Showing papers in "Origins of Life and Evolution of Biospheres in 2019"
University of Nevada, Reno1, National Autonomous University of Mexico2, Ochanomizu University3, Tokyo Institute of Technology4, Middle East Technical University5, California Institute of Technology6, Aix-Marseille University7, Institute of Chemical Technology in Prague8, National University of Malaysia9, University of Colorado Boulder10, Howard Hughes Medical Institute11, University of Cambridge12, Johns Hopkins University13, Helen Wills Neuroscience Institute14, Institute for Advanced Study15, Osaka University16, Pierre-and-Marie-Curie University17, University of Southern California18, University of the Basque Country19, University of Valencia20, Max Planck Society21
TL;DR: Some of the central philosophical issues facing origins-of-life research are described and a targeted history of the developments that have led to the multidisciplinary field of origins- of-life studies is provided to guide researchers and students from all fields.
Abstract: In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wohler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Ganti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.
28 citations
TL;DR: The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history.
Abstract: A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA's working definition of life, which postulates that life is a "self-sustaining chemical system capable of Darwinian evolution". The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.
21 citations
TL;DR: In this paper, the effects of fluctuations on achieving homochirality were investigated using a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included.
Abstract: To understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included. The results of earlier work either without autocatalysis or without cross-inhibition are reproduced. Bifurcation diagrams and the dependencies of the number of reaction steps on parameters are studied. In systems with 30,000 molecules, for example, up to a billion reaction steps may be needed to achieve homochirality without autocatalysis.
11 citations
TL;DR: It is concluded that the four AntiC-SLs were the first primeval tRNAs, which originated from four anticodon stem-loops translating GNC codons to the corresponding four amino acid sequence of a protein.
Abstract: The riddle of the origin of life is unsolved as yet. One of the best ways to solve the riddle would be to find a vestige of the first life from databases of DNA and/or protein of modern organisms. It would be, especially, important to know the origin of tRNA, because it mediates between genetic information and the amino acid sequence of a protein. Here I attempt to find a vestige of the origin and evolution of tRNA from base sequences of Pseudomonas aeruginosa tRNA gene. It was first perceived that 5' anticodon (AntiC) stem sequences of P. aeruginosa tRNA for translation of G-start codon (GNN) are intimately and mutually related. Then, mutual relations among all of the forty-two 5' AntiC stem sequences of P. aeruginosa tRNA were examined. These relationships imply that P. aeruginosa tRNA originated from four anticodon stem-loops (AntiC-SL) translating GNC codons to the corresponding four amino acids, Gly, Ala, Asp and Val (where N is G, C, A, or T). In contrast to the case of AntiC-stem sequence, a mutual relation map could not be drawn with D-, T- and acceptor-stem sequences of P. aeruginosa tRNA. Thus I conclude that the four AntiC-SLs were the first primeval tRNAs.
10 citations
TL;DR: A hypothetical mechanism explaining the amplification of the initial enantiomeric excess, as well as chiral and chemical purification of the substances which were essential for the evolution of Life to start are proposed.
Abstract: This work addresses the supramolecular self-organization in the xerogels of formose reaction products. The UV-induced formose reaction was held in over-saturated formaldehyde solutions at 70∘C without a catalyst. The solutions of the obtained carbohydrates were dried on a glass slide, and the obtained xerogels demonstrated a prominent optical activity, while the initial solutions were optically inactive. The xerogels contained highly elongated crystalline elements of a helical structure as well as the isometric ones. Thus xerogel formation was accompanied by a spontaneous resolution of enantiomers and separation of different-shaped supramolecular structures. The thick helices were twisted of thinner ones, while the latter were twisted of elementary structures having a diameter much smaller than 400 nm. Similar structural hierarchy is typical of biological macromolecules (DNA, proteins, and cellulose). Summarizing the obtained results, we proposed a hypothetical mechanism explaining the amplification of the initial enantiomeric excess, as well as chiral and chemical purification of the substances which were essential for the evolution of Life to start.
10 citations
TL;DR: It was concluded that life could have originated due to the impact of meteorites on alkaline water-formamide lakes located near volcanoes on the early Earth.
Abstract: Syntheses under shock in nitrogen bubbled samples of the water – formamide – bicarbonate – sodium hydroxide system at pH 8.63, 9.46 and 10.44 were performed in the stainless steel preservation capsules. The maximum temperature and pressure in the capsules reached 545 K and 12.5 GPa respectively. Using the LC-MS-MS analysis, the 21 synthesis products have been identified, including amines and polyamines, carboxamide, acetamide and urea derivatives, compounds containing aniline, pyrrolidine, pyrrole, imidazole, as well as alcohol groups. It was found that the Fischer-Tropsch-type syntheses with catalysis on the surface of the stainless steel of the conservation capsule associated with the adsorbed hydrogen cyanide reactions and transamidation processes play the main role in the shock syntheses. Formation reactions of all the above-mentioned compounds have been suggested. It was proposed that hydrogen cyanide, ammonia, isocyanic acid, aminonitrile, aminoacetonitrile, as well as adsorbed species H(a), CH(a), CH2(a), CHOH(a), NH2(a) and H2CNH(a) are especially important for the formation of the products. A reduction reaction of adsorbed bicarbonate with hydrogen to formaldehyde has been first postulated. In the studied system also classical reactions take place – Wohler’s synthesis of urea and Butlerov’s synthesis of methenamine. It was suggest that material of meteorites may be an effective catalyst in the Fischer-Tropsch-type syntheses at falling of the iron-nickel meteorites in the water – formamide regions on the early Earth. It was concluded that life could have originated due to the impact of meteorites on alkaline water-formamide lakes located near volcanoes on the early Earth.
8 citations
TL;DR: The proposed reaction paths are exothermic and barrierless which indicates the possibility of carbodiimide formation in ISM, and the isotropic and anisotropic polarizabilities have been calculated from relevant tensor components for both reaction mechanisms.
Abstract: The Structure of carbodiimide has been studied by using quantum chemical methods. Carbodiimide (HNCNH) has been detected towards Sagittarius B2 (N) in interstellar medium (ISM). Two reaction mechanisms have been proposed to study the formation of interstellar Carbodiimide. The first reaction mechanism is based on molecule-radical and the second one is a radical-radical mechanism, through previously detected interstellar molecules or radicals. Quantum chemical calculations have been performed by using density functional theory (DFT) and Moller-Plesset second order perturbation (MP2) theory, in gas phase as well as in polarizable continuum model (PCM). The proposed reaction paths are exothermic and barrierless which indicates the possibility of carbodiimide formation in ISM. Several basis sets have been used to verify the validity and accuracy of the results. The isotropic and anisotropic polarizabilities of carbodiimide have been calculated from relevant tensor components for both reaction mechanisms with the help of data obtained by DFT/B3LYP and MP2 methods using aug-cc-pVTZ basis sets in gaseous phase as well as in PCM.
7 citations
TL;DR: The one-pot synthesis of purine and pyrimidine nucleic acid bases in the presence of pre-biologically significant binary metal oxide nanoparticles, metal ferrites is described and the ability of isocytosine (a constitutional isomer of cytosine) to recognize cyto and guanine through normal and reversed Watson-Crick pairing respectively, demonstrates an important storyline for the genesis of ancient nucleic acids.
Abstract: The synthesis of prebiotic molecules from simple precursors is believed to be a crucial scheme in order to study the origin of life processes. The present study describes the one-pot synthesis of purine and pyrimidine nucleic acid bases in the presence of pre-biologically significant binary metal oxide nanoparticles, metal ferrites, namely NiFe2O4, CoFe2O4, CuFe2O4, ZnFe2O4 and MnFe2O4. The products identified are cytosine, isocytosine, 4(3H)-pyrimidinone, adenine, hypoxanthine and purine. The ability of isocytosine (a constitutional isomer of cytosine) to recognize cytosine and guanine through normal and reversed Watson-Crick pairing respectively, demonstrates an important storyline for the genesis of ancient nucleic acids. The relevance of other synthesized nucleic acid bases with respect to the origin of life is also discussed. The divalent metal ions in iron oxide make it an appropriate catalytic system because it demonstrates excellent catalytic performance for the nucleic acid bases synthesis with significantly high yield, as compared to pure iron oxide and some other minerals like silica, alumina, manganese oxides and double metal cyanide complexes.
5 citations
TL;DR: The acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01 M HCl at 50 °C leads to the formation of oligosacCharides containing up to eight monomeric units identified by high resolution mass spectrometry.
Abstract: The prebiotic origin of polysaccharides, the largest class of biopolymers by mass in extant biology, has seldom been investigated experimentally. Herein, we report on the acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01 M HCl at 50 °C. This protocol leads to the formation of oligosaccharides containing up to eight monomeric units identified by high resolution mass spectrometry. The regio- and stereochemistry of the oligomeric acetal linkages, as well as the quantitative analysis of glucose conversion, are elucidated by combining 1H, 13C and 2D NMR spectroscopy. Ten out of eleven possible acetal linkages, including α- and β- anomers, have been identified with the α- and β- 1,6-acetals being the dominant linkages observed. In addition, the acid-catalyzed oligomerization of several glucose disaccharides such as cellobiose, maltose, and gentiobiose are presented along with an accompanying comparison with the corresponding oligomerization of glucose.
5 citations
TL;DR: The present data may support established abiogenesis models suggesting that pyrite surfaces carried out primitive metabolic cycles in suitable environments of the early Earth, such as endolithic recesses in mafic rocks permeated by hydrothermal fluids.
Abstract: Pyrite and organic matter closely coexist in some hydrothermally-altered gabbroic xenoliths from the Hyblean Plateau, Sicily The representative sample consists of plagioclase, Fe-oxides, clinopyroxene, pyrite and minor amounts of many other minerals Plagioclase displays incipient albitization, clinopyroxene is deeply corroded Pyrite grains are widely replaced by spongy-textured magnetite, which locally hosts Ca-(and Fe-)sulfate micrograins and blebs of condensed organic matter Whole-rock trace element distribution evidences that incompatible elements, particularly the fluid-mobile Ba, U and Pb, are significantly enriched with respect to N-MORB values The mineralogical and geochemical characteristics of the sample, and its U-Pb zircon age of 2169 ± 67 MA, conform to the xenolith-based viewpoint that the unexposed Hyblean basement is a relict of the Ionian Tethys lithospheric domain, mostly consisting of abyssal-type serpentinized peridotites with small gabbroic intrusions Circulating hydrothermal fluids there favored the formation of hydrocarbons trough Fischer-Tropsch-type organic synthesis, giving also rise to sulfidization episodes Subsequent variations in temperature and redox conditions of the system induced partial de-sulfidization, Fe-oxides precipitation and sulfate-forming reactions, also promoting poly-condensation and aromatization of the already-formed hydrocarbons Here we show organic matter adhering to a crystal face of a microscopic pyrite grain Pyrite surfaces, as abiotic analogues of enzymes, can adsorb and concentrate organic molecules, also acting as catalysts for a broad range of proto-biochemical reactions The present data therefore may support established abiogenesis models suggesting that pyrite surfaces carried out primitive metabolic cycles in suitable environments of the early Earth, such as endolithic recesses in mafic rocks permeated by hydrothermal fluids
4 citations
TL;DR: A potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids is shown.
Abstract: In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.
TL;DR: It is proposed that cytosine residues could have stably existed in the primordial world in the RNA i-motif, a four-stranded quadruplex structure formed by base-pairing of protonated and unprotonated cytOSine residues under acidic conditions.
Abstract: The primordial RNA world is a hypothetical era prior to the appearance of protein and DNA, when RNA molecules were the sole building blocks for early forms of life on Earth. A critical concern with the RNA-world hypothesis is the instability of the cytosine nucleobase compared to the other three bases (adenine, guanine, and uracil). The author proposes that cytosine residues could have stably existed in the primordial world in the RNA i-motif, a four-stranded quadruplex structure formed by base-pairing of protonated and unprotonated cytosine residues under acidic conditions. The i-motif structure not only increases the lifetime of cytosine residues by slowing their deamination rate, but could also allow RNA polymers to bind to certain ligands (e.g., anions) to perform critical functions. Future studies focused on determining the rate of cytosine deamination in RNA i-motifs over a range of pH, temperature, and pressure conditions, and on interrogating the interactions between ligands and RNA i-motifs, could uncover new evidence of the origin of life on Earth.
TL;DR: The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.
Abstract: Amino acids and peptides have been demonstrated to form lipoamino acids and lipopeptides under presumed prebiotic conditions, and readily form liposomes. Of the common nucleobases, adenine forms a liponucleobase even below 100 °C. Adenine as well as other nucleobases can also be derivatized with ethylene carbonate (and likely other similar compounds) onto which fatty acids can be attached. The fatty acid tails along with appropriately functionalized nucleobases provide some solubility of liponucleobases in membranes. Such membranes would provide a structure in which three of biology’s major components are closely associated and available for chemical interactions. Nucleobase-to-nucleobase interactions would ensure that the liponucleobases would have a uniquely different head-group relationship than other amphiphiles within a membrane, likely forming rafts due their π-π interactions and providing surface discontinuities that could serve as catalytic sites. The π-π bond distance in aromatic compounds is typically 0.34 nm, commensurate with that of the amine to carboxylate distance in alpha amino acids. This would have provided opportunity for hydrogen bonding between amino acids and the distal primary amines or tautomeric carbonyl/hydroxyl groups of two π-bonded nucleobases. Such bonding would weaken the covalent linkages within the amino acids, making them susceptible to forming peptide bonds with an adjacent amino acid, likely a lipoamino acid or lipopeptide. Were this second lipoamino acid bound to a third π-bonded nucleobase, it could result in orientation, destabilization and peptide formation. The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.
TL;DR: This work reproduces amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study, and shows that the sequence-selectivity and stereoselectivity of the amyloids-Templated reaction is similar for both activation chemistries.
Abstract: Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We have previously reported on the role that short peptide amyloids could have played in a template-based chemical elongation. Here we take a step closer to the goal by reproducing amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study. Our investigation shows that the sequence-selectivity and stereoselectivity of the amyloid-templated reaction is similar for both activation chemistries. Notably, the amyloid protects the peptides from some of the side-reactions that take place with the COS-activation.
TL;DR: Investigation of the one-pot 1-ethyl-3-methylimidazolium acetate catalyzed synthesis of 1,3-dibutyl-4,5-difuryl-imidazolia acetate shows that the highest yield of DBDFIM-Ac was obtained when the mole ratio of n-butylamine, formaldehyde, and acetic acid relative to furfural was respectively.
Abstract: The chemistry of imidazolium-catalyzed imidazolium synthesis was studied as part of an effort to develop a plausible prebiotic synthesis of a small catalytic molecule capable of catalyzing its own synthesis. Specifically, we investigated the one-pot 1-ethyl-3-methylimidazolium acetate (EMIM-Ac) catalyzed synthesis of 1,3-dibutyl-4,5-difuryl-imidazolium acetate (DBDFIM-Ac) from furfural, n-butylamine, formaldehyde, and acetic acid at 80 °C. Liu et al. (2012) had previously demonstrated the first reaction of the synthetic process, the EMIM-Ac catalyzed benzoin condensation of furfural that yields furoin. Our early studies established the second reaction of the synthetic process, the multicomponent reaction of furoin, n-butylamine, formaldehyde, and acetic acid that yields the imidazolium salt, DBDFIM-Ac. Studies of the complete two-reaction process that uses furfural for the synthesis of DBDFIM-Ac showed that the highest yield of DBDFIM-Ac was obtained when the mole ratio of n-butylamine, formaldehyde, and acetic acid relative to furfural was respectively (0.5:0.25:0.25:1.0-furfural), or one-half of the stoichiometric ratio (1.0:0.5:0.5:1.0-furfural). A time course study of the process showed transient formation of furoin, the obligatory reaction intermediate. DBDFIM-Ac and the imidazolium side product, 1,3-dibutyl-4,5-trifuryl-imidazolium acetate (DBTFIM-Ac), were stable under the reaction conditions. Imidazolium products (DBDFIM and DBTFIM) and the furoin intermediate were not formed in control reactions (80 °C, 24 h) in which EMIM catalyst was either absent or replaced with an equal volume of acetonitrile or DMF. The imidazolium product, DBDFIM-Ac, was shown to catalyze the synthesis of structurally similar 1,3-dipentyl-4,5-difuryl-imidazolium acetate (DPDFIM-Ac) from furfural, n-pentylamine, formaldehyde, and acetic acid at 80 °C.
TL;DR: The author reveals that his mother was a religious believer, that his father was an agnostic mathematician, and that he himself is a believer, and one of the most interesting questions that the author poses is the question of how theology might be affected if life is discovered elsewhere in the Universe.
Abstract: Two of the best science conferences that I ever attended were the last two Trieste Conferences on Chemical Evolution and the Origins of Life, in 2001 and 2003, both of which were organized and hosted by Julian Chela-Flores in a superb manner. So I looked forward to a good experience as I read ASTROBIOLOGY AND HUMANISM: Conversations on Science, Philosophy and Theology. The Trieste Conferences on Chemical Evolution and the Origins of Life were initiated in the 1980s at the Trieste International Center for Theoretical Physics by Cyril Ponnamperuma at the behest of Abdus Salam, the Director of the Center, and were continued after Ponnamperuma by Chela-Flores. Every 3 years, in the beautiful ancient Roman port city of Trieste, Chela-Flores managed to attract a stunning, eclectic array of scientists, philosophers, and theologians to discuss the origins-of-life, astrobiology, and their interactions with the humanities since the 1990s. In 2001, Chela-Flores published THENEW SCIENCEOFASTROBIOLOGY: FromGenesis of the Living Cell to Evolution of Intelligent Behavior in the Universe, Kluwer Academic Publishers, which was an important overview of this new and multidisciplinary field of science. Chela-Flores’ newest book ASTROBIOLOGY AND HUMANISM, a sleek hardback of 150 pages at a list price of $119.95, is an interesting sequel to his earlier books, in that his earlier books were comprehensive and technical whereas the new book is a highly personal philosophical memoir of his voyage from his doctorate in quantum physics at the University of London, through his participation in several influential scientific organizations, to the present time. For example, Chela-Flores reveals that his mother was a religious believer, that his father was an agnostic mathematician, and that he himself is a believer. Undoubtedly, such religious belief is largely responsible for the ecumenical nature of the Trieste Conferences under ChelaFlores’ leadership. Thus, one of the most interesting questions that the author poses is the question of how theology might be affected if life is discovered elsewhere in the Universe. Origins of Life and Evolution of Biospheres https://doi.org/10.1007/s11084-019-09584-7