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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Incubator Lifescape

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

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)

Gompper, Gompper, Gerhard, et al. The 2019 Motile Active Matter Roadmap. Journal of Physics: Condensed Matter. 32/29, 2020. This is a broadly European state of the art collection for this fluid field, which is hardly a decade old. As the quotes note, some 40 researches post papers such as Active Brownian Particles: From Collective Phenomena to Fundamental Physics by Thomas Speck, Self-organized Collective Patterns by Fernando Peruani, and Patterns of Collective Motion in Huge Flocks of Starlings by Charlotte Hemelrijk. Its popularity and expansive subject increasingly attest to an animate, lively natural materiality.

Activity and autonomous motion are fundamental in living and engineering systems. The new field of active matter now focuses on the physical aspects of propulsion mechanisms, and on motility-induced collective behavior of a larger number of member agents. The scale ranges from microswimmers to cells, fish, birds, and people. A major challenge for understanding and designing active matter is their nonequilibrium nature due to persistent energy consumption. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active systems comprises a major challenge. Hence, going forward this important research area requires a concerted, synergetic, interdisciplinary approach. (Abstract excerpt)

Active matter is a novel class of nonequilibrium systems composed of a large number of autonomous agents. The scale of agents ranges from nanomotors, microswimmers, and cells, to crowds of fish, birds, and humans. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. Recent progress in experimental and simulation methods, and theoretical advances, now allow for new insights into this behavior, which should ultimately lead to the design of novel synthetic active agents and materials. This Roadmap provides an overview of the state of the art, and discusses future research directions on natural and artificial active agents, and their collective behavior. (Gerhard Gompper, Roland Winkler, 3)

Hagan, Michael and Aparna Baskaran. Emergent Self-Organization in Active Materials. Current Opinion in Cell Biology. 38/74, 2016. For the record, we ought to note that just a decade ago, as earlier entries show, a evidential recognition of such cellular spontaneity was rare and in abeyance. Here Brandeis University physicists provide a 2017 example of its common acceptance as metabolic physiology and anatomy becomes an exemplar of nonlinear complexity.

Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically driven nonequilibrium materials, with emergent properties comparable to those of living systems. This review will describe two recently developed classes of active matter systems, in which simple building blocks — self-propelled colloidal particles or extensile rod-like particles — self-organize to form macroscopic structures with features not possible in equilibrium systems. We summarize the recent experimental and theoretical progress on each of these systems, and we present simple descriptions of the physics underlying their emergent behaviors. (Abstract)

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)

Hallatschek, Oskar, et al. Proliferating Active Matter. Nature Reviews Physics. May, 2023. Some 15 years after this field gained recognition (S. Ramaswamy), UC Berkeley, Leipzig University, University of Basel, MIT, University of Edinburgh, and Princeton University researchers including Ned Wingreen provide an extensive, 200 reference survey of a wealth of evidence across all manner of physical and biological phases such as particulate, colloidal, cellular flows and even avian flocks to acquire their own self-organized patterns and processes. Once more in mid 2023 a robust, organic integrity becomes well established.

Active matter locally dissipates energy to produce systematic motion. This Perspective highlights proliferation as a special type of activity that breaks particle number conservation and thereby gives rise to a unique set of collective phenomena characteristic of life. (editor)

The patterns of collective motion created by autonomous particles have fuelled active-matter research for two decades. But so far these studies have focused on candidate entities. In reality, living systems involve the growth and evolution of microbial biofilms, expansion of a tumour, the development from a fertilized egg into an embryo. Here we argue that unique features emerge because proliferation represents a distinct activity that consumes and dissipates energy, injects biomass, and leads to myriad dynamic scenarios. Complex, collective phenomena in these soft-matter phases moves us to propose expansive generation as another direction of active-matter physics, worthy of new dynamical universality classes. (Abstract edits)

Examples of Active Matter Proliferation: Growing cells, shapes and populations have often been studied in mathematical biology at a meanfield level so to observe phenomena in microbiology, development, ecology, epidemiology, group dynamics and evolution. Several generic model systems of active matter collectives have thus emerged. One prototypical example combining soft matter and growth is provided by microbial biofilms on solid, semisolid or liquid substrates into resilient communities. These surface bacteria are abundant in nature composed either of clonal cells or diverse species. Complex physical properties contribute to their expansive presence, evolutionary success and their
important role in human disease. (5)

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)

Huelga, Susana and Martin Plenio. Vibrations, Quanta and Biology. Contemporary Physics.. 54/4, 2013. University of Ulm, and Center for Integrated Quantum Science and Technologies, Ulm (Albert Einstein’s birthplace), researchers contribute to interlacing “open system, hierarchical, network” affinities between quantum phenomena and lively evolving organisms.

Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme -- the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology. (Abstract)

The clear demonstration that Nature makes use of quantum effects would bring about the necessity for a significant change of thinking for biologists as they would be required to grasp quantum concepts in order to understand some fundamental biological processes. The very same fact would however also present the opportunity to learn from biology by unraveling the mechanisms by which quantum dynamics and its interplay with environments lead to enhanced performance. The resulting design principles have the potential to lead to the development of new applications at the bio-nano scale. (182)

Jarvis, Peter and Jeremy Sumner. Systematics and Symmetry in Molecular Phylogenetic Modeling: Perspectives from Physics. Journal of Physics A. 54/45, 2019. University of Tasmania physicists scope out a broad and deep affinity between entanglement, Markov invariance and other phenomena with life’s mathematically rooted course as the extended Abstract explains. See also Quantum Channel Simulation of Phylogenetic Branching Models by Jarvis and D. Ellinas in this journal (52/11, 2019).

Phylogenetics is the suite of mathematical and computational methods by which biologists infer past evolutionary relationships between observed species. Here we wish to emphasize the many features of multipartite entanglement which are shared between descriptions of quantum states on the physics side, and the multi-way tensor probability arrays arising in phylogenetics. In some instances, well-known objects such as the Cayley hyperdeterminant can be directly imported into the formalism. In other cases new objects appear, such as the remarkable 'squangle' invariants for quartet tree discrimination, which for DNA data are of quintic degree, with their own unique interpretation in the phylogenetic modelling context. All this hints strongly at the natural and universal presence of entanglement as a phenomenon which reaches across disciplines. (Abstract excerpt)

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