Showing papers in "Origins of Life and Evolution of Biospheres in 2015"
TL;DR: Observations highlight that water-splitting in photosystem II evolved independently from a homodimeric ancestral type II reaction center capable of high potential photosynthesis and Mn(II) oxidation, which is required by the presence of homologous redox-active tyrosines in the modern heterodimer.
Abstract: Oxygenic photosynthesis is the most important bioenergetic event in the history of our planet-it evolved once within the Cyanobacteria, and remained largely unchanged as it was transferred to algae and plants via endosymbiosis. Manganese plays a fundamental role in this history because it lends the critical redox behavior of the water-oxidizing complex of photosystem II. Constraints from the photoassembly of the Mn-bearing water-oxidizing complex fuel the hypothesis that Mn(II) once played a key role as an electron donor for anoxygenic photosynthesis prior to the evolution of oxygenic photosynthesis. Here we review the growing body of geological and geochemical evidence from the Archean and Paleoproterozoic sedimentary records that supports this idea and demonstrates that the oxidative branch of the Mn cycle switched on prior to the rise of oxygen. This Mn-oxidizing phototrophy hypothesis also receives support from the biological record of extant phototrophs, and can be made more explicit by leveraging constraints from structural biology and biochemistry of photosystem II in Cyanobacteria. These observations highlight that water-splitting in photosystem II evolved independently from a homodimeric ancestral type II reaction center capable of high potential photosynthesis and Mn(II) oxidation, which is required by the presence of homologous redox-active tyrosines in the modern heterodimer. The ancestral homodimer reaction center also evolved a C-terminal extension that sterically precluded standard phototrophic electron donors like cytochrome c, cupredoxins, or high-potential iron-sulfur proteins, and could only complete direct oxidation of small molecules like Mn(2+), and ultimately water.
50 citations
TL;DR: The meteoritic mineral schreibersite has been proposed as an important source of reactive P on the early earth and several high-energy P intermediates may have provided the reactive material necessary for incorporating P into prebiotic molecules.
Abstract: The ubiquity of phosphorus (P) in modern biochemistry suggests that P may have participated in prebiotic chemistry prior to the emergence of life. Of the major biogenic elements, phosphorus alone lacks a substantial volatile phase and its ultimate source therefore had to have been a mineral. However, as most native P minerals are chemically un-reactive within the temperature-pressure-pH regimes of contemporary life, it begs the question as to whether the most primitive early living systems on earth had access to a more chemically reactive P-mineral inventory. The meteoritic mineral schreibersite has been proposed as an important source of reactive P on the early earth. The chemistry of schreibersite as a P source is summarized and reviewed here. Recent work has also shown that reduced oxidation state P compounds were present on the early earth; these compounds lend credence to the relevance of schreibersite as a prebiotic mineral. Ultimately, schreibersite will oxidize to phosphate, but several high-energy P intermediates may have provided the reactive material necessary for incorporating P into prebiotic molecules.
30 citations
TL;DR: The natural regimes of pressure and temperature fluctuations in Kamchatka hydrothermal systems can guide future experiments on prebiotic chemistry under oscillating conditions.
Abstract: The composition of organic matter and fluctuations of thermodynamic parameters were investigated in the hydrothermal systems of the Kamchatka peninsula in the context of the origin of life. Organics were analyzed by gas-chromatography/mass spectrometry, and 111 organic compounds belonging to 14 homologous series (aromatic hydrocarbons, alkanes and isoalkanes, halogenated aromatic hydrocarbons, carboxylic acids, esters, etc.) were found in hot springs inhabited by Archaeal and Bacterial thermophiles. The organics detected in the sterile condensate of water-steam mixture taken from deep boreholes (temperature 108–175 °C) consisted of 69 compounds of 11 homologous series, with aromatic hydrocarbons and alkanes being prevalent. The organic material included important prebiotic components such as nitrogen-containing compounds and lipid precursors. A separate organic phase (oil) was discovered in the Uzon Caldera. A biogenic origin is supported by the presence of sterane and hopane biomarkers and the δ13C value of the bulk oil; its age determined by 14C measurements was 1030 ± 40 years. Multilevel fluctuations of thermodynamic parameters proposed to be required for the origin of life were determined in the Mutnovsky and Pauzhetsky hydrothermal systems. The low-frequency component of the hydrothermal fluid pressure varied by up to 2 bars over periods of hours to days, while mid-frequency variations had regular micro-oscillations with periods of about 20 min; the high-frequency component displayed sharp changes of pressure and microfluctuations with periods less than 5 min. The correlation coefficient between pressure and temperature ranges from 0.89 to 0.99 (average 0.96). The natural regimes of pressure and temperature fluctuations in Kamchatka hydrothermal systems can guide future experiments on prebiotic chemistry under oscillating conditions.
26 citations
TL;DR: Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline Hydrothermal fluids at the vent–ocean interface, may be the most suitable environment for the synthesis and polymerization of amino acids.
Abstract: Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson–Kirkham–Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent–ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.
25 citations
TL;DR: The process of periodic formation and destruction of vesicles could offer a perfect environment for molecular evolution in small compartments and for the generation of protocells.
Abstract: Tectonic fault systems in the continental crust offer huge networks of interconnected channels and cavities. Filled mainly with water and carbon dioxide (CO2), containing a wide variety of hydrothermal chemistry and numerous catalytic surfaces, they may offer ideal reaction conditions for prebiotic chemistry. In these systems, an accumulation zone for organic compounds will develop at a depth of approximately 1 km where CO2 turns sub-critical and dissolved components precipitate. At this point, periodic pressure changes caused for example by tidal influences or geyser activity may generate a cyclic process involving repeated phase transitions of carbon dioxide. In the presence of amphiphilic compounds, this will necessarily lead to the transient formation of coated water droplets in the gas phase and corresponding vesicular structures in the aqueous environment. During this process, the concentration of organic components inside the droplets and vesicles would be drastically increased, allowing for favorable reaction conditions and, in case of the vesicles generated, large trans-membrane concentration gradients. Altogether, the process of periodic formation and destruction of vesicles could offer a perfect environment for molecular evolution in small compartments and for the generation of protocells. The basic process of vesicle formation is reproduced experimentally with a lipid in a water/CO2 system.
25 citations
TL;DR: It is shown (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers, and the likelihood of such a replicator being discovered by chance is increased by many orders of magnitude.
Abstract: Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.
22 citations
TL;DR: It is found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation, and remarkable LC-enhanced chain lengthening is observed, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.
Abstract: The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5'-hydroxy-3'-phosphate partially self-complementary DNA 14mers with 3'-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.
19 citations
TL;DR: It is argued that the phospholipid glycerol headgroups of archaea and bacteria are both exclusively homochiral, and that the reason for this “dual homochirality” was a simple evolutionary choice at the independent origin of the two synthesizing enzymes.
Abstract: Homochirality, the single-handedness of optically asymmetric chemical structures, is present in all major biological macromolecules Terrestrial life's preference for one isomer over its mirror image in D-sugars and L-amino acids has both fascinated and puzzled biochemists for over a century But the contrasting case of the equally fundamental phospholipids has received less attention Although the phospholipid glycerol headgroups of archaea and bacteria are both exclusively homochiral, the stereochemistries between the two domains are opposite Here I argue that the reason for this "dual homochirality" was a simple evolutionary choice at the independent origin of the two synthesizing enzymes More broadly, this points to a trivial biogenic cause for the evolution of homochirality: the enzymatic processes that produce chiral biomolecules are stereospecific in nature Once an orientation has been favored, shifting to the opposite is both difficult and unnecessary Homochirality is thus the simplest and most parsimonious evolutionary case
18 citations
TL;DR: Part (a) of the property, the code degeneracy, is derived from the synthetase character of developing specificities directed initially to the principal dinucleotides of the triplets, resulting in tetracodonic degeneracy.
Abstract: The distribution of the triplet to amino acid correspondences in the genetic code matrix contains blocks of similarity. There are (a) groups of similar triplets coding for the same amino acid, which is called code degeneracy, and (b) clusters of similar amino acids corresponding to similar triplets. Processes that led to this regionalization have been investigated through a variety of perspectives but no consensus has been reached and no model has been convincing enough to drive experimental tests. Most traditional has been the hypothesis that the code was derived from the standard evolutionary processes of testing variations in the correspondences through the fitness measure of reaching distributions in the matrix space in an optimal manner so that the effects of mutations on protein phenotypes would be minimized, that is, with reduction of the intensity or of the deviant quality of the functional alterations associated with variations. In contrast, the self-referential model for the formation of the code is based on an original regionalization of characters through the concerted superposition of the two components of the encodings: the four modules of dimers of tRNAs are occupied sequentially by sets of amino acids that are also sequentially devoted to fulfilling specific functions in the protein sites and motifs to which they preferentially belong. Therewith, part (b) of the error-minimizing property follows. Part (a) of the property, the code degeneracy, is derived from the synthetase character of developing specificities directed initially to the principal dinucleotides of the triplets, resulting in tetracodonic degeneracy. This was later partly modified during evolution according to the developments of codon usage and the introduction of new amino acids.
18 citations
TL;DR: The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios.
Abstract: The hypothesis that RNA played a significant role in the origin of life requires effective and efficient abiotic pathways to produce RNA oligomers. The most successful abiotic oligomerization reactions to date have utilized high-energy, modified, or pre-activated ribonucleotides to generate strands of RNA up to 50-mers in length. In spite of their success, these modifications and pre-activation reactions significantly alter the ribonucleotides in ways that are highly unlikely to have occurred on a prebiotic Earth. This research seeks to address this problem by exploring an aqueous based method for activating the canonical ribonucleotides in situ using 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and imidazole. The reactions were run with and without a montmorillonite clay catalyst and compared to reactions that used ribonucleotides that were pre-activated with imidazole. The effects of pH and ribonucleotide concentration were also investigated. The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios.
18 citations
TL;DR: The origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events are explored.
Abstract: We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. Genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term “quasispecies symmetry breaking” to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step.
TL;DR: The two usually separate worlds of rocks and life are shown to be connected through molecular and thermodynamic chemical evolution.
Abstract: In the context of the origin of life, rocks are considered mainly for catalysis and adsorption-desorption processes. Here it is shown how some rocks evolve in energy and might induce synthesis of molecules of biological interest. Radioactive rocks are a source of thermal energy and water radiolysis producing molecular hydrogen, H2. Mafic and ultramafic rocks evolve in water and dissolved carbon dioxide releasing thermal energy and H2. Peridotites and basalts contain ferromagnesian minerals which transform through exothermic reactions with the generation of heat. These reactions might be triggered by any heating process such as radioactive decay, hydrothermal and subduction zones or post-shock of meteorite impacts. H2 might then be generated from endothermic hydrolyses of the ferromagnesian minerals olivine and pyroxene. In both cases of mafic and radioactive rocks, production of CO might occur through high temperature hydrogenation of CO2. CO, instead of CO2, was proven to be necessary in experiments synthesizing biological-type macromolecules with a gaseous mixture of CO, N2 and H2O. In the geological context, N2 is present in the environment, and the activation source might arise from cosmic radiation and/or radionuclides. Ferromagnesian and radioactive rocks might consequently be a starting point of an hydrothermal chemical evolution towards the abiotic formation of biological molecules. The two usually separate worlds of rocks and life are shown to be connected through molecular and thermodynamic chemical evolution. This concept has been proposed earlier by the author (Bassez J Phys: Condens Matter 15:L353–L361, 2003, 2008a, 2008b; Bassez Orig Life Evol Biosph 39(3–4):223–225, 2009; Bassez et al. 2011; Bassez et al. Orig Life Evol Biosph 42(4):307–316, 2012, Bassez 2013) without thermodynamic details. This concept leads to signatures of prebiotic chemistry such as radionuclides and also iron and magnesium carbonates associated with serpentine and/or talc, which were discussed at the 2014 European Astrobiology Network Association conference on Signatures of Life.
TL;DR: A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters, and appeared to protect natural zeolite from thermal degradation.
Abstract: There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.
TL;DR: Two of the most fundamental questions concerning the origin of life, how biologically important molecules find their unique spatial configuration, and how coding sequences can evolve beyond a certain critical length, have not been solved.
Abstract: Two of the most fundamental questions concerning the origin of life, how biologically important molecules (RNA, proteins) find their unique spatial configuration, and how coding sequences can evolve beyond a certain critical length, are discussed. It is shown that both of these problems have not been solved. Experiments that could clarify the mechanisms of interaction between biologically important molecules in the simplest cells are discussed.
TL;DR: It is shown that chiral symmetry breaking using circularly polarized light is dependent on both the helicity and the wavelength of incident light, and time-dependent density functional theory was used to calculate anisotropy spectra.
Abstract: All life on Earth is characterized by its asymmetry – both the genetic material and proteins are composed of homochiral monomers. Understanding how this molecular asymmetry initially arose is a key question related to the origins of life. Cometary ice simulations, l-enantiomeric enriched amino acids in meteorites and the detection of circularly polarized electromagnetic radiation in star-forming regions point to a possible interstellar/protostellar generation of stereochemical asymmetry. Based upon our recently recorded anisotropy spectra g(λ) of amino acids in the vacuum-UV range, we subjected amorphous films of racemic 13C-alanine to far-UV circularly polarized synchrotron radiation to probe the asymmetric photon-molecule interaction under interstellar conditions. Optical purities of up to 4 % were reached, which correlate with our theoretical predictions. Importantly, we show that chiral symmetry breaking using circularly polarized light is dependent on both the helicity and the wavelength of incident light. In order to predict such stereocontrol, time-dependent density functional theory was used to calculate anisotropy spectra. The calculated anisotropy spectra show good agreement with the experimental ones. The European Space Agency’s Rosetta mission, which successfully landed Philae on comet 67P/Churyumov-Gerasimenko on 12 November 2014, will investigate the configuration of chiral compounds and thereby obtain data that are to be interpreted in the context of the results presented here.
TL;DR: Moves of centrality of the 12 graphs indicate that all amino acids were equally relevant irrespective of its chronological order of its appearance and therefore the genetic code at this stage was already frozen.
Abstract: The 12 different types of graphs of the 8 amino acids encoded by the presumably primeval RNY code are derived. The symmetry groups of these graphs are analyzed and coincide with the corresponding values of polar requirement for each amino acid. The symmetry groups at the codon level are partially carried over as a group or subgroup at the amino acid level. Measures of centrality of the 12 graphs indicate that all amino acids were equally relevant irrespective of its chronological order of its appearance. The elimination of any amino acid would be strongly selected against and therefore the genetic code at this stage was already frozen.
TL;DR: Radio and millimeter-wave astronomical observations suggest that gas-phase polyatomic, carbon-containing molecules survive the planetary nebula phase and subsequently are transported into the interstellar medium, seeding the chemistry of diffuse and then dense clouds.
Abstract: An ever increasing amount of molecular material is being discovered in the interstellar medium, associated with the birth and death of stars and planetary systems. Radio and millimeter-wave astronomical observations, made possible by high-resolution laboratory spectroscopy, uniquely trace the history of gas-phase molecules with biogenic elements. Using a combination of both disciplines, the full extent of the cycling of molecular matter, from circumstellar ejecta of dying stars - objects which expel large amounts of carbon - to nascent solar systems, has been investigated. Such stellar ejecta have been found to exhibit a rich and varied chemical content. Observations demonstrate that this molecular material is passed onto planetary nebulae, the final phase of stellar evolution. Here the star sheds almost its entire original mass, becoming an ultraviolet-emitting white dwarf. Molecules such as H2CO, HCN, HCO(+), and CCH are present in significant concentrations across the entire age span of such nebulae. These data suggest that gas-phase polyatomic, carbon-containing molecules survive the planetary nebula phase and subsequently are transported into the interstellar medium, seeding the chemistry of diffuse and then dense clouds. The extent of the chemical complexity in dense clouds is unknown, hindered by the high spectral line density. Organic species such as acetamide and methyl amine are present in such objects, and NH2CHO has a wide Galactic distribution. However, organophosphorus compounds have not yet been detected in dense clouds. Based on carbon and nitrogen isotope ratios, molecular material from the ISM appears to become incorporated into solar system planetesimals. It is therefore likely that interstellar synthesis influences prebiotic chemistry on planet surfaces.
TL;DR: This study focuses on glycerol-citric acid HBPs synthesized via moderate heating in the dry state, and proposes that the chelating properties of citric acid govern the makeup of the resulting polymer, turning the polymerization system into a rudimentary smart material.
Abstract: Proteins are responsible multiple biological functions, such as ligand binding, catalysis, and ion channeling. This functionality is enabled by proteins’ three-dimensional structures that require long polypeptides. Since plausibly prebiotic synthesis of functional polypeptides has proven challenging in the laboratory, we propose that these functions may have been initially performed by alternative macromolecular constructs, namely hyperbranched polymers (HBPs), during early stages of chemical evolution. HBPs can be straightforwardly synthesized in one-pot processes, possess globular structures determined by their architecture as opposed to folding in proteins, and have documented ligand binding and catalytic properties. Our initial study focuses on glycerol-citric acid HBPs synthesized via moderate heating in the dry state. The polymerization products consisted of a mixture of isomeric structures of varying molar mass as evidenced by NMR, mass spectrometry and size-exclusion chromatography. Addition of divalent cations during polymerization resulted in increased incorporation of citric acid into the HBPs and the possible formation of cation-oligomer complexes. The chelating properties of citric acid govern the makeup of the resulting polymer, turning the polymerization system into a rudimentary smart material.
TL;DR: A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup and indicating that REMD simulations can be used for the structural investigation of short peptides.
Abstract: The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides.
TL;DR: It is argued that a linkage directing process will be found for a lipid membrane and may in the right environment result in initial evolution, including initiation of α-helices, the development of a single chirality and NTPs, and so satisfies the prior requirement.
Abstract: It is proposed that processes characteristic of biology today, autocatalysis, selection of molecules for linkage by their electrical shape, and evolution by survival selection were also the processes that initiated biology. A reconnaissance is made of both paradoxes and potential questions. It is argued that the minimal requirement for initiating Darwinian evolution is not a molecule copying process, but a linkage copying process. Survival selection evolution does not require a heterocatalytic polymer and a separate replicase process until there is uncertainty where molecular additions will occur. It is argued that a linkage directing process will be found for a lipid membrane (though this needs to be verified) and may in the right environment result in initial evolution, including initiation of α-helices, the development of a single chirality and NTPs. The system has at this point become sufficiently complex that higher precision copying is needed. However it seems likely that this state is able to generate the first miniature ribozymes and their replicases, and so satisfies the prior requirement. With the proposed requirements, it is likely that the development of polymers was within membranes.
TL;DR: Progress is reported in developing a silica-aerogel-based cosmic dust capture panel for use in the Tanpopo experiment on the International Space Station and qualification tests for an engineering model of the capture panel as an instrument aboard the ISS were successful.
Abstract: In this paper, we report the progress in developing a silica-aerogel-based cosmic dust capture panel for use in the Tanpopo experiment on the International Space Station (ISS). Previous studies revealed that ultralow-density silica aerogel tiles, comprising two layers with densities of 0.01 and 0.03 g/cm(3) developed using our production technique, were suitable for achieving the scientific objectives of the astrobiological mission. A special density configuration (i.e., box framing) aerogel with a holder was designed to construct the capture panels. Qualification tests for an engineering model of the capture panel as an instrument aboard the ISS were successful. Sixty box-framing aerogel tiles were manufactured in a contamination-controlled environment.
TL;DR: From space infrared spectroscopic observations, it is found that complex organics can be synthesized in the late stages of stellar evolution, and the chemical structures of the stellar organics show strong similarity to the insoluble organic matter found in meteorites.
Abstract: Recent research has discovered that complex organic matter is prevalent throughout the Universe. In the Solar System, it is found in meteorites, comets, interplanetary dust particles, and planetary satellites. Spectroscopic signatures of organics with aromatic/aliphatic structures are also found in stellar ejecta, diffuse interstellar medium, and external galaxies. From space infrared spectroscopic observations, we have found that complex organics can be synthesized in the late stages of stellar evolution. Shortly after the nuclear synthesis of the element carbon, organic gas-phase molecules are formed in the stellar winds, which later condense into solid organic particles. This organic synthesis occurs over very short time scales of about a thousand years. In order to determine the chemical structures of these stellar organics, comparisons are made with particles produced in the laboratory. Using the technique of chemical vapor deposition, artificial organic particles have been created by injecting energy into gas-phase hydrocarbon molecules. These comparisons led us to believe that the stellar organics are best described as amorphous carbonaceous nanoparticles with mixed aromatic and aliphatic components. The chemical structures of the stellar organics show strong similarity to the insoluble organic matter found in meteorites. Isotopic analysis of meteorites and interplanetary dust collected in the upper atmospheres have revealed the presence of pre-solar grains similar to those formed in old stars. This provides a direct link between star dust and the Solar System and raises the possibility that the early Solar System was chemically enriched by stellar ejecta with the potential of influencing the origin of life on Earth.
TL;DR: This study explores the sensitivity of the precipitation climatology of Titan-like exomoons to these moons’ orbital configuration using a global climate model and finds that precipitation on exomoon with dense atmospheres generally occurs at any longitude in contrast to tidally locked exoplanets.
Abstract: The availability of liquid water on the surface on Earth's continents in part relies on the precipitation of water This implies that the habitability of exomoons has to consider not only the surface temperature and atmospheric pressure for the presence of liquid water, but also the global precipitation climatology This study explores the sensitivity of the precipitation climatology of Titan-like exomoons to these moons' orbital configuration using a global climate model The precipitation rate primarily depends on latitude and is sensitive to the planet's obliquity and the moon's rotation rate On slowly rotating moons the precipitation shifts to higher latitudes as obliquity is increased, whereas on quickly rotating moons the latitudinal distribution does not strongly depend on obliquity Stellar eclipse can cause a longitudinal variation in the mean surface temperature and surface pressure between the subplanetary and antiplanetary side if the planet's obliquity and the moon's orbital distance are small In this particular condition the antiplanetary side generally receives more precipitation than the subplanetary side However, precipitation on exomoons with dense atmospheres generally occurs at any longitude in contrast to tidally locked exoplanets
TL;DR: It is demonstrated that when a fatty acid is heated with various amino acids, optimally in the presence of suitable salts or minerals, lipoamino acids are formed.
Abstract: Researchers have formed peptide bonds under a variety of presumed prebiotic conditions. Here it is proposed that these same conditions would have also formed amide bonds between fatty acids and amino acids, producing phosphate-free amphipathic lipoamino acids and lipopeptides. These compounds are known to form vesicles and are ubiquitous in living organisms. They could represent molecules that provided protection by membranes as well as possibilities for proto-life metabolism . It is here demonstrated that when a fatty acid is heated with various amino acids, optimally in the presence of suitable salts or minerals, lipoamino acids are formed. Magnesium and potassium carbonates as well as iron (II) sulfide are found to be particularly useful in these reactions. In this manner N-lauroylglycine, N-lauroylalanine, N-stearoylalanine and several other lipoamino acids have been synthesized. Similarly, when glycylglycine was heated with lauric acid in the presence of magnesium carbonate, the lipopeptide N-lauroylglycylglycine was formed. Such compounds are proposed to have been critical precursors to the development of life.
TL;DR: This work has performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using UNSW Australia’s Katana supercomputing facility to follow the dynamical evolution of a model inner disk comprising 300,298 particles for a period of 60 Ma.
Abstract: The HR 8799 system, with its four giant planets and two debris belts, has an architecture closely mirroring that of our Solar system where the inner, warm asteroid belt and outer, cool Edgeworth-Kuiper belt bracket the giant planets. As such, it is a valuable laboratory for examining exoplanetary dynamics and debris disk-exoplanet interactions. Whilst the outer debris belt of HR 8799 has been well resolved by previous observations, the spatial extent of the inner disk remains unknown. This leaves a significant question mark over both the location of the planetesimals responsible for producing the belt's visible dust and the physical properties of those grains. We have performed the most extensive simulations to date of the inner, unresolved debris belt around HR 8799, using UNSW Australia's Katana supercomputing facility to follow the dynamical evolution of a model inner disk comprising 300,298 particles for a period of 60 Ma. These simulations have enabled the characterisation of the extent and structure of the inner disk in detail, and will in future allow us to provide a first estimate of the small-body impact rate and water delivery prospects for possible (as-yet undetected) terrestrial planet (s) in the inner system.
TL;DR: This work discusses recently described autocatalytic systems where self-reproducing micelles are driven by bond-forming reactions, which generate increased complexity on both the molecular level, through covalent bond formation, and the supramolecularlevel, through spontaneous self-assembly into functional aggregates.
Abstract: The autocatalytic self-reproduction of micelles and vesicles has been studied for several decades. These systems are vital components of certain protocell models and some models for how life may have begun from mixtures of simple chemicals. Here we discuss our recently described autocatalytic systems where self-reproducing micelles are driven by bond-forming reactions. These systems generate increased complexity on both the molecular level, through covalent bond formation, and the supramolecular level, through spontaneous self-assembly into functional aggregates. This provides the conceptual basis for novel studies of the potential roles of self-reproducing lipid aggregates in the prebiotic world.
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TL;DR: The evolution of the structural motifs responsible for redox reactions (the biological “transistors”) across the tree of life, and the photogeochemical reactions on minerals that ultimately came to be the driving force for these biological reactions are examined.
Abstract: The biogeochemical cycles of H, C, N, O and S are coupled via biologically catalyzed electron transfer (redox) reactions far from thermodynamic equilibrium. In this paper I examine the evolution of the structural motifs responsible for redox reactions (the biological “transistors”) across the tree of life, and the photogeochemical reactions on minerals that ultimately came to be the driving force for these biological reactions.
TL;DR: This work aims to construct a chemical system called “protometabolism,” which would be a precursor of metabolism, and abstract some principles from biology and statistical physics to guide this approach.
Abstract: The key issue of the origin of life is the origin of a complex system rather than the abiotic formation of various organic substances, small and large. To consider this “origin problem” it is advantageous to abstract some principles from biology and statistical physics to guide our approach. Referring to these principles, we aim to construct a chemical system called “protometabolism,” which would be a precursor of metabolism.
TL;DR: “AmoebaChem,” a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner, is proposed, which explores a variety of metastable molecule in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules.
Abstract: We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called “AmoebaSAT [Aono et al. 2013],” which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], “the satisfiability problem,” and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [http://www.cs.ubc.ca/~hoos/5/benchm.html]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate “AmoebaChem,” which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.
TL;DR: This work searches for new dynamical configurations—where planets may stay in stable orbits—to increase the probability to find a planet like the Earth.
Abstract: Approximately 60 % of all stars in the solar neighbourhood (up to 80 % in our Milky Way) are members of binary or multiple star systems. This fact led to the speculations that many more planets may exist in binary systems than are currently known. To estimate the habitability of exoplanetary systems, we have to define the so-called habitable zone (HZ). The HZ is defined as a region around a star where a planet would receive enough radiation to maintain liquid water on its surface and to be able to build a stable atmosphere. We search for new dynamical configurations—where planets may stay in stable orbits—to increase the probability to find a planet like the Earth.