020",
    journal = "Life",
    abstract = {The question of where life originated has been contentious for a very long time. Scientists have invoked many environments to address this question. Often, we find ourselves beholden to a location, especially if we think life originated once and then evolved into the myriad forms we now know today. In this brief commentary, we wish to lay out the following understanding: hydrothermal environments are energetically robust locations for the origins and early evolution of life as we know it. Two environments typify hydrothermal conditions, hydrothermal fields on dry land and submarine hydrothermal vents. If life originated only once, then we must choose between these two environments; however, there is no reason to assume life emerged only once. We conclude with the idea that rather than having an "either or" mind set about the origin of life a "yes and" mind set might be a better paradigm with which to problem solve within this field. Finally, we shall discuss further research with regards to both environments.},
    url = "https://doi.org/10.3390/life10040036",
    doi = "10.3390/life10040036",
    openalex = "W3015340286",
    references = "cartwright2019the, doi103390life10030020"
}

@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 field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.

@article{doi101089ast20210079,
    author = "Barge, Laura M. and Rodriguez, Laura E. and Weber, Jessica M. and Theiling, Bethany",
    title = "Determining the “Biosignature Threshold” for Life Detection on Biotic, Abiotic, or Prebiotic Worlds",
    year = "2021",
    journal = "Astrobiology",
    abstract = {The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.},
    url = "https://doi.org/10.1089/ast.2021.0079",
    doi = "10.1089/ast.2021.0079",
    openalex = "W4200321682",
    references = "doi101038216029a0, doi103390life10040042"
}

The non-equilibrium thermodynamics and the photochemical reaction mechanisms are described which may have been involved in the dissipative structuring, proliferation and complexation of the fundamental molecules of life from simpler and more common precursors under the UVC photon flux prevalent at the Earth's surface at the origin of life. Dissipative structuring of the fundamental molecules is evidenced by their strong and broad wavelength absorption bands in the UVC and rapid radiationless deexcitation. Proliferation arises from the auto- and cross-catalytic nature of the intermediate products. Inherent non-linearity gives rise to numerous stationary states permitting the system to evolve, on amplification of a fluctuation, towards concentration profiles providing generally greater photon dissipation through a thermodynamic selection of dissipative efficacy. An example is given of photochemical dissipative abiogenesis of adenine from the precursor HCN in water solvent within a fatty acid vesicle floating on a hot ocean surface and driven far from equilibrium by the incident UVC light. The kinetic equations for the photochemical reactions with diffusion are resolved under different environmental conditions and the results analyzed within the framework of non-linear Classical Irreversible Thermodynamic theory.

@article{doi103390e23020217,
    author = "Michaelian, Karo",
    title = "The Dissipative Photochemical Origin of Life: UVC Abiogenesis of Adenine",
    year = "2021",
    journal = "Entropy",
    abstract = "The non-equilibrium thermodynamics and the photochemical reaction mechanisms are described which may have been involved in the dissipative structuring, proliferation and complexation of the fundamental molecules of life from simpler and more common precursors under the UVC photon flux prevalent at the Earth's surface at the origin of life. Dissipative structuring of the fundamental molecules is evidenced by their strong and broad wavelength absorption bands in the UVC and rapid radiationless deexcitation. Proliferation arises from the auto- and cross-catalytic nature of the intermediate products. Inherent non-linearity gives rise to numerous stationary states permitting the system to evolve, on amplification of a fluctuation, towards concentration profiles providing generally greater photon dissipation through a thermodynamic selection of dissipative efficacy. An example is given of photochemical dissipative abiogenesis of adenine from the precursor HCN in water solvent within a fatty acid vesicle floating on a hot ocean surface and driven far from equilibrium by the incident UVC light. The kinetic equations for the photochemical reactions with diffusion are resolved under different environmental conditions and the results analyzed within the framework of non-linear Classical Irreversible Thermodynamic theory.",
    url = "https://doi.org/10.3390/e23020217",
    doi = "10.3390/e23020217",
    openalex = "W3113314209",
    references = "doi101002andp19053220806, doi10108800344885291306, doi101098rstb19520012, doi101103physrev37405, doi101103physrev382265, doi101103physrev8334, doi10111911987158, doi101126science1173046528, doi10114912425756, openalexw1556913189"
}

Publications related to the origin of life are mostly products of laboratory research and have the tacit assumption that the same reactions would have been possible on the early Earth some 4 billion years ago. Can this assumption be tested? We cannot go back in time, but we are able to venture out of the laboratory and perform experiments in natural conditions that are presumably analogous to the prebiotic environment. This brief review describes initial attempts to undertake such studies and some of the lessons we have learned.

@article{doi103390life11020134,
    author = "Deamer, David W.",
    title = "Where Did Life Begin? Testing Ideas in Prebiotic Analogue Conditions",
    year = "2021",
    journal = "Life",
    abstract = "Publications related to the origin of life are mostly products of laboratory research and have the tacit assumption that the same reactions would have been possible on the early Earth some 4 billion years ago. Can this assumption be tested? We cannot go back in time, but we are able to venture out of the laboratory and perform experiments in natural conditions that are presumably analogous to the prebiotic environment. This brief review describes initial attempts to undertake such studies and some of the lessons we have learned.",
    url = "https://doi.org/10.3390/life11020134",
    doi = "10.3390/life11020134",
    openalex = "W3128786289",
    references = "doi103390life10110291"
}

The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.

@article{doi103390life11050429,
    author = "Russell, Michael J.",
    title = "The “Water Problem”(sic), the Illusory Pond and Life’s Submarine Emergence—A Review",
    year = "2021",
    journal = "Life",
    abstract = {The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.},
    url = "https://doi.org/10.3390/life11050429",
    doi = "10.3390/life11050429",
    openalex = "W3163572428",
    references = "doi101002j146020751982tb01276x, doi101007s0041000500258, doi101016096800049090281f, doi101021cr0503658, doi10103835084000, doi101038384055a0, doi101038nature08013, doi101038s41467018077710, doi101073pnas9083334, doi101126science1102556, doi103390life10110291"
}

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

@article{doi103390life11070690,
    author = "Brunk, Clifford F. and Marshall, Charles R.",
    title = "‘Whole Organism’, Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life",
    year = "2021",
    journal = "Life",
    abstract = "While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.",
    url = "https://doi.org/10.3390/life11070690",
    doi = "10.3390/life11070690",
    openalex = "W3178442375",
    references = "doi103390life11050429"
}

Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.

@article{doi103390life11080777,
    author = "Altair, Thiago and Borges, Luiz G. F. and Galante, Douglas and Varela, Hamilton",
    title = "Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents",
    year = "2021",
    journal = "Life",
    abstract = "Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (\textasciitilde 4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.",
    url = "https://doi.org/10.3390/life11080777",
    doi = "10.3390/life11080777",
    openalex = "W3193123880",
    references = "baltscheffsky1981stepwise, branscomb2018frankenstein, doi101002bies201700179, doi101002bies201700182, doi1010160020711x94901198, doi101021cr0503658, doi101021cr2004844, doi101038191144a0, doi10103835084000, doi101038nrmicro1991, doi101039c3sc50205h, doi101126science1102556, doi101126science1303370245, doi101128mr5244524841988, doi103390life10110291, doi103390life11050429, doi103390life8040046, fox1995thermal"
}

"Prebiotic soup" often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both "assembled" mixtures, which are made by mixing reagent grade chemicals, and "synthesized" mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were "tamed" during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures.

@article{doi103390life11111221,
    author = "Vincent, Lena and Colón‐Santos, Stephanie and Cleaves, Henderson James and Baum, David and Maurer, Sarah",
    title = "The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses",
    year = "2021",
    journal = "Life",
    abstract = {"Prebiotic soup" often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both "assembled" mixtures, which are made by mixing reagent grade chemicals, and "synthesized" mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were "tamed" during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures.},
    url = "https://doi.org/10.3390/life11111221",
    doi = "10.3390/life11111221",
    openalex = "W3212542712",
    references = "doi103390life10030020"
}

If life developed in hydrothermal vents, it would have been within mineral membranes. The first proto-cells must have evolved to manipulate the mineral membranes that formed their compartments in order to control their metabolism. There must have occurred a biological takeover of the self-assembled mineral structures of the vents, with the incorporation of proto-biological molecules within the mineral membranes to alter their properties for life's purposes. Here, we study a laboratory analogue of this process: chemical-garden precipitation of the amino acids arginine and tryptophan with the metal salt iron chloride and sodium silicate. We produced these chemical gardens using different methodologies in order to determine the dependence of the morphology and chemistry on the growth conditions, as well as the effect of the amino acids on the formation of the iron-silicate chemical garden. We compared the effects of having amino acids initially within the forming chemical garden, corresponding to the internal zones of hydrothermal vents, or else outside, corresponding to the surrounding ocean. The characterization of the formed chemical gardens using X-ray diffraction, Fourier transform infrared spectroscopy, elemental analysis, and scanning electron microscopy demonstrates the presence of amino acids in these structures. The growth method in which the amino acid is initially in the tablet with the iron salt is that which generated chemical gardens with more amino acids in their structures.

@article{doi101021acslangmuir2c01345,
    author = "Borrego‐Sánchez, Ana and Gutiérrez‐Ariza, Carlos and Sainz‐Díaz, C. Ignacio and Cartwright, Julyan H. E.",
    title = "The Effect of the Presence of Amino Acids on the Precipitation of Inorganic Chemical-Garden Membranes: Biomineralization at the Origin of Life",
    year = "2022",
    journal = "Langmuir",
    abstract = "If life developed in hydrothermal vents, it would have been within mineral membranes. The first proto-cells must have evolved to manipulate the mineral membranes that formed their compartments in order to control their metabolism. There must have occurred a biological takeover of the self-assembled mineral structures of the vents, with the incorporation of proto-biological molecules within the mineral membranes to alter their properties for life's purposes. Here, we study a laboratory analogue of this process: chemical-garden precipitation of the amino acids arginine and tryptophan with the metal salt iron chloride and sodium silicate. We produced these chemical gardens using different methodologies in order to determine the dependence of the morphology and chemistry on the growth conditions, as well as the effect of the amino acids on the formation of the iron-silicate chemical garden. We compared the effects of having amino acids initially within the forming chemical garden, corresponding to the internal zones of hydrothermal vents, or else outside, corresponding to the surrounding ocean. The characterization of the formed chemical gardens using X-ray diffraction, Fourier transform infrared spectroscopy, elemental analysis, and scanning electron microscopy demonstrates the presence of amino acids in these structures. The growth method in which the amino acid is initially in the tablet with the iron salt is that which generated chemical gardens with more amino acids in their structures.",
    url = "https://doi.org/10.1021/acs.langmuir.2c01345",
    doi = "10.1021/acs.langmuir.2c01345",
    openalex = "W4292314302",
    references = "cartwright2019the"
}

@article{doi101038s41561022010671,
    author = "Barge, Laura M. and Price, R.E.",
    title = "Diverse geochemical conditions for prebiotic chemistry in shallow-sea alkaline hydrothermal vents",
    year = "2022",
    journal = "Nature Geoscience",
    url = "https://doi.org/10.1038/s41561-022-01067-1",
    doi = "10.1038/s41561-022-01067-1",
    openalex = "W4309760581",
    references = "doi103390life11050429"
}

Abstract Iron (II) sulfide minerals have gained attention in the last decades due to their relevance in hypotheses for the emergence of life on the early Earth around 4 billion years ago. In the submarine vent theory, it has been proposed that those minerals, especially mackinawite, had a key role in prebiotic processes. Those are estimated to be present in a natural electrochemical setting, analogous to a chemiosmotic one, formed in the interface between the early ocean and the interior of the alkaline hydrothermal systems, the early vent-ocean interface. To evaluate this and other hypotheses, voltammetric studies were performed to better understand the electrochemical behavior of minerals under conditions analogous to the vent-ocean interface. The preliminary results presented here indicate that, in the potential range estimated to exist in that interface, mackinawite can transition to other mineral phases and may posibly coexist with other minerals, resulting from its oxidation. This can create a local chemical diversity. In addition, it has been tested a protocol for Ni incorporation in mackinawite structure, resulting in a surface that showed an interesting behavior in the presence of CO 2, although definitive experiments showed necessary for a deeper comprehension of that behavior. Overall, the results are consistent with previous results on electrocatalytical properties of Fe-Ni-S materials for CO 2 reduction, and also could lead to the emergence of a protometabolism on early Earth.

@article{doi10108826331357ac79e7,
    author = "Altair, Thiago and Galante, Douglas and Varela, Hamilton",
    title = "Voltammetric investigation on iron-(nickel-)sulfur surface under conditions for the emergence of life",
    year = "2022",
    journal = "IOP SciNotes",
    abstract = "Abstract Iron (II) sulfide minerals have gained attention in the last decades due to their relevance in hypotheses for the emergence of life on the early Earth around 4 billion years ago. In the submarine vent theory, it has been proposed that those minerals, especially mackinawite, had a key role in prebiotic processes. Those are estimated to be present in a natural electrochemical setting, analogous to a chemiosmotic one, formed in the interface between the early ocean and the interior of the alkaline hydrothermal systems, the early vent-ocean interface. To evaluate this and other hypotheses, voltammetric studies were performed to better understand the electrochemical behavior of minerals under conditions analogous to the vent-ocean interface. The preliminary results presented here indicate that, in the potential range estimated to exist in that interface, mackinawite can transition to other mineral phases and may posibly coexist with other minerals, resulting from its oxidation. This can create a local chemical diversity. In addition, it has been tested a protocol for Ni incorporation in mackinawite structure, resulting in a surface that showed an interesting behavior in the presence of CO 2, although definitive experiments showed necessary for a deeper comprehension of that behavior. Overall, the results are consistent with previous results on electrocatalytical properties of Fe-Ni-S materials for CO 2 reduction, and also could lead to the emergence of a protometabolism on early Earth.",
    url = "https://doi.org/10.1088/2633-1357/ac79e7",
    doi = "10.1088/2633-1357/ac79e7",
    openalex = "W4283068526",
    references = "doi103390life11080777"
}

The concept of habitability is now widely used to describe zones in a solar system in which planets with liquid water can sustain life. Because habitability does not explicitly incorporate the origin of life, this article proposes a new word-urability-which refers to the conditions that allow life to begin. The utility of the word is tested by applying it to combinations of multiple geophysical and geochemical factors that support plausible localized zones that are conducive to the chemical reactions and molecular assembly processes required for the origin of life. The concept of urable worlds, planetary bodies that can sustain an arising of life, is considered for bodies in our own solar system and exoplanets beyond.

@article{doi101089ast20210173,
    author = "Deamer, David W. and Cary, Francesca and Damer, Bruce",
    title = "Urability: A Property of Planetary Bodies That Can Support an Origin of Life",
    year = "2022",
    journal = "Astrobiology",
    abstract = "The concept of habitability is now widely used to describe zones in a solar system in which planets with liquid water can sustain life. Because habitability does not explicitly incorporate the origin of life, this article proposes a new word-urability-which refers to the conditions that allow life to begin. The utility of the word is tested by applying it to combinations of multiple geophysical and geochemical factors that support plausible localized zones that are conducive to the chemical reactions and molecular assembly processes required for the origin of life. The concept of urable worlds, planetary bodies that can sustain an arising of life, is considered for bodies in our own solar system and exoplanets beyond.",
    url = "https://doi.org/10.1089/ast.2021.0173",
    doi = "10.1089/ast.2021.0173",
    openalex = "W4282915451",
    references = "doi103390life11050429"
}

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"
}

Adenosine triphosphate (ATP) may be the most important biological small molecule. Since it was discovered in 1929, ATP has been regarded as life's energy reservoir. However, this compound means more to life. Its legend starts at the dawn of life and lasts to this day. ATP must be the basic component of ancient ribozymes and may facilitate the origin of structured proteins. In the existing organisms, ATP continues to construct ribonucleic acid (RNA) and work as a protein cofactor. ATP also functions as a biological hydrotrope, which may keep macromolecules soluble in the primitive environment and can regulate phase separation in modern cells. These functions are involved in the pathogenesis of aging-related diseases and breast cancer, providing clues to discovering anti-aging agents and precision medicine tactics for breast cancer.

@article{doi103390metabo12050461,
    author = "Chu, Xin‐Yi and Xu, Yuanyuan and Tong, Xinyu and Wang, Gang and Zhang, Hongyu",
    title = "The Legend of ATP: From Origin of Life to Precision Medicine",
    year = "2022",
    journal = "Metabolites",
    abstract = "Adenosine triphosphate (ATP) may be the most important biological small molecule. Since it was discovered in 1929, ATP has been regarded as life's energy reservoir. However, this compound means more to life. Its legend starts at the dawn of life and lasts to this day. ATP must be the basic component of ancient ribozymes and may facilitate the origin of structured proteins. In the existing organisms, ATP continues to construct ribonucleic acid (RNA) and work as a protein cofactor. ATP also functions as a biological hydrotrope, which may keep macromolecules soluble in the primitive environment and can regulate phase separation in modern cells. These functions are involved in the pathogenesis of aging-related diseases and breast cancer, providing clues to discovering anti-aging agents and precision medicine tactics for breast cancer.",
    url = "https://doi.org/10.3390/metabo12050461",
    doi = "10.3390/metabo12050461",
    openalex = "W4280649924",
    references = "doi103390life10030020"
}

The construction of hypothetical environments to produce organic molecules such as metabolic intermediates or amino acids is the subject of ongoing research into the emergence of life. Experiments specifically focused on an anabolic approach typically rely on a mineral catalyst to facilitate the supply of organics that may have produced prebiotic building blocks for life. Alternatively to a true catalytic system, a mineral could be sacrificially oxidized in the production of organics, necessitating the emergent 'life' to turn to virgin materials for each iteration of metabolic processes. The aim of this perspective is to view the current 'metabolism-first' literature through the lens of materials chemistry to evaluate the need for higher catalytic activity and materials analyses. While many elegant studies have detailed the production of chemical building blocks under geologically plausible and biologically relevant conditions, few appear to do so with sub-stoichiometric amounts of metals or minerals. Moving toward sub-stoichiometric metals with rigorous materials analyses is necessary to demonstrate the viability of an elusive cornerstone of the 'metabolism-first' hypotheses: catalysis. We emphasize that future work should aim to demonstrate decreased catalyst loading, increased productivity, and/or rigorous materials analyses for evidence of true catalysis.

@article{doi101002chem202301447,
    author = "de Graaf, Ruvan and Decker, Yannick De and Sojo, Víctor and Hudson, Reuben",
    title = "Quantifying Catalysis at the Origin of Life**",
    year = "2023",
    journal = "Chemistry - A European Journal",
    abstract = "The construction of hypothetical environments to produce organic molecules such as metabolic intermediates or amino acids is the subject of ongoing research into the emergence of life. Experiments specifically focused on an anabolic approach typically rely on a mineral catalyst to facilitate the supply of organics that may have produced prebiotic building blocks for life. Alternatively to a true catalytic system, a mineral could be sacrificially oxidized in the production of organics, necessitating the emergent 'life' to turn to virgin materials for each iteration of metabolic processes. The aim of this perspective is to view the current 'metabolism-first' literature through the lens of materials chemistry to evaluate the need for higher catalytic activity and materials analyses. While many elegant studies have detailed the production of chemical building blocks under geologically plausible and biologically relevant conditions, few appear to do so with sub-stoichiometric amounts of metals or minerals. Moving toward sub-stoichiometric metals with rigorous materials analyses is necessary to demonstrate the viability of an elusive cornerstone of the 'metabolism-first' hypotheses: catalysis. We emphasize that future work should aim to demonstrate decreased catalyst loading, increased productivity, and/or rigorous materials analyses for evidence of true catalysis.",
    url = "https://doi.org/10.1002/chem.202301447",
    doi = "10.1002/chem.202301447",
    openalex = "W4385799227",
    references = "doi103390life10030020, doi103390life8040046"
}

@article{doi101016jbiosystems2023104927,
    author = "Fields, Chris and Levin, Michael",
    title = "Regulative development as a model for origin of life and artificial life studies",
    year = "2023",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2023.104927",
    doi = "10.1016/j.biosystems.2023.104927",
    openalex = "W4377101719",
    references = "doi103390life10040042"
}

Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.

@article{doi101126sciadvadi1884,
    author = "Weingart, Maximilian and Chen, Siyu and Donat, Clara and Helmbrecht, Vanessa and Orsi, William D. and Braun, Dieter and Alim, Karen",
    title = "Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation",
    year = "2023",
    journal = "Science Advances",
    abstract = "Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.",
    url = "https://doi.org/10.1126/sciadv.adi1884",
    doi = "10.1126/sciadv.adi1884",
    openalex = "W4387164918",
    references = "doi101016jearscirev2021103910, 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"
}

The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.

@article{doi103389fspas20221095701,
    author = "Westall, Francès and Brack, André and Fairén, Alberto González and Schulte, M.",
    title = "Setting the geological scene for the origin of life and continuing open questions about its emergence",
    year = "2023",
    journal = "Frontiers in Astronomy and Space Sciences",
    abstract = "The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.",
    url = "https://doi.org/10.3389/fspas.2022.1095701",
    doi = "10.3389/fspas.2022.1095701",
    openalex = "W4313560149",
    references = "doi101007s1121401906248, doi101016jprecamres201804007"
}

Abstract The origin of life (OoL) has always been a mysterious and challenging topic that puzzles human beings. Clay minerals have unique properties and wide distribution in early Earth environments. They can not only adsorb biological small molecules to catalyze their polymerization, but play an active role in the formation and evolution of protocells. In this review, the research progress on the interactions of clay minerals with biomolecules and protocells complex structures in the field of the OoL based on chemical evolution theory is summarized. The types, structures and properties of clay minerals, biological molecules and protocell models related to the OoL are introduced in detail. The mechanism of interaction between clay minerals and biological molecules, the construction of protocells and the role of clay minerals in the formation, structure and stability of protocells are systematically described. Finally, the future research priorities and challenges in the field of OoL based on clay minerals, biomolecules and protocells are discussed. It is aspired that this review can further advance the exploration of the OoL from a new perspective, and can also bring some interesting findings and ideas to the interdisciplinary research of materials, biology, chemistry and other related disciplines.Clay minerals have a variety of interactions with small biomolecules, which can be used as structural and functional templates to promote the organic synthesis of biomolecules and the formation and evolution of protocells, playing a non‐negligible role in the field of the OoL.

@article{doi101002adfm202406210,
    author = "Yan, Ying and Yang, Huaming",
    title = "Interactions of Clay Minerals with Biomolecules and Protocells Complex Structures in the Origin of Life: A Review",
    year = "2024",
    journal = "Advanced Functional Materials",
    abstract = "Abstract The origin of life (OoL) has always been a mysterious and challenging topic that puzzles human beings. Clay minerals have unique properties and wide distribution in early Earth environments. They can not only adsorb biological small molecules to catalyze their polymerization, but play an active role in the formation and evolution of protocells. In this review, the research progress on the interactions of clay minerals with biomolecules and protocells complex structures in the field of the OoL based on chemical evolution theory is summarized. The types, structures and properties of clay minerals, biological molecules and protocell models related to the OoL are introduced in detail. The mechanism of interaction between clay minerals and biological molecules, the construction of protocells and the role of clay minerals in the formation, structure and stability of protocells are systematically described. Finally, the future research priorities and challenges in the field of OoL based on clay minerals, biomolecules and protocells are discussed. It is aspired that this review can further advance the exploration of the OoL from a new perspective, and can also bring some interesting findings and ideas to the interdisciplinary research of materials, biology, chemistry and other related disciplines.Clay minerals have a variety of interactions with small biomolecules, which can be used as structural and functional templates to promote the organic synthesis of biomolecules and the formation and evolution of protocells, playing a non‐negligible role in the field of the OoL.",
    url = "https://doi.org/10.1002/adfm.202406210",
    doi = "10.1002/adfm.202406210",
    openalex = "W4400869036",
    references = "doi101016jbiosystems2019104063, doi101089ast20210162"
}

@article{doi101038d41586024005444,
    author = "Lane, Nick and Xavier, Joana C.",
    title = "To unravel the origin of life, treat findings as pieces of a bigger puzzle",
    year = "2024",
    journal = "Nature",
    url = "https://doi.org/10.1038/d41586-024-00544-4",
    doi = "10.1038/d41586-024-00544-4",
    openalex = "W4392168243",
    references = "doi103390life10030020"
}

The origin of life required membrane-bound compartments to allow the separation and concentration of internal biochemistry from the external environment and establish energy-harnessing ion gradients. Long-chain amphiphilic molecules, such as fatty acids, appear strong candidates to have formed the first cell membranes although how they were first generated remains unclear. Here we show that the reaction of dissolved hydrogen and bicarbonate with the iron-rich mineral magnetite under conditions of continuous flow, alkaline pH and relatively low temperatures (90 °C) generate a range of functionalised long-chain aliphatic compounds, including mixed fatty acids up to 18 carbon atoms in length. Readily generated membrane-forming amphiphilic organic molecules in the first cellular life may have been driven by similar chemistry generated from the mixing of bicarbonate-rich water (equilibrated with a carbon dioxide-enriched atmosphere) with alkaline hydrogen-rich fluids fed by the serpentinisation of the Earth's iron-rich early crust.

@article{doi101038s43247023011964,
    author = "Purvis, Graham and Šiller, Lidija and Crosskey, Archie and Vincent, J. Bryan and Wills, Corinne and Sheriff, Jake and Xavier, Cijo M. and Telling, Jon",
    title = "RETRACTED ARTICLE: Generation of long-chain fatty acids by hydrogen-driven bicarbonate reduction in ancient alkaline hydrothermal vents",
    year = "2024",
    journal = "Communications Earth \& Environment",
    abstract = "The origin of life required membrane-bound compartments to allow the separation and concentration of internal biochemistry from the external environment and establish energy-harnessing ion gradients. Long-chain amphiphilic molecules, such as fatty acids, appear strong candidates to have formed the first cell membranes although how they were first generated remains unclear. Here we show that the reaction of dissolved hydrogen and bicarbonate with the iron-rich mineral magnetite under conditions of continuous flow, alkaline pH and relatively low temperatures (90 °C) generate a range of functionalised long-chain aliphatic compounds, including mixed fatty acids up to 18 carbon atoms in length. Readily generated membrane-forming amphiphilic organic molecules in the first cellular life may have been driven by similar chemistry generated from the mixing of bicarbonate-rich water (equilibrated with a carbon dioxide-enriched atmosphere) with alkaline hydrogen-rich fluids fed by the serpentinisation of the Earth's iron-rich early crust.",
    url = "https://doi.org/10.1038/s43247-023-01196-4",
    doi = "10.1038/s43247-023-01196-4",
    openalex = "W4390819649",
    references = "doi103390life10110291"
}

Abstract The Strytan Hydrothermal Field (SHF) in basaltic terrain in Iceland is one of the extant alkaline submarine hydrothermal vent systems favoured as analogues for where life on Earth may have begun. To test this hypothesis we analyse the composition, structure, and mineralogy of samples from hydrothermal chimneys generated at the SHF. We find that the chimney precipitates are composed of Mg-silicates including clays of the saponite-stevensite group (high Mg and Si, low Fe and Al), Ca-carbonates and Ca-sulfates. The chimneys comprise permeable structures with pores sizes down to 1 µm or less. Their complex interiors as observed with SEM (Scanning Electron Microscopy) and X-ray CT (computed tomography scanning), exhibit high internal surface areas. EDX (energy-dispersive X-ray spectroscopy) analysis reveals an increase in the Mg/Si ratio toward the chimney exteriors. Chemical garden analogue experiments produce similar Mg–silicate chimneys with porous internal structures, indicating that injection-precipitation experiments can be high-fidelity analogues for natural hydrothermal chimneys at the SHF. We conclude that SHF chimneys could have facilitated prebiotic reactions comparable to those proposed for clays and silica gels at putative Hadean to Eoarchean alkaline vents. Analysis of the fluid dynamics shows that these chimneys are intermediate in growth rate compared to faster black smokers though slower than those at Lost City. The SHF is proposed as a prebiotic alkaline vent analogue for basaltic terrains on the early Earth.

@article{doi101186s4064502300603w,
    author = "Gutiérrez‐Ariza, Carlos and Barge, Laura M. and Ding, Yang and Cardoso, Silvana S. S. and McGlynn, Shawn E. and Nakamura, Ryuhei and Giovanelli, Donato and Price, R.E. and Lee, Hye‐Eun and Huertas, F. Javier and Sainz‐Díaz, C. Ignacio and Cartwright, Julyan H. E.",
    title = "Magnesium silicate chimneys at the Strytan hydrothermal field, Iceland, as analogues for prebiotic chemistry at alkaline submarine hydrothermal vents on the early Earth",
    year = "2024",
    journal = "Progress in Earth and Planetary Science",
    abstract = "Abstract The Strytan Hydrothermal Field (SHF) in basaltic terrain in Iceland is one of the extant alkaline submarine hydrothermal vent systems favoured as analogues for where life on Earth may have begun. To test this hypothesis we analyse the composition, structure, and mineralogy of samples from hydrothermal chimneys generated at the SHF. We find that the chimney precipitates are composed of Mg-silicates including clays of the saponite-stevensite group (high Mg and Si, low Fe and Al), Ca-carbonates and Ca-sulfates. The chimneys comprise permeable structures with pores sizes down to 1 µm or less. Their complex interiors as observed with SEM (Scanning Electron Microscopy) and X-ray CT (computed tomography scanning), exhibit high internal surface areas. EDX (energy-dispersive X-ray spectroscopy) analysis reveals an increase in the Mg/Si ratio toward the chimney exteriors. Chemical garden analogue experiments produce similar Mg–silicate chimneys with porous internal structures, indicating that injection-precipitation experiments can be high-fidelity analogues for natural hydrothermal chimneys at the SHF. We conclude that SHF chimneys could have facilitated prebiotic reactions comparable to those proposed for clays and silica gels at putative Hadean to Eoarchean alkaline vents. Analysis of the fluid dynamics shows that these chimneys are intermediate in growth rate compared to faster black smokers though slower than those at Lost City. The SHF is proposed as a prebiotic alkaline vent analogue for basaltic terrains on the early Earth.",
    url = "https://doi.org/10.1186/s40645-023-00603-w",
    doi = "10.1186/s40645-023-00603-w",
    openalex = "W4392298409",
    references = "doi101016jearscirev2021103910, doi103389fmicb20231145915"
}

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.

@article{doi103390life14020175,
    author = "Schoenmakers, Ludo L. J. and Reydon, Thomas A. C. and Kirschning, Andreas",
    title = "Evolution at the Origins of Life?",
    year = "2024",
    journal = "Life",
    abstract = "The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.",
    url = "https://doi.org/10.3390/life14020175",
    doi = "10.3390/life14020175",
    openalex = "W4391224728",
    references = "doi101007s1121401906248"
}

The path from life's origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life's anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life's biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.

@article{doi103390life14020226,
    author = "Brunk, Clifford F. and Marshall, Charles R.",
    title = "Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell",
    year = "2024",
    journal = "Life",
    abstract = "The path from life's origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life's anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life's biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.",
    url = "https://doi.org/10.3390/life14020226",
    doi = "10.3390/life14020226",
    openalex = "W4391530903",
    references = "doi101073pnas2300491120"
}

Humanity’s strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin’s Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the “organic-molecules-paradigm” became increasingly difficult to ignore, culminating in Erwin Schrödinger’s 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.

@article{doi103390life14050607,
    author = "Nitschke, Wolfgang and Farr, Orion and Gaudu, Nil and Truong, Chloé and Guyot, François and Russell, Michael J. and Duval, Simon",
    title = "The Winding Road from Origin to Emergence (of Life)",
    year = "2024",
    journal = "Life",
    abstract = "Humanity’s strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin’s Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the “organic-molecules-paradigm” became increasingly difficult to ignore, culminating in Erwin Schrödinger’s 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.",
    url = "https://doi.org/10.3390/life14050607",
    doi = "10.3390/life14050607",
    openalex = "W4396805282",
    references = "branscomb2018frankenstein, doi101002bies201700179, doi101016jcell201211050, doi101038191144a0, doi101038nrmicro201810, doi101038s4146702229612x, doi101038s41467023369043, doi101098rstb20021183, doi101098rstb20061881, doi101126sciadv1600285, doi101126science1173046528, doi101126science1303370245, doi101128br4111001801977, doi101144gsjgs15430377, doi103389fmicb20231145915"
}

Chemical and geological processes on prebiotic Earth are believed to have resulted in the emergence of life through the increasing organization and functionality of organic molecules. This primer provides an overview of some key abiotic chemical and physical processes that could have contributed to life's building blocks (amino acids, nucleotides, fatty acids, and monosaccharides) becoming more ordered during the early stages in the origin of life. The processes considered include polymerization, intramolecular folding, multimolecular assembly, and chemical evolution through various selective mechanisms. Our goal is to provide an accessible, high-level synopsis of these key general concepts for a diverse audience.

@article{doi10117715311074251365943,
    author = "Edri, Rotem and Joshi, Manesh Prakash and Frenkel‐Pinter, Moran and Hud, Nicholas V. and Keating, Christine D. and Leman, Luke J.",
    title = "From Polymerization-Enabled Folding and Assembly to Chemical Evolution: Key Processes for Emergence of Functional Polymers in the Origin of Life",
    year = "2025",
    journal = "Astrobiology",
    abstract = "Chemical and geological processes on prebiotic Earth are believed to have resulted in the emergence of life through the increasing organization and functionality of organic molecules. This primer provides an overview of some key abiotic chemical and physical processes that could have contributed to life's building blocks (amino acids, nucleotides, fatty acids, and monosaccharides) becoming more ordered during the early stages in the origin of life. The processes considered include polymerization, intramolecular folding, multimolecular assembly, and chemical evolution through various selective mechanisms. Our goal is to provide an accessible, high-level synopsis of these key general concepts for a diverse audience.",
    url = "https://doi.org/10.1177/15311074251365943",
    doi = "10.1177/15311074251365943",
    openalex = "W4413970213",
    references = "doi103390life14050607"
}

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"
}