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

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

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)

Ross, Tyler, et al. Controlling Organization and Forces in Active Matter through Optically-defined Boundaries. Nature. 572/224, 2019. CalTech bioengineers uncover non-equilibrium phenomena and principles by optically controlling structures and fluid flow in an engineered system of active biomolecules which led to views of an innate tendency to spontaneously organize into animate structures and movements.

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)

Saclioglu, Cihan, et al. Group Behavior in Physical, Chemical and Biological Systems. Journal of Biosciences. 39/2, 2014. In an issue on Individuals and Groups (search S. Newman), biophysicists Saclioglu, Sabanci Universitesi, Istanbul with Onder Pekcan, Kadir Has Universitesi, Istanbul and Vidyanand Nanjundiah, Indian Institute of Science, Bangalore scope out how to situate and root in substantial nature, as must be the case, life’s persistent evolutionary formation of social assembles at each and every stage and instance. Section 2, for example, is Physical principles underlying collective behavior: Elementary particles and emergent macroscopic manifestations. Maybe in this Indian journal and milieu, an Eastern mind can better perceive how obvious this holistic unity must be. It goes on to a similar Group Behavior in Chemistry, Groups in Biology segment and more, altogether akin to 2017 papers by van Gestel/Tarnita and Sebe-Pedros, et al of a universal, independent recurrence from universe to us.

Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such ‘emergent’ properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck’s constant is discrete, not zero. Groups of molecules in solution, in particular polymers (‘sols’), can form viscous clusters that behave like elastic solids (‘gels’). Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. (Abstract excerpt)

Schweitzer, Frank. An Agent-Based Framework of Active Matter with Applications in Biological and Social Systems. arXiv:1806.10829. The ETH Zurich Chair of Systems Design has been a pioneer theorist and practitioner of the complexity revolution since the 1990s. As this paper conveys, a latest phase is an on-going rooting in and synthesis with physical phenomena, along with a strong inclusion of ubiquitous network features. Elemental agents, aka nodes, thus engage in “binary interactions” in the guise of a manifest statistical physics. Their persistent non-equilibrium dynamics can then reveal common, general principles across micro and macro perspectives. In living instantiations, they foster aggregation, cross-communication, self-assemblies, and so on.

Active matter, as other types of self-organizing systems, relies on the take-up of energy that can be used for different actions, such as motion or structure formation. Here we provide a dynamic agent-based approach for these processes at different levels of organization, physical, biological and social. Nonlinear driving variables describe the take-up, storage and conversion of energy, whereas driven variables describe the energy consuming activities. To demonstrate, we recast a number of existing models of Brownian agents and Active Brownian Particles such as clustering and self-wiring of networks based on chemotactic interactions, online communication and polarization of opinions based on emotional influence. The framework obtains critical parameters for active motion and the emergence of collective phenomena and the role of energy take-up and dissipation in dynamic regimes. (Abstract edits)

Selesnick, Stephen, et al. Quantum-like Behavior without Quantum Physics. Journal of Biological Physics. Online July, 2017. As the Abstract notes, mathematician Selesnick, and physicist Gualtiero Piccinini, University of Missouri, with philosopher J. P. Rawling, Florida State University, consider ways that quantum effects, as they become better understood into the 21st century, can be noticed and quantified across classical phenomena such as neural activities.

Recently there has been much interest in the possible quantum-like behavior of the human brain in such functions as cognition, the mental lexicon, memory, etc., producing a vast literature. These studies are both empirical and theoretical, the tenets of the theory in question being mainly, and apparently inevitably, those of quantum physics itself, for lack of other arenas in which quantum-like properties are presumed to obtain. However, attempts to explain this behavior on the basis of actual quantum physics going on at the atomic or molecular level within some element of brain or neuronal anatomy do not seem to survive much scrutiny. In this paper we lay the groundwork for a theory that might explain the provenance of quantum-like behavior in complex systems whose internal structure is essentially hidden or inaccessible. The results reveal certain effects in such systems which, though quantum-like, are not identical to the kinds of quantum effects found in physics. (Abstract)

Seoane, Luis. Fate of Duplicated Neural Structures. arXiv:2008.00531. The Barcelona systems theorist is presently a postdoc at MIT’s Center for Brains Minds + Machines (search LS and visit the CBMM site). After prior collaborations with Ricard Sole (see arXiv site) and others, he continues his project to give life’s evolutionary biology and cognition a deeper statistical and computational physics basis, as it necessarily has to have. His innovative 2020 entry is a good instance of this scientific frontier as it seeks to quantify and join human and universe into a unified organic genesis. Its sections course through bilateral hemispheres, reactive and/or predictive brains, cortical columns, active algorithms, linguistics and more as each form and move by an energetic flow. The 193 references over the 2000s and 2010s document a 21st century worldwise revolution from everything in pieces to altogether now. So this panicky year seems also a time of historic local, global and ecosmic synthesis which, if we could witness, read and avail might help mitigate and guide.

Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism percolates throughout biological processes and set limits to effective computation. Under specific conditions, self-replicating and computationally complex patterns become favored which yields life, cognition, and Darwinian evolution. Neurons and neural circuits then reside between statistical mechanics, computation, and cognitively in natural selection. A statistical physics theory of neural circuits would tell what kinds of brains to expect under set energetic, evolutionary, and computational conditions.

With this big picture in mind, we focus on the fate of duplicated neural circuits. We look at central nervous systems with a stress on computational thresholds that might prompt this redundancy and at duplicated circuits for complex phenotypes. From this we derive phase diagrams and transitions between single and duplicated circuits, which constrain evolutionary paths that lead to complex cognition. Similar phase diagrams and transitions might constrain internal connectivity patterns of neural circuits at large. Thus the formalism of statistical mechanics seems a natural framework for this promising line of research. (Abstract)

Siva, Karthnik, et al. Spin Glass Models of Syntax and Language Evolution. arXiv:1508.00504. We note this paper by Caltech mathematicians as a good example of the cosmic synthesis of physics and people, condensed matter and cultural discourse, a rooting of life and us in a fertile uniVerse. The Principles and Parameters model of Generative Linguistics due to Noam Chomsky is applied from Albanian to Zulu which leads to subject-verb language networks. If linguistics can be described by way of particles in relative motions, then this affinity would imply in turn that physical substance is literally textual in kind. The senior coauthor is Professor Matilde Marcolli. If there is any doubt that women can do STEM studies, check her website publications page where you will find work on Multifractals, Mumford Curves, Eternal Inflation and much more. For an April 2016 edition see her Syntactic Parameters and a Coding theory Perspective on Entropy and Complexity of Language Families paper in Entropy. And for even more see Semantic Spaces at 1605.0504238 and Syntactic Phylogenetic Trees at 1607.02791..

Using the SSWL database of syntactic parameters of world languages, and the MIT Media Lab data on language interactions, we construct a spin glass model of language evolution. We treat binary syntactic parameters as spin states, with languages as vertices of a graph, and assigned interaction energies along the edges. We study a rough model of syntax evolution, under the assumption that a strong interaction energy tends to cause parameters to align, as in the case of ferromagnetic materials. We also study how the spin glass model needs to be modified to account for entailment relations between syntactic parameters. This modification leads naturally to a generalization of Potts models with external magnetic field, which consists of a coupling at the vertices of an Ising model and a Potts model with q=3, that have the same edge interactions. We describe the results of simulations of the dynamics of these models, in different temperature and energy regimes. We discuss the linguistic interpretation of the parameters of the physical model. (Abstract)

Skjeltorp, Arne and Geir Helgesen. Editorial. European Physical Journal Special Topics. 225/4, 2016. An introduction to an issue on Cooperative Particles with papers such as Entangled Active Matter: From Cells to Ants and Patchy Colloidosomes – An Emerging Class of Structures, see abstract below. For another case, see Emergent Behavior in Active Colloids by Andreas Zotti and Holger Stark in the Journal of Physics: Condensed Matter (28/253001, 2016).

Both cells and ants belong to the broad field of active matter, a novel class of non-equilibrium materials composed of many interacting units that individually consume energy and collectively generate motion or mechanical stresses. However cells and ants differ from fish and birds in that they can support static loads. This is because cells and ants can be entangled, so that individual units are bound by transient links. Entanglement gives cells and ants a set of remarkable properties usually not found together, such as the ability to flow like a fluid, spring back like an elastic solid, and self-heal. In this review, we present the biology, mechanics and dynamics of both entangled cells and ants. We apply concepts from soft matter physics and wetting to characterize these systems as well as to point out their differences, which arise from their differences in size.

Smerlak, Matteo. Natural Selection as Coarsening. arXiv:1707.05317. A Perimeter Institute for Theoretical Physics senior postdoctoral researcher deftly considers how life’s seemingly vicarious evolution might actually be rooted in and exemplify fundamental physical phenomena. A concern is a somewhat arcane terminology, better definitions and translations would help, as they might apply to biological systems. But in the later 2010s, evinced by entries here and throughout, a salutary synthesis, long foreseen, is at last coming together. See also Limiting Fitness Distributions to Evolutionary Dynamics by Smerlak and Ahmed Youssef at 1511.00296.

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening---scaling and self-similarity---have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model. (Abstract)

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