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

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

Kolakowska, Alice. Deciphering Dynamical Patterns of Growth Processes. European Journal of Physics. 30/1353, 2009. A Florida Institute of Technology physicist contends that since similar nonlinear phenomena seem to occur everywhere from universe to human, in ways much akin to the field of statistical mechanics, undergraduate physics curriculums ought now to include this significant expansion.

Many large-scale complex systems exhibit similar dynamical patterns. Examples include man-made structures such as, e.g., the Internet, social networks, programming dependences in computer operating system or stock market. Nature-made complex structures provide examples from the animate world such as, e.g., heart-beat patterns, growth of cell colonies and living tissues, or dynamical patterns in fish population: and, numerous mechanistic examples coming from the inanimate world such as, e.g., earthquake patterns, avalanches or dynamics of magnetization in a sample material. What may those diverse systems have in common? Elementary components of one system are quite different to the components of another system, and so is the physical nature of interactions between elementary components. Despite these transparent differences, when the systems of enormously large numbers of elementary components are analysed statistically they amazingly demonstrate similar statistical patterns or scaling laws. (1353-1354)

Koonin, Eugene. The Logic of Chance: The Nature and Origin of Biological Evolution. Upper Saddle River, NJ: FT Press Science, 2011. The National Center for Biotechnology Information, Evolutionary Genomics Research Group director, molecular biologist gathers many articles and thoughts into a work that epitomizes the vying cosmic revolutions. A Preface espouses a “postmodern” evolutionary synthesis of “constrained randomness” so to join a vicarious multiverse with intrinsic patterns that yet seem to underlie genomic activities. Although well intended, thus begins the array of contradictions that beset us today. Postmodernism is noted for its ban of any “metanarrative,” which a stochastic, chancy multiverse assumed by Koonin implies. Yet he perceptively goes on to propose deep affinities between evolutionary dynamics and statistical physics. Both natural realms proceed via many elements in interaction, from which arises an orderly result. It is thus inferred that “universal laws” must exist for such generative effect. Several of Koonin’s papers, often with colleagues, herein tend to favor an independent source. But life’s contingent ascent against the second law is explainable within an infinity of universes. Once again, in so many words, “chance and necessity,” but the ultimate question is again not asked or answered.

The characteristic exponents of the three broad functional classes of genes show little variation across prokaryotic lineages, suggesting that the differential evolutionary dynamics of genes with different functions reflect fundamental “laws” of evolution of cellular organization – or, in other words, distinct, strong constraints on the functional composition of genomes. Eukaryotic genes show similar, if less pronounced, patterns of power law gene scaling. All things considered, these distinct scaling laws represent another set of universals of genome evolution. (97) The parallels between evolutionary biology and statistical physics appear to be both detailed and fundamental to the degree that the conclusion seems to be justified that this is not an analogy, but rather a manifestation of the general statistical principles (it is tempting to call them “laws”) of the behavior of large ensembles of weakly interacting entities. (102)

Koorehdavoudi, Hana and Paul Bogdan. A Statistical Physics Characterization of the Complex Systems Dynamics. Nature Scientific Reports. 6/27602, 2016. As the quotes explain, in a good example of the living networks turn in physical theories, University of Southern California engineers advance an algorithmic quantification of active complexities from spatio-temporal interactions. See also herein a 2017 entry Reliable Multi-Fractal Characterization of Weighted Complex Networks by Bogdan and Yuankun Xue in this journal (7/7487).

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. (Abstract excerpts)

The remaining of this paper is organized as follows: In the first section of results, we present our framework to extract the possible states in the collective motion and the strategy to build the corresponding energy landscape for transitions between them. To demonstrate the benefits of our approach, we first apply this strategy to quantify the energy landscape of a self-organizing model of a simulated group of agents based on local interactions among its individuals. Next, we define the missing information for the group structure. In the second section, we apply the same framework to three natural groups of swimming bacteria, flying pigeons and ants and study their energy landscapes. We define emergence, self-organization, and quantify the complexity of a collective motion based on
these newly introduced metrics. (2)

Kresic, Ivor, et al.. Generating Multiparticle Entangled States by Self-Organization of Driven Ultracold Atoms. arXiv:2208.10111. As the Abstract conveys, Vienna University of Technology and University of Strathclyde, Scotland physicists expand the frontier presence of spontaneous orderings into atomic depths to an extent that nature’s every depth and breadth seems to exhibit and be moved by these one, same phenomena.

We study a methodology for guiding the dynamical evolution of ultracold atomic motional degrees of freedom towards multiparticle entangled Dicke-like states, via nonlinear self-organization under external driving. In the first model the external drive is an oscillating magnetic field, leading to self-organization by interatomic scattering. In the second model the drive is a pump laser, leading to self-organization by photon-atom scattering in a ring cavity. We demonstrate highly efficient generation of multiparticle entangled states of atomic motion and discuss prospective experimental realizations of the models. Our results highlight the potential for using the self-organization of atomic motion in quantum technological applications.

Krioukov, Dmitri, et al. Network Cosmology. Nature Scientific Reports. 2/793, November, 2012. As the quotes express, mathematical physicists Krioukov, along with Maksim Kitsak, Robert Sinkovits, David Rideout, David Meyer, University of California, San Diego, and Marian Boguna, University of Barcelona, deftly apply the generic scale-free network phenomena that distinguishes everywhere else in nature and society to the realm of celestial topologies and dynamics. As a result, by a finesse of de Sitter spacetime theories, even cosmic reaches are revealed to seamlessly draw upon, apply and exemplify these universal formative principles.

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology. (Abstract)

We show here that there exists a very simple but completely unexpected connection between networks and cosmology. In cosmology, de Sitter spacetime plays a central role as the exact solution of Einstein’s equations for an empty universe, to which our universe asymptotically converges. Here we show that graphs encoding the large-scale causal structure of de Sitter spacetime and our universe have structure common to many complex networks, and that the large-scale growth dynamics of these causal graphs and complex networks are asymptotically the same. (1)

In short, past light cones of new nodes, shown by green in Fig. 2, are asymptotically equal to the corresponding hyperbolic discs, shown by red. The green light cone bounds the set of nodes to which node P connects as a new causet element. The red hyperbolic disc bounds the set of nodes to which P connects as a new node in the hyperbolic network model that accurately describes the growth of real networks. Since these two sets are asymptotically the same, we conclude that not only the structure, but also the growth dynamics of complex networks and de Sitter causets are asymptotically identical. (5)

Kwapien, Jaroslaw and Stanislaw Drozdz. Physical Approach to Complex Systems. Physics Reports. 515/3-4, 2012. By virtue of this 153 page treatise, Kwapien, Complex Systems Theory Group, Polish Academy of Sciences, and Drozdz, Institute of Computer Science, Cracow University of Technology, could be fairly seen to broach a 21st cosmic revolution from the homeland of Nicolai Copernicus. A retrospective of the nonlinear sciences is now possible, as the authors accomplish, of their incipient occasion in the 1980s, wide divergence through the 1990s and early 2000s, to their convergent clarification. A case is made that physics, with its quest for fundamental theories and laws, is well suited for this task. From this vantage can be viewed, often in local terms and emphasizing certain aspects, how each dedicated field of nature and society from galaxies to Gaia, has reinvented themselves by way of a dynamical, integral emergence. This is treated by first citing prime attributes such as self-organization, criticality, hierarchical structure, scale invariance, nested networks, fractal geometries, and so on. So put, their presence can be drawn from and exemplified by, for example, quantitative linguistics, financial markets, and the “archetypal” human brain. All of which, one might muse, implies a radically different creative cosmos.

These expansive studies over past years could be seen to sort into two phases or methods. Much of the work was to find evidences of complex phenomena, as noted, in each realm and stage from cosmos to civilization, as this website documents. From these advances could then be distilled, by obvious inference, a common, independent, source. Apropos, I visited the Santa Fe Institute in 1987, heard a talk by Harold Morowitz, with Stuart Kauffman in the audience, when its incentive was the grail hope of uncovering and deciphering such a natural, reliable consistency. This proved elusive over intervening years as work fractionated but from 2005 on, merging with statistical physics, a universal recurrence of much depth and breath has been achieved. This paper is strong theoretical statement in regard, auguring an epochal discovery by humankind of nature’s implicate, creative agency, revealed by its ubiquitous manifestation. A large next step, within a natural genesis universe, is to perceive all this phenomena as a cosmic to children Genetic Code.

Typically, complex systems are natural or social systems which consist of a large number of nonlinearly interacting elements. These systems are open, they interchange information or mass with environment and constantly modify their internal structure and patterns of activity in the process of self-organization. However, the most striking property of such systems is the existence of emergent phenomena which cannot be simply derived or predicted solely from the knowledge of the systems’ structure and the interactions among their individual elements. This property points to the holistic approaches which require giving parallel descriptions of the same system on different levels of its organization. There is strong evidence - consolidated also in the present review - that different, even apparently disparate complex systems can have astonishingly similar characteristics both in their structure and in their behaviour. One can thus expect the existence of some common, universal laws that govern their properties. (Abstract, 1)

Now based on the phenomenon of emergence we may formulate a working definition of a complex system; this definition will be used throughout the present work. According to it, a complex system is a system built from a large number of nonlinearly interacting constituents, which exhibits collective behavior and, due to an exchange of energy or information with the environment, can easily modify its internal structure and patterns of activity. (3) In this section we shall review a few of the most characteristic properties of the structure and behaviour of the systems which are commonly referred to as complex. Presenting such a review is possible because of the fact that complex systems differing in morphology, being built from distinct elements on a microscopic level, and even occupying of the hierarchical organization of matter can exhibit amazingly similar macroscopic structure and also similar behaviour in specific situations. This may constitute a manifestation of universality of the physical phenomena underlying existence of such systems. (6)

Scale Invariance. There is another common property of complex systems which is related to the hierarchical structure discussed above: a lack of characteristic scale. This means that both the structure of, and processes taking place inside such systems are the same over a broad range of spatial and temporal scales. (11)

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)

Mandal, Niladri, et al. A molecular origin of non-reciprocal interactions between interacting active catalysts. Chem. 10/4, 2024. In this Cell Press journal, Penn State and University of Maine (R. Dean Astumian) biophysicists add explanatory reasons for the apparent innate propensity of flowing material systems (microbes, swarms) to take on an organized liveliness of their own. In addition, these phenomena seem to possess autocatalytic features. See also Self-organization of primitive metabolic cycles due to non-reciprocal interactions at arXiv:2303.09832 for a similar analysis. Altogether a natural presence of a biological, self-making spontaneity becomes deeply quantified.

Non-reciprocal interactions are ubiquitous in the living world. These interactions occur as an apparent violation of Newton’s third law of equal and opposite reaction to every action and are responsible for several phenomena including flocking of birds and swarming of fish. Our work suggests that nonreciprocity is not limited to complex and evolved life forms but can occur in systems where external forcing agents are absent. These interactions could have self-originated in the very beginning of life in the absence of information-coding when variations in the physical and chemical environments must have played a critical role in the matter-to-life transition. (Big Picture)

Recent work suggests that nonreciprocal interactions are universally present in living systems and constitute an important part of active matter. Here we elucidate how thermodynamic disequilibrium gives rise to non-reciprocal interactions in molecular systems where the individual molecules remain in mechanical equilibrium. We use a kinase/phosphatase enzyme pair as an illustrative example and show that non-reciprocal interactions between the two arise due to diffusion and kinetic asymmetries in the presence of self-generated substrate and product gradients. (Abstract excerpt)

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)

Previous   1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10  Next