A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems

The core of the origin-of-life problem is to explain how a complex dissipative system could emerge spontaneously from a simple environment, perpetuate itself, and complexify over time. This would only be possible, we argue, if prebiotic chemical reaction networks had autocatalytic features organized in a way that permitted the accretion of complexity even in the absence of genetic control. To evaluate this claim, we developed tools to analyze the autocatalytic organization of food-driven reaction networks and applied these tools to both abiotic and biotic networks. Both networks contained seed-dependent autocatalytic systems (SDASs), which are subnetworks that can use a flux of food chemicals to self-propagate if, and only if, they are first seeded by some non-food chemicals. Moreover, SDASs were organized such that the activation of a lower-tier SDAS could render new higher-tier SDASs accessible. The organization of SDASs is, thus, similar to trophic levels (producer, primary consumer, etc.) in a biological ecosystem. Furthermore, similar to ecological succession, we found that higher-tier SDASs may produce chemicals that enhance the ability of the entire chemical ecosystem to utilize food more efficiently. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify even without genetic polymers. This framework predicts that it ought to be possible to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems in the laboratory. Additionally, SDAS theory may be useful for exploring general properties of other complex systems.

Prebiotic experiments simulating hydrothermal vents: Influence of olivine in the decomposition of simple carboxylic acids

Hydrothermal systems have been proposed as keen environments on the early Earth where chemical evolution processes could have occurred. The presence of minerals and a continuous energy flux stand out among the most remarkable conditions in such environments. In this research the decomposition of two organic acids was studied. Ionizing radiation and thermal energy were the sources selected for decomposition tests, as both are naturally present on hydrothermal systems and probably, they were present on early Earth. Radiation could come from unstable elements in minerals, and heat is the most abundant energy source in hydrothermal systems. As minerals play a key role in prebiotic chemistry experiments and are an essential component on hydrothermal environments, the role of olivine in decomposition was tested. Results indicate that both organic acids highly decomposed when irradiated or heated. Radiation is more efficient than heating in decomposing the carboxylic acids and forming other carboxylic acids. Interestingly, the occurrence of olivine affects decomposition on both heated and irradiated samples, as both the rate of decomposition, and the amount and type of products vary compared with experiments without the mineral. The formation of other carboxylic acids was followed in all samples. Succinic, tricarballilic, citric and carboxisuccinic acids were detected in radiolysis experiments of acetic acid. The radiolysis of formic acid produced oxalic and tartronic. The heating of acetic acid solutions formed succinic, tricarballilic, citric and carboxisuccinic acids. However, the heating of formic acids only generated oxalic acid. The presence of olivine affected the amount and type of carboxylic acids formed in radiation and heating experiments. Natural hydrothermal systems are complex environments and many variables are present in them. Our results reinforce the idea that a combination of variables is necessary to better simulate these environments in prebiotic chemistry experiments. All variables could have affected the prebiotic chemical reactions; and hence, the role of hydrothermal systems in prebiotic chemistry could be much more complex that thought.

Life’s Origins and the Search for Life on Rocky Exoplanets

The study of the origin(s) of life on Earth and the search for life on other planets are closely linked. Prebiotic chemical scenarios can help priori-tize target planets for the search for life (as we know it) and can provide informative prior probabilities to help us assess the likelihood that particular spectroscopic features are evidence of life. The prerequisites for origins scenarios themselves predict characteristic spectral signatures. The interplay between origins research and the search for extraterrestrial life starts with laboratory work to guide exploration within our own Solar System, which will then inform future exoplanet observations and laboratory research. Exoplanet research will, in turn, provide statistical context to conclusions about the nature and origins of life.

Abiotic RNA Formation in Natural Nanoconfinements of Water: Overcoming the Water Paradox via a Nanofluidic Bridge Between Geochemistry and Biochemistry

<p class="western">The "water paradox" is an obstinate problem in the research on the chemical evolution towards the emergence of life. It states that although aqueous environments are essential for life, they hamper key condensation reactions such as nucleotide polymerisation. To overcome this paradox several hypotheses have been proposed, including scenarios based on alternative solvents like formamide, condensing agents like cyanamide, high temperatures of over 150 °C or wet/dry cycles in surface ponds. However, when appraising the prebiotic plausibility of such scenarios some general weaknesses appear. Besides the fact that all known life manages the water paradox without needing such proposed conditions, the principle that evolution builds on existing pathways indicates that the same physicochemical effects were probably involved in the abiotic origin of biopolymers as now being tapped by life via complex enzymes.</p> <p class="western">Here we show that abiotic temporal nanoconfinements of water can act as natural reactions vessels for prebiotic RNA formation. We present evidence for spontaneous, abiotic polymerisation of nucleotides in water. According to our results the reaction is enabled by the rise of anomalous properties of water when being temporarily confined between nanoscale separated particles of geological ubiquity within aqueous suspensions. These findings can solve the water paradox in such a way that nanofluidic effects in aqueous particle suspensions open up an abiotic route to biopolymerisation and polymer stabilisation under chemical and thermodynamic conditions which also exist within the intracellular environment of living cells. The fact that polymerase enzymes also form temporal nanoconfined water clusters inside their active site implies that the same physico-chemical effects are tapped for nucleotide condensation in water both by biochemical pathways and the reported abiotic route. This indicates that our model is consistent with evolutionary conservatism stretching back to the era of prebiotic chemical evolution. The consistency is further supported by the fact that water is not trapped by nanoconfinements within the polymerase core but can exchange with the surrounding intracellular fluid – a situation which is also prevalent in nanofluidic environments within aqueous particle suspensions. Our experimental finding that under the reported conditions an amino acid catalyses the abiotic polymerisation of nucleotides may give a hint to a nanofluidic origin of cooperation between amino acids and nucleotides evolving to the interdependent synthesis of proteins and nucleic acids in living cells.</p> <p class="western">The effect of abiotic RNA polymerisation in temporal nanoconfined water does not depend on highly specific mineral species and geological environments as watery suspensions of micro- and nanoparticles are virtually ubiquitous – they exist, for example, in the form of sediments with pore water, hydrothermal vent fluids containing precipitated inorganic and polyaromatic particles or dispersed aggregates inside water-filled cracks in the crust of the earth and possibly of icy moons in the outer solar system.</p> <p class="western"><strong>References</strong></p> <p class="western">Greiner de Herrera, A., Markert, T. & Trixler, F. Temporal nanofluidic confinements induce prebiotic condensation in water. Preprint, DOI: 10.21203/rs.3.rs-163645/v3</p>

Cyanide as a Primordial Reductant enables a Protometabolic Reductive Glyoxylate Pathway

Investigation of prebiotic chemical pathways leading to protometabolic forerunners of metabolism has been largely based on bio-inspired (iron-mediated) reductive conversion of carbon dioxide and of carboxylic acid substrates.1,2 While attractive from a parsimony point of view, this approach has been challenging with debatable outcomes.3,4 Herein, we show that cyanide reacts with citric acid cycle (TCA) intermediates and derivatives and acts as a primordial reducing agent mediating abiotic reductive transformations. The hydrolysis of the cyanide adducts followed by decarboxylation enables the efficient reductive-decarboxylative transformation of oxaloacetate to malate and fumarate to succinate while pyruvate and α-ketoglutarate are not reduced. In the presence of glyoxylate,5,6 malonate7 and malononitrile,8 alternative pathways emerge, which after decarboxylation produce metabolic intermediates and related compounds also found in meteorites.9 These results, along with the previous demonstration of the metal-free alpha-keto analog of the reverse-TCA cycle,4,6 suggest that (a) alternative paradigms of cyanide-based protometabolic reactions bypassing the abiotic reductive-carboxylation steps can be prebiotically viable, (b) a novel reductive glyoxylate pathway can be a precursor to the r-TCA cycle and (c) the type of sophisticated carboxylation and reduction chemistries which are part of extant metabolic cycles10,11 are an evolutionary invention mediated by complex metalloproteins11.

The Grayness of the Origin of Life

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent “grayness” blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.

Prebiotic Chemical Refugia: Multifaceted Scenario for the Formation of Biomolecules in Primitive Earth

The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is to glimpse in which chemical scenarios the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as a homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades as nucleotides are complex though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named “Prebiotic Chemical Refugia”. A prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic biomolecules. Plus, this higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. This different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity; among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks of biological molecules might be accumulated are reviewed and discussed.