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

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

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)

Jusup, Marko, et al. Physics Of Metabolic Organization. Physics of Life Reviews. 20/1, 2017. Mathematical biologists from Japan, Portugal, and Croatia scope out the pursuit of a deeper rooting and common cause of life within physical and energetic phenomena. Along with 14 peer comments, the integrative project appears on its way, which hints of universalities such as the von Bertalanffy growth curve.

Karamouzas, Ioannis, et al. Universal Power Law Governing Pedestrian Interactions. Physical Review Letters. 113/238701, 2014. It is worth notice, as this letter by University of Minnesota and Argonne National Laboratory physicists exemplifies, how often statistical mechanics is being applied to a widest range of phenomena and occasions. A result is the discovery of a constant recurrence in kind from physical substrates to social commerce. In this case a deeper mathematics is found to guide even our walk and talk.

Human crowds often bear a striking resemblance to interacting particle systems, and this has prompted many researchers to describe pedestrian dynamics in terms of interaction forces and potential energies. The correct quantitative form of this interaction, however, has remained an open question. Here, we introduce a novel statistical-mechanical approach to directly measure the interaction energy between pedestrians. This analysis, when applied to a large collection of human motion data, reveals a simple power-law interaction that is based not on the physical separation between pedestrians but on their projected time to a potential future collision, and is therefore fundamentally anticipatory in nature. Remarkably, this simple law is able to describe human interactions across a wide variety of situations, speeds, and densities. We further show, through simulations, that the interaction law we identify is sufficient to reproduce many known crowd phenomena. (Abstract)

Katsnelson, Mikhail, et al. Towards Physical Principles of Biological Evolution. Physica Scripta. 93/4, 2018. An entry in a Focus Issue on 21st Century Frontiers (search Lidstrom) by MK, Radboud University along with Yuri Wolf and Eugene Koonin, National Center for Biotechnology Information. While the traditional realms of inorganic and organic have long been apart, seemingly unbreachable, nowadays a robust (re)unification at last seems possible. A first step is to allow the very idea and integration at all. As often, it will involve a clarification of concepts and definitions, such as a thermodynamic basis for population genetic, along with affinities to the major evolutionary transitions scale. Another convergence might be spin-glass complexity theories with life’s emergence from proteins to organisms and the biosphere. The presence of “percolation effects and criticalities,” and natural selection as “measurement” is also suggested. Another version of this paper, Physical Foundations of Biological Complexity, appears in the Proceedings of the National Academy of Sciences (115/E8678, 2018, also at arXiv:1803.0997).

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in 'emergent phenomena'. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. (Abstract excerpt)

Biological evolution by no means defies any laws of physics but the emergent biological phenomena appear to call for extension of physics itself. Biological entities and their evolution do not simply follow the ‘more is different’ principle but, in some respects, appear to be qualitatively different from non-biological phenomena, indicative of distinct forms of emergence that require new physical theory. Following the analogy outlined above, in biology as inphysics, measurement generates the arrow of time and necessitates evolution. However, biological evolution has substantial special features, some of which we tried to capture here, in particular, by applying concepts of condensed matter physics, such as frustration and percolation, to central processes of biological evolution. Evidently, tn analysis and discussion presented here are only prolegomena to the sustained, concerted effort which is required to unite biology and physics. (9-10)

Klopper, Abigail. Physics of Living Systems. Nature Physics. July, 2018. An editor introduces an Insight collection on this current, vital synthesis of figure and ground as it gains collaborative veracity. The entries include Biophysics Across Time and Space by Ewa Paluch, Ethology as a Physical Science by Andre Brown and Ben de Bivort, Mesoscale Physical Principles of Collective Cell Organization by Joe Chin-Hun Kuo, et al and The Physics of Cooperative Transport in Ants by Ofer Feinerman, et al.

Klotsa, Daphne. As Above, So Below, and also in Between: Mesoscale Active Matter in Fluids. Soft Matter. 15/8946, 2019. After a decade of diverse particle (molecules, colloids, microbes, swimmers) studies, a University of North Carolina biomaterials physicist extends the approach onto macro systems such as bird flocks, insect swarms and whale pods. By so doing, it is found that the same phenomena can be observed at each and every wide scale and instance. Into the 21st century this traditional adage can gain its worldwise quantification. See also The Most Active Matter of All by Nicholas Ouellette in the new Cell Press journal Matter (1/2, 2019, third quote).

Living matter, such as biological tissue, can be viewed as a nonequilibrium hierarchical assembly, where self-driven components come together by consuming energy to form increasingly complex structures. The remarkable properties of such living or “active-matter” systems have prompted these questions: (1) do we understand the biology and biophysics that give rise to these properties? (2) can we achieve similar functionality with synthetic active materials? Here we study active matter in liquids and gases for aquatic and avian movements with finite inertia and expect collective behavior to emerge by way of nonlinearities and many-body interactions. The organisms/particles can become quite complex leading to flocking states and nonequilibrium phase transitions. (Abstract edits)

Nature has perfected obtaining robust collective behavior and global order from simple local interactions. The challenge for us is to engineer similar systems at various scales that are composed of many agents, ranging from self-propelled nanoparticles in solution to cars in traffic, and to be able to control their emergent collective properties, their emergent “intelligence.” Our group does computational research on active matter and related topics in order to bridge the gap between emergent phenomena, smart materials and robot swarming. (DK lab website)

The term “matter” encompasses everything from molecules to mountains. It also includes living, sentient beings. If matter composes all physical things, and materials science considers the behavior of such things, can materials science describe the most active matter of all? (Ouellette)

Krisnanda, Tanjung, et al. Probing Quantum Features of Photosynthetic Organisms. arXiv:1711.06485. We cite this entry by theoretical physicists from Singapore and the UK including Chiara Marletto and Vlatko Vedral to emphasize a current cross-integration and fertilization of macro-classical and micro-quantum phases. Its opening sentence is There is no a priori limit on the complexity, size or mass of objects to which quantum theory is applicable. If to observe, a worldwise sapiensphere is well on her/his way to finally, actually expressing a unified, animate, genesis universe.

Recent experiments have demonstrated strong coupling between living bacteria and light. Here we propose a scheme to infer quantumness of the light-bacteria correlations, as characterised by the presence of quantum discord, without requiring any knowledge of their mutual interactions, and by measuring only the light's degrees of freedom. This is achieved by monitoring the dynamics of the entanglement between few optical modes (probes) that interact independently with the bacteria. When the (light-sensitive part of) bacterium is modelled as a collection of two-level atoms we find that the steady state entanglement between the probes is independent of the initial conditions, is accompanied by entanglement between probes and bacteria, and provides independent evidence of the strong coupling between them. (Abstract)

Le Bihan, Denis. Is the Brain Relativistic?. arXiv:1908.04290. The senior French philosophical neuroscientist is posted at NEUROSPIN: From Physics to the Human Brain, a CEA Parisian research and clinical project, especially for autism studies, by way of novel intense field imaging techniques. In search of a broader natural context of service to cerebral research, the author notes that while cosmic physics has a conceptual basis, a global theory of the working brain to account for cognition, behavior, and consciousness does not exist. A sense of a deep affinity between our human faculty and the extant universe informs the text, as the second and third quotes allude. Neural network theories are engaged, along with genetic (alphabetic) factors in a connectome mode, along with synaptic pruning and visual capacities. As this imaginative rooting goes forward, we visit quantum phenomena, Minkowski diagrams, hyperspace geodesics, and more to show how akin a vital universe and our microcosmic human acumen might actually be. Thus the paper closes with the thought:To paraphrase (physicist) J. A. Wheeler one may conclude that brain spacetime tells activity how to flow while activity tells brain spacetime how to curve. (29)

Due to the large body of knowledge which neuroimaging has achieved over the last three decades, we have gained a fresh view of the brain which could help us make predictions for new imaging instruments to come, such as ultra high field MRI. By doing so, switching back and forth between physics and neurobiology, we come to a sense that time and space in the brain, as in the Universe, are, indeed, tightly mingled, and could be unified through a brain 'spacetime'. Thinking about a speed limit for action potentials flowing along myelinated axons led us to envision a 4-dimensional brain spacetime which holds to a relativistic pseudo-diffusion principle and functional curvature governed by brain activity, in a similar way gravitational masses give our 4-dimensional Universe spacetime its curvature. (Abstract excerpts, edits).

In consideration of neuroimaging achievements over the last 3 decades we thought that we could perhaps look at the brain with a fresh view which could unveil those “old” things in a new framework. By doing so, switching back and forth between physics and neurobiology, we came across the view that time and space in the brain, as in the Universe, were, indeed, tightly mingled, and might fade away to be unified through a brain “spacetime”. Further thinking led us to realize that this 4-dimensional brain spacetime would obey a kind of relativistic principle and present a functional curvature generated by brain activity, in a similar way gravitational masses give our 4-dimensional Universe spacetime its curvature. We then looked at how this whole-brain framework may shed light on clinical observations of dysfunctions and disorders. (2, edits)

Following the arguments developed above one should not find it objectionable, we hope, that the brain may be viewed in some way as a physical “object” embedded in a 4D enclosure. As such, the brain which is part of the Universe must obey Universephysical laws. After all, the perceptionwe have of the external world, the Universe, comes from our internal world, that is our mind in our brain, and it should not come as a surprise that our understanding of the Universe and our brain are irremediably connected. Hence, considering that the brain represents a kind of Universe itself one may envision how physical laws could be revisited, directly or through analogical derivations to provide a framework useful to better represent and perhaps understand how the brain works as a whole system. (10)

Lee, Chiu Fan and Jean David Wurtz. Novel Physics Arising From Phase Transitions in Biology. Journal of Physics D. 52/2, 2019. In a Special Issue on Collective Behaviour of Living Matter, Imperial College London bioengineers enter another example of the current synthesis of physical phenomena with living systems via a formative agency whence life transitions in kind through serial evolutionary and developmental phases. Thus, universal behaviors previously noted at condensed matter critical points can likewise be seen to occur in biological activities. A further aspect is that many free, contingent entities are yet seen to give rise to an overall coherence. By turns, as worldwide physical and biological sciences cross-inform, a unitary organic procreative ecosmos gains a revolutionary veracity. The work merited notice in Nature Physics (Jan. 2019) as Biological Transitions by Mark Buchanan. Also in this issue, e.g., see Phase Transitions in Huddling Emperor Penguins, Density Distributions and Depth in Flocks, and Emergence of Cooperativity in a Model Biofilm in this collection. See also Physical Principles of Intracellular Organization via Active and Passive Phase Transitions by Joel Berry, et al in Reports on Progress in Physics (81/4, 2018). The third quote is the Issue proposal by Ben Fabry, et al.

Phase transitions, such as the freezing of water and the magnetisation of a ferromagnet due to temperature changes, are familiar physical phenomena. Lately, such collective behaviours at a phase transition are similarly found in effect for living systems. From cytoplasmic organisation inside a cell to the migration of cell tissue during development, phase transitions have emerged as key mechanisms underlying many biological processes. However, a living system is fundamentally different from a thermal system, with metabolism and motility being two hallmarks of its nonequilibrium nature. In this review, we will discuss how such driven chemical reactions can arrest universal coarsening kinetics expected from thermal phase separation, and how motility leads to the emergence of a novel universality class when the rotational symmetry is spontaneously broken. (Abstract edits)

Collective phenomena are intimately linked to the phenomenon of phase transitions in physics. At a typical phase transition, a many-body system with constituents that interact only locally with their neighbours, be they molecules or living organisms, can collectively change their behaviour upon change of a single parameter, such that the universal behaviour is modified. By universal, we mean that certain properties of the system are independent of the microscopic details. Recently, phase transitions in living systems have come under attention, whence the generic non-equilibrium nature of biological systems gives rise to novel collectivities not seen before. (1)

Biological systems are becoming primarily known as networks of interacting genes and proteins. Yet a simple analysis of fundamental genetic programs fails to explain higher-level functions such as multi-cellular aggregation, tissue organization, embryonic development, and whole-scale behaviour of groups of individuals. Such collective processes are often insensitive to microscopic details of the underlying system and instead are emergent properties that arise from local interactions between cells or individuals. In recent years, novel theoretical and experimental approaches have spurred the development of statistical models of complex biological systems and generated much progress in our understanding of emergent collective processes in biology. (Issue Summary)

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