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

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

Coleman, Piers. Frontier at Your Fingertips. Nature. 446/379, 2007. A note that physics and biology are converging as materiality becomes reinvented as a self-similar expression of universal collaborative principles. See also the Emergent Universe Project website noted in this section.

Some believe that emergence implies an abandonment of reductionism in favour of a more hierarchical structure of science, with disconnected principles developing at each level. Perhaps. But in almost every branch of physics, from string theory to condensed-matter physics, we find examples of collective, emergent behavior that share common principles. (379) To me, this suggests that emergence does not spell the end for reductionism, but rather indicates that it be realigned to embrace collective behavior as in integral part of our Universe. (379)

Costa, Luciano da Fontoura, et al. Analyzing and Modeling Real-World Phenomena with Complex Networks. Advances in Physics. 60/3, 2011. Drawing upon a departmental focus on this field, eight University of Sao Paulo physicists provide a 108 page survey, with 565 references, of this real dynamic materiality across nature and society. After noting Basic Concepts, topical areas are Social, Communications, Economy, Finance, Computers, Internet, World Wide Web, Citations, Transportation Power Grids, Biomolecular, Medicine, Ecology, Neuroscience, Linguistics, Earthquakes, Physics, Chemistry, Mathematics, Climate, and Epidemics – that is everywhere. From these many exemplars can be distilled a common, independent, complex system topology. Circa 2012, how could it dawn upon international collaborative science that this ubiquitous discovery is actually revealing a procreative genesis universe? In such regard, other such citations lately weigh in, e.g., Li and Peng in Complex Human Societies, Dorogovtsev, the Nature Physics Insight review, all herein, boding a critical credence. We append extended quotes.

The many achievements of physics over the last few centuries have been based on reductionist approaches, whereby the system of interest is reduced to a small, isolated portion of the world, with full control of the parameters involved (e.g., temperature, pressure, electric field). An interesting instance of reductionism, which is seldom realized, is the modeling of non-linear phenomena with linear models by restricting the parameters and variables in terms of a linear approximation. In establishing the structure of matter with the quantum theory in the first few decades of the 20th century, for example, reductionism was key to reaching quantitative treatment of the properties of atoms, molecules and then sophisticated structures such as crystalline solids. Indeed, deciphering the structure of matter was decisive for many developments – not only in physics but also in chemistry, materials science and more recently in biology. Nevertheless, with reductionist approaches only limited classes of real-world systems may be treated, for the complexity inherent in naturally-occurring phenomena cannot be embedded in the theoretical analysis. (4)

The success of complex networks is therefore to a large extent a consequence of their natural suitability to represent virtually any discrete system. Moreover, the organization and evolution of such networks, as well as dynamical processes on them, involve non-linear models and effects. The connectivity of networks is ultimately decisive in constraining and defining many aspects of systems dynamics. For instance, the behavior of biological neuronal networks, one of the greatest remaining scientific challenges, is largely defined by connectivity. Because of its virtually unlimited generality for representing connectivity in the most diverse real systems in an integrative way, complex networks are promising for integration and unification of several aspects of modern science, including the inter-relationships between structure and dynamics. Such a potential has been confirmed with a diversity of applications for complex networks, encompassing areas such as ecology, genetics, epidemiology, physics, the Internet and WWW, computing, etc. In fact, applications of complex networks are redefining the scientific method through incorporation of dynamic and multidisciplinary aspects of statistical physics and computer science. (4-5)

Frequently, the success of new areas of physics are judged not only from their theoretical contributions, but also from their potential for applications to real-world data and problems. Despite its relatively young age, the area of complex network research has already established itself, especially through its close relationship with formal theoretical fields such as statistical mechanics and graph theory, as a general and powerful theoretical framework for representing and modeling complex systems. It has been capable of taking into account not only the connectivity structure of those systems, but also intricate dynamics. Judging by the large number of areas and articles reviewed in the present survey, complex networks have performed equally well (if not better) with respect to their application potential. Indeed, the generality and flexibility of complex networks extends to virtually every real-world problems, from neuroscience to earthquakes, encompassing at least the 22 areas considered in the present work. (71)

Crosato, Emanuele, at al. Thermodynamics of Emergent Structure in Active Matter. Physical Review E. Online October, 2019. Nine years after this title phrase came about, University of Sydney, Complex Systems Research Group theorists EC, Mikhail Prokopenko, and Richard Spinney quantify energetic properties that further distinguish this spontaneously animate materiality. As the quotes say, as 2020 near, our website survey is well able to report a truly organic, fertile ecosmos from which phenomenal persons arise, awaken and discover.

Active matter is rapidly becoming a key paradigm of out-of-equilibrium soft matter exhibiting complex collective phenomena, yet the thermodynamics of such systems remain poorly understood. In this letter we study the nonequilbrium thermodynamics of large scale active systems capable of mobility-induced phase separation and polar alignment, using a fully under-damped model which exhibits hidden entropy productions not previously reported in the literature. We quantify steady state entropy production at each point in the phase diagram, revealing characteristic dissipation rates associated with the distinct phases and configurational structure. This reveals sharp discontinuities in the entropy production at phase transitions and facilitates identification of the thermodynamics of micro-features, such as defects in the emergent structure. (Abstract)

In this letter we have explored the thermodynamic character that emerges from the rich collective dynamics exhibited by active matter and highlighted a hidden entropy production where rotational timescales impact dissipation in the translational degrees of freedom. Our results suggest that the richness, commonly associated with the phase structure of active matter, is mirrored in its thermodynamics, opening up a new tool to study collective phenomena on both a micro and macroscopic scale. Important questions remain, including the delicate issue of TRS which we have shown to dramatically influence any thermodynamic interpretation. We hope that the work will contribute to a deeper understanding of the thermodynamics of active systems and, more broadly, the dynamics that can lead to emergent structures. (5)

Domokos, Gabor, et al. Soft cells and the geometry of seashells. arXiv:2402.04190.. Morphodynamics Research Group, Budapest University of Technology members cleverly identify and enhance a heretofore unappreciated pervasive phase of natural, animate topologies.

A central problem of geometry is the tiling of space with simple structures. Triangles, squares, and hexagons in the plane and cubes and other polyhedra in three-dimensional space have sharp corners and flat faces. However, many tilings in Nature are shapes with curved edges, non-flat faces, and corners. Here, we resolve this dissonance by a new class of shapes named soft cells to minimize edges and add contours. We prove that an infinite class of polyhedral tilings can be smoothly deformed into soft versions. These ideal soft shapes, born out of geometry, are found abundantly in nature, from cells to shells.

Drossel, Barbara. Strong Emergence in Condensed Matter Physics. arXiv:1909.01134. In a contribution to appear in a Synthese issue on Top-Down Causation, the Technical University Darmstadt theoretical physicist (search) contends that from a 2019 vista this basic field, aka many-body physics, by virtue of integrative summations of myriad particles (entities), does inherently give rise to macroscopic formations. See also How Downwards Causation Occurs in Digital Computers by George Ellis and the author at 1908.10186 and Emergent Quasiparticles by Alexandre Guay and Olivier Sartenaer in Individuation, Process, and Scientific Practices by Otavio Bueno, et al, eds. (Oxford UP, 2018).

This paper argues that the physics of condensed matter cannot be reduced to the supposedly fundamental quantum mechanical theory for all the atoms of which the system consists. In fact, there are many reasons to reject the idea that the world of physics is causally closed with everything being determined by bottom-up by microscopic laws. In actual practice condensed-matter theory does not start with atomic interactions. Instead, plausible assumptions, intuitive models, and phenomena are used to mathematically describe the properties of systems that consist of a macroscopic number of particles. The paper thus includes a list of arguments in favor of strong emergence and top-down causation within the realm of physics. (Abstract excerpt)

Elaiw, Ahmed, et al. On Entropy Dynamics for Active “Living” Particles. Entropy. Online October, 2017. King Abdulaziz University, Saudi Arabia system physicists including Nicola Bellomo (search) consider this newly perceived feature of physical materiality to inherently self-organize into animate assemblies. If to consider this work, and e.g., a cosmology paper by the Iranian physicists Khanpour and Yusofi (search), might a palliative 21st century renaissance of Islamic science be actually be underway? See also these concurrent books by the authors: A Quest Towards a Mathematical Theory of Living Systems and Active Particles: Advances in theory, Models, and Applications, see second quote, both from Springer/Birkhauser.

This paper presents a modeling approach, followed by entropy calculations of the dynamics of large systems of interacting active particles viewed as living—hence, complex—systems. Active particles are partitioned into functional subsystems, while their state is modeled by a discrete scalar variable, while the state of the overall system is defined by a probability distribution function over the state of the particles. The aim of this paper consists of contributing to a further development of the mathematical kinetic theory of active particles. (Abstract)

This volume collects ten surveys on the modeling, simulation, and applications of active particles using methods ranging from mathematical kinetic theory to nonequilibrium statistical mechanics. The contributing authors are leading experts working in this challenging field, and each of their chapters provides a review of the most recent results in their areas and looks ahead to future research directions. The approaches to studying active matter are presented here from many different perspectives, such as individual-based models, evolutionary games, Brownian motion, and continuum theories, as well as various combinations of these. Applications covered include biological network formation and network theory; opinion formation and social systems; control theory of sparse systems; theory and applications of mean field games; population learning; dynamics of flocking systems; vehicular traffic flow; and stochastic particles and mean field approximation. (AP summary)

Ellis, George F. R. Physics and the Real World. Foundations of Physics. 36/2, 2006. A brief version appeared in Physics Today, July 2005. An exercise to better relate and square physical reality with the presence of risen life. But what kind of universe is Ellis trying to describe. Not the moribund megaverse of string theory whereof human beings are the most fleeting, insignificant anomaly. By such inherent animate properties cosmic matter is seen to develop into emergent modular hierarchies of sentient and creative entities, in so many words a natural genesis.

The challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures, with top-down causation and memory effects allowing autonomous higher levels of order to emerge with genuine causal powers. (227)

Eom, Young-Ho, et al. Network-Based Model of the Growth of Termite Nests. Physical Review E. 92/6, 2015. Systems scientists across Europe including Santo Fortunato and Guy Theraulaz analyze social insect structures in terms of local node and interactive link complexity, which is then seen as a generic instance of a universal self-organization phenomena. We cite as another example of mid 2010s abilities to study and perceive both these specific instantiations and their common, independent mathematics.

We present a model for the growth of the transportation network inside nests of the social insect subfamily Termitinae (Isoptera, termitidae). These nests consist of large chambers (nodes) connected by tunnels (edges). The model based on the empirical analysis of the real nest networks combined with pruning (edge removal, either random or weighted by betweenness centrality) and a memory effect (preferential growth from the latest added chambers) successfully predicts emergent nest properties (degree distribution, size of the largest connected component, average path lengths, backbone link ratios, and local graph redundancy). Our results provide an example of how complex network organization and efficient network properties can be generated from simple building rules based on local interactions and contribute to our understanding of the mechanisms that come into play for the formation of termite networks and of biological transportation networks in general. (Abstract)

Faldor, Maxence and Antoine Cully. TowarArtificial Open-Ended Evolution within Lenia using Quality-Diversity.. arXiv:2406.04235. We cite this paper by Imperial College London mathematicians to record the use of advanced computational programs as a way to facilitate and quantify a current notice of self-organizing generative dynamics in universal effect from quantum to embryonic to media phases. See also Hierarchically Organized Latent Modules for Exploratory Search in Morphogenetic Systems at arXiv:2007.01195 and Meta-Diversity Search in Complex Systems, A Recipe for Artificial Open-Endedness? at 2312.00455 by Inria, Univ. Ensta ParisTech (Flowers Team) members including Pierre-Yves Oudeyer.

In the quest to understand how complexity can self-organize from simple rules, computational models, such as Lenia cellular automata, have been developed. In this paper, we show that Quality-Diversity (QD), a family of Evolutionary Algorithms, is an effective framework to find diverse self-organizing patterns in complex systems. QD algorithms can evolve a large entity population adapted to their ecological niche. Our combined method achieved an array of lifelike self-organizing autonomous patterns similar to complex biological evolution. (Excerpt Edit)

Fontaine, Quentin, et al.. Kardar-Parisi-Zhang Universality in a One-Dimensional Polariton Condensate. Nature. August 24, 2022. Sixteen physicists in France, Belgium and Italy mainly at the University of Paris-Saclay cite experimental instances of consistent, reliable formations that occur across many “physical” occasions. (a reason why we added Statistical Organics to the section title). See a review A New Phase for the Universal Growth of Interfaces by Sebastian Diehl in the same issue which lauds the quality and wider significance of these findings.

Revealing universal behaviours is a hallmark of statistical physics. Phenomena such as the stochastic growth of crystalline surfaces and of interfaces in bacterial colonies, and spin transport in quantum magnets all belong to the same universality class, despite wide microscopic differences. In each systems, space–time correlations show power-law scalings with similar critical exponents, a dynamic commonality governed by the nonlinear stochastic Kardar–Parisi–Zhang (KPZ) equation (see Wikipedia, G. Parisi is a 2021 Nobel winner). Our empirical studies show that phase evolutions in a driven-dissipative one-dimensional polariton condensate indeed holds to the KPZ universality class. (Abstract excerpt)

Freivogel, Ben. A Multiverse of Probabilities. Physics World. March, 2010. I put this paper here to emphasize the present absence of systems thinking in physical cosmology. For the situation is dire. Physicists seem to be spinning their 11 dimension, string, brane, tangled theories to incoherent extremes, quite unawares, with no faculty, quality control, or philosophical oversight as a reality check. The postmodern humanities cheer because don’t you know there is no reality to check, only bubble cosmoses, each with vicarious laws and constants. And this article is not isolated, in the April 2010 issue of Discover magazine three “Beyond Einstein” articles traipse hypotheses all over matter, space and time. While the March 30 news, as I write, proclaims the LHC is finally smashing atoms, in this same PW issue it is lamented that the supposed keystone Higgs boson may be more elusive than thought. Just how Ptolemaic will physics become, spinning epicycles from particles to parsecs, sans any admissible sense, the very idea, of a greater knowable genesis creation.

Frey, Erwin. Evolutionary Game Theory: Theoretical Concepts and Applications to Microbial Communities. Physica A.. 389/4265, 2010. A Ludwig-Maximilians-Universität München biophysicist provides a 33 page tutorial on the merger of stochastic physics with nonlinear complex network science. The material was presented at 2009 summer schools such as “Condensed Matter and Materials Physics” in Boulder, Colorado, and “Steps in Evolution: Perspectives from Physics, Biochemistry and Cell Biology 150 Years after Darwin” at Jacobs University, Bremen. By what worldwide natural philosophy might we begin to realize the actual discovery of a genesis cosmos with such vital propensities from universe to human?

Ecological systems are complex assemblies of large numbers of individuals, interacting competitively under multifaceted environmental conditions. Recent studies using microbial laboratory communities have revealed some of the self-organization principles underneath the complexity of these systems. A major role of the inherent stochasticity of its dynamics and the spatial segregation of different interacting species into distinct patterns has thereby been established. It ensures the viability of microbial colonies by allowing for species diversity, cooperative behavior and other kinds of “social” behavior. A synthesis of evolutionary game theory, nonlinear dynamics, and the theory of stochastic processes provides the mathematical tools and a conceptual framework for a deeper understanding of these ecological systems. We conclude with a perspective on the current challenges in quantifying bacterial pattern formation, and how this might have an impact on fundamental research in non-equilibrium physics. (Abstract excerpts)

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