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Origin of Life in Chemically Complex Messy Environments: 2nd Edition
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Origin of Life in Chemically Complex Messy Environments: 2nd Edition

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 23840

Special Issue Editors

Dr. Ranajay Saha

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Guest Editor
Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
Interests: origin of life; prebiotic evolution; RNA world; minimal synthetic cells; molecular biology; protein and RNA biophysics; macromolecular crowding and confinement; UV damage; fluorescence spectroscopy
Special Issues, Collections and Topics in MDPI journals
Dr. Alberto Vázquez-Salazar

E-Mail Website
Guest Editor
Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
Interests: origin of life; RNA world; early evolution of life
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The first volume of the Special Issue “Origin of Life in Chemically Complex Messy Environments” (https://www.mdpi.com/journal/life/special_issues/Origin_of_Life ) was a success, and it is our pleasure to announce the second volume.

Traditionally, the vast majority of prebiotic chemistry research has consisted of experiments focused on the behavior of a restricted spectrum of organic molecules, usually studying the components of life separately, where the results are limited by the simulated scenario, also described as "clean and isolated" experiments. However, research on the origin of life needs to be expanded in order to enable continuous progress in the field. Considering the prebiotic Earth four billion years ago (a messy atmosphere, in other words), a chaotic mélange of diverse starting materials appears to be realistic. As prebiotic chemists and origin-of-life researchers, we must modify our current approach and consider more chemical and geological scenarios in which both physical processes and driving forces toward primitive life formation are examined. In this Special Issue, we welcome the submission of original research papers, comprehensive reviews, and perspectives that demonstrate or summarize advances related to the origin of life in various complex chemical and prebiotically feasible environments.

Dr. Ranajay Saha
Dr. Alberto Vázquez-Salazar
Guest Editors

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Keywords

  • origin of life
  • complex chemical systems
  • prebiotic chemistry
  • prebiotic metabolisms
  • chemical evolution
  • prebiotic catalysts

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Published Papers (10 papers)

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Research

31 pages, 4371 KiB  
Article
Biological, Equilibrium and Photochemical Signatures of C, N and S Isotopes in the Early Earth and Exoplanet Atmospheres
by James R. Lyons
Life 2025, 15(3), 398; https://doi.org/10.3390/life15030398 - 3 Mar 2025
Viewed by 722
Abstract
The unambiguous detection of biosignatures in exoplanet atmospheres is a primary objective for astrobiologists and exoplanet astronomers. The primary methodology is the observation of combinations of gases considered unlikely to coexist in an atmosphere or individual gases considered to be highly biogenic. Earth-like [...] Read more.
The unambiguous detection of biosignatures in exoplanet atmospheres is a primary objective for astrobiologists and exoplanet astronomers. The primary methodology is the observation of combinations of gases considered unlikely to coexist in an atmosphere or individual gases considered to be highly biogenic. Earth-like examples of the former include CH4 and O3, and the latter includes dimethyl sulfide (DMS). To improve the plausibility of the detection of life, I argue that the isotope ratios of key atmospheric species are needed. The C isotope ratios of CO2 and CH4 are especially valuable. On Earth, thermogenesis and volcanism result in a substantial difference in δ13C between atmospheric CH4 and CO2 of ~−25‰. This difference could have changed significantly, perhaps as large as −95‰ after the evolution of hydrogenotrophic methanogens. In contrast, nitrogen fixation by nitrogenase results in a relatively small difference in δ15N between N2 and NH3. Isotopic biosignatures on ancient Earth and rocky exoplanets likely coexist with much larger photochemical signatures. Extreme δ15N enrichment in HCN may be due to photochemical self-shielding in N2, a purely abiotic process. Spin-forbidden photolysis of CO2 produces CO with δ13C < −200‰, as has been observed in the Venus mesosphere. Self-shielding in SO2 may generate detectable 34S enrichment in SO in atmospheres similar to that of WASP-39b. Sufficiently precise isotope ratio measurements of these and related gases in terrestrial-type exoplanet atmospheres will require instruments with significantly higher spectral resolutions and light-collecting areas than those currently available. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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16 pages, 1216 KiB  
Article
The Origin(s) of LUCA: Computer Simulation of a New Theory
by Shiping Tang and Ming Gao
Life 2025, 15(1), 75; https://doi.org/10.3390/life15010075 - 10 Jan 2025
Viewed by 1926
Abstract
Carl Woese’s thesis of cellular evolution emphasized that the last universal common/cellular ancestor (LUCA) must have evolved by drawing from “global inventions”. Yet, existing theories regarding the origin(s) of LUCA have mostly centered upon scenarios that LUCA had evolved mostly independently. In an [...] Read more.
Carl Woese’s thesis of cellular evolution emphasized that the last universal common/cellular ancestor (LUCA) must have evolved by drawing from “global inventions”. Yet, existing theories regarding the origin(s) of LUCA have mostly centered upon scenarios that LUCA had evolved mostly independently. In an earlier paper, we advanced a new theory regarding the origin(s) of LUCA that extends Woese’s original insights. Our theory centers upon the possibility that different vesicles and protocells can merge with and acquire each other as a form of variation, selection, and retention, driven by wet-and-dry cycles and other similar cyclical processes. In this paper, we use computer simulation to show that under a variety of simulated conditions, LUCA can indeed be produced by our proposed processes. We hope that our study can stimulate laboratory testing of some key hypotheses that vesicles’ absorption, acquisition, and merger has indeed been a central force in driving the evolution of LUCA. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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17 pages, 8483 KiB  
Article
Groundwater-Driven Evolution of Prebiotic Alkaline Lake Environments
by Benjamin M. Tutolo, Robert Perrin, Rachel Lauer, Shane Bossaer, Nicholas J. Tosca, Alec Hutchings, Serhat Sevgen, Michael Nightingale, Daniel Ilg, Eric B. Mott and Thomas Wilson
Life 2024, 14(12), 1624; https://doi.org/10.3390/life14121624 - 7 Dec 2024
Cited by 2 | Viewed by 1783
Abstract
Alkaline lakes are thought to have facilitated prebiotic synthesis reactions on the early Earth because their modern analogs accumulate vital chemical feedstocks such as phosphate through the evaporation of dilute groundwaters. Yet, the conditions required for some building block synthesis reactions are distinct [...] Read more.
Alkaline lakes are thought to have facilitated prebiotic synthesis reactions on the early Earth because their modern analogs accumulate vital chemical feedstocks such as phosphate through the evaporation of dilute groundwaters. Yet, the conditions required for some building block synthesis reactions are distinct from others, and these conditions are generally incompatible with those permissible for nascent cellular function. However, because current scenarios for prebiotic synthesis have not taken account of the physical processes that drive the chemical evolution of alkaline lakes, the potential for the co-occurrence of both prebiotic synthesis and the origins and early evolution of life in prebiotic alkaline lake environments remains poorly constrained. Here, we investigate the dynamics of active, prebiotically relevant alkaline lakes using near-surface geophysics, aqueous geochemistry, and hydrogeologic modeling. Due to their small size, representative range of chemistry, and contrasting evaporation behavior, the investigated, neighboring Last Chance and Goodenough Lakes in British Columbia, Canada offer a uniquely tractable environment for investigating the dynamics of alkaline lake behavior. The results show that the required, extreme phosphate enrichments in alkaline lake waters demand geomorphologically-driven vulnerability to evaporation, while the resultant contrast between evaporated brines and inflowing groundwaters yields Rayleigh–Taylor instabilities and vigorous surface–subsurface cycling and mixing of lake and groundwaters. These results provide a quantitative basis to reconcile conflicting prebiotic requirements of UV light, salinity, metal concentration, and pH in alkaline lake environments. The complex physical and chemical processing inherent to prebiotic alkaline lake environments thus may have not only facilitated prebiotic reaction networks, but also provided habitable environments for the earliest evolution of life. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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15 pages, 3940 KiB  
Article
Light-Assisted Formation of Nucleosides and Nucleotides from Formamide in the Presence of Cerium Phosphate
by Shoval Gilboa, Larisa Panz, Nitai Arbell and Yaron Paz
Life 2024, 14(7), 846; https://doi.org/10.3390/life14070846 - 5 Jul 2024
Viewed by 1200
Abstract
The abiotic formation of nucleotides from small, simple molecules is of large interest in the context of elucidating the origin of life scenario. In what follows, it is shown that nucleosides and nucleotides can be formed from formamide in a one-pot reaction utilizing [...] Read more.
The abiotic formation of nucleotides from small, simple molecules is of large interest in the context of elucidating the origin of life scenario. In what follows, it is shown that nucleosides and nucleotides can be formed from formamide in a one-pot reaction utilizing the mineral cerium phosphate (CePO4) as a photocatalyst, a catalyst and a reactant that supplies the necessary phosphate groups. While the most abundant RNA/DNA building blocks were thymidine and thymidine monophosphate, considerable yields of other building blocks such as cytidine, cytidine monophosphate, and adenosine cyclic monophosphate were found. Comparing the yield of nucleosides and nucleotides under light conditions to that in the dark suggests that in the presence of cerium phosphate, light promotes the formation of nucleobases, whereas the formation of nucleotides from nucleosides take place even in the absence of light. The scenario described herein is considerably simpler than other scenarios involving several steps and several reactants. Therefore, by virtue of the principle of Occam’s razor, it should be of large interest for the community. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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14 pages, 4788 KiB  
Article
From Zero to Hero: The Cyanide-Free Formation of Amino Acids and Amides from Acetylene, Ammonia and Carbon Monoxide in Aqueous Environments in a Simulated Hadean Scenario
by Christian Seitz, Thomas Geisberger, Alexander Richard West, Jessica Fertl, Wolfgang Eisenreich and Claudia Huber
Life 2024, 14(6), 719; https://doi.org/10.3390/life14060719 - 1 Jun 2024
Cited by 1 | Viewed by 1579
Abstract
Amino acids are one of the most important building blocks of life. During the biochemical process of translation, cells sequentially connect amino acids via amide bonds to synthesize proteins, using the genetic information in messenger RNA (mRNA) as a template. From a prebiotic [...] Read more.
Amino acids are one of the most important building blocks of life. During the biochemical process of translation, cells sequentially connect amino acids via amide bonds to synthesize proteins, using the genetic information in messenger RNA (mRNA) as a template. From a prebiotic perspective (i.e., without enzymatic catalysis), joining amino acids to peptides via amide bonds is difficult due to the highly endergonic nature of the condensation reaction. We show here that amides can be formed in reactions catalyzed by the transition metal sulfides from acetylene, carbon monoxide and ammonia under aqueous conditions. Some α- and β-amino acids were also formed under the same conditions, demonstrating an alternative cyanide-free path for the formation of amino acids in prebiotic environments. Experiments performed with stable isotope labeled precursors, like 15NH4Cl and 13C-acetylene, enabled the accurate mass spectroscopic identification of the products formed from the starting materials and their composition. Reactions catalyzed using the transition metal sulfides seem to offer a promising alternative pathway for the formation of amides and amino acids in prebiotic environments, bypassing the challenges posed by the highly endergonic condensation reaction. These findings shed light on the potential mechanisms by which the building blocks of life could have originated on early Earth. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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19 pages, 1439 KiB  
Article
A Surface Hydrothermal Source of Nitriles and Isonitriles
by Paul B. Rimmer and Oliver Shorttle
Life 2024, 14(4), 498; https://doi.org/10.3390/life14040498 - 11 Apr 2024
Cited by 8 | Viewed by 5744
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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23 pages, 2745 KiB  
Article
Prebiotic Syntheses of Organophosphorus Compounds from Reduced Source of Phosphorus in Non-Aqueous Solvents
by Maheen Gull, Tian Feng, Benjamin Smith, Laurent Calcul and Matthew A. Pasek
Life 2023, 13(11), 2134; https://doi.org/10.3390/life13112134 - 29 Oct 2023
Cited by 1 | Viewed by 1991
Abstract
Reduced-oxidation-state phosphorus (reduced P, hereafter) compounds were likely available on the early Earth via meteorites or through various geologic processes. Due to their reactivity and high solubility, these compounds could have played a significant role in the origin of various organophosphorus compounds of [...] Read more.
Reduced-oxidation-state phosphorus (reduced P, hereafter) compounds were likely available on the early Earth via meteorites or through various geologic processes. Due to their reactivity and high solubility, these compounds could have played a significant role in the origin of various organophosphorus compounds of biochemical significance. In the present work, we study the reactions between reduced P compounds and their oxidation products, with the three nucleosides (uridine, adenosine, and cytidine), with organic alcohols (glycerol and ethanolamine), and with the tertiary ammonium organic compound, choline chloride. These reactions were studied in the non-aqueous solvent formamide and in a semi-aqueous solvent comprised of urea: ammonium formate: water (UAFW, hereafter) at temperatures of 55–68 °C. The inorganic P compounds generated through Fenton chemistry readily dissolve in the non-aqueous and semi-aqueous solvents and react with organics to form organophosphites and organophosphates, including those which are identified as phosphate diesters. This dual approach (1) use of non-aqueous and semi-aqueous solvents and (2) use of a reactive inorganic P source to promote phosphorylation and phosphonylation reactions of organics readily promoted anhydrous chemistry and condensation reactions, without requiring any additive, catalyst, or other promoting agent under mild heating conditions. We also present a comparative study of the release of P from various prebiotically relevant phosphate minerals and phosphite salts (e.g., vivianite, apatite, and phosphites of iron and calcium) into formamide and UAFW. These results have direct implications for the origin of biological P compounds from non-aqueous solvents of prebiotic provenance. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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17 pages, 6790 KiB  
Article
RETRACTED: Metal Catalysis Acting on Nitriles in Early Earth Hydrothermal Systems
by Miranda Sturtz and Christopher House
Life 2023, 13(7), 1524; https://doi.org/10.3390/life13071524 - 7 Jul 2023
Cited by 1 | Viewed by 2225 | Retraction
Abstract
Hydrothermal systems are areas in which heated fluids and organic molecules rush through basaltic material rich in metals and minerals. By studying malononitrile and acetonitrile, we examine the effects of metal and mineral nanoparticles on nitrile compounds in anoxic, hydrothermal conditions representing a [...] Read more.
Hydrothermal systems are areas in which heated fluids and organic molecules rush through basaltic material rich in metals and minerals. By studying malononitrile and acetonitrile, we examine the effects of metal and mineral nanoparticles on nitrile compounds in anoxic, hydrothermal conditions representing a prebiotic environment of early Earth. Polymerization, reduction, cyclization, and a phenomenon colloquially known as ‘chemical gardening’ (structure building via reprecipitation of metal compounds or complexing with organics) are all potential outcomes with the addition of metals and minerals. Reduction occurs with the addition of rhodium (Rh) or iron (II) sulfide (FeS), with positive identification of ethanol and ethylamine forming from acetonitrile reduction. We find that polymerization and insoluble product formation were associated with oxide minerals, metallic nickel (Ni), and metallic cobalt (Co) acting as catalysts. Oxide minerals strongly promoted polymerization into insoluble, tar-like products of nitriles. FeS, iron-nickel alloy (FeNi), and rhodium are unique cases that appear to act as reagents by actively participating in chemical gardening without returning to their initial state. Further, FeS tentatively had a phase change into the mineral parabutlerite. This research aims to identify metals and metal minerals that could best serve nitrile catalysis and reactions on early Earth. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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13 pages, 4968 KiB  
Article
Serpentinization-Associated Mineral Catalysis of the Protometabolic Formose System
by Arthur Omran, Asbell Gonzalez, Cesar Menor-Salvan, Michael Gaylor, Jing Wang, Jerzy Leszczynski and Tian Feng
Life 2023, 13(6), 1297; https://doi.org/10.3390/life13061297 - 31 May 2023
Cited by 4 | Viewed by 3318
Abstract
The formose reaction is a plausible prebiotic chemistry, famed for its production of sugars. In this work, we demonstrate that the Cannizzaro process is the dominant process in the formose reaction under many different conditions, thus necessitating a catalyst for the formose reaction [...] Read more.
The formose reaction is a plausible prebiotic chemistry, famed for its production of sugars. In this work, we demonstrate that the Cannizzaro process is the dominant process in the formose reaction under many different conditions, thus necessitating a catalyst for the formose reaction under various environmental circumstances. The investigated formose reactions produce primarily organic acids associated with metabolism, a protometabolic system, and yield very little sugar left over. This is due to many of the acids forming from the degradation and Cannizaro reactions of many of the sugars produced during the formose reaction. We also show the heterogeneous Lewis-acid-based catalysis of the formose reaction by mineral systems associated with serpentinization. The minerals that showed catalytic activity include olivine, serpentinite, and calcium, and magnesium minerals including dolomite, calcite, and our Ca/Mg-chemical gardens. In addition, computational studies were performed for the first step of the formose reaction to investigate the reaction of formaldehyde, to either form methanol and formic acid under a Cannizzaro reaction or to react to form glycolaldehyde. Here, we postulate that serpentinization is therefore the startup process necessary to kick off a simple proto metabolic system—the formose protometabolic system. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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16 pages, 8397 KiB  
Article
Straightforward Creation of Possibly Prebiotic Complex Mixtures of Thiol-Rich Peptides
by Ibrahim Shalayel, Naoual Leqraa, Véronique Blandin and Yannick Vallée
Life 2023, 13(4), 983; https://doi.org/10.3390/life13040983 - 10 Apr 2023
Cited by 2 | Viewed by 2065
Abstract
At the origin of life, extremely diverse mixtures of oligomers and polymers could be obtained from relatively simple molecular bricks. Here, we present an example of the polymerization of two amidonitriles derived from cysteine, Cys-Ala-CN and Cys-Met-CN. The thiol function in a molecule [...] Read more.
At the origin of life, extremely diverse mixtures of oligomers and polymers could be obtained from relatively simple molecular bricks. Here, we present an example of the polymerization of two amidonitriles derived from cysteine, Cys-Ala-CN and Cys-Met-CN. The thiol function in a molecule adds onto the nitrile group of another one, allowing efficient condensation reactions and making available an extensive range of polymers containing amide bonds and/or five-membered heterocycles, namely thiazolines. Macrocycles were also identified, the biggest one containing sixteen residues (cyclo(Cys-Met)8). MALDI-TOF mass spectrometry was used to identify all the present species. What these examples show is that complex mixtures are likely to have formed on the primitive Earth and that, ultimately, the selection that must have followed may have been an even more crucial step towards life than the synthesis of the pre-biological species themselves. Full article
(This article belongs to the Special Issue Origin of Life in Chemically Complex Messy Environments: 2nd Edition)
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