Life | Special Issue : Feature Papers in Origins of Life 2024

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9 pages, 355 KiB

Open AccessCommunication

Possibilities for Methanogenic and Acetogenic Life in Molecular Clouds

by Lei Feng

Life 2024, 14(11), 1364; https://doi.org/10.3390/life14111364 - 24 Oct 2024

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Abstract

According to panspermia, life on Earth may have originated from life forms transported through space from elsewhere. These life forms could have passed through molecular clouds, where the process of methanogenesis could have provided enough energy to sustain living organisms. In this study, [...] Read more.

According to panspermia, life on Earth may have originated from life forms transported through space from elsewhere. These life forms could have passed through molecular clouds, where the process of methanogenesis could have provided enough energy to sustain living organisms. In this study, we calculate the Gibbs free energy released from synthesizing hydrocarbons for methanogenic (acetogenic) life in a molecular cloud, with methane (acetic acid) as the final metabolic product. Our calculations demonstrate that the chemical reactions during methanogenesis can release enough free energy to support living organisms. The methanogenic life may have served as the predecessor of life on Earth, and there is some preliminary evidence from various molecular biology studies to support this idea. Furthermore, we propose a potential distinguishing signal to test our model. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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18 pages, 1864 KiB

Open AccessArticle

Exploring the Core Formose Cycle: Catalysis and Competition

by Jeremy Kua and L. Philip Tripoli

Life 2024, 14(8), 933; https://doi.org/10.3390/life14080933 - 25 Jul 2024

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Abstract

The core autocatalytic cycle of the formose reaction may be enhanced or eroded by the presence of simple molecules at life’s origin. Utilizing quantum chemistry, we calculate the thermodynamics and kinetics of reactions both within the core cycle and those that deplete the [...] Read more.

The core autocatalytic cycle of the formose reaction may be enhanced or eroded by the presence of simple molecules at life’s origin. Utilizing quantum chemistry, we calculate the thermodynamics and kinetics of reactions both within the core cycle and those that deplete the reactants and intermediates, such as the Cannizzaro reaction. We find that via disproportionation of aldehydes into carboxylic acids and alcohols, the Cannizzaro reaction furnishes simple catalysts for a variety of reactions. We also find that ammonia can catalyze both in-cycle and Cannizzaro reactions while hydrogen sulfide does not; both, however, play a role in sequestering reactants and intermediates in the web of potential reactions. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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24 pages, 1640 KiB

Open AccessArticle

The Pigment World: Life’s Origins as Photon-Dissipating Pigments

by Karo Michaelian

Life 2024, 14(7), 912; https://doi.org/10.3390/life14070912 - 22 Jul 2024

Viewed by 1920

Abstract

Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been [...] Read more.

Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been attributed to a “natural selection” of molecules resistant to the dangerous UV-C light incident on Earth’s surface during the Archean. In contrast, the “thermodynamic dissipation theory for the origin of life” argues that, far from being detrimental, UV-C light was, in fact, the thermodynamic potential driving the dissipative structuring of life at its origin. The optical properties were thus the thermodynamic “design goals” of microscopic dissipative structuring of organic UV-C pigments, today known as the “fundamental molecules of life”, from common precursors under this light. This “UV-C Pigment World” evolved towards greater solar photon dissipation through more complex dissipative structuring pathways, eventually producing visible pigments to dissipate less energetic, but higher intensity, visible photons up to wavelengths of the “red edge”. The propagation and dispersal of organic pigments, catalyzed by animals, and their coupling with abiotic dissipative processes, such as the water cycle, culminated in the apex photon dissipative structure, today’s biosphere. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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17 pages, 2209 KiB

Open AccessArticle

Autocatalytic Selection as a Driver for the Origin of Life

by Mike P. Williamson

Life 2024, 14(5), 590; https://doi.org/10.3390/life14050590 - 6 May 2024

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Abstract

Darwin’s theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable [...] Read more.

Darwin’s theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable alternative mechanism for prebiotic systems: autocatalytic selection, in which molecules catalyze reactions and processes that lead to increases in their concentration. Crucially, this provides a driver for increases in concentrations of molecules to a level that permits prebiotic metabolism. We show how this can produce high levels of amino acids, sugar phosphates, nucleotides and lipids and then lead on to polymers. Our outline is supported by a set of guidelines to support the identification of the most likely prebiotic routes. Most of the steps in this pathway are already supported by experimental results. These proposals generate a coherent and viable set of pathways that run from established Hadean geochemistry to the beginning of life. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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Review

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25 pages, 11108 KiB

Open AccessReview

Pioneers of Origin of Life Studies—Darwin, Oparin, Haldane, Miller, Oró—And the Oldest Known Records of Life

by J. William Schopf

Life 2024, 14(10), 1345; https://doi.org/10.3390/life14101345 - 21 Oct 2024

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Abstract

The two basic approaches to elucidating how life began both date from Darwin. The first, that of the experimentalists, stems from Darwin’s famous “warm little pond” letter to Joseph Hooker of 1871. This approach, an attempt to replicate the sequential events leading to [...] Read more.

The two basic approaches to elucidating how life began both date from Darwin. The first, that of the experimentalists, stems from Darwin’s famous “warm little pond” letter to Joseph Hooker of 1871. This approach, an attempt to replicate the sequential events leading to life’s origin, is exemplified by the “primordial soup” hypothesis of A.I. Oparin (1924) and J.B.S. Haldane (1929); the Miller–Urey laboratory synthesis of amino acids under possible primitive Earth conditions (1953); and Joan Oró’s nonbiological synthesis of the nucleic acid adenine (1959). The second approach, that of the observationalists who search for relevant evidence in the geological record, dates from Darwin’s 1859 On the Origin of Species, in which he laments the “inexplicable” absence of a pre-Cambrian fossil record. Darwin’s concern spurred a century of search that was ultimately rewarded by Stanley Tyler’s 1953 discovery of diverse microscopic fossils in the ~1900 Ma Gunflint Chert of southern Canada. Tyler’s find was soon followed by a cascade of discoveries worldwide; the establishment of a new field of science, Precambrian paleobiology; and, more recently, the discovery of 3400 and ~3465 Ma Paleoarchean microfossils, establishing that primordial life evolved early, far, and fast. Though progress has been made, much remains to be learned in the foci of this Origin of Life 2024 volume, for which this essay is the history-reviewing “stage setter”. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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18 pages, 1836 KiB

Open AccessReview

The Winding Road from Origin to Emergence (of Life)

by Wolfgang Nitschke, Orion Farr, Nil Gaudu, Chloé Truong, François Guyot, Michael J. Russell and Simon Duval

Life 2024, 14(5), 607; https://doi.org/10.3390/life14050607 - 9 May 2024

Cited by 1 | Viewed by 2174

Abstract

Humanity’s strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin’s Theory of Evolution and the paradigm that the [...] Read more.

Humanity’s strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin’s Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the “organic-molecules-paradigm” became increasingly difficult to ignore, culminating in Erwin Schrödinger’s 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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Other

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10 pages, 2952 KiB

Open AccessBrief Report

The HOMO-LUMO Gap as Discriminator of Biotic from Abiotic Chemistries

by Roman Abrosimov and Bernd Moosmann

Life 2024, 14(10), 1330; https://doi.org/10.3390/life14101330 - 18 Oct 2024

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Abstract

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), [...] Read more.

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (−10.4 ± 0.9 eV versus −12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The “hydrophilic reactivity” quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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24 pages, 996 KiB

Open AccessOpinion

Hunting the Cell Cycle Snark

by Vic Norris

Life 2024, 14(10), 1213; https://doi.org/10.3390/life14101213 - 24 Sep 2024

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Abstract

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics [...] Read more.

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the ‘prebiotic ecology’ and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like “why do cells replicate their DNA?”, “why is DNA replication semi-conservative?”, “why is DNA a double helix?”, “why do cells divide?”, “is cell division a spandrel?”, and “how are catabolism and anabolism balanced?”. Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life 2024)

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