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

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

Cocco, Simona, et al. Inverse Statistical Physics of Protein Sequences. arXiv:1703.01222. Sorbonne University, Paris, computational theorists post a “Key Issues Review” of humanity’s project, by way of translating and clarifying terms and concepts, to realize nature’s animate and physical systems as a singular, self-conceiving uniVerse.

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. (Abstract)

Coveney, Peter, et al. Bridging the Gaps at the Physics-Chemistry-Biology Interface. Philosophical Transactions of the Royal Society A. Vol. 374/Iss. 2080, 2016. Senior theorists Coveney (search), University College London, with Jean-Pierre Boon, Free University of Brussels, and Sauro Succi, Harvard, introduce a subject issue of papers from an April 2016 Solvay Workshop in Belgium. An opener, Big Data Need Big Theory Too by Coveney, et al, argues that myriad pieces have little worth without a coherent model to make sense of them. Further technical entries are Kinetics and Thermodynamics of Living Copolymerization, Multiscale Simulation of Molecular Processes in Cellular Environments, and Chimera Simulation of Complex States of Flowing Matter. The edition appears concurrently with The Science of Complexity and the Role of Mathematics in the European Physical Journal Special Topics. See also Complex Systems: Physics Beyond Physics by Yurij Holovatch, Ralph Kenna, and Stefan Thurner at arXiv.1610.01002 for another synthesis.

It is commonly agreed that the most challenging problems in modern science and engineering involve the concurrent and nonlinear interaction of multiple phenomena, acting on a broad and disparate spectrum of scales in space and time. It is also understood that such phenomena lie at the interface between different disciplines, such as physics, chemistry, material science and biology. The multiscale and multi-level nature of these problems commands a paradigm shift in the way they need to be handled, both conceptually and in terms of the corresponding problem-solving computational tools. The above phenomena take place far from equilibrium, where the organizing power of nonlinearity is fully exposed and macroscopic universality is compromised by the necessary degrees of microscopic (molecular) individualism. Indeed, the ability to integrate universality and molecular individualism is perhaps the most challenging task of modern multiscale modelling. At the same time, the recent decades have also witnessed substantial progress in the development of modelling methodologies at all scales, including, for example, ab initio molecular dynamics and quantum mechanics/molecular mechanics techniques for atomic and nano-scales, and dissipative particle dynamics for mesoscales, and various grid-based methods for the several macroscales. (Abstract)

De Magistris, Giulio and Davide Marenduzzo. An Introduction to the Physics of Active Matter. Physica A. Online July, 2014. As the Abstract notes, University of Edinburgh physicists offer a tutorial upon the intrinsic dynamics of “active particles,” self-motile systems, hydrodynamics of active gels, and so on.

In these notes we provide an introductory description of the physics of active matter, focusing on theoretical aspects, and on some methods which are often used in the field. We discuss a selection of active systems, where activity comes from different microscopic sources (mainly self-replication, self-propulsion, non-thermal forces), and in all cases we focus on their statistical physics and emergent collective behaviour, which is often linked to underlying nonequilibrium phase transitions. We hope to convey the idea that this field is a fascinating growing area of research at the interphase between statistical, soft matter and biological physics, and that active matter systems can possess, in general, a much richer physics than their passive counterparts. (Abstract)

Deem, Michael. Statistical Mechanics of Modularity and Horizontal Gene Transfer. Annual Review of Condensed Matter Physics. 4/287, 2013. The Rice University biophysicist is a leading advocate of and researcher for the cross-fertilization of these seemingly disparate fields. As an increasing number realize and profess, a newly spontaneous physical matter can join with and serve as a fertile source for emergent biological vitality.

Biological structure organizes over evolutionary timescales. This review discusses the spontaneous emergence of hierarchical structure in biology as a result of environmental change. A body of theoretical and experimental work on evolutionary dynamics is reviewed, and a theory for these results based on a principle of least action is discussed. The structure that has emerged in biology is complementary to a type of evolutionary dynamics known as horizontal gene transfer. How horizontal gene transfer ameliorates the difficulty that finite populations would otherwise have to evolve on rugged fitness landscapes is also discussed. (Abstract)

A pervasive theme in biology is the ubiquity of structured bits of material. This structuring appears at all scales of life. Proteins are comprised of atoms, amino acids, secondary structures, and domains. At yet higher levels of structure, there are multiprotein complexes, pathways, organelles, and cells. Depending on the type of species, there can be a number of further structural levels before the complete individual is reached. Individuals may then form colonies and interact with other species of an ecosystem. (288)

Complementary to this structural hierarchy is a hierarchical database of structured bits of information. This information at least partially encodes the structural features. This hierarchy of genetic material, including nucleic acids, codons, exons, genes, operons, and genomes, maps to a hierarchy of protein structures. There are yet higher levels of information. For example, within a complex species there is information encoded in the physiological state. At the level of populations, the union of all individual genomes is termed the supragenome, and it is often significantly larger than the intersection of all the individual genomes. (387)

Research Interests: Theoretical methods of statistical mechanics are developed and applied at Rice to study the collective properties of biological systems. Both computational and analytical methods are of interest. Natural systems from our world and engineered systems from biotechnology offer a wide variety of phenomena for study. New field-theoretic techniques, new computer simulation methods, and new random energy models have resulted. Current areas of interest include: Newton's laws of biology, Personalized critical care, Physical theories of pathogen evolution. (Deem’s Lab page)

Deng, Pan, et al. The Ecological Basis of Morphogenesis: Branching Patterns in Swarming Colonies of Bacteria.. New Journal of Physics. 16/015006, 2014. In a Focus on the Physics of Biofilms section, Memorial Sloan-Kettering Cancer Center researchers offer another contribution, by way of microbial assemblies, that joins life’s communal developments with physical substrates and mathematical principles. And it is worth noting that this Institute of Physics IOP periodical, as others, contains a good percentage of articles on biological and complexity phenomena, as scientific pursuits now reconverge.

Understanding how large-scale shapes in tissues, organs and bacterial colonies emerge from local interactions among cells and how these shapes remain stable over time are two fundamental problems in biology. Here we investigate branching morphogenesis in an experimental model system, swarming colonies of the bacterium Pseudomonas aeruginosa. We combine experiments and computer simulation to show that a simple ecological model of population dispersal can describe the emergence of branching patterns. In our system, morphogenesis depends on two counteracting processes that act on different length-scales: (i) colony expansion, which increases the likelihood of colonizing a patch at a close distance and (ii) colony repulsion, which decreases the colonization likelihood over a longer distance. The two processes are included in a kernel-based mathematical model using an integro-differential approach borrowed from ecological theory. (Abstract)

This focus issue of New Journal of Physics, devoted to the 'Physics of Biofilms', aims to highlight this research field by collecting selected contributions from leading authors in the field that tackle either physical processes or the coupling of physical and biological processes underpinning biofilm formation. We hope that, by demonstrating the richness of the physics involved in biofilm formation and the importance of understanding them, this focus issue will serve to attract a broad range of researchers from (but not limited to) the fields of soft condensed matter, complex fluids, polymer physics and statistical mechanics, to augment today's interdisciplinary efforts towards understanding and controlling the formation of biofilms. (Overview)

Diaz, Jorge and Roberto Mulet. Statistical Mechanics of Interacting Metabolic Networks. Physical Review E. 101/042401, 2020. A University of Havana systems biologist and a physicist discern an array of affinities between cellular processes and condensed matter as life’s complexity and animate cosmos proceed to reunite and grow together. See also Characterizing Steady States of Genome Scale Metabolic Networks in PLoS Computational Biology (November 2017) and A Physical Model of Cell Metabolism in Nature Scientific Reports (8/8349, 2018) by the authors and colleagues.

We cast the metabolism of interacting cells within a statistical mechanics framework with regard to the phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of spin vectors, whose values are constrained by stochiometry and energy requirements of the metabolism. Within this picture, the phenotypic states of the population are equivalent to the equilibrium states of a disordered spin model. We apply this solution to a simplified model of metabolism and a complex metabolic network, the central core of Escherichia coli, to demonstrate that the combination of selective pressure and interactions defines a complex phenotypic space. Cells may specialize in producing or consuming metabolites, which is described by an equilibrium phase space akin to a spin-glass model. (Abstract excerpt)

Dorogovtsev, Sergei, et al. Critical Phenomena in Complex Networks. Reviews of Modern Physics. 80/4, 2008. Universidade de Aveiro, Portugal physicists provide a detailed tutorial for the evident ubiquity of scale-free nets to persist in a state of self-organized criticality.

Critical phenomena in networks include a wide range of issues: structural changes in networks, the emergence of critical—scale-free—network architectures, various percolation phenomena, epidemic thresholds, phase transitions in cooperative models defined on networks, critical points of diverse optimization problems, transitions in co-evolving couples—a cooperative model and its network substrate, transitions between different regimes in processes taking place on networks, and many others. We will show that many of these critical effects are closely related and universal for different models and may be described and explained in the framework of a unified approach. (1277)

Eckmann, Jean-Pierre, et al. Proteins: The Physics of Amorphous Evolving Matter. Reviews of Modern Physics. 91/031001, 2019. J-P E and Jacques Rougemont, University of Geneva and Tsvi Tlusty, Ulsan National Institute of Science and Technology, post a tutorial paper which traces a pathway by which to join and root life’s biochemical processes within fundamental condensed matter principles. In this computational view, proteins arise from collective many-body interactions in amino acid matter as the outcome of an evolutionary search in a high-dimensional space of gene sequences. In regard, an evolutionary learning process is seen to act as a combinatorial search within an optimization process. See also Physical Model of the Genotype to Phenotype Map of Proteins by the authors with Albert Libchaber in Physical Review X (7/021037, 2017). These and many other insightful efforts are presently revealing a unified, lively ovoGenesis uniVerse.

Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function performed by the protein within a hierarchy of interwoven interaction networks of the cell, the organism and the population. A physical theory of proteins therefore needs to unify both the biophysical and the evolutionary. We review physical approaches by way of a mechanical framework which treats proteins as evolvable condensed matter: Mutations introduce localized perturbations in the gene, which are similarly translated into the protein matter. A natural tool seems to be Green's functions (Wikipedia)as they map the evolutionary linkage among mutations in the gene to cooperative physical interactions among the amino acids. (Abstract excerpt)

England, Jeremy. Statistical Physics of Self-Replication. Journal of Chemical Physics. 139/121923, 2013. A young MIT physicist forges ahead with the persuasion that living systems must be sourced in and explained by nature’s far-from-equilibrium phenomena via thermodynamic energies and entropies. His project received much notice in the online Quanta Magazine in a January 2014 article “A New Physics Theory of Life” by Natalie Wolchover. See also an endorsement Biology and Nonequilibrium by the mathematician David Ruelle in European Physical Journal Special Topics, (224/935, 2015). I heard Jeremy speak at the University of Massachusetts, Amherst in April 2016 on the Statistical Physics of Adaptation (second quote) where he saw his work as a continuance of Ilya Prigogine’s theories, and more recently of Gavin Crooks (search) and other colleagues.

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids. (Article Abstract)

Many-body systems that are driven far from thermal equilibrium can exhibit a seemingly endless range of different "self-organization" phenomena, whether during long periods of transient relaxation over a hierarchy of timescales, or in an ergodic steady-state. Indeed, the range of possible behaviors is so diverse that it includes (but is not limited to) everything that living things do! In the face of such phenomenological diversity, it is difficult to articulate any thermodynamic commonality that might be analogous to the tendency to minimize free energy observed in equilibrated systems. Here, we try to exploit recent fundamental progress in our understanding of far-from-equilibrium dynamics to develop predictive thermodynamic principles for a general class of driven self-organized systems. We find there is a language in which Darwinian selection in biological systems may be thought of as a special case of a more general physical tendency for "dissipative adaptation" that arises from the correlation between irreversible changes in shape and the absorption of external work. (Talk Abstract)

Fleming, Graham, chair. Quantum Effects in Chemistry and Biology. Procedia Chemistry. 3/1, 2011. As the proceedings of this 22nd Solvay Conference on Chemistry, after the 1911 Solvay Conference on Physics that initiated the legendary series. A century later quantum phenomena is being assimilated into these macro domains, at the same time it si rooting, informing and expanding their essence. Notable papers are Quantum Effects in Biology by Fleming, et al, Quantum Effects in Chemistry by Mark Ratner and Ronnie Kosloff, and Quantum Correlations in Biomolecules by Vlatko Vedral.

Fodor, Etienne and M. Cristina Marchetti. The Statistical Physics of Active Matter: From Self-Catalytic Colloids to Living Cells. arXiv:1708.08652. Some seven years since Sriram Ramaswamy (search) recognized and named this facility of organic physiologies to exhibit spontaneous formations traceable to physical forces, Cambridge University and Cornell University researchers provide a tutorial overview with 101 references of the now popular field, aka Soft Matter. I enter a day after hearing Dr. Marchetti speak at the University of Massachusetts, Amherst, second quote, where she reported on their common recurrence over a range of lively movements from tissue cultures and embryogenesis to starling flocks. An independent, universal source thus seems to be implied as interactive elements proceed to dynamically cooperate and self-organize. The third quote is a capsule for her Soft Matter Laboratory.

These lecture notes are designed to provide a brief introduction into the phenomenology of active matter and to present some of the analytical tools used to rationalize the emergent behavior of active systems. Such systems are made of interacting agents able to extract energy stored in the environment to produce sustained directed motion. The local conversion of energy into mechanical work drives the system far from equilibrium, yielding new dynamics and phases. The emerging phenomena can be classified depending on the symmetry of the active particles and on the type of microscopic interactions. We focus here on steric and aligning interactions, as well as interactions driven by shape changes. The models that we present are all inspired by experimental realizations of either synthetic, biomimetic or living systems. Based on minimal ingredients, they are meant to bring a simple and synthetic understanding of the complex phenomenology of active matter. (Abstract)

Collections of self-propelled entities, from living cells to engineered microswimmers, organize in a rich variety of active fluid and solid states, with unusual properties. For instance, active fluids can flow with no externally applied driving forces and active gases do not fill their container. In this talk I will describe the behavior of such “active materials” and highlight two examples of active phase transitions. The first is the formation of cohesive matter with no cohesive forces in collections of purely repulsive active colloids. The second is a new density-independent solid-liquid transition in epithelial tissues controlled by cell motility and a cell-shape parameter measuring the interplay of cortical tension and cell-cell adhesion. An important insight of this work is that cell shape correlates with the mechanical properties of living tissues. (MCM Presentation – U Mass Amherst, Sept. 13, 2017)

Our (MCM) group is interested in the emergent behavior of soft and biological materials that are driven out of equilibrium by an external drive, internal activity or quenched disorder. We use theory and computation to investigate the rich dynamics of a broad range of systems, from vibrated granular matter to bacterial suspensions, the cell cytoskeleton and living tissues. Our work makes complementary use of bottom-up modeling and top-down phenomenology to highlight the role of physical interactions relative to genetically and biochemically- regulated signaling in controlling the large scale structural organization and the mechanical properties of these complex systems. (https://mcmarche.expressions.syr.edu/)

Fort, Hugo. Statistical Mechanics Ideas and Techniques Applied to Selected Problems in Ecology. Entropy. Online December, 2013. A Universidad de la República, Uruguay, physicist and Complex Systems Group leader with international collaborations such as Marten Scheffer, contributes to a recent, growing trend to uncover deep consistencies between condensed matter principles and all areas of life’s organic and social evolution (e.g., search Moretti). In this case, three ecosystem features, as the Abstract explains, can be seen to take on quite similar forms to physical phenomena. By this overdue merger a worldwide systems project begins to reassemble the sciences and a common natural cosmos.

Ecosystem dynamics provides an interesting arena for the application of a plethora concepts and techniques from statistical mechanics. Here I review three examples corresponding each one to an important problem in ecology. First, I start with an analytical derivation of clumpy patterns for species relative abundances (SRA) empirically observed in several ecological communities involving a high number n of species, a phenomenon which have puzzled ecologists for decades. An interesting point is that this derivation uses results obtained from a statistical mechanics model for ferromagnets. Second, going beyond the mean field approximation, I study the spatial version of a popular ecological model involving just one species representing vegetation.

It is shown that different quantities—like the variance, the two-point correlation function and the patchiness—may serve as early warnings for the desertification of arid lands. Remarkably, in the onset of a desertification transition the distribution of vegetation patches exhibits scale invariance typical of many physical systems in the vicinity a phase transition. I comment on similarities of and differences between these catastrophic shifts and paradigmatic thermodynamic phase transitions like the liquid-vapor change of state for a fluid. Third, I analyze the case of many species interacting in space. I choose tropical forests, which are mega-diverse ecosystems that exhibit remarkable dynamics. Therefore these ecosystems represent a research paradigm both for studies of complex systems dynamics as well as to unveil the mechanisms responsible for the assembly of species-rich communities. The more classical equilibrium approaches are compared versus non-equilibrium ones and in particular I discuss a recently introduced cellular automaton model in which species compete both locally in physical space and along a niche axis. (Abstract excerpts)

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