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IV. Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic Code-Script Source

1. Network Physics: A Vital Interlinked Anatomy and Physiology

Laurent, Hebert-Dufresne, et al. Complex Networks as an Emerging Property of Hierarchical Preferential Attachment. Physical Review E. 92/6, 2015. Cited also in Universality Affirmations, University of Laval, Quebec and University of Barcelona physicists open this survey on the state of complexity science by tracing its advent to a 1962 paper The Architecture of Complexity by the pioneer theorist Herbert Simon in the Proceedings of the American Philosophical Society (106/467). Some half century later, as this 2015 section documents, the Grail goal of one, same, infinitely iterated, self-organizing system has been proven from quantum to human to cosmic realms, so as to imply a common, independent, universally manifest, source.

Laurienti, Paul, et al. Universal Fractal Scaling of Self-Organized Networks. Physica A. 390/20, 2011. Cited more in Common Code, after some two decades of complex systems studies from every angle, in disparate fields and terms, on every continent, a maturity is lately being reached so it is possible, for example, for this team of Wake Forest University biomedical researchers to propose a natural “universality” of “node and interaction” dynamic network phenomena. To wit, the same fractal pattern and process faithfully recurs across broad Biological, Information, Social, and Technological domains. These extended quotes might portend, circa 2011, a new animate nature suffused with intrinsic creativities that repeat and reiterate across every regnant realm. At what point, and by what insight, might this realization become a revolution, and its spontaneity be appreciated as genetic in kind?

Lee, Kyu-Min, et al. Towards Real-World Complexity: An Introduction to Multiplex Networks. European Physical Journal B. 88/2, 2015. In this edition for Condensed Matter and Complex Systems, Korea University physicists offer a succinct tutorial for these novel findings of a lively nature from cosmos to cerebral to culture as graced by nested networks in iterative hierarchies. With statistical and nonlinear physics as Keywords, the paper joins a mid 2010s revolution from mechanical particles only to pervasive animate, neural interconnections, whose latest epitome of human persons and societies is able to achieve its own vital self-realization.

Many real-world complex systems are best modeled by multiplex networks of interacting network layers. The multiplex network study is one of the newest and hottest themes in the statistical physics of complex networks. Pioneering studies have proven that the multiplexity has broad impact on the system’s structure and function. In this Colloquium paper, we present an organized review of the growing body of current literature on multiplex networks by categorizing existing studies broadly according to the type of layer coupling in the problem. Major recent advances in the field are surveyed and some outstanding open challenges and future perspectives will be proposed. (Abstract)

Lee, Sang Hoon. Network Nested as Generalized Core-Periphery Structures. arXiv:1602.00093. We cite this entry by a Korea Institute for Advanced Study physicist as an example of how such a generic recurrent scale, which seeks and reaches complementary fast dense and slower expanse phases, are gaining notice as natural archetypes from universe to human. See also later entries on this eprint site by the author and colleagues for practical applications such as 3D chromosome and power-grid geometries.

The concept of nestedness, in particular for ecological and economical networks, has been introduced as a structural characteristic of real interacting systems. We suggest that the nestedness is in fact another way to express a mesoscale network property called the core-periphery structure. With real ecological mutualistic networks and synthetic model networks, we define the network-level measures for nestedness and core-periphery-ness in the case of weighted and bipartite networks. Therefore, there must exist structurally interwoven properties in more fundamental levels of network formation, behind this seemingly obvious relation between nestedness and core-periphery structures. (Abstract)

Lee, UnCheol and George Mashour. Role of Network Science in the Study of Anesthetic State Transitions. Anesthesiology. 129/1029, 2018. University of Michigan Medical School neuroscientists, who are involved with consciousness studies at UMMS (search each author), illustrate how the common multiplex networks found everywhere also provide functional structures as brains pass into and out of relatively unconscious states. It is then affirmed that as these conditions exhibit a self-organized criticality with scale-free power laws, this phenomena appears to manifestly arise from universal, lawful principles. Within this approach, the array of nodes, links, hubs, and dynamic topologies are cited as a major determinant of global information processing.

University of Michigan Medical School neuroscientists, who are involved with consciousness studies at UMMS (search each author), illustrate how the common multiplex networks found everywhere also provide functional structures as brains pass into and out of relatively unconscious states. It is then affirmed that as these conditions exhibit a self-organized criticality with scale-free power laws, this phenomena appears to manifestly arise from universal, lawful principles. Within this approach, the array of nodes, links, hubs, and dynamic topologies are cited as a major determinant of global information processing.

Leli, Vito, et al. Deep Learning Super-Diffusion in Multiplex Networks. arXiv:1811.04104. As the Abstract details, VL, Saeed Osat and Timur Tlyachev, Skolkovo Institute of Science and Technology, Moscow and Jacob Biamonte, Deep Quantum AI, Moscow conceive a working method based on natural phenomena so to better analyze and design intricate nets of many kinds.

Complex network theory has shown success in understanding the emergent and collective behavior of complex systems. Many real-world complex systems were recently discovered to be more accurately modeled as multiplex networks in which each interaction type is mapped to its own network layer such as transportation networks, coupled social networks, metabolic and regulatory networks, etc. A salient physical phenomena emerging from multiplexity is super-diffusion via an accelerated diffusion by the multi-layer structure as compared to any single layer. Here we show that modern machine (deep) learning, such as fully connected and convolutional neural networks, can classify and predict the presence of super-diffusion in multiplex networks. (Abstract excerpts)

Li, Aming, et al. Evolution of Cooperation on Temporal Networks. Nature Communications. 11/2259, 2020. By a novel application of network science to social activities, an eight person team from Peking University, Northeastern University, Harvard Medical School and Princeton University (Simon Levin) illuminates a deeper natural basis for beneficial behaviors to both members and groups. As the quotes says, these heretofore unknown features can aid better explanations and usage.

Population structure is a key determinant in fostering cooperation among naturally self-interested individuals in microbial populations, social insect groups, and human societies. Prior research has focused on static structures, and yet most interactions are changing in time and form a temporal network. Surprisingly, we find that network temporality actually enhances the evolution of cooperation relative to comparable static networks, despite the fact that bursty interaction patterns generally impede. We resolve this tension by a measure which quantifies the amount of temporality in a network, so to reveal an intermediate level that boosts cooperation. (Abstract excerpt)

Explaining the evolution of durable, widespread cooperative behaviour in groups of self-interested individuals has been a challenge since the time of Darwin. In response, researchers have turned to the critical role played by the underlying interaction networks, in which nodes represent individuals and links represent interactions. It has been shown that the nontrivial population structures represented by both homogeneous and heterogeneous networks permit the formation of stable clusters of cooperators (altruists), with higher individual payoffs while also resisting defectors (egoists). As such, both theoretical analysis and behavioural experiments point to network structure as a key ingredient for the emergence of cooperation. (2)

Li, Angsheng, et al. Discovering Natural Communities in Networks. Physica A. Online May, 2015. We note this paper amongst many to exemplify a robust maturity of complexity system science. Chinese Academy of Sciences, Beijing, theorists treat these pervasive relational formations as an independent, universal phenomena from which generic principles and properties can be identified. The upshot would be to wonder where does this dynamic mathematical geometry come from, what kind of a universe to human self-realizing procreation?

Natural or true communities are basic to many interacting systems in nature, society and networks. Identifying and analyzing natural communities of real world networks are essential to understanding the networks, with potential applications in understanding, for instance: the roles and functions of the modules of social and technological systems, the roles and mechanisms of social groups in nature and society, the mechanisms of group intelligence, the mechanisms of interacting learning and games among social groups, diagnosing and curing of complex diseases, and designing of new medicines etc. Our algorithm provides for the first time a method which may exactly identify or precisely approximate the natural or true communities of many real world networks and interacting system in nature and society. (2)

Liu, Chuang, et al. Computational Network Biology. Physics Reports. December, 2019. A seven member international team posted in China, Switzerland and the USA (Ruth Nussinov, National Cancer Institute) provide an 80 page tutorial across scientific techniques and real applications as life’s intricate anatomy and physiology becomes understood by these revolutionary 2010s features.

Biological entities are involved in intricate and complex interactions, in which uncovering the biological information from the network concepts are of great significance. In this review, we summarize the recent developments of this vital, copious field, first introducing various types of biological network structural properties. We then review the network-based approaches, ranging from metrics to machine-learning methods, and how to use these algorithms to gain new insights. We highlight the application in neuroscience, human disease, and drug developments and discuss some major challenges and future directions. (Abstract excerpt)

Liu, Jin-Long, et al. Fractal and Multifractal Analyses of Bipartite Networks. Nature Scientific Reports. 7/45588, 2017. As nature’s webworks from condensed matter to Internet cultures become evident and quantified, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, China researchers finesse their iconic complexities. Our interest is then a pervasive presence of a universal repetition in kind of one common code motif comprised of archetypal nodal and connective (gender) complements. See also for example in this journal SO2 Emissions in China – Their Network and Hierarchical Structures for another take (Shaomin Yan & Guang Wu, 2017).

Bipartite network, as a special kind of complex networks, has also attracted a great deal of attention from researchers in the fields of scientific research, engineering application, e-commerce, etc. The difference with the unipartite networks is the fact that the nodes of a bipartite network can be separated into two classes and its edges exist only between nodes of different classes. In real world, there are many systems, which can be modeled naturally by a bipartite network, such as the metabolic network, the human sexual network, actor-movie network, scientist-paper network, web-user network, and so on. (1)

Although a lot of research works have been done on the study of bipartite networks, there is no a systematic framework for it compared with the unipartite networks. It is well known that, after the small-world character and scale-free property, self-similarity has become the third basic characteristic of complex networks. Many complex networks such as the World-Wide-Web, social networks, protein-protein interaction networks (PINs), and cellular networks consist of self-repeating patterns. (1)

Liu, Xueming, et al. Network Resilience. arXiv:2007.14464. Six theorists from Chinese Universities and Rensselaer Polytechnic Institute including Jianxi Gao and Boleslaw Szymanski post a 113 page, 859 reference 2020 tutorial about this pervasive ability of natural node/link complexities to restore and maintain themselves. Typical sections are Tipping Points in Ecological Networks, Phase Transitions in Biological Networks, Behavior Transitions in Animal and Human Networks and Resilience, Robustness and Stability. In the midst of epochal perils, this entry reports a concurrent worldwise finding of a revolutionary genesis ecosmos with its own bigender genomic code.

Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems, and social convention changes in human and animal networks. Such a regime shift demonstrates a system's ability to adjust activities so to retain its basic functionality in the face of internal or external changes. Only in recent years by way of network theory and lavish data sets, have complexity scientists been able to study real-world multidimensional systems, early warning indicators and resilient responses. This report reviews resilience function and regime shift of complex systems in domains such as ecology, biology, social systems and infrastructure. (Abstract excerpt)

The nature and the world in which we live are filled with changes and crises. Examples are the global pandemic of the novel coronavirus, the catastrophe in east Africa caused by the infestation by desert locusts, and the 2019 bushfire in Australia that burned through some 10 million hectares of land. In addition, these threats and crisises are not independent but related with one another. For example, the Australia bushfire and locust swarms are linked to the oscillations of the Indian Ocean Dipole, which is one aspect of the growing of the global climate change. How the nature or societies response to such threats and crises is defined by their resilience, which characterizes the ability of a system to adjust its activity to retain its basic functionality in the face of internal disturbances or external changes. (2)

Mac Carron, Padraig and Ralph Kenna. Universal Properties of Mythological Networks. Europhysics Letters EPL. 99/28002, 2012. Reported more in Universality, Coventry University physicists apply condensed matter theories in the form of complex systems to the historic corpus of epic fabled and storied mythic literatures. The second quote is a also exemplifies how such papers now open as the range and reach of nonlinear phenomena extends across every natural and social domain. As a result, a true cosmos to culture “universality” is at last becoming evident and proven.

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