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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Lifescape

1. A Consilience of Biology and Physics: Active Matter

Katsnelson, Mikhail, et al. Towards Physical Principles of Biological Evolution. Physica Scripta. 93/4, 2018. An entry in a Focus Issue on 21st Century Frontiers (search Lidstrom) by MK, Radboud University along with Yuri Wolf and Eugene Koonin, National Center for Biotechnology Information. While the traditional realms of inorganic and organic have long been apart, seemingly unbreachable, nowadays a robust (re)unification at last seems possible. A first step is to allow the very idea and integration at all. As often, it will involve a clarification of concepts and definitions, such as a thermodynamic basis for population genetic, along with affinities to the major evolutionary transitions scale. Another convergence might be spin-glass complexity theories with life’s emergence from proteins to organisms and the biosphere. The presence of “percolation effects and criticalities,” and natural selection as “measurement” is also suggested. Another version of this paper, Physical Foundations of Biological Complexity, appears in the Proceedings of the National Academy of Sciences (115/E8678, 2018, also at arXiv:1803.0997).

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in 'emergent phenomena'. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. (Abstract excerpt)

Biological evolution by no means defies any laws of physics but the emergent biological phenomena appear to call for extension of physics itself. Biological entities and their evolution do not simply follow the ‘more is different’ principle but, in some respects, appear to be qualitatively different from non-biological phenomena, indicative of distinct forms of emergence that require new physical theory. Following the analogy outlined above, in biology as inphysics, measurement generates the arrow of time and necessitates evolution. However, biological evolution has substantial special features, some of which we tried to capture here, in particular, by applying concepts of condensed matter physics, such as frustration and percolation, to central processes of biological evolution. Evidently, tn analysis and discussion presented here are only prolegomena to the sustained, concerted effort which is required to unite biology and physics. (9-10)

Klopper, Abigail. Physics of Living Systems. Nature Physics. July, 2018. An editor introduces an Insight collection on this current, vital synthesis of figure and ground as it gains collaborative veracity. The entries include Biophysics Across Time and Space by Ewa Paluch, Ethology as a Physical Science by Andre Brown and Ben de Bivort, Mesoscale Physical Principles of Collective Cell Organization by Joe Chin-Hun Kuo, et al and The Physics of Cooperative Transport in Ants by Ofer Feinerman, et al.

Klotsa, Daphne. As Above, So Below, and also in Between: Mesoscale Active Matter in Fluids. Soft Matter. 15/8946, 2019. After a decade of diverse particle (molecules, colloids, microbes, swimmers) studies, a University of North Carolina biomaterials physicist extends the approach onto macro systems such as bird flocks, insect swarms and whale pods. By so doing, it is found that the same phenomena can be observed at each and every wide scale and instance. Into the 21st century this traditional adage can gain its worldwise quantification. See also The Most Active Matter of All by Nicholas Ouellette in the new Cell Press journal Matter (1/2, 2019, third quote).

Living matter, such as biological tissue, can be viewed as a nonequilibrium hierarchical assembly, where self-driven components come together by consuming energy to form increasingly complex structures. The remarkable properties of such living or “active-matter” systems have prompted these questions: (1) do we understand the biology and biophysics that give rise to these properties? (2) can we achieve similar functionality with synthetic active materials? Here we study active matter in liquids and gases for aquatic and avian movements with finite inertia and expect collective behavior to emerge by way of nonlinearities and many-body interactions. The organisms/particles can become quite complex leading to flocking states and nonequilibrium phase transitions. (Abstract edits)

Nature has perfected obtaining robust collective behavior and global order from simple local interactions. The challenge for us is to engineer similar systems at various scales that are composed of many agents, ranging from self-propelled nanoparticles in solution to cars in traffic, and to be able to control their emergent collective properties, their emergent “intelligence.” Our group does computational research on active matter and related topics in order to bridge the gap between emergent phenomena, smart materials and robot swarming. (DK lab website)

The term “matter” encompasses everything from molecules to mountains. It also includes living, sentient beings. If matter composes all physical things, and materials science considers the behavior of such things, can materials science describe the most active matter of all? (Ouellette)

Krisnanda, Tanjung, et al. Probing Quantum Features of Photosynthetic Organisms. arXiv:1711.06485. We cite this entry by theoretical physicists from Singapore and the UK including Chiara Marletto and Vlatko Vedral to emphasize a current cross-integration and fertilization of macro-classical and micro-quantum phases. Its opening sentence is There is no a priori limit on the complexity, size or mass of objects to which quantum theory is applicable. If to observe, a worldwise sapiensphere is well on her/his way to finally, actually expressing a unified, animate, genesis universe.

Recent experiments have demonstrated strong coupling between living bacteria and light. Here we propose a scheme to infer quantumness of the light-bacteria correlations, as characterised by the presence of quantum discord, without requiring any knowledge of their mutual interactions, and by measuring only the light's degrees of freedom. This is achieved by monitoring the dynamics of the entanglement between few optical modes (probes) that interact independently with the bacteria. When the (light-sensitive part of) bacterium is modelled as a collection of two-level atoms we find that the steady state entanglement between the probes is independent of the initial conditions, is accompanied by entanglement between probes and bacteria, and provides independent evidence of the strong coupling between them. (Abstract)

Le Bihan, Denis. Is the Brain Relativistic?. arXiv:1908.04290. The senior French philosophical neuroscientist is posted at NEUROSPIN: From Physics to the Human Brain, a CEA Parisian research and clinical project, especially for autism studies, by way of novel intense field imaging techniques. In search of a broader natural context of service to cerebral research, the author notes that while cosmic physics has a conceptual basis, a global theory of the working brain to account for cognition, behavior, and consciousness does not exist. A sense of a deep affinity between our human faculty and the extant universe informs the text, as the second and third quotes allude. Neural network theories are engaged, along with genetic (alphabetic) factors in a connectome mode, along with synaptic pruning and visual capacities. As this imaginative rooting goes forward, we visit quantum phenomena, Minkowski diagrams, hyperspace geodesics, and more to show how akin a vital universe and our microcosmic human acumen might actually be. Thus the paper closes with the thought:To paraphrase (physicist) J. A. Wheeler one may conclude that brain spacetime tells activity how to flow while activity tells brain spacetime how to curve. (29)

Due to the large body of knowledge which neuroimaging has achieved over the last three decades, we have gained a fresh view of the brain which could help us make predictions for new imaging instruments to come, such as ultra high field MRI. By doing so, switching back and forth between physics and neurobiology, we come to a sense that time and space in the brain, as in the Universe, are, indeed, tightly mingled, and could be unified through a brain 'spacetime'. Thinking about a speed limit for action potentials flowing along myelinated axons led us to envision a 4-dimensional brain spacetime which holds to a relativistic pseudo-diffusion principle and functional curvature governed by brain activity, in a similar way gravitational masses give our 4-dimensional Universe spacetime its curvature. (Abstract excerpts, edits).

In consideration of neuroimaging achievements over the last 3 decades we thought that we could perhaps look at the brain with a fresh view which could unveil those “old” things in a new framework. By doing so, switching back and forth between physics and neurobiology, we came across the view that time and space in the brain, as in the Universe, were, indeed, tightly mingled, and might fade away to be unified through a brain “spacetime”. Further thinking led us to realize that this 4-dimensional brain spacetime would obey a kind of relativistic principle and present a functional curvature generated by brain activity, in a similar way gravitational masses give our 4-dimensional Universe spacetime its curvature. We then looked at how this whole-brain framework may shed light on clinical observations of dysfunctions and disorders. (2, edits)

Following the arguments developed above one should not find it objectionable, we hope, that the brain may be viewed in some way as a physical “object” embedded in a 4D enclosure. As such, the brain which is part of the Universe must obey Universephysical laws. After all, the perceptionwe have of the external world, the Universe, comes from our internal world, that is our mind in our brain, and it should not come as a surprise that our understanding of the Universe and our brain are irremediably connected. Hence, considering that the brain represents a kind of Universe itself one may envision how physical laws could be revisited, directly or through analogical derivations to provide a framework useful to better represent and perhaps understand how the brain works as a whole system. (10)

Lee, Chiu Fan and Jean David Wurtz. Novel Physics Arising From Phase Transitions in Biology. Journal of Physics D. 52/2, 2019. In a Special Issue on Collective Behaviour of Living Matter, Imperial College London bioengineers enter another example of the current synthesis of physical phenomena with living systems via a formative agency whence life transitions in kind through serial evolutionary and developmental phases. Thus, universal behaviors previously noted at condensed matter critical points can likewise be seen to occur in biological activities. A further aspect is that many free, contingent entities are yet seen to give rise to an overall coherence. By turns, as worldwide physical and biological sciences cross-inform, a unitary organic procreative ecosmos gains a revolutionary veracity. The work merited notice in Nature Physics (Jan. 2019) as Biological Transitions by Mark Buchanan. Also in this issue, e.g., see Phase Transitions in Huddling Emperor Penguins, Density Distributions and Depth in Flocks, and Emergence of Cooperativity in a Model Biofilm in this collection. See also Physical Principles of Intracellular Organization via Active and Passive Phase Transitions by Joel Berry, et al in Reports on Progress in Physics (81/4, 2018). The third quote is the Issue proposal by Ben Fabry, et al.

Phase transitions, such as the freezing of water and the magnetisation of a ferromagnet due to temperature changes, are familiar physical phenomena. Lately, such collective behaviours at a phase transition are similarly found in effect for living systems. From cytoplasmic organisation inside a cell to the migration of cell tissue during development, phase transitions have emerged as key mechanisms underlying many biological processes. However, a living system is fundamentally different from a thermal system, with metabolism and motility being two hallmarks of its nonequilibrium nature. In this review, we will discuss how such driven chemical reactions can arrest universal coarsening kinetics expected from thermal phase separation, and how motility leads to the emergence of a novel universality class when the rotational symmetry is spontaneously broken. (Abstract edits)

Collective phenomena are intimately linked to the phenomenon of phase transitions in physics. At a typical phase transition, a many-body system with constituents that interact only locally with their neighbours, be they molecules or living organisms, can collectively change their behaviour upon change of a single parameter, such that the universal behaviour is modified. By universal, we mean that certain properties of the system are independent of the microscopic details. Recently, phase transitions in living systems have come under attention, whence the generic non-equilibrium nature of biological systems gives rise to novel collectivities not seen before. (1)

Biological systems are becoming primarily known as networks of interacting genes and proteins. Yet a simple analysis of fundamental genetic programs fails to explain higher-level functions such as multi-cellular aggregation, tissue organization, embryonic development, and whole-scale behaviour of groups of individuals. Such collective processes are often insensitive to microscopic details of the underlying system and instead are emergent properties that arise from local interactions between cells or individuals. In recent years, novel theoretical and experimental approaches have spurred the development of statistical models of complex biological systems and generated much progress in our understanding of emergent collective processes in biology. (Issue Summary)

Leng, Biao, et al. Gravitational Scaling in Beijing Subway Network. arXiv:1606.01208. Beihang University (a major public research facility in Beijing) physicists, along with Shlomo Havlin, the veteran Israeli systems theorist, draw upon the physics of Newtonian gravity, self-organized criticality, and network dynamics to discern an independent motive source which serves to organize commuter traffic. The study follows up a similar work as Scaling and Renormalization in the Seoul Bus System by Segun Goh, et al (PLoS One 9/3, 2014), second Abstract. And to reflect, these findings, among many more, infer a double domain of human activities which are actually guided by and exemplify an independent self-organizing mathematics.

Recently, with the availability of various traffic datasets, human mobility has been studied in different contexts. Researchers attempt to understand the collective behaviors of human movement with respect to the spatio-temporal distribution in traffic dynamics, from which a gravitational scaling law characterizing the relation between the traffic flow, population and distance has been found. However, most studies focus on the integrated properties of gravitational scaling, neglecting its dynamical evolution during different hours of a day. Investigating the hourly traffic flow data of Beijing subway network, based on the hop-count distance of passengers, we find that the scaling exponent of the gravitational law is smaller in Beijing subway system compared to that reported in Seoul subway system. This means that traffic demand in Beijing is much stronger and less sensitive to the travel distance. Furthermore, we analyzed the temporal evolution of the scaling exponents in weekdays and weekends. Our findings may help to understand and improve the traffic congestion control in different subway systems. (Leng abstract)

Social systems have recently attracted much attention, with attempts to understand social behavior with the aid of statistical mechanics applied to complex systems. Collective properties of such systems emerge from couplings between components, for example, individual persons, transportation nodes such as airports or subway stations, and administrative districts. Among various collective properties, criticality is known as a characteristic property of a complex system, which helps the systems to respond flexibly to external perturbations. This work considers the criticality of the urban transportation system entailed in the massive smart card data on the Seoul transportation network. Analyzing the passenger flow on the Seoul bus system during one week, we find explicit power-law correlations in the system, that is, power-law behavior of the strength correlation function of bus stops and verify scale invariance of the strength fluctuations. Such criticality is probed by means of the scaling and renormalization analysis of the modified gravity model applied to the system. Here a group of nearby (bare) bus stops are transformed into a (renormalized) “block stop” and the scaling relations of the network density turn out to be closely related to the fractal dimensions of the system, revealing the underlying structure. It is thus demonstrated that such ideas of physics as scaling and renormalization can be applied successfully to social phenomena exemplified by the passenger flow. (Goh abstract)

Lou, Yuting, et al. Homeostasis and Systematic Ageing as Non-equilibrium Phase Transitions in Computational Multicellular Organizations. Royal Society Open Science. Online July 10, 2019. University of Tokyo and Fudan University, Shanghai systems biologists provide another notice of physical principles at work throughout life’s somatic activities and long developmental course.

The breakdown of homeostasis in tissues involves multiscale factors ranging from the accumulation of genetic damages to the deregulation of metabolic processes. Here, we present a multicellular homeostasis model in the form of a two-dimensional stochastic cellular automaton with three cellular states, cell division, cell death and cell cycle arrest. Our model illustrates how organisms can develop into diverse homeostatic patterns with distinct morphologies, turnover rates and lifespans without considering genetic, metabolic or other variations. Those homeostatic states exist in extinctive, proliferative and degenerative phases, which undergo a systematic ageing akin to a transition in non-equilibrium physical systems. (Abstract excerpt)

Love, Alan, et al. Perspectives on Integrating Genetic and Physical Explanations of Evolution and Development. Integrative & Comparative Biology. 57/6, 2017. In this Oxford Academic journal, Love, Thomas Stewart, Gunter Wagner, and Stuart Newman introduce this symposium, notably a century after D’Arcy Thompson’s On Growth and Form, about many intrinsic structural constraints that do in fact affect life’s anatomy and physiology. See, herein for example, The Origin of Novelty through the Evolution of Scaling Relationships, by Fred Nijhout and Ken McKenna.

In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium “Physical and Genetic Mechanisms for Evolutionary Novelty” that was dedicated to exploring empirical cases where both biological physics and developmental genetic considerations are crucial. We conclude by arguing that intentional reflection on conceptual questions about investigation, explanation, and integration is critical to achieving significant empirical and theoretical advances in our understanding of how novel forms originate across the tree of life. (Abstract)

Manning, Lisa and Eva-Maria Schoetz Collins. Focus on Physical Models in Biology: Multicellularity and Active Matter. New Journal of Physics. Circa 2013 –, 2014. Syracuse University and UCSD biophysicists introduce an on-going posting of articles that contribute to this 21st century integration of a conducive cosmos with evolutionary life. A typical paper is “The Origin of Traveling Waves in an Emperor Penguin Huddle” (15/125022). Of interest is how readily scientists have adopted the “active matter” phrase since 2010, and in the quote, a sense of “living materials.” See also Tsimring, et al, herein, for another (re)unification of these premier sciences. Search the March 2014 issue to find.

Living materials, from individual cells to flocks of animals, are a form of 'active matter', i.e. self-propelled entities which exhibit complex behaviors and interactions, and whose understanding is an active area of interdisciplinary research. New imaging techniques such as confocal, multiphoton, SPIM and 3D traction force microscopy have allowed an unprecedented look at the motions and forces that occur in a variety of multicellular systems. To complement the experimental advances on how groups of cells organize and interact at medium to high densities, theories and models are needed which scale up from single-cell behaviors to collective, emergent phenomena at the multi-cell level and allow us to make testable predictions. Much can also be learned by comparing and contrasting groups of cells with other active matter systems. In addition, new and sophisticated image and data analysis techniques are required to pinpoint, in multiple dimensions, features of cell mechanics, interactions and motility in these dense 'living materials'. These active, non-equilibrium systems might also generate new types of physical behavior that simply cannot be observed in inert systems and thus enable us to learn exciting new physics. (Excerpt)

Marais, Adriana, et al. The Future of Quantum Biology. Journal of the Royal Society Interface. Vol.15/Iss.148, 2018. A dozen scientists from the University of KwaZulu-Natal, Durban, VU University, Amsterdam, and Cambridge University offer a latest report with 133 references of how a quantum transfer of energy and charge which involves superposition, coherence and entanglement can be seen at work in such areas as photosynthesis, enzyme catalysis, olfaction, respiration, neuronal sensations and onto cognition. Still another instance is their presence at life’s biophysical and biochemical origin and complexification.

Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions. (Abstract)

Marchetti, Cristina, et al. Hydrodynamics of Soft Active Matter. Reviews of Modern Physics. 85/3, 2013. Theorists and researchers from Syracuse University (CM), University of Pierre and Marie Curie, Paris, Indian Institute of Science (S. Ramaswamy), TIFR Centre for Interdisciplinary Sciences, Hyperabad, Raman Research Institute, Bangalore, and the University of Bristol, UK, provide an extensive review of this growing sense that base materiality is not a lumpen passivity, only moved by external forces. Rather, by a decade of convergent findings from complex systems science about groupings from biomolecules and microbes to animal flocks, herds, troops, and tribes, physical substance is actually to be seen as innately proactive. As physics and biology again become one, this blending of animate organic and an “inorganic analogue” portends a natural cosmos of revolutionary liveliness.

In this review we summarize theoretical progress in the field of active matter, placing it in the context of recent experiments. Our approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of the review is to integrate the several approaches proposed in the literature, from semi-microscopic to phenomenological. In particular, we first consider dry systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium, and clarify the differences and similarities between two types of orientationally ordered states, the nematic and the polar.

We then consider the active hydrodynamics of a suspension, and relate as well as contrast it with the dry case. We further highlight various large-scale instabilities of these nonequilibrium states of matter. We discuss and connect various semi-microscopic derivations of the continuum theory, highlighting the unifying and generic nature of the continuum model. Throughout the review, we discuss the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular materials. We suggest promising extensions towards greater realism in specific contexts from cell biology to animal behavior, and remark on some exotic active-matter analogues. Lastly, we summarize the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents. (Abstract)

The goal of this article is to introduce the reader to a general framework and viewpoint for the study of the mechanical and statistical properties of living matter and of some remarkable non-living imitations, on length scales from sub-cellular to oceanic. The ubiquitous nonequilibrium condensed systems that this review is concerned with have come to be known as active matter (Ramaswamy, 2010). Their unifying characteristic is that they are composed of self-driven units - active particles - each capable of converting stored or ambient free energy into systematic movement. (2)

Active systems exhibit a wealth of intriguing nonequilibrium properties, including emergent structures with collective behavior qualitatively different from that of the individual constituents, bizarre fluctuation statistics, nonequilibrium order-disorder transitions, pattern formation on mesoscopic scales, unusual mechanical and rheological properties, and wave propagation and sustained oscillations even in the absence of inertia in the strict sense. (2)

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