III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

2. A Consilience Unity as Physics, Biology and People Become One

Kruse, Karsten, et al. Acto-myosin clusters as active units shaping living matter. arXiv:2408.05119.. arXiv:2408.05119. University of Geneva and University of Strasbourg biologists including Daniel Riveline provide an exercise whereby these title entities are treated as a self-assembling form of mobile matter.

Stress generation by the actin cytoskeleton shapes cells and tissues. Despite progress in live imaging and quantitative descriptions of cytoskeletal network dynamics, the connection between molecular scales and cell-scale spatio-temporal patterns is still unclear. Here we review studies of acto-myosin clusters at micrometer size and with lifetimes of several minutes in organisms from fission yeast to humans. We propose that tracking these clusters can serve as a simple readout for living matter such as morphogenetic processes that play similar roles in diverse organisms. (Abstract)

We have reviewed experimental and theoretical studies showing that self-organised acto-myosin clusters in a wide range of species behave locally and globally according to common rules. Apart from their biological significance, we speculate that acto-myosin clusters can also be applied to physical parameters. As such, we propose that acto-myosin clusters might act as appropriate quasi-particles on which general principles underlying morphogenesis can be built. It will be interesting to test these ideas in embryos while outlining the mechanisms securing robust morphogenesis with outstanding precisions over time and space. (9, 10)

Kulkarni, Suman and Dani Bassett.. Towards principles of brain network organization and function. arXiv:2408.02640l. As many fields this year seek and gain a deeper substantial ground in a conducive nature, here University of Pennsylvania prolific neuroscientists (search both) proceed to connect cerebral topologies and cognitive behaviors with a meld of many-body physics (organics), multiplex nets as they actively process knowledge content.

Understanding patterns of complex interactions and how they support collective neural activity and function is vital to parse human and animal behavior, treat mental illness, and develop artificial intelligence. Here, we take stock of recent progress in statistical physics, network geometry and information theory. Our discussion scales from individual neurons to mappings across brain regions. We examine the organizing principles and constraints that shape the biological structure and function of neural circuits and close with a look ahead at further integrities.

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)

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)

Marson, G. Ajmone, et al. Stochastic Evolutionary Differential Games toward a System of Behavioral Social Dynamics. Mathematical Models and Methods in Applied Sciences. 26/6, 2016. In a well rated World Scientific journal, this paper by mathematicians G. A. Marsan, Organization for Economic Cooperation and Development OECD, Paris, Nicola Bellomo, King Abdulaziz University, Jeddah, and Livio Gibelli, Polytechnic University of Turin was cited as the most read of the year. Also at arXiv:1506.05699. It is an inquiry into how novel theories of self-active kinetic matter might, by way of “big data” networks, be applied far afield to a range of social and economic systems. See also Mathematical Models of Self-Propelled Particles by N. Bellomo and F. Brezzi in this journal (27/6, 2017).

This paper proposes a systems approach to social sciences based on a mathematical framework derived from a generalization of the mathematical kinetic theory and of theoretical tools of game theory. Social systems are modeled as a living evolutionary ensemble composed of many individuals, who express specific strategies, cooperate, compete and might aggregate into groups which pursue a common interest. A critical analysis on the complexity features of social system is developed and a differential structure is derived to provide a general framework toward modeling. (Abstract)

McFadden, Johnjoe and Jim Al-Khalili. Life on the Edge: The Coming of Age of Quantum Biology. New York: Bantam, 2014. A geneticist and a physicist, both at the University of Surrey, draw upon the leading edges of biological and physical science to explain a grand cross-integration of evolutionary organisms and a lively natural cosmos.

McFadden, Johnjoe and Jim Al-Khalili. The Origins of Quantum Biology. Proceedings of the Royal Society A. Vol.474/Iss.2220, 2018. A University of Surrey, UK biologist and a physicist who have each authored prior works (search) achieve a unique, thorough history of this incipient synthesis from A. N. Whitehead, Erwin Schrodinger and others such as organicists and vitalists, aka the Cambridge Theoretical Biology Club, to its worldwise fruition today. From this retro-vista, an Order from Order phrase can be coined, which is seen in effect by a flow of recent findings, as the abstract notes.

Quantum biology is usually considered to be a new discipline, arising from recent research that suggests that biological phenomena such as photosynthesis, enzyme catalysis, avian navigation or olfaction may not only operate within the bounds of classical physics but also make use of a number of the non-trivial features of quantum mechanics, such as coherence, tunnelling and, perhaps, entanglement. However, although the most significant findings have emerged in the past two decades, the roots of quantum biology go much deeper—to the quantum pioneers of the early twentieth century. We will argue that some of the insights provided by these pioneering physicists remain relevant to our understanding of quantum biology today. (Abstract)

Clearly, quantization applies to all matter at the microscopic scale and has long been assimilated into standard molecular biology and biochemistry. Today, quantum biology refers to a small, but growing, number of rather more specific phenomena, well known in physics and chemistry, but until recently thought not to play any meaningful role within the complex environment of living cells. (1)

What remains indisputable is that the quantum dynamics that are undoubtedly taking place within living systems have been subject to 3.5 billion years of optimizing evolution. It is likely that, in that time, life has learned to manipulate quantum systems to its advantage in ways that we do not yet fully understand. They may have had to wait many decades, but the quantum pioneers were indeed right to be excited about the future of quantum biology. (11)

Melkikh, Alexey and Andrei Khrennikov. Mechanisms of Directed Evolution of Morphological Structures and the Problems of Morphogenesis. Biosystems. 168/26, 2018. Reviewed more in Systems Evolution, a latest essay by the Ural Federal University, Russia and Linnaeus University, Sweden theorists.

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