The evolution of organic matter in space

An experimental and numerical model of the behavior of cytosine in aqueous solution under gamma radiation. Relevance in prebiotic chemistry

Cytosine is an essential chemical molecule in living systems, such as DNA and RNA, it is essential in astrobiology to study how it behaves under probable primitive conditions. We looked at how cytosine broke down in aqueous solutions exposed to high radiation levels to learn more about how stable it might have been on the early Earth. We conducted various types of analysis, such as ultraviolet-visible spectroscopy and high-pressure liquid chromatography. We also developed a computer model to describe the kinetic processes and learn more about the molecules involved in the system. This model fits the results of experiments and lets us study cytosine's stability when it is exposed to gamma radiation. It enables researchers to theorize processes that are hard to test in the laboratory and is essential for studying how stable cytosine behaves in high-radiation settings.

Carbon Monoxide Poisoning: From Occupational Health to Emergency Medicine

Carbon monoxide poisoning remains a leading cause of accidental poisoning worldwide (both at home and at work), and it is also a cause of suicidal poisoning. Such poisoning can arise following prolonged exposure to low levels of CO or following brief exposure to high concentrations of the gas. In fact, despite exposure limits, high safety standards, and the availability of CO alarms, nearly 50,000 people in the United States visit the emergency department each year due to poisoning. Additionally, CO poisoning in the United States causes up to 500 deaths each year. Despite the widespread nature of this form of poisoning, known about for centuries and whose damage mechanisms have been recognized (or rather hypothesized about) since the 1800s, early recognition, especially of late complications, and treatment remain a medical challenge. A well-designed therapeutic diagnostic process is necessary so that indication for hyperbaric or normobaric therapy is correctly made and so that patients are followed up even after acute exposure to diagnose late complications early. Furthermore, it is necessary to consider that in the setting of emergency medicine, CO poisoning can be part of a differential diagnosis along with other more frequent conditions, making its recognition difficult. The last thirty years have been marked by a significant increase in knowledge regarding the toxicity of CO, as well as its functioning and its importance at physiological concentrations in mammalian systems. This review, taking into account the significant progress made in recent years, aims to reconsider the pathogenicity of CO, which is not trivially just poisonous to tissues. A revision of the paradigm, especially as regards treatment and sequelae, appears necessary, and new studies should focus on this new point of view.

Results of an Eight-Year Extraction of Phosphorus Minerals within the Seymchan Meteorite

In-fall of extraterrestrial material including meteorites and interstellar dust particles during the late heavy bombardment are known to have brought substantial amounts of reduced oxidation-state phosphorus to the early Earth in the form of siderophilic minerals, e.g., schreibersite ((FeNi)₃P). In this report, we present results on the reaction of meteoritic phosphide minerals in the Seymchan meteorite in ultrapure water for 8 years. The ions produced during schreibersite corrosion (phosphite, hypophosphate, pyrophosphate, and phosphate) are stable and persistent in aqueous solution over this timescale. These results were also compared with the short-term corrosion reactions of the meteoritic mineral schreibersite's synthetic analog Fe₃P in aqueous and non-aqueous solutions (ultrapure water and formamide). This finding suggests that the reduced-oxidation-state phosphorus (P) compounds including phosphite could be ubiquitous and stable on the early Earth over a long span of time and such compounds could be readily available on the early Earth.

How Did Life Emerge in Chemically Complex Messy Environments?

One of the problems that make it difficult to solve the mystery of the origin of life is determining how life emerged in chemically complex messy environments on primitive Earth. In this article, the “chemically complex messy environments” that are focused on are a mixed state of various organic compounds produced via prebiotic means and accumulated on primitive earth. The five factors described below are thought to have contributed to opening the way for the emergence of life: (1) A characteristic inherent in [GADV]-amino acids, which are easily produced via prebiotic means. [GADV] stands for four amino acids, Gly [G], Ala [A], Asp [D] and Val [V], which are indicated by a one-letter symbol. (2) The protein 0th-order structure or a [GADV]-amino acid composition generating water-soluble globular protein with some flexibility, which can be produced even by the random joining of [GADV]-amino acids. (3) The formation of versatile [GADV]-microspheres, which can grow, divide and proliferate even without a genetic system, was the emergence of proto-life. (4) The [GADV]-microspheres with a higher proliferation ability than others were able to be selected. Proto-Darwin evolution made it possible to proceed forward to the creation of a core life system composed of the (GNC)_n gene, anticodon stem-loop tRNA or AntiC-SL tRNA (GNC genetic code), and [GADV]-protein. (5) Eventually, the first genuine life with a core life system emerged. Thus, the formation processes of [GADV]-protein and the (GNC)_n gene in chemically complex messy environments were the steps to the emergence of genuine life.

Velocity-tunable beam of continuously decelerated polar molecules for cold ion-molecule reaction studies

Producing high densities of molecules is a fundamental challenge for low-temperature, ion-molecule reaction studies. Traveling-wave Stark decelerators promise to deliver high density beams of cold, polar molecules but require non-trivial control of high-voltage potentials. We have overcome this experimental challenge and demonstrate continuous deceleration of ND₃ from 385 to 10 m/s, while driving the decelerator electrodes with a 10 kV amplitude sinewave. In addition, we test an alternative slowing scheme, which increases the time delay between decelerated packets of ND₃ and non-decelerated molecules, allowing for better energy resolution of subsequent reaction studies. We characterize this source of neutral, polar molecules suitable for energy-resolved reaction studies with trapped ions at cold translational temperatures. We also propose a combined apparatus consisting of the traveling-wave decelerator and a linear ion trap with a time-of-flight mass spectrometer and discuss to what extent it may achieve cold, energy-resolved, ion-neutral reactions.

The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life

The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.

Polypeptide formation in clusters of β-alanine amino acids by single ion impact

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.

One-carbon metabolism, folate, zinc and translation

The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.

Cold and controlled chemical reaction dynamics

State-to-state chemical reaction dynamics, with complete control over the reaction parameters, offers unparalleled insight into fundamental reactivity.

Introduction to virus origins and their role in biological evolution

Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.

Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate

A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al., 2018, Nature 558:564-568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin ("prebiotic soup"). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.

An Evolutionary Perspective of Neoplastic Diseases in the Universe

The existence of exoplanets orbiting low mass-stars is one of the most significant discoveries of our time. Especially intriguing to us is the possibility that Earth-sized exoplanets within a habitable zone might harbor life-forms that resemble our own RNA/DNA-based species. We further narrow this theoretical possibility with the following question: if alien life does indeed exist elsewhere, would extraterrestrial life be burdened with earthly diseases? Given that the chemistry of the universe is subject to specific rules, restraints, and predictable outcomes, we argue that cancer-signaling pathways might be programmed into the life cycle of habitable exoplanets. This hypothetical prediction is also based on evolutionary convergence, the repeated emergence of biological similarity that occurs when disparate life-forms adapt to comparable selection pressures. The possibility that mutations and nucleotide base rearrangements that drive cancer growth might be fixed in the chemical hardware of alien life provides us with the opportunity to wonder and consider the origins, evolution, and ubiquity of disease beyond Earth.

Constraining the Prebiotic Cell Size Limits in Extremely Hostile Environments: A Dynamical Perspective

The ability to support a replicator population in an extremely hostile environment is considered in a simple model of a prebiotic cell. We explore from a classical approach how the replicator viability changes as a function of the cell radius. The model includes the interaction between two different species: a substrate that flows from the exterior and a replicator that feeds on the substrate and is readily destroyed in the environment outside the cell. According to our results, replicators in the cell only exist when the radius exceeds some critical value [Formula: see text] being, in general, a function of the substrate concentration, the diffusion constant of the replicator species, and the reproduction rate coefficient. Additionally, the influence of other parameters on the replicator population is also considered. The viability of chemical replicators under such drastic conditions could be crucial in understanding the origin of the first primitive cells and the ulterior development of life on our planet. Key Words: Prebiotic cell-Chemical replicator-Environment-Reproduction rate. Astrobiology 18, 403-411.

Relevance and Significance of Extraterrestrial Abiological Hydrocarbon Chemistry

Astrophysical observations show similarity of observed abiological "organics"-i.e., hydrocarbons, their derivatives, and ions (carbocations and carbanions)-with studied terrestrial chemistry. Their formation pathways, their related extraterrestrial hydrocarbon chemistry originating from carbon and other elements after the Big Bang, their parent hydrocarbon and derivative (methane and methanol, respectively), and transportation of derived building blocks of life by meteorites or comets to planet Earth are discussed in this Perspective. Their subsequent evolution on Earth under favorable "Goldilocks" conditions led to more complex molecules and biological systems, and eventually to humans. The relevance and significance of extraterrestrial hydrocarbon chemistry to the limits of science in relation to the physical aspects of evolution on our planet Earth are also discussed.

The Role of Ultrahigh Resolution Fourier Transform Mass Spectrometry (FT-MS) in Astrobiology-Related Research: Analysis of Meteorites and Tholins

It is an important but also a challenging analytical problem to understand the chemical composition and structure of prebiotic organic matter that is present in extraterrestrial materials. Its formation, evolution and content in the building blocks ("seeds") for more complex molecules, such as proteins and DNA, are key questions in the field of exobiology. Ultrahigh resolution mass spectrometry is one of the best analytical techniques that can be applied because it provides reliable information on the chemical composition and structure of individual components of complex organic mixtures. Prebiotic organic material is delivered to Earth by meteorites or generated in laboratories in simulation (model) experiments that mimic space or atmospheric conditions. Recent representative examples for ultrahigh resolution mass spectrometry studies using Fourier-transform (FT) mass spectrometers such as Orbitrap and ion cyclotron resonance (ICR) mass spectrometers are shown and discussed in the present article, including: (i) the analysis of organic matter of meteorites; (ii) modeling atmospheric processes in ICR cells; and (iii) the structural analysis of laboratory made tholins that might be present in the atmosphere and surface of Saturn's largest moon, Titan.

Introduction to Virus Origins and Their Role in Biological Evolution

Viruses are extremely abundant and diverse parasites of cells. They might have arisen during an early phase of the evolution of life on Earth dominated by RNA or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate: viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via lateral transfers of genes. These two models bear on considering viruses predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.

Emergence of life from multicomponent mixtures of chemicals: the case for experiments with cycling physicochemical gradients

The emergence of life from planetary multicomponent mixtures of chemicals is arguably the most complicated and least understood natural phenomenon. The fact that living cells are non-equilibrium systems suggests that life can emerge only from non-equilibrium chemical systems. From an astrobiological standpoint, non-equilibrium chemical systems arise naturally when solar irradiation strikes rotating surfaces of habitable planets: the resulting cycling physicochemical gradients persistently drive planetary chemistries toward "embryonic" living systems and an eventual emergence of life. To better understand the factors that lead to the emergence of life, I argue for cycling non-equilibrium experiments with multicomponent chemical systems designed to represent the evolving chemistry of Hadean Earth ("prebiotic soups"). Specifically, I suggest experimentation with chemical engineering simulators of Hadean Earth to observe and analyze (i) the appearances and phase separations of surface active and polymeric materials as precursors of the first "cell envelopes" (membranes) and (ii) the accumulations, commingling, and co-reactivity of chemicals from atmospheric, oceanic, and terrestrial locations.

Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth

The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.

Radiolytic studies of naphthalene in the presence of water

Naphthalene is an interesting candidate to study in the framework of organic delivery to planetary surfaces as well as in the origin of life. Additionally, naphthalene is of environmental interest, because of its chronic and acute effects on living systems, such as humans and animals (e.g. moths). Naphthalene has been well studied in both fields. In this paper we give an overview of radiolytic studies of naphthalene in the presence of both liquid water and water ice. From our review it appears that OH radicals are formed both in liquid water and in interstellar ices and that these radicals play a considerable role in the degradation of naphthalene. However, it also appears that upon irradiation of naphthalene in liquid water, hydrogen peroxide, a species that accelerates naphthalene degradation, is formed. Based on this review we suggest that the role of hydrogen peroxide in interstellar ices should be further investigated.

Links between hydrothermal environments, pyrophosphate, na(+), and early evolution

The discovery that photosynthetic bacterial membrane-bound inorganic pyrophosphatase (PPase) catalyzed light-induced phosphorylation of orthophosphate (Pi) to pyrophosphate (PPi) and the capability of PPi to drive energy requiring dark reactions supported PPi as a possible early alternative to ATP. Like the proton-pumping ATPase, the corresponding membrane-bound PPase also is a H⁺-pump, and like the Na⁺-pumping ATPase, it can be a Na⁺-pump, both in archaeal and bacterial membranes. We suggest that PPi and Na⁺ transport preceded ATP and H⁺ transport in association with geochemistry of the Earth at the time of the origin and early evolution of life. Life may have started in connection with early plate tectonic processes coupled to alkaline hydrothermal activity. A hydrothermal environment in which Na⁺ is abundant exists in sediment-starved subduction zones, like the Mariana forearc in the W Pacific Ocean. It is considered to mimic the Archean Earth. The forearc pore fluids have a pH up to 12.6, a Na⁺-concentration of 0.7 mol/kg seawater. PPi could have been formed during early subduction of oceanic lithosphere by dehydration of protonated orthophosphates. A key to PPi formation in these geological environments is a low local activity of water.

The composition and organization of cytoplasm in prebiotic cells

This article discusses the hypothesized composition and organization of cytoplasm in prebiotic cells from a theoretical perspective and also based upon what is currently known about bacterial cytoplasm. It is unknown if the first prebiotic, microscopic scale, cytoplasm was initially contained within a primitive, continuous, semipermeable membrane, or was an uncontained gel substance, that later became enclosed by a continuous membrane. Another possibility is that the first cytoplasm in prebiotic cells and a primitive membrane organized at the same time, permitting a rapid transition to the first cell(s) capable of growth and division, thus assisting with the emergence of life on Earth less than a billion years after the formation of the Earth. It is hypothesized that the organization and composition of cytoplasm progressed initially from an unstructured, microscopic hydrogel to a more complex cytoplasm, that may have been in the volume magnitude of about 0.1-0.2 μm(3) (possibly less if a nanocell) prior to the first cell division.

Chemical methods for searching for evidence of extra-terrestrial life

This paper describes the chemical concepts used for the purpose of detecting life in extra-terrestrial situations. These methods, developed initially within the oil industry, have been used to determine when life began on Earth and for investigating the Moon and Mars via space missions. In the case of Mars, the Viking missions led to the realization that we had meteorites from Mars on Earth. The study of Martian meteorites in the laboratory provides tantalizing clues for life on Mars in both the ancient and recent past. Meteorite analyses led to the launch of the Beagle 2 spacecraft, which was designed to prove that life-detection results obtained on Earth were authentic and not confused by terrestrial contamination. Some suggestions are made for future work.

The detection of extra-terrestrial life and the consequences for science and society

Astronomers are now able to detect planets orbiting stars other than the Sun where life may exist, and living generations could see the signatures of extra-terrestrial life being detected. Should it turn out that we are not alone in the Universe, it will fundamentally affect how humanity understands itself--and we need to be prepared for the consequences. A Discussion Meeting held at the Royal Society in London, 6-9 Carlton House Terrace, on 25-26 January 2010, addressed not only the scientific but also the societal agenda, with presentations covering a large diversity of topics.