Origin Of Life Research Articles

Boundary versus enabling conditions for the origins of life: Comment on "Mineral self-organization on a lifeless planet" by García-Ruiz et al.

Boundary versus enabling conditions for the origins of life: Comment on "Mineral self-organization on a lifeless planet" by García-Ruiz et al.

Crystals and the debates on the nature, recognition and origin of life: Comment on "Mineral self-organization on a lifeless planet" by J.M. García-Ruiz et al.

Crystals and the debates on the nature, recognition and origin of life: Comment on "Mineral self-organization on a lifeless planet" by J.M. García-Ruiz et al.

Human Adaptation to Deep Space Environment: An Evolutionary Perspective of the Foreseen Interplanetary Exploration.

Long-term and deep space exploration is a prevailing dream that is becoming a reality. Is that so? The answer to this question depends on how the main actors of space exploration, i.e., politicians, scientists, and engineers, define “long-term” and the ultimate goals of the current space programs. Presently, long-term refers to few months or years, which is equivalent to the time necessary for a manned mission to reach another planet and return to Earth. Such a space mission is a tremendous scientific challenge associated with multidisciplinary issues spanning from technology to medicine biology, social, and psychological science. It has been a priority of the main westernized societies that has attracted the brightest and most innovative scientific minds since World War II. At first the stakes were mainly political in order to demonstrate to other countries power and strength. It progressively became a scientific motivation to uncover the secrets of the Universe and life's origin, and potentially to find traces of distant life. More recently, a desire to colonize space and exploit resources on other planets has emerged as a new dream. Although the journey to Mars is still a prospective and traveling in deep space a further elusive goal, one can question the ultimate implications of deep space exploration over the long-term.

The Hot Spring Hypothesis for an Origin of Life.

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus.“To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic.”—Leslie Orgel

Autocatalytic chemical networks at the origin of metabolism.

Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)—self-sustaining networks that collectively catalyse all their reactions—embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and furthermore indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.

Prebiotic Peptides: Molecular Hubs in the Origin of Life.

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

A Central Role for Peptides and Proteins in the Chemistry to Biology Transition of the Origins of Life

A Central Role for Peptides and Proteins in the Chemistry to Biology Transition of the Origins of Life

EXPERIÊNCIA DO ENSINO DE BIOLOGIA PELA EXPERIMENTAÇÃO EM UMA ESCOLA ESTADUAL DE EDUCAÇÃO PROFISSIONAL

O presente trabalho trata-se de um relato de experiência docente de umprofessor de biologia, realizada em uma Escola Estadual de Educação Profissionalde um município da Região Norte do Estado do Ceará, com alunos de 1° ano doensino médio. Procurou-se abordar o processo de ensino-aprendizagem com aexperimentação no Laboratório de Biologia da escola. Aborda-se neste trabalho aaplicação de atividades experimentais como forma de recurso didático durante operíodo do ano letivo de 2018. Para este relato, utilizou-se um diário de campodurante todo o ano e realizou-se neste trabalho 82 horas de métodos práticos deensino sobre os seguintes temas: Origem da Vida, Bioquímica Celular, Citologia eMetabolismo Energético, para um total de 160 alunos, de modo a inovar edespertar o interesse destes, sedimentando a aprendizagem de conceitos debiologia trabalhados no 1° ano. Destaca-se que o ensino por meio deexperimentação, desperta o interesse dos alunos e desenvolve competências ehabilidades relacionadas ao conhecimento biológico.

The origin of life: The conditions that sparked life on Earth

The origin of life: The conditions that sparked life on Earth

On the possible origin of protein homochirality, structure, and biochemical function

Living systems have chiral molecules, e.g., native proteins that almost entirely contain L-amino acids. How protein homochirality emerged from a background of equal numbers of L and D amino acids is among many questions about life's origin. The origin of homochirality and its implications are explored in computer simulations examining the stability and structural and functional properties of an artificial library of compact proteins containing 1:1 (termed demi-chiral), 3:1, and 1:3 ratios of D:L and purely L or D amino acids generated without functional selection. Demi-chiral proteins have shorter secondary structures and fewer internal hydrogen bonds and are less stable than homochiral proteins. Selection for hydrogen bonding yields a preponderance of L or D amino acids. Demi-chiral proteins have native global folds, including similarity to early ribosomal proteins, similar small molecule ligand binding pocket geometries, and many constellations of L-chiral amino acids with a 1.0-Å RMSD to native enzyme active sites. For a representative subset containing 550 active site geometries matching 457 (2) 4-digit (3-digit) enzyme classification (E.C.) numbers, native active site amino acids were generated at random for 472 of 550 cases. This increases to 548 of 550 cases when similar residues are allowed. The most frequently generated sequences correspond to ancient enzymatic functions, e.g., glycolysis, replication, and nucleotide biosynthesis. Surprisingly, even without selection, demi-chiral proteins possess the requisite marginal biochemical function and structure of modern proteins, but were thermodynamically less stable. If demi-chiral proteins were present, they could engage in early metabolism, which created the feedback loop for transcription and cell formation.

Earth's earliest and deepest purported fossils may be iron-mineralized chemical gardens.

Recognizing fossil microorganisms is essential to the study of life's origin and evolution and to the ongoing search for life on Mars. Purported fossil microbes in ancient rocks include common assemblages of iron-mineral filaments and tubes. Recently, such assemblages have been interpreted to represent Earth's oldest body fossils, Earth's oldest fossil fungi, and Earth's best analogues for fossils that might form in the basaltic Martian subsurface. Many of these putative fossils exhibit hollow circular cross-sections, lifelike (non-crystallographic, constant-thickness, and bifurcate) branching, anastomosis, nestedness within ‘sheaths’, and other features interpreted as strong evidence for a biological origin, since no abiotic process consistent with the composition of the filaments has been shown to produce these specific lifelike features either in nature or in the laboratory. Here, I show experimentally that abiotic chemical gardening can mimic such purported fossils in both morphology and composition. In particular, chemical gardens meet morphological criteria previously proposed to establish biogenicity, while also producing the precursors to the iron minerals most commonly constitutive of filaments in the rock record. Chemical gardening is likely to occur in nature. Such microstructures should therefore not be assumed to represent fossil microbes without independent corroborating evidence.

Hydrothermal Chemistry and the Origin of Cellular Life.

Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.

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.

Time Out

Should researchers who study the origins of life take a time-out? Chemist James Tour says they should hit pause on their work, in order to critically assess what they have accomplished, and what more is even possible to accomplish.

The new physics needed to probe the origins of life

Stuart Kauffman’s provocative take on emergence and evolution energizes Sara Imari Walker. Stuart Kauffman’s provocative take on emergence and evolution energizes Sara Imari Walker.

Recent Advances in Origins of Life Research by Biophysicists in Japan

Biophysics research tends to focus on utilizing multidisciplinary technologies and interdisciplinary collaborations to study biological phenomena through the lens of chemistry and physics. Although most current biophysics work is focused on studying extant biology, the fact remains that modern biological systems at some point were descended from a universal common ancestor. At the core of modern biology is the important question of how the earliest life on (or off) Earth emerged. Recent technological and methodological advances developed by biophysicists in Japan have allowed researchers to gain a new suite of knowledge related to the origins of life (OoL). Using these reports as inspiration, here, we highlight some of the significant OoL advances contributed by members of the biophysical research field in Japan with respect to the synthesis and assembly of biological (or pre-biological) components on early Earth, the co-assembly of primitive compartments with biopolymer systems, and the evolution of early genetic systems. We hope to provide inspiration to other biophysicists to not only use the always-advancing suite of available multidisciplinary technologies to continue their own line of work, but to also consider how their work or techniques can contribute to the ever-growing field of OoL research.

Prebiotic Oligomer Assembly: What Was the Energy Source?

Polymerization of nucleotides and amino acids to form large, complex, and potentially functional products was an early and essential event on the paths leading to life's origin. The standard Gibbs energies of the condensation reactions are uphill, however, and at equilibrium will yield only declining sequences of small, nonfunctional oligomers. Geochemically produced condensing agents such as carbonyl sulfide, cyanamide, and polyphosphates have been proposed to invert the unfavorable condensation Gibbs energies and thereby activate exergonic condensation. We argue, however, that although activators may provide modest yields of oligomers, the inherently episodic nature of their sources throttles their effectiveness, and the fundamental hydrolytic instabilities of oligonucleotides and peptides ultimately prevail to yield decreasing product sequences. Notably, the Gibbs energy governing oligomer formation is antientropic. Accordingly, we propose that declining progression can be surmounted in evaporating pools in which a favorable entropy change is produced when high surface/volume ratios concentrate reactants at the air/water interface in continuous cycles of wetting and drying. The severely reduced configurational freedom of the solutes then inverts the antientropic nature of the condensation reactions, pivoting them to exergonic states and thus to the production of ascending sequences of complex polymeric products.

Autocatalytic Networks at the Basis of Life's Origin and Organization.

Life is more than the sum of its constituent molecules. Living systems depend on a particular chemical organization, i.e., the ways in which their constituent molecules interact and cooperate with each other through catalyzed chemical reactions. Several abstract models of minimal life, based on this idea of chemical organization and also in the context of the origin of life, were developed independently in the 1960s and 1970s. These models include hypercycles, chemotons, autopoietic systems, (M,R)-systems, and autocatalytic sets. We briefly compare these various models, and then focus more specifically on the concept of autocatalytic sets and their mathematical formalization, RAF theory. We argue that autocatalytic sets are a necessary (although not sufficient) condition for life-like behavior. We then elaborate on the suggestion that simple inorganic molecules like metals and minerals may have been the earliest catalysts in the formation of prebiotic autocatalytic sets, and how RAF theory may also be applied to systems beyond chemistry, such as ecology, economics, and cognition.

The setting for the origin of life: a geological– geochemical perspective

There are many different scientific aspects involved in the challenge of understanding the origin of life (OoL). These include organic geochemistry – how to make RNA and DNA molecules from the simple organic building blocks delivered from space in the form of amino acids and some other compounds. Other aspects involve the study of inorganic geochemistry – how elements are made available to promote organic molecule complexification, under what conditions will lipid membranes form and how to bring together the different components that make a functioning cell.

The origin of life revisited: from metabolites to cells

The origin of life revisited: from metabolites to cells