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Organic Chemical Evolution regarding the Origin(s) of Life

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

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 34376

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Special Issue Editors

Dr. Alexander Ruf

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Guest Editor

1. Institute of Space Astrophysics, Aix-Marseille University, PIIM group/ASTRO, 13007 Marseille, France
2. Ludwig-Maximilians-University, Department of Chemistry and Pharmacy, 80539 Munich, Germany
Interests: astrochemistry; astrobiology; analytical chemistry; computational chemistry; data analysis

Prof. Dr. Oliver Trapp

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Guest Editor

Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
Interests: origin of homochirality; autocatalysis; self-amplification; molecular evolution

Dr. Louis B. Le Sergeant D'Hendecourt

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Guest Editor

Institute of Space Astrophysics, Aix-Marseille University, PIIM group/ASTRO, 13007 Marseille, France
Interests: astrochemistry; interstellar ices; organic materials; laboratory simulations

Special Issue Information

Dear Colleagues,

A great challenge in Origin(s) of Life research is to identify the transition between inanimate molecules and prebiotic/biotic material. With increasing technology, including space-based telescopes or laboratory instruments, the molecular complexity in space is steadily being unraveled in greater detail. However, a single molecule does not represent life (e.g., no storage of information or emergent functions), but understanding the molecule's evolution through space enables one to probe the emergence of prebiotic chemistry in principle.

This Special Issue is split into two parts:

(i) Astrochemistry --> "Organic Chemical Evolution"

(ii) Prebiotic Chemistry --> "Regarding the Origin(s) of Life"

We will address the evolution of organic molecules along the astronomical timeline, and we will discuss the processes from individual molecules to prebiotic functions. Thus, we have teamed up to combine expertise from Astrochemistry (Louis d'Hendecourt), Prebiotic Chemistry (Oliver Trapp) and respective state-of-the-art (data) analysis (Alexander Ruf).

With respect to Astrochemistry, we will address three topics: (i) Organic Chemistry in Our Galaxy (Molecular Clouds, Protoplanetary Disks); (ii) Organic Chemistry in Our Solar System (Mars, Asteroids/Meteorites, Titan, Comets); (iii) Organic Delivery to Early Earth.

The Prebiotic Chemistry Section will focus on the formation of the first molecules of life. The appearance of complexity and self-organization, the oligomerization of nucleotides, amino acids and sugars leading to functional polymers and building of potential metabolic networks will be addressed. An important aspect here is the fundamental understanding of processes leading to the formation of homochirality.

Chemical (data) analysis has become an increasingly important topic in Origin(s) of Life research, using more powerful instruments and data analytical methods. Here, we will address strategies that target both observational and laboratory data.

Research or review articles are encouraged for submission.

Dr. Alexander Ruf
Prof. Dr. Oliver Trapp
Dr. Louis B. Le Sergeant D'Hendecourt
Guest Editors

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Keywords

astrochemistry
self-organization
prebiotic chemistry
data analysis
origin(s) of life

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Published Papers (9 papers)

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Research

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18 pages, 3504 KiB

Open AccessArticle

Deuterium Isotope Fractionation of Polycyclic Aromatic Hydrocarbons in Meteorites as an Indicator of Interstellar/Protosolar Processing History

by Heather V. Graham, Jamie E. Elsila, Jason P. Dworkin, Scott A. Sandford and Jose C. Aponte

Life 2022, 12(9), 1368; https://doi.org/10.3390/life12091368 - 1 Sep 2022

Cited by 5 | Viewed by 2515

Abstract

The stable isotope composition of soluble and insoluble organic compounds in carbonaceous chondrites can be used to determine the provenance of organic molecules in space. Deuterium enrichment in meteoritic organics could be a residual signal of synthetic reactions occurring in the cold interstellar medium or an indicator of hydrothermal parent-body reactions. δD values have been measured in grains and bulk samples for a wide range of meteorites; however, these reservoirs are highly variable and may have experienced fractionation during thermal and/or aqueous alteration. Among the plethora of organic compounds in meteorites are polycyclic aromatic hydrocarbons (PAHs), which are stable and abundant in carbonaceous chondrites, and their δD ratio may preserve evidence about their formation environment as well as the influence of parent-body processes. This study tests hypotheses about the potential links between PAHs-deuteration concentrations and their formation conditions by examining the δD ratio of PAHs in three CM carbonaceous chondrites representing an aqueous alteration gradient. We use deuterium enrichments in soluble 2–5-ring PAHs as an indicator of either photon-driven deuteration due to unimolecular photodissociation in warm regions of space, gas-phase ion–molecule reactions in cold interstellar regions of space, or UV photolysis in ices. We also test hypothesized reaction pathways during parent-body processing that differ between partially and fully aromatized PAHs. New methodological approaches were developed to extract small, volatile PAHs without fractionation. Our results suggest that meteoritic PAHs could have formed through reactions in cold regions, with possible overprinting of deuterium enrichment during aqueous parent-body alteration, but the data could not rule out PAH alteration in icy mantles as well. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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8 pages, 988 KiB

Open AccessArticle

Aliphatic Aldehydes in the Earth’s Crust—Remains of Prebiotic Chemistry?

by Yildiz Großmann, Ulrich Schreiber, Christian Mayer and Oliver J. Schmitz

Life 2022, 12(7), 925; https://doi.org/10.3390/life12070925 - 21 Jun 2022

Cited by 2 | Viewed by 2848

Abstract

The origin of life is a mystery that has not yet been solved in the natural sciences. Some promising interpretative approaches are related to hydrothermal activities. Hydrothermal environments contain all necessary elements for the development of precursor molecules. There are surfaces with possible catalytic activity, and wide ranges of pressure and temperature conditions. The chemical composition of hydrothermal fluids together with periodically fluctuating physical conditions should open up multiple pathways towards prebiotic molecules. In 2017, we detected potentially prebiotic organic substances, including a homologous series of aldehydes in Archean quartz crystals from Western Australia, more than 3 billion years old. In order to approach the question of whether the transformation of inorganic into organic substances is an ongoing process, we investigated a drill core from the geologically young Wehr caldera in Germany at a depth of 1000 m. Here, we show the existence of a similar homologous series of aldehydes (C₈ to C₁₆) in the fluid inclusions of the drill core calcites, a finding that supports the thesis that hydrothermal environments could possibly be the material source for the origin of life. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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39 pages, 2663 KiB

Open AccessArticle

Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor

by Tobias Göppel, Joachim H. Rosenberger, Bernhard Altaner and Ulrich Gerland

Life 2022, 12(4), 567; https://doi.org/10.3390/life12040567 - 10 Apr 2022

Cited by 5 | Viewed by 3050

Abstract

The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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22 pages, 802 KiB

Open AccessArticle

Possible Ribose Synthesis in Carbonaceous Planetesimals

by Klaus Paschek, Kai Kohler, Ben K. D. Pearce, Kevin Lange, Thomas K. Henning, Oliver Trapp, Ralph E. Pudritz and Dmitry A. Semenov

Life 2022, 12(3), 404; https://doi.org/10.3390/life12030404 - 10 Mar 2022

Cited by 7 | Viewed by 4433

Abstract

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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15 pages, 2218 KiB

Open AccessArticle

Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions

by Moran Frenkel-Pinter, Kaitlin C. Jacobson, Jonathan Eskew-Martin, Jay G. Forsythe, Martha A. Grover, Loren Dean Williams and Nicholas V. Hud

Life 2022, 12(2), 265; https://doi.org/10.3390/life12020265 - 10 Feb 2022

Cited by 7 | Viewed by 4941

Abstract

The origin of biopolymers is a central question in origins of life research. In extant life, proteins are coded linear polymers made of a fixed set of twenty alpha-_L-amino acids. It is likely that the prebiotic forerunners of proteins, or protopeptides, were more heterogenous polymers with a greater diversity of building blocks and linkage stereochemistry. To investigate a possible chemical selection for alpha versus beta amino acids in abiotic polymerization reactions, we subjected mixtures of alpha and beta hydroxy and amino acids to single-step dry-down or wet-dry cycling conditions. The resulting model protopeptide mixtures were analyzed by a variety of analytical techniques, including mass spectrometry and NMR spectroscopy. We observed that amino acids typically exhibited a higher extent of polymerization in reactions that also contained alpha hydroxy acids over beta hydroxy acids, whereas the extent of polymerization by beta amino acids was higher compared to their alpha amino acid analogs. Our results suggest that a variety of heterogenous protopeptide backbones existed during the prebiotic epoch, and that selection towards alpha backbones occurred later as a result of polymer evolution. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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10 pages, 1740 KiB

Open AccessArticle

The Abiotic Formation of Pyrrole under Volcanic, Hydrothermal Conditions—An Initial Step towards Life’s First Breath?

by Christian Seitz, Wolfgang Eisenreich and Claudia Huber

Life 2021, 11(9), 980; https://doi.org/10.3390/life11090980 - 17 Sep 2021

Cited by 5 | Viewed by 2953

Abstract

Porphyrins, corrins, and tetrapyrroles constitute macrocycles in essential biomolecules such as heme, chlorophyll, cobalamin, and cofactor F430. The chemical synthesis as well as the enzymatic synthesis of these macrocycles starts from pyrrole derivatives. We here show that pyrrole and dimethyl pyrrole can be formed under the simulated volcanic, hydrothermal conditions of Early Earth, starting from acetylene, propyne, and ammonium salts in the presence of NiS or CoS as catalysts. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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Review

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24 pages, 1618 KiB

Open AccessReview

Sources of Nitrogen-, Sulfur-, and Phosphorus-Containing Feedstocks for Prebiotic Chemistry in the Planetary Environment

by Zoe R. Todd

Life 2022, 12(8), 1268; https://doi.org/10.3390/life12081268 - 19 Aug 2022

Cited by 11 | Viewed by 4056

Abstract

Biochemistry on Earth makes use of the key elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (or CHONPS). Chemically accessible molecules containing these key elements would presumably have been necessary for prebiotic chemistry and the origins of life on Earth. For example, feedstock molecules including fixed nitrogen (e.g., ammonia, nitrite, nitrate), accessible forms of phosphorus (e.g., phosphate, phosphite, etc.), and sources of sulfur (e.g., sulfide, sulfite) may have been necessary for the origins of life, given the biochemistry seen in Earth life today. This review describes potential sources of nitrogen-, sulfur-, and phosphorus-containing molecules in the context of planetary environments. For the early Earth, such considerations may be able to aid in the understanding of our own origins. Additionally, as we learn more about potential environments on other planets (for example, with upcoming next-generation telescope observations or new missions to explore other bodies in our Solar System), evaluating potential sources for elements necessary for life (as we know it) can help constrain the potential habitability of these worlds. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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18 pages, 648 KiB

Open AccessReview

The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses

by Lena Vincent, Stephanie Colón-Santos, H. James Cleaves II, David A. Baum and Sarah E. Maurer

Life 2021, 11(11), 1221; https://doi.org/10.3390/life11111221 - 11 Nov 2021

Cited by 10 | Viewed by 4830

Abstract

“Prebiotic soup” often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both “assembled” mixtures, which are made by mixing reagent grade chemicals, and “synthesized” mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were “tamed” during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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Other

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23 pages, 1730 KiB

Open AccessHypothesis

Natural Selection and Scale Invariance

by Adrian F. Tuck

Life 2023, 13(4), 917; https://doi.org/10.3390/life13040917 - 31 Mar 2023

Cited by 1 | Viewed by 2617

Abstract

This review points out that three of the essential features of natural selection—competition for a finite resource, variation, and transmission of memory—occur in an extremely simple, thermalized molecular population, one of colliding “billiard balls” subject to an anisotropy, a directional flux of energetic molecules. The emergence of scaling behavior, scale invariance, in such systems is considered in the context of the emergence of complexity driven by Gibbs free energy, the origins of life, and known chemistries in planetary and astrophysical conditions. It is suggested that the thermodynamic formalism of statistical multifractality offers a parallel between the microscopic and macroscopic views of non-equilibrium systems and their evolution, different from, empirically determinable, and therefore complementing traditional definitions of entropy and its production in living systems. Further, the approach supports the existence of a bridge between microscopic and macroscopic scales, the missing mesoscopic scale. It is argued that natural selection consequently operates on all scales—whether or not life results will depend on both the initial and the evolving boundary conditions. That life alters the boundary conditions ensures nonlinearity and scale invariance. Evolution by natural selection will have taken place in Earth’s fluid envelope; both air and water display scale invariance and are far from chemical equilibrium, a complex condition driven by the Gibbs free energy arising from the entropy difference between the incoming solar beam and the outgoing infrared radiation to the cold sink of space acting on the initial conditions within evolving boundary conditions. Symmetry breaking’s role in the atmospheric state is discussed, particularly in regard to aerosol fission in the context of airborne bacteria and viruses in both current and prebiotic times. Over 4.4 billion years, the factors operating to support natural selection will have evolved along with the entire system from relative simplicity to the current complexity. Full article

(This article belongs to the Special Issue Organic Chemical Evolution regarding the Origin(s) of Life)

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