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

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

Lancichinetti, Andrea, et al. Detecting the Overlapping and Hierarchical Community Structure in Complex Networks. New Journal of Physics. 11/033015, 2009. From the Complex Networks Lagrange Laboratory, Institute for Scientific Interchange, Torino, and the Budapest University of Technology and Economics, an example of how physicists are lately articulating the natural universalities of nested nets composed of cellular-like entities.

Many networks in nature, society and technology are characterized by a mesoscopic level of organization, with groups of nodes forming tightly connected units, called communities or modules, that are only weakly linked to each other. Uncovering this community structure is one of the most important problems in the field of complex networks. Networks often show a hierarchical organization, with communities embedded within other communities; moreover, nodes can be shared between different communities. (033015)

Laughlin, Robert. A Different Universe. New York: Basic Books, 2005. When a Nobel Laureate in Physics announces a revolutionary new science and worldview, it is of significant notice. The 20th century phase of looking down into matter in search of fundamental particles and lawful certainty has run its course. Although a necessary step and not wrong, reducing the world to fragments misses its true character. Drawing upon novel conceptions of quantum physics, along with advances in nonlinear science, Laughlin takes the opposite viewpoint that nature is to be understood through an emergent, stratified complexity. In addition to things, innate principles of organization and relationship are at work. From many imperfect, inexact entities (molecules, organisms) yet arises a more predictable, collective order. It is just this nascent turn of perspective from mechanism to dynamic emergence that Natural Genesis is trying to express. (An endorsement by another physics laurate, Philip Anderson, can be found in Nature 434/701, 2005.)

Thus the tendency of nature to form a hierarchical society of physical laws is much more than an academic debating point. It is why the world is knowable. (8) In other words, superconducting behavior reveals to us through its exactness, that everyday reality is a collective organizational phenomenon. (32) What we are seeing is a transformation of worldview in which the objective of understanding nature by breaking it down into ever smaller parts is supplanted by the objective of understanding how nature organizes itself. (76) Emergence means complex organizational structure growing out of simple rules. (200) …I think a good case can be made that science has now moved from an Age of Reductionism to an Age of Emergence, a time when the search for ultimate causes of things shifts from the behavior of parts to the behavior of the collective. (208)

Licata, Ignazio. Almost-Anywhere Theories: Reduction and Universality of Emergence. Ecological Complexity. 15/6, 2010. The author is a physicist founder of the Institute for Scientific Methodology, Palermo, Italy, which is concerned with intersections of scientific worldviews and their cultural understanding. In such regard, this paper seeks to move beyond a “Theory of Everything” based on bottom level determinants to a complementary addition of dynamic interrelations at each and all risen, sequential realms of a creative evolution. A certain portal is said to be a proper appreciation of renormalization group theory, not easy to do, as a good way to express nature’s phenomenal self-similarity.

Here, we aim to show that reductionism and emergence play a complementary role in understanding natural processes and in the dynamics of science explanation. In particular, we will show that the renormalization group - one of the most refined tools of Theoretical Physics - allows (us) to understand the importance of emergent processes' role in Nature identifying them as universal organization processes, that is, they are scale independent. (Abstract, 11)

Thus, grasping the complexity of the world requires a theoretical scenario which reconciles the quantum veritas of reductionism with radical emergence processes. The key starting point to understand such scenario is that the world is not made of cellular automata, chess pieces or Newtonian particles, but it is fundamentally quantum-based, informationally open to the observer (entanglement and nonlocal information) and is affected by measurements. (14)

Strictly speaking, in QFT (quantum field theory), similarly and even more radically than in QM, a particle is not a nomological fundamental “object,” but an event fixed by a network of relations whose conditions of existence are set by the dynamics of the interacting fundamental fields. (15)

Mainzer, Klaus. Thinking in Complexity: The Computational Dynamics of Matter, Mind, and Mankind. Berlin: Springer, 2007. Although emphasizing informational aspects, a good entry to the nascent perception that all natural realms are graced by such a self-similar theory of every when and where.

The theory of nonlinear, complex systems has become by now a proven problem-solving approach in the natural sciences. It is also recognized that many, if not most, of our social, ecological, economical and political problems are essentially of a global, complex and nonlinear nature. And it is now further accepted than any holistic perspective of the human mind and brain can hardly be achieved by any other approach. In this wide-ranging, scholarly but very concise treatment, Klaus Mainzer (physicist, computer scientist and philosopher) discusses, in essentially nontechnical language, the common framework behind these ideas and challenges. Emphasis is given to the evolution of new structures in natural and cultural systems, and we are lead to see clearly how the new integrative approach can give insights not available from traditional reductionistic methods. The fifth edition enlarges and revises almost all sections and include an entirely new chapter on the complexity of economic systems. (Publisher)

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)

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)

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)

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