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Nunn AV, Guy GW, Bell JD. Bioelectric Fields at the Beginnings of Life. Bioelectricity 2022; 4:237-247. [PMID: 36636557 PMCID: PMC9810354 DOI: 10.1089/bioe.2022.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The consensus on the origins of life is that it involved organization of prebiotic chemicals according to the underlying principles of thermodynamics to dissipate energy derived from photochemical and/or geochemical sources. Leading theories tend to be chemistry-centric, revolving around either metabolism or information-containing polymers first. However, experimental data also suggest that bioelectricity and quantum effects play an important role in biology, which might suggest that a further factor is required to explain how life began. Intriguingly, in the early part of 20th century, the concept of the "morphogenetic field" was proposed by Gurwitsch to explain how the shape of an organism was determined, while a role for quantum mechanics in biology was suggested by Bohr and Schrödinger, among others. This raises the question as to the potential of these phenomena, especially bioelectric fields, to have been involved in the origin of life. It points to the possibility that as bioelectricity is universally prevalent in biological systems today, it represents a more complex echo of an electromagnetic skeleton which helped shape life into being. It could be argued that as a flow of ions creates an electric field, this could have been pivotal in the formation of an energy dissipating structure, for instance, in deep sea thermal vents. Moreover, a field theory might also hint at the potential involvement of nontrivial quantum effects in life. Not only might this perspective help indicate the origins of morphogenetic fields, but also perhaps suggest where life may have started, and whether metabolism or information came first. It might also help to provide an insight into aging, cancer, consciousness, and, perhaps, how we might identify life beyond our planet. In short, when thinking about life, not only do we have to consider the accepted chemistry, but also the fields that must also shape it. In effect, to fully understand life, as well as the yin of accepted particle-based chemistry, there is a yang of field-based interaction and an ethereal skeleton.
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Affiliation(s)
- Alistair V.W. Nunn
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, United Kingdom.,Address correspondence to: Alistair V.W. Nunn, PhD, Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | | | - Jimmy D. Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, United Kingdom
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The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene. Life (Basel) 2022; 12:life12060834. [PMID: 35743865 PMCID: PMC9225589 DOI: 10.3390/life12060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons ‘remembered’ their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.
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Clark BC, Kolb VM, Steele A, House CH, Lanza NL, Gasda PJ, VanBommel SJ, Newsom HE, Martínez-Frías J. Origin of Life on Mars: Suitability and Opportunities. Life (Basel) 2021; 11:539. [PMID: 34207658 PMCID: PMC8227854 DOI: 10.3390/life11060539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL.
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Affiliation(s)
| | - Vera M. Kolb
- Department of Chemistry, University of Wisconsin—Parkside, Kenosha, WI 53141, USA;
| | - Andrew Steele
- Earth and Planetary Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA;
| | - Christopher H. House
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16807, USA;
| | - Nina L. Lanza
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (N.L.L.); (P.J.G.)
| | - Patrick J. Gasda
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (N.L.L.); (P.J.G.)
| | - Scott J. VanBommel
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Horton E. Newsom
- Institute of Meteoritics, Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 88033, USA;
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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6
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Clark BC, Kolb VM. Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere. Life (Basel) 2020; 10:life10110278. [PMID: 33198206 PMCID: PMC7697624 DOI: 10.3390/life10110278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Although the cellular microorganism is the fundamental unit of biology, the origin of life (OoL) itself is unlikely to have occurred in a microscale environment. The macrobiont (MB) is the macro-scale setting where life originated. Guided by the methodologies of Systems Analysis, we focus on subaerial ponds of scale 3 to 300 m diameter. Within such ponds, there can be substantial heterogeneity, on the vertical, horizontal, and temporal scales, which enable multi-pot prebiotic chemical evolution. Pond size-sensitivities for several figures of merit are mathematically formulated, leading to the expectation that the optimum pond size for the OoL is intermediate, but biased toward smaller sizes. Sensitivities include relative access to nutrients, energy sources, and catalysts, as sourced from geological, atmospheric, hydrospheric, and astronomical contributors. Foreshores, especially with mudcracks, are identified as a favorable component for the success of the macrobiont. To bridge the gap between inanimate matter and a planetary-scale biosphere, five stages of evolution within the macrobiont are hypothesized: prebiotic chemistry → molecular replicator → protocell → macrobiont cell → colonizer cell. Comparison of ponds with other macrobionts, including hydrothermal and meteorite settings, allows a conclusion that more than one possible macrobiont locale could enable an OoL.
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Affiliation(s)
- Benton C. Clark
- Space Science Institute, Boulder, CO 80301, USA
- Correspondence:
| | - Vera M. Kolb
- Department of Chemistry, University of Wisconsin—Parkside, Kenosha, WI 53141, USA;
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7
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Li Y, Li Y, Liu Y, Wu Y, Wu J, Wang B, Ye H, Jia H, Wang X, Li L, Zhu M, Ding H, Lai Y, Wang C, Dick J, Lu A. Photoreduction of inorganic carbon(+IV) by elemental sulfur: Implications for prebiotic synthesis in terrestrial hot springs. SCIENCE ADVANCES 2020; 6:6/47/eabc3687. [PMID: 33208363 PMCID: PMC7673799 DOI: 10.1126/sciadv.abc3687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Terrestrial hydrothermal systems have been proposed as alternative birthplaces for early life but lacked reasonable scenarios for the supply of biomolecules. Here, we show that elemental sulfur (S0), as the dominant mineral in terrestrial hot springs, can reduce carbon dioxide (CO2) into formic acid (HCOOH) under ultraviolet (UV) light below 280 nm. The semiconducting S0 is indicated to have a direct bandgap of 4.4 eV. The UV-excited S0 produces photoelectrons with a highly negative potential of -2.34 V (versus NHE, pH 7), which could reduce CO2 after accepting electrons from electron donors such as reducing sulfur species. Simultaneously, UV light breaks sulfur bonds, benefiting the adsorption of charged carbonates onto S0 and assisting their photoreduction. Assuming that terrestrial hot springs covered 1% of primitive Earth's surface, S0 at 10 μM could have produced maximal 109 kg/year HCOOH within 10-cm-thick photic zones, underlying its remarkable contributions to the accumulation of prebiotic biomolecules.
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Affiliation(s)
- Yanzhang Li
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yan Li
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China.
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yi Liu
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yifu Wu
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Junqi Wu
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Bin Wang
- Sinopec Beijing Research Institute of Chemical Industry, Beijing 100013, People's Republic of China
| | - Huan Ye
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Haoning Jia
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiao Wang
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Linghui Li
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Meixiang Zhu
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Hongrui Ding
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yong Lai
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Changqiu Wang
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jeffrey Dick
- The Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, School of Geosciences and Info-Physics, Central South University, Changsha 410083, People's Republic of China
| | - Anhuai Lu
- Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China.
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, People's Republic of China
- The Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, School of Geosciences and Info-Physics, Central South University, Changsha 410083, People's Republic of China
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8
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Osinski G, Cockell C, Pontefract A, Sapers H. The Role of Meteorite Impacts in the Origin of Life. ASTROBIOLOGY 2020; 20:1121-1149. [PMID: 32876492 PMCID: PMC7499892 DOI: 10.1089/ast.2019.2203] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The conditions, timing, and setting for the origin of life on Earth and whether life exists elsewhere in our solar system and beyond represent some of the most fundamental scientific questions of our time. Although the bombardment of planets and satellites by asteroids and comets has long been viewed as a destructive process that would have presented a barrier to the emergence of life and frustrated or extinguished life, we provide a comprehensive synthesis of data and observations on the beneficial role of impacts in a wide range of prebiotic and biological processes. In the context of previously proposed environments for the origin of life on Earth, we discuss how meteorite impacts can generate both subaerial and submarine hydrothermal vents, abundant hydrothermal-sedimentary settings, and impact analogues for volcanic pumice rafts and splash pools. Impact events can also deliver and/or generate many of the necessary chemical ingredients for life and catalytic substrates such as clays as well. The role that impact cratering plays in fracturing planetary crusts and its effects on deep subsurface habitats for life are also discussed. In summary, we propose that meteorite impact events are a fundamental geobiological process in planetary evolution that played an important role in the origin of life on Earth. We conclude with the recommendation that impact craters should be considered prime sites in the search for evidence of past life on Mars. Furthermore, unlike other geological processes such as volcanism or plate tectonics, impact cratering is ubiquitous on planetary bodies throughout the Universe and is independent of size, composition, and distance from the host star. Impact events thus provide a mechanism with the potential to generate habitable planets, moons, and asteroids throughout the Solar System and beyond.
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Affiliation(s)
- G.R. Osinski
- Institute for Earth and Space Exploration, University of Western Ontario, London, Canada
- Department of Earth Sciences, University of Western Ontario, London, Canada
- Address correspondence to: Dr. Gordon Osinski, Department of Earth Sciences, 1151 Richmond Street, University of Western Ontario, London ON, N6A 5B7, Canada
| | - C.S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - A. Pontefract
- Department of Biology, Georgetown University, Washington, DC, USA
| | - H.M. Sapers
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
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Nunn AVW, Guy GW, Botchway SW, Bell JD. From sunscreens to medicines: Can a dissipation hypothesis explain the beneficial aspects of many plant compounds? Phytother Res 2020; 34:1868-1888. [PMID: 32166791 PMCID: PMC7496984 DOI: 10.1002/ptr.6654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 01/16/2020] [Accepted: 02/16/2020] [Indexed: 12/17/2022]
Abstract
Medicine has utilised plant‐based treatments for millennia, but precisely how they work is unclear. One approach is to use a thermodynamic viewpoint that life arose by dissipating geothermal and/or solar potential. Hence, the ability to dissipate energy to maintain homeostasis is a fundamental principle in all life, which can be viewed as an accretion system where layers of complexity have built upon core abiotic molecules. Many of these compounds are chromophoric and are now involved in multiple pathways. Plants have further evolved a plethora of chromophoric compounds that can not only act as sunscreens and redox modifiers, but also have now become integrated into a generalised stress adaptive system. This could be an extension of the dissipative process. In animals, many of these compounds are hormetic, modulating mitochondria and calcium signalling. They can also display anti‐pathogen effects. They could therefore modulate bioenergetics across all life due to the conserved electron transport chain and proton gradient. In this review paper, we focus on well‐described medicinal compounds, such as salicylic acid and cannabidiol and suggest, at least in animals, their activity reflects their evolved function in plants in relation to stress adaptation, which itself evolved to maintain dissipative homeostasis.
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Affiliation(s)
- Alistair V W Nunn
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
| | | | - Stanley W Botchway
- STFC, UKRI & Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Jimmy D Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
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Chatterjee S, Yadav S. The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code. Life (Basel) 2019; 9:E25. [PMID: 30832272 PMCID: PMC6463137 DOI: 10.3390/life9010025] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/09/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic information age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code.
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Affiliation(s)
- Sankar Chatterjee
- Department of Geosciences, Museum of Texas Tech University, Box 43191, 3301 4th Street, Lubbock, TX 79409, USA.
| | - Surya Yadav
- Rawls College of Business, Texas Tech University, Box 42101, 703 Flint Avenue, Lubbock, TX 79409, USA.
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Ball R, Brindley J. Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170141. [PMID: 29291048 PMCID: PMC5717622 DOI: 10.1098/rsos.170141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution 'Goldilocks'. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system.
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Affiliation(s)
- Rowena Ball
- Mathematical Sciences Institute and Research School of Chemistry, The Australian National University, Canberra 2602, Australia
| | - John Brindley
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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