Origins of life: An operational definition

Is Life Binary or Gradual?

The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living.

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

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.

From autocatalysis to survival of the fittest in self-reproducing lipid systems

Studying autocatalysis - in which molecules catalyse their own formation - might help to explain the emergence of chemical systems that exhibit traits normally associated with biology. When coupled to other processes, autocatalysis can lead to complex systems-level behaviour in apparently simple mixtures. Lipids are an important class of chemicals that appear simple in isolation, but collectively show complex supramolecular and mesoscale dynamics. Here we discuss autocatalytic lipids as a source of extraordinary behaviour such as primitive chemical evolution, chemotaxis, temporally controllable materials and even as supramolecular catalysts for continuous synthesis. We survey the literature since the first examples of lipid autocatalysis and highlight state-of-the-art synthetic systems that emulate life, displaying behaviour such as metabolism and homeostasis, with special consideration for generating structural complexity and out-of-equilibrium models of life. Autocatalytic lipid systems have enormous potential for building complexity from simple components, and connections between physical effects and molecular reactivity are only just beginning to be discovered.

Venus, an Astrobiology Target

We present a case for the exploration of Venus as an astrobiology target-(1) investigations focused on the likelihood that liquid water existed on the surface in the past, leading to the potential for the origin and evolution of life, (2) investigations into the potential for habitable zones within Venus' present-day clouds and Venus-like exo atmospheres, (3) theoretical investigations into how active aerobiology may impact the radiative energy balance of Venus' clouds and Venus-like atmospheres, and (4) application of these investigative approaches toward better understanding the atmospheric dynamics and habitability of exoplanets. The proximity of Venus to Earth, guidance for exoplanet habitability investigations, and access to the potential cloud habitable layer and surface for prolonged in situ extended measurements together make the planet a very attractive target for near term astrobiological exploration.

Physical autocatalysis driven by a bond-forming thiol-ene reaction

Autocatalysis has been extensively studied because it is central to the propagation of living systems. Chemical systems which self-reproduce like living cells would offer insight into principles underlying biology and its emergence from inanimate matter. Protocellular models feature a surfactant boundary, providing compartmentalization in the form of a micelle or vesicle and any model of the emergence of cellular life must account for the appearance, and evolution of, such boundaries. Here, we describe an autocatalytic system where two relatively simple components combine to form a more complex product. The reaction products aggregate into micelles that catalyse molecular self-reproduction. Study of the reaction kinetics and aggregation behaviour suggests a mechanism involving micelle-mediated physical autocatalysis and led to the rational design of a second-generation system. These reactions are driven by irreversible bond formation and provide a working model for the autocatalytic formation of protocells from the coupling of two simple molecular components.

Imperfect identity of autonomous living system

We usually think that there is a clear cut between known facts and unknown facts. In category theory, this can correspond to equivalence of categories for partial map and pointed set. If this relation is satisfied, we implicitly ignore the difference of "before encoding" and "after encoding". In this paper, we admit this discrepancy in the context of organizational endo-perspective, and make weak condition of equivalence of categories for partial map and pointed set to connect learning systems.

Thirty years of computational autopoiesis: a review

Computational autopoiesis--the realization of autopoietic entities in computational media--holds an important and distinctive role within the field of artificial life. Its earliest formulation by Francisco Varela, Humberto Maturana, and Ricardo Uribe was seminal in demonstrating the use of an artificial, computational medium to explore the most basic question of the abstract nature of living systems--over a decade in advance of the first Santa Fe Workshop on Artificial Life. The research program it originated has generated substantive demonstrations of progressively richer, lifelike phenomena. It has also sharply illuminated both conceptual and methodological problems in the field. This article provides an integrative overview of the sometimes disparate work in this area, and argues that computational autopoiesis continues to provide an effective framework for addressing key open problems in artificial life.

Basic autonomy as a fundamental step in the synthesis of life

In the search for the primary roots of autonomy (a pivotal concept in Varela's comprehensive understanding of living beings), the theory of autopoiesis provided an explicit criterion to define minimal life in universal terms, and was taken as a guideline in the research program for the artificial synthesis of biological systems. Acknowledging the invaluable contribution of the autopoietic school to present biological thinking, we offer an alternative way of conceiving the most basic forms of autonomy. We give a bottom-up account of the origins of "self-production" (or self-construction, as we propose to call it), pointing out which are the minimal material and energetic requirements for the constitution of basic autonomous systems. This account is, indeed, committed to the project of developing a general theory of biology, but well grounded in the universal laws of physics and chemistry. We consider that the autopoietic theory was formulated in highly abstract terms and, in order to advance in the implementation of minimal autonomous systems (and, at the same time, make major progress in exploring the origins of life), a more specific characterization of minimal autonomous systems is required. Such a characterization will not be drawn from a review of the autopoietic criteria and terminology (à la Fleischaker) but demands a whole reformulation of the question: a proper naturalization of the concept of autonomy. Finally, we also discuss why basic autonomy, according to our account, is necessary but not sufficient for life, in contrast with Varela's idea that autopoiesis was a necessary and sufficient condition for it.

Autopoietic and (M,R) systems

From the many attempts to produce a conceptual framework for the organization of living systems, the notions of (M,R) systems and Autopoiesis stand out for their rigor, their presupposition of the circularity of metabolism, and the new epistemologies that they imply. From their inceptions, these two notions have been essentially disconnected because each has defined its own language and tools. Here we demonstrate the existence of a deep conceptual link between (M,R) systems and Autopoietic systems. This relationship permits us to posit that Autopoietic systems, which have been advanced as capturing the central aspects of living systems, are a subset of (M,R) systems. This result, in conjunction with previous theorems proved by Rosen, can be used to outline a demonstration that the operation of Autopoietic systems cannot be simulated by Turing machines. This powerful result shows the potential of linking these two models. Finally, we suggest that the formalism of (M,R) systems could be used to model the circularity of metabolism.

Membrane self-assembly processes: steps toward the first cellular life

This review addresses the question of the origin of life, with emphasis on plausible boundary structures that may have initially provided cellular compartmentation. Some form of compartmentation is a necessary prerequisite for maintaining the integrity of interdependent molecular systems that are associated with metabolism, and for permitting variations required for speciation. The fact that lipid-bilayer membranes define boundaries of all contemporary living cells suggests that protocellular compartments were likely to have required similar, self-assembled boundaries. Amphiphiles such as short-chain fatty acids, which were presumably available on the early Earth, can self-assemble into stable vesicles that encapsulate hydrophilic solutes with catalytic activity. Their suspensions in aqueous media have therefore been used to investigate nutrient uptake across simple membranes and encapsulated catalyzed reactions, both of which would be essential processes in protocellular life forms.

What makes plants different? Principles of extracellular matrix function in 'soft' plant tissues

An overview of the biomechanic and morphogenetic function of the plant extracellular matrix (ECM) in its primary state is given. ECMs can play a pivotal role in cellular osmo- and volume-regulation, if they enclose the cell hermetically and constrain hydrostatic pressure evoked by osmotic gradients between the cell and its environment. From an engineering viewpoint, such cell walls turn cells into hydraulic machines, which establishes a crucial functional differences between cell walls and other cellular surface structures. Examples of such hydraulic machineries are discussed. The function of cell walls in the control of pressure, volume, and shape establishes constructional evolutionary constraints, which can explain aspects commonly considered typical of plants (sessility, autotrophy). In plants, 'cell division' by insertion of a new cell wall is a process of internal cytoplasmic differentiation. As such it differs fundamentally from cell separation during cytokinesis in animals, by leaving the coherence of the dividing protoplast basically intact. The resulting symplastic coherence appears more important for plant morphogenesis than histological structure; similar morphologies are realized on the basis of distinct tissue architectures in different plant taxa. The shape of a plant cell is determined by the shape its cell wall attains under multiaxial tensile stress. Consequently, the development of form in plants is achieved by a differential plastic deformation of the complex ECM in response to this multiaxial force (hydrostatic pressure). Current concepts of the regulation of these deformation processes are briefly evaluated.

Protein expression in liposomes

Compartmentalization is one of the key steps in the evolution of cellular structures and, so far, only few attempts have been made to model this kind of "compartmentalized chemistry" using liposomes. The present work shows that even such complex reactions as the ribosomal synthesis of polypeptides can be carried out in liposomes. A method is described for incorporating into 1-palmitoyl-2-oleoyl-sn-3-phosphocholine (POPC) liposomes the ribosomal complex together with the other components necessary for protein expression. Synthesis of poly(Phe) in the liposomes is monitored by trichloroacetic acid of the (14)C-labelled products. Control experiments carried out in the absence of one of the ribosomal subunits show by contrast no significant polypeptide expression. This methodology opens up the possibility of using liposomes as minimal cell bioreactors with growing degree of synthetic complexity, which may be relevant for the field of origin of life as well as for biotechnological applications.

How did bacteria come to be?

Bacteria in the modern taxonomic sense are one of the three Domains. They must have split from the other two after the bulk of the development of biochemistry and cell biology had taken place. Up to the time of the Last Universal Ancestor (LUA) the world had been monophyletic with little stable diversity. This is to say that as advances took place the older forms were eliminated and diversity was only temporary. Two kinds of events could, in principle, permit stable diversity to arise. One kind occurs when two nearly simultaneous, different advances occur, both of which overcome the same problem. While the previous type would be supplanted, if the new types did not compete with each other, new niches and habitats could lead to stable diversity. The second kind is a saltation or macroevolutionary event that greatly expands the biota and reduces previous constraints and thereby drastically reduces competition; this generally leads to a 'species radiation' and results in the development of a spectrum of biological types some of which persist and do not compete with each other. It is proposed that the two splits to yield the three Domains of Bacteria, Archaea, and Eukarya, resulted from one of each of these two processes leading to diversity. One arose from the consequences of cells accumulating substances from the environment, thus increasing their internal osmotic pressure. This resulted in two nearly simultaneous biological solutions: one (Bacteria) was the development of the external sacculus, i.e. the formation of a stress-bearing exoskeleton. The other (Eukarya) was the development of cytoskeletons and mechanoenzymes, i.e. formation of an endoskeleton. The other event causing diversity was the invention of an effective way to tap a new energy source and allow the biomass to increase extensively permitting a radiation of many different types of organisms. I suggest that this seminal advance was the development of methanogenesis. This caused a short-lived expansion and radiation before oxygen-producing photosynthesis allowed a still more major expansion and decreased the number of methanogens. Some details of these processes are elaborated. In particular, the evolutionary process that permitted the development of a sacculus, interpreted in light of the bacterial physiology of today's organisms is presented. It is argued that many great advances arise by developing a number of totally different processes for other purposes that can then each be modified to combine for yet another purpose.

Enzyme-containing liposomes can endogenously produce membrane-constituting lipids

BACKGROUND

'Giant vesicles' are liposomes that have diameters of several micrometers. It is possible to microinject biochemicals into a single vesicle and follow the progress of a chemical reaction in real time by light microscopy. We have previously used this technique to inject phospholipase A2 into giant vesicles; the vesicles disappeared as their components were hydrolyzed. Here we investigate whether the lipid components of a vesicle can be synthesized inside it.

RESULTS

Giant vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC) and palmitoyl-CoA were prepared in a solution containing sn-glycerol-3-phosphate. Microinjection of the enzyme sn-glycerol-3-phosphate-acyltransferase into the vesicle catalyzes the in situ production of the lipid membrane precursor 1-palmitoyl-sn-glycerol-3-phosphate, which remains incorporated in the membrane. The altered membrane chemistry causes shrinkage of the vesicle and formation of smaller liposomes on the inner surface at the site of injection. Similar transformations were seen when the enzyme was added to the outside of the vesicle.

CONCLUSIONS

We have used the first step of the 'salvage pathway' for synthesis of POPC to demonstrate that it is possible to localize the synthesis of a lipid membrane precursor inside a giant vesicle. In the future it may be possible to combine the necessary enzymes and substrates to carry out the reactions for a complete metabolic pathway within a liposome.

Production of RNA by a polymerase protein encapsulated within phospholipid vesicles

Catalyzed polymerization reactions represent a primary anabolic activity of all cells. It can be assumed that early cells carried out such reactions, in which macromolecular catalysts were encapsulated within some type of boundary membrane. In the experiments described here, we show that a template-independent RNA polymerase (polynucleotide phosphorylase) can be encapsulated in dimyristoyl phosphatidylcholine vesicles without substrate. When the substrate adenosine diphosphate (ADP) was provided externally, long-chain RNA polymers were synthesized within the vesicles. Substrate flux was maximized by maintaining the vesicles at the phase transition temperature of the component lipid. A protease was introduced externally as an additional control. Free enzyme was inactivated under identical conditions. RNA products were visualized in situ by ethidium bromide fluorescence. The products were harvested from the liposomes, radiolabeled, and analyzed by polyacrylamide gel electrophoresis. Encapsulated catalysts represent a model for primitive cellular systems in which an RNA polymerase was entrapped within a protected microenvironment.