Origins of Life and Evolution of Biospheres最新文献

{"title":"Plausibility of the Formose Reaction in Alkaline Hydrothermal Vent Environments.","authors":"Arthur Omran","doi":"10.1007/s11084-020-09599-5","DOIUrl":"10.1007/s11084-020-09599-5","url":null,"abstract":"<p><p>Prebiotic processes required a reliable source of free energy and complex chemical mixtures that may have included sugars. The formose reaction is a potential source of those sugars. At moderate to elevated temperature and pH ranges, these sugars rapidly decay. Here it is shown that CaCO₃-based chemical gardens catalyze the formose reaction to produce glucose, ribose, and other monosaccharides. These thin inorganic membranes are explored as analogs of hydrothermal vent materials-a possible place for the origin of life-and similarly exposed to very steep pH gradients. Supported by simulations of a simple reaction-diffusion model, this study shows that such gradients allow for the dynamic accumulation of sugars in specific layers of the thin membrane, effectively protecting formose sugar yields. Therefore, the formose reaction may be a plausible prebiotic reaction in alkaline hydrothermal vent environments, possibly setting the stage for an RNA world.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11084-020-09599-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10225029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Possible Role of Anoxic Alkaline High Subcritical Water in the Formation of Ferric Minerals, Methane and Disordered Graphitic Carbon in a BARB3 Drilled Sample of the 3.4 Ga Buck Reef Chert.","authors":"Marie-Paule Bassez","doi":"10.1007/s11084-023-09638-x","DOIUrl":"10.1007/s11084-023-09638-x","url":null,"abstract":"<p><p>The present article reports Raman spectroscopic observations of siderite, hematite, disordered graphitic carbon and possibly greenalite inside the quartz matrix of a banded iron sample from the BARB3 core drilled inside the 3.4 Ga Buck Reef Chert of the Barberton Greenstone Belt in South Africa. The article also reports Raman spectroscopic observations of quartz cavities, concluding in the presence of water, methane and sodium hydroxide at high concentration leading to pH ~ 15 inside the inclusion, suggesting an Archean water which was strongly basic. Fe^III-greenalite may also be present inside the inclusion. The possible role of anoxic alkaline high subcritical water in the formation of ferric minerals and the CO required for the synthesis of molecules of biological interest has been demonstrated theoretically since 2013 and summarized in the concept of Geobiotropy. The present article experimentally confirms the importance of considering water in its anoxic strongly alkaline high subcritical domain for the formation of quartz, hematite, Fe^III-greenalite, methane and disordered graphitic carbon. Methane is proposed to form locally when the carbon dioxide that is dissolved in the Archean anoxic alkaline high subcritical water, interacts with the molecular hydrogen that is emitted during the anoxic alkaline oxidation of ferrous silicates. The carbon matter is proposed to form as deposition from the anoxic methane-rich fluid. A detailed study of carbon matter from diverse origins is presented in a supplementary file. The study shows that the BARB3_23B sample has been submitted to ~ 335 °C, a temperature of the high subcritical domain, and that the graphitic structure contains very low amounts of oxygen and no hydroxyl functional groups. The importance of considering the structure of water is applied to the constructions of the Neoproterozoic and Archean banded iron formations. It is proposed that their minerals are produced inside chemical reaction chambers containing ferrous silicates, and ejected from the Earth's oceanic crust or upper mantle, during processes involving subduction events or not.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10292018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Behaviour and the Origin of Organisms.","authors":"Matthew Egbert,&nbsp;Martin M Hanczyc,&nbsp;Inman Harvey,&nbsp;Nathaniel Virgo,&nbsp;Emily C Parke,&nbsp;Tom Froese,&nbsp;Hiroki Sayama,&nbsp;Alexandra S Penn,&nbsp;Stuart Bartlett","doi":"10.1007/s11084-023-09635-0","DOIUrl":"10.1007/s11084-023-09635-0","url":null,"abstract":"<p><p>It is common in origins of life research to view the first stages of life as the passive result of particular environmental conditions. This paper considers the alternative possibility: that the antecedents of life were already actively regulating their environment to maintain the conditions necessary for their own persistence. In support of this proposal, we describe 'viability-based behaviour': a way that simple entities can adaptively regulate their environment in response to their health, and in so doing, increase the likelihood of their survival. Drawing on empirical investigations of simple self-preserving abiological systems, we argue that these viability-based behaviours are simple enough to precede neo-Darwinian evolution. We also explain how their operation can reduce the demanding requirements that mainstream theories place upon the environment(s) in which life emerged.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10237777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments.","authors":"Hayley Boigenzahn,&nbsp;John Yin","doi":"10.1007/s11084-022-09634-7","DOIUrl":"https://doi.org/10.1007/s11084-022-09634-7","url":null,"abstract":"<p><p>Polyphosphate-mediated peptide bond formation is central to protein synthesis in modern organisms, but a simpler form of activation likely preceded the emergence of proteins and RNA. One suggested scenario involves trimetaphosphate (TP), an inorganic phosphate that promotes peptide condensation. Peptide bond formation can also be promoted by high pH and drying, but the interaction of these factors with TP has yet to be characterized kinetically. We studied the formation of glycine oligomers formed under initially alkaline conditions in the presence of TP during the process of drying. Oligopeptide products sampled over 24 h were analyzed by functionalization and high-performance liquid chromatography with ultraviolet absorption (UV-HPLC). As they dried, two different pH-dependent mechanisms dominated during different stages of the process. The first mechanism occurs in alkaline solutions and activates monomer amino acids to form dimers while reducing the pH. Our results then become consistent with a second mechanism that proceeds at neutral pH and consumes dimers to form longer products. The possibility that a series of reactions might occur where the first reaction changes the environment to favor the second, and so on, may have broader implications for prebiotic polymerization. Studying how the environment changes during time-varying conditions, like drying, could help us understand how organic polymers formed during the origin of life.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10381183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thymine Adsorption onto Cation Exchanged Montmorillonite Clay: Role of Biogenic Divalent Metal Cations in Prebiotic Processes of Chemical Evolution.","authors":"Satish Chandra Sati,&nbsp;Chandra Kala Pant,&nbsp;Preeti Bhatt,&nbsp;Yogesh Pandey","doi":"10.1007/s11084-022-09633-8","DOIUrl":"https://doi.org/10.1007/s11084-022-09633-8","url":null,"abstract":"<p><p>The adsorption of thymine, a key pyrimidine base of deoxyribonucleic acid (DNA) on montmorillonite clay (Mnt) exchanged with metal ions (Mnt-M²⁺, M²⁺  = Fe²⁺, Co²⁺, Cu²⁺, Ca²⁺, and Mg²⁺) over a range of concentration (7.0 × 10^-5 M to 12.0 × 10^-5 M) and pH (4.0 - 9.0) at ambient temperature has been investigated in aqueous environment spectrophotometrically (UV, FTIR, XRD, SEM-EDX). The effectiveness of various adsorbents was determined in terms of percent (%) binding and Langmuir constants (K_L and X_m) using Langmuir adsorption isotherm at their respective pH of maximum adsorption. Transition metal ions incorporated Mnt, particularly Fe²⁺ have shown better adsorption ability than alkaline earth metal ions. The present study reveals the significant role of divalent metal cation exchanged Mnt clay in the chemical evolution of biomolecules of genetic continuity and self-replication which might have occurred through the adsorption of thymine on and between their silicate layers to protect and achieve biocompatibility.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10371057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical Models of Chiral Symmetry-breaking - A Review of General Theories, and Adiabatic Approximations of the APED System.","authors":"Priscila C Diniz,&nbsp;Jonathan A D Wattis,&nbsp;Fernando P da Costa","doi":"10.1007/s11084-022-09631-w","DOIUrl":"https://doi.org/10.1007/s11084-022-09631-w","url":null,"abstract":"<p><p>We review the literature surrounding chiral symmetry-breaking in chemical systems, with a focus on understanding the mathematical models underlying these chemical processes. We comment in particular on the toy model of Sandars, Viedma's crystal grinding systems and the APED model. We include a few new results based on asymptotic analysis of the APED system.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10729929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary Approach to Biological Homochirality.","authors":"Konstantin K Konstantinov,&nbsp;Alisa F Konstantinova","doi":"10.1007/s11084-022-09632-9","DOIUrl":"https://doi.org/10.1007/s11084-022-09632-9","url":null,"abstract":"<p><p>We study a very simple linear evolutionary model based on distribution of protocells by total enantiomeric excess and without any mutual inhibition and show that such model can produce two species with values of total enantiomeric excess in each of the species approaching [Formula: see text] when there is a global [Formula: see text] symmetry. We then consider a scenario when there is a small external global asymmetry factor, like weak interaction, and show that only one of the species remains in such a case, and that is the one, which is more efficient in replication. We perform an estimate of the time necessary to reach homochirality in such a model and show that reasonable assumptions lead to an estimate of around 300 thousand years plus or minus a couple of orders of magnitude. Despite this seemingly large time to reach homochirality, the model is immune to racemization because amino acids in the model follow the lifespan of the protocells rather than the time needed to reach homochirality. We show that not needing mutual inhibition in such evolutionary model is due to the difference in the topology of the spaces in which considered model and many known models of biological homochirality operate. Bifurcation-based models operate in disconnected zero-dimensional space (the space is just two points with enantiomeric excess equal [Formula: see text] and [Formula: see text]), whereas considered evolutionary model (in its continuous representation) operates in one-dimensional connected space, that is the whole interval between [Formula: see text] and [Formula: see text] of total enantiomeric excess. We then proceed with the analysis of the replication process in non-homochiral environment and show that replication errors (the probability to attach an amino acid of wrong chirality) result in a smooth decrease of replication time when total enantiomeric excess of the replicated structure moves away from zero. We show that this decrease in replication time is sufficient for considered model to work.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10729907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution.","authors":"Kenneth N McGuinness,&nbsp;Gunnar W Klau,&nbsp;Shaunna M Morrison,&nbsp;Elisha K Moore,&nbsp;Jan Seipp,&nbsp;Paul G Falkowski,&nbsp;Vikas Nanda","doi":"10.1007/s11084-022-09630-x","DOIUrl":"https://doi.org/10.1007/s11084-022-09630-x","url":null,"abstract":"<p><p>Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10380659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological Homochirality and the Search for Extraterrestrial Biosignatures.","authors":"Marcelo Gleiser","doi":"10.1007/s11084-022-09623-w","DOIUrl":"https://doi.org/10.1007/s11084-022-09623-w","url":null,"abstract":"<p><p>Most amino acids and sugar molecules occur in mirror, or chiral, images of each other, knowns as enantiomers. However, life on Earth is mostly homochiral: proteins contain almost exclusively L-amino acids, while only D-sugars appear in RNA and DNA. The mechanism behind this fundamental asymmetry of life remains unknown, despite much progress in the theoretical and experimental understanding of homochirality in the past decades. We review three potential mechanisms for the emergence of biological homochirality on primal Earth and explore their implications for astrobiology: the first, that biological homochirality is a stochastic process driven by local environmental fluctuations; the second, that it is driven by circularly-polarized ultraviolet radiation in star-forming regions; and the third, that it is driven by parity violation at the elementary particle level. We argue that each of these mechanisms leads to different observational consequences for the existence of enantiomeric excesses in our solar system and in exoplanets, pointing to the possibility that the search for life elsewhere will help elucidate the origins of homochirality on Earth.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40699979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetry Breaking by Consecutive Amplification: Efficient Paths to Homochirality.","authors":"Laura Huber,&nbsp;Oliver Trapp","doi":"10.1007/s11084-022-09627-6","DOIUrl":"https://doi.org/10.1007/s11084-022-09627-6","url":null,"abstract":"<p><p>To understand chiral symmetry breaking on the molecular level, we developed a method to efficiently investigate reaction kinetics of single molecules. The model systems include autocatalysis as well as a reaction cascade to gain further insight into the prebiotic origin of homochirality. The simulated reactions start with a substrate and only a single catalyst molecule, and the occurrence of symmetry breaking was examined for its degree of dependence on randomness. The results demonstrate that interlocking processes, which e.g., form catalysts, autocatalytic systems, or reaction cascades that build on each other and lead to a kinetic acceleration, can very well amplify a statistically occurring symmetry breaking. These results suggest a promising direction for the experimental implementation and identification of such processes, which could have led to a shift out of thermodynamic equilibrium in the emergence of life.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10615881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}