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

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

Berg, Howard and Krastan Balgoev. Perspectives on Working at the Physics-Biology Interface. Physical Biology. 11/5, 2014. An introduction to a very special issue of reflections by senior scientists who had shifted careers from physical science to research on active biological phenomena. Their efforts are now seen much in accord with a 21st century turn to revive and reintegrate life within a conducive material nature. It opens with the exemplary work of Harold Morowitz in The Emergence of a New Kind of Biology. I first heard HM speak in 1972 in New York City on Biology as a Cosmological Imperative. Other veterans are John Hopfield, Hans Frauenfelder, Robert Austin, and Herbert Levine who foresaw long ago this course correction.

We note contributions by Robert Laughlin who extols an emergent universe by virtue of manifest life, Universal Relations in the Self-Assembly of Proteins and DNA by David Thirumalai, and Geoffrey West’s path from high energy physics at LANL to president of the Santa Fe Institute in From Quarks and Strings to Cells and Whales. Research on communal bacteria as an interdisciplinary endeavor is cited by Bonnie Bassler and Ned Wingreen in Working Together at the Interface of Physics and Biology. An especial advocate is Eshel Ben-Jacob, past president of the Israel Physics Society, in My Encounters with Bacteria – Learning about Communication, Cooperation and Choice. He is lately applying his insights into self-organizing, intelligent microbial systems as a novel approach to cure cancer.

One knows for certain that this is happening in living things because their genomes are not large enough to encrypt the endlessly complex details of their form and function. There is nothing vague or imprecise about these concepts. They are codified in a body of mathematics known as the renormalization group. It is highly quantitative and well tested in systems that one can control precisely and measure accurately. The renormalization group came to us originally from elementary particle theory, where it was inferred from the scale invariance of quantum fields. (Laughlin)

My journey into the physics of living systems began with the most fundamental organisms on Earth, bacteria, that three decades ago were perceived as solitary, primitive creatures of limited capabilities. A decade later this notion had faded away and bacteria came to be recognized as the smart beasts they are, engaging in intricate social life through a sophisticated chemical language. Acting jointly, these tiny organisms can sense the environment, process information, solve problems and make decisions so as to thrive in harsh environments. The bacterial power of cooperation manifests in their ability to develop large colonies of astonishing complexity. The number of bacteria in a colony can amount to many billions, yet they exchange 'chemical tweets' that reach each and every one of them so they all know what they're all doing, each cell being both actor and spectator in the bacterial Game of Life. (Ben Jacob)

Bettencourt, Luis, et al. Professional Diversity and the Productivity of Cities. Nature Scientific Reports. 4/5393, 2014. The lead sentence “A fundamental theme across the study of complex systems - from ecosystems to human behavior and socioeconomic organization - deals with the mechanisms by which diversity arises and is sustained” is how many papers open today. Just as every other realm from cosmos to civilization is known to exemplify self-organizing complexities, so does this urban prototype. Once again both a dynamic and structural universality, and its specific instantiation are cited. In this case, Santa Fe Institute and LANL system physicists describe an organic scale-invariance than spans from neighborhoods to cities with regard to distributions of knowledge skills and vital services. See also by the authors, with Geoffrey West, the May posting The Systematic Structure and Predictability of Urban Business Diversity at arXiv:1405.3202.

Attempts to understand the relationship between diversity, productivity and scale have remained limited due to the scheme-dependent nature of the taxonomies describing complex systems. We analyze the diversity of US metropolitan areas in terms of profession diversity and employment to show how this frequency distribution takes a universal scale-invariant form, common to all cities, in the limit of infinite resolution of occupational taxonomies. We show that this limit is obtained under general conditions that follow from the analysis of the variation of the occupational frequency across taxonomies at different resolutions in a way analogous to finite-size scaling in statistical physical systems. We propose a theoretical framework that derives the form and parameters of the limiting distribution of professions based on the appearance, in urban social networks, of new occupations as the result of specialization and coordination of labor. By deriving classification scheme-independent measures of functional diversity and modeling cities as social networks embedded in infrastructural space, these results show how standard economic arguments of division and coordination of labor can be articulated in detail in cities and provide a microscopic basis for explaining increasing returns to population scale observed at the level of entire metropolitan areas. (Abstract)

Bialek, William. Perspectives on Theory at the Interface of Physics and Biology. arXiv:1512.08954. The Princeton University, John Archibald Wheeler/Battelle professor of physics, is a leading practitioner and advocate of a 21st century reintegration of vital life and fertile ground. As the quotes convey, revisions of both domains as they cross-inform is necessary such as statistical physics with evolutionary dynamics. By this view, one can notice that any and all realms of nature and society, say bird flock or social media collective behaviors, is can be realized to exemplify similar principles. As the guns of January 2016 now ready, as markets crash, demigods bluster, and worse, here is an imminent epochal discovery by virtue of imagining its presence as due to our worldwise humankinder.

Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. I'm an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples. (Abstract)

But theoretical physics is not a collection of disparate models for particular systems, or a catalogue of special cases. There is a growing community of theorists who want, as it were, more out of life. We want a theoretical physics of biological systems that reaches the level of predictive power that has become the standard in other areas of physics. We want to reconcile the physicists' desire for concise, unifying theoretical principles with the obvious complexity and diversity of life. (1)

Turning from the past to the present and future, I will argue this is an auspicious time: theory is having a real impact on experiment, related theoretical ideas are emerging in very different biological contexts, and we can see hints of ideas that have the power to unify and deepen our understanding of diverse phenomena. What is emerging from our community goes beyond the application of physics to the problems of biology. (1)

To summarize, the classical examples are inspiring, but the challenge for theory in our time is (at least) three fold. First, we have to identify principles that organize our thinking at a systems level. Second, we have to express these principles in mathematical terms. Third, if we expect our mathematical theories to make quantitative predictions, we have to push our experimentalist friends to expand the range of life's phenomena that are accessible to correspondingly quantitative measurement. (5)

Bialek, William, Chair. Physics of Life. Washington, DC: National Academies Press., 2022. This volume is a current edition of the NAS Biological Physics/Physics of Living Systems: A Decadal Survey program. The document can be read online or purchased in paper as an informative survey of the 2020s reunion of living, evolving, sensing systems with the conducive ground it has arisen from.

Bialek, William, et al. Social Interactions Dominate Speed Control in Driving Natural Flocks toward Criticality. arXiv:1307.5563. Online July 2013. An American-European team from Princeton University, Sapienza University of Rome, and the University of Paris, including Andrea Cavagna and Alkesandra Walczak (search each for more), has come together to contribute several papers to the growing application of statistical physics to every other natural and social domain. In this case, it is remarkable that the same phenomena found in liquid helium, magnetic materials, and so on, equally apply to and guide many-body animal behaviors. See also “Dynamical Maximum Entropy Approach to Flocking” by Andrea Cavagna, et al, (arXiv:1310.3810).

Flocks of birds exhibit a remarkable degree of coordination and collective response. It is not just that thousands of individuals fly, on average, in the same direction and at the same speed, but that even the fluctuations around the mean velocity are correlated over long distances. Quantitative measurements on flocks of starlings, in particular, show that these fluctuations are scale-free, with effective correlation lengths proportional to the linear size of the flock. These models are mathematically equivalent to statistical physics models for ordering in magnets, and the correct prediction of scale-free correlations arises because the parameters - completely determined by the data - are in the critical regime. In biological terms, criticality allows the flock to achieve maximal correlation across long distances with limited speed fluctuations. (Abstract)

Bouchaud, Jean-Philippe, et al. On the Emergence of an “Intention Field” for Socially Cohesive Agents. arXiv:1311.0810. French systems scientists are able to connect universe and human by showing how all manner of group activities can be modeled by way of statistical, condensed matter, physical theories.

The understanding that unremarkable individual elements can give rise, through interactions, to remarkable collective emergent phenomena is arguably the most important contribution of statistical physics to science. These collective effects are often so ordinary that we do not think of them as surprising, like for example the rigidity of a solid, which is still one of the most remarkable properties of interacting atoms. Some exotic states of matter are more astonishing, such as superfluidity or superconductivity, liquid crystals, etc. But this concept outreaches far beyond physics and is relevant to understand a host of situations, ranging from avalanches, the functioning of the brain, traffic jams, bird flocks, to all kinds of social phenomena. (1)

Recently, (we) analyzed the spatial correlations of the turnout rate in many elections and in different European countries. We found in all cases a slow, logarithmic decay of the correlation function as a function of distance. This logarithmic behaviour was very recently confirmed on US data by another group. This empirical regularity not only means that the behavioral pattern of individuals is far from random, but also suggests that some universal underlying mechanism must be at play for such a non-trivial characteristic pattern to appear. (1)

Bowler, Michael and Colleen Kelly. On the Statistical Mechanics of Species Abundance Distributions. Theoretical Population Biology. 82/2, 2012. An Oxford University physicist and a zoologist contribute to dawning realizations of how much physical principles and biological phenomena, via translations, have in common. See also by the authors a major volume Temporal Dynamics and Ecological Process due from Cambridge University Press in early 2014.

A central issue in ecology is that of the factors determining the relative abundance of species within a natural community. The proper application of the principles of statistical physics to species abundance distributions (SADs) shows that simple ecological properties could account for the near universal features observed. These properties are (i) a limit on the number of individuals in an ecological guild and (ii) per capita birth and death rates. They underpin the neutral theory of Hubbell (2001), the master equation approach of Volkov et al. (2003, 2005) and the idiosyncratic (extreme niche) theory of Pueyo et al. (2007); they result in an underlying log series SAD, regardless of neutral or niche dynamics. The success of statistical mechanics in this application implies that communities are in dynamic equilibrium and hence that niches must be flexible and that temporal fluctuations on all sorts of scales are likely to be important in community structure. (Abstract)

Cartwright, Julyan, et al. DNA as Information: At the Crossroads between Biology, Mathematics, Physics and Chemistry. Philosophical Transactions of the Royal Society A. Vol.374/Iss.2063, 2016. University of Granada, and University of Bologna scientists introduce an issue on growing abilities to connect and explain genetic phenomena with an encompassing physical, chemical, and mathematical domains. As the quotes allude, both life and cosmos phases proceed to cross-inform each other. The natural universe increasingly appears as biologically conducive in essence, living systems become theoretically amenable and describable by these disciplines. The authors go on to recognize an historic revolution, or paradigm shift in the making, which ought to be facilitated and pursued forthright. It is worth noting that language and book is once more a metaphor for both the genetic code, and by extension for a conducive nature. The copious issue contains papers such as The Meaning of Biological Information by Eugene Koonin, DNA as Information by Peter Wills, and Pragmatic Information in Biology and Physics by Juan Roederer.

On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems—or parts of them—within a theoretical framework. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. (Abstract)

Biology at present is embarked on an experimental search that we may define as functionalist; that is to say that it is attempting to understand how the functions of living material link together. This search is based upon data that are harder and harder to classify, and above all to interpret. We may compare the situation to that of the comprehension of inanimate matter before the advent of the modern atomic theory. We may thus ask ourselves: were those theoretical efforts to understand and classify matter using physico-mathematical concepts useful? The answer is of course affirmative, and indeed theoretical methods used by biology today originated in the revolution—the paradigm shift—produced by the knowledge of the atomic structure of matter, without which molecular biology would not exist. We argue that another paradigm shift is needed to understand biology: its mathematization. (5)

A common metaphor refers to DNA as the ‘book of life’. Of course, we know that the main information that represents an organism is contained or carried by nucleic acid molecules. In this respect, DNA can be considered as a book, but curiously, such a metaphor has scientific basis only in the concept of the genetic code. However, the genetic code is not a book nor a part of it; rather it is a translation dictionary between two different worlds (languages), i.e. the world of nucleic acids and the world of proteins. Hence, the genetic code allows the translation of a book written in a language into an abridged version of the same book in a different language. Moreover, little is known about the grammar, the syntax and even the orthography of the book of life. Still, we know that the genetic code is involved in the transmission of the information contained in such book and configures a relevant part of the process that defines the central dogma of molecular biology. (7)

Caticha, Nestor, et al. Phase Transition from Egalitarian to Hierarchical Societies Driven by Competition between Cognitive and Social Constraints. arXiv:1608.03637. This posting by University of Sao Paulo mathematicians is an example of current rootings of life’s evolving social complexities in an increasingly lively, informative physical cosmos.

Behavioral phylogenetics makes it plausible that the common ancestor of Homo and Pan genera had a hierarchical social structure. Paleolithic humans with a foraging lifestyle, however, most likely had a largely egalitarian society and yet hierarchical structures became again common in the Neolithic period. Contemporary illiterate societies ll the ethological spectrum [6] from egalitarian to authoritarian and despotic. This non-monotonic journey, a so called U-shaped trajectory, along the egalitarian-hierarchical spectrum during human evolution, was stressed by Knauft and has defied theory despite several attempts of anthropological explanation. Our approach to the study of social organization uses tools of information theory and statistical mechanics. (1)

Cavagna, Andrea and Irene Giardina. Bird Flocks as Condensed Matter Systems. Annual Review of Condensed Matter Physics. Volume 5, 2014. Online in January, University of Rome La Sapienza physicists realize that their prior studies (search) by sophisticated video imagery and complex system science of startling starling aerial maneuvers can be similarly appreciated within the theoretical corpus of statistical mechanics. In this survey, such iconic swarm dynamics is taken as an example of an innately creative materiality in couched in the new phrase “active matter” (search Marchetti). In which regard, by a natural philosophy view even more is implied – a grand new genesis universe that these unified sciences are finally becoming able to express.

Flocking is a paradigmatic case of self-organized collective behavior in biology, and a living example of active matter. Several models and theories have been developed in the last years to address these kind of systems. However, contrary to granular materials and biological systems at the microscale, experiments have been scarce until recently, preventing the necessary comparison between theory and data. In this review, we discuss a novel approach to flocking, where experimental data are used as a starting point, to empirically characterize flocking as a statistical physics collective phenomenon, and build models directly from the data. (Abstract)

In this review, we describe and summarize a novel approach to collective animal behavior and flocking that is based on experiments and empirically grounded modeling. The main philosophy is to start from experimental data and quantify the collective patterns using concepts and methodologies from statistical and condensed matter physics. (23) To conclude this long marathon on flocking, let’s summarize the understanding gathered so far on natural flocks and discuss how it connects to existing research in active matter. When looking at flocks as condensed matter systems, there are two main paradigms that come to mind: the paradigm of liquids and particles interacting with attraction-repulsion potentials and the paradigm of ferromagnetism, in which vectorial degrees of freedom try to align with neighbors. These two paradigms are in fact beautifully integrated in the modeling approaches that have been developed in the past ten years to treat active matter systems. (24)

Cavagna, Andrea, et al. Flocking and Turning: A New Model for Self-Organized Collective Motion. Journal of Statistical Physics. 158/3, 2015. Systems physicists from Italy, Argentina, France, and the USA including Irene Giardina, Thierry Mora and Aleksandra Walczak, proceed to study composite avian flight as a form of active physical matter. As this international project goes forward, life and cosmos again become an integral unity with a single scientific basis, as the same dynamics are found to infinitely repeat in kind at every scale and instance.

What we have done here is to push one step further the ambitious program to tame the vast richness of biological phenomena using the powerful conceptual framework of theoretical physics. (625)

Choi, Jeong-Mo, et al. Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions. Annual Review of Biophysics. 49/107, 2020. Washington University, St. Louis biomedical scientists describe and illustrate another way that life’s intrinsic genetic, metabolic vitality can be traced to, rooted in and manifestly exhibit this substantial phenomena.

Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated compositions. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. (Abstract excerpt)

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