abstract: The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life. / Dissertation/Thesis / Doctoral Dissertation Physics 2018

L'étude de la photochimie dans le système solaire est de toute première importance pour appréhender la chimie organique complexe au sein d'un environnement extraterrestre. Parmi ces environnements, les comètes revêtent un intérêt particulier en exobiologie puisqu'elles ont pu, ainsi que leurs grains, être des vecteurs de matière organique sur la Terre primitive et ainsi contribuer à l'émergence de la vie. Mais dans quelle mesure, la matière organique potentiellement présente au sein des grains survit-elle face aux rayonnements solaires? Ma thèse porte sur l'étude de la dégradation photochimique de trois bases azotées (adénine, guanine et uracile) et d'un acide aminé (glycine) dans les conditions du système solaire, c'est à dire soumis à des rayonnements énergétiques VUV/UV ( <300 nm). Les études conduites lors de ce travail peuvent aussi être appliquées à l'interprétation des mesures du le spectromètre de masse COSIMA présent sur l'orbiteur de la mission cométaire ROSETTA et dont l'objectif est l'analyse de la surface de grains cométaires capturés dans l'environnement de la comète 67P/Churyomov-Gerasimenko. Ce travail présente les spectres de sections efficaces d'absorption mesurés dans les domaines VUV/UV pour des films organiques purs. Ces spectres ont mené à la déduction de constantes de photolyse, ainsi qu'à l'élaboration d'un modèle simulant la cinétique de destruction globale d'un film organique optiquement épais. La confrontation entre ce modèle et les données expérimentales d'irradiation en orbite basse terrestre ainsi qu'en laboratoire a permis d'estimer les temps de vie des molécules considérées à 1 ua puis extrapolés à différentes distances héliocentriques. Les résultats obtenus ont montré que la glycine, l'adénine et la guanine, potentiellement présentes au sein des grains cométaires, seraient totalement détruites entre le moment de l'éjection des grains du noyau cométaire et l'arrivée sur Terre si elles sont en surface. En sous-surface, elles sont au contraire très stables, de part la protection efficace que leur confèrent les minéraux constitutifs du grain contre les rayonnements solaires. Dans le cadre de la mission ROSETTA, les résultats diffèrent. Au plus loin du soleil, à 3,5 ua, l'abondance des molécules ne diminuerait pas de façon significative pendant le temps de parcours des grains entre le noyau et l'orbiteur. Au périhélie, la "survie" des molécules dépendra fortement de la distance noyau-orbiteur. Les pertes significatives des 3 molécules par photochimie n'auraient lieu que si l'orbiteur se situe au moins à quelques centaines de kilomètres du noyau / The study of photochemistry in the solar system is of prime importance to assess complex organic chemistry in an extraterrestrial environment. Among those environments, comets are subject to a particular interest in the context of exobiology, along with their grains, as they could have bring organic matter on the primitive earth, and hence contribute to the emergence of life. But to what extent does the organic matter potentially with in grains survive face to solar radiation? My thesis deals with the study of photochemical degradation of three nitrogenous bases (adenine, guanine and uracil) and one amino acid ( glycine) in the conditions of the solar system, which means subject to VUV/UV energetically radiations ( <300 nm). Studies performed during this work can also be applied to the interpretation of COSIMA mass spectrometer, present on the cometary mission ROSETTA, which aims to analyze the surface of cometary grains captured in the environment of the 67P/Churyomov-Gerasimenko comet. This work present absorption cross section spectrum measured in the VUV/UV range, for pure organic films. These spectrum led to the deduction of photolysis rate constants, and to the elaboration of a model simulating the global kinetic of destruction of a optically thick organic film. The comparison between this model and experimental data of low earth orbit irradiation as well as laboratory data allowed to estimates lifetimes for the considered molecules at 1 AU, and then extrapolated at different heliocentrically distances. Results show that glycine, adenine and guanine, potentially existing inside the cometary grains, would be entirely destroyed between the ejection of the grains and the arrival on earth if they exist at the surface. Below the surface, they are at the contrary very stable, thanks the effective protection of the mineral constitutive of the grain against solar radiations. In the frame of ROSETTA mission, results differ. At the farther of the sun, at 3.5 AU, the abundance of the molecule would not significantly decrease during the time of travel of grains between the core and the orbiter. At the perihelia, the survival of molecule strongly depends of the core-orbiter distance. Significant loss of the 3 molecules by photochemistry would only occurred if the orbiter is at more than hundred of kilometers from the core

Na Antártica e no Ártico, a vida microbiana é presente e diversificada, tendo se adaptado a condições similares às encontradas em mundos que despertam interesse à astrobiologia. Este estudo investigou as alterações fisiológicas e fenotípicas do extremófilo psicrotrófico Exiguobacterium antarcticum B7 sob diferentes temperaturas. Foram utilizadas técnicas de eletroforese de proteínas em duas dimensões associada a espectrometria de massa, juntamente com técnicas de microscopia. E. antarcticum foi também submetida a condições físicas encontradas em Marte e no ambiente interplanetário. Seguindo evidências de que micro-organismos psicrotróficos podem também ser resistentes a períodos prolongados de dessecação, foi investigada a presença de linhagens microbianas resistentes a anidrobiose em solos da Antártica e permafrost do Ártico. Por fim, voltando-se à ecologia microbiana de solos polares permanentemente congelados, foi estudada a diversidade microbiana de três estratos de permafrost do ártico canadense com o uso de sequenciamento de DNA de nova geração. / In Antarctica and the Arctic, microbial life is present and diverse, having adapted to low temperature and low humidity conditions, similar to the worlds that arouse more interest to astrobiology. This study investigated the physiological changes of the psychrotrophic extremophile Exiguobacterium antarcticum B7 at different temperatures. Two dimensional protein electrophoresis techniques was used for proteome analysis in conjunction with mass spectrometry, as well as microscopy techniques. E. antarcticum was also subjected to physical parameters found on Mars and in the interplanetary environment. Following evidence that psychrotrophic microorganisms may also be resistant to prolonged periods of desiccation, it was investigated the presence of microbial strains resistant to anhydrobiosis on Antarctic soils and Arctic permafrost. At last, turning the attention to the microbial ecology of permanently frozen polar soils, it was studied the bacterial diversity of three Arctic permafrost strata with next-generation high throughput DNA sequencing.

The identification and characterization of molecular biomarkers using mass spectrometry on an orbiting or fly-by spacecraft is one of the preferred analytical techniques in the search for life beyond the Earth. However, analysis is complicated by unwanted molecular dissociation occurring when sampled native molecules impact the instrument at high velocity. The mechanisms of chemical changes produced in high velocity impacts have been studied experimentally in some cases; however, there are significant experimental limitations to these techniques. Here I present the design, construction, and testing of a new experimental technique to produce high velocity molecular and microparticle collisions under a controlled lab setting using a high-speed spinning rotor. Chapter 1 of this manuscript gives a scientific review of the astrobiological importance of this project for future and current space missions as well as describing previous techniques used to produced hypervelocity impacts and their limitations. Chapter 2 presents the design, construction, calibration, and preliminary experiments of the new technique involving the high-speed rotor. Chapter 3 describes the fabrication of a molecular beam system from the ground up to be coupled with the high-speed rotor. Chapter 4, describes future project directions and presents future experiments using the rotor as a stand-alone instrument. Lastly, the appendix contains the standard operation procedures and design notes regarding the operation of these two instruments.

The McMurdo Dry Valley region is the largest ice-free area of Antarctica. Harsh abiotic conditions of the polar desert ecosystem, including extreme cold, aridity, and limited nutrient availability select for unique taxa. The comparatively simple terrestrial ecosystem is well-suited for investigating edaphic influences on microbial presence, activity, and community structuring. The Dry Valleys are viewed as a useful analog for Mars astrobiology investigations. However, most biotic investigations have been focused on lower elevations, where an understanding of edaphic effects on microbial communities within its generally more favorable conditions has emerged. Transiently wetted Dry Valley water tracks may be analogous to recurring slope lineae on Mars. Dry permafrost is rare on Earth, and unique to high-elevation Antarctica soils, but is ubiquitous on Mars. Identifying if abiotic properties known to structure microbial communities within low elevation soils holds true for water tracks and dry permafrost is not known. My dissertation investigates edaphic effects on microbial communities within water track soils and dry permafrost. First, I review the ecological effects of transient wetting within hyperarid environments of the Atacama Desert of Chile and the Dry Valleys of Antarctica and apply the findings to possible habitability of modern and early (i.e., ~3.5 bya) Mars surface environments. I show that deliquescent hygroscopic salts facilitate biological response where little or no biotic activity would occur otherwise, yet the salts can also inhibit life. Transient wetting alone may also not be enough to support life. Secondly, I examine bacterial community composition, richness, and diversity on and off water track soils in Taylor Valley and show they are significantly different in composition, which likely influence ecosystem functioning. Salinity is shown as the best predictor of composition. Third, I examine a bacterial community from a Beacon Valley water track, which we believe is among the highest, driest, and coldest soils on Earth that still experiences brief seasonal wetting. I show a small but diverse community is present, with some viable cells, yet no detectable RNA is expressed by the community when tested within a suite of simulated Martin soils. Finally, I examine bacterial and fungal communities in dry permafrost of Arena Valley. I show a strikingly minimal microbial community severely restricted by the extreme cold, oligotrophy, and aridity. Several abundant taxa are related to those within maritime, costal, and endolithic habitats, indicating that they are foreign inoculum. The communities appear to be inactive to such a degree that they are not meaningfully structured by the broad suite of measured abiotic properties. Dry permafrost soils and water track environments are extremely challenging habitats, but they are generally more favorable than conditions observed on Mars. My research has important ecological value for investigating terrestrial thresholds of microbial habitability on Earth and for Mars astrobiology investigations.

Raman spectroscopy has been used to characterise both organic and geological samples in order to build a database for the future characterization of biomarker molecules that are of astrobiological relevance. Characteristic geological features and hydrated minerals recently found on the surface of Mars by the NASA planetary rovers Spirit and Opportunity suggest that a possible biosphere could have once existed there. Analytical instrumentation protocols for the unequivocal detection of biomarkers in suitable geological matrices are critical for future unmanned explorations, including the forthcoming ESA ExoMars mission scheduled for 2018. Several geological features found on the surface of Mars by planetary rovers suggest that a possible extinct biosphere could exist based on similar sources of energy as occurred on Earth. For this reason, analytical instrumental protocols for the detection of isolated biomarkers preserved in suitable geological matrices unequivocally and non-destructively have to be evaluated for future unmanned missions. Raman spectroscopy is currently part of the Pasteur instrumentation suite of the ExoMars mission for the remote detection of extant or extinct life signatures in the Martian surface and subsurface. Terrestrial analogues of Martian sites have been identified and the biogeological modifications resulting from extremophilic survival activity have been studied. Here we present the Raman spectral characterization of several examples of organic compounds which have been recorded using 785 nm, 633 nm and 514 nm laser excitation -polycyclic aromatic hydrocarbons (PAHs), organic acids, chlorophyll and carotenoids. Experimental mixtures of ß-carotene in usnic acid, PAHs in usnic acid and PAHs in mineral matrices have also been investigated. Organic compounds and PAHs located under crystalline minerals samples were identified using a 5x objective lens and 785 nm III excitation. The pure compounds and compound mixtures were also analysed using X-ray powder diffraction and scanning electron microscopy (SEM). The results of this study indicate that near infrared laser at 785 nm provided the clearest and the most informative spectra due to the reduction of fluorescence emission. Higher energy lasers operating in the visible region have resulted in the emission of significant background fluorescence. Few samples fluoresce even with the use of 785 nm excitation and FT-Raman spectroscopy remains the instrument of choice for the analysis of these samples.

<p>Investigating the presence of microbial communities in the Earth's deep terrestrial subsurface and the metabolic processes taking place in these environments provides insight into the some of the ultimate limits for life on Earth, as well as the potential for microbial life to exist within the subsurface of other planetary bodies. This Master's thesis project utilized phospholipid fatty acid (PLFA) analysis, in combination with carbon isotope analyses (δ¹³C and Δ¹⁴C), to explore the presence and activity of microbial communities living within deep terrestrial subsurface fracture water systems and low permeability, deep sedimentary rocks. Deep fracture water systems, ranging from 0.9 to 3.2 km below land surface, were sampled for microbial communities via deep mine boreholes in the Witwatersrand Basin of South Africa. PLFA concentrations revealed low biomass microbial communities, ranging from 2x10¹ to 5x10⁴ cells per mL and the PLFA profiles contained indicators for environmental stressors, including high temperatures and nutrient deprivation. δ¹³C and Δ¹⁴C analyses of PLFAs and potential carbon sources (dissolved inorganic carbon (DIC), dissolved organic carbon (DOC) and methane) identified microbial utilization of methane in some systems and utilization of DIC in others. Evidence for microbial oxidation of methane and chemoautotrophy in these systems is consistent with a self-sustaining deep terrestrial subsurface biosphere that is capable of surviving independent of the photosphere. Viable microbial communities were also identified within deep (334 to 694 m depth) sedimentary rock cores sampled from the Michigan Basin, Canada. PLFA analyses revealed microbial cell densities ranging from 1-3 x 10⁵ cells/mL and identified PLFA indicators for environmental stressors. These results demonstrate the ubiquity of microbial life in the deep terrestrial subsurface and provide insight into microbial carbon sources and cycling in deep microbial systems which may persist in isolation over geologic timescales.</p> / Master of Science (MSc)

Life on Earth likely began as an RNA world, where cell-free or compartmentalized ribonucleic acid (RNA) molecules dominated as the replicating and evolving lifeforms prior to the emergence of DNA- and protein-based life. The focus of this thesis is on when and how this RNA world emerged. We use astrophysical and geophysical studies to constrain when the Earth was habitable, and biosignature studies to constrain when the Earth was inhabited. From this we obtain a time interval for the emergence of life. Considering all these constraints, we find that the Earth was habitable as early as 4.5 Ga, or as late as 3.9 Ga, depending on whether the early influx of asteroids inhibited life from emerging. The time that the Earth was inhabited is more precisely constrained to 3.7 Ga. This suggests life emerged within 800 Myr, and possibly in < 200 Myr. Between 4.5–3.7 Ga, the continental crust was slowly rising up from the global ocean, providing dry land on which warm little ponds could form. We develop the theory for the emergence of RNA polymers in these pond environments, whose wet-dry cycles promote polymerization. RNA is comprised of chains of nucleotides, and the latter is made up of ribose, phosphate, and a characteristic nucleobase. We numerically model the survival and evolution of nucleobases in warm little ponds from meteorite and interplanetary dust sources. The wet-dry cycles of our ponds are controlled by precipitation, evaporation, and seepage. The nucleobase sinks include photodissociation, seepage, and hydrolysis. Nucleobase and nucleotide seepage is efficient, therefore nucleotides and RNA molecules must have emerged rapidly (< a few years) in order to avoid falling through pores at the base of the pond. We find that meteorites, not interplanetary dust particles, are the dominant source of nucleobases used for RNA synthesis. Finally, under these conditions, we find that first RNA polymers likely emerged before 4.17 Ga. / Thesis / Master of Science (MSc)

No / The first Raman spectrometers to be used for in situ analysis of planetary material will be launched as part of powerful, rover-based analytical laboratories within the next 6 years. There are a number of significant challenges associated with building spectrometers for space applications, including limited volume, power and mass budgets, the need to operate in harsh environments and the need to operate independently and intelligently for long periods of time (due to communication limitations). Here, we give an overview of the technical capabilities of the Raman instruments planned for future planetary missions and give a review of the preparatory work being pursued to ensure that such instruments are operated successfully and optimally. This includes analysis of extremophile samples containing pigments associated with biological processes, synthetic materials which incorporate biological material within a mineral matrix, planetary analogues containing low levels of reduced carbon and samples coated with desert varnish that incorporate both geo-markers and biomarkers. We discuss the scientific importance of each sample type and the challenges using portable/flight-prototype instrumentation. We also report on technical development work undertaken to enable the next generation of Raman instruments to reach higher levels of sensitivity and operational efficiency.

Esta tese se insere no contexto da química prebiótica, que estuda a evolução química que ocorreu antes do surgimento da vida na Terra. Tal área pertence ao ramo de pesquisa da Astrobiologia, que estuda o surgimento, a evolução, distribuição e futuro da vida na Terra ou em outro lugar do Universo. Dentre as várias hipóteses abordadas na química prebiótica, a hipótese mineral é foco de estudo deste trabalho, ou seja, se os minerais podem ter agido como preconcentradores ou protetores de moléculas biologicamente relevantes para a química prebiótica e como catalisadores de reações. A classe mineral de hidróxidos duplo lamelares (HDL) é estudada inicialmente considerando se sua síntese seria possível em um ambiente prebiótico. Desta forma, o HDL foi sintetizado por dois métodos de síntese (coprecipitação e reconstrução) e em quatro composições distintas de água do mar sintética, que mimetizam diferentes fases geológicas da Terra, os resultados mostraram a formação deste mineral em todas as composições de água do mar analisadas. Posteriormente, o estudo da interação de biomoléculas com HDL foi feito visando caracterizar se estas poderiam estar inseridas no espaço interlamelar deste mineral. O íon tiocianato, precursor de biomoléculas, e as bases nitrogenadas adenina, timina, e uracila mostraram-se presentes nas amostras de HDL sintetizadas pelos dois métodos, coprecipitação e reconstrução. As amostras foram caracterizadas por difratometria de raios X, análise termogravimétrica, análise elementar e por espectroscopia vibracional, Raman e no infravermelho. Embora os resultados iniciais indiquem que as biomoléculas possam estar interagindo com o mineral por adsorção e não necessariamente estejam intercaladas, estudos com lavagem das amostras com carbonato de sódio mostraram a troca iônica das biomoléculas pelo ânion inorgânico e sugerem que estas encontravam-se realmente no espaço interlamelar do mineral. Foram feitas então simulações de ambientes extremos nos sistemas HDL + biomoléculas para avaliar se a presença do mineral aumenta a estabilidade das biomoléculas frente a aquecimento, radiação UVC e radiação ionizante já que tais condições extremas estariam presentes na Terra primitiva / This thesis subject is related to prebiotic chemistry, which studies the chemical evolution that happened before the origin of life on Earth. This subject belongs to the Astrobiology research area, which studies the origin, evolution, distribution and future of life on Earth and elsewhere in the Universe. Among the many hypothesis that prebiotic chemistry encompass, the mineral hypothesis is the aim of this thesis, that is, if minerals could have had a role in preconcentrating and protecting molecules relevant to prebiotic chemistry, and also if they could have acted as catalists. The layered double hydroxide (LDH) minerals are studied and the first question is if they could have been synthetized in a prebiotic environment. Four different seawater compositions are analyzed, considering many geological periods of Earth, and two synthesis methods were studied: coprecipitation and reconstruction. The results showed that the LDHs are formed in all seawater types studied. Following these studies, we discuss whether biomolecules could be in the interlayer space of this mineral. Thiocyanate, a biomolecule precursor, and the nucleic acids adenine, thymine and uracil were present in the LDH samples synthetized either by coprecipitation and reconstruction, and they were characterized by X-Ray diffraction, thermogravimetric analysis, elemental analysis and by vibrational spectroscopy: IR and Raman. Although the preliminary results showed that the biomolecules are not necessarily intercalated, but may simply be adsorbed on the minerals, after washing with a sodium carbonate solution, the biomolecules were replaced by the inorganic anion, suggesting that the former was in fact intercalated in the mineral. Extreme conditions simulations were then performed on the LDH plus biomolecules systems to evaluate whether the mineral may act as a protector and stabilize the biomolecules when these were heated or irradiated with UV-C and ionizing radiation, since such scenarios would be common on early Earth