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

2. Computational Systems Physics: Self-Organization, Active Matter

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)

Martin, David, et al. Fluctuation-induced first order transition to collective motion.. Journal of Statistical Mechanics. August, 2024. University of Chicago, Sorbonne, Paris-Saclay and MIT biophysicists including Frédéric van Wijland give another twist to matter on the move by way ofdiscerning turbulences which seem to percolate through the stream.

The nature of the transition to collective motion in assemblies of aligning self-propelled particles remains an open issue. In this article, we focus on dry active matter and show that weak fluctuations suffice to turn mean-field transitions into a 'discontinuous' coexistence scenario. Our theory shows how a density-dependence of the polar-field mass is induced which in turn, triggers a feedback loop between ordering and advection motion and the emergence of inhomogeneous travelling bands. Finally, we confirm our predictions by numerical simulations of fluctuating hydrodynamics as well as of topological particle models. (Excerpt)

Masucci, Adolfo, et al. Extracting Directed Information Flow Networks. Physical Review E. 83/026103, 2011. Researchers from Spain and Greece identify a universally applicable, seemingly independent, feature of complex systems in repetitive evidence across widely separate domains of genomic webs and the worldwide web. See also Masucci, et al “Wikipedia Information Flow Analysis Reveals the Scale-Free Architecture of the Semantic Space” in PLoS One (6/2, 2011).

We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge. (026103)

Matek, Christian. Searching for a Conceptual Language in Systems Biology: Hints from Statistical Mechanics? Progress in Biophysics and Molecular Biology. Online September, 2012. In a brief note, a Rudolf Peierls Centre for Theoretical Physics, Oxford, researcher draws a strong affinity between these seemingly disparate biological and physical domains. Altogether now might they infer an innate, expansive “systems cosmology,” a many-body, condensed matter cosmos from animating spontaneous organization to creaturely organisms and we peoples?

The search for an underlying conceptual framework in systems Biology inspired by the lessons from Statistical Mechanics may not only guide the intuition towards new experimental ideas. It could also provide a potentially cleared and simpler understanding of the rich structures of biology, telling relevant from irrelevant aspects of large systems and their function, and thus helping to recognize the simple behind the seemingly complex. (3)

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)

Mukherjee, Siddhartha. The Song of the Cell: An Exploration of Medicine and the New Human. New York: Scribners, 2022. The author is a renowned cancer physician and awarded science writer. This volume proceeds from his The Gene (2016) to enter a history of how life’s actual cellular basis became known. The account runs from 17th century discoveries onto its many vital findings such as immunity. But it is not until page 360 that a song and dance begins as a dynamic network interconnectivity can now be factored in. As Dr. Mukherjee views their physiological effect, these many interrelations are of equal importance as the discrete cells. So the work winds up with a 2020s somatic version of nature’s particle/wave, me/We incarnate complementarity. As our societies become torn asunder by their polarity, such realizations might well salve the body politic

Many readers might read the word song as metaphorical. But in my view, it is far from a metaphor. What the young man laments is that he hasn’t learned the interconnectedness of the individual inhabitants of the rain forest – their ecology and interdependence- how the forest acts and lives as a whole. A “song” can be both an internal message and also an external one: a message sent out from one being to another rto signal connective cooperativity. We can name cell, and their contents but have yet to learn such songs of cell biology. (362)

But powerful as it might be, “atomism” is reaching its explanatory limits, We can learn much about the physical, chemical and biological worlds through evolutionary agglomerations of atomistic units but these methods are straining at their limits. Genes, by themselves, are quite incomplete explanations of the complexities and diversities of organisms; we need to add gene-gene and gene-environment to explain organismical physiology and fates. (364-365)

The laws that govern the Newtonian ball are as real and tangible as they were during the conception of the universe. By the same logic, a cell and a gene are real. It’s just that they aren’t real in isolation. They are fundamentally cooperative, integrating units and together they they build, maintain and repair organisms. (365)

Perhaps one manifesto for the future of cell biology is to integrate “atomism” and “holism.” Multicellularity evolved again and again, because cells while retaining their boundaries could find multiple benefits in citizenship. That, more than any other, is the advantage of understanding cellular system, and beyond to cellular ecosystems. (365-366)

Siddhartha Mukherjee is a professor of medicine at the Irving Cancer Research Institute, Columbia University. A Rhodes scholar, he graduated from Stanford University, University of Oxford, and Harvard Medical School. He is the author of The Gene: An Intimate History, and The Emperor of All Maladies: A Biography of Cancer, a 2011 Pulitzer Prize winner..


Siddhartha Mukherjee is a professor of medicine at the Irving Cancer Research Institute, Columbia University. A Rhodes scholar, he graduated from Stanford University, University of Oxford, and Harvard Medical School. He is the author of The Gene: An Intimate History, and The Emperor of All Maladies: A Biography of Cancer, a 2011 Pulitzer Prize winner..

Nakamura, Eita and Kunihiko Kaneko. Statistical Evolutionary Laws in Music Styles. Nature Scientific Reports.. 9/15993, 2019. In late 2019, Kyoto University and University of Tokyo, Universal Biology Institute offer a good example of our 21st century worldwise project reaching a systemic synthesis across these widest ecosmos to cultural occasions, and every other natural and social phase in between. In significant regard, a reciprocal presence even in musical compositions of dual phases of conserved tradition, and a creative originality is recorded. So once again an iconic reciprocity akin to physical energy and our bicameral brains is found to grace score and song. See also Cultural Evolution of Music by Patrick Savage in Nature Communications (5/16, 2019).

If a cultural feature is transmitted over generations and exposed to stochastic selection, its evolution may be governed by statistical laws. Music exhibits steady changes of styles over time, with new characteristics developing from traditions. Here we analyze Western classical music data and find statistical evolutionary laws. We then study an evolutionary model where creators learn from past data so to generate new data to be socially selected according to the content dissimilarity (novelty) and style conformity (typicality). The model reproduces the observed statistical laws and can make predictions for independent musical features. In addition, the same model with different parameters can predict the evolution of Japanese enka music. Our results suggest that the evolution of musical styles can partly be explained and predicted by the evolutionary model incorporating statistical learning. (Abstract excerpts)

In the evolutionary process studied here, the balance between novelty and typicality (i.e. content dissimilarity and style conformity) plays an essential role. As we saw in the classical music data and enka music data, relative values can influence the direction and speed of evolution. The novelty and typicality biases can then be important for other types of culture. Evolutionary dynamics of language, other genres of music, scientific topics, and sociological phenomena are among topics under investigation. Another relevant topic is the evolution of bird songs, where selection-based learning is important. Bird song dynamics have been studied to describe the interaction between generators (singing birds) and imitators, which is similar to the novelty-typicality dyad in this study. (7, edits)

Naldi, Giovanni, et al, eds. Mathematical Modeling of Collective Behavior in Socio-Economic and Life Sciences. Boston: Birkhauser. 2010. University of Milan (Naldi), Ferrera (Lorenzo Pareschi), and Pavia (Guiseppe Toscani) systems physicists provide, per the Preface quotes next, a cogent update on the worldwide discovery of a universality of complex dynamical systems of agents and affairs. As an emergent convergence, statistical mechanics and complexity science now flow together to reveal a new genesis nature from molecule to metropolis.

The description of emerging collective behaviors and self–organization in a group of interacting individuals has gained increasing interest from various research communities in biology, engineering, physics, as well as sociology and economics. In the biological context, swarming behavior of bird flocks, fish schools, insects, bacteria, and people is a major research topic in behavioral ecology with applications to artificial intelligence. Likewise, emergent economic behaviors, such as distribution of wealth in a modern society and price formation dynamics, or challenging social phenomena such as the formation of choices and opinions are also problems in which the emergence of collective behaviors and universal equilibria has been shown. (v)

The novelty here is that important phenomena in seemingly different areas such as sociology, economy and biology can be described by closely related mathematical models. In this book we present selected research topics that can be regarded as new and challenging frontiers of applied mathematics. These topics have been chosen to elucidate the common methodological background underlining the main idea of this book: to identify similar modeling approaches, similar analytical and numerical techniques, for systems made out of a large number of “individuals” that show a “collective behavior,” and obtain from them “average” information. The expertise obtained from dealing with physical situations is considered as the basis for the modeling and simulation of problems for applications in the socio-economic and life sciences, as a newly emerging research field. In most of the selected contributions, the main idea is that the collective behaviors of a group composed of a sufficiently large number of individuals (agents) could be described using the laws of statistical mechanics as it happens in a physical system composed of many interacting particles. This opens a bridge between classical statistical physics and the socio-economic and life sciences. (v-vi)

Nardini, Cesare, et al. Entropy Production in Field Theories without Time Reversal Symmetry: Quantifying the Non-Equilibrium Character of Active Matter. Physical Review X. 7/021007, 2017. A six member team with postings in the UK, Scotland, and France press this theoretical frontier researching these lively propensities of material nature as they engender self-emergent animate behaviors.

Needleman, Daniel and Zvonimir Dogic. Active Matter at the Interface between Materials Science and Cell Biology. Nature Reviews Materials. 2/17048, 2017. We cite this entry by Harvard and Brandeis University physicists as a latest iconic case of human endeavors to learn and express what innate essence that extant nature might actually have. In regard, the paper opens with a quote by Gottfried Leibniz from Jessica Riskin’s fine history The Restless Clock (2016 herein) that intertwines machine and organism aspects. We add three quotes which reflect the conflation. The consideration is that this novel 2010s perception of intrinsic, non-equilibrium, self-organized vitalities may finally achieve a quantified meld of physical matter and animate biology.

The remarkable processes that characterize living organisms, such as motility, self-healing and reproduction, are fuelled by a continuous injection of energy at the microscale. The field of active matter focuses on understanding how the collective behaviours of internally driven components can give rise to these biological phenomena, while also striving to produce synthetic materials composed of active energy-consuming components. The synergistic approach of studying active matter in both living cells and reconstituted systems assembled from biochemical building blocks has the potential to transform our understanding of both cell biology and materials science. This methodology can provide insight into the fundamental principles that govern the dynamical behaviours of self-organizing subcellular structures, and can lead to the design of artificial materials and machines that operate away from equilibrium and can thus attain life-like properties. In this Review, we focus on active materials made of cytoskeletal components, highlighting the role of active stresses and how they drive self-organization of both cellular structures and macroscale materials, which are machines powered by nanomachines. (Abstract)

Figure 1: Organisms are machines made from machines. Organisms are composed of tissues, which are non-equilibrium assemblages of cells. Cells are built from non-equilibrium self-organized structures, and subcellular structures are composed of energy-transducing molecular motors and filaments. In the schematic, one cell is undergoing cell division and contains a spindle (a structure that segregates chromosomes during cell division), which is made of microtubules (filament structures in the cytoskeleton) and molecular motors. The close-up views show a molecular motor that is crosslinking and sliding between two microtubules and the end of a microtubule that is dynamically shrinking. (2)

Here we review recent advances that have transformed active matter into a mature and rapidly expanding research field that spans diverse disciplines, ranging from soft matter physics to cell biology, to materials science, and to engineering. We focus on experimental
work at the interface between cell biology and materials science, as well as on the potential for each of these lines of research to influence and benefit the others. We first provide a brief historical perspective on the importance of active processes in the biological organization of cells. Next, we discuss active materials assembled from purified cytoskeletal components, which are classified according to the symmetries of their structures and stresses, and we review advances that demonstrate the essential role of active stresses and out-of-equilibrium self-organization in cytoskeletal systems in cells. We conclude by placing these topics in the broader context of other realizations of active matter. We also note that active matter is a much broader field that is being investigated using a wide array of synthetic model systems that are either externally or internally driven. (2)

Nemenman, Ilya. Information Theory and Adaptation. Wall, Michael, ed. Quantitative Biology: From Molecular to Cellular Systems. Boca Raton: CRC Press, 2012. In this chapter, the Emory University, Departments of Physics, Biology, Computational and Life Sciences Strategic Initiative, theorist embarks on this mission to understand the many ways that communicated content plays a major role in biological viability.

In this Chapter, we ask questions (1) What is the right way to measure the quality of information processing in a biological system? and (2) What can real-life organisms do in order to improve their performance in information-processing tasks? We then review the body of work that investigates these questions experimentally, computationally, and theoretically in biological domains as diverse as cell biology, population biology, and computational neuroscience. (Abstract, arXiv:1011.5466)

“What is physics? ... -- The idea ... that the world is understandable.” John J. Hopfield. I am a physicist working to understand how biological systems, such as cells, organisms, and populations, learn from their surrounding environment and respond to it (we call this "biological information processing"). I am interested in physical problems in this biological domain. That is “Are there phenomenological, coarse-grained, and yet functionally accurate representations of biological processes, or are we forever doomed to every detail mattering?” I hope to achieve some quantitative understanding of such complex phenomena as evolution, sensory processes, animal behavior, human cognition, and, who knows, maybe one day even human consciousness. (Ilya Nemenman website)

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