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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

A. A Survey of Common Principles

Deisboeck, Thomas and J. Yasha Kresh, eds. Complex Systems Science in Biomedicine. New York: Springer, 2006. An 850 page compendium which covers both the range of nonlinear complexity, especially network phenomena, and their dynamic presence in organisms from genes and cells to developmental, metabolic, neurological, cardiac, immune, and other functions. These novel understandings of anatomy and physiology by way of complex adaptive systems then opens up new approaches to treat diseases, cancer, the aging process, genetic disorders, and so on. A luminous array of authors includes mathematical theorists and physician researchers, along with a preface by Stuart Kauffman, MD. As befitting, the full text can be accessed in the cyberspace noosphere through Google Book Search, via title and editors.

Dobrescu, R. and Purcarea, V. Emergence, Self-Organization and Morphogenesis in Biological Structures. Journal of Medicine and Life. 4/82, 2011. When I spoke at in 2005 at Palacky University in the Czech Republic (slides on home page) a professor from the close by University of Brno, where Gregor Mendel’s garden resides, told me in so many words that Eastern Europe does not accept a Western (US & UK, Dawkins & Co.) evolutionary theory that rejects any formative cause other than post-selection. “We know it is wrong.” This paper by Polytechnic University of Bucharest and Carol Davila University of Medicine, Bucharest, researchers is cited as an exemplary witness of a prior dynamic agency that provides a universal, repetitive source. We ought to remember how much science is bent by personalities, biases, preconditions, and so on, which govern what can be seen and permitted or not. The text is online in full at the journal site.

The paper discusses the connection between emergence, pattern formation and nonlinear dynamics, focusing on the similarity between discrete patterns and fractal structures, and then describes different solutions to model reaction-diffusion systems as representative processes in morphogenesis. A specific example is the diffusion limited aggregation growth process, illustrated by the simulation of the evolution of a bacterial colony that shows the roles of instability and sensitivity in non-equilibrium pattern formation. Based on this particular case, it is shown how self-organization could be achieved from non-organized agglomeration of separate entities, in a region of space. We conclude with some brief remarks about universality, predictability and long-term prospects for this field of research. (Abstract)

It is important to note that the main properties such as the existence of distinct cell types, the homeostatic stability of cell types, the number of cell types in an organism, the similarity in gene expression patterns in different cell types, the fact that development from the fertilized egg is organized around branching pathways of cell differentiation, and many other aspects of differentiation are all consequences of properties of self organization, so profoundly immanent in complex regulatory networks whose order selection cannot avoid. All aspects of differentiation appear to be properties of complex parallel–processing systems lying in the ordered regime. These properties may therefore reflect quasi–universal features of organisms due not to selection alone, but also to the spontaneous order of the systems on which selection has been privileged to act. (89)

Dorit, Robert. The Humpty-Dumpty Problem. American Scientist. July-August, 2011. The Smith College biologist muses that a major, dedicated effort is overdue to put life and everything back together again, after centuries of partitioning and fragmenting. Lately driven by computer prowess, such an interactionist perspective for living systems can illume and quantify, within a “new harmony,” a reciprocal interplay of parts and their iterative, modular, vital organizations.

Earnest, Tyler, et al. Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies. Reports on Progress in Physics. 81/5, 2018. University of Illinois, Urbana computational physicists and chemists including Zaida Luthey-Schulten pursue a translational interpretation of (multi) cellular biology by way of dynamic physical principles. Per the second quote, their goal is to quantify living phenomena in a way to better join and assimilate life within the encompassing natural cosmos. If to reflect, the past decades and centuries of scientific studies now appear as a single endeavor from individuals and groups to our global collaboration so as to achieve this integral, imperative organic unity.

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge to the complex forms and behaviors in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recently stochastic modeling has grow into a major subdiscipline within biological physics. We describe how stochasticity impacts key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, as they may be coupled into a comprehensive model of a 'minimal cell'. We consider the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches to understand life across a range of length and time scales. (Abstract edited excerpts)

The ultimate goal of constructing whole-cell simulations is to describe life in the language of physics. The vocabulary is, of course, well known – we speak of thermodynamic potentials, molecular conformations, chemical transformations and reactions – but the grammar, the system of integrating methods that span vastly different time and length scales, and whose applicabilities are often mutually exclusive, into a cohesive picture of the living cell remains elusive. This final section is intended to outline in broad terms our expectations for the future of the field. (28)

Eisler, Zoltan, et al. Fluctuation Scaling in Complex Systems. Advances in Physics. 57/1, 2008. In the study of nonlinear phenomena from galaxies to Gaia, two approaches can be taken: to view each subject tree (scientific field) or the whole (temporal cosmos) forest. Most often, metabolic networks e.g., the task is to quantify patterns and processes in a specific domain. The other approach, which might be termed ‘systems physics,’ reported in journals such as Physical Review E and the above, is to distill and extract common generalities across nature’s nested hierarchy from universe to human. Researchers from Hungary, France and the U.S. here pursue the latter path as they emphasize a salient feature whereby “the fluctuation in the activity of an (interactive) element grows monotonically with the average activity” and go on to show this quality indeed characterizes dynamic nature everywhere.

Interacting systems of many units with emergent collective behavior are often termed ‘complex.’ Such complex systems are ubiquitous in many fields of research ranging from engineering sciences through physics and biology to sociology. An advantage of the related multi-disciplinary approach is that the universal appearance of several phenomena can be revealed more easily. Such generally observed characteristics include (multi-)fractality or scale invariance, the related Pareto or Zipf laws, self-organized and critical behavior. (91) We believe that a possible common origin of all FS laws is the generality of these underlying mean-field mathematical structures. (134)

Etxeberria, Arantza and Kepa Ruiz-Moreno. The Challenging Biology of Transients. EMBO Reports. 10/Special Issue, 2009. Within an issue on “Science and Society,” University of the Basque Country philosophers content that the systems turn in many fields, notably biological and genetics research, can offer new appreciations of cooperative, autopoietic relations which actually enhance an autonomous individuality for members. By these lights, a better definition of living organisms is gained, to further distinguish from mere machines. As a result, self-organized life can be seen to spread deeper roots into basic physical realms.

Feagin, R. A., et al. Individual versus Community Level Processes and Pattern Formation in a Model of Sand Dune Succession. Ecological Modelling. 183/4, 2005. This specific study provides a microcosm of nature’s reciprocal interplay of entity (plant, person) and relevant group. Pierre Teilhard de Chardin termed this “creative union.” In so doing, nature can teach a common principle and wisdom that could well serve our human abide.

The results showed that the plant patterns were due to individual plant responses to their environment within their local neighborhood, yet these responses were constrained by the global history of the community. (Abstract 435) The results of this study are an important contribution to the theoretical debate over whether individualistic or community-unit processes drive the formation of pattern in plant communities. The model demonstrates that within sand dune plant communities, both processes affect pattern formation. (447)

Ferrer-i-Cancho, Ramon, et al. Compression as a Universal Principle of Animal Behavior. Cognitive Science. Online July, 2013. Universitat Politècnica de Catalunya, University of Aberdeen, Tajen University, Taiwan, National Sun Yat-sen University, and University of Roehampton, London, systems linguists and field biologists describe common, cross-disciplinary patterns between creaturely social activities and human language. A similar communicative coding law or topology is found to be independently present in both stages and every instance.

A key aim in biology and psychology is to identify fundamental principles underpinning the behavior of animals, including humans. Analyses of human language and the behavior of a range of non-human animal species have provided evidence for a common pattern underlying diverse behavioral phenomena: words follow Zipf's law of brevity (the tendency of more frequently used words to be shorter), and conformity to this general pattern has been seen in the behavior of a number of other animals. It has been argued that the presence of this law is a sign of efficient coding in the information theoretic sense. However, no strong direct connection has been demonstrated between the law and compression, “the information theoretic principle of minimizing the expected length of a code.” Here we show that minimizing the expected code length implies that the length of a word cannot increase as its frequency increases. Furthermore, we show that the mean code length or duration is significantly small in human language, and also in the behavior of other species in all cases where agreement with the law of brevity has been found. We argue that compression is a general principle of animal behavior, that reflects selection for efficiency of coding. (Abstract)

Figueiredo, P. H., et al. Self-Affine Analysis of Protein Energy. Physica A. 389/2682, 2010. In a similar theoretical fashion as everywhere else across a procreative nature and nurture, Universidade Federal Rural de Pernambuco, Programa de Modelagem Computacional - SENAI - Cimatec, Universidade Federal do Rio de Janeiro, Universidade Federal da Bahia, physicists find life’s fertile biochemical milieu to abide in and fluoresce by webwork dances of enfolded molecules and relational partners.

In recent years, there has been a growing evidence that many complex physical, economical, and biological systems manifest self-affinity characterized by long-range power-law correlations. In such a context, the detrended fluctuation analysis (DFA) was recently proposed [1] to analyze long-range power-law correlations in nonstationary systems. One advantage of the DFA method is that it allows the long-range power-law correlations in signals with embedded polynomial trends that can mask the true correlations in the fluctuations of a noise signal. The DFA method has been applied to analyze the DNA and its evolution [1,2], file editions in computer diskettes [3], economics [4,5], climate temperature behavior [6], phase transition [7], astrophysics sources [8,9] and cardiac dynamics [10,11], among others. (2682)

The study of fractal characteristics of the proteins provides countless results. The fractal analysis uncovered self-similarity in many research fields such as cluster dimension of proteins [12], anomalous temperature dependence of the Raman spin–lattice relaxation rates [13], relation between the fractal dimension and the number of hydrogen bridges [14], multifractality in the energy hypersurface of the proteins [15], packing of small protein fragments [16], surface volume [17], degree of compactness of the proteins [18], measurement of the average packing density [19] as well as a hydrophobicity scale [20] among others. Furthermore, the fractal methods identify different states of the same system according to its different scaling behaviors, e.g., the fractal dimension is different for structures with (without) hydrogen bonds [14,15]. In this sense, the correct interpretation of the scaling results obtained by the fractal analysis is crucial to understand the intrinsic geometry (and sometimes dynamics) of the systems under study.

Fortunato, Santo and Claudio Castellano. Scaling and Universality in Proportional Elections. Physical Review Letters. 99/138701, 2007. As Galileo famously noted, nature’s philosophy is written with a mathematical quill. In this paper, scientists from Torino and Roma quantify that underlying and informing our seemingly chaotic political elections is a constantly recurrent, systematic geometry. A proposal of this website is that a persistent gridlock thus occurs along archetypal lines of so-called right conservative and left liberal poles, when their resolve is an obvious complementarity.

We show that, in proportional elections, the distribution of the number of votes received by candidates is a universal scaling function, identical in different countries and years. This finding reveals the existence in the voting process of a general microscopic dynamics that does not depend on the historical, political, and/or economical context where voters operate. (Abstract, 138701)

Many social nontrivial phenomena emerge spontaneously out of the mutual influence of a large number of individuals, similarly to large-scale thermodynamic behavior resulting from the interaction of a huge number of atoms or molecules. However, human interactions are neither purely mechanical nor reproducible, both typical requirements for a physical description of a process. Nevertheless the collective behavior of large groups of individuals may be independent of the details of social interactions and individual psychological attributes, and be instead the consequence of generic properties of the elementary interactions, allowing for a simple ‘‘statistical physics’’ modeling. (138701)

Frank, Steven. All of Life is Social. Current Biology. 17/16, 2007. An introduction to a special section on Social Biology which records that the complementary interplay of selfish or selfless behavior found from bees to baboons occurs across an expanded spectrum from genomes, viruses, bacteria, to human cognitive and linguistic discourse.

For example, multicellularity originated through a complex evolutionary history of cellular aggregations, in which the opposing social forces of conflict and cooperation likely played a key role. Similarly, genomes arose through social histories of genetic aggregations and organelle symbioses. Several aspects of multicellularity, of genomes, of societies, and of cognition can be understood only within the social history of conflict and cooperation. (R648)

Frank, Steven. The Common Patterns of Nature. Journal of Evolutionary Biology. Online July 17, 2009. The University of California, Irvine ecologist contends that a realm of mathematical formulae underlies animate activity from “amino acid substitutions to ecological communities” with the result that generic forms and functions can be found in occurrence everywhere.

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