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

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

Hernandez-Bermejo, Benito. Renormalization Group Approach to Power-Law Modeling of Complex Metabolic Networks. Journal of Theoretical Biology. Article in Press, 2010. A Universidad Rey Juan Carlos, Madrid, physicist identifies common parallels between this physical method and nature’s self-similarity, to wit each and all are trying to explain with disparate terms, the one same ubiquitous phenomena.

In the modeling of complex biological systems, and especially in the framework of the description of metabolic pathways, the use of power-law models often provides a remarkable accuracy over several orders of magnitude in concentrations, an unusually broad range not fully understood at present. In order to provide additional insight in this sense, this article is devoted to the renormalization group analysis of reactions in fractal or self-similar media. (Abstract)

This explains also the close relationship of the renormalization group invariant solutions and fractality. In fact, historically the notions of fractal and renormalization group appeared independently, but both were intended to analyze what is invariant under the change of scale of observation: fractal for geometrical objects, and renormalization group for physical quantities. (2)

Heylighen, Francis. The Self-Organization of Time and Causality. Foundations of Science. 15/4, 2010. Within this complexity revolution, the Vrije Universiteit Brussel systems thinker and director of its Evolution, Complexity, & Cognition Group seeks more formally stated, albeit abstract, explanations of a cosmic and earthly nature that evidently seems to be not expiring but somehow winding itself up in a developmental way. In this Autumn 2010 paper, theories can lately be extended to imagine an innately self-arranging and creating universe.

In the case of causality, the variations can be conceived as causal agents that embody different condition-action or cause-effects. In the case of basic laws of physics, the agents are likely to represent elementary particles or fields. Since the agents interact, in the sense that the effect of one’s action forms an initial condition or cause for another one’s subsequent action, they together form a complex dynamical system. These systems are known to necessarily self-organize, in the sense that the overall dynamics settles into an attractor. (355)

As yet, we know too little about the dynamics of such a primordial complex dynamical system to say anything about what kind of causal rules might emerge from such a self-organization at the cosmic scale. However, the general notion of self-organization based on variation and selection suggests some general features of the resulting order, such as the fact that it will be partly contingent, partly predictable, and context-dependent rather than absolute. (355)

Hidalgo, Jorge, et al. Cooperation, Competition and the Emergence of Criticality in Communities of Adaptive Systems. Journal of Statistical Mechanics. March, 033203, 2016. As the quotes describe, a theorist team of Hidalgo and Miguel Munoz, University of Granada and Jacopo Grilli, Samir Suweis, and Amos Maritan, University of Padova (search for prior papers) continues their project to quantify the features and propensities of life’s finely poised dynamic phenomena. As this paper and many others express, in accord with traditional wisdom, a universal balance of harmony and disorder does seem to be evident everywhere.

The hypothesis that living systems can benefit from operating at the vicinity of critical points has gained momentum in recent years. Criticality may confer an optimal balance between too ordered and exceedingly noisy states. Here we present a model, based on information theory and statistical mechanics, illustrating how and why a community of agents aimed at understanding and communicating with each other converges to a globally coherent state in which all individuals are close to an internal critical state, i.e. at the borderline between order and disorder. We study—both analytically and computationally—the circumstances under which criticality is the best possible outcome of the dynamical process, confirming the convergence to critical points under very generic conditions. Finally, we analyze the effect of cooperation (agents trying to enhance not only their fitness, but also that of other individuals) and competition (agents trying to improve their own fitness and to diminish those of competitors) within our setting. (Abstract)

In a recent work with a fresh perspective [29], criticality has been shown to emerge in communities of individuals/agents trying to communicate with each other and creating a collective entity. This approach considers a community of individuals equipped with a (genetic, neural, regulation...) network representing the internal configuration of each individual agent. The state of each of such networks is controlled by some parameters that completely determine the steady state probability distribution function of internal con figurations. It is assumed that the state of each single agent is defined by such a probability distribution. Each individual of the community tries to mimic, i.e. to infer or “understand", the state of others within a community. With unexpected generality, under this dynamics, the community experiences a drift toward the critical point of the network dynamics, i.e. at the edge between ordered and disordered states. (3)

Hidalgo, Jorge, et al. Emergence of Criticality in Living Systems through Adaptation and Evolution: Practice Makes Critical. arXiv:1307.4325. A posting in its Condensed Matter: Statistical Mechanics section by systems physicists Hidalgo and Miguel Munoz, University of Granada, Spain, Jacopo Grilli, Samir Suweis, and Amos Maritan, University of Padova, Italy, and Jaynath Banavar, University of Maryland, USA. In regard, a contribution to this scientific synthesis – a material cosmos which is innately conducive for life, and a universality of critically poised, self-organized, dynamic networks that grace such bodies, brains and societies.

Empirical evidence has proliferated that living systems might operate at the vicinity of critical points with examples ranging from spontaneous brain activity to flock dynamics. Such systems need to cope with and respond to a complex ever-changing environment through the construction of useful internal maps of the world. Here we employ tools from statistical mechanics and information theory to prove that systems poised at criticality are much more efficient in ensuring that their internal maps are good proxies of reality. Analytical and computational evolutionary models vividly illustrate that a community of such systems dynamically self-tunes toward a critical state either as the complexity of the environment increases or even upon attempting to map with fidelity the other agents in the community. Our approach constitutes a general explanation for the emergence of critical-like behavior in complex adaptive systems. (Abstract)

These general ideas can be exploited to construct a quantitative framework, which clearly demonstrates that self-tuning to criticality is a strategy adopted by living systems to effectively represent the external world. The critical point reached in this way represents a borderline between a disordered phase in which perturbations and noise propagate unboundedly and an ordered phase whereas changes are rapidly erased –hindering plasticity– thereby providing an excellent compromise between flexibility and accuracy. (2)

Janson, Natalia. Non-Linear Dynamics of Biological Systems. Contemporary Physics. 53/2, 2012. As a cosmic and vital spontaneities flow together, a Loughborough University, UK, mathematical physicist, with a doctorate from Saratov State University, Russia, contributes a technical tutorial upon exemplary phenomena such as “oscillatory dynamics” in cardiac physiology, respiration, and metabolism. With Ilya Prigogine, Herman Haken, and earlier Leonid Mandelstam as guides, living systems are seen to progressively arise from non-equilibrium, self-organizing thermodynamics.

All living systems, their parts, or their populations, have three properties in common. Firstly, they feed on externally supplied nutrients, regularly remove the products of decay, and exchange signals with the surrounding objects. In other words, they exchange matter, energy, and information with the environment and thus belong to the wide class of open systems. Secondly, even if they do not demonstrate any obvious activity, they constantly lose energy to the external world, and are thus dissipative systems. Thirdly, all living systems are non-linear, which means, broadly speaking, that their response to a sum of external inputs is not equivalent to a sum of their responses to the individual inputs. It is the combination of these three features that lead to the remarkable properties that we observe in living systems, such as the ability to live and survive, and to develop and learn. (137)

Here we look at biological systems from the viewpoint of the discipline known under a variety of names: complexity theory, synergetics, self-organization theory, chaos theory, or nonlinear dynamics – in what follows we will use the latter name. It is based on a vast number of discoveries in mathematics and physics made during as many as five centuries. (137)

Jensen, Henrik and Elsa Arcaute. Complexity, Collective Effects, and Modeling of Ecosystems. Annals of the New York Academy of Sciences. Vol. 1195, 2010. In an edition entitled Ecological Complexity and Sustainability, Imperial College London mathematicians proceed with a dual purpose of showing how a “Tangled Nature” can in fact be explicated by an adept apply of complex system theories. They go on to perceptively note that such nonlinear phenomena is much the same subject as treated by statistical mechanics. This fertile melding across scales from galaxies to Gaia which is well underway, e.g., Dirk Helbing and Claudino Castellano herein, then portends more than another methodology. Rather what is implied is a new kind of universe distinguished by an independent, implicate spontaneity that explicate, natural phenotypes from molecules to a metropolis emerge from and exemplify. These worldwide collaborations over the past few years can now robustly qualify a cosmic Copernican revolution from a moribund Ptolemaic multiverse to a procreative genesis synthesis.

We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions among large numbers of components, leading to ecosystems that possess the prototypical characteristics of complex systems. We argue that statistical mechanics is at present the best methodology available to obtain a quantitative description of complex systems, and that ecology is in urgent need of "integrative" approaches that are quantitative and nonstationary. We describe examples where combining statistical mechanics and ecology has led to improved ecological modeling and, at the same time, broadened the scope of statistical mechanics. (E19 Abstract)

Complex Systems consist of a large number of interacting components. The interactions give rise to emergent hierarchical structures. Statistical Mechanics seeks to understand how properties at systems level emerge from the level of the system-components and their interactions. (E19) This will allow us to demonstrate how macroevolution can be modeled as emerging from the interacting microevolution, which consists of individual organism influencing each other and undergoing reproduction which is prone to mutation. (E20)

Josephson, Brian. Biological Aspects of Fundamental Reality. http://sms.cam.ac.uk/media/715532. A video lecture by the Nobel laureate on October 28, 2009 at the Freiburg Institute for Advanced Studies. The main thesis is that life can and ought to be theoretically seen as a fundamental feature of cosmic nature, not as an alien or secondary anomaly. But after three decades on the physics staff at Cambridge University, he understandably proceeds by trying to tease out of the standard model such novel propensities for cooperative, emergent complexity that will not be found in the LHC. Thus, life is seen to exist beyond particles alone as “relational systems suffused with informational webs.” A more animate physics of our universe may then arise from deeper, different dimensions than quirky quanta.

But Josephson, a fine, sincere fellow, who I met once in 2006, notes that his expansive ideas do not curry favor with his “hostile” physics department. As this site tries to document, nothing less than a Copernican revolution from a Ptolemaic, barren, mechanical multiverse to a universal reality that is inherently organic in kind would seem to do. In which case excuses do not have to be made for an increasingly fertile materiality from which, as Josephson notes, regnant beings may evolve so as to become J. A. Wheeler’s intended observers needed to bring this self-creating genesis into full florescence.

Reductionism is the dominant paradigm of many fields of modern science. The main assumption is that a complex system can be explained in terms of the sum of its parts. On the basis of this idea we can conclude that all the natural phenomena can be explained in terms of some fundamental law of physics. However, this reductionist approach fails when applied to very complex systems such as biological ones. Thus, new paths to the formulation of a theory of everything could include complexity as the basic element.

On the basis of this concept, Prof. Brian D. Josephson offered in his lecture a different "non-orthodox" biological prospective for understanding the laws of nature. His approach is based on the concept that “life" is a new fundamental aspect of reality. Unitary elements behave in several complex ways such as reforming, reshaping, dissolving etc. All these elements represent the basic bricks of a new — although yet unshaped — approach that could lead our knowledge beyond the "standard model". (Talk Abstract)

Karl, Markus, et al. Tuning Universality Far from Equilibrium. Nature Scientific Reports. 3/2394, 2013. With Boris Nowak and Thomas Gasenzer, Ruprecht-Karls-Universitat, Heidelberg physicists show how open systems in this regime have a deep propensity for common scale-free dynamics and topologies at each and every natural stage and instance. The main point carrying through the article is that such similar phenomena appear everywhere as seemingly “independent” of certain specific detail.

Possible universal dynamics of a many-body system far from thermal equilibrium are explored. A focus is set on meta-stable non-thermal states exhibiting critical properties such as self-similarity and independence of the details of how the respective state has been reached. It is proposed that universal dynamics far from equilibrium can be tuned to exhibit a dynamical phase transition where these critical properties change qualitatively. This is demonstrated for the case of a superfluid two-component Bose gas exhibiting dfferent types of long-lived but non-thermal critical order. Scaling exponents controlled by the ratio of experimentally tuneable coupling parameters offer themselves as natural smoking guns. The results shed light on the wealth of universal phenomena expected to exist in the far-from-equilibrium realm. (Abstract)

The concept of universality has been extremely successful in classifying and characterising equilibrium states of matter. For example, there are different types of order in a magnetic material separated by a second-order phase transition at which the relevant physical properties become independent of the microscopic details of the system. This constitutes universality and allows to characterise an extensive range of different phenomena in terms of just a few classes governed by the same critical properties. In view of the intensifying discussion on the dynamics of many-body systems it is a pressing question whether also far away from the thermal limit the character of dynamical evolution can become independent of the microscopic details. (1)

Kelty-Stephen, Damian and James Dixon. When Physics is Not "Just Physics": Complexity Science Invites New Measurement Frames for Exploring the Physics of Cognitive and Biological Development. Critical Reviews in Biomedical Engineering. 40/6, 2012. By a parting of paths centuries ago, physics and biology went separate ways in their studies of moribund matter and quickening life. Here Harvard University and University of Connecticut ecological psychologists contribute to their growing reintegration and reunion in an increasingly holistic genesis universe from singularity to sentience.

The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena. (Abstract)

Khasseh, Reyhaneh, et al. Active quantum flocks. arXiv:2308.01603. University of Augsburg, Germany and MPI Physics of Complex Systems researchers including Markus Heyl describe an array of theoretical and empirical affinities between macro classical and micro quantum realms whereby the same non-equilibrium formative dynamics can be commonly seen to occur in both phases. As many nascent findings across the widest expanses now come together they achieve an historic witness of how nature does in fact avail and recycle a universal optimum viability as it arises from an independent, implicate source code.

Flocks of animals represent an archetype of collective behavior in the macroscopic classical world, which concertedly perform motions and actions as if one single entity. Here, we address whether flocks can also form in the microscopic world at the quantum level. For that purpose, we introduce the concept of active quantum matter as models of quantum particles on a one-dimensional lattice. We provide analytical evidence that these systems can indeed give rise to similar assemblies. A key finding is that such flocks, unlike classical ones, develop a strong coherence over long distances. Our work thus realizes collective behaviors of biological active particles in quantum matter and opens a path towards a class of nonequilibrium quantum many-body systems with unique properties. (Abstract)

In the quantum world, remarkable advances in simulators have been able to probe the real-time dynamics of quantum matter. Among important developments is the observation of nonequilibrium phases of matter such as many-body localization and discrete time crystals. In the classical world, the understanding of dynamical processes away from equilibrium in the context of active materials and the physics of biological systems has been impressive. So far, these nonequilibrium many-body physics of quantum and classical systems have evolved independently, leaving open the question at their interface: is it also possible for quantum particles to exhibit flocking, similar to birds or fish in the classical world? (1)

In two or higher-dimensional classical active matter, such propagating waves can be seen as a phase separation phenomenon resulting from positive feedback between density and polarization, leading to a discontinuous flocking transition. For classical active matter in one dimension, such waves randomly flip the direction leading to continuous phase transitions, consistent with our one-dimensional active quantum flocks. (5)

Kibble, Tom and Ajit Srivastava. Condensed Matter Analogues of Cosmology. Journal of Physics: Condensed Matter. 25/400301, 2013. Imperial College, London, and Institute of Physics, Bhubaneswar, India, physicists introduce an issue on recent correspondences in form and process found across these micro and macro realms. Examples are “The Multiverse Transition in Superfluid 3He” by Yury Bunkov, and Causality and Non-Equilibrium Second-Order Phase Transitions in Inhomogeneous Systems” by Adolfo del Campo, Tom Kibble, and Wojciech Zurek. Leading loci in the American southwest are the Center for Nonlinear Studies, Los Alamos Laboratory, and Texas A & M University, Computational Physics Group. For these articles, and many arXiv postings, their essence is a profusion of nonlinear, self-organized criticalities that repeat in kind from fractal galaxies and geologies to natural biota and social media, so as to imply a dynamic universality drawn from an independent source. Might we then just wonder at a worldwide human acumen able to study such expanse and depth, and altogether begin to realize it is one integral, vital, ultimately self-witnessing creation.

It is always exciting when developments in one branch of physics turn out to have relevance in a quite different branch. It would be hard to find two branches farther apart in terms of energy scales than early-universe cosmology and low-temperature condensed matter physics. Nevertheless ideas about the formation of topological defects during rapid phase transitions that originated in the context of the very early universe have proved remarkably fruitful when applied to a variety of condensed matter systems. The mathematical frameworks for describing these systems can be very similar. This interconnection has led to a deeper understanding of the phenomena in condensed matter systems utilizing ideas from cosmology.

Kohestani, Havva and Alessandro Giuliani. Organization Principles of Biological Networks. BioSystems. Online March, 2016. In another paper which could well represent an international collaboration and scientific synthesis, University of Tabriz, Iran, and National Institute of Health, Italy, theorists identify a wide array of common network features. These include number of nodes, shortest paths, degree of connections, net density, clustering coefficient, net centrality, diameter, heterogeneity, modularity, transmission load, and so on. This distillation is drawn from lattice, Barabasi-Albert, Erdos-Renyi, social, neural and brain, metabolic, protein interaction, amino-acid, gene regulatory, and cancer metabolic networks. On the basis of this exemplary invariance, a separate, universal source domain can now be recognized and specified.

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