1
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Sabater B. Entropy Perspectives of Molecular and Evolutionary Biology. Int J Mol Sci 2022; 23:ijms23084098. [PMID: 35456917 PMCID: PMC9029946 DOI: 10.3390/ijms23084098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. The absolute entropy of the mixed components of non-living biomass (approximately −1.6 × 103 J K−1 L−1) is the reference to which other entropy decreases would be ascribed to life. The compartmentation of metabolites and the departure from the equilibrium of metabolic reactions account for reductions in entropy of 1 and 40–50 J K−1 L−1, respectively, and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases in thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated with life. The photosynthetic conversion of radiant energy to biomass energy accounts for most entropy (2.8 × 105 J K−1 carbon kg−1) produced by living beings. The comparatively very low entropy produced in other processes (approximately 4.8 × 102 J K−1 L−1 day−1 in the human body) must be rapidly exported outside as heat to preserve low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described, whose control minimizes the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.
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Affiliation(s)
- Bartolomé Sabater
- Department of Life Sciences, University of Alcalá, 28805 Alcalá de Henares, Madrid, Spain
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2
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Núñez-Corrales S, Jakobsson E. Entropic boundary conditions towards safe artificial superintelligence. J EXP THEOR ARTIF IN 2021. [DOI: 10.1080/0952813x.2021.1952653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Santiago Núñez-Corrales
- Illinois Informatics and National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana IL, USA
| | - Eric Jakobsson
- Molecular and Cellular Biology and National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana IL, USA
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3
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Kunnev D. Origin of Life: The Point of No Return. Life (Basel) 2020; 10:life10110269. [PMID: 33153087 PMCID: PMC7693465 DOI: 10.3390/life10110269] [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: 10/19/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022] Open
Abstract
Origin of life research is one of the greatest scientific frontiers of mankind. Many hypotheses have been proposed to explain how life began. Although different hypotheses emphasize different initial phenomena, all of them agree around one important concept: at some point, along with the chain of events toward life, Darwinian evolution emerged. There is no consensus, however, how this occurred. Frequently, the mechanism leading to Darwinian evolution is not addressed and it is assumed that this problem could be solved later, with experimental proof of the hypothesis. Here, the author first defines the minimum components required for Darwinian evolution and then from this standpoint, analyzes some of the hypotheses for the origin of life. Distinctive features of Darwinian evolution and life rooted in the interaction between information and its corresponding structure/function are then reviewed. Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. One of the most distinctive characteristics of Darwinian evolution in comparison with all other processes is the establishment of a fundamentally new level of matter capable of evolving and adapting. Therefore, the initiation of Darwinian evolution is the "point of no return" after which life begins. In summary: a definition and a mechanism for Darwinian evolution are provided together with a critical analysis of some of the hypotheses for the origin of life.
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Affiliation(s)
- Dimiter Kunnev
- Department of Oral Biology, University at Buffalo, Buffalo, NY 14263, USA
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4
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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: 11] [Impact Index Per Article: 2.8] [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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5
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Kahana A, Schmitt-Kopplin P, Lancet D. Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate. ASTROBIOLOGY 2019; 19:1263-1278. [PMID: 31328961 PMCID: PMC6785169 DOI: 10.1089/ast.2019.2029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al., 2018, Nature 558:564-568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin ("prebiotic soup"). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.
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Affiliation(s)
- Amit Kahana
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, Israel
| | - Philippe Schmitt-Kopplin
- Helmholtz Zentrum Muenchen, Research Unit Analytical BioGeoChemistry, Neuherberg, Germany
- Technische Universität München, Chair of Analytical Food Chemistry, Freising-Weihenstephan, Germany
| | - Doron Lancet
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, Israel
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6
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Rosas F, Mediano PA, Ugarte M, Jensen HJ. An Information-Theoretic Approach to Self-Organisation: Emergence of Complex Interdependencies in Coupled Dynamical Systems. ENTROPY 2018; 20:e20100793. [PMID: 33265882 PMCID: PMC7512355 DOI: 10.3390/e20100793] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 01/14/2023]
Abstract
Self-organisation lies at the core of fundamental but still unresolved scientific questions, and holds the promise of de-centralised paradigms crucial for future technological developments. While self-organising processes have been traditionally explained by the tendency of dynamical systems to evolve towards specific configurations, or attractors, we see self-organisation as a consequence of the interdependencies that those attractors induce. Building on this intuition, in this work we develop a theoretical framework for understanding and quantifying self-organisation based on coupled dynamical systems and multivariate information theory. We propose a metric of global structural strength that identifies when self-organisation appears, and a multi-layered decomposition that explains the emergent structure in terms of redundant and synergistic interdependencies. We illustrate our framework on elementary cellular automata, showing how it can detect and characterise the emergence of complex structures.
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Affiliation(s)
- Fernando Rosas
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
- Centre of Complexity Science, Imperial College London, London SW7 2AZ, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
- Correspondence: ; Tel.: +44-020-7589-5111
| | | | - Martín Ugarte
- CoDE Department, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Henrik J. Jensen
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
- Centre of Complexity Science, Imperial College London, London SW7 2AZ, UK
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8502, Japan
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7
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The Main Agroecological Structure (MAS) of the Agroecosystems: Concept, Methodology and Applications. SUSTAINABILITY 2018. [DOI: 10.3390/su10093131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This document presents the concept of the Main Agroecological Structure of agroecosystems (MAS) from the perspective of environmental thinking (ecosystem-culture relationships) and considered as a dissipative cultural structure. It discusses the possible applications of this concept (resilience, production, diversity) both inside and outside the farms. The potential MAS can be useful in the planning processes of the farms because it allows the quantification of the internal and external corridors, including natural vegetation. At the same time, it can be an important tool in the context of landscape management because it shows a series of cultural relations (economic, social, symbolic and technological) that are normally overlooked by the partial analysis of landscape ecology.
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Lancet D, Zidovetzki R, Markovitch O. Systems protobiology: origin of life in lipid catalytic networks. J R Soc Interface 2018; 15:20180159. [PMID: 30045888 PMCID: PMC6073634 DOI: 10.1098/rsif.2018.0159] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022] Open
Abstract
Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Zidovetzki
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Omer Markovitch
- Origins Center, Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
- Blue Marble Space Institute of Science, Seattle, WA, USA
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9
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Armstrong DL, Lancet D, Zidovetzki R. Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition. ASTROBIOLOGY 2018; 18:419-430. [PMID: 29634319 PMCID: PMC5910049 DOI: 10.1089/ast.2016.1615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/03/2017] [Indexed: 06/08/2023]
Abstract
We studied the simulated replication and growth of prebiotic vesicles composed of 140 phospholipids and cholesterol using our R-GARD (Real Graded Autocatalysis Replication Domain) formalism that utilizes currently extant lipids that have known rate constants of lipid-vesicle interactions from published experimental data. R-GARD normally modifies kinetic parameters of lipid-vesicle interactions based on vesicle composition and properties. Our original R-GARD model tracked the growth and division of one vesicle at a time in an environment with unlimited lipids at a constant concentration. We explore here a modified model where vesicles compete for a finite supply of lipids. We observed that vesicles exhibit complex behavior including initial fast unrestricted growth, followed by intervesicle competition for diminishing resources, then a second growth burst driven by better-adapted vesicles, and ending with a final steady state. Furthermore, in simulations without kinetic parameter modifications ("invariant kinetics"), the initial replication was an order of magnitude slower, and vesicles' composition variability at the final steady state was much lower. The complex kinetic behavior was not observed either in the previously published R-GARD simulations or in additional simulations presented here with only one lipid component. This demonstrates that both a finite environment (inducing selection) and multiple components (providing variation for selection to act upon) are crucial for portraying evolution-like behavior. Such properties can improve survival in a changing environment by increasing the ability of early protocellular entities to respond to rapid environmental fluctuations likely present during abiogenesis both on Earth and possibly on other planets. This in silico simulation predicts that a relatively simple in vitro chemical system containing only lipid molecules might exhibit properties that are relevant to prebiotic processes. Key Words: Phospholipid vesicles-Prebiotic compartments-Prebiotic vesicle competition-Prebiotic vesicle variability. Astrobiology 18, 419-430.
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Affiliation(s)
- Don L. Armstrong
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Cell Biology and Neuroscience, University of California, Riverside, California, USA
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Zidovetzki
- Department of Cell Biology and Neuroscience, University of California, Riverside, California, USA
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10
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Monroy-Ata A, Peña-Becerril JC. ON THE NATURE OF EVOLUTION: AN EXPLICATIVE MODEL. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2016. [DOI: 10.1016/j.recqb.2016.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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Zubarev DY, Pachón LA. Sustainability of Transient Kinetic Regimes and Origins of Death. Sci Rep 2016; 6:20562. [PMID: 26853459 PMCID: PMC4744936 DOI: 10.1038/srep20562] [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: 08/11/2015] [Accepted: 01/06/2016] [Indexed: 11/12/2022] Open
Abstract
It is generally recognized that a distinguishing feature of life is its peculiar capability to avoid equilibration. The origin of this capability and its evolution along the timeline of abiogenesis is not yet understood. We propose to study an analog of this phenomenon that could emerge in non-biological systems. To this end, we introduce the concept of sustainability of transient kinetic regimes. This concept is illustrated via investigation of cooperative effects in an extended system of compartmentalized chemical oscillators under batch and semi-batch conditions. The computational study of a model system shows robust enhancement of lifetimes of the decaying oscillations which translates into the evolution of the survival function of the transient non-equilibrium regime. This model does not rely on any form of replication. Rather, it explores the role of a structured effective environment as a contributor to the system-bath interactions that define non-equilibrium regimes. We implicate the noise produced by the effective environment of a compartmentalized oscillator as the cause of the lifetime extension.
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Affiliation(s)
- Dmitry Yu Zubarev
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
| | - Leonardo A Pachón
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA; Calle 70 No. 52-21, Medellín, Colombia
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12
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On the thermodynamics of multilevel evolution. Biosystems 2013; 113:140-3. [PMID: 23751978 DOI: 10.1016/j.biosystems.2013.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 10/26/2022]
Abstract
Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term "evolution" employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization.
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13
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Michel D. Life is a self-organizing machine driven by the informational cycle of Brillouin. ORIGINS LIFE EVOL B 2013; 43:137-50. [PMID: 23625038 DOI: 10.1007/s11084-013-9329-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/04/2013] [Indexed: 01/04/2023]
Abstract
Acquiring information is indisputably energy-consuming and conversely, the availability of information permits greater efficiency. Strangely, the scientific community long remained reluctant to establish a physical equivalence between the abstract notion of information and sensible thermodynamics. However, certain physicists such as Szilard and Brillouin proposed: (i) to give to information the status of a genuine thermodynamic entity (k B T ln2 joules/bit) and (ii) to link the capacity of storing information inferred from correlated systems, to that of indefinitely increasing organization. This positive feedback coupled to the self-templating molecular potential could provide a universal basis for the spontaneous rise of highly organized structures, typified by the emergence of life from a prebiotic chemical soup. Once established, this mechanism ensures the longevity and robustness of life envisioned as a general system, by allowing it to accumulate and optimize microstate-reducing recipes, thereby giving rise to strong nonlinearity, decisional capacity and multistability. Mechanisms possibly involved in priming this cycle are proposed.
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Affiliation(s)
- Denis Michel
- Université de Rennes 1 IRSET U1085 Transcription, Environment and Cancer, Campus de Beaulieu, Bat 13, 35042 Rennes Cedex, France.
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14
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Froese T, Virgo N, Ikegami T. Motility at the origin of life: its characterization and a model. ARTIFICIAL LIFE 2013; 20:55-76. [PMID: 23373982 DOI: 10.1162/artl_a_00096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an ximpoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.
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Affiliation(s)
- Tom Froese
- Universidad Nacional Autónoma de Mexico and, University of Tokyo
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15
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Cimpoiasu VM, Popa R. Biotic Abstract Dual Automata (BiADA): a novel tool for studying the evolution of porebiotic order (and the origin of life). ASTROBIOLOGY 2012; 12:1123-1134. [PMID: 23167567 DOI: 10.1089/ast.2012.0882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biotic Abstract Dual Automata (BiADA), a novel simulation concept for studying the evolution of prebiotic order, has four main attributes. (1) The energy of each form of organization is the sum of two stocks: entropy-associated energy (E(s)) and free energy (E(g)), with dissimilar meaning, energy conductive, and energy exchange properties; (2) E(s) and E(g) have user-defined absolute values and are not derived from the relative thermodynamic parameters standard entropy and standard Gibbs free energy; (3) BiADA analyzes changes in both units of transformation and units of organization; and (4) BiADA-based models analyze forward and reverse transformations separately and the brut production of forms of organization. We discuss quantitative relationships between energy, information, and order parameters proposed in BiADA-based simulations. The example we show is that of a simple system with two forms of organization. The model monitors the energy flow and budget, the evolution of order and information capacity, and the energy cost of producing and maintaining the system's state. We show the effect of six prebiotic factors on the evolution of order and energy dissipative potential of the system. These are the initial state of the system, energy availability, the intrinsic energy conductivity, catalysis of "A to B" transformations, B autocatalysis, and the terminal heat sink. We discuss benefits of employing BiADA principles in the study of the origin of order in more complex networks.
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16
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Rull V. Time, evolution and physical reductionism. The arrow of evolutionary time challenges an eventual physical theory of everything. EMBO Rep 2012; 13:181-5. [PMID: 22302015 DOI: 10.1038/embor.2012.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Valentí Rull
- Botanic Institute of Barcelona (IBB-CSIC-ICUB), Spain.
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17
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de la Fuente IM. Quantitative analysis of cellular metabolic dissipative, self-organized structures. Int J Mol Sci 2010; 11:3540-99. [PMID: 20957111 PMCID: PMC2956111 DOI: 10.3390/ijms11093540] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 09/11/2010] [Accepted: 09/12/2010] [Indexed: 11/16/2022] Open
Abstract
One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso Martínez de la Fuente
- Institute of Parasitology and Biomedicine "López-Neyra" (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento s/n, 18100 Armilla (Granada), Spain; E-Mail: ; Tel.: +34-958-18-16-21
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18
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Marín D, Martín M, Sabater B. Entropy decrease associated to solute compartmentalization in the cell. Biosystems 2009; 98:31-6. [DOI: 10.1016/j.biosystems.2009.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/01/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
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