This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Benner SA. Paradoxes in the origin of life. Origins of Life and Evolution of Biospheres. 2014;44: 339–343. doi: 10.1007/s11084-014-9379-0BennerSAParadoxes in the origin of lifeOrigins of Life and Evolution of Biospheres20144433934310.1007/s11084-014-9379-0Open DOISearch in Google Scholar
Lee H-E, Russell M, Nakamura R. Water chemistry at the nanoscale: clues for resolving the “water paradox” underlying the emergence of life. ChemistryEurope. 2024;2: e202400038. (7pp). doi: 10.1002/ceur.202400038LeeH-ERussellMNakamuraRWater chemistry at the nanoscale: clues for resolving the “water paradox” underlying the emergence of lifeChemistryEurope20242e202400038(7pp).10.1002/ceur.202400038Open DOISearch in Google Scholar
Bernhardt HS. The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biology Direct. 2012;7: 23. doi: 10.1186/1745-6150-7-23BernhardtHSThe RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)Biology Direct201272310.1186/1745-6150-7-23Open DOISearch in Google Scholar
Ross DS, Deamer D. Dry/wet cycling and the thermodynamics and kinetics of prebiotic polymer synthesis. Life (Basel, Switzerland). 2016;6: 28. (12pp). doi: 10.3390/life6030028RossDSDeamerDDry/wet cycling and the thermodynamics and kinetics of prebiotic polymer synthesisLife (Basel, Switzerland)2016628(12pp).10.3390/life6030028Open DOISearch in Google Scholar
Whitaker D, Powner MW. On the aqueous origins of the condensation polymers of life. Nature Reviews Chemistry. 2024;8: 817–832. doi: 10.1038/s41570-024-00648-5WhitakerDPownerMWOn the aqueous origins of the condensation polymers of lifeNature Reviews Chemistry2024881783210.1038/s41570-024-00648-5Open DOISearch in Google Scholar
Ianeselli A, Salditt A, Mast C, Ercolano B, Kufner CL, Scheu B, et al. Physical non-equilibria for prebiotic nucleic acid chemistry. Nature Reviews Physics. 2023;5: 185–195. doi: 10.1038/s42254-022-00550-3IaneselliASaldittAMastCErcolanoBKufnerCLScheuBPhysical non-equilibria for prebiotic nucleic acid chemistryNature Reviews Physics2023518519510.1038/s42254-022-00550-3Open DOISearch in Google Scholar
Song X, Simonis P, Deamer D, Zare RN. Wet-dry cycles cause nucleic acid monomers to polymerize into long chains. Proceedings of the National Academy of Sciences of the United States of America. 2024;121: e2412784121. doi: 10.1073/pnas.2412784121SongXSimonisPDeamerDZareRNWet-dry cycles cause nucleic acid monomers to polymerize into long chainsProceedings of the National Academy of Sciences of the United States of America2024121e241278412110.1073/pnas.2412784121Open DOISearch in Google Scholar
Eigen M, Schuster P. The hypercycle. Die Naturwissenschaften. 1978;65: 341–369. doi: 10.1007/bf00439699EigenMSchusterPThe hypercycleDie Naturwissenschaften19786534136910.1007/bf00439699Open DOISearch in Google Scholar
Riggi VS, Bruce Watson E, Steele A, Rogers KL. Mineral-mediated oligoribonucleotide condensation: broadening the scope of prebiotic possibilities on the early earth. Life (Basel, Switzerland). 2023;13: 1899. (15pp). doi: 10.3390/life13091899RiggiVSBruce WatsonESteeleARogersKLMineral-mediated oligoribonucleotide condensation: broadening the scope of prebiotic possibilities on the early earthLife (Basel, Switzerland)2023131899(15pp).10.3390/life13091899Open DOISearch in Google Scholar
Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Letters. 2023;597: 2879–2896. doi: 10.1002/1873-3468.14766EdriRFisherSMenor-SalvanCWilliamsLDFrenkel-PinterMAssembly-driven protection from hydrolysis as key selective force during chemical evolutionFEBS Letters20235972879289610.1002/1873-3468.14766Open DOISearch in Google Scholar
Miller SL. A production of amino acids under possible primitive earth conditions. Science (New York, N.Y.). 1953;117: 528–529. doi: 10.1126/science.117.3046.528MillerSLA production of amino acids under possible primitive earth conditionsScience (New York, N.Y.)195311752852910.1126/science.117.3046.528Open DOISearch in Google Scholar
Okamoto R, Haraguchi T, Nomura K, Maki Y, Izumi M, Kajihara Y. Regioselective α-peptide bond formation through the oxidation of amino thioacids. Biochemistry. 2019;58: 1672–1678. doi: 10.1021/acs.biochem.8b01239OkamotoRHaraguchiTNomuraKMakiYIzumiMKajiharaYRegioselective α-peptide bond formation through the oxidation of amino thioacidsBiochemistry2019581672167810.1021/acs.biochem.8b01239Open DOISearch in Google Scholar
Du X, Cui J, Han Y, Li F, Liang H, Jin J, et al. Effects of monomer purity on AA-BB polycondensation: a Monte Carlo study. Polymer Bulletin. 2024;81: 6423–6436. doi: 10.1007/s00289-023-05015-wDuXCuiJHanYLiFLiangHJinJEffects of monomer purity on AA-BB polycondensation: a Monte Carlo studyPolymer Bulletin2024816423643610.1007/s00289-023-05015-wOpen DOISearch in Google Scholar
Orgel LE. The origins of life: molecules and natural selection. London: Chapman & Hall; 1973.OrgelLEThe origins of life: molecules and natural selectionLondonChapman & Hall1973Search in Google Scholar
Rich A. On the problems of evolution and biochemical information transfer. In: Kasha M, Pullman B. (eds.) Horizons in biochemistry: Albert Szent-Györgyi dedicatory volume. (Cambridge, Mass.) is an imprint of Elsevier: Academic Press; 1962. p.103–125.RichAOn the problems of evolution and biochemical information transferIn:KashaMPullmanB.(eds.)Horizons in biochemistry: Albert Szent-Györgyi dedicatory volume(Cambridge, Mass.) is an imprint of ElsevierAcademic Press1962103125Search in Google Scholar
Woese C. The genetic code: the molecular basis for genetic expression. London: Harper & Row; 1967.WoeseCThe genetic code: the molecular basis for genetic expressionLondonHarper & Row1967Search in Google Scholar
Orgel LE. Evolution of the genetic apparatus. Journal of Molecular Biology. 1968;38: 381–393. doi: 10.1016/0022-2836(68)90393-8OrgelLEEvolution of the genetic apparatusJournal of Molecular Biology19683838139310.1016/0022-2836(68)90393-8Open DOISearch in Google Scholar
Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, et al. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. eLife. 2024;12: RP90316. (27pp). doi: 10.7554/eLife.90316.3ZhangKEldinPCieslaJHBriantLLentiniJMRamosJProteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main proteaseeLife202412RP90316(27pp).10.7554/eLife.90316.3Open DOISearch in Google Scholar
Benner SA, Kim H-J, Carrigan MA. Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. Accounts of Chemical Research. 2012;45: 2025–2034. doi: 10.1021/ar200332wBennerSAKimH-JCarriganMAAsphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNAAccounts of Chemical Research2012452025203410.1021/ar200332wOpen DOISearch in Google Scholar
Wang C, Liu H. Factors influencing degradation kinetics of mRNAs and half-lives of microRNAs, circRNAs, lncRNAs in blood in vitro using quantitative PCR. Scientific Reports. 2022;12: 7259. (11pp). doi: 10.1038/s41598-022-11339-wWangCLiuHFactors influencing degradation kinetics of mRNAs and half-lives of microRNAs, circRNAs, lncRNAs in blood in vitro using quantitative PCRScientific Reports2022127259(11pp).10.1038/s41598-022-11339-wOpen DOISearch in Google Scholar
Kahne D, Still WC. Hydrolysis of a peptide bond in neutral water. Journal of the American Chemical Society. 1988;10: 7529–7534. doi: 10.1021/ja00230a041KahneDStillWCHydrolysis of a peptide bond in neutral waterJournal of the American Chemical Society1988107529753410.1021/ja00230a041Open DOISearch in Google Scholar
Williams DA, Hartquist TW. The cosmic-chemical bond. London: Royal Society of Chemistry; 2013. doi: 10.1039/9781839169144WilliamsDAHartquistTWThe cosmic-chemical bondLondonRoyal Society of Chemistry201310.1039/9781839169144Open DOISearch in Google Scholar
Howard KT, Bailey MJ, Berhanu D, Bland PA, Cressey G, Howard LE, et al. Biomass preservation in distal impact melt ejecta. Nature Geoscience. 2013;6: 1018–1022. doi: 10.1038/ngeo1996HowardKTBaileyMJBerhanuDBlandPACresseyGHowardLEBiomass preservation in distal impact melt ejectaNature Geoscience201361018102210.1038/ngeo1996Open DOISearch in Google Scholar
Benner SA, Bell EA, Biondi E, Brasser R, Carell T, Kim H-J, et al. When did life likely emerge on earth in an RNA-first process? ChemSystemsChem. 2020;2: e1900035. doi: 10.1002/syst.201900035BennerSABellEABiondiEBrasserRCarellTKimH-JWhen did life likely emerge on earth in an RNA-first process?ChemSystemsChem20202e190003510.1002/syst.201900035Open DOISearch in Google Scholar
Cronin JR, Pizzarello S. Amino acid enantiomer excesses in meteorites: origin and significance. Advances in Space Research. 1999;23: 293–299. doi: 10.1016/S0273-1177(99)00050-2CroninJRPizzarelloSAmino acid enantiomer excesses in meteorites: origin and significanceAdvances in Space Research19992329329910.1016/S0273-1177(99)00050-2Open DOISearch in Google Scholar
Parker MC, Jeynes C. A relativistic entropic Hamiltonian–Lagrangian approach to the entropy production of spiral galaxies in hyperbolic spacetime. Universe. 2021;7: 325. (15pp). doi: 10.3390/universe7090325ParkerMCJeynesCA relativistic entropic Hamiltonian–Lagrangian approach to the entropy production of spiral galaxies in hyperbolic spacetimeUniverse20217325(15pp).10.3390/universe7090325Open DOISearch in Google Scholar
Parker MC, Jeynes C. Maximum entropy (most likely) double helical and double logarithmic spiral trajectories in space-time. Scientific Reports. 2019;9: 10779. doi: 10.1038/s41598-019-46765-wParkerMCJeynesCMaximum entropy (most likely) double helical and double logarithmic spiral trajectories in space-timeScientific Reports201991077910.1038/s41598-019-46765-wOpen DOISearch in Google Scholar
Parker MC, Jeynes C. ab initio thermodynamics calculation of beta decay rates. Annalen Der Physik. 2023;535: 2300259. (11pp). doi: 10.1002/andp.202300259ParkerMCJeynesCab initio thermodynamics calculation of beta decay ratesAnnalen Der Physik20235352300259(11pp).10.1002/andp.202300259Open DOISearch in Google Scholar
Auffray C, Nottale L. Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws. Progress in Biophysics and Molecular Biology. 2008;97: 79–114. doi: 10.1016/j.pbiomolbio.2007.09.002AuffrayCNottaleLScale relativity theory and integrative systems biology: 1. Founding principles and scale lawsProgress in Biophysics and Molecular Biology2008977911410.1016/j.pbiomolbio.2007.09.002Open DOISearch in Google Scholar
Parker MC, Jeynes C. A maximum entropy resolution to the wine/water paradox. Entropy (Basel, Switzerland). 2023;25: 1242. (10pp). doi: 10.3390/e25081242ParkerMCJeynesCA maximum entropy resolution to the wine/water paradoxEntropy (Basel, Switzerland)2023251242(10pp).10.3390/e25081242Open DOISearch in Google Scholar
Parker MC, Jeynes C. Entropic uncertainty principle, partition function and holographic principle derived from Liouville’s theorem. Physics Open. 2021;7: 100068. (11pp). doi: 10.1016/j.physo.2021.100068ParkerMCJeynesCEntropic uncertainty principle, partition function and holographic principle derived from Liouville’s theoremPhysics Open20217100068(11pp).10.1016/j.physo.2021.100068Open DOISearch in Google Scholar
Parker MC, Jeynes C, Catford WN. Halo properties in helium nuclei from the perspective of geometrical thermodynamics. Annalen Der Physik. 2022;534: 2100278. (11pp). doi: 10.1002/andp.202100278ParkerMCJeynesCCatfordWNHalo properties in helium nuclei from the perspective of geometrical thermodynamicsAnnalen Der Physik20225342100278(11pp).10.1002/andp.202100278Open DOISearch in Google Scholar
Parker MC, Jeynes C. Relating a system’s Hamiltonian to its entropy production using a complex-time approach. Entropy. April 2023;25: 629. (19pp). doi: 10.3390/e25040629ParkerMCJeynesCRelating a system’s Hamiltonian to its entropy production using a complex-time approachEntropyApril202325629(19pp).10.3390/e25040629Open DOISearch in Google Scholar
Chatterjee A, Zhang K, Rao Y, Sharma N, Giammar DE, Parker KM. Metal-catalyzed hydrolysis of RNA in aqueous environments. Environmental Science & Technology. 2022;56: 3564–3574. doi: 10.1021/acs.est.1c08468ChatterjeeAZhangKRaoYSharmaNGiammarDEParkerKMMetal-catalyzed hydrolysis of RNA in aqueous environmentsEnvironmental Science & Technology2022563564357410.1021/acs.est.1c08468Open DOISearch in Google Scholar
Sun Y, Frenkel-Pinter M, Liotta CL, Grover MA. The pH dependent mechanisms of non-enzymatic peptide bond cleavage reactions. Physical Chemistry Chemical Physics. 2019;22: 107–113. doi: 10.1039/c9cp05240bSunYFrenkel-PinterMLiottaCLGroverMAThe pH dependent mechanisms of non-enzymatic peptide bond cleavage reactionsPhysical Chemistry Chemical Physics20192210711310.1039/c9cp05240bOpen DOISearch in Google Scholar
Beardslee PC, Dhamdhere G, Jiang J, Ogbonna EC, Presloid CJ, Prorok M, et al. Enzymes & CLP proteases. In: Jez J. (ed.) Encyclopedia of biological chemistry III. 3rd ed., Vol. 3. Oxford: Elsevier; 2021. p.292–306. doi: 10.1016/B978-0-12-819460-7.00156-0BeardsleePCDhamdhereGJiangJOgbonnaECPresloidCJProrokMEnzymes & CLP proteasesIn:JezJ.(ed.)Encyclopedia of biological chemistry III3rd ed.3OxfordElsevier202129230610.1016/B978-0-12-819460-7.00156-0Open DOISearch in Google Scholar
Bruce Martin R. Free energies and equilibria of peptide bond hydrolysis and formation. Biopolymers. 1998;45: 351–353. doi: 10.1002/(SICI)1097-0282(19980415)45:5<351:AID-BIP3>3.0.CO;2-KBruce MartinRFree energies and equilibria of peptide bond hydrolysis and formationBiopolymers19984535135310.1002/(SICI)1097-0282(19980415)45:5<351:AID-BIP3>3.0.CO;2-KOpen DOISearch in Google Scholar
Radzicka A, Wolfenden R. Rates of uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteases. Journal of the American Chemical Society. 1996;118: 6105–6109. doi: 10.1021/ja954077cRadzickaAWolfendenRRates of uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteasesJournal of the American Chemical Society19961186105610910.1021/ja954077cOpen DOISearch in Google Scholar
Xu Z, Asakawa S. Release and degradation of dissolved environmental RNAs from zebrafish cells. RNA Biology. 2025;22(1): 1–12. doi: 10.1080/15476286.2025.2486281XuZAsakawaSRelease and degradation of dissolved environmental RNAs from zebrafish cellsRNA Biology202522111210.1080/15476286.2025.2486281Open DOISearch in Google Scholar
Brigiano FS, Gierada M, Tielens F, Pietrucci F. Mechanism and free-energy landscape of peptide bond formation at the silica−water interface. ACSCatalysis. 2022;12: 2821–2830. doi: 10.1021/acscatal.1c05635BrigianoFSGieradaMTielensFPietrucciFMechanism and free-energy landscape of peptide bond formation at the silica−water interfaceACSCatalysis2022122821283010.1021/acscatal.1c05635Open DOISearch in Google Scholar
Forsythe JG, Yu S-S, Mamajanov I, Grover MA, Krishnamurthy R, Fernández FM, et al. Ester-mediated amide bond formation driven by wet–dry cycles: a possible path to polypeptides on the prebiotic earth. Angewandte Chemie. 2015;54: 9871–9875. doi: 10.1002/anie.201503792ForsytheJGYuS-SMamajanovIGroverMAKrishnamurthyRFernándezFMEster-mediated amide bond formation driven by wet–dry cycles: a possible path to polypeptides on the prebiotic earthAngewandte Chemie2015549871987510.1002/anie.201503792Open DOISearch in Google Scholar
Zagrovic B, Adlhart M, Kapral TH. Coding from binding? Molecular interactions at the heart of translation. Annual Review of Biophysics. 2023;52: 69–89. doi: 10.1146/annurev-biophys-090622-102329ZagrovicBAdlhartMKapralTHCoding from binding? Molecular interactions at the heart of translationAnnual Review of Biophysics202352698910.1146/annurev-biophys-090622-102329Open DOISearch in Google Scholar
Guo X, Su M. The origin of translation: bridging the nucleotides and peptides. International Journal of Molecular Sciences. 2023;24: 197. (16pp). doi: 10.3390/ijms24010197GuoXSuMThe origin of translation: bridging the nucleotides and peptidesInternational Journal of Molecular Sciences202324197(16pp).10.3390/ijms24010197Open DOISearch in Google Scholar
Parker MC, Jeynes C. Fullerene stability by geometrical thermodynamics. ChemistrySelect. 2020;5: 514. doi: 10.1002/slct.201903633ParkerMCJeynesCFullerene stability by geometrical thermodynamicsChemistrySelect2020551410.1002/slct.201903633Open DOISearch in Google Scholar
Parker MC, Jeynes C, Walker SD. A metric for the entropic purpose of a system. Entropy (Basel, Switzerland). 2025;27: 131. (40pp). doi: 10.3390/e27020131ParkerMCJeynesCWalkerSDA metric for the entropic purpose of a systemEntropy (Basel, Switzerland)202527131(40pp).10.3390/e27020131Open DOISearch in Google Scholar