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

2. A Consilience as Physics and Biology Grow Together: Active Matter

Wright, Katherine. Life is Physics. physics.aps.org/articles/v12/2. Physicists are on the hunt for a “theory of life” that explains why life can exist. A senior editor for the American Physical Society (APS)reviews the many ways this historic re-convergence and theoretical closure is underway in our midst as biology and physics, vibrant life and material animations become one again.

(Ramin) Golestanian and (Nigel) Goldenfeld both believe that the traits of life, such as replication, evolution, and using energy to move, are examples of what condensed-matter physicists call “emergent phenomena”—complex properties that arise from the interactions of a large number of simpler components. For example, superconductivity is a macroscopic property that arises in metals from attractive interactions among its electrons, which lead to a state with zero electrical resistance. In the case of life, the emergent behaviors arise from interactions among molecules and from how the molecules group together to form structures or carry out functions.

Xue, Chi, et al. Scale-invariant Topology and Bursty Branching of Evolutionary Trees Emerge from Niche Construction. Proceedings of the National Academy of Sciences. 117/7679, 2020. University of Illinois genome biologists including Nigel Goldenfeld provide an exercise to show how, by way of statistical physics and network principles, that life’s circuitous, diverse, adaptive course can yet be found to have an intrinsic, self similar topology.

Phylogenetic trees describe both the evolutionary process and community diversity. Recent work has established that they exhibit scale-invariant topology, which quantifies the fact that their branching lies in between balanced binary trees and maximally unbalanced ones. Here, we present a simple, coarse-grained statistical model of niche construction coupled to speciation. Finite-size scaling analysis of the dynamics shows that the resultant phylogenetic tree topology is scale-invariant due to a singularity arising from large niche construction fluctuations that follow extinction events. The same model recapitulates the bursty pattern of diversification in time. (Abstract)

Yukalov, Vyacheslav. Selected Topics of Social Physics: Nonequilibrium Systems. arXiv:2307.10833. The author is a senior complexity expert (search) who was at ETH Zurich in collaboration with Didier Sornette and is now jointly at the Bogolubov Laboratory of Theoretical Physics, Dubna, Russia and the University of Sao Paulo, Brazil. Three main sections are Dynamical Social Systems, Generalized Evolution Equations and Models of Financial Markets. See also Quantum Operation of Affective Artificial Intelligence by YY at 2305.08112. In many formats, we record a growing realization that universe and human from enlivened substance to political populace are deep (wo)manifestations of implicate codified patterns and processes.

This review article is the second part of the project Selected Topics of Social Physics. The first part has been devoted to equilibrium systems. The present part considers nonequilibrium systems. The style of the paper is a tutorial which makes it easy to read for nonspecialists to grasping the basics of social physics and describes recent original models that could be of interest to experienced researchers in the field. The present material is based on the lectures that the author had been giving during several years at the Swiss Federal Institute of Technology in Zurich (Abstract)

Zeravcic, Zorana, et al. Toward Living Matter with Colloidal Particles. Reviews of Modern Physics. 89/031001, 2017. Zeravcic, CNRS, Paris, with Vinothan Manoharan and Michael Brenner, Harvard, contribute an array of sophisticated insights as physical materiality becomes increasingly imbued with innate organic structures and movements. A persistent tendency to achieve self-replicative and metabolic states is evident. One may add that in turn well infers an animate, procreative ecosmos.

A fundamental unsolved problem is to understand the differences between inanimate matter and living matter. Although this question might be framed as philosophical, there are many fundamental and practical reasons to pursue the development of synthetic materials with the properties of living ones. There are three fundamental properties of living materials that we seek to reproduce: The ability to spontaneously assemble complex structures, the ability to self-replicate, and the ability to perform complex and coordinated reactions that enable transformations impossible to realize if a single structure acted alone. The conditions that are required for a synthetic material to have these properties are currently unknown. This Colloquium examines whether these phenomena could emerge by programming interactions between colloidal particles, an approach that bootstraps off of recent advances in DNA nanotechnology and in the mathematics of sphere packings. (Abstract excerpt)

Zhou, Cangqi, et al. Cumulative Dynamics of Independent Information Spreading Behavior: A Physical Perspective. Nature Scientific Reports. 7/5530, 2017. Tsinghua University, Beijing, information theorists achieve a novel synthesis across these widely apart realms by which to associate our daily social media with natural complexity dynamics. As the quotes allude, an apparent independent, invariant source is implied, more than analogous, which seems in exemplary effect at each stage and instance.

The popularization of information spreading in online social networks facilitates daily communication among people. Although much work has been done to study the effect of interactions among people on spreading, there is less work that considers the pattern of spreading behaviour when people independently make their decisions. By comparing microblogging, an important medium for information spreading, with the disordered spin glass system, we find that there exist interesting corresponding relationships between them. Based on the analogy with the Trap Model of spin glasses, we derive a model with a unified power-function form for the growth of independent spreading activities. Our model takes several key factors into consideration, including memory effect, the dynamics of human interest, and the fact that older messages are more difficult to discover. Our work indicates that, other than various features, some invariable rules should be considered during spreading prediction. (Abstract)

Our work contributes a useful methodology, the analogy with physical systems, for studying human dynamics. The discovered rule, that applies to the growth of different retweeting activities with a unified form, reveals the nature of complexity in retweeting activities. We hope that our work will shed some light on the study of human dynamics. Our work also indicates that, other than various features adopted in well-tuned machine learning models, some invariable rules, such as the power-law growth of independent retweeting activities, the memory effect in human behaviour, should be taken into consideration during the prediction of information spreading. (2)

Zhou, Shuang. Lyotropic Chromonic Liquid Crystals. International: Springer, 2017. The edition is a Kent State University, Liquid Crystal Institute, award-winning doctoral thesis by a physical chemist now at Harvard. Besides clever understandings of nature’s lively materiality, the first chapter notes how such dynamic and topological propensities can be seen to similarly arise and array across emergent groupings of microbes, fish swarms, avian flocks and ungulate herds. he work thus exemplifies current studies as they find deep connections between biological, animal life and increasingly conducive physical substrates. We cite book summary edits, some chemical definitions, and an Abstract from a talk that Zhou gave at UM Amherst in February, 2018.

This thesis describes lyotropic chromonic liquid crystals (LCLCs) with exotic elastic and viscous properties. The first part presents a thorough analysis of LCLCs as functions of concentration, temperature and ionic contents, while the second part explores an active nematic system: living liquid crystals, which represent a combination of LCLC and living bacteria. LCLCs are an emerging class of liquid crystals that have shown profound connections to biological systems in two aspects. First, the process of chromonic aggregation is similar to DNA oligomers and other super-molecular assemblies of biological origin. Second, LCLCs are biocompatible, serving as a unique anisotropic matrix to interface with living systems. (Abstract excerpts and edits)

In this talk, I will introduce a new active matter system, called living liquid crystals, which combine lyotropic chromonic liquid crystals with living bacteria Bacillus Subtilis. Such system offers independent control of the orientational order – through the nematic liquid crystal, and activity – through the concentration of bacteria and oxygen. The long range nematic order profoundly changes the particle-particle and particle-fluid interactions, and results in a wealth of intriguing phenomena, such as 1) controlling bacteria trajectories through liquid crystal director field, 2) optical visualization of the motion of nanometer-thick bacteria flagella, 3) local melting of the liquid crystal by bacteria flow, 3) cargo particle transportation, 4) bend instability, and 5) low Reynolds number turbulence, among others. Living liquid crystals provide a unique angle to understand active matters physics from particle level to macroscopic level. (Abstract excerpts)

Liquid crystals (LCs) are matter in a state which has properties between those of conventional liquids and those of solid crystals. For instance, a liquid crystal may flow like a liquid, but its molecules may be oriented in a crystal-like way. Lyotropic LCs exhibit phase transitions as a function of both temperature and concentration of the liquid-crystal molecules in a solvent. Nematic denotes a state of a liquid crystal in which the molecules are oriented in parallel but not arranged in well-defined planes.

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