Biochemistry

@misc{valleryradot1922fermentations84,
    author = "Vallery-Radot, P",
    title = "Fermentations et Gnrations dites Spontanes",
    year = "1922",
    howpublished = "Paris, Masson et Cie, v. II",
    note = "talkorigins\_source = {true}; raw\_reference = {Vallery-Radot, P., 1922, Fermentations et Gnrations dites Spontanes: Paris, Masson et Cie, v. II.}"
}

@article{cousen1924biochemistry,
    author = "Cousen, A.",
    title = "Biochemistry",
    year = "1924",
    journal = "Journal of the Chemical Society, Abstracts",
    url = "https://doi.org/10.1039/ca9242600892",
    doi = "10.1039/ca9242600892",
    pages = "i892",
    volume = "126"
}

@article{huffman1942thermal51,
    author = "Huffman, H. M",
    title = "Thermal data XV. The heats of combustion and free energies of some compounds containing the peptide bond",
    year = "1942",
    journal = "Journal of Physical Chemistry, v. 46, p. 885-891",
    note = "talkorigins\_source = {true}; raw\_reference = {Huffman, H. M., 1942, Thermal data XV. The heats of combustion and free energies of some compounds containing the peptide bond: Journal of Physical Chemistry, v. 46, p. 885-891.}"
}

@article{crossref1952biochemistry,
    title = "BIOCHEMISTRY",
    year = "1952",
    journal = "Medical Journal of Australia",
    url = "https://doi.org/10.5694/j.1326-5377.1952.tb100094.x",
    doi = "10.5694/j.1326-5377.1952.tb100094.x",
    number = "3",
    pages = "98-99",
    volume = "2"
}

@article{sanger1953amino76,
    author = "Sanger, F. and Thompson, E. O. P",
    title = "Amino acids in the glycyl chain of insulin. II Peptides from enzymic hydrolyzates",
    year = "1953",
    journal = "Biochemical Journal, v. 53, p. 366-374",
    note = "talkorigins\_source = {true}; raw\_reference = {Sanger, F., and Thompson, E. O. P., 1953, Amino acids in the glycyl chain of insulin. II Peptides from enzymic hydrolyzates: Biochemical Journal, v. 53, p. 366-374.}"
}

@misc{gamow1956problem42,
    author = "Gamow, G. and Rich, A. and Yas, M",
    title = "Problem of information transfer from nucleic acids to proteins",
    year = "1956",
    howpublished = "Advances in Biological and Medical Physics, v. 4, p. 23-68",
    note = "talkorigins\_source = {true}; raw\_reference = {Gamow, G., Rich, A., and Yas, M., 1956, Problem of information transfer from nucleic acids to proteins: Advances in Biological and Medical Physics, v. 4, p. 23-68.}"
}

@article{fox1957the9,
    author = "Fox, S. W",
    title = "The chemical problem of spontaneous generation",
    year = "1957",
    journal = "Journal of Chemical Education, v. 34, p. 472-479",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1957, The chemical problem of spontaneous generation: Journal of Chemical Education, v. 34, p. 472-479.}"
}

@misc{fox1958thermal29,
    author = "Fox, S. W. and Harada, K",
    title = "Thermal copolymerization of amino acids to a product resembling protein",
    year = "1958",
    howpublished = "Science, v. 128, p. 1214",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Harada, K., 1958, Thermal copolymerization of amino acids to a product resembling protein: Science, v. 128, p. 1214.}"
}

@article{fox1959review10,
    author = "Fox, S. W",
    title = "Review of the book The Biological Replication of Macromolecules",
    year = "1959",
    journal = "Journal of Chemical Education, v. 36, p. 706A",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1959, Review of the book The Biological Replication of Macromolecules: Journal of Chemical Education, v. 36, p. 706A.}"
}

@book{fox1962the31,
    author = "Fox, S. W. and Harada, K. and Rohlfing, D. L",
    title = "The thermal copolymerization of -amino acids, in Stahmann, M. A., ed., Polyamino Acids, Polypeptides, and Proteins",
    year = "1962",
    publisher = "Madison, Wisconsin, University of Wisconsin Press, p. 47-54",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Harada, K., and Rohlfing, D. L., 1962, The thermal copolymerization of -amino acids, in Stahmann, M. A., ed., Polyamino Acids, Polypeptides, and Proteins: Madison, Wisconsin, University of Wisconsin Press, p. 47-54.}"
}

@article{jb1962biochemistry,
    author = "J B, \\&NA;",
    title = "Biochemistry",
    year = "1962",
    journal = "The American Journal of the Medical Sciences",
    url = "https://doi.org/10.1097/00000441-196209000-00042",
    doi = "10.1097/00000441-196209000-00042",
    number = "3",
    pages = "396",
    volume = "244"
}

@incollection{vegotsky1962protein85,
    author = "Vegotsky, A. and Fox, S. W",
    editor = "Florkin, M. and Mason, H. S.",
    title = "Protein molecules: intraspecific and interspecific variations",
    year = "1962",
    booktitle = "Comparative Biochemistry",
    publisher = "New York, Academic Press, v. IV, p. 185-224",
    note = "talkorigins\_source = {true}; raw\_reference = {Vegotsky, A., and Fox, S. W., 1962, Protein molecules: intraspecific and interspecific variations, in Florkin, M., and Mason, H. S., eds., Comparative Biochemistry: New York, Academic Press, v. IV, p. 185-224.}"
}

@misc{fox1963abiotic41,
    author = "Fox, S. W. and Yuyama, S",
    title = "Abiotic production of primitive protein and formed microparticles",
    year = "1963",
    howpublished = "Annals of the New York Academy of Sciences, v. 108, p. 487-494",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Yuyama, S., 1963, Abiotic production of primitive protein and formed microparticles: Annals of the New York Academy of Sciences, v. 108, p. 487-494.}"
}

@article{fox1963effects40,
    author = "Fox, S. W. and Yuyama, S",
    title = "Effects of the Gram stain on microspheres from thermal polyamino acids",
    year = "1963",
    journal = "Journal of Bacteriology, v. 85, p. 279-283",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Yuyama, S., 1963, Effects of the Gram stain on microspheres from thermal polyamino acids: Journal of Bacteriology, v. 85, p. 279-283.}"
}

@misc{fox1964the34,
    author = "Fox, S. W. and Krampitz, G",
    title = "The catalytic decomposition of glucose in aqueous solution by thermal proteinoids",
    year = "1964",
    howpublished = "Nature, v. 203, p. 1362-1364",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Krampitz, G., 1964, The catalytic decomposition of glucose in aqueous solution by thermal proteinoids: Nature, v. 203, p. 1362-1364.}"
}

@misc{fox1964thermal11,
    author = "Fox, S. W",
    title = "Thermal polymerization of amino acids and production of formed microparticles on lava",
    year = "1964",
    howpublished = "Nature, v. 201, p. 336-337",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1964, Thermal polymerization of amino acids and production of formed microparticles on lava: Nature, v. 201, p. 336-337.}"
}

@book{fox1965experiments12,
    author = "Fox, S. W",
    title = "Experiments suggesting evolution to protein, in Bryson, V., and Vogel, H. J., eds., Evolving Genes and Proteins",
    year = "1965",
    publisher = "New York, Academic Press, p. 359-369",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1965, Experiments suggesting evolution to protein, in Bryson, V., and Vogel, H. J., eds., Evolving Genes and Proteins: New York, Academic Press, p. 359-369.}"
}

@book{harada1965thermal45,
    author = "Harada, K. and Fox, S. W",
    title = "Thermal polycondensation of free amino acids with polyphosphatic acid, in Fox, S. W., ed., The Origins of Prebiological Systems",
    year = "1965",
    publisher = "New York, Academic Press, p. 289-308",
    note = "talkorigins\_source = {true}; raw\_reference = {Harada, K., and Fox, S. W., 1965, Thermal polycondensation of free amino acids with polyphosphatic acid, in Fox, S. W., ed., The Origins of Prebiological Systems: New York, Academic Press, p. 289-308.}"
}

@misc{fox1966simulation32,
    author = "Fox, S. W. and Joseph, D. and McCauley, R. J. and Windsor, C. R. and Yuyama, S",
    title = "Simulation of organismic morphology and behavior by synthetic poly--amino acids, in Brown, A. H., and Florkin, M., eds., Life Sciences and Space Research",
    year = "1966",
    howpublished = "Washington, D.C., Spartan Books, v. IV, p. 111-120",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Joseph, D., McCauley, R. J., Windsor, C. R., and Yuyama, S., 1966, Simulation of organismic morphology and behavior by synthetic poly--amino acids, in Brown, A. H., and Florkin, M., eds., Life Sciences and Space Research: Washington, D.C., Spartan Books, v. IV, p. 111-120.}"
}

@misc{fox1967a36,
    author = "Fox, S. W. and McCauley, R. J. and Wood, A",
    title = "A model of primitive heterotrophic proliferation",
    year = "1967",
    howpublished = "Comparative Biochemistry and Physiology, v. 20, p. 773-778",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., McCauley, R. J., and Wood, A., 1967, A model of primitive heterotrophic proliferation: Comparative Biochemistry and Physiology, v. 20, p. 773-778.}"
}

@misc{hayakawa1967copolymerization48,
    author = "Hayakawa, T. and Windsor, C. R. and Fox, S. W",
    title = "Copolymerization of the Leuchs anhydrides of the eighteen amino acids common to protein",
    year = "1967",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 118, p. 265-272",
    note = "talkorigins\_source = {true}; raw\_reference = {Hayakawa, T., Windsor, C. R., and Fox, S. W., 1967, Copolymerization of the Leuchs anhydrides of the eighteen amino acids common to protein: Archives of Biochemistry and Biophysiology, v. 118, p. 265-272.}"
}

@misc{rohlfing1967the73,
    author = "Rohlfing, D. L",
    title = "The catalytic decarboxylation of oxaloacetic acid by thermally prepared poly--aminoacids",
    year = "1967",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 118, p. 468-474",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1967, The catalytic decarboxylation of oxaloacetic acid by thermally prepared poly--aminoacids: Archives of Biochemistry and Biophysiology, v. 118, p. 468-474.}"
}

@misc{rohlfing1967thermal72,
    author = "Rohlfing, D. L",
    title = "Thermal poly--amino acids containing low proportions of aspartic acid",
    year = "1967",
    howpublished = "Nature, v. 216, p. 657-659",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1967, Thermal poly--amino acids containing low proportions of aspartic acid: Nature, v. 216, p. 657-659.}"
}

@misc{usdin1967inhibition83,
    author = "Usdin, V. R. and Mitz, M. A. and Killos, P. J",
    title = "Inhibition and reactivation of the catalytic activity of a thermal -amino acid copolymer",
    year = "1967",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 122, p. 258-261",
    note = "talkorigins\_source = {true}; raw\_reference = {Usdin, V. R., Mitz, M. A., and Killos, P. J., 1967, Inhibition and reactivation of the catalytic activity of a thermal -amino acid copolymer: Archives of Biochemistry and Biophysiology, v. 122, p. 258-261.}"
}

@misc{fox1968melanocytestimulating39,
    author = "Fox, S. W. and Wang, C.-T",
    title = "Melanocyte-stimulating hormone activity on thermal properties of -amino acids",
    year = "1968",
    howpublished = "Science, v. 160, p. 547-548",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Wang, C.-T., 1968, Melanocyte-stimulating hormone activity on thermal properties of -amino acids: Science, v. 160, p. 547-548.}"
}

@misc{fox1968spontaneous13,
    author = "Fox, S. W",
    title = "Spontaneous generation, the origin of life, and self assembly",
    year = "1968",
    howpublished = "Current Models in Biology [Now BioSystems], v. 2, p. 235-240; Now BioSystems",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1968, Spontaneous generation, the origin of life, and self assembly: Current Models in Biology [Now BioSystems], v. 2, p. 235-240; Now BioSystems.}"
}

@misc{hardebeck1968decarboxylation46,
    author = "Hardebeck, H. G. and Krampitz, G. and Wulf, L",
    title = "Decarboxylation of pyruvic acid in aqueous solutions by thermal proteinoids",
    year = "1968",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 123, p. 72-81",
    note = "talkorigins\_source = {true}; raw\_reference = {Hardebeck, H. G., Krampitz, G., and Wulf, L., 1968, Decarboxylation of pyruvic acid in aqueous solutions by thermal proteinoids: Archives of Biochemistry and Biophysiology, v. 123, p. 72-81.}"
}

@misc{karmpitz1968aminotransferase54,
    author = "Karmpitz, G. and Baars-Diehl, S. and Haas, W. and Nakashima, T",
    title = "Aminotransferase activity of thermal polylysine",
    year = "1968",
    howpublished = "Experientia, v. 24, p. 140-142",
    note = "talkorigins\_source = {true}; raw\_reference = {Karmpitz, G., Baars-Diehl, S., Haas, W., and Nakashima, T., 1968, Aminotransferase activity of thermal polylysine: Experientia, v. 24, p. 140-142.}"
}

@misc{karmpitz1968glutaminsureoxydoreductase55,
    author = "Karmpitz, G. and Haas, W. and Baars-Diehl, S",
    title = "Glutaminsure-Oxydoreductase- Aktivitt von Polyanhydro--Aminosuren (Proteinoiden)",
    year = "1968",
    howpublished = "Naturwissenschaften, v. 55, p. 345-346",
    note = "talkorigins\_source = {true}; raw\_reference = {Karmpitz, G., Haas, W., and Baars-Diehl, S., 1968, Glutaminsure-Oxydoreductase- Aktivitt von Polyanhydro--Aminosuren (Proteinoiden): Naturwissenschaften, v. 55, p. 345-346.}"
}

@misc{oshima1968the67,
    author = "Oshima, T",
    title = "The catalytic hydrolysis of phosphate ester bonds by thermal polymers of amino acids",
    year = "1968",
    howpublished = "Archives of Biochemistry and Biophysiology, v. 126, p. 478-485",
    note = "talkorigins\_source = {true}; raw\_reference = {Oshima, T., 1968, The catalytic hydrolysis of phosphate ester bonds by thermal polymers of amino acids: Archives of Biochemistry and Biophysiology, v. 126, p. 478-485.}"
}

@misc{dayhoff1969atlas5,
    author = "Dayhoff, M. O",
    title = "Atlas of Protein Sequence and Structure",
    year = "1969",
    howpublished = "Silver Spring, Md., National Biomedical Research Foundation, v. 4",
    note = "talkorigins\_source = {true}; raw\_reference = {Dayhoff, M. O., 1969, Atlas of Protein Sequence and Structure: Silver Spring, Md., National Biomedical Research Foundation, v. 4.}"
}

@misc{fox1969membranelike35,
    author = "Fox, S. W. and McCauley, R. J. and Montgomery, P. O'B. and Fukushima, T. and Harada, K. and Windsor, C. R",
    title = "Membrane-like properties in microsystems assembled from synthetic protein-like polymer, in Snell, F., Wolken, J., Iverson, G. J., and Lam, J., eds., Physical Principles of Biological Membranes",
    year = "1969",
    howpublished = "New York, Gordon \& Breach, p. 417-430",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., McCauley, R. J., Montgomery, P. O'B., Fukushima, T., Harada, K., and Windsor, C. R., 1969, Membrane-like properties in microsystems assembled from synthetic protein-like polymer, in Snell, F., Wolken, J., Iverson, G. J., and Lam, J., eds., Physical Principles of Biological Membranes: New York, Gordon \& Breach, p. 417-430.}"
}

@misc{fox1969selfordered14,
    author = "Fox, S. W",
    title = "Self-ordered polymers and propagative cell-like systems",
    year = "1969",
    howpublished = "Naturwissenschaften, v. 56, p. 1-9",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1969, Self-ordered polymers and propagative cell-like systems: Naturwissenschaften, v. 56, p. 1-9.}"
}

@misc{rohlfing1969catalytic75,
    author = "Rohlfing, D. L. and Fox, S. W",
    title = "Catalytic activities of thermal polyanhydro--amino acids",
    year = "1969",
    howpublished = "Advances in Catalysis, v. 20, p. 373-418",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., and Fox, S. W., 1969, Catalytic activities of thermal polyanhydro--amino acids: Advances in Catalysis, v. 20, p. 373-418.}"
}

@book{chambers1970biochemical4,
    author = "Chambers, K. L",
    title = "Biochemical Coevolution",
    year = "1970",
    publisher = "Eugene, Oregon State University Press, 117 p.; 29th Biology Colloquium",
    note = "talkorigins\_source = {true}; raw\_reference = {Chambers, K. L., 1970, Biochemical Coevolution: Eugene, Oregon State University Press, 117 p.; 29th Biology Colloquium.}"
}

@misc{lehninger1970biochemistry60,
    author = "Lehninger, A. L",
    title = "Biochemistry",
    year = "1970",
    howpublished = "New York, Worth and Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Lehninger, A. L., 1970, Biochemistry: New York, Worth and Co.}"
}

@misc{hsu1971conjugation50,
    author = "Hsu, L. L. and Brooke, S. and Fox, S. W",
    title = "Conjugation of proteinoid microspheres",
    year = "1971",
    howpublished = "a model of primordial communication: Current Models in Biology [Now BioSystems], v. 4, p. 12-25",
    note = "talkorigins\_source = {true}; raw\_reference = {Hsu, L. L., Brooke, S., and Fox, S. W., 1971, Conjugation of proteinoid microspheres: a model of primordial communication: Current Models in Biology [Now BioSystems], v. 4, p. 12-25.}"
}

@misc{dayhoff1972atlas6,
    author = "Dayhoff, M. O",
    title = "Atlas of Protein Sequence and Structure",
    year = "1972",
    howpublished = "Sliver Spring, Md., National Biomedical Research Foundation, v. 5",
    note = "talkorigins\_source = {true}; raw\_reference = {Dayhoff, M. O., 1972, Atlas of Protein Sequence and Structure: Sliver Spring, Md., National Biomedical Research Foundation, v. 5.}"
}

@article{osterberg1972polyphosphate68,
    author = "Osterberg, R. and Orgel, L. E",
    title = "Polyphosphate and trimetaphosphate formation under potetially prebiotic conditions",
    year = "1972",
    journal = "Journal of Molecular Evolution, v. 1, p. 241-248",
    note = "talkorigins\_source = {true}; raw\_reference = {Osterberg, R., and Orgel, L. E., 1972, Polyphosphate and trimetaphosphate formation under potetially prebiotic conditions: Journal of Molecular Evolution, v. 1, p. 241-248.}"
}

@book{wood1972light87,
    author = "Wood, A. and Hardebeck, H. G",
    title = "Light enhanced decarboxylations by proteinoids, in Rohlfing, D. L., and Oparin, A. I., eds., Molecular Evolution",
    year = "1972",
    publisher = "New York, Plenum Press, p. 233-245",
    note = "talkorigins\_source = {true}; raw\_reference = {Wood, A., and Hardebeck, H. G., 1972, Light enhanced decarboxylations by proteinoids, in Rohlfing, D. L., and Oparin, A. I., eds., Molecular Evolution: New York, Plenum Press, p. 233-245.}"
}

@misc{fox1973molecular15,
    author = "Fox, S. W",
    title = "Molecular evolution to the first cells",
    year = "1973",
    howpublished = "Pure Applied Chemistry, v. 34, p. 641-669",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1973, Molecular evolution to the first cells: Pure Applied Chemistry, v. 34, p. 641-669.}"
}

@phdthesis{junck1973synthesis53,
    author = "Junck, J. R. and Fox, S. W",
    title = "Synthesis of oligonucleotides by proteinoid microspheres acting on ATP",
    year = "1973",
    publisher = "Naturwissenschaften, v. 60, p. 425-427",
    note = "talkorigins\_source = {true}; raw\_reference = {Junck, J. R., and Fox, S. W., 1973, Synthesis of oligonucleotides by proteinoid microspheres acting on ATP: Naturwissenschaften, v. 60, p. 425-427.}"
}

@misc{schopf1973the77,
    author = "Schopf, J. W",
    title = "The evolution of the earliest cells",
    year = "1973",
    howpublished = "Scientific American, v. 239, no. 3, p. 111-138",
    note = "talkorigins\_source = {true}; raw\_reference = {Schopf, J. W., 1973, The evolution of the earliest cells: Scientific American, v. 239, no. 3, p. 111-138.}"
}

@book{barrington1974biochemistry1,
    author = "Barrington, E. J. W",
    title = "Biochemistry of Primitive Deuterostomians, in Florkin, M., and Scheer, B. T., eds., Chemical Zoology",
    year = "1974",
    publisher = "London, Academic Press, v. VIII, p. 61-95",
    note = "talkorigins\_source = {true}; raw\_reference = {Barrington, E. J. W., 1974, Biochemistry of Primitive Deuterostomians, in Florkin, M., and Scheer, B. T., eds., Chemical Zoology: London, Academic Press, v. VIII, p. 61-95.}"
}

@misc{fox1974from33,
    author = "Fox, S. W. and Jungck, J. R. and Nakashima, T",
    title = "From proteinoid microsphere to comtemporary cell",
    year = "1974",
    howpublished = "formation of internucleotide and peptide bonds by proteinoid particles: Origins Life, v. 5, p. 227-237",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Jungck, J. R., and Nakashima, T., 1974, From proteinoid microsphere to comtemporary cell: formation of internucleotide and peptide bonds by proteinoid particles: Origins Life, v. 5, p. 227-237.}"
}

@article{griffith1974serum43,
    author = "Griffith, R. W. and Umminger, B. L. and Grant, B. F. and Pang, P. K. T. and Pickford, G. E",
    title = "Serum composition of the coelacanth Latimeria chalumnae Smith",
    year = "1974",
    journal = "Journal of Experimental Zoology, v. 187, p. 87-102",
    note = "talkorigins\_source = {true}; raw\_reference = {Griffith, R. W., Umminger, B. L., Grant, B. F., Pang, P. K. T., and Pickford, G. E., 1974, Serum composition of the coelacanth Latimeria chalumnae Smith: Journal of Experimental Zoology, v. 187, p. 87-102.}"
}

@book{kenyon1974prefigured56,
    author = "Kenyon, D. H",
    title = "Prefigured ordering and protoselection in the origin of life, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry",
    year = "1974",
    publisher = "New York, Plenum Press, p. 207-220",
    note = "talkorigins\_source = {true}; raw\_reference = {Kenyon, D. H., 1974, Prefigured ordering and protoselection in the origin of life, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry: New York, Plenum Press, p. 207-220.}"
}

@book{keosian1974lifes57,
    author = "Keosian, J",
    title = "Life's beginnings-origin or evolution?, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry",
    year = "1974",
    publisher = "New York, Plenum Press, p. 221-231",
    note = "talkorigins\_source = {true}; raw\_reference = {Keosian, J., 1974, Life's beginnings-origin or evolution?, in Dose, K., Fox, S. W., Deborin, G. A., and Pavlovskaya, T. E., eds., The Origins of Life and Evolutionary Biochemistry: New York, Plenum Press, p. 221-231.}"
}

@incollection{kittredge1974comparative,
    author = "Kittredge, James S.",
    title = "Comparative Biochemistry: Marine Biochemistry",
    year = "1974",
    booktitle = "Experimental Marine Biology",
    url = "https://doi.org/10.1016/b978-0-12-472450-1.50011-7",
    doi = "10.1016/b978-0-12-472450-1.50011-7",
    pages = "225-267"
}

@phdthesis{price1974synthesis71,
    author = "Price, C. C",
    title = "Synthesis of Life",
    year = "1974",
    publisher = "Stroudsburg, Pa., Dowden, Hutchinson \& Ross",
    note = "talkorigins\_source = {true}; raw\_reference = {Price, C. C., 1974, Synthesis of Life: Stroudsburg, Pa., Dowden, Hutchinson \& Ross.}"
}

@book{florkin1975comprehensive7,
    author = "Florkin, M",
    title = "Comprehensive Biochemistry",
    year = "1975",
    publisher = "Amsterdam, Elsevier, v. 29B",
    note = "talkorigins\_source = {true}; raw\_reference = {Florkin, M., 1975, Comprehensive Biochemistry: Amsterdam, Elsevier, v. 29B.}"
}

@phdthesis{hennen1975the49,
    author = "Hennen, G. and Plaquet, R. and Biserte, G",
    title = "The synthesis of amino acid polymers by thermal condensation at 105° without a catalyst",
    year = "1975",
    publisher = "Biochimie, v. 57, p. 1395-1396",
    note = "talkorigins\_source = {true}; raw\_reference = {Hennen, G., Plaquet, R., and Biserte, G., 1975, The synthesis of amino acid polymers by thermal condensation at 105° without a catalyst: Biochimie, v. 57, p. 1395-1396.}"
}

@misc{lehninger1975biochemistry61,
    author = "Lehninger, A. L",
    title = "Biochemistry [2nd ed.]",
    year = "1975",
    howpublished = "New York, Worth and Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Lehninger, A. L., 1975, Biochemistry [2nd ed.]: New York, Worth and Co.}"
}

@misc{melius1975thermal63,
    author = "Melius, P. and Sheng, Y. Y.-P",
    title = "Thermal condensation of a mixture of six amino acids",
    year = "1975",
    howpublished = "Bioorganic Chemistry, v. 4, p. 385-391",
    note = "talkorigins\_source = {true}; raw\_reference = {Melius, P., and Sheng, Y. Y.-P., 1975, Thermal condensation of a mixture of six amino acids: Bioorganic Chemistry, v. 4, p. 385-391.}"
}

@misc{snyder1975a79,
    author = "Snyder, W. D. and Fox, S",
    title = "A model for the origin of stable protocells in a primitive alkaline ocean",
    year = "1975",
    howpublished = "BioSystems, v. 7, p. 222-229",
    note = "talkorigins\_source = {true}; raw\_reference = {Snyder, W. D., and Fox, S., 1975, A model for the origin of stable protocells in a primitive alkaline ocean: BioSystems, v. 7, p. 222-229.}"
}

@inproceedings{watts1975evolution86,
    author = "Watts, D. C",
    title = "Evolution of phosphagen kinases in the chordate line",
    year = "1975",
    booktitle = "Symposium of the Zoological Society, London, v. 36, p. 105-127",
    note = "talkorigins\_source = {true}; raw\_reference = {Watts, D. C., 1975, Evolution of phosphagen kinases in the chordate line: Symposium of the Zoological Society, London, v. 36, p. 105-127.}"
}

@misc{fox1976the16,
    author = "Fox, S. W",
    title = "The evolutionary significance of phase-separated microsystems",
    year = "1976",
    howpublished = "Origins Life, v. 7, p. 49-68",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1976, The evolutionary significance of phase-separated microsystems: Origins Life, v. 7, p. 49-68.}"
}

@phdthesis{rohlfing1976thermal74,
    author = "Rohlfing, D. L",
    title = "Thermal polyamino acids",
    year = "1976",
    publisher = "synthesis at less than 100° C: Science, v. 193, p. 68-70",
    note = "talkorigins\_source = {true}; raw\_reference = {Rohlfing, D. L., 1976, Thermal polyamino acids: synthesis at less than 100° C: Science, v. 193, p. 68-70.}"
}

@misc{tashian1976evolution80,
    author = "Tashian, R. E. and Goodman, M. and Ferrell, R. E. and Tanis, R. J",
    title = "Evolution of Carbonic Anhydrase in Primates and Other Mammals, in Goodman, M., and Tashian, R. E., eds., Molecular Anthropology",
    year = "1976",
    howpublished = "New York, Plenum",
    note = "talkorigins\_source = {true}; raw\_reference = {Tashian, R. E., Goodman, M., Ferrell, R. E., and Tanis, R. J., 1976, Evolution of Carbonic Anhydrase in Primates and Other Mammals, in Goodman, M., and Tashian, R. E., eds., Molecular Anthropology: New York, Plenum.}"
}

@article{temussi1976structural82,
    author = "Temussi, P. A. and Paolillo, L. and Ferrara, L. and Benedetti, E. and Andini, S",
    title = "Structural characterization of thermal prebiotic polypeptides",
    year = "1976",
    journal = "Journal of Molecular Evolution, v. 7, p. 105-110",
    note = "talkorigins\_source = {true}; raw\_reference = {Temussi, P. A., Paolillo, L., Ferrara, L., Benedetti, E., and Andini, S., 1976, Structural characterization of thermal prebiotic polypeptides: Journal of Molecular Evolution, v. 7, p. 105-110.}"
}

@book{fox1977bioorganic17,
    author = "Fox, S. W",
    title = "Bioorganic chemistry and the emergence of the first cell, in van Tamelan, E. E., ed., Bioorganic Chemistry",
    year = "1977",
    publisher = "New York, Academic Press, v. III, p. 21-32",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1977, Bioorganic chemistry and the emergence of the first cell, in van Tamelan, E. E., ed., Bioorganic Chemistry: New York, Academic Press, v. III, p. 21-32.}"
}

@misc{kimura1977causes58,
    author = "Kimura, M",
    title = "Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism",
    year = "1977",
    howpublished = "Mishima, Japan, National Institute of Genetics, p. 1-28",
    note = "talkorigins\_source = {true}; raw\_reference = {Kimura, M., 1977, Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism: Mishima, Japan, National Institute of Genetics, p. 1-28.}"
}

@article{nakashima1977a66,
    author = "Nakashima, T. and Jungck, J. R. and Fox, S. W. and Lederer, E. and Das, B. C",
    title = "A test for randomness in peptides isolated from a thermal polyamino acid",
    year = "1977",
    journal = "International Journal of Quantum Chemistry, v. QBS4, p. 65-72",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., Jungck, J. R., Fox, S. W., Lederer, E., and Das, B. C., 1977, A test for randomness in peptides isolated from a thermal polyamino acid: International Journal of Quantum Chemistry, v. QBS4, p. 65-72.}"
}

@misc{grote1978effect44,
    author = "Grote, J. R. and Syren, R. M. and Fox, S. W",
    title = "Effect of product from heated amino acids on conductance in lipid bilayer membrenes and nonaqueous solvents",
    year = "1978",
    howpublished = "BioSystems, v. 10, p. 287-292",
    note = "talkorigins\_source = {true}; raw\_reference = {Grote, J. R., Syren, R. M., and Fox, S. W., 1978, Effect of product from heated amino acids on conductance in lipid bilayer membrenes and nonaqueous solvents: BioSystems, v. 10, p. 287-292.}"
}

@misc{powers1978biochemical70,
    author = "Powers, D. A. and Place, A. R",
    title = "Biochemical genetics of Fundulus heteroclitus (L.). 1. Temporal and spatial variation in gene frequencies of Ldh-B, Mdh-A, Gpi-B and Pgm-A",
    year = "1978",
    howpublished = "Biochemical Genetics, v. 16, p. 593-607",
    note = "talkorigins\_source = {true}; raw\_reference = {Powers, D. A., and Place, A. R., 1978, Biochemical genetics of Fundulus heteroclitus (L.). 1. Temporal and spatial variation in gene frequencies of Ldh-B, Mdh-A, Gpi-B and Pgm-A: Biochemical Genetics, v. 16, p. 593-607.}"
}

@misc{schopf1978the78,
    author = "Schopf, J. W",
    title = "The evolution of the earliest cells",
    year = "1978",
    howpublished = "Scientific American, v. 239, p. 110-135",
    note = "talkorigins\_source = {true}; raw\_reference = {Schopf, J. W., 1978, The evolution of the earliest cells: Scientific American, v. 239, p. 110-135.}"
}

@book{barrington1979hormones2,
    author = "Barrington, E. J. W",
    title = "Hormones and Evolution",
    year = "1979",
    publisher = "New York, Academic Press; 2 Volumes",
    note = "talkorigins\_source = {true}; raw\_reference = {Barrington, E. J. W., 1979, Hormones and Evolution: New York, Academic Press; 2 Volumes.}"
}

@inproceedings{hartley1979evolution47,
    author = "Hartley, B. S",
    title = "Evolution of enzyme structure",
    year = "1979",
    booktitle = "Proceedings of the Royal Society, v. B205, p. 443-452",
    note = "talkorigins\_source = {true}; raw\_reference = {Hartley, B. S., 1979, Evolution of enzyme structure: Proceedings of the Royal Society, v. B205, p. 443-452.}"
}

@book{fox1980a28,
    author = "Fox, S. W. and Adachi, T. and Stillwell, W",
    title = "A quinone-assisted photoformation of energy-rich chemical bonds, in Veziroglu, T. N., ed., Solar Energy",
    year = "1980",
    publisher = "International Progress: New York, Pergamon Press, v. 2, p. 1056-1074",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Adachi, T., and Stillwell, W., 1980, A quinone-assisted photoformation of energy-rich chemical bonds, in Veziroglu, T. N., ed., Solar Energy: International Progress: New York, Pergamon Press, v. 2, p. 1056-1074.}"
}

@misc{fox1980introductory18,
    author = "Fox, S. W",
    title = "Introductory remarks to the special issue on 'assembly mechanisms",
    year = "1980",
    howpublished = "BioSystems, v. 12, p. 131",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1980, Introductory remarks to the special issue on 'assembly mechanisms': BioSystems, v. 12, p. 131.}"
}

@misc{fox1980metabolic21,
    author = "Fox, S. W",
    title = "Metabolic microspheres",
    year = "1980",
    howpublished = "Naturwissenschaften, v. 67, p. 378-383",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1980, Metabolic microspheres: Naturwissenschaften, v. 67, p. 378-383.}"
}

@article{fox1980response19,
    author = "Fox, S. W",
    title = "Response to repeated statements on temperatures required for polycondensation of amino acids",
    year = "1980",
    journal = "Journal of Molecular Evolution, v. 15, p. 539",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1980, Response to repeated statements on temperatures required for polycondensation of amino acids: Journal of Molecular Evolution, v. 15, p. 539.}"
}

@misc{fox1980the20,
    author = "Fox, S. W",
    title = "The origins of behavior in macromolecules and protocells",
    year = "1980",
    howpublished = "Comparative Biochemistry and Physiology, v. 67B, p. 423-436",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1980, The origins of behavior in macromolecules and protocells: Comparative Biochemistry and Physiology, v. 67B, p. 423-436.}"
}

@phdthesis{fox1980the37,
    author = "Fox, S. W. and Nakashima, T",
    title = "The assembly and properties of protobiological structures",
    year = "1980",
    publisher = "the beginnings of cellular peptide synthesis: BioSystems, v. 12, p. 155-166",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., and Nakashima, T., 1980, The assembly and properties of protobiological structures: the beginnings of cellular peptide synthesis: BioSystems, v. 12, p. 155-166.}"
}

@phdthesis{nakashima1980synthesis64,
    author = "Nakashima, T. and Fox, S. W",
    title = "Synthesis of peptides from amino acids and ATP with lysine-rich protenoid",
    year = "1980",
    publisher = "Journal of Molecular Evolution, v. 15, p. 161-168",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., and Fox, S. W., 1980, Synthesis of peptides from amino acids and ATP with lysine-rich protenoid: Journal of Molecular Evolution, v. 15, p. 161-168.}"
}

@phdthesis{fox1981a26,
    author = "Fox, S. W",
    title = "A model for protocellular coordination of nucleic acid and protein synthesis, in Kageyama, M., Nakamura, K., Oshima, T., and Uchida, T., eds., Science and Scientists",
    year = "1981",
    publisher = "Tokyo, Japan Science Society Press, p. 39-45",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, A model for protocellular coordination of nucleic acid and protein synthesis, in Kageyama, M., Nakamura, K., Oshima, T., and Uchida, T., eds., Science and Scientists: Tokyo, Japan Science Society Press, p. 39-45.}"
}

@misc{fox1981amino30,
    author = "Fox, S. W. and Harada, K. and Hare, P. E",
    title = "Amino acids from the Moon",
    year = "1981",
    howpublished = "Notes on meteorites: Subcellular Biochemistry, v. 8, p. 357-373",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Harada, K., and Hare, P. E., 1981, Amino acids from the Moon: Notes on meteorites: Subcellular Biochemistry, v. 8, p. 357-373.}"
}

@misc{fox1981an22,
    author = "Fox, S. W",
    title = "An acid test",
    year = "1981",
    howpublished = "Nature, v. 294, p. 688",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, An acid test: Nature, v. 294, p. 688.}"
}

@misc{fox1981creation24,
    author = "Fox, S. W",
    title = {Creation "copout},
    year = "1981",
    howpublished = "Nature, v. 292, p. 490",
    note = {talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, Creation "copout": Nature, v. 292, p. 490.}}
}

@phdthesis{fox1981creationism25,
    author = "Fox, S. W",
    title = "Creationism, the random hypothesis and experiments",
    year = "1981",
    publisher = "Science, v. 213, p. 290",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, Creationism, the random hypothesis and experiments: Science, v. 213, p. 290.}"
}

@misc{fox1981from23,
    author = "Fox, S. W",
    title = "From inanimate matter to living systems",
    year = "1981",
    howpublished = "American Biology Teacher, v. 43, no. 3, p. 127-135, 140",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, From inanimate matter to living systems: American Biology Teacher, v. 43, no. 3, p. 127-135, 140.}"
}

@book{fox1981how27,
    author = "Fox, S. W",
    title = "How many theories for the origin of (proto)life?, in Srinivasan, R., ed., Biomolecular Structure, Conformation, Function and Evolution",
    year = "1981",
    publisher = "Oxford, Pergamon Press, p. 643-646",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1981, How many theories for the origin of (proto)life?, in Srinivasan, R., ed., Biomolecular Structure, Conformation, Function and Evolution: Oxford, Pergamon Press, p. 643-646.}"
}

@misc{ishima1981electrical52,
    author = "Ishima, Y. and Pryzbylski, A. and Fox, S. W",
    title = "Electrical membrane phenomena in spherules from protenoid and lecithin",
    year = "1981",
    howpublished = "BioSystems, v. 13, p. 243-251",
    note = "talkorigins\_source = {true}; raw\_reference = {Ishima, Y., Pryzbylski, A., and Fox, S. W., 1981, Electrical membrane phenomena in spherules from protenoid and lecithin: BioSystems, v. 13, p. 243-251.}"
}

@misc{kuhn1981molecular59,
    author = "Kuhn, H",
    title = "Molecular self-organization and the origin of life",
    year = "1981",
    howpublished = "Agnew. Chem. Internat. Ed. Engl., v. 20, p. 500-520",
    note = "talkorigins\_source = {true}; raw\_reference = {Kuhn, H., 1981, Molecular self-organization and the origin of life: Agnew. Chem. Internat. Ed. Engl., v. 20, p. 500-520.}"
}

@misc{matsuno1981material62,
    author = "Matsuno, K",
    title = "Material self-assembly as a physicochemical process",
    year = "1981",
    howpublished = "BioSystems, v. 13, p. 237-241",
    note = "talkorigins\_source = {true}; raw\_reference = {Matsuno, K., 1981, Material self-assembly as a physicochemical process: BioSystems, v. 13, p. 237-241.}"
}

@misc{nakashima1981formulation65,
    author = "Nakashima, T. and Fox, S. W",
    title = "Formulation of peptides by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles",
    year = "1981",
    howpublished = "BioSystems, v. 14, p. 151- 161",
    note = "talkorigins\_source = {true}; raw\_reference = {Nakashima, T., and Fox, S. W., 1981, Formulation of peptides by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles: BioSystems, v. 14, p. 151- 161.}"
}

@misc{pivcova1981nmr69,
    author = "Pivcova, H. and Saudek, V. and Drobnik, J. and Vlasak, J",
    title = "NMR study of poly (aspartic acid) I. - and -peptide bonds in poly (aspartic acid) prepared by thermal polycondensation",
    year = "1981",
    howpublished = "Biopolymers, v. 20, p. 1605-1614",
    note = "talkorigins\_source = {true}; raw\_reference = {Pivcova, H., Saudek, V., Drobnik, J., and Vlasak, J., 1981, NMR study of poly (aspartic acid) I. - and -peptide bonds in poly (aspartic acid) prepared by thermal polycondensation: Biopolymers, v. 20, p. 1605-1614.}"
}

@article{yockey1981self88,
    author = "Yockey, H. P",
    title = "Self organization origin of life scenarios and information theory",
    year = "1981",
    journal = "Journal of Theoretical Biology, v. 91, p. 13-31",
    note = "talkorigins\_source = {true}; raw\_reference = {Yockey, H. P., 1981, Self organization origin of life scenarios and information theory: Journal of Theoretical Biology, v. 91, p. 13-31.}"
}

@phdthesis{follmann1982deoxyribonucleotide8,
    author = "Follmann, H",
    title = "Deoxyribonucleotide systhesis and the emergence of DNA in molecular evolution",
    year = "1982",
    publisher = "Naturwissenschaften, v. 69, p. 75-81",
    note = "talkorigins\_source = {true}; raw\_reference = {Follmann, H., 1982, Deoxyribonucleotide systhesis and the emergence of DNA in molecular evolution: Naturwissenschaften, v. 69, p. 75-81.}"
}

@article{fox1982the38,
    author = "Fox, S. W. and Nakashima, T. and Przyblyski, A. and Syren, R. M",
    title = "The updated experimental proteinoid model",
    year = "1982",
    journal = "International Journal of Quantum Chemistry, v. QBS 9, p. 195-204",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Nakashima, T., Przyblyski, A., and Syren, R. M., 1982, The updated experimental proteinoid model: International Journal of Quantum Chemistry, v. QBS 9, p. 195-204.}"
}

@misc{templeton1983phylogenetic81,
    author = "Templeton, A. R",
    title = "Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes",
    year = "1983",
    howpublished = "Evolution, v. 37, p. 221-244",
    note = "talkorigins\_source = {true}; raw\_reference = {Templeton, A. R., 1983, Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes: Evolution, v. 37, p. 221-244.}"
}

@article{crossref1987biochemistry,
    title = "Biochemistry",
    year = "1987",
    journal = "Science News",
    url = "https://doi.org/10.2307/3972125",
    doi = "10.2307/3972125",
    number = "1",
    pages = "8",
    volume = "132"
}

@misc{brauman1988frontiers3,
    author = "Brauman, J. L",
    title = "Frontiers in Chemistry",
    year = "1988",
    howpublished = "Science, v. 240, no. 373",
    note = "talkorigins\_source = {true}; raw\_reference = {Brauman, J. L., 1988, Frontiers in Chemistry: Science, v. 240, no. 373.}"
}

@article{sodja1996biochemistry,
    author = "Sodja, Ann",
    title = "Biochemistry",
    year = "1996",
    journal = "International Biodeterioration \& Biodegradation",
    url = "https://doi.org/10.1016/0964-8305(96)88252-7",
    doi = "10.1016/0964-8305(96)88252-7",
    number = "3-4",
    pages = "233-235",
    volume = "37"
}

@article{crossref1998biochemistry,
    title = "Biochemistry",
    year = "1998",
    journal = "Science News",
    url = "https://doi.org/10.2307/4011044",
    doi = "10.2307/4011044",
    number = "17",
    pages = "266-266",
    volume = "154"
}

@incollection{abdel2009biochemistry,
    author = "Abdel, Ahmad Wagih",
    title = "Biochemistry",
    year = "2009",
    booktitle = "Passing the USMLE",
    url = "https://doi.org/10.1007/978-0-387-68980-7\_11",
    doi = "10.1007/978-0-387-68980-7\_11",
    pages = "1-24"
}

The dual information-function nature of nucleic acids has been exploited in the laboratory to isolate novel receptors and catalysts from random DNA and RNA sequences by cycles of in vitro selection and amplification. This strategy is particularly effective because, unlike polypeptides with random amino acid sequences, nucleic acids with random base sequences are often capable of stably folding into defined three-dimensional structures. However, the pervasive base-pairing potential of nucleic acids is also known to lead to kinetic traps in their folding landscapes. That is, the same DNA or RNA sequence can often adopt alternative base-paired structures that are local energy minima, and these folds may interconvert very slowly. We have used simulations with nucleic acid folding algorithms to evaluate the effect of misfolding on in vitro selection experiments. We demonstrate that kinetic traps can prevent the recovery of novel families of complex functional motifs by two mechanisms. First, misfolding can lead to the stochastic loss of unique sequences in the first round of selection. Second, frequent misfolding can reduce the average activity of multiple copies of a sequence to such an extent that it will be outcompeted after multiple rounds of selection. In these simulations, adding thermal cycling to sample multiple folds of one sequence during a selection for a self-modifying catalytic activity can improve the recovery of rare examples of more complex structures. Although newly isolated sequences may fold poorly, they can represent footholds in sequence space that can be improved to reliably fold after a few mutations. Thus, it is plausible that thermal cycling by day-night cycles or other mechanisms on the primordial earth may have been important for the evolution of the first RNA catalysts, and a fold sampling strategy might be used to search for more effective nucleic acid catalysts in the laboratory today.

@article{doi1075519780262310505ch062,
    author = "Reba, Aaron and Meyer, Austin G and Barrick, Jeffrey E",
    title = "Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection.",
    year = "2013",
    journal = "Artificial life 13: proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems. International Conference on the Simulation and Synthesis of Living Systems (13th: 2012: East Lansing, Mich.)",
    abstract = "The dual information-function nature of nucleic acids has been exploited in the laboratory to isolate novel receptors and catalysts from random DNA and RNA sequences by cycles of in vitro selection and amplification. This strategy is particularly effective because, unlike polypeptides with random amino acid sequences, nucleic acids with random base sequences are often capable of stably folding into defined three-dimensional structures. However, the pervasive base-pairing potential of nucleic acids is also known to lead to kinetic traps in their folding landscapes. That is, the same DNA or RNA sequence can often adopt alternative base-paired structures that are local energy minima, and these folds may interconvert very slowly. We have used simulations with nucleic acid folding algorithms to evaluate the effect of misfolding on in vitro selection experiments. We demonstrate that kinetic traps can prevent the recovery of novel families of complex functional motifs by two mechanisms. First, misfolding can lead to the stochastic loss of unique sequences in the first round of selection. Second, frequent misfolding can reduce the average activity of multiple copies of a sequence to such an extent that it will be outcompeted after multiple rounds of selection. In these simulations, adding thermal cycling to sample multiple folds of one sequence during a selection for a self-modifying catalytic activity can improve the recovery of rare examples of more complex structures. Although newly isolated sequences may fold poorly, they can represent footholds in sequence space that can be improved to reliably fold after a few mutations. Thus, it is plausible that thermal cycling by day-night cycles or other mechanisms on the primordial earth may have been important for the evolution of the first RNA catalysts, and a fold sampling strategy might be used to search for more effective nucleic acid catalysts in the laboratory today.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC9484335/",
    doi = "10.7551/978-0-262-31050-5-ch062",
    pmcid = "PMC9484335",
    pmid = "36129423"
}

The hydrophobicities of the 20 common amino acids are reflected in their tendencies to appear in interior positions in globular proteins and in deeply buried positions of membrane proteins. To determine whether these relationships might also have been valid in the warm surroundings where life may have originated, we examined the effect of temperature on the hydrophobicities of the amino acids as measured by the equilibrium constants for transfer of their side-chains from neutral solution to cyclohexane (K(w > c)). The hydrophobicities of most amino acids were found to increase with increasing temperature. Because that effect is more pronounced for the more polar amino acids, the numerical range of K(w > c) values decreases with increasing temperature. There are also modest changes in the ordering of the more polar amino acids. However, those changes are such that they would have tended to minimize the otherwise disruptive effects of a changing thermal environment on the evolution of protein structure. Earlier, the genetic code was found to be organized in such a way that--with a single exception (threonine)--the side-chain dichotomy polar/nonpolar matches the nucleic acid base dichotomy purine/pyrimidine at the second position of each coding triplet at 25 °C. That dichotomy is preserved at 100 °C. The accessible surface areas of amino acid side-chains in folded proteins are moderately correlated with hydrophobicity, but when free energies of vapor-to-cyclohexane transfer (corresponding to size) are taken into consideration, a closer relationship becomes apparent.

@article{doi101073pnas1507565112,
    author = "Wolfenden, Richard and Lewis, Charles A and Yuan, Yang and Carter, Charles W",
    title = "Temperature dependence of amino acid hydrophobicities.",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    abstract = "The hydrophobicities of the 20 common amino acids are reflected in their tendencies to appear in interior positions in globular proteins and in deeply buried positions of membrane proteins. To determine whether these relationships might also have been valid in the warm surroundings where life may have originated, we examined the effect of temperature on the hydrophobicities of the amino acids as measured by the equilibrium constants for transfer of their side-chains from neutral solution to cyclohexane (K(w > c)). The hydrophobicities of most amino acids were found to increase with increasing temperature. Because that effect is more pronounced for the more polar amino acids, the numerical range of K(w > c) values decreases with increasing temperature. There are also modest changes in the ordering of the more polar amino acids. However, those changes are such that they would have tended to minimize the otherwise disruptive effects of a changing thermal environment on the evolution of protein structure. Earlier, the genetic code was found to be organized in such a way that--with a single exception (threonine)--the side-chain dichotomy polar/nonpolar matches the nucleic acid base dichotomy purine/pyrimidine at the second position of each coding triplet at 25 °C. That dichotomy is preserved at 100 °C. The accessible surface areas of amino acid side-chains in folded proteins are moderately correlated with hydrophobicity, but when free energies of vapor-to-cyclohexane transfer (corresponding to size) are taken into consideration, a closer relationship becomes apparent.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC4475965/",
    doi = "10.1073/pnas.1507565112",
    pmcid = "PMC4475965",
    pmid = "26034278"
}

A general framework for conventional models of the origin of life (OOL) is the specification of a 'privileged function.' A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients. In Membrane Worlds, the privileged function is compartmentalization. In evaluating these models, we consider the contents and properties of the Universal Gene Set of life, which is the set of orthologous genes conserved throughout the tree of life and found in every living system. We also consider the components and properties of the Molecular Toolbox of Life, which contains twenty amino acids, eight nucleotides, glucose, polypeptide, polynucleotide, and several other components. OOL models based on privileged functions necessarily depend on "takeovers" to transition from previous genetic and catalytic systems to the extant DNA/RNA/protein system, requiring replacement of one Molecular Toolbox with another and of one Universal Gene Set with another. The observed robustness and contents of the Toolbox of Life and the Universal Gene Set over the last 3.7 billion years are thought to be post hoc phenomena. Once the takeover processes are acknowledged and are reasonably considered, the privileged function models are seen to be extremely complex with low predictive power. These models require indeterminacy and plasticity of biological and chemical processes.

@article{doi101007s002390179783y,
    author = "Lanier, Kathryn A and Williams, Loren Dean",
    title = "The Origin of Life: Models and Data.",
    year = "2017",
    journal = "Journal of molecular evolution",
    abstract = {A general framework for conventional models of the origin of life (OOL) is the specification of a 'privileged function.' A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients. In Membrane Worlds, the privileged function is compartmentalization. In evaluating these models, we consider the contents and properties of the Universal Gene Set of life, which is the set of orthologous genes conserved throughout the tree of life and found in every living system. We also consider the components and properties of the Molecular Toolbox of Life, which contains twenty amino acids, eight nucleotides, glucose, polypeptide, polynucleotide, and several other components. OOL models based on privileged functions necessarily depend on "takeovers" to transition from previous genetic and catalytic systems to the extant DNA/RNA/protein system, requiring replacement of one Molecular Toolbox with another and of one Universal Gene Set with another. The observed robustness and contents of the Toolbox of Life and the Universal Gene Set over the last 3.7 billion years are thought to be post hoc phenomena. Once the takeover processes are acknowledged and are reasonably considered, the privileged function models are seen to be extremely complex with low predictive power. These models require indeterminacy and plasticity of biological and chemical processes.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC5371624/",
    doi = "10.1007/s00239-017-9783-y",
    pmcid = "PMC5371624",
    pmid = "28243688"
}

@misc{crossrefNonebiochemistry,
    title = "Biochemistry \& Analytical Biochemistry",
    year = "None",
    url = "https://doi.org/10.4172/2161-1009",
    doi = "10.4172/2161-1009"
}