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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

Baruchi, Itay, et al. Functional Holography of Complex Networks Activity – From Cultures to the Human Brain. Complexity. 10/3, 2005. In a similar way to holographic universe theories (see Quantum Cosmology) Baruchi, along with Vernon Towle and Eshel Ben-Jacob, find that biological and neural networks, in their algorithmic processes, take on the typical properties of a hologram. Here is still another approach which finds nature to be distinguished by the same pattern and process at each scale and instance.

In a similar way to holographic universe theories (see Quantum Cosmology) Baruchi, along with Vernon Towle and Eshel Ben-Jacob, find that biological and neural networks, in their algorithmic processes, take on the typical properties of a hologram. Here is still another approach which finds nature to be distinguished by the same pattern and process at each scale and instance.

Bhattacharyya, Pratip, et al. A Common Mode of Origin of Power Laws in Models of Market and Earthquake. Physica A. 381/377, 2007. From the Theoretical Condensed Matter Physics Division and Centre for Applied Mathematics and Computational Science, Saha Instute of Nuclear Physics, and the Physics Department, Gurudas College, Kolkata, India, comes this report of widely separated natural and social domains which are yet seen hold to the same dynamic topologies.

We show that there is a common mode of origin for the power laws observed in two different models: (i) the Pareto law for the distribution of money among the agents with random-saving propensities in an ideal gas-like market model and (ii) the Gutenberg–Richter law for the distribution of overlaps in a fractal-overlap model for earthquakes. The identification of the generic origin of the power laws helps in better understanding and in developing generalized views of phenomena in such diverse areas as economics and geophysics. (377)

Bickhard, Mark. Interactivism: Introduction to the Special Issue. Synthese. 166/449, 2009. This citation could also apply to “Does Process Matter? An Introduction to the Special Issue on Interactivism” of Aximathes (21/1-2, 2011). For each edition, the Lehigh University philosopher views the scene and articles with regard to the title turn from preoccupations with particulate matter to give equal worth to the real presence of dynamical interrelations between elements. In both issues, Australian systems scholar Cliff Hooker pens a large chapter on a bio-cognitive rationality. Another sample could be “Physicalism, Emergence and Downward Causation.”

Blagus, Neli, et al. Self-Similar Scaling of Density in Complex Real-World Networks. Physica A. 391/8, 2011. As an example of our instant, worldwide science collaboration, as if a global brain/mind learning on her/his own, University of Ljubljana, Slovenia, Computer and Information scientists contribute to the current distillation and discovery (search herein, Systems Physics, and throughout) from a decade of theory and evidence of a genesis nature innately distinguished by such a dynamic network anatomy and physiology. With total online access, the authors could drawn on a vast array of social, citation, web graph, commerce, communication, information, software, technological, biological, microbial, protein web, modular, hierarchical living systems to make their case. Compare, e.g., with Kim, J., et al. “Fractality and Self-Similarity in Scale-Free Networks” in New Journal of Physics. (9/6, 2007).

Despite their diverse origin, networks of large real-world systems reveal a number of common properties including small-world phenomena, scale-free degree distributions and modularity. Recently, network self-similarity as a natural outcome of the evolution of real-world systems has also attracted much attention within the physics literature. Here we investigate the scaling of density in complex networks under two classical box-covering renormalizations - network coarse-graining - and also different community-based renormalizations. The analysis on over 50 real-world networks reveals a power-law scaling of network density and size under adequate renormalization technique, yet irrespective of network type and origin. The results thus advance a recent discovery of a universal scaling of density among different real-world networks (search Laurienti) and imply an existence of a scale-free density also within - among different self-similar scales of - complex real-world networks. (Abstract, 1)

Self-similarity is primarily studied under the framework of network renormalization. As already discussed, renormalization is an iterative coarse-graining technique, where the original network is covered with boxes, thus each node belongs to exactly one box. Boxes are then replaced by super-nodes that are linked when a corresponding link also exists in the (original) network. The entire process repeats until no links remain and the number of nodes equals to the number of connected components. (3)

Boettiger, Alistair and George Oster. Emergent Complexity in Simple Neural Systems. Communicative & Integrative Biology. 2/6, 2009. University of California, Berkeley, biophysicists find seashell patternings and our cortical neural activities to spring from and express the same fractal-like geometries and dynamics.

The ornate and diverse patterns of seashells testify to the complexity of living systems. Provocative computational explorations have shown that similarly complex patterns may arise from the collective interaction of a small number of rules. This suggests that, although a system may appear complex, it may still be understood in terms of simple principles. (467)

Boldini, Alain, et al. Application of Symbolic Recurrence to Experimental Data from Firearm Prevalence to Fish Swimming. Chaos. 29/113128, 2019. NYU and Technical University of Cartagena, Spain bioengineers finesse mathematical techniques in search of better ways to parse and compare complex interactive phenomena across wide scales and instances. And coincidently we log in on the December 14 date of the 2012 Newton school shooting, which is mentioned in the paper. However then might a breadth and depth of credible, sufficient, phenomenal proof be achieved so we peoples could realize and implement an independent, universal naturome code? See also Symbolic Recurrence Plots to Analyze Dynamical Systems by Victoria Caballero-Pintado, et al in Chaos (28/063112, 2018).

Recurrence plots and recurrence quantification analysis are powerful tools to study the behavior of nonlinear dynamical systems. Previous usages, however, have led to arbitrary definitions of recurrence. Here we describe a symbolic recurrence to overcome this issue, and to better book-keep recurrent portions of the phase space and real time series. We illustrate by examining a wide range of experimental datasets from firearm prevalence and media coverage to the sexual interaction of swimming fish. These results demonstrate the potential of symbolic recurrence in real-world applications across research fields. (Abstract excerpt)

Bransburg-Zabary, Sharron, et al. Individual and Meta-Immune Networks. Physical Biology. 10/2, 2013. In this 21st century journal, an international team from Tel Aviv University, Boston University, Harvard Medical School, Weismann Institute, and Rice University, including Alfred Tauber and Eshel Ben-Jacob, provide a strong affirmation of the similarly nonlinear essence of immune systems. Indeed, it is noted that the 1970s network theories of Danish immunologist Niels Jerne, for which he received the 1984 Nobel Prize in Medicine, are now well explicated and quite proven.

In recent years, network theory has become one of the central theoretical frameworks that can be applied to the description, analysis and understanding of complex systems and in particular in strongly coupled multi-level complex systems. Complex networks can be found everywhere, in man-made systems and in human social systems, in organic and non-organic matter, in natural and anthropogenic structures as well as in biological systems. Examples include linked molecular or cellular structures, climate networks, communication and infrastructure networks, social and economic networks, gene networks, neuron networks and immune networks. The understanding of the growth, structure, dynamics and functioning of these networks, and their mutual interrelationships, is critical. (1)

Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems.

Brummer, Alexander, et al. A General Model for Metabolic Scaling in Self-Similar Asymmetric Networks. PLoS Computational Biology. 13/3, 2017. Brummer, University of Arizona physics, Van Savage, UCLA biomathematics, and Brian Enquist, UA ecology expand and finesse the WBE (West, Geoffrey, Brown, James H. and Enquist) theory of life’s nested recurrences. Since its inception in 1997 (search), this well researched and tested explanation has become basically verified and established. The new National Geographic TV program Xray Earth, available on You Tube, has segments by Enguist and West about these luminous findings.

We have derived a more general form of the WBE model. It incorporates different branching geometries reflected in differences in branching asymmetry. We believe that our approach can offer a more general theory that can better relate variation in organismal form and function than the original WBE model. Our definition of asymmetry in a strictly bifurcating network allows for a more accurate analysis of biological branching networks. In addition, the theory makes a set of novel predictions for the type of branching asymmetry favored under different fluid flow types/transfer regimes. (19)

Buchanan, Mark. The Mathematical Mirror to Animal Nature. Nature. 453/714, 2008. A note on the growing perception of universally recurrent behavior patterns from social insects and migratory birds to financial investors and mobile phone users. The subject here involves “Levy flights” as “random walks” distinguished by a probability distribution that generates a scale invariance. These many findings lead investigators to postulate the presence of an independent, underlying source. A companion article, "The Cambrian Smorgasbord" by Arran Frood, cites the work of ecologist Jennifer Dunne as illuminating common recurrences across evolutionary time and space.

Caetano-Anolles, Derek, et al. Evolution of Macromolecular Structure: A ‘Double Tale’ of Biological Accretion. arXiv:1805.06487. A son Derek, MPI Evolutionary Biology, daughter Kelsey, Seoul National University agricultural biotechnology, and father Gustavo (search), University of Illinois plant sciences, collaborate on an iterative cosmic to organic to cultural synthesis just becoming evident. The entry draws on earlier versions such as Piecemeal Buildup of the Genetic Code (Life, 6/43, 2016), Early History and Emergence of Molecular Functions (Nature Scientific Reports, 6/25058, 2016), Computing the Origin and Evolution of the Ribosome (Computational and Structural Biotechnology, 13/427, 2015), and Structural Phylogenomics Retrodicts the Origin of the Genetic Code (PLoS One, 8/8, 2013). An initial notice is that, akin to Geoffrey West 2017, Naoki Sato 2018, and others, it is lately possible to view the entire course of universe to human evolution as a single, complex, emergent phenomenon which springs from, and exemplifies, its own procreative qualities.

The essay opens by citing how orbital planets have been found to form by accretive condensations from dusty, peeble-filled clouds. Earth life evolution is then seen to similarly gather, clump, and accrete, as it self-organizes into episodic nested hierarchies of (multi)cellular modularity. This iconic structure and process occurs from genomic RNA biochemistry, complex proteins, metabolic networks all the way to urban civilizations. An illustration compares an affinity between 3D ribosome helices and high-rise buildings in Manhattan. To wit, a natural philosophy surmise is that our collective learned kindermind is beginning to achieve her/his visionary witness of a greater familial genesis with its own genomic propensities meant for we peoples to discover, decipher, read and intentionally carry forth.

The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that are responsible for a 'double tale' of evolutionary accretion at various levels of complexity, from proteins and nucleic acids to high-rise building structures in cities. Parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organization. Evolutionary genomics and network biology support the 'double tale' of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules. (Abstract)

Callebaut, Werner and Diego Rasskin-Gutman, eds. Modularity: Understanding the Development and Evolution of Natural Complex Systems. Cambridge: MIT Press, 2005. Reviewed more in Part V, this volume complements: Schlosser, Gerhard and Gunter Wagner, eds. Modularity in Development and Evolution. (2003). Altogether they report in detail and breadth the discovery that nature repeats, by way of semiautonomous components and entities, the same universal pattern and process over and over. Still another aspect and perspective serves to reveal an iterative, “modular” universe.

Camazine, Scott, et al, eds. Self-Organization in Biological Systems. Princeton: Princeton University Press, 2001. A primer for generic self-emergent systems whose many interactions between simpler components and local rules give rise to global degrees of order. The book moves on to describe their presence throughout the natural kingdom from shell patterns to social insect structures.

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