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Yang X, Mao Z, Huang J, Wang R, Dong H, Zhang Y, Ma H. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol 2023; 8:597-605. [PMID: 37743907 PMCID: PMC10514394 DOI: 10.1016/j.synbio.2023.09.002] [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] [Received: 05/16/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Metabolic network models have become increasingly precise and accurate as the most widespread and practical digital representations of living cells. The prediction functions were significantly expanded by integrating cellular resources and abiotic constraints in recent years. However, if unreasonable modeling methods were adopted due to a lack of consideration of biological knowledge, the conflicts between stoichiometric and other constraints, such as thermodynamic feasibility and enzyme resource availability, would lead to distorted predictions. In this work, we investigated a prediction anomaly of EcoETM, a constraints-based metabolic network model, and introduced the idea of enzyme compartmentalization into the analysis process. Through rational combination of reactions, we avoid the false prediction of pathway feasibility caused by the unrealistic assumption of free intermediate metabolites. This allowed us to correct the pathway structures of l-serine and l-tryptophan. A specific analysis explains the application method of the EcoETM-like model and demonstrates its potential and value in correcting the prediction results in pathway structure by resolving the conflict between different constraints and incorporating the evolved roles of enzymes as reaction compartments. Notably, this work also reveals the trade-off between product yield and thermodynamic feasibility. Our work is of great value for the structural improvement of constraints-based models.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Ruoyu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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2
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Gyllingberg L, Birhane A, Sumpter DJT. The lost art of mathematical modelling. Math Biosci 2023:109033. [PMID: 37257641 DOI: 10.1016/j.mbs.2023.109033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
We provide a critique of mathematical biology in light of rapid developments in modern machine learning. We argue that out of the three modelling activities - (1) formulating models; (2) analysing models; and (3) fitting or comparing models to data - inherent to mathematical biology, researchers currently focus too much on activity (2) at the cost of (1). This trend, we propose, can be reversed by realising that any given biological phenomenon can be modelled in an infinite number of different ways, through the adoption of an pluralistic approach, where we view a system from multiple, different points of view. We explain this pluralistic approach using fish locomotion as a case study and illustrate some of the pitfalls - universalism, creating models of models, etc. - that hinder mathematical biology. We then ask how we might rediscover a lost art: that of creative mathematical modelling.
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Affiliation(s)
| | - Abeba Birhane
- Mozilla Foundation, 2 Harrison Street, Suite 175, San Francisco, CA 94105, USA
| | - David J T Sumpter
- Department of Information Technology, Uppsala University, Box 337, Uppsala, SE-751 05, Sweden.
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3
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Paradis E. Information-energy equivalence and the emergence of self-replicating biological systems. Biosystems 2023; 226:104885. [PMID: 36935033 DOI: 10.1016/j.biosystems.2023.104885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Biological processes are characterized by a decrease in entropy in apparent violation of the second law of thermodynamics. Information stored in genomes help to solve this paradox when interpreted under the relationship between information and energy stated by Brillouin in the 1950's. However, the origins of living forms from inanimate matter which have no information storage device remains an open question. In this paper, a theoretical approach is developed on this issue. The replication of a simple entity with a binary genome is assumed to require an information-equivalent energy in addition to the standard activation energy. It is found that, in some conditions, a decrease in entropy can be accomplished together with a decrease in Gibbs free energy. An equation of the total energy for the replication of this entity is derived. Three factors are predicted to lower this energy: a small number of states of the coding sequence, a lower temperature, and a high ratio of the reaction on diffusion coefficients. These factors may have favoured the emergence of evolutionary demons-information storage devices that are able to decrease entropy. It is evaluated that some short, single-stranded RNA sequences made only of G and of C may conform to this model. The consequences of this model and its predictions on the origins of life on Earth and on other planets are discussed.
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Narushin VG, Griffin AW, Romanov MN, Griffin DK. Measurement of the neutral axis in avian eggshells reveals which species conform to the golden ratio. Ann N Y Acad Sci 2022; 1517:143-153. [PMID: 36052445 PMCID: PMC9826523 DOI: 10.1111/nyas.14895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Avian eggs represent a striking evolutionary adaptation for which shell thickness is crucial. An understudied eggshell property includes the neutral axis, a line that is drawn through any bent structure and whose precise location is characterized by the k-factor. Previous studies have established that, for chicken eggs, mean k corresponds to the golden ratio (Φ = 1.618, or 0.618 in its reciprocal form). We hypothesized whether such an arrangement of the neutral axis conforms to the eggshell of any bird or only to eggshells with a certain set of geometric parameters. Implementing a suite of innovative methodological approaches, we investigated variations in k of 435 avian species, exploring which correspond to Φ. We found that mean k is highly variable among birds and does not always conform to Φ, being much lower in spherical and ellipsoid eggs and higher in pyriform eggs. While 21 species had k values within 0.618 ± 0.02 (including four falcon species) and the Falconinae subfamily (six species) revealed a mean of 0.618, it is predominantly domesticated species (chicken, ducks, and geese) that lay eggs whose neutral axis corresponds to the golden ratio. Thus, the study of the mathematical secrets of the eggshell related to the golden ratio of its neutral axis suggests its species-specific signatures in birds.
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Affiliation(s)
- Valeriy G. Narushin
- Research Institute for Environment TreatmentZaporozhyeUkraine,Vita‐Market LtdZaporozhyeUkraine
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5
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The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life. PLoS Comput Biol 2022; 18:e1010498. [PMID: 36084149 PMCID: PMC9491600 DOI: 10.1371/journal.pcbi.1010498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/21/2022] [Accepted: 08/18/2022] [Indexed: 12/16/2022] Open
Abstract
Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds.” We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab. The level of complexity seen in even the simplest living system is too great to have arisen in its current form without a long history of complexification. In this paper, we explore the view that open environments on the early Earth that received an ongoing flux of food chemicals could have complexified gradually by the sequential activation of autocatalytic chemical reaction systems. We develop the concept of seed-dependent autocatalytic systems (SDASs)–subnetworks whose components can self-propagate once activated by “seed” molecules, which might result from rare reactions or import from other environments. We developed new computational tools for detecting SDASs in reaction databases and determining if they are hierarchically organized, such that the activation of a lower-tier SDAS allows a higher-tier SDAS to then be seeded, much like the relationship between producers and consumers in an ecosystem. We apply our algorithms to two chemical reaction networks, one biological and the other abiotic, and find that both contain hierarchically organized SDASs. These results support the fundamental continuity of the way that the chemistry of non-life and life is organized and suggest new classes of laboratory experiment.
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6
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Liu Y, Di Z, Gerlee P. Ladderpath Approach: How Tinkering and Reuse Increase Complexity and Information. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1082. [PMID: 36010747 PMCID: PMC9407278 DOI: 10.3390/e24081082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The notion of information and complexity are important concepts in many scientific fields such as molecular biology, evolutionary theory and exobiology. Many measures of these quantities are either difficult to compute, rely on the statistical notion of information, or can only be applied to strings. Based on assembly theory, we propose the notion of a ladderpath, which describes how an object can be decomposed into hierarchical structures using repetitive elements. From the ladderpath, two measures naturally emerge: the ladderpath-index and the order-index, which represent two axes of complexity. We show how the ladderpath approach can be applied to both strings and spatial patterns and argue that all systems that undergo evolution can be described as ladderpaths. Further, we discuss possible applications to human language and the origin of life. The ladderpath approach provides an alternative characterization of the information that is contained in a single object (or a system) and could aid in our understanding of evolving systems and the origin of life in particular.
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Affiliation(s)
- Yu Liu
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Zengru Di
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Philip Gerlee
- Department of Mathematical Sciences, Chalmers University of Technology, 405 30 Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
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7
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Martínez RF, Cuccia LA, Viedma C, Cintas P. On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review. ORIGINS LIFE EVOL B 2022; 52:21-56. [PMID: 35796896 DOI: 10.1007/s11084-022-09624-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.
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Affiliation(s)
- R Fernando Martínez
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
| | - Louis A Cuccia
- Department of Chemistry and Biochemistry, Quebec Centre for Advanced Materials (QCAM/CQMF), FRQNT, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Cristóbal Viedma
- Department of Crystallography and Mineralogy, University Complutense, 28040, Madrid, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
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8
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Charlat S, Ariew A, Bourrat P, Ferreira Ruiz M, Heams T, Huneman P, Krishna S, Lachmann M, Lartillot N, Le Sergeant d’Hendecourt L, Malaterre C, Nghe P, Rajon E, Rivoire O, Smerlak M, Zeravcic Z. Natural Selection beyond Life? A Workshop Report. Life (Basel) 2021; 11:life11101051. [PMID: 34685422 PMCID: PMC8538383 DOI: 10.3390/life11101051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of “heritable variation in fitness among individuals”. Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions. Here we relate the major questions that were debated during a three-day workshop devoted to discussing whether natural selection may take place in non-living physical systems. We start this report with a brief overview of research fields dealing with “life-like” or “proto-biotic” systems, where mimicking evolution by natural selection in test tubes stands as a major objective. We contend the challenge may be as much conceptual as technical. Taking the problem from a physical angle, we then discuss the framework of dissipative structures. Although life is viewed in this context as a particular case within a larger ensemble of physical phenomena, this approach does not provide general principles from which natural selection can be derived. Turning back to evolutionary biology, we ask to what extent the most general formulations of the necessary conditions or signatures of natural selection may be applicable beyond biology. In our view, such a cross-disciplinary jump is impeded by reliance on individuality as a central yet implicit and loosely defined concept. Overall, these discussions thus lead us to conjecture that understanding, in physico-chemical terms, how individuality emerges and how it can be recognised, will be essential in the search for instances of evolution by natural selection outside of living systems.
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Affiliation(s)
- Sylvain Charlat
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
- Correspondence:
| | - André Ariew
- Department of Philosophy, University of Missouri, 438 Strickland Hall, Columbia, MO 65211, USA;
| | - Pierrick Bourrat
- Department of Philosophy, Macquarie University, Balaclava Road, North Ryde, NSW 2109, Australia;
- Charles Perkins Centre, Department of Philosophy, The University of Sydney, Camperdown, NSW 2006, Australia
| | - María Ferreira Ruiz
- Department of Philosophy, University of Bielefeld, 33615 Bielefeld, Germany;
| | - Thomas Heams
- INRAE, Domaine de Vilvert Bâtiment 211, 78352 Jouy-en-Josas, France;
| | - Philippe Huneman
- Institut d’Histoire et de Philosophie des Sciences et des Techniques, CNRS (Centre National de la Recherche Scientifique), Université Paris I Sorbonne, 13 Rue du Four, 75006 Paris, France;
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | | | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
| | - Louis Le Sergeant d’Hendecourt
- Centre de St-Jérôme, Laboratoire de Physique des Interactions Ioniques et Moléculaires, Aix-Marseille Université, CNRS, UMR 7345, 13013 Marseille, France;
| | - Christophe Malaterre
- Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Département de Philosophie, Université du Québec à Montréal (UQAM), 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada;
| | - Philippe Nghe
- Laboratoire Biophysique et Evolution, CNRS UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, 10 Rue Vauquelin, 75005 Paris, France;
| | - Etienne Rajon
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75005 Paris, France;
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 04103 Leipzig, Germany;
| | - Zorana Zeravcic
- Gulliver Lab, CNRS UMR 7083, ESPCI Paris, PSL University, 75005 Paris, France;
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9
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Steel M, Xavier JC, Huson DH. The structure of autocatalytic networks, with application to early biochemistry. J R Soc Interface 2020; 17:20200488. [PMID: 33023395 DOI: 10.1098/rsif.2020.0488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronized fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organization of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualize RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualize the core aspects of primitive biochemistry.
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Affiliation(s)
- Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich Heine Universität, Dusseldorf, Germany
| | - Daniel H Huson
- Center for Bioinformatics, University of Tübingen, Tubingen, Germany
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10
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Liu Y. On the definition of a self-sustaining chemical reaction system and its role in heredity. Biol Direct 2020; 15:15. [PMID: 33023641 PMCID: PMC7541320 DOI: 10.1186/s13062-020-00269-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Background The ability to self-sustain is one of the essential properties of life. However, a consistent and satisfying definition of self-sustainability is still missing. Currently, self-sustainability refers to either “no-intervention by a higher entity” or “regeneration of all the system’s components”. How to connect self-sustainability with heredity, another essential of life, is another problem, as they are often considered to be independent of each other. Last but not least, current definitions of self-sustainability failed to provide a practical method to empirically discern whether a chemical system is self-sustaining or not. Results Here I propose a definition of self-sustainability. It takes into account the chemical reaction network itself and the external environment which is simplified as a continuous-flow stirred tank reactor. One distinct property of self-sustaining systems is that the system can only proceed if molecular triggers (or called, seeds) are present initially. The molecular triggers are able to establish the whole system, indicating that they carry the preliminary heredity of the system. Consequently, life and a large group of fires (and other dissipative systems) can be distinguished. Besides, the general properties and various real-life examples of self-sustaining systems discussed here together indicate that self-sustaining systems are not uncommon. Conclusions The definition I proposed here naturally connects self-sustainability with heredity. As this definition involves the continuous-flow stirred tank reactor, it gives a simple way to empirically test whether a system is self-sustaining or not. Moreover, the general properties and various real-life examples of self-sustaining systems discussed here provide practical guidance on how to construct and detect such systems in real biology and chemistry. Reviewers This article was reviewed by Wentao Ma and David Baum.
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Affiliation(s)
- Yu Liu
- Institut Mittag-Leffler, Auravägen 17, Djursholm, 18260, Sweden.
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11
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An ecological framework for the analysis of prebiotic chemical reaction networks. J Theor Biol 2020; 507:110451. [PMID: 32800733 DOI: 10.1016/j.jtbi.2020.110451] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/18/2020] [Accepted: 08/09/2020] [Indexed: 01/29/2023]
Abstract
It is becoming widely accepted that very early in life's origin, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this possibility, we formalize the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. To capture the idea that life-like chemical systems are maintained out of equilibrium by fluxes of energy-rich food chemicals, we model chemical ecosystems in well-mixed compartments that are subject to constant dilution by a solution with a fixed concentration of input chemicals. Modelling all chemical reactions as fully reversible, we show that seeding an autocatalytic cycle with tiny amounts of one or more of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding justifies drawing an instructive analogy between an autocatalytic cycle and a biological species. We extend this finding to show that pairs of autocatalytic cycles can exhibit competitive, predator-prey, or mutualistic associations just like biological species. Furthermore, when there is stochasticity in the environment, particularly in the seeding of autocatalytic cycles, chemical ecosystems can show complex dynamics that can resemble evolution. The evolutionary character is especially clear when the network architecture results in ecological precedence, which makes a system's trajectory historically contingent on the order in which cycles are seeded. For all its simplicity, the framework developed here helps explain the onset of adaptive evolution in prebiotic chemical reaction networks, and can shed light on the origin of key biological attributes such as thermodynamic irreversibility and genetic encoding.
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12
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Liu Y, Hjerpe D, Lundh T. Side Reactions Do Not Completely Disrupt Linear Self-Replicating Chemical Reaction Systems. ARTIFICIAL LIFE 2020; 26:327-337. [PMID: 32697159 DOI: 10.1162/artl_a_00327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A crucial question within the fields of origins of life and metabolic networks is whether or not a self-replicating chemical reaction system is able to persist in the presence of side reactions. Due to the strong nonlinear effects involved in such systems, they are often difficult to study analytically. There are however certain conditions that allow for a wide range of these reaction systems to be well described by a set of linear ordinary differential equations. In this article, we elucidate these conditions and present a method to construct and solve such equations. For those linear self-replicating systems, we quantitatively find that the growth rate of the system is simply proportional to the sum of all the rate constants of the reactions that constitute the system (but is nontrivially determined by the relative values). We also give quantitative descriptions of how strongly side reactions need to be coupled with the system in order to completely disrupt the system.
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Affiliation(s)
| | | | - Torbjörn Lundh
- Institut Mittag-Leffler
- Chalmers University of Technology
- University of Gothenburg, Mathematical Sciences
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13
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Seshasai P, Kurle MM, Verma N, Pushpavanam S. Multiplicity, travelling waves and spatial patterns in coupled autocatalytic reaction systems. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Pavlović RZ, Border SE, Li Y, Li X, Badjić JD. Photoinduced interruption of interannular cooperativity for delivery of cationic guests in water. Chem Commun (Camb) 2020; 56:2987-2990. [DOI: 10.1039/c9cc09903d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Photoinduced decarboxylation of two hexaanionic baskets, surrounding a divalent cationic guest, reduced the interannular cooperativity (i.e. multivalency) holding the complex together to result in the release of guests.
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Affiliation(s)
- Radoslav Z. Pavlović
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus 43210
- USA
| | - Sarah E. Border
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus 43210
- USA
| | - Yiming Li
- Department of Chemistry
- University of South Florida
- 33620 Tampa
- USA
| | - Xiaopeng Li
- Department of Chemistry
- University of South Florida
- 33620 Tampa
- USA
| | - Jovica D. Badjić
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus 43210
- USA
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