1. Cairns-Smith, A. G, 1971, The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal As an Ancestor: Toronto, University of Toronto Press, 165 p.

BibTeX
@book{cairnssmith1971the1,
    author = "Cairns-Smith, A. G",
    title = "The Life Puzzle",
    year = "1971",
    publisher = "On Crystals and Organisms and on the Possibility of a Crystal As an Ancestor: Toronto, University of Toronto Press, 165 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Cairns-Smith, A. G., 1971, The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal As an Ancestor: Toronto, University of Toronto Press, 165 p.}"
}

2. Cairns-Smith, A. G., 1971, The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal as an Ancestor: Project Muse (Johns Hopkins University).

Abstract

What is the origin of life? Molecular biology shows us one kind, but in thinking about it we must consider those generalised aspects of living organisation that are common to all conceivable forms of life. The author believes that only a combination of general biological theory and particular chemical knowledge can solve the problems of the origin and re-creation of life. This book does not fall into either the classical Haldane or Oparin schools of thought on the origin of life, but advances a thesis of its own, which, according to Professor C.H. Waddington, is one of the most important recent intellectual developments in this field.Part I considers the role of molecular biology in formulating a view of life as it exists now. Part II turns to more general aspects of the organisation of matter. In Part III the author advances his own theories on the origin of life-theories which are both revolutionary and reactionary. As he remarks, 'If my conclusions are correct it may be difficult to find the right system, but it would be easy to make a very simple organism once we have.'

BibTeX
@book{doi1031389781487589684,
    author = "Cairns-Smith, A. G.",
    title = "The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal as an Ancestor",
    year = "1971",
    booktitle = "Project Muse (Johns Hopkins University)",
    abstract = "What is the origin of life? Molecular biology shows us one kind, but in thinking about it we must consider those generalised aspects of living organisation that are common to all conceivable forms of life. The author believes that only a combination of general biological theory and particular chemical knowledge can solve the problems of the origin and re-creation of life. This book does not fall into either the classical Haldane or Oparin schools of thought on the origin of life, but advances a thesis of its own, which, according to Professor C.H. Waddington, is one of the most important recent intellectual developments in this field.Part I considers the role of molecular biology in formulating a view of life as it exists now. Part II turns to more general aspects of the organisation of matter. In Part III the author advances his own theories on the origin of life-theories which are both revolutionary and reactionary. As he remarks, 'If my conclusions are correct it may be difficult to find the right system, but it would be easy to make a very simple organism once we have.'",
    url = "https://doi.org/10.3138/9781487589684",
    doi = "10.3138/9781487589684",
    openalex = "W149028925"
}

3. Bunn, C. W., 1972, Life from Crystals: Nature.

BibTeX
@article{doi101038236239a0,
    author = "Bunn, C. W.",
    title = "Life from Crystals",
    year = "1972",
    journal = "Nature",
    url = "https://doi.org/10.1038/236239a0",
    doi = "10.1038/236239a0",
    openalex = "W165208592"
}

4. Russell, Michael J. and Hall, A. J., 1997, The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front: Journal of the Geological Society.

Abstract

Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150 degrees C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90 degrees C), iron-hearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS-, H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (delta Eh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural delta pH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.

BibTeX
@article{doi101144gsjgs15430377,
    author = "Russell, Michael J. and Hall, A. J.",
    title = "The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front",
    year = "1997",
    journal = "Journal of the Geological Society",
    abstract = "Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150 degrees C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90 degrees C), iron-hearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS-, H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (delta Eh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural delta pH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.",
    url = "https://doi.org/10.1144/gsjgs.154.3.0377",
    doi = "10.1144/gsjgs.154.3.0377",
    openalex = "W2145198797",
    references = "darwin2009the, doi10100797894015805408, doi101007bf00032643, doi101007bf01140180, doi101007bf01808177, doi1010160003986161900339, doi1010160016703789901506, doi1010160016703794902887, doi1010160020711x94901198, doi1010160076687987550236, doi1010161074552195900314, doi101016s0022283667800378, doi101038191144a0, doi101038319618a0, doi101038331612a0, doi101038336117a0, doi101038343129a0, doi101038355125a0, doi101073pnas87124576, doi101111j174966321936tb56976x, doi101126science1173046528, doi101128br4111001801977, doi101130001676061951621111ghosw20co2, doi1023073514674, fox1995thermal, openalexw1491459594, openalexw1882072473, openalexw1986779979, openalexw2139291338"
}

5. Fuchs, Georg, 2010, Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?: Annual Review of Microbiology.

Abstract

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

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

6. Schulman, Rebecca and Yurke, Bernard and Winfree, Erik, 2012, Robust self-replication of combinatorial information via crystal growth and scission: Proceedings of the National Academy of Sciences.

Abstract

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.

BibTeX
@article{doi101073pnas1117813109,
    author = "Schulman, Rebecca and Yurke, Bernard and Winfree, Erik",
    title = "Robust self-replication of combinatorial information via crystal growth and scission",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98\% of bits are copied correctly and 78\% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50\% yield, replication of longer sequences, and darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.",
    url = "https://doi.org/10.1073/pnas.1117813109",
    doi = "10.1073/pnas.1117813109",
    openalex = "W2070783600",
    references = "doi101137070680266"
}

7. 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., 2014, The Drive to Life on Wet and Icy Worlds: 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).

BibTeX
@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"
}

8. Mariscal, Carlos and Barahona, Ana and Aubert-Kato, Nathanaël and Aydınoğlu, Arsev Umur and Bartlett, Stuart and Cárdenas, Marı́a Luz and Chandru, Kuhan and Cleland, Carol E. and Cocanougher, Ben and Comfort, Nathaniel and Cornish‐Bowden, Athel and Deacon, Terrence W. and Froese, Tom and Giovannelli, Donato and Hernlund, J. W. and Hut, Piet and Kimura, Jun and Maurel, Marie-Christine and Merino, Nancy and Moreno, Álvaro and Nakagawa, Mayuko and Peretό, Juli and Virgo, Nathaniel and Witkowski, Olaf and Cleaves, Henderson James, 2019, Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report: Origins of Life and Evolution of Biospheres.

BibTeX
@article{doi101007s1108401909580x,
    author = "Mariscal, Carlos and Barahona, Ana and Aubert-Kato, Nathanaël and Aydınoğlu, Arsev Umur and Bartlett, Stuart and Cárdenas, Marı́a Luz and Chandru, Kuhan and Cleland, Carol E. and Cocanougher, Ben and Comfort, Nathaniel and Cornish‐Bowden, Athel and Deacon, Terrence W. and Froese, Tom and Giovannelli, Donato and Hernlund, J. W. and Hut, Piet and Kimura, Jun and Maurel, Marie-Christine and Merino, Nancy and Moreno, Álvaro and Nakagawa, Mayuko and Peretό, Juli and Virgo, Nathaniel and Witkowski, Olaf and Cleaves, Henderson James",
    title = "Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report",
    year = "2019",
    journal = "Origins of Life and Evolution of Biospheres",
    url = "https://doi.org/10.1007/s11084-019-09580-x",
    doi = "10.1007/s11084-019-09580-x",
    openalex = "W2967455602",
    references = "doi1010079789400989474, doi1010160020711x94901198, doi101038171737a0, doi101038scientificamerican117998, doi10106313050879, doi101103physrevlett59381, doi1023072005041, doi1031389781487589684, openalexw1916207017"
}

9. 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., 2020, The Future of Origin of Life Research: Bridging Decades-Old Divisions: 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.

BibTeX
@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"
}

10. Lei, Lei and Burton, Zachary F., 2020, Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code: Life.

Abstract

Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an ~16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to ~16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation.

BibTeX
@article{doi103390life10030021,
    author = "Lei, Lei and Burton, Zachary F.",
    title = "Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code",
    year = "2020",
    journal = "Life",
    abstract = "Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an \textasciitilde 16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to \textasciitilde 16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation.",
    url = "https://doi.org/10.3390/life10030021",
    doi = "10.3390/life10030021",
    openalex = "W3009119289",
    references = "doi101007s1108401909580x"
}

11. Colón‐Santos, Stephanie and Vázquez-Salazar, Alberto and Adams, Alyssa and Campillo-Balderas, José Alberto and Hernández-Morales, Ricardo and Jácome, Rodrigo and Muñoz‐Velasco, Israel and Rodriguez, Laura E. and Schaible, Micah J. and Schaible, George A. and Szeinbaum, Nadia and Thweatt, Jennifer L. and Trubl, Gareth, 2024, Chapter 2: What Is Life?: Astrobiology.

Abstract

The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.

BibTeX
@article{doi101089ast20210116,
    author = "Colón‐Santos, Stephanie and Vázquez-Salazar, Alberto and Adams, Alyssa and Campillo-Balderas, José Alberto and Hernández-Morales, Ricardo and Jácome, Rodrigo and Muñoz‐Velasco, Israel and Rodriguez, Laura E. and Schaible, Micah J. and Schaible, George A. and Szeinbaum, Nadia and Thweatt, Jennifer L. and Trubl, Gareth",
    title = "Chapter 2: What Is Life?",
    year = "2024",
    journal = "Astrobiology",
    abstract = {The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.},
    url = "https://doi.org/10.1089/ast.2021.0116",
    doi = "10.1089/ast.2021.0116",
    openalex = "W4392930411",
    references = "doi101007s1108401909580x"
}