Origin Of Life Research Articles

Chemical Evolution in Big History

Unfortunately, there is insufficient research on the course of chemical evolution within the framework of the study of both Big History and evolution. The lack of attention to chemical evolution is all the more disappointing since it is a very important part of megaevolution and Big History, which at some of its stages even act as the leading line (in particular, in the formation of pre-life on the Earth five billion years ago). The paper presents a brief history of chemical evolution: from the formation of the first atoms in the Universe to abiogenesis on the Earth, that is, the stage of pre-life and the formation of prerequisites for the emergence of the first living organisms. The history of chemical evolution before life's origin can be divided into three stages: the formation of atoms (pre-evolution); history before the start of the abiogenic phase on the Earth; and abiogenic chemical evolution. However, the author aims to elaborate a more detailed periodization of chemical evolution before life's origin. One should also pay attention to the important feature of chemical evolution which distinguishes it from other lines of evolution, namely, its co-evolutionary nature. The author demonstrates that chemical evolution at all its stages acted as a part of a co-evolutionary tandem: first, as a part of cosmic and stellar-galactic evolution, then as a part of planetary evolution since it is on planets (where temperature parameters are much more comfortable for chemical reactions) that a new qualitative stage in the development of chemical evolution begins. Finally, on the Earth, it developed first as a part of geochemical evolution, and then as a part of bio-chemical evolution, and this development continues until now.

Different Scenarios for the Origin and the Subsequent Succession of a Hypothetical Microbial Community in the Cloud Layer of Venus.

The possible existence of a microbial community in the venusian clouds is one of the most intriguing hypotheses in modern astrobiology. Such a community must be characterized by a high survivability potential under severe environmental conditions, the most extreme of which are very low pH levels and water activity. Considering different scenarios for the origin of life and geological history of our planet, a few of these scenarios are discussed in the context of the origin of hypothetical microbial life within the venusian cloud layer. The existence of liquid water on the surface of ancient Venus is one of the key outstanding questions influencing this possibility. We link the inherent attributes of microbial life as we know it that favor the persistence of life in such an environment and review the possible scenarios of life's origin and its evolution under a strong greenhouse effect and loss of water on Venus. We also propose a roadmap and describe a novel methodological approach for astrobiological research in the framework of future missions to Venus with the intent to reveal whether life exists today on the planet.

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri.

Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS-). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS2). Recently, paradigm-shifting studies indicate that Fe and S in FeS2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS2, as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS2, Fe(II)/HS-, or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS-, either as a component of the growth medium [Fe(II)/HS-] or generated through reduction of FeS2, were likely a major factor underpinning these phenotypic differences.IMPORTANCEThe methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life's origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

Biosignature, Technosignature, Event: Deconstruction, Astrobiology, and the Search for a Wholly Other Origin

Here I pursue a deconstructive reading of astrobiology, the emerging science dedicated to a double quest: solving the mystery of life's origin and discovering life beyond Earth. Astrobiology, I argue, is organized as a response to the aporetic formulation assumed by the origin of life in modern molecular biology, where (as Derrida's argues in Life Death) it becomes the origin of textuality. Because all Earth life shares a single genetic code, astrobiologists are seeking a second; hoping that a sort of multi-planetary comparative genomics may reveal the secret to life's origin. But the aporia repeats in the figure of the biosignature, the trace of life.

Which came first: the chicken, the egg, or guanine?

The main goal of the origin of life (OoL) hypothesis is to reconstruct the missing link between the primordial soup and the extant biology. However, the OoL itself is just the initial part of the link representing the bootstrapping operation of Darwinian evolution. The rest of the link is the emergence of the evolution to the present day primary biological system-the ribosome-based translation apparatus. A valid hypothesis must (i) not invoke Darwinian evolution in the bootstrapping and (ii) transform the ab initio life form into the translation apparatus without violating the principle of continuity (i.e., only incremental steps without foresight). Currently, no such hypothesis exists. Here, I discuss the Quadruplex World hypothesis, which fully complies with these requirements and suggests a spontaneous emergence of the ab initio life form. The spontaneity of OoL arises from the physicochemical properties of guanine monomers in a manner of causal determinism: each step of the process (i.e., scaffolding, polymerization, and folding) is caused by the most recent past step such that in the end only the specific 3D architecture forms. The architecture (i) has a length-independent folding pattern; (ii) can play the role of the predecessor of tRNA and single-handedly conduct a primitive form of translation; and (iii) can evolve into the extant translation apparatus without any paradoxes.

Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles.

RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.

On the origin of life: an RNA-focused synthesis and narrative.

Darwin's assertion that "it is mere rubbish thinking, at present, of origin of life" is no longer valid. By synthesizing origin of life (OoL) research from its inception to recent findings, with a focus on (i) proof-of-principle prebiotically plausible syntheses and (ii) molecular relics of the ancient RNA World, we present a comprehensive up-to-date description of science's understanding of the OoL and the RNA World hypothesis. Based on these observations, we solidify the consensus that RNA evolved before coded proteins and DNA genomes, such that the biosphere began with an RNA core where much of the translation apparatus and related RNA architecture arose before RNA transcription and DNA replication. This supports the conclusion that the OoL was a gradual process of chemical evolution involving a series of transitional forms between prebiotic chemistry and the last universal common ancestor (LUCA) during which RNA played a central role, and that many of the events and their relative order of occurrence along this pathway are known. The integrative nature of this synthesis also extends previous descriptions and concepts and should help inform future questions and experiments about the ancient RNA World and the OoL.

Protobiotic Network Reproducers Are Compositional Attractors: Enhanced Probability for Life's Origin

Protobiotic Network Reproducers Are Compositional Attractors: Enhanced Probability for Life's Origin

A Primer on Building Life‐Like Systems

AbstractThe quest to understand life and recreate it in vitro has been undertaken through many different routes. These different approaches for experimental investigation of life aim to piece together the puzzle either by tracing life's origin or by synthesizing life‐like systems from non‐living components. Unlike efforts to define life, these experimental inquiries aim to recapture specific features of living cells, such as reproduction, self‐organization or metabolic functions that operate far from thermodynamic equilibrium. As such, these efforts have generated significant insights that shed light on crucial aspects of biological functions. For observers outside these specific research fields, it sometimes remains puzzling what properties an artificial system would need to have in order to be recognized as most similar to life. In this Perspective, we discuss properties whose realization would, in our view, allow the best possible experimental emulation of a minimal form of biological life.

Gamma-Ray-Induced Amino Acid Formation in Aqueous Small Bodies in the Early Solar System.

Carbonaceous chondrites contain life's essential building blocks, including amino acids, and their delivery of organic compounds would have played a key role in life's emergence on Earth. Aqueous alteration of carbonaceous chondrites is a widespread process induced by the heat produced by radioactive decay of nuclides like 26Al. Simple ubiquitous molecules like formaldehyde and ammonia could produce various organic compounds, including amino acids and complex organic macromolecules. However, the effects of radiation on such organic chemistry are unknown. Hence, the effects of gamma rays from radioactive decays on the formation of amino acids in meteorite parent bodies are demonstrated here. We discovered that gamma-ray irradiation of aqueous formaldehyde and ammonia solutions afforded a variety of amino acids. The amino acid yields had a linear relationship with the total gamma-ray dose but were unaffected by the irradiation dose rates. Given the gamma-ray production rates in the meteorite parent bodies, we estimated that the production rates were reasonable compared to amino acid abundances in carbonaceous chondrites. Our findings indicate that gamma rays may contribute to amino acid formation in parent bodies during aqueous alteration. In this paper, we propose a new prebiotic amino acid formation pathway that contributes to life's origin.

A Nonenzymatic Analog of Pyrimidine Nucleobase Biosynthesis

AbstractMetabolic theories for the origin of life posit that inorganic catalysts enabled self‐organized chemical precursors to the pathways of metabolism, including those that make genetic molecules. Recently, experiments showing nonenzymatic versions of a number of core metabolic pathways have started to support this idea. However, experimental demonstrations of nonenzymatic reaction sequences along the de novo ribonucleotide biosynthesis pathways are limited. Here we show that all three reactions of pyrimidine nucleobase biosynthesis that convert aspartate to orotate proceed at 60 °C without photochemistry under aqueous conditions in the presence of metals such as Cu2+and Mn4+. Combining reactions into one‐pot variants is also possible. Life may not have invented pyrimidine nucleobase biosynthesis from scratch, but simply refined existing nonenzymatic reaction channels. This work is a first step towards uniting metabolic theories of life's origin with those centered around genetic molecules.

A material-based panspermia hypothesis: The potential of polymer gels and membraneless droplets.

The Panspermia hypothesis posits that either life's building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetarily transferred to facilitate the origins of life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely "seed" a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) as a theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: (1) survive spaceflight and (2) "function", i.e., contingently drive chemical evolution toward some form of abiogenesis once arriving on a foreign planet. We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels' capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.

Undefining life's biochemistry: implications for abiogenesis.

In the mid-twentieth century, multiple Nobel Prizes rewarded discoveries of a seemingly universal set of molecules and interactions that collectively defined the chemical basis for life. Twenty-first-century science knows that every detail of this Central Dogma of Molecular Biology can vary through either biological evolution, human engineering (synthetic biology) or both. Clearly the material, molecular basis of replicating, evolving entities can be different. There is far less clarity yet for what constitutes this set of possibilities. One approach to better understand the limits and scope of moving beyond life's central dogma comes from those who study life's origins. RNA, proteins and the genetic code that binds them each look like products of natural selection. This raises the question of what step(s) preceded these particular components? Answers here will clarify whether any discrete point in time or biochemical evolution will objectively merit the label of life's origin, or whether life unfolds seamlessly from the non-living universe.

Benesh Joseph.

"I am waiting for the day when someone will discover the mystery of life's origin … My biggest motivation is the excitement of making a new observation …" Find out more about Benesh Joseph in his Introducing … Profile.

Benesh Joseph

Abstract “I am waiting for the day when someone will discover the mystery of life's origin … My biggest motivation is the excitement of making a new observation …” Find out more about Benesh Joseph in his Introducing … Profile.

Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP.

The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3’,5’‐cyclic guanosine monophosphate (3’,5’‐cGMP) has been proposed as a candidate to create oligonucleotides of 15–20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.

Self-reproducing catalytic micelles as nanoscopic protocell precursors.

Protocells at life's origin are often conceived as bilayer-enclosed precursors of life, whose self-reproduction rests on the early advent of replicating catalytic biopolymers. This Perspective describes an alternative scenario, wherein reproducing nanoscopic lipid micelles with catalytic capabilities were forerunners of biopolymer-containing protocells. This postulate gains considerable support from experiments describing micellar catalysis and autocatalytic proliferation, and, more recently, from reports on cross-catalysis in mixed micelles that lead to life-like steady-state dynamics. Such results, along with evidence for micellar prebiotic compatibility, synergize with predictions of our chemically stringent computer-simulated model, illustrating how mutually catalytic lipid networks may enable micellar compositional reproduction that could underlie primal selection and evolution. Finally, we highlight studies on how endogenously catalysed lipid modifications could guide further protocellular complexification, including micelle to vesicle transition and monomer to biopolymer progression. These portrayals substantiate the possibility that protocellular evolution could have been seeded by pre-RNA lipid assemblies.

The Significance of The Mystery of Life's Origin

The Significance of The Mystery of Life's Origin

"Minimal metabolism": A key concept to investigate the origins and nature of biological systems.

The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of "minimal metabolism", in contrast to previous, top-down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here: https://youtu.be/DP7VMKk2qpA.

A Corollary of the Conant-Ashby Theorem Applied to Abiogenesis

From the Conant-Ashby theorem about the "good regulator" is possible to derive a corollary about the origin of life (OOL). This corollary introduces the concept of "good constructor." Thenit is shown as nature, seen as a material system ruled by the laws of physics, cannot be a "good constructor" of the basic machinery necessary for a living cell. As a consequence OOL needs intelligent design.