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

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

Pauls, James, et al. Quantum Coherence and Entanglement in the Avian Compass. Physical Review E. 87/062704, 2013. Reviewed more in Cooperative Societies, Purdue University and LANL physicists including Sabre Kais advance the reconception and unity of physics and life as they find deep similarities and explanations. The artificial quantum-classical barrier is being removed to reveal a creative reiteration in kind and time from universe to human.

Perunov, Nikolai, et al. Statistical Physics of Adaption. arXiv.1412.1875. As the Abstract notes, MIT Physics of Living Systems Group researchers including Jeremy England contribute to the ongoing synthesis of these fields of study which serve to integrate and root life’s evolution, and our collaborative comprehension, within a fertile cosmic ground.

All living things exhibit adaptations that enable them to survive and reproduce in the natural environment that they inhabit. From a biological standpoint, it has long been understood that adaptation comes from natural selection, whereby maladapted individuals do not pass their traits effectively to future generations. However, we may also consider the phenomenon of adaptation from the standpoint of physics, and ask whether it is possible to delineate what the difference is in terms of physical properties between something that is well-adapted to its surrounding environment, and something that is not. In this work, we undertake to address this question from a theoretical standpoint. Building on past fundamental results in far-from-equilibrium statistical mechanics, we demonstrate a generalization of the Helmholtz free energy for the finite-time stochastic evolution of driven Newtonian matter. By analyzing this expression term by term, we are able to argue for a general tendency in driven many-particle systems towards self-organization into states formed through exceptionally reliable absorption and dissipation of work energy from the surrounding environment. (Abstract)

Picoli, Sergio, et al. Universal Bursty Behavior in Human Violent Conflicts. Nature Scientific Reports. 4/4773, 2014. Universidade Estadual de Maringa, Brazil, and Universidad Nacional Autonoma de Mexico, systems physicists quantify that even the most chaotic carnage can yet be seen to exhibit a common structure and activity. However and whenever might we finally altogether come to realize and understand, as so implied, that an independent mathematical source is in formative effect everywhere? Then as so edified be able to at last to declare a truce and break free from this obsession?

Understanding the mechanisms and processes underlying the dynamics of collective violence is of considerable current interest. Recent studies indicated the presence of robust patterns characterizing the size and timing of violent events in human conflicts. Since the size and timing of violent events arises as the result of a dynamical process, we explore the possibility of unifying these observations. By analyzing available catalogs on violent events in Iraq (2003–2005), Afghanistan (2008–2010) and Northern Ireland (1969–2001), we show that the inter-event time distributions (calculated for a range of minimum sizes) obeys approximately a simple scaling law which holds for more than three orders of magnitude. This robust pattern suggests a hierarchical organization in size and time providing a unified picture of the dynamics of violent conflicts. (Abstract)

Despite the fact that human activities and natural phenomena are very different in nature, it has been suggested that both could be described by a common approach. For example, the occurrence of earthquakes has been related to the relaxation of accumulated stress after reaching a threshold as in self-organized criticality (SOC). Analogously, violent events in human conflicts could be associated with a threshold mechanism. In this scenario, a description of human conflicts in terms of SOC seems plausible. Our findings are consistent with this possibility, providing quantitative support for the analogy between patterns in human conflicts and natural phenomena exhibiting SOC. (3)

Popkin, Gabriel. The Physics of Life. Nature. 529/16, 2016. A report on the growing realization of inherent material propensities, via the new field of “active matter” research, to organize and arrange into similar biological forms and motions from proteins to people.

From flocking birds to swarming molecules, physicists are seeking to understand ‘active matter’ – and looking for a fundamental theory of the living world.

Prechl, Jozsef. Statistical thermodynamics of self-organization in the adaptive immune system. arXiv:2306.04665. A senior Eotvos Lorand University, Budapest researcher contributes to the ongoing integral rooting of viable, persistent organisms withi a conducive, substantial milieu which is then seen to spontaneously vivify into a processive animate development. A Table of cardinal features from physical self-organization to an adaptive immunity enlists a thermal energy, dynamic non-linearity, multiple interactions, and more.

A steady flow of energy can be seen to arrange matter and information in particular ways by a process known as self-organization. Adaptive immunity is an instance implemented as a complex adaptive biological system that vivifies and informs itself by the maintenance of a steady state which can be modeled mathematically and physically. Here I summarize arguments for such a statistical thermodynamic interpretation of immune function and key variables that characterize self-organization in the context of biochemical energies, and network structurations. (Abstract)

Provata, Astero, et al. DNA Viewed as an Out-of-Equilibrium Structure. Physical Review E. 89/052105, 2014. Reviewed more in Genome Complex Systems as a good example of an integral synthesis of life and law.

Pruessner, Gunnar. Complex Systems, Non-Equilibrium Dynamics and Self-Organization. Entropy. Online January, 2017. The Imperial College London mathematician invites papers for a Special mid 2017 Issue on this subject phenomena. We record because its description note Active Matter as an exemplary instance.

Over the last two decades or so, the notion of complex systems has found its way into many different areas of science and humanities, allowing for a quantitative understanding of phenomena that were traditionally studied in a more qualitative fashion. A particularly attractive aspect of complex systems is the emergence of co-operative phenomena, or self-organisation, often driven by non-equilibrium dynamics that relies on an external (energy) source. Such systems seem to be all around us, and govern and represent all that we do and are. Particular interest in self-organisation and non-equilibrium systems in the form of "active matter" has been generated within the biological sciences with the continued emphasis of more quantitative methods. Pattern or tissue formation may be a particularly good example of a phenomenon suitable for the present issue. Other good examples may be entropy production in sociological and financial systems or recent developments in self-organised criticality.

Ramaswamy, Sriram. The Mechanics and Statistics of Active Matter. Annual Review of Condensed Matter Physics. 1/323, 2010. The Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore, biophysicist introduces the concept of “active matter” to represent novel appreciations, as the quotes say, of a natural materiality suffused by its own internal agency and dynamic motion. The phrase has gained currency in such 2013 writings by Cristina Marchetti, et al and Mark Buchanan (search each).

Active particles contain internal degrees of freedom with the ability to take in and dissipate energy and, in the process, execute systematic movement. Examples include all living organisms and their motile constituents such as molecular motors. This article reviews recent progress in applying the principles of nonequilibrium statistical mechanics and hydrodynamics to form a systematic theory of the behaviour of collections of active particles -- active matter -- with only minimal regard to microscopic details. A unified view of the many kinds of active matter is presented, encompassing not only living systems but inanimate analogues. (Abstract)

The viewpoint of this review is that living matter can fruitfully be regarded as a kind of material and studied using the tools of condensed matter physics and statistical mechanics; that there is a practical way to encode into such a description those features of the living state that are relevant to materials science; and that the results of such an endeavour will help us better understand, control and perhaps mimic active cellular matter. (325).

A comprehensive theory of this ubiquitous type of condensed matter is a natural imperative for the physicist, and should yield a catalogue of the generic behaviours, such as nonequilibrium phases and phase transitions, the nature of correlations and response, and characteristic instabilities. Second, therefore, the generic tendencies emerging from the theory of active matter, unless suppressed by specific mechanisms, must arise in vivo, which is why biologists should care about it. (325-326) The reader should keep in mind that theories of active matter were formulated not in response to a specific puzzle posed by experiments but rather to incorporate living, metabolizing, spontaneously moving matter into the condensed-matter fold. (326)

Riiska, Calvin, et al. The Physics of Animal Behavior: Form, Function, and Interactions. Annual Review of Condensed Matter Physics. Volume 13, 2024. In this latest chapter Emory University and University of Colorado biophysicists including Orit Peleg contribute to a current consilience of nonlinear complex system phenomena as it becomes amenable to and reflective of, in this exemplary case, with a deep physical source.

Understanding the physics of behavior in animals that has lately gained much attention. As a result, in this review we delve into the intricate temporal and spatial scales for both individual members and collective assemblies. Our work involves experimental and theoretical approaches which highlight the importance of feedback loops, emergent behavior, and environmental factors. Novel technologies such as high-speed imaging and tracking can then be used to validate physics-based models of complex 3D network dynamics across many species. We also consider applications in artificial intelligence, identify new areas for study, and envision further breakthroughs that reveal nature’s clever, cooperative behavioral repertoire. (Excerpt)

Rossi, Paolo. Surname Distribution in Population Genetics and in Statistical Physics. Physics of Life Reviews. Online June, 2013. As the Abstract notes, a University of Pisa physicist finds parallels between a person’s family name, genomic sources, and onto condensed material phenomena. We enter as an example of a growing incidence of such studies that draw common correspondences from disparate physical realms to personal lives. A further reason, as many entries attest, is a recognition of a mathematical domain that, unbeknownst, underlies, guides, channels, our individual and collective days and destinies, see herein Callegari about migrations, and Bohorquez about insurgencies.

Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from geneticists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents. (Abstract)

Rosso, Osvaldo, et al. Topics on Non-Equilibrium Statistical Mechanics and Nonlinear Physics II. Philosophical Transactions of the Royal Society A. 373/Iss. 2056, 2015. An introduction to papers from a 2014 conference in Brazil on these concerns, Google “Medyfinol” for info. Among the contributions is Causal Information Quantification of Prominent Dynamical Features of Biological Neurons by Fernando Montani, et al, which can represent this union and cross-invigoration of emergent persons able to learn this with a conducive physical materiality.

The research in non-equilibrium statistical mechanics and nonlinear physics is a scientific approach to the investigation of how relationships between parts give rise to the collective behaviour of a system, and how the system interacts and forms relationships with its environment. Such problems are tackled, mostly with new concepts and tools related to information theory, statistical mechanics and nonlinear dynamics. They aim at representing and understanding the organized albeit unpredictable behaviour of natural systems that are considered intrinsically complex. In fact, the exciting fields of complexity, chaos and nonlinear science have experienced impressive growth in recent decades. (Abstract)

Rotrattanadumrong, Rachapun and Robert Endres. Emergence of Cooperativity in a Model Bioflim. Journal of Physics D: Applied Physics. 50/234006, 2017. As the quotes say, Imperial College, London system biophysicists trace an insistent tendency even at this bacterial stage to get along with each other as a way to improve group survival benefits. See also a note added below about the Special Issue on Collective Behavior of Living Matter of which it is part edited by Ben Fabry, Daniel Zitterbart and R. Endres. And it well serves this section when a paper that joins microbes and physical phenomena can appear in a Physics journal.

Evolution to multicellularity from an aggregate of cells involves altruistic cooperation between individual cells, which is in conflict with Darwinian evolution. How cooperation arises and how a cell community resolves such conflicts remains unclear. In this study, we investigated the spontaneous emergence of cell differentiation and the subsequent division of labour in evolving cellular metabolic networks. In spatially extended cell aggregates, our findings reveal that resource limitation can lead to the formation of subpopulations and cooperation of cells, and hence multicellular communities. A specific example of our model can explain the recently observed oscillatory growth in Bacillus subtilis biofilms. (Abstract)

Biological systems are usually conceptualized as networks of interacting genes and proteins. Yet an analysis of genetic programs fails to explain higher-level functions such as multi-cellular aggregation, tissue organization, embryonic development, and collective behaviour of individuals. Such collective processes are often insensitive to microscopic details of the underlying system and are emergent properties that arise from the 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 progress in our understanding of emergent collective processes in biology. (Special Issue)

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