What Is Life?

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: 9 August 2024 | Viewed by 7583

Special Issue Editors


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Guest Editor
Department of Biology, Faculty of Medicine, University of Aix-Marseille, INSERM UMR_S 1072, 13015 Marseille, France
Interests: virus-host interactions; lipid rafts; gangliosides; virus receptors; RNA viruses; SARS-CoV-2 variants; antivirals; vaccines
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Guest Editor
CBM Centre de Biophysique Moléculaire, 4301 Orleans, France
Interests: astrobiology; chirality; prebiotics; organic chemistry; evolution; synthetic organic chemistry; meteorites; organic synthesis; chromatography; mars

Special Issue Information

Dear Colleagues,

In 1944, Erwin Schrödinger published his seminal book “What is life?” which inspired generations of biologists. Despite amazing discoveries in biology (the DNA double helix, the genetic code, whole genomes sequencing, the structure of proteins, epigenetics...) we still struggle to define exactly what life is. The 80th anniversary of Schrödinger's essay seems to us the ideal time to ask the question again, in light of today’s knowlege. In this Special Issue we want to focus on selected parameters of biology that are often neglected, such as water, time, electrostatic potential or quantum mechanisms. These parameters control many (and often unsuspected) biological mechanisms and they are intimately linked to life processes and life definition. This Special Issue plans to give an overview of the most recent advances in this research field as well as new considerations in the definition of life. This Special Issue is aimed at providing selected contributions on the basic but neglected parameters of biology that are critical for better understanding what life is, and how it handles order and chaos through a combination of genetic and epigenetic mechanisms. Potential topics include, but are not limited to: The definition of life The role of water in biological mechanisms; How living organisms handle time constraints; Electrostatic potential in biology; Quantum mechanisms in biology; Impact of silent mutations in evolution; Intrinsically disordered proteins, moonlighting proteins and their roles in biology; New insights in the origin of life - astrobiology; Synthetic biology; Are viruses alive?

Prof. Dr. Jacques Fantini
Dr. André Brack
Guest Editors

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Keywords

  • definition of life
  • origins of life
  • synthetic biology
  • theoretical biology
  • quantum biology
  • water, time
  • electrostatic potential
  • DNA
  • mutations
  • molecular interactions

Published Papers (6 papers)

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Research

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26 pages, 1698 KiB  
Article
Effects of Activation Barriers on Quenching to Stabilize Prebiotic Chemical Systems
by Qianyi Sheng, Ben Fredrick Intoy and J. W. Halley
Life 2024, 14(1), 116; https://doi.org/10.3390/life14010116 - 12 Jan 2024
Viewed by 630
Abstract
We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, [...] Read more.
We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, giving an efficient mechanism for natural sorting through enormous numbers of nonequilibrium chemistries from which the most lifelike ones could be naturally selected. However, the model used for these studies did not take account of activation barriers to polymer scission (peptide bond hydrolysis in the case of proteins). Such barriers are known to exist and are expected to enhance the quenching effect. Here, we introduce a modified model which takes activation barriers into account and we compare the results to data from experiments on quenched systems of amino acids. We find that the model results turn out to be sensitive to the width of the distribution of barrier heights but quite insensitive to its average value. The results of the new model are in significantly better agreement with the experiments than those found using our previous model. The new parametrization of the model only requires one new parameter and the parametrization is more physical than the previous one, providing a chemical interpretation of the parameter p in our previous models. Within the model, a characteristic temperature Tc emerges such that if the temperature of the hot stage is above Tc and the temperature of the cold stage is below it, then the ‘freezing out’, in a quench, of a disequilibrium ensemble of long polymers is expected. We discuss the possible relevance of this to models of the origin of life in emissions from deep ocean rifts. Full article
(This article belongs to the Special Issue What Is Life?)
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38 pages, 5235 KiB  
Article
Mineral Indicators of Geologically Recent Past Habitability on Mars
by Roger Hart and Dawn Cardace
Life 2023, 13(12), 2349; https://doi.org/10.3390/life13122349 - 15 Dec 2023
Viewed by 1151
Abstract
We provide new support for habitable microenvironments in the near-subsurface of Mars, hosted in Fe- and Mg-rich rock units, and present a list of minerals that can serve as indicators of specific water–rock reactions in recent geologic paleohabitats for follow-on study. We modeled, [...] Read more.
We provide new support for habitable microenvironments in the near-subsurface of Mars, hosted in Fe- and Mg-rich rock units, and present a list of minerals that can serve as indicators of specific water–rock reactions in recent geologic paleohabitats for follow-on study. We modeled, using a thermodynamic basis without selective phase suppression, the reactions of published Martian meteorites and Jezero Crater igneous rock compositions and reasonable planetary waters (saline, alkaline waters) using Geochemist’s Workbench Ver. 12.0. Solid-phase inputs were meteorite compositions for ALH 77005, Nakhla, and Chassigny, and two rock units from the Mars 2020 Perseverance rover sites, Máaz and Séítah. Six plausible Martian groundwater types [NaClO4, Mg(ClO4)2, Ca(ClO4)2, Mg-Na2(ClO4)2, Ca-Na2(ClO4)2, Mg-Ca(ClO4)2] and a unique Mars soil-water analog solution (dilute saline solution) named “Rosy Red”, related to the Phoenix Lander mission, were the aqueous-phase inputs. Geophysical conditions were tuned to near-subsurface Mars (100 °C or 373.15 K, associated with residual heat from a magmatic system, impact event, or a concentration of radionuclides, and 101.3 kPa, similar to <10 m depth). Mineral products were dominated by phyllosilicates such as serpentine-group minerals in most reaction paths, but differed in some important indicator minerals. Modeled products varied in physicochemical properties (pH, Eh, conductivity), major ion activities, and related gas fugacities, with different ecological implications. The microbial habitability of pore spaces in subsurface groundwater percolation systems was interrogated at equilibrium in a thermodynamic framework, based on Gibbs Free Energy Minimization. Models run with the Chassigny meteorite produced the overall highest H2 fugacity. Models reliant on the Rosy Red soil-water analog produced the highest sustained CH4 fugacity (maximum values observed for reactant ALH 77005). In general, Chassigny meteorite protoliths produced the best yield regarding Gibbs Free Energy, from an astrobiological perspective. Occurrences of serpentine and saponite across models are key: these minerals have been observed using CRISM spectral data, and their formation via serpentinization would be consistent with geologically recent-past H2 and CH4 production and sustained energy sources for microbial life. We list index minerals to be used as diagnostic for paleo water–rock models that could have supported geologically recent-past microbial activity, and suggest their application as criteria for future astrobiology study-site selections. Full article
(This article belongs to the Special Issue What Is Life?)
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15 pages, 2737 KiB  
Article
Infrared Spectral Signatures of Nucleobases in Interstellar Ices I: Purines
by Caroline Antunes Rosa, Alexandre Bergantini, Péter Herczku, Duncan V. Mifsud, Gergő Lakatos, Sándor T. S. Kovács, Béla Sulik, Zoltán Juhász, Sergio Ioppolo, Heidy M. Quitián-Lara, Nigel J. Mason and Claudia Lage
Life 2023, 13(11), 2208; https://doi.org/10.3390/life13112208 - 14 Nov 2023
Viewed by 1116
Abstract
The purine nucleobases adenine and guanine are complex organic molecules that are essential for life. Despite their ubiquitous presence on Earth, purines have yet to be detected in observations of astronomical environments. This work therefore proposes to study the infrared spectra of purines [...] Read more.
The purine nucleobases adenine and guanine are complex organic molecules that are essential for life. Despite their ubiquitous presence on Earth, purines have yet to be detected in observations of astronomical environments. This work therefore proposes to study the infrared spectra of purines linked to terrestrial biochemical processes under conditions analogous to those found in the interstellar medium. The infrared spectra of adenine and guanine, both in neat form and embedded within an ice made of H2O:NH3:CH4:CO:CH3OH (10:1:1:1:1), were analysed with the aim of determining which bands attributable to adenine and/or guanine can be observed in the infrared spectrum of an astrophysical ice analogue rich in other volatile species known to be abundant in dense molecular clouds. The spectrum of adenine and guanine mixed together was also analysed. This study has identified three purine nucleobase infrared absorption bands that do not overlap with bands attributable to the volatiles that are ubiquitous in the dense interstellar medium. Therefore, these three bands, which are located at 1255, 940, and 878 cm−1, are proposed as an infrared spectral signature for adenine, guanine, or a mixture of these molecules in astrophysical ices. All three bands have integrated molar absorptivity values (ψ) greater than 4 km mol−1, meaning that they should be readily observable in astronomical targets. Therefore, if these three bands were to be observed together in the same target, then it is possible to propose the presence of a purine molecule (i.e., adenine or guanine) there. Full article
(This article belongs to the Special Issue What Is Life?)
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18 pages, 761 KiB  
Article
On the Emergence of Autonomous Chemical Systems through Dissipation Kinetics
by Addy Pross and Robert Pascal
Life 2023, 13(11), 2171; https://doi.org/10.3390/life13112171 - 06 Nov 2023
Cited by 2 | Viewed by 929
Abstract
This work addresses the kinetic requirements for compensating the entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic and evolutionary features of life cannot therefore be separated from an origin of life perspective. Growth, self-organization, evolution and [...] Read more.
This work addresses the kinetic requirements for compensating the entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic and evolutionary features of life cannot therefore be separated from an origin of life perspective. Growth, self-organization, evolution and dissipation processes need to be metabolically coupled and fueled by low-entropy energy harvested from the environment. The evolutionary process requires a reproduction cycle involving out-of-equilibrium intermediates and kinetic barriers that prevent the reproductive cycle from proceeding in reverse. Model analysis leads to the unexpectedly simple relationship that the system should be fed energy with a potential exceeding a value related to the ratio of the generation time to the transition state lifetime, thereby enabling a process mimicking natural selection to take place. Reproducing life’s main features, in particular its Darwinian behavior, therefore requires satisfying constraints that relate to time and energy. Irreversible reaction cycles made only of unstable entities reproduce some of these essential features, thereby offering a physical/chemical basis for the possible emergence of autonomy. Such Emerging Autonomous Systems (EASs) are found to be capable of maintaining and reproducing their kind through the transmission of a stable kinetic state, thereby offering a physical/chemical basis for what could be deemed an epigenetic process. Full article
(This article belongs to the Special Issue What Is Life?)
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18 pages, 4371 KiB  
Article
Evolution of Intrinsic Disorder in Protein Loops
by Fizza Mughal and Gustavo Caetano-Anollés
Life 2023, 13(10), 2055; https://doi.org/10.3390/life13102055 - 14 Oct 2023
Viewed by 823
Abstract
Intrinsic disorder accounts for the flexibility of protein loops, molecular building blocks that are largely responsible for the processes and molecular functions of the living world. While loops likely represent early structural forms that served as intermediates in the emergence of protein structural [...] Read more.
Intrinsic disorder accounts for the flexibility of protein loops, molecular building blocks that are largely responsible for the processes and molecular functions of the living world. While loops likely represent early structural forms that served as intermediates in the emergence of protein structural domains, their origin and evolution remain poorly understood. Here, we conduct a phylogenomic survey of disorder in loop prototypes sourced from the ArchDB classification. Tracing prototypes associated with protein fold families along an evolutionary chronology revealed that ancient prototypes tended to be more disordered than their derived counterparts, with ordered prototypes developing later in evolution. This highlights the central evolutionary role of disorder and flexibility. While mean disorder increased with time, a minority of ordered prototypes exist that emerged early in evolutionary history, possibly driven by the need to preserve specific molecular functions. We also revealed the percolation of evolutionary constraints from higher to lower levels of organization. Percolation resulted in trade-offs between flexibility and rigidity that impacted prototype structure and geometry. Our findings provide a deep evolutionary view of the link between structure, disorder, flexibility, and function, as well as insights into the evolutionary role of intrinsic disorder in loops and their contribution to protein structure and function. Full article
(This article belongs to the Special Issue What Is Life?)
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Review

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21 pages, 2722 KiB  
Review
What Is life? Rethinking Biology in Light of Fundamental Parameters
by Jacques Fantini, Mélanie Matveeva, Marine Lefebvre and Henri Chahinian
Life 2024, 14(3), 280; https://doi.org/10.3390/life14030280 - 20 Feb 2024
Viewed by 1787
Abstract
Defining life is an arduous task that has puzzled philosophers and scientists for centuries. Yet biology suffers from a lack of clear definition, putting biologists in a paradoxical situation where one can describe at the atomic level complex objects that remain globally poorly [...] Read more.
Defining life is an arduous task that has puzzled philosophers and scientists for centuries. Yet biology suffers from a lack of clear definition, putting biologists in a paradoxical situation where one can describe at the atomic level complex objects that remain globally poorly defined. One could assume that such descriptions make it possible to perfectly characterize living systems. However, many cases of misinterpretation put this assumption into perspective. In this article, we focus on critical parameters such as time, water, entropy, space, quantum properties, and electrostatic potential to redefine the nature of living matter, with special emphasis on biological coding. Where does the DNA double helix come from, why cannot the reproduction of living organisms occur without mutations, what are the limitations of the genetic code, and why do not all proteins have a stable three-dimensional structure? There are so many questions that cannot be resolved without considering the aforementioned parameters. Indeed, (i) time and space constrain many biological mechanisms and impose drastic solutions on living beings (enzymes, transporters); (ii) water controls the fidelity of DNA replication and the structure/disorder balance of proteins; (iii) entropy is the driving force of many enzymatic reactions and molecular interactions; (iv) quantum mechanisms explain why a molecule as simple as hydrocyanic acid (HCN) foreshadows the helical structure of DNA, how DNA is stabilized, why mutations occur, and how the Earth magnetic field can influence the migration of birds; (v) electrostatic potential controls epigenetic mechanisms, lipid raft functions, and virus infections. We consider that raising awareness of these basic parameters is critical for better understanding what life is, and how it handles order and chaos through a combination of genetic and epigenetic mechanisms. Thus, we propose to incorporate these parameters into the definition of life. Full article
(This article belongs to the Special Issue What Is Life?)
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