Extended Criticality, Phase Spaces and Enablement in Biology

This paper analyzes, in terms of critical transitions, the phase spaces of biological dynamics. The phase space is the space where the scientific description and determination of a phenomenon is given. We argue that one major aspect of biological evolution is the continual change of the pertinent phase space and the unpredictability of these changes. This analysis will be based on the theoretical symmetries in biology and on their critical instability along evolution. Our hypothesis deeply modifies the tools and concepts used in physical theorizing, when adapted to biology. In particular, we argue that causality has to be understood di erently, and we discuss two notions to do so: di erential causality and enablement. In this context constraints play a key role: on one side, they restrict possibilities, on the other, they enable biological systems to integrate changing constraints in their organization, by correlated variations, in un-prestatable ways. This corresponds to the formation of new phenotypes and organisms.

[1]  Francis Bailly,et al.  A 2-dimensional geometry for biological time. , 2011, Progress in biophysics and molecular biology.

[2]  C. Sonnenschein,et al.  The society of cells cancer and control of cell proliferation , 2013 .

[3]  Fleury.  Branching morphogenesis in a reaction-diffusion model , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[4]  Henrik Jeldtoft Jensen,et al.  Glassy dynamics , 2007, Scholarpedia.

[5]  E. Allin,et al.  Evolution of the mammalian middle ear , 1975, Journal of morphology.

[6]  H. Maturana,et al.  Autopoiesis: the organization of living systems, its characterization and a model. , 1974, Currents in modern biology.

[7]  Denis Jacquemin,et al.  Double proton transfer mechanism in the adenine-uracil base pair and spontaneous mutation in RNA duplex , 2009 .

[8]  G. Longo,et al.  Mathematics and the Natural Sciences. The Physical Singularity of Life. Introduction , 2006 .

[9]  N. Ouyang,et al.  Expression and regulation of αB-crystallin in the kidney in vivo and in vitro , 2006, Pflügers Archiv.

[10]  Neil Rooney,et al.  From energetics to ecosystems : the dynamics and structure of ecological systems , 2006 .

[11]  R. Goldschmidt,et al.  Richard Goldschmidt : hopeful monsters and other ‘ heresies , 2002 .

[12]  G. Longo,et al.  From physics to biology by extending criticality and symmetry breakings. , 2011, Progress in biophysics and molecular biology.

[13]  J. Sethna,et al.  Minimal model of plasma membrane heterogeneity requires coupling cortical actin to criticality. , 2010, Biophysical journal.

[14]  Gerhard Werner,et al.  Consciousness Viewed in the Framework of Brain Phase Space Dynamics, Criticality, and the Renormalization Group , 2011, 1103.2366.

[15]  A. Páldi.  Stochastic gene expression during cell differentiation: order from disorder? , 2003, Cellular and Molecular Life Sciences CMLS.

[16]  A. Oudenaarden,et al.  Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.

[17]  Giuseppe Longo,et al.  Protention and retention in biological systems , 2010, Theory in Biosciences.

[18]  R. V. Jean,et al.  Phyllotaxis: A Systemic Study in Plant Morphogenesis , 1995 .

[19]  Giuseppe Longo,et al.  From Bottom-Up Approaches to Levels of Organization and Extended Critical Transitions , 2012, Front. Physio..

[20]  Bruce J. West.  Where Medicine Went Wrong: Rediscovering the Path to Complexity , 2006 .

[21]  David N. Beratan,et al.  Electron Transfer through Proteins , 2005 .

[22]  J. Sethna.  Statistical Mechanics: Entropy, Order Parameters, and Complexity , 2021 .

[23]  P. Grangier,et al.  Experimental Realization of Einstein-Podolsky-Rosen-Bohm Gedankenexperiment : A New Violation of Bell's Inequalities , 1982 .

[24]  J. Petitot.  The neurogeometry of pinwheels as a sub-Riemannian contact structure , 2003, Journal of Physiology-Paris.

[25]  V. Weiss.  Major genes of general intelligence , 1992 .

[26]  N. Bohr.  II - Can Quantum-Mechanical Description of Physical Reality be Considered Complete? , 1935 .

[27]  G. Longo,et al.  EXTENDED CRITICAL SITUATIONS: THE PHYSICAL SINGULARITY OF LIFE PHENOMENA , 2008 .

[28]  Giuseppe Longo.  On the Relevance of Negative Results 1 , 2012 .

[29]  J. Laskar.  Large-scale chaos in the solar system. , 1994 .

[30]  J. Sethna,et al.  Statistical Mechanics: Entropy, Order Parameters , 2007 .

[31]  D. Heeger,et al.  Spatial attention affects brain activity in human primary visual cortex. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A. Lesne.  Robustness: confronting lessons from physics and biology , 2008, Biological reviews of the Cambridge Philosophical Society.

[33]  Giuseppe Longo,et al.  Randomness Increases Order in Biological Evolution , 2012, Computation, Physics and Beyond.

[34]  John M. Greally,et al.  Genomics: Encyclopaedia of humble DNA , 2007, Nature.

[35]  E. Brouzes,et al.  Interplay of mechanical deformation and patterned gene expression in developing embryos. , 2004, Current opinion in genetics & development.

[36]  R. Batterman.  Hydrodynamics versus Molecular Dynamics: Intertheory Relations in Condensed Matter Physics , 2006, Philosophy of Science.

[37]  Harry B Gray,et al.  Electron tunneling through proteins , 2003, Quarterly Reviews of Biophysics.

[38]  Franco Strocchi,et al.  Symmetry Breaking , 2021, Theoretical and Mathematical Physics.

[39]  A. Moreno,et al.  Organisational closure in biological organisms. , 2010, History and philosophy of the life sciences.

[40]  T. Mančal,et al.  Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems , 2007, Nature.

[41]  G. Longo,et al.  In search of principles for a Theory of Organisms , 2015, Journal of Biosciences.

[42]  G. Longo,et al.  Some Bridging Results and Challenges in Classical, Quantum and Computational Randomness , 2011 .

[43]  Bruce J. West,et al.  From Self-Organized to Extended Criticality , 2012, Front. Physio..

[44]  N. Ouyang,et al.  Expression and regulation of alphaB-crystallin in the kidney in vivo and in vitro. , 2006, Pflugers Archiv : European journal of physiology.

[45]  G Longo,et al.  Is information a proper observable for biological organization? , 2012, Progress in biophysics and molecular biology.

[46]  Stephen Jay Gould,et al.  The Return of Hopeful Monsters , 2006 .

[47]  H. Ochman,et al.  Stepwise formation of the bacterial flagellar system , 2007, Proceedings of the National Academy of Sciences.

[48]  Giuseppe Longo,et al.  No entailing laws, but enablement in the evolution of the biosphere , 2012, GECCO '12.

[49]  Gerhard Werner,et al.  Fractals in the Nervous System: Conceptual Implications for Theoretical Neuroscience , 2009, Front. Physiology.

[50]  G. Longo.  On the relevance of negative results , 2011 .

[51]  R. Kucharski,et al.  Nutritional Control of Reproductive Status in Honeybees via DNA Methylation , 2008, Science.

[52]  Francis Bailly,et al.  BIOLOGICAL ORGANIZATION AND ANTI-ENTROPY , 2009 .

[53]  Denis Noble,et al.  Could there be a Synthesis between Western and Oriental Medicine, and with Sasang Constitutional Medicine in Particular? , 2009, Evidence-based complementary and alternative medicine : eCAM.

[54]  Thomas Heams,et al.  Randomness in biology , 2014, Mathematical Structures in Computer Science.

[55]  Van Fraassen,et al.  Laws and symmetry , 1989 .

[56]  Giuseppe Longo,et al.  Randomness and multilevel interactions in biology , 2011, Theory in Biosciences.

[57]  Gregory D. Scholes,et al.  Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature , 2010, Nature.

[58]  François Taddei,et al.  Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch , 2010, Molecular systems biology.