The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the spontaneous generation of an RNA World (e.g., strand-cyclization, heterogeneous backbones, non-selective ligation of activated nucleotides). The Molecular Midwife hypothesis, proposed by Hud and Anet in 2000, provides a possible solution to several problems associated with the assembly of the first nucleic acids. In this hypothesis, nucleic acid base pairs are assembled by small, planar molecules that resemble molecules which are known today to intercalate the base pairs of nucleic acid duplexes. Thus, the validity and merits of the Molecular Midwife hypothesis can be, to some extent, explored by studying the effects of intercalation on the non-covalent assembly of nucleic acids. In this thesis, I explore the role of the sugar-phosphate backbone in dictating the structure and thermodynamics of nucleic acid intercalation by using 2′,5′-linked RNA intercalation as a model system of non-natural nucleic acid intercalation. The solution structure of an intercalator-bound 2′,5′ RNA duplex reveals structural and thermodynamic aspects of intercalation that provide insight into the origin of the nearest-neighbor exclusion principle, a principle that is uniformly obeyed upon the intercalation of natural (i.e. 3′,5′-linked) RNA and DNA. I also demonstrate the ability of intercalator-mediated assembly to circumvent the strand-cyclization problem, a problem that otherwise greatly limits the polymerization of short oligonucleotides into long polymers. Together, the data presented in this thesis illustrate the important role that the nucleic acid backbone plays in governing the thermodynamics of intercalation, and provide support for the proposed role of intercalator-mediated assembly in the prebiotic formation of nucleic acids.

Syftet med studien är att synliggöra hur barn tänker om liv och död och deras uppfattning om livets uppkomst. Genom att utgå från ett biologiskt- och ett filosofiskt perspektiv så är mitt syfte att synliggöra barns oliktänkande i ämnet. Min valda metod till studien är semistrukturerad intervju integrerat med bildskapande med barn mellan 5-7 år. I resultatet av min studie så synliggörs barns olika sätt att förstå och uttrycka livsnära fenomen på. Resultatet visade också på barns oliktänkande genom en naturalistisk-, evolutionär- eller en skapelsekopplad beskrivning av livets och människans uppkomst. De medverkande barnen visade en nyfikenhet, engagemang och en tydlig vilja till att reflektera i givna ämnen. Den insamlade data utgjorde en tydlig bild av barns oliktänkande runt begreppen levande, liv och död och livets uppkomst. / The main purpose of this study is to make children’s thoughts about life, death and their concept of origin of life visible. Through a combined biological- and philosophical perspective my aim is to make children’s diversity of thoughts visual. My chosen method for my study is semi-structured interviews integrated with drawings with children between 5-7 years old. In the result of the study children´s different way of understanding and expressing their thoughts about life become visible. The result also shows children’s different concept about origin of life connected to a naturalistic-, an evolutionary -and a creationist theory. I noticed a great curiosity and engagement from the participating children and a distinct commitment to reflect over given topics. The collected data gave a clear illustration of children’s different kind of thoughts of being alive, life and death and their understanding of origin of life.

One chemoautotrophic origin of life theory posits the abiotic formation of alkyl thiols as an initial step to forming biomolecules and eventually a simple chemoautotrophic cell. The premise of this theory is that a recurring reaction on the charged surfaces of pyrite served as a primordial metabolism analogous to the reductive acetyl-CoA pathway (Wächtershäuser 1988) that was later enveloped by a primitive cellular membrane. Alkyl thiols have not previously been identified in terrestrial hot springs as unequivocally abiogenic, but they have been produced in the laboratory under hydrothermal conditions in the presence of a catalyst. I analyzed the dissolved gas content of several hot springs and conducted sterile laboratory experiments in order to evaluate the abiogenic formation of methanethiol (CH3SH), the simplest of the alkyl thiols. Specifically of interest was Cinder Pool, an acid-sulfate-chloride hot spring in Yellowstone National Park. This spring is unusual in that it contains a subaqueous molten sulfur layer (~18 m depth) and thousands of iron- vii sulfur-spherules floating on the surface, which are created by gas bubbling through the molten floor of the spring. This material could potentially serve as a reactive and catalytic surface for abiogenic CH3SH formation in Cinder Pool. Gas samples were collected from Cinder Pool and an adjacent hydrothermal feature in fall of 2011 using the bubble strip method. Two samples contained measurable quantities of CH3SH and other organic sulfur gases, with concentrations of all gases generally higher at the bottom of the pool. Laboratory microcosm experiments were conducted to replicate these findings in a sterile environment. Analog Cinder Pool water was injected into serum bottles containing different iron-sulfur compounds, including cinders collected from the pool itself, as catalytic surfaces for the CH3SH generating reaction. The bottles were then charged with hydrogen (H2), carbon dioxide (CO2), and carbon disulfide (CS2) as reaction gases and incubated for a week at temperatures between 60 and 100oC. Bottles used either powdered FeS, FeS2 (pyrite) or cinder material as a catalytic surface, and all of these surfaces were capable of catalyzing CH3SH formation. In bottles without imposed CS2, however, cinder material was the only surface that produced any detectable CH3SH. While CH3SH is central to the autotroph-first theory and has been synthesized in the laboratory (e.g. Heinen and Lauwers 1996), it has not previously been observed to form abiotically in natural systems. I have identified CH3SH in a natural hydrothermal feature where it is unlikely to have formed secondary to microbial activity, and I have duplicated these field findings in sterile laboratory experiments using the cinders as a reactive surface for formation. / text

Cells use lipid membranes to organize and define their chemical environments. All cell membranes are based on a common structure: bilayers composed of phospholipids with two hydrocarbon chains. How did biology converge on this particular solution for cellular encapsulation? The first cell membranes are proposed to have assembled from simple, single-chain lipids, such as fatty acids and their derivatives, which would have been available in the prebiotic environment. Here we argue that the physical properties of fatty acid membranes would have made them well suited for a role as primitive cell membranes and predisposed their evolution to modern, phospholipid-based membranes. We first considered models for primitive membrane self-assembly, which faces significant concentration barriers due to the entropic cost of aggregation and the solubility of single-chain lipids. We therefore identified two physical mechanisms by which fatty acid membrane assembly can proceed from dilute solutions. Thermal diffusion columns, a proposed prebiotic concentration method, drive the formation of fatty acid vesicles by concentrating an initially isotropic solution past the critical concentration necessary for aggregation. Alternatively, mixtures of fatty acids with varying chain lengths, the expected products of abiotic lipid synthesis, intrinsically reduce the concentration barrier to aggregation through their polydispersity. These results motivated us to better understand the phase behavior of fatty acids in solutions. We found that the composition of fatty acid aggregates, whether vesicles or micelles, is also determined by concentration. Fatty acid vesicles feature significant amounts of coexisting micelles, whose abundance is enriched in low concentration solutions. We utilized this micelle-vesicle equilibrium to drive the growth of pre-existing fatty acid vesicles by changing amphiphile concentration. We next considered the evolution of phospholipid membranes, which was a critical and necessary step for the early evolution of cells. We found that the incorporation of even small amounts of phospholipids drives the growth of fatty acid vesicles by competition for monomers with neighboring vesicles lacking phospholipids. This competitive growth would have provided a strong selective advantage for primitive cells to evolve the catalytic machinery needed to synthesize phospholipids from their single-chain precursors. Growth is caused by any relative difference in phospholipid content, suggesting an evolutionary arms race among primitive cells for increasingly phospholipid membranes. What would have been the consequences for early cells of such a transition in membrane composition? We found that increasing phospholipid content inhibits the permeability of fatty acid membranes through changes in bilayer fluidity. For early heterotrophic cells, the emergence of increasingly phospholipid membranes would have therefore imposed new selective pressures for the evolution of membrane transport machinery and metabolism. Our model for early membrane evolution led us to develop prebiotic models for phospholipid chemistry. The assembly of phospholipids from single-chain substrates requires a single reaction: the acyltransfer of an activated fatty acid onto a glycerol monoester or lysophospholipid. We developed a synthetic model for this reaction that incorporates a copper-catalyzed azide-alkyne cycloaddition and showed that it drives de novo vesicle assembly.

Methane (CH4) plays an important role in regulating Earth’s climate. Its atmospheric concentrations are related to both biotic and abiotic processes. The biotic one can be formed either by chemoautotrophic or heterotrophic pathways by methanogens. Abiotic CH4 formation can occur from several sequential reactions starting with H2 production by serpentinization of Fe-bearing minerals followed by Fischer-Tropsch Type reactions or thermogenic reactions from hydrocarbons. In the presence of suitable electron acceptors, microbial oxidation utilizes CH4 and contributes to regulating its emission.  From the perspectives of astrobiology and Earth climate regulation, this thesis focuses on: (1) Dynamics of CH4 formation and oxidation in lake sediments (Paper I), (2) Constructing an automatic flux chamber to facilitate its emission measurements (Paper II), (3) dynamics of both abiotic and biotic CH4 formation processes related to olivine water interaction in temperature range 30 - 70°C (Paper III and IV). Paper I showed that potential CH4 oxidation strongly correlated to in situ its formation rates across a wide variety of lake sediments. This means that the oxidation rates could be enhanced in environments having the high formation rates. Thereby, the oxidation would likely be able to keep up with potentially increasing the formation rates, as a result diffusive CH4 release from freshwater sediments might not necessarily increase due to global warming. Paper II presented a new automated approach to assess temporal variability of its aquatic fluxes. Paper III and IV together revealed that H2 can be formed via olivine-water interaction. Abiotic CH4 formation was formed likely by Fischer-Tropsch Type reactions at low inorganic carbon concentration but by thermogenic processes at high inorganic carbon concentration. Paper IV showed that biotic methanogenic metabolism could harvest H2 and produce CH4. The dynamics of these processes seemed strongly affected by carbonate chemistry. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Submitted.

Esta pesquisa apresenta os resultados de um levantamento empírico de livros didáticos de Biologia e Química aprovados no PNLEM 2007, no sentido de investigar as demandas de conceitos químicos no estudo de uma temática própria da disciplina de Biologia: a origem da vida. Adicionalmente, esta dissertação coteja essas demandas conceituais com os correspondentes saberes químicos sequenciados nos capítulos das coleções de Química e discute a potencial interlocução entre os conjuntos de saberes das duas disciplinas, visto que fazem parte da mesma área do conhecimento escolar. Considerando-se todas as obras divididas em três volumes um para cada ano do Ensino Médio e excetuando-se os volumes únicos, foram analisados os capítulos que tratam da origem da vida em quatro coleções de Biologia e todo o conteúdo programático de duas obras de Química. Reconhecendo a relevância do livro didático no cenário educacional brasileiro, o caráter notadamente disciplinar do currículo e as especificidades do ensino de Ciências, este trabalho reúne argumentos teóricos que fundamentam a necessidade de um olhar abrangente sobre a realidade, sempre complexa e multifacetada. / This research presents the results of an empirical survey from textbooks of Biology and Chemistry approved in PNLEM 2007, to investigate the demands of chemical concepts in the study of one the subjects in Biology: the origin of life. In addition to that, this dissertation collates these conceptual demands with the corresponding chemical knowledge sequenced in chapters of the chemical collections and discusses the potential dialogue between the sets of knowledge of those two disciplines, as part of the same area of school knowledge. Considering the works divided into three volumes one for each year of high school and except for the single volumes, were analyzed the chapters dealing with the origin of life in four collections of Biology and whole academic program in two works of Chemistry. Recognizing the relevance of the textbook in Brazilian educational scenario, the notably disciplinary character of the curriculum and the specificities of Natural Sciences who originated the school disciplines of Biology and Chemistry, this work gathers theoretical arguments that justify the need for a comprehensive look at the reality, always complex and multifaceted.

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

The TiO2-catalyzed synthesis of nucleosides in non-aqueous formamide environ- ment via so-called acyclonucleoside intermediates represents an alternative way for the emergence of nucleic acids monomeric units, which could address the the fundamental problem associated with the formation of a --glycosidic bond between a nucleobase and a sugar moiety. In this computational contribution we present a plausible reaction route for the prebiotic TiO2-catalyzed synthesis of purine C2- and C3-acyclonucleosides in formamide, which does not require photocatalytic or radical chain mechanisms. The maximum computed activation energy along the proposed reaction channel is ≥ 32 kcal·mol≠1 , which is clearly feasible under the experimental conditions of the Saladino synthesis. We show that the rate determining step of the entire reaction path is the deprotonation of the formaldehyde hydrate methylene carbon occurring likely on defective binding sites of an anatase surface. Our calculations thus support the view of Saladino et al. about the catalytic role of the TiO2 surface in the one-pot synthesis of purine acyclonucleosides in heat formamide solution.

All known living cells contain a complex set of molecular machinery to support their growth and replication. However, the earliest cells must have been much simpler, consisting of a compartment and a genetic material to allow for Darwinian evolution. To study these intermediates, plausible model `protocells' must be synthesized in the laboratory since no fossils remain. Recent work has shown that fatty acids can self-assemble into vesicles that are able to grow and divide through simple mechanisms. However, a self-replicating protocell genome has not yet been developed. Here we discuss studies of systems that allow for the copying of nucleic acid templates without enzymes and how they could be developed into a genetic material.

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2015-10-21T23:19:34Z No. of bitstreams: 1 Saladina Amoedo Athayde - Disserta??o de Mestrado.pdf: 1649534 bytes, checksum: bd2a63d306451ca97d675a7b1decb6ab (MD5) / Made available in DSpace on 2015-10-21T23:19:34Z (GMT). No. of bitstreams: 1 Saladina Amoedo Athayde - Disserta??o de Mestrado.pdf: 1649534 bytes, checksum: bd2a63d306451ca97d675a7b1decb6ab (MD5) Previous issue date: 2015-08-27 / This paper presents a proposal of educational process, developed through applied research in order to seek the improvement about teaching Science and Biology in Basic School implementing current themes and concepts, interrelated to cross-cutting issues, going back to the origin of life, living beings, their interaction with the physical environment and the prospects for life elsewhere other than Earth. The project had as target students from elementary and high school from two public schools in the district of Feira de Santana-BA. It is justified by the low rates of our schools PISA (Programme for International Student Assessment) and IDEB (Education Development Index Basic) evaluations. The Vigotsky Knowledge Theory and Ausubel Learning Theory were used to guiding the educational process and pedagogical actions. Questionnaires were used as a data collection tool and the structured work by the construction and application of four activities, developed from the perspective of life on Mars. The choice of this planet is because of its importance for the study and teaching of astronomy through discoveries made since the first civilizations in search of understanding about planetary evolution and pre and post biotic ecosystems. Data analysis showed satisfactory results, it was possible to detect an improvement in the recognition of current concepts as a source of technological knowledge and as a result it expected to occur changes on educational indicators. Due to dissemination among teacher were demand applications in schools out of the winning ones, allowing viewing this proposal as reference in the quest for improving the teaching of Science and Biology. / Este trabalho apresenta uma proposta de processo educacional, elaborado por meio de pesquisa aplicada, no intuito de buscar a melhoria do ensino de Ci?ncias e Biologia da Escola B?sica implementando temas e conceitos atuais, interrelacionados a temas transversais, remontando a origem da vida, seres vivos, sua intera??o com o ambiente f?sico e as perspectivas de vida em outros lugares al?m da Terra. O projeto teve como p?blico alvo estudantes do Ensino Fundamental e M?dio de duas escolas p?blicas do munic?pio de Feira de Santana-BA. Est? justificado pelos baixos ?ndices das nossas escolas nas avalia??es do PISA (Programa Internacional de Avalia??o de Estudantes) e do IDEB (?ndice de Desenvolvimento da Educa??o B?sica). O Processo Educacional utilizado est? fundamentado na teoria do conhecimento Vigotsky e da aprendizagem de Ausubel, as quais nortearam as a??es pedag?gicas. Foram usados question?rios como ferramenta de coleta de dados e o trabalho estruturado pela constru??o e aplica??o de quatro atividades, desenvolvidas a partir da perspectiva de vida em Marte. A escolha deste planeta se deve ao fato da import?ncia dele para o estudo e ensino da Astronomia, mediante descobertas realizadas desde as primeiras civiliza??es em busca do entendimento sobre evolu??o planet?ria e ecossistemas pr? e p?s bi?ticos. A an?lise dos dados mostrou resultados satisfat?rios, foi poss?vel detectar uma melhora no reconhecimento dos conceitos atuais como fonte de conhecimento tecnol?gico e em decorr?ncia disto esperar que ocorra mudan?a dos ?ndices educacionais. Devido a divulga??o entre os professores, foram geradas demandas de aplica??o em escolas n?o contempladas, permitindo visionar esta proposta como refer?ncia na busca pela melhoria do ensino de Ci?ncias e Biologia.