Showing papers in "Origins of Life and Evolution of Biospheres in 2020"

The Prebiotic Provenance of Semi-Aqueous Solvents.

Abstract: The numerous and varied roles of phosphorylated organic molecules in biochemistry suggest they may have been important to the origin of life. The prominence of phosphorylated molecules presents a conundrum given that phosphorylation is a thermodynamically unfavorable, endergonic process in water, and most natural sources of phosphate are poorly soluble. We recently demonstrated that a semi-aqueous solvent consisting of urea, ammonium formate, and water (UAFW) supports the dissolution of phosphate and the phosphorylation of nucleosides. However, the prebiotic feasibility and robustness of the UAFW system are unclear. Here, we study the UAFW system as a medium in which phosphate minerals are potentially solubilized. Specifically, we conduct a series of chemical experiments alongside thermodynamic models that simulate the formation of ammonium formate from the hydrolysis of hydrogen cyanide, and demonstrate the stability of formamide in such solvents (as an aqueous mixture). The dissolution of hydroxylapatite requires a liquid medium, and we investigate whether a UAFW system is solid or liquid over varied conditions, finding that this characteristic is controlled by the molar ratios of the three components. For liquid UAFW mixtures, we also find the solubility of phosphate is higher when the quantity of ammonium formate is greater than urea. We suggest the urea within the system can lower the activity of water, help create a stable and persistent solution, and may act as a condensing agent/catalyst to improve nucleoside phosphorylation yields.

Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions

Abstract: Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.

Unexpected Thiocyanate Adsorption onto Ferrihydrite Under Prebiotic Chemistry Conditions.

Abstract: The most crucial role played by minerals was in the preconcentration of biomolecules or precursors of biomolecules in prebiotic seas. If this step had not occurred, molecular evolution would not have occurred. Thiocyanate is an important molecule in the formation of biomolecules as well as a catalyst for prebiotic reactions. The adsorption of thiocyanate onto ferrihydrite was carried out under pH and ion composition conditions in seawater that resembled those of prebiotic Earth. The seawater used in this work had high Mg2+, Ca2+ and SO42− concentrations. The most important result of this work was that ferrihydrite adsorbed thiocyanateata pH value (7.2 ± 0.2) that usually does not adsorb thiocyanate. The high adsorptivity of Mg2+, Ca2+ and SO42−onto ferrihydrite showed that seawater ions can act as carriers of thiocyanate to the ferrihydrite surface, creating a huge outer-sphere complex. Kinetic adsorption and isotherm experiments showed the best fit for the pseudo-second-order model and an activation energy of 23.8 kJ mol−1forthe Langmuir-Freundlich model, respectively. Thermodynamic data showed positive ΔG values, which apparently contradict the adsorption isotherm data and kinetic data that was obtained. The adsorption of thiocyanate onto ferrihydrite could be explained by coupling with the exergonic SO42− adsorption onto ferrihydrite. The FTIR spectra showed no difference between the C≡N stretching peaks of adsorbed thiocyanate and free thiocyanate, corroborating the formation of an outer-sphere complex. All the results demonstrated the importance of the artificial seawater composition for the adsorption of thiocyanate and for understanding prebiotic chemistry.

Plausibility of the Formose Reaction in Alkaline Hydrothermal Vent Environments.

Abstract: 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.

On A Hypothetical Mechanism of Interstellar Life Transfer Trough Nomadic Objects.

Abstract: Lethal radiation, low vacuum pressure and low temperatures – this is how space welcomes organisms. Crossing of immense interstellar distances inflates the exposure time of biological material to harmful space conditions. This paper discusses the intriguing possibility of a life-bearing exoplanet being ejected from its planetary system and carrying life across interstellar distances (nomadic = free floating = rogue planet). The proposed interstellar panspermia mechanism reduces the exposure time to space conditions and provides multiple chances for interactions between microbes-bearing rock debris and exoplanets within system the nomadic object encountered on its way. The testing strategy is outlined and discussed in the paper, including testable predictions the proposed hypothesis makes.

Survival of the Halophilic Archaeon Halovarius luteus after Desiccation, Simulated Martian UV Radiation and Vacuum in Comparison to Bacillus atrophaeus.

Abstract: Extraterrestrial environments influence the biochemistry of organisms through a variety of factors, including high levels of radiation and vacuum, temperature extremes and a lack of water and nutrients. A wide variety of terrestrial microorganisms, including those counted amongst the most ancient inhabitants of Earth, can cope with high levels of salinity, extreme temperatures, desiccation and high levels of radiation. Key among these are the haloarchaea, considered particularly relevant for astrobiological studies due to their ability to thrive in hypersaline environments. In this study, a novel haloarchaea isolated from Urmia Salt Lake, Iran, Halovarius luteus strain DA50T, was exposed to varying levels of simulated extraterrestrial conditions and compared to that of the bacteria Bacillus atrophaeus. Bacillus atrophaeus was selected for comparison due to its well-described resistance to extreme conditions and its ability to produce strong spore structures. Thin films were produced to investigate viability without the protective influence of cell multi-layers. Late exponential phase cultures of Hvr. luteus and B. atrophaeus were placed in brine and phosphate buffered saline media, respectively. The solutions were allowed to evaporate and cells were encapsulated and exposed to radiation, desiccation and vacuum conditions, and their post-exposure viability was studied by the Most Probable Number method. The protein profile using High Performance Liquid Chromatography and Matrix Assisted Laser Desorption/Ionization bench top reflector time-of-flight are explored after vacuum and UV-radiation exposure. Results showed that the change in viability of the spore-forming bacteria B. atrophaeus was only minor whereas Hvr. luteus demonstrated a range of viability under different conditions. At the peak radiation flux of 105 J/m2 under nitrogen flow and after two weeks of desiccation, Hvr. luteus demonstrated the greatest decrease in viability. This study further expands our understanding of the boundary conditions of astrobiologically relevant organisms in the harsh space environment.

Chirality Driven Twisting as a Driving Force of Primitive Folding in Binary Mixtures

Abstract: The N-trifluoroacetylated α-aminoalcohols (TFAAAs) are able to form quasi-one-dimensional supramolecular fibers (strings) when chirally pure, and isometric precipitates in the racemate. The strings’ formation leads to the reversible gelation of the solution. The fresh gels occupy all the available volume, however during the incubation, they contract and concentrate in the central region of the tube. The microscopic observations revealed the growth of the strings’ diameter and their rotation in the course of the incubation at the hour time-scale. The rotation provides for the hairpins forming that serve as hooks on the rotating string, which provides for coiling of the strings, which was observed as gel contraction. The morphology of the twisted strings resembles the structures observed in modern proteins, which allows drawing an analogy between the folding of biopolymers and the formation of the clew of strings. In addition, the rotation found in the TFAAA gels is an example of a simple system converting the energy of intermolecular agglutination to the rotational movement, so they could be considered as molecular motors.

Chiral Symmetry Breaking in Large Peptide Systems.

Abstract: Chiral symmetry breaking in far from equilibrium systems with large number of amino acids and peptides, like a prebiotic Earth, was considered. It was shown that if organic catalysts were abundant, then effective averaging of enantioselectivity would prohibit any symmetry breaking in such systems. It was further argued that non-linear (catalytic) reactions must be very scarce (called the abundance parameter) and catalysts should work on small groups of similar reactions (called the similarity parameter) in order to chiral symmetry breaking have a chance to occur. Models with 20 amino acids and peptide lengths up to three were considered. It was shown that there are preferred ranges of abundance and similarity parameters where the symmetry breaking can occur in the models with catalytic synthesis / catalytic destruction / both catalytic synthesis and catalytic destruction. It was further shown that models with catalytic synthesis and catalytic destruction statistically result in a substantially higher percentage of the models where the symmetry breaking can occur in comparison to the models with just catalytic synthesis or catalytic destruction. It was also shown that when chiral symmetry breaking occurs, then concentrations of some amino acids, which collectively have some mutually beneficial properties, go up, whereas the concentrations of the ones, which don't have such properties, go down. An open source code of the whole system was provided to ensure that the results can be checked, repeated, and extended further if needed.

Alteration and Stability of Complex Macromolecular Amino Acid Precursors in Hydrothermal Environments

Abstract: The early Solar System comprised a broad area of abiotically created organic compounds, including interstellar organics which were integrated into planetesimals and parent bodies of meteorites, and eventually delivered to the early Earth. In this study, we simulated interstellar complex organic compounds synthesized by proton irradiation of a gas mixture of CO, NH3, and H2O, which are known to release amino acids after acid hydrolysis on the basis of Kobayashi et al. (1999) who reported that at the first stage of chemical evolution, the main compounds formed abiotically are complex organic compounds with high molecular weights. We examined their possible hydrothermal alteration and stabilities as amino acid precursors under high temperature and pressure conditions simulating parent bodies of meteorites by using an autoclave. We reported that all samples treated at 200–300 °C predominantly released glycine and alanine, followed by α-aminobutyric acid, and serine. After heating, amino acid concentrations decreased in general; however, the recovery ratios of γ-aminobutyric acid increased with temperature. The interstellar complex organic analog could maintain as amino acid precursors after being treated at high temperature (200–300 °C) and pressure (8–14 MPa). However, the molecular structures were altered during heating to form organic compounds that are more stable and can survive in elevated hydrothermal conditions.

Symphony in C: Carbon and the Evolution of (Almost) Everything by Robert M. Hazen, W.W. Norton & Company, 2019

Abstract: I have to admit that I am a fan of Robert Hazen. In 2005 I favorably reviewed his bookGenesis and in 2013 I favorably reviewed his DVD course The Origin and Evolution of Earth. Hazen is executive director of the Deep Carbon Observatory at the Carnegie Institution and Professor of Earth Science at George Mason University. He is also a trumpet player of symphonies by Beethoven, Brahms, Schuman, and Mendelssohn. What I like about Hazen, who has produced a number of books and DVDs, is that I am always learning new things from his works which are always delivered in superlative style. In addition, Hazen’s expositions of science always include fascinating descriptions of its practitioner scientists. So, when I ordered a copy of his latest book, I knew I was in for a good read. In Symphony in C Hazen presents us with a carbon-centered view of Planet Earth in analogy to a symphony in four movements, which he entitles Earth, Air, Fire, and Water. Earth recounts how carbon became the fourth most abundant element in the Universe, produced by stellar evolution, and subsequently became a major element of the Earth from the beginning of its evolution 4 1⁄2 billion years ago. The Earth contains more than 400 carbon minerals. Carbon, in the form of calcium carbonate, or limestone, comprises the largest repository of carbon in the Earth’s crust, roughly 100 million billion tons of such rock. Air shows how carbon in the Earth began circulating as carbon dioxide through the Earth via its oceans and solid carbonate rocks. Fire describes a number of thermal chemical reactions undergone by carbon within the Earth and also in chemists’ laboratories. Carbon, Element No. 6, has a unique capacity to form a near infinite number of chemicals, some of which are: dry ice (frozen carbon dioxide), super glue (cyanoacrylate), wax, grease, oils, graphite, graphene, diamonds, dynamite (nitroglycerin absorbed on a stable substrate), Fullerenes, Bucky Balls, nanotubes, Bakelite, plastic, rubber, aspirin (acetylsalicylic acid), cellophane, neoprene, nylon, and pasta, to name just a few. Finally, Water describes how carbon, within Earth’s watery milieu, displayed its most extraordinary property of all, namely this element’s ability to form life with the participation of the other Origins of Life and Evolution of Biospheres https://doi.org/10.1007/s11084-020-09592-y

Parity Violation Energy of Biomolecules - V: Protein Metal Centers.

Abstract: The parity-violation difference between mirror images of chiral metal centers found in naturally occurring proteins and enzymes is computed at the Dirac-Hartree-Fock level, for both equilibrium and transition state configurations The systems, selected on the likelihood of yielding high parity violation energies based on atomic mass and coordination geometry, are extracted from: type I Blue Copper Protein active site, Zn and Cd Carbon Anhydrase, Ni Acetyl-Coenzyme-A Synthase, and Mo based CO-Dehydrogenase Our values provide an approximate upper limit to possible parity-violation effects in biological systems based on static effects

Investigating the Evolution and Development of Biological Systems from the Perspective of Thermo-Kinetics and Systems Theory

Abstract: Life itself is grander than the sum of its constituent molecules. Any living organism may be regarded as a part of a dissipative process that connects irreversible energy consumption with growth, reproduction, and evolution. Under energy-fuelled, far-from-equilibrium conditions, chemical systems capable of exponential growth can manifest a specific form of stability- dynamic kinetic stability (DKS) - indicating the persistence of self-reproducible entities. This kinetic behavior is associated with thermodynamic conditions far from equilibrium leading to an evolutionary view of the origin of life in which increasing entities have to be associated with the dissipation of free energy. This review aims to reformulate Darwinian theory in physicochemical terms so that it can handle both animate and inanimate systems, thus helping to overcome this theoretical divide. The expanded formulation is based on the principle of dynamic kinetic stability and evidence from the emerging field of systems chemistry. Although the classic Darwinian theory is useful for understanding the origins and evolution of species, it is not meant to primarily build an explicit framework for predicting potential evolution routes. Throughout the last century, the inherently systemic and dynamic nature of the biological systems has been brought to the attention of researchers. During the last decades, "systems" approaches to biology and genome evolution are gaining ever greater significance providing the possibility of a deeper interpretation of the basic concepts of life. Further progress of this approach depends on crossing disciplinary boundaries and complex simulations of biological systems. Evolutionary systems biology (ESB) through the integration of methods from evolutionary biology and systems biology aims to the understanding of the fundamental principles of life as well as the prediction of biological systems evolution.