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

2. A Consilience as Physics, Biology and People Become One

Freeman, Walter, et al. Brain Dynamics, Chaos and Bessel Functions. Journal of Physics: Conference Series. 626/012069, 2015. A paper presented at the 7th International Workshop on Spacetime – Matter – Quantum Mechanics, September 2014, Castiglioncello, Italy. Walter Freeman is a UC Berkeley systems neuroscientist, now 88 years young, a third generation of a legendary family of brain researchers and physicians. Coauthors are Antonio Capolupo, Robert Kozma, Andres Olivares del Campo and Giuseppe Vitiello. (Bessel functions are complex differential equations, please Google.) We cite in this section for its representation of neural qualities in statistical physics and mathematical terms, which can show how much our own brains and thought are rooted in and a continuance of this cosmic cerebral essence. See also arXiv:1506.04393 for more.

A paper presented at the 7th International Workshop on Spacetime – Matter – Quantum Mechanics, September 2014, Castiglioncello, Italy. Walter Freeman is a UC Berkeley systems neuroscientist, now 88 years young, a third generation of a legendary family of brain researchers and physicians. Coauthors are Antonio Capolupo, Robert Kozma, Andres Olivares del Campo and Giuseppe Vitiello. (Bessel functions are complex differential equations, please Google.) We cite in this section for its representation of neural qualities in statistical physics and mathematical terms, which can show how much our own brains and thought are rooted in and a continuance of this cosmic cerebral essence. See also arXiv:1506.04393 for more.

Frey, Erwin and Tobias Reichenbach. Bacterial Games. Meyer-Ortmanns, Hildegard and Stefan Thurner, eds. Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Berlin: Springer, 2011. Ludwig-Maximilians-Universitat biophysicists view communal bacteria as an exemplar of interactive agent, nonlinear self-organization, to which an “evolutionary game theory” such as public goods games can then contribute. All this on-going phenomena is further seen as a facet of a “nonequilibrium physics.”

Microbial laboratory communities have become model systems for studying the complex interplay between nonlinear dynamics of evolutionary selection forces, stochastic fluctuations arising from the probabilistic nature of interactions, and spatial organization. Major research goals are to identify and understand mechanisms that ensure 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 conceptual framework for a deeper understanding of these ecological systems. We give an introduction to the modern formulation of these theories and illustrate their effectiveness, focusing on selected examples of microbial systems. (297)

Microbial systems are complex assemblies of large numbers of individuals, interacting competitively under multifaceted environmental conditions. Bacteria often grow in complex, dynamical communities, pervading the earth’s ecological systems, from hot springs to rivers and the human body. (298) The ensuing complexity of bacterial communities has conveyed the idea that they constitute “social groups,” where the coordinated action of individuals leads to various kinds of system-level functionalities. (298)

Gadiyaram, Vasundhara, et al. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. arXiv:1912.11609. Indian Institute of Science, Karnataka and University of Illinois, Urbana researchers provide a good example of the present integrative frontiers as 2020 science fulfills its stage of common unification from universe to humankinder.

This perspective presents a multidisciplinary characterization of protein structure networks. Our approach will be to synthesize concepts from quantum chemistry, polymer conformations, matrix mathematics, and percolation theory. We then construct protein networks in terms of non-covalently interacting amino acid side chains and to distill information from their graph spectra such as structural integrity. In conclusion, we suggest a further unifying approach to protein structure analyses for larger, more complex networks, such as metabolic and disease networks. (Abstract excerpt)

Garcia-Ojalvo, Jordi and Alfonso Martinex Arias. Towards a Statistical Mechanics of Cell Fate Decisions. Current Opinion in Genetics and Development. 22/6, 2012. In a special issue on the Genetics of System Biology (Briscoe), Pompeu Fabra University, Barcelona, and Cambridge University, UK biomedical researchers offer another example of affinities between biological and physical phenomena. By these insights, cellular dynamics can take on the guise of universal, critical phase transitions. A graphic image is used to depict parallels between the title domains. A notable surmise is that in both cases a stochastic variability on a micro level – say molecules or cells – will average out to a predictable macroscopic order. See also a cited paper Origin and Function of Fluctuations in Cell Behaviour and the Emergence of Patterns by Ana Mateus, et al in Seminars in Cell & Developmental Biology (20/877, 2009).

The spatiotemporal organization of a developing organism requires carefully orchestrated sequences of cellular differentiation events. These events are triggered by decisions made by individual cells about their fate, which are in turn controlled by gene and protein regulation processes. While these cell fate decisions are subject to stochasticity and are not reproducible at the single-cell level, they result in highly consistent, almost deterministic patterns at the level of the whole cell population. The question of how this macroscopic order arises from a disordered microscopic behaviour is still outstanding, and is reminiscent of problems in physical systems that are readily addressed by statistical mechanics. (Abstract)

Geyer, Delphine, et al. Freezing a Flock: Motility-Induced Phase Separation in Polar Active Liquids. Physical Review X.. 9/031043, 2019. University of Lyon and University of Paris researchers including Denis Bartolo deftly perceive in their experimental setup how particulate densities in a flowing stream seem to exhibit their an inherent propensity to transform into more organized groupings. The work merited an editorial Viewpoint: A Crowd Freezes Up which highlights deep affinities between physics and people.

Combining experiments and theory, we investigate the dense phases of polar active matter beyond the conventional flocking picture. We show that above a critical density flocks assembled from self-propelled colloids arrest their collective motion, lose their orientational order, and form solids that actively rearrange their local structure while continuously melting and freezing at their boundaries. We argue that the suppression of collective motion in the form of solid jams is a generic feature of flocks assembled from motile units that reduce their speed as density increases, a feature common to a broad class of active bodies, from synthetic colloids to living creatures. (Abstract)

Gilpin, William and Marcus Feldman. A Phase Transition Induces Chaos in a Predator-Prey Ecosystem with a Dynamic Fitness landscape. PLoS Computational Biology. July, 2017. A Stanford University physicist and a biologist contribute to later 2010s rootings of life’s creaturely development and eco-activities into a naturally conducive cosmos. As the Abstract cites, by this view statistical physical phenomena are manifestly in effect in evolutionary and environmental processes.

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the “edge of chaos” while creating a wide distribution of opportunities for speciation during epochs of disruptive selection. (Abstract)

Goldenfeld, Nigel and Carl Woese. Life is Physics: Evolution as a Collective Phenomenon Far from Equilibrium. Annual Review of Condensed Matter Physics. Volume 2, 2011. This extensive paper by a University of Illinois biophysicist and a microbiologist is one of the strongest statements of a much overdue reunion of these physical and animate realms. Carl Woese (1928-2012) was a premier biological theorist of the past half century. Credits say the paper was also vetted by Freeman Dyson, Barbara Drossel, James Shapiro, Leo Kadanoff, Michael Deem, and others. While these fields long co-existed as separate, contradictory domains, today as complexity science joins with statistical, many-body concepts, a grand synthesis is at hand. Section headings include Evolution as a Problem in Condensed Matter Physics, The Need for a Physics of Living Systems, Beyond the Modern Synthesis, and Is Evolution Random?. To wit “There is compelling evidence that not only may mutations be non-random, but horizontal gene transfer too need not be random.” As a consequence, more than another theory or model, a creative genesis universe seems on the implied horizon.

Apropos, I heard Nigel Goldenfeld speak at a University of Massachusetts, Amherst, physics colloquium on October 9, 2013 on “Collective Dynamics and Phase Transitions in Early Life: Clues to the Genetic Code.” He indeed advised, two days after the Nobel Prize for the Higgs boson, that “biology is the new condensed matter physics.” As a field that studies collective phenomena, life’s evolution ought to be seen more as an on-going “process.” From an initial regime of “horizontal gene transfer,” the molecular DNA version appears to be in an optimum form. In this physical sense then, a genome can be dubbed an “information-sharing protocol.” Might we imagine closure to a past century of necessary particle, relativity, and quantum phases, which has ran its course, and on cue a 21st century “systems physics” of matter come to life again? Goldenfeld tacitly alluded that life’s common genome is universally suitable because it has manifestly arisen from a conducive cosmos.

This review focuses on evolution as a problem in non-equilibrium statistical mechanics, where the key dynamical modes are collective, as evidenced by the plethora of mobile genetic elements whose role in shaping evolution has been revealed by modern genomic surveys. We discuss how condensed matter physics concepts might provide a useful perspective in evolutionary biology, the conceptual failings of the modern evolutionary synthesis, the open-ended growth of complexity, and the quintessentially self-referential nature of evolutionary dynamics. (Abstract)

With the growing recognition of the importance of collective phenomena in evolution,, but also in ecology, immunology, microbiology and even global climate change, it is timely to assess the extent to which a condensed matter physics perspective—with its unifying principles of collective behavior arising from interactions—can be illuminating in biology. Equally fascinating is the notion that biology may extend the frontier of non-equilibrium physics, revealing principles of self-organization that seem absent in purely physical processes such as pattern formation. (376)

Physics was able to delay serious consideration of collective effects for nearly 300 years, and only in the past 30 years or so has it confronted complex collective phenomena involving multiple scales of space and time, unpredictable dynamics, and large fluctuations. Biology was not so lucky: At its outset, complex phenomena were encountered, but tools were lacking to cope with the difficulty. Rather than abiding by ignorance, a language culture was developed to explain away the conceptual difficulties using guesswork solutions such as “natural selection.” Today the development of sophisticated technology has allowed biology to take refuge in single-molecule biophysics, genomics, and molecular biology. But the stultifying language culture still remains. This sanctuary is an illusionary respite: The core problems of biology remain irksome to some and are inextricably interwoven with evolution. Indeed, the very existence of biological phenomena is an expression of physical laws that represent a new asymptotic realm in nonequilibrium statistical physics. (392)

Hakim, Vincent and Pascal Silberzan. Collective Cell Migration: A Physics Perspective. Reports on Progress in Physics. 80/7, 2017. CNRS Research University, Paris biophysicists quantify how individual cells actually abide and move in a cohesive group phase manner.

Cells have traditionally been viewed either as independently moving entities or as somewhat static parts of tissues. However, it is now clear that in many cases, multiple cells coordinate their motions and move as collective entities. Well-studied examples comprise development events, as well as physiological and pathological situations. Different ex vivo model systems have also been investigated. Several recent advances have taken place at the interface between biology and physics, and have benefitted from progress in imaging and microscopy, from the use of microfabrication techniques, as well as from the introduction of quantitative tools and models. We review these interesting developments in quantitative cell biology that also provide rich examples of collective out-of-equilibrium motion. (Abstract)

Harder, Malte and Daniel Polani. Self-Organizing Particle Systems. Advances in Complex Systems. 16/2, 2013. Adaptive Systems Research Group, University of Hertfortshire computer scientists contribute another example of scientific reevaluations of the nature of cellular biology by way of the prior activity of self-organizing physical and informational processes.

The self-organization of cells into a living organism is a very intricate process. Under the surface of orchestrating regulatory networks there are physical processes which make the information processing possible, that is required to organize such a multitude of individual entities. We use a quantitative information theoretic approach to assess self-organization of a collective system. In particular, we consider an interacting particle system, that roughly mimics biological cells by exhibiting differential adhesion behavior. Employing techniques related to shape analysis, we show that these systems in most cases exhibit self-organization. Moreover, we consider spatial constraints of interactions, and additionally show that particle systems can self-organize without the emergence of pattern-like structures. However, we will see that regular pattern-like structures help to overcome limitations of self-organization that are imposed by the spatial structure of interactions. (Abstract)

Hauser, Marcus and Lutz Schimansky-Geier. Statistical Physics of Self-Propelled Particles. European Physical Journal Special Topics. 224/7, 2015. Otto von Guericke University, and Humboldt University biophysicists introduce an issue on realizations of a natural materiality that seems to exhibit biological behaviors. Papers include Active Particles in Heterogeneous Media Display New Physics, and The Unlikely High Efficiency of a Molecular Motor Based on Active Motion.

Heffern, Elleard, et al. Phase Transitions in Biology: From Bird Flocks to Population Dynamics. Proceedings of the Royal Society B. October, 2021. We note this entry by University of Missouri physicists and biologists including Sonya Bahar provide a good example of the robust, self-similar fulfillments of a wide-ranging universe to us dynamic complexity network revolution which is just now possible, and well underway.

Phase transitions from one condition to another are a significant concept in physical reality. Insights derived from many past studies are lately being well applied to diverse phenomena in living systems. We provide a brief review of phase transitions and their new role in explaining biological processes from collective behaviour in animal flocks to neuronal firings in cerebral activity. We also highlight a novel area of their presence in population collapse and extinction due to climate change or microbial responses to antibiotic treatments. (Abstract)

Hirst, Linda. Active Matter in Biology. Nature. 544/164, 2017. A UC Merced biophysicist comments on a research paper, Topological Defects in Epithelia Govern Cell Death and Extrusion, by Thuan Beng Saw, et al in the same issue about fertile interconnections between condensed matter theories and living systems, aka soft matter and human beings.

Saw and colleagues’ study demonstrates how the physics of soft matter can contribute to a deeper understanding of biological systems. The authors show that compressive stresses
induced by orientational ordering and defects in the epithelium provide a physical trigger for cell death. What makes this paper particularly exciting is its resonance with an emerging field in condensed-matter physics: active matter. (164) There are many examples of active matter in nature, ranging from flocks of birds and insect swarms to cells and combinations of biopolymers and molecular motors. The unifying theme is that collections of subunits (birds, cells, biopolymers, and so on) take in energy locally, and then translate that energy into movement that can, in turn, produce large-scale dynamic motion. Internal motion throughout an active material can also result in the formation of emergent dynamic structures, including topological defects at which local order breaks down. (164)

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