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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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Systems biology of eukaryotic superorganisms and the holobiont concept. Theory Biosci 2018; 137:117-131. [DOI: 10.1007/s12064-018-0265-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/05/2018] [Indexed: 01/25/2023]
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3
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Gho YS, Lee C. Emergent properties of extracellular vesicles: a holistic approach to decode the complexity of intercellular communication networks. MOLECULAR BIOSYSTEMS 2017; 13:1291-1296. [DOI: 10.1039/c7mb00146k] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Holistic approaches to decode emergent properties of extracellular vesicles either at a single vesicle level or at a systems level.
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Affiliation(s)
- Yong Song Gho
- Department of Life Sciences
- Pohang University of Science and Technology
- Pohang
- Republic of Korea
| | - Changjin Lee
- Department of Life Sciences
- Pohang University of Science and Technology
- Pohang
- Republic of Korea
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4
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Swimming performance of Bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems. Sci Rep 2016; 6:23841. [PMID: 27053439 PMCID: PMC4823718 DOI: 10.1038/srep23841] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/16/2016] [Indexed: 01/05/2023] Open
Abstract
Many bacterial species use flagella for self-propulsion in aqueous media. In the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. Therefore, the motility of soil bacteria might have special requirements. An important soil bacterial genus is Bradyrhizobium, with species that possess one flagellar system and others with two different flagellar systems. Among the latter is B. diazoefficiens, which may express its subpolar and lateral flagella simultaneously in liquid medium, although its swimming behaviour was not described yet. These two flagellar systems were observed here as functionally integrated in a swimming performance that emerged as an epistatic interaction between those appendages. In addition, each flagellum seemed engaged in a particular task that might be required for swimming oriented toward chemoattractants near the soil inner surfaces at viscosities that may occur after the loss of soil gravitational water. Because the possession of two flagellar systems is not general in Bradyrhizobium or in related genera that coexist in the same environment, there may be an adaptive tradeoff between energetic costs and ecological benefits among these different species.
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Annila A, Baverstock K. Genes without prominence: a reappraisal of the foundations of biology. J R Soc Interface 2014; 11:20131017. [PMID: 24554573 PMCID: PMC3973354 DOI: 10.1098/rsif.2013.1017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/28/2014] [Indexed: 01/08/2023] Open
Abstract
The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin's proportional numbers are influencing their ecosystems. Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype. In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.
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Affiliation(s)
- Arto Annila
- Department of Biosciences, University of Helsinki, POB 64, Gustaf Hälströmin katu 2, 00560 Helsinki, Finland
- Department of Physics, University of Helsinki, POB 64, Gustaf Hälströmin katu 2, 00560 Helsinki, Finland
| | - Keith Baverstock
- Department of Environmental Science, University of Eastern Finland, POB 1627, Yliopistonranta 1, 70211 Kuopio, Finland
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Moenke G, Falcke M, Thurley K. Hierarchic stochastic modelling applied to intracellular Ca(2+) signals. PLoS One 2012; 7:e51178. [PMID: 23300536 PMCID: PMC3531454 DOI: 10.1371/journal.pone.0051178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
Important biological processes like cell signalling and gene expression have noisy components and are very complex at the same time. Mathematical analysis of such systems has often been limited to the study of isolated subsystems, or approximations are used that are difficult to justify. Here we extend a recently published method (Thurley and Falcke, PNAS 2011) which is formulated in observable system configurations instead of molecular transitions. This reduces the number of system states by several orders of magnitude and avoids fitting of kinetic parameters. The method is applied to Ca(2+) signalling. Ca(2+) is a ubiquitous second messenger transmitting information by stochastic sequences of concentration spikes, which arise by coupling of subcellular Ca(2+) release events (puffs). We derive analytical expressions for a mechanistic Ca(2+) model, based on recent data from live cell imaging, and calculate Ca(2+) spike statistics in dependence on cellular parameters like stimulus strength or number of Ca(2+) channels. The new approach substantiates a generic Ca(2+) model, which is a very convenient way to simulate Ca(2+) spike sequences with correct spiking statistics.
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Affiliation(s)
- Gregor Moenke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Keven Thurley
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin, Berlin, Germany
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Skupin A, Thurley K. Calcium signaling: from single channels to pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 740:531-51. [PMID: 22453959 DOI: 10.1007/978-94-007-2888-2_24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ca(2+) is not only one of the most versatile and ubiquitous second messengers but also a well-established representative example of cell signaling. The identification of most key elements involved in Ca(2+) signaling enables a mechanistic and quantitative understanding of this particular pathway. Cellular behavior relies in general on the orchestration of molecular behavior leading to reliable cellular responses that allow for regulation and adaptation. Ca(2+) signaling uses a hierarchical organization to transform single molecule behavior into cell wide signals. We have recently shown experimentally that this organization carries single channel signatures onto the whole cell level and renders Ca(2+) oscillations stochastic. Here, we briefly review the co-evolution of experimental and theoretical studies in Ca(2+) -signaling and show how dynamic bottom-up modeling can be used to address -biological questions and illuminate biological principles of cell signaling.
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Affiliation(s)
- Alexander Skupin
- Luxembourg Centre of Systems Biomedicine, University Luxembourg, Luxembourg.
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Trevors JT, Saier MH. Thermodynamic perspectives on genetic instructions, the laws of biology and diseased states. C R Biol 2010; 334:1-5. [PMID: 21262480 DOI: 10.1016/j.crvi.2010.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 11/28/2010] [Accepted: 11/29/2010] [Indexed: 10/18/2022]
Abstract
This article examines in a broad perspective entropy and some examples of its relationship to evolution, genetic instructions and how we view diseases. Living organisms are programmed by functional genetic instructions (FGI), through cellular communication pathways, to grow and reproduce by maintaining a variety of hemistable, ordered structures (low entropy). Living organisms are far from equilibrium with their surrounding environmental systems, which tends towards increasing disorder (increasing entropy). Organisms free themselves from high entropy (high disorder) to maintain their cellular structures for a period of time sufficient to allow reproduction and the resultant offspring to reach reproductive ages. This time interval varies for different species. Bacteria, for example need no sexual parents; dividing cells are nearly identical to the previous generation of cells, and can begin a new cell cycle without delay under appropriate conditions. By contrast, human infants require years of care before they can reproduce. Living organisms maintain order in spite of their changing surrounding environment that decreases order according to the second law of thermodynamics. These events actually work together since living organisms create ordered biological structures by increasing local entropy. From a disease perspective, viruses and other disease agents interrupt the normal functioning of cells. The pressure for survival may result in mechanisms that allow organisms to resist attacks by viruses, other pathogens, destructive chemicals and physical agents such as radiation. However, when the attack is successful, the organism can be damaged until the cell, tissue, organ or entire organism is no longer functional and entropy increases.
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Affiliation(s)
- Jack T Trevors
- School of Environmental Sciences, University of Guelph, N1G 2W1, Guelph, Ontario, Canada.
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Trevors JT. Generalizations about bacteriology: thermodynamic, open systems, genetic instructions, and evolution. Antonie Van Leeuwenhoek 2010; 97:313-8. [DOI: 10.1007/s10482-010-9419-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 01/27/2010] [Indexed: 11/30/2022]
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Abstract
This paper explores the issue of life and its relevance to nursing, through Aristotle's philosophy and an Aristotelian interpretation of Nightingale's Notes on Nursing. Life as process and becoming has ontological status in Aristotle's philosophy and this dynamism is particularly relevant for nursing. The paper presents aspects of Aristotle's philosophy of life: his account of life as inherent powers of the individual, his analysis of change and time, and his understanding of sickness and health as qualitative states of living beings. It is shown how the Greek medical-philosophical tradition, continued by Galenic medicine and hygiene into modern time, influenced Nightingale's nursing. Individuals' life-maintaining metabolic relations to their surroundings are investigated through Aristotle and modern philosophy of biology and through Nightingale's nursing emphasis on the patient's relation to her or his immediate surroundings. It is argued that Nightingale's concern is really the processes of individual life, which in sickness necessitate temporally continuous nursing observation. Humans' radical dependency on their surroundings is actualized as interpersonal interdependency. The paper argues that the end of nursing care, the telos for which sake it is practised, is inherent in the individual course of the patients' life. When life processes are affected by sickness, infirmity, medical interventions or mental suffering, individuals need competent help to live - and to live as well as possible. It is suggested that the special responsibility of nursing is to facilitate, relieve and protect individual life continuously during such times.
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Affiliation(s)
- Ingunn Elstad
- Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
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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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12
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Follmann H, Brownson C. Darwin’s warm little pond revisited: from molecules to the origin of life. Naturwissenschaften 2009; 96:1265-92. [PMID: 19760276 DOI: 10.1007/s00114-009-0602-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/05/2009] [Accepted: 08/10/2009] [Indexed: 11/26/2022]
Affiliation(s)
- Hartmut Follmann
- Institute of Biology, University of Kassel, 34109, Kassel, Germany.
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Alberghina L, Höfer T, Vanoni M. Molecular networks and system-level properties. J Biotechnol 2009; 144:224-33. [PMID: 19616593 DOI: 10.1016/j.jbiotec.2009.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/07/2009] [Accepted: 07/10/2009] [Indexed: 11/17/2022]
Abstract
Molecular systems biology aims to describe the functions of complex biological processes through recursive integration of molecular analysis, modeling, simulation and theory. It focuses on networks that originate from interconnection of genes, proteins and metabolites whose dynamic interactions generate, as an emergent property of the system, the corresponding function. Although evolutionary optimized, intracellular biochemical parameters, such as the expression level of gene products or the affinity between two or more proteins, must have a permissible range that gives robustness against perturbations to the system. Using the yeast G(1)-to-S transition network as an example we show that sophisticated relations exist among network structure, emergent property and robustness. Different emergent properties are generated from the same network by changing the strength of its interactions, not only by altering expression level, but also through mono and multi-site phosphorylation/dephosphorylation. Besides, multi-site protein phosphorylation modules, widespread in cell cycle, may ensure robust and coherent timing of cell cycle transitions as it happens for the onset of DNA replication. In conclusion, the modulation of biological function/emergent property by modifying interaction strength provides an efficient, highly tunable device to regulate biological processes. Furthermore, the principles outlined herein may provide new insight to network analysis in drug discovery.
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Affiliation(s)
- Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy.
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