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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, Incubator Lifescape

2. A Consilience as Physics and Biology Grow Together: Active Matter

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)

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.

Menon, Gautam. Active Matter. Krishnan, J. Murali, et al, eds. Rheology of Complex Fluids. Berlin: Springer, 2010. A Chennai Institute of Technology, India, mathematician draws upon this novel conception of natural spontaneities to better characterize dynamic, animate phenomena. The chapter was informed by discussions with Sriram Ramaswamy, its founder, Cristina Marchetti, and other colleagues. As this section conveys, from many instances across every scale, independent general principles can be distilled.

The term active matter describes diverse systems, spanning macroscopic (e.g. shoals of fish and flocks of birds) to microscopic scales (e.g. migrating cells, motile bacteria and gels formed through the interaction of nanoscale molecular motors with cytoskeletal filaments within cells). Such systems are often idealizable in terms of collections of individual units, referred to as active particles or self-propelled particles, which take energy from an internal replenishable energy depot or ambient medium and transduce it into useful work performed on the environment, in addition to dissipating a fraction of this energy into heat. Active particles can exhibit remarkable collective behaviour as a consequence of these interactions, including non-equilibrium phase transitions between novel dynamical phases, large fluctuations violating expectations from the central limit theorem and substantial robustness against the disordering effects of thermal fluctuations. (Abstract)

Rheology is the branch of physics that deals with the deformation and flow of matter, especially the non-Newtonian flow of liquids and the plastic flow of solids.

Menzel, Andreas. Tuned, Driven, and Active Soft Matter. Physics Reports. 554/1, 2015. The Heinrich Heine University theorist quantifies an inherent materiality that seems to act much as a living organism with internal propensities, responses and self-motility. Candidates such as colloids, nematic liquid crystals, ferrogels, magnetic elastomers, vesicles in shear flow, copolymers engage in self-propelled, variable movement, interactive, emergent organizations, and so on. The paper goes on to the Collective Behavior of Animals whence insects, fish, and birds are found to exhibit similar non-equilibrium phenomena. By turns, might we imagine the physical cosmos by nature to be organic and alive. See also his later paper On the Way of Classifying New States of Active Matter in New Journal of Physics (18/071001, 2016) as a further summary with a copious bibliography.

One characteristic feature of soft matter systems is their strong response to external stimuli. As a consequence they are comparatively easily driven out of their ground state and out of equilibrium, which leads to many of their fascinating properties. Here, we review illustrative examples. This review is structured by an increasing distance from the equilibrium ground state. On each level, examples of increasing degree of complexity are considered. Finally, we focus on systems that are “active” and “self-driven”. Here our range spans from idealized self-propelled point particles, via sterically interacting particles like granular hoppers, via microswimmers such as self-phoretically driven artificial Janus particles or biological microorganisms, via deformable self-propelled particles like droplets, up to the collective behavior of insects, fish, and birds. As we emphasize, similarities emerge in the features and behavior of systems that at first glance may not necessarily appear related. We thus hope that our overview will further stimulate the search for basic unifying principles underlying the physics of these soft materials out of their equilibrium ground state. (Abstract excerpts)

Mohseni, Masoud, et al. Quantum Effects in Biology. Cambridge: Cambridge University Press,, 2014. Among the editors and authors are Martin Plenio, Seth Lloyd, Graham Fleming, and Elisabet Romero (See Nature Physics 10/9, 2014). One of the first book-length collections which gathers years of research and realizations that, if properly understood, “quantum” phenomena are not arcane and off-putting. Instead, as the quote notes, their creative presence can then be found across all realms of living, quickening nature.

Quantum biology, as introduced in the previous chapter, mainly studies the dynamical influence of quantum effects in biological systems. In processes such as exciton transport in photosynthetic complexes, radical pair spin dynamics in magnetoreception, and photo-induced retinal isomerization in the rhodopsin protein, a quantum description is a necessity rather than an option. The quantum modelling of biological processes is not limited to solving the Schrödinger equation for an isolated molecular structure. Natural systems are open to the exchange of particles, energy or information with their surrounding environments that often have complex structures. Therefore the theory of open quantum systems plays a key role in dynamical modelling of quantum-biological systems. Research in quantum biology and open quantum system theory have found a bilateral relationship. Quantum biology employs open quantum system methods to a great extent while serving as a new paradigm for development of advanced formalisms for non-equilibrium biological processes. (Chapter 2, Open Quantum System Approaches to Biological Systems)

Mora, Thierry, et al. Questioning the Activity of Active Matter in Natural Flocks of Birds. arXiv:1511.01958. A team of nine physicists across Europe including Irene Giardina, Leonardo Parisi, Aleksandra Walczak, and Andrea Cavagna continue to expand and finesse a viewing animal groupings as exemplars of complex adaptive self-organizing systems. For a philosophical surmise, one might imagine a universally iterative nature not as only a book, an encyclopedia testament, but as a three dimensional, graphic revelation which our phenomenal human phase is meant to read, and to enhance anew.

The correlated motion of large bird flocks is an instance of self-organization where global order emerges from local interactions. Despite the analogy with ferromagnetic systems, a major difference is that flocks are active -- animals move relative to each other, thereby dynamically rearranging their interaction network. Although the theoretical importance of this off-equilibrium ingredient has long been appreciated, its relevance to actual biological flocks remains unexplored. Here we introduce a novel dynamical inference technique based on the principle of maximum entropy, which takes into account network reshuffling and overcomes the limitations of slow experimental sampling rates. We apply this method to three-dimensional data of large natural flocks of starlings, inferring independently the strength of the social alignment forces, the range of these forces, and the noise.

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