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

2. A Consilience Unity 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.

Kadmom, Jonathon. Efficient coding with chaotic neural networks: A journey from neuroscience to physics and back. arXiv:2408.01949. A Center for Brain Sciences, Hebrew University, Jerusalem polythreorist posts his workshop paper as this broadest, integral unification gains credence and comes together into these 2020s. A robust legitimacy is evident as many clarified aspects in both domains are found to readily be assimilated across this widest human to universe to Earthuman expanse.

This essay is derived from my lecture at "The Physics Modeling of Thought" workshop in Berlin in winter 2023. In regard, it explores a mutually beneficial relationship between theoretical neuroscience and statistical physics through the lens of computation in cortical circuits. It highlights how the study of neural networks has enhanced our understanding of complex, nonequilibrium, and disordered systems and how brain research has led to developments in physics such as phase transitions and critical phenomena. (Excerpt)

Workshop on Physics Modeling of Thought This is the first of a series within a four-year program at the MPI History of Science dedicated to this subject. For some years now, the Institute has carried out a historical-critical investigation of the theory and practices of modeling in different scientific realms from fundamental physics to earth systems. The general themes of the workshop include: The Neural Network Paradigm: The Complex and Dynamic Brain, Macro vs. Micro and Space-time Representations.

Kaneko, Kunihiko. Constructing universal phenomenology for biological cellular systems by evolutionary dimensional reduction.. Journal of Statistical Mechanics. February, 2024. A veteran biophysicist with postings at the Niels Bohr Institute, Copenhagen and the University of Tokyo contributes a paper to the STATPHYS 28 meeting held in August 2023 in Tokyo which can serve as another instance of current expansive integral rootings of life’s organismic and development in this conducive, many-body ground. See also Evolutionary accessibility of random and structured fitness landscapes by Joachim Krug and Daniel Oros.

The possibility of a macroscopic phenomenological theory for biological systems, akin to a thermodynamic framework is reviewed. Weround. introduce the concept of an evolutionary fluctuation–response relationship, which highlights the variance between phenotypic traits caused by genetic mutations. The universality of evolutionary dimensional reduction is presented along with theoretical formulations. We conclude with the prospects of a macroscopic basis that conveys biological robustness and irreversibility in cell differentiation. (Excerpt)

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)

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