Thermodynamical journey in plant biology

Nonequilibrium irreversible thermodynamics constitute a meaningful point of view suitable to explore life with a rich paradigm. This analytical framework can be used to span the gap from molecular processes to plant function and shows great promise to create a holistic description of life. Since living organisms dissipate energy, exchange entropy and matter with their environment, they can be assimilated to dissipative structures. This concept inherited from nonequilibrium thermodynamics has four properties which defines a scale independent framework suitable to provide a simpler and more comprehensive view of the highly complex plant biology. According to this approach, a biological function is modeled as a cascade of dissipative structures. Each dissipative structure, corresponds to a biological process, which is initiated by the amplification of a fluctuation. Evolution of the process leads to the breakage of the system symmetry and to the export of entropy. Exporting entropy to the surrounding environment corresponds to collecting information about it. Biological actors which break the symmetry of the system and which store information are by consequence, key actors on which experiments and data analysis focus most. This paper aims at illustrating properties of dissipative structure through familiar examples and thus initiating the dialogue between nonequilibrium thermodynamics and plant biology.

[1]  Pierre Fayant,et al.  Finite Element Model of Polar Growth in Pollen Tubes[C][W] , 2010, Plant Cell.

[2]  M. Tazawa,et al.  Studies on water permeability of a single plant cell by means of transcellular osmosis , 1956, Protoplasma.

[3]  Ben Scheres,et al.  Polar PIN Localization Directs Auxin Flow in Plants , 2006, Science.

[4]  W. Plaxton,et al.  THE ORGANIZATION AND REGULATION OF PLANT GLYCOLYSIS. , 1996, Annual review of plant physiology and plant molecular biology.

[5]  G. Mouille,et al.  Arabidopsis Phyllotaxis Is Controlled by the Methyl-Esterification Status of Cell-Wall Pectins , 2008, Current Biology.

[6]  E. Tulving How many memory systems are there , 1985 .

[7]  E. Jovanov,et al.  Plant electrical memory. , 2009, Plant signaling & behavior.

[8]  T. Gisiger Scale invariance in biology: coincidence or footprint of a universal mechanism? , 2001, Biological reviews of the Cambridge Philosophical Society.

[9]  Roderick C. Dewar,et al.  Maximum entropy production and plant optimization theories , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[10]  Jacques Dumais,et al.  Quantifying Green Life: Grand Challenges in Plant Biophysics and Modeling , 2011, Front. Plant Sci..

[11]  J. Wolfe Cellular Thermodynamics: the molecular and macroscopic views , 2015 .

[12]  J. Ziman Bridging the Culture Gap , 1973, Nature.

[13]  J. Dunlap Molecular Bases for Circadian Clocks Review review word for the late 80 s and early 90 s would have , 1999 .

[14]  Kathy Chen,et al.  Network dynamics and cell physiology , 2001, Nature Reviews Molecular Cell Biology.

[15]  Frank Jülicher,et al.  Oscillations in cell biology. , 2005, Current opinion in cell biology.

[16]  E. Le Deunff,et al.  Breaking conceptual locks in modelling root absorption of nutrients: reopening the thermodynamic viewpoint of ion transport across the root. , 2014, Annals of botany.

[17]  F. Gzil Introduction à l'étude de la médecine expérimentale , 2008 .

[18]  K. Bennett,et al.  The power of movement in plants. , 1998, Trends in ecology & evolution.

[19]  Ilya Prigogine,et al.  What is entropy? , 2004, Naturwissenschaften.

[20]  J. L. Jackson,et al.  Dissipative structure: an explanation and an ecological example. , 1972, Journal of theoretical biology.

[21]  D. Turcotte,et al.  Self-organized criticality , 1999 .

[22]  Y. Couder,et al.  Phyllotaxis as a Dynamical Self Organizing Process Part II: The Spontaneous Formation of a Periodicity and the Coexistence of Spiral and Whorled Patterns , 1996 .

[23]  E. D. Schneider,et al.  The thermodynamics and evolution of complexity in biological systems. , 1998, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.

[24]  H. Qian,et al.  Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. , 2005, Biophysical chemistry.

[25]  Grégoire Nicolis,et al.  Self-Organization in nonequilibrium systems , 1977 .

[26]  B. Meyer The water relations of plant cells , 1938, The Botanical Review.

[27]  U. Zimmermann,et al.  Physical Aspects of Water Relations of Plant Cells , 1979 .

[28]  Edmund Taylor Whittaker The Nature of the Physical World , 1929, Nature.

[29]  D J Cosgrove,et al.  A model of cell wall expansion based on thermodynamics of polymer networks. , 1998, Biophysical journal.

[30]  T. Mizuno,et al.  Comparative transcriptome of diurnally oscillating genes and hormone-responsive genes in Arabidopsis thaliana: insight into circadian clock-controlled daily responses to common ambient stresses in plants. , 2008, Plant & cell physiology.

[31]  R. Bonhomme,et al.  Bases and limits to using 'degree.day' units , 2000 .

[32]  L. Mahadevan,et al.  How the Venus flytrap snaps , 2005, Nature.

[33]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[34]  Chas A. Egan,et al.  Life, gravity and the second law of thermodynamics , 2008, Physics of Life Reviews.

[35]  M. Tyree The Thermodynamics of Short-distance Translocation in Plants , 1969 .

[36]  Sebastian E. Ahnert,et al.  - Risueno Root Branching Arabidopsis Oscillating Gene Expression Determines Competence for Periodic , 2014 .

[37]  Anja Geitmann,et al.  Experimental approaches used to quantify physical parameters at cellular and subcellular levels. , 2006, American journal of botany.

[38]  M. Born Statistical Thermodynamics , 1944, Nature.

[39]  Bruno Moulia,et al.  Leaves as Shell Structures: Double Curvature, Auto-Stresses, and Minimal Mechanical Energy Constraints on Leaf Rolling in Grasses , 2000, Journal of Plant Growth Regulation.

[40]  Brian G. Henning,et al.  Beyond Mechanism: Putting Life Back Into Biology , 2013 .

[41]  F. Crick,et al.  Molecular structure of nucleic acids , 2004, JAMA.

[42]  Keng C. Soh,et al.  Network thermodynamics in the post-genomic era. , 2010, Current opinion in microbiology.

[43]  J. Dumais,et al.  Chemically mediated mechanical expansion of the pollen tube cell wall. , 2011, Biophysical journal.

[44]  C. Wolgemuth Does cell biology need physicists , 2011 .

[45]  B. Palsson,et al.  The evolution of molecular biology into systems biology , 2004, Nature Biotechnology.

[46]  James H. Brown,et al.  A general model for the structure and allometry of plant vascular systems , 1999, Nature.

[47]  D. Walker,et al.  A mathematical model of electron transport. Thermodynamic necessity for photosystem II regulation: 'light stomata’ , 1989, Proceedings of the Royal Society of London. B. Biological Sciences.

[48]  J. Boyer,et al.  Calcium pectate chemistry causes growth to be stored in Chara corallina: a test of the pectate cycle. , 2008, Plant, cell & environment.

[49]  A. Bird,et al.  Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.

[50]  C. Pillet,et al.  Entropy Production , 2020, Encyclopedia of Continuum Mechanics.

[51]  H. Callen Thermodynamics and an Introduction to Thermostatistics , 1988 .

[52]  T. Long,et al.  RÉFLEXIONS SUR LA PUISSANCE MOTRICE DU FEU, ET SUR LES MACHINES PROPRES A DÉVELOPPER CETTE PUISSANCE. , 1903 .

[53]  G. Cai,et al.  No Stress! Relax! Mechanisms Governing Growth and Shape in Plant Cells , 2014, International journal of molecular sciences.

[54]  J. Halley Ecology, evolution and 1 f -noise. , 1996, Trends in ecology & evolution.

[55]  B. Moulia,et al.  The power and control of gravitropic movements in plants: a biomechanical and systems biology view. , 2009, Journal of experimental botany.

[56]  M. Lahaye,et al.  Another Brick in the Cell Wall: Biosynthesis Dependent Growth Model , 2013, PloS one.

[57]  A. Geitmann,et al.  Polar growth in pollen tubes is associated with spatially confined dynamic changes in cell mechanical properties. , 2009, Developmental biology.

[58]  Raffaella Barone,et al.  General Model , 2005, Encyclopedia of Biometrics.

[59]  F. Tardieu,et al.  Circadian rhythms of hydraulic conductance and growth are enhanced by drought and improve plant performance , 2014, Nature Communications.

[60]  L. Demetrius Thermodynamics and evolution. , 2000, Journal of theoretical biology.

[61]  T. Bohr,et al.  Unifying model of shoot gravitropism reveals proprioception as a central feature of posture control in plants , 2012, Proceedings of the National Academy of Sciences.

[62]  Jean Baptiste Pierre Antoine de Monet de Lamarck,et al.  Système Analytique des Connaissances Positives de L'Homme , 1820 .

[63]  N. Sugimoto Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. , 2014, International review of cell and molecular biology.