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The Emergence of Life
The origin of life from inanimate matter has been the focus of much research for decades, both experimentally and philosophically. Luisi takes the reader through the consecutive stages from prebiotic chemistry to synthetic biology, uniquely combining both approaches. This book presents a systematic course discussing the successive stages of self-organisation, emergence, self-replication, autopoiesis, synthetic compartments and construction of cellular models, in order to demonstrate the spontaneous increase in complexity from inanimate matter to the first cellular life forms. A chapter is dedicated to each of these steps, using a number of synthetic and biological examples. With end-of-chapter review questions to aid reader comprehension, this book will appeal to graduate students and academics researching the origin of life and related areas such as evolutionary biology, biochemistry, molecular biology, biophysics and natural sciences.
eBook
Formation of nucleobases in a Miller–Urey reducing atmosphere
The Miller–Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH₃ + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.
Journal Article
Membraneless polyester microdroplets as primordial compartments at the origins of life
Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets’ potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a “messy” prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.
Journal Article
Quarks to Culture
Our world is nested, both physically and socially, and at each level we find innovations that are necessary for the next. Consider: atoms combine to form molecules, molecules combine to form single-celled organisms; when people come together, they build societies. Physics has gone far in mapping the basic mechanics of the simplest things and the dynamics of the overall nesting, as have biology and the social sciences for their fields. But what can we say about this beautifully complex whole? How does one stage shape another, and what can we learn about human existence through understanding an enlarged field of creation and being?InQuarks to Culture, Tyler Volk answers these questions, revealing how a universal natural rhythm-building from smaller things into larger, more complex things-resulted in a grand sequence of twelve fundamental levels across the realms of physics, biology, and culture. He introduces the key concept of \"combogenesis,\" the building-up from combination and integration to produce new things with innovative relations. He explores common themes in how physics and chemistry led to biological evolution, and biological evolution to cultural evolution. Volk also provides insights into linkages across the sciences and fields of scholarship, and presents an exciting synthesis of ideas along a sequence of things and relations, from physical to living to cultural. The resulting inclusive natural philosophy brings clarity to our place in the world, offering a roadmap for those who seek to understand big history and wrestle with questions of how we came to be.
eBook
The Plausibility of Life
In the 150 years since Darwin, the field of evolutionary biology has left a glaring gap in understanding how animals developed their astounding variety and complexity. The standard answer has been that small genetic mutations accumulate over time to produce wondrous innovations such as eyes and wings. Drawing on cutting-edge research across the spectrum of modern biology, Marc Kirschner and John Gerhart demonstrate how this stock answer is woefully inadequate. Rather they offer an original solution to the longstanding puzzle of how small random genetic change can be converted into complex, useful innovations.In a new theory they call \"facilitated variation,\" Kirschner and Gerhart elevate the individual organism from a passive target of natural selection to a central player in the 3-billion-year history of evolution. In clear, accessible language, the authors invite every reader to contemplate daring new ideas about evolution. By closing the major gap in Darwin's theory Kirschner and Gerhart also provide a timely scientific rebuttal to modern critics of evolution who champion \"intelligent design.\"
eBook
The singularity of nature : a convergence of biology, chemistry and physics
The Singularity of Nature: A Convergence of Biology, Chemistry and Physics takes a systems-based approach to the origin and evolution of complex life. Readers will gain a novel understanding of physiologic evolution and the limits to our current understanding.
eBook
Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases
Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22): 9346–9351].We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45–90 d, starting with an initial formamide weight fraction of 10−3 wt % that is typical for concentrations in shallow lakes on early Earth.
Journal Article
A Surface Hydrothermal Source of Nitriles and Isonitriles
Giant impacts can generate transient hydrogen-rich atmospheres, reducing atmospheric carbon. The reduced carbon will form hazes that rain out onto the surface and can become incorporated into the crust. Once heated, a large fraction of the carbon is converted into graphite. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences of such a crust for a prebiotic surface hydrothermal vent scenario. We model a surface vent fed by nitrogen-rich volcanic gas from high-temperature magmas passing through graphite-saturated crust. We consider this occurring at pressures of 1–1000bar and temperatures of 1500–1700 ∘C. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles (0.1% HCN and 1ppm HC3N) and isonitriles (0.01% HNC) relevant for prebiotic chemistry. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm. Methyl isocyanide can participate in the non-enzymatic activation and ligation of the monomeric building blocks of life, and surface or shallow hydrothermal environments provide its only known equilibrium geochemical source.
Journal Article