IV. Ecosmomics: Independent Complex Network Systems, Computational Programs, Genetic Ecode Scripts

5. Common Code: A Further Report of Reliable, Invariant Occasions

Szabo, Gyorgy and Gabor Fath. Evolutionary Games on Graphs. Physics Reports. 446/4-6, 2007. An extensive tutorial on game theory as seen from a statistical physics viewpoint, which could be viewed as another encounter with, in translation, nature’s non-equilibrium, agent-based, self-organizing emergence.

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games. (97)

Talaga, Szymon and Andrzej Nowak. Structural Measure of Similarity and Complementarity in Complex Networks. Nature Scientific Reports. 12/16580, 2022. We note this current entry by University of Warsaw and Florida Atlantic University complexity scholars (search AN), while densely theoretic, as an example to natural tendencies to commonly avail these creative reciprocities. See also Budel, Gabriel, et al. Topological Properties and Organizing Principles of Semantic Networks by Gabriel Budel, et al (2023) herein.

The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3 cycles). However, many phenomena from division of labor to protein-protein interactions (PPI) are driven by complementarities and synergies. Here we show that the first principle is linked to the abundance of quadrangles (4-cycles) and dense bipartite subgraphs. Using multiple social and biological networks, we demonstrate that our similarity coefficients capture structural properties related to domain-specific phenomena. (Excerpt)

In summary, we showed that both similarity and complementarity are important organizational principles shaping the structure of social and biological networks and can be linked to interpretable, domain-specific phenomena. (14)

Tao, Terence. E pluribus unum: From Complexity, Universality. Daedalus. 141/3, 2012. In a special issue on Science in the 21st Century, the UCLA polymathematician draws on the latest statistical physics to at last confirm this extant Nature is in fact grounded in and distinguished by an intelligible, recurrent, programmatic quality. Whatever the material realm or substrate the same phenomenal organization appears due to the constant interactions of many communicative entities. As a result, it becomes strongly evident that such an independent formative source or agency must be involved. And how could one not notice, quite fittingly, here anew is the very essence of our archetypal Taoist wisdom.

In this brief survey, I discuss some examples of the fascinating phenomenon of universality in complex systems, in which universal macroscopic laws of nature emerge from a variety of different microscopic dynamics. This phenomenon is widely observed empirically, but the rigorous mathematical foundation for universality is not yet satisfactory in all cases. (Abstract, 23)

A remarkable phenomenon often occurs once the number of components becomes large enough: that is, the aggregate properties of the complex system can mysteriously become predictable again, governed by simple laws of nature. Even more surprising, these macroscopic laws for the overall system are often largely independent of their microscopic counterparts that govern the individual components of that system. One could replace the microscopic components by completely different types of objects and obtain the same governing law at the macroscopic level. When this occurs, we say that the macroscopic law is universal. The universality phenomenon has been observed both empirically and mathematically in many different contexts, several of which I discuss below. In some cases, the phenomenon is well understood, but in many situations, the underlying source of universality is mysterious and remains an active area of mathematical research. (24)

The law of large numbers is one of the simplest and best understood of the universal laws in mathematics and nature, but it is by no means the only one. Over the decades, many such universal laws have been found to govern the behavior of wide classes of complex systems, regardless of the components of a system or how they interact with each other. (25) That the macroscopic behavior of a large, complex system can be almost totally independent of its microscopic structure is the essence of universality. (25)

Tauber, Uwe. Critical Dynamics: A Field Theory Approach to Equilibrium and Non-Equilibrium Scaling Behavior. Cambridge: Cambridge University Press, 2014. A Virginia Tech physicist contributes a technical text that well quantifies the latest and deepest theoretical basis for nature’s self-similar “scale invariance” from physical to planetary realms.

Introducing a unified framework for describing and understanding complex interacting systems common in physics, chemistry, biology, ecology, and the social sciences, this comprehensive overview of dynamic critical phenomena covers the description of systems at thermal equilibrium, quantum systems, and non-equilibrium systems. Powerful mathematical techniques for dealing with complex dynamic systems are carefully introduced, including field-theoretic tools and the perturbative dynamical renormalization group approach, rapidly building up a mathematical toolbox of relevant skills. Heuristic and qualitative arguments outlining the essential theory behind each type of system are introduced at the start of each chapter, alongside real-world numerical and experimental data, firmly linking new mathematical techniques to their practical applications.

Tero, Atsushi, et al. Rules for Biologically Inspired Adaptive Network Design. Science. 327/439, 2010. Along with a news note “Amoeba-Inspired Network Design” in the same issue, how such microbial colonies can be seen as exemplars of self-organizing systems, which are being found to recur throughout nature’s ascendant nest, especially for viable human societies. All of which it is said seems to spring from an independent, universal mathematical source.

Troisi, Alessandro, et al. An Agent-based Approach for Modeling Molecular Self-organization. Proceedings of the National Academy of Sciences. 102/255, 2010. In another example from the recent nonlinear dynamics shift in physics, University of Bologna and Northwestern University researchers search ways to independently articulate and define the universally prevalent, nested complexity that is being found everywhere to distinguish a genesis nature.

Self-organization is one of the most fascinating phenomena in nature. It appears in such apparently disparate arenas as crystal growth, the regulation of metabolism, and dynamics of animal and human behavior. One of the great challenges in the field of complexity is the definition of the common patterns that make possible the emergence of order from apparently disordered systems. One example is given by the scale invariant networks that appear to offer a good perspective for many complex systems. Another possibility is the study of emergent phenomena through agent-based (AB) modeling. In this paper, after defining briefly the principles of AB modeling, we explore the possibility that such a modeling paradigm could be useful for the study of self-organizing chemical systems, complementing the currently used stochastic (Monte Carlo) or deterministic (molecular dynamics) methods. (255)

Tsuchiya, Masa, et al. Local and Global Responses in Complex Gene Regulation Networks. Physica A. 388/1738, 2009. Keio University, Japan, and Istituto Superiore di Sanita, Italy, researchers, including Kumar Selvarajoo and Alessandro Giuliani, employ a statistical physics approach to reveal a network paradigm an intrinsic genome-wide dynamical essence.

One relevant feature of the high degree of connectivity of gene regulation networks is the emergence of collective ordered phenomena influencing the entire genome and not only a specific portion of transcripts. The great majority of existing gene regulation models give the impression of purely local ‘hard-wired’ mechanisms disregarding the emergence of global ordered behavior encompassing thousands of genes while the general, genome wide, aspects are less known. (Abstract)

Biological phenomena, at every scale of definition from protein folding to the structure of ecological systems passing through gene expression regulation and physiology, display two seemingly alternative functioning modes. The first mode can be called “hard wired,” for the possibility to be efficiently described by the node-arrow representation prevalent in modern biology and the second mode (statistical mechanics-like) in which collective phenomena are more important than the specific elements involved. This second (collective) mode, despite successful application in different fields of cell biology still appears under adopted by the scientific community. (1738)

The demonstration that within a clonal population of multipotent progenitor cells, spontaneous non-genetic population heterogeneity primes the cells for different lineage choices and that , in turn, the progression along the differentiation pathways happens in terms of a genome-wide transcriptome displacement asks for a complementation of the classical gene-specific approach to cellular biology with a much wider statistical-mechanics like perspective. (1745)

Valverde, Sergi and Ricard Sole. Self-Organization versus Hierarchy in Open-Source Networks. Physical Review E. 76/046118, 2007. Over the past few years, scale-free networks composed of elemental nodes, which themselves can be complex nets, and are joined in dynamic, interactive linkage, have been found to distinguish every natural and social plane. In this case, email exchanges on the Internet, in contrast to ‘bottom-up’ biologically self-organized systems, can be observed to exhibit a ‘top-down’ degree of centralized direction. Might we then be able to note, I add circa 2008, an evolutionary vector of increasing intention and guidance? Sole, Valverde and their colleagues, based at the Universitat Pompeu Fabra in Barcelona, with international collaboration such as the Santa Fe Institute, are making significant contributions toward the theoretical explanation of a natural genesis. (But in the Physics and Astronomy Classification Scheme (PACS) this journal employs, this work is tacked on to an alien cosmos at the very end as category ‘89.75.Hc.’)

Valverde, Sergi, et al. Structural Determinants of Criticality in Biological Networks. Frontiers of Physiology. May 8, 2015. Valverde and Jordi Garcia-Ojalvo, University of Pompeu Fabra, Barcelona, Sebastian Ohse, Albert-Ludwigs University, Freiburg, along with Malgorzata Turalska and Bruce West, Duke University, finesse these generic anatomical dynamics which seem to universally appear in every development phase of universe and human. Figure 3, Gene Network Evolution has this caption: Natural selection pushes gene regulatory networks toward the critical regime due to the opposing forces of conserving essential network function and allowing for the evolution of potentially beneficial modifications. A favored middle state is then shown as poised between Ordered and Chaotic, once more as a reciprocal, metastable reciprocity.

Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. (Abstract)

Villegas, Pablo, et al. Evolution in the Debian GNU/Linux Software Network: Analogies and Differences with Gene Regulatory Networks. Journal of the Royal Society Interface. February, 2020. In this visionary, consummate year, University of Granada, Spain including Miguel Munoz (search) proceed to recognize many structural and operational parallels between these widely separate domains as they both engage in information processing and conveyance. Convergent comparisons such as this quite imply the reality of an independent mathematical program with a generic neural and genomic essence across all natural and social realms. See also Keil, Petr, et al. Macroecological and Macroevolutionary Patterns Emerge in the Universe of GNU/Linux Operating Systems by Petr Keil et al in Ecography (41/11, 2018).

Gene regulatory networks GRN as they process information in the cell display non-trivial architectural features such as scale-free degree distributions, high modularity and low average distance between connected genes. Such networks result from complex evolutionary and adaptive processes difficult to track empirically. On the other hand, the developmental (or evolutionary) stages of open-software networks that result from self-organized growth across versions are well known. Here, we study the evolution of the Debian GNU/Linux software network, focusing on changes of key structural and statistical features over time. Our results show that this has led to a structure in which the out-degree distribution is scale-free and the in-degree distribution is a stretched exponential. These features resemble closely those shown by GRNs, which suggests the existence of common adaptive pathways for the architectural design of information-processing networks. (Abstract)

Understanding the collective properties stemming from the interactions of a large number of units such as genes, proteins or metabolites is of paramount importance in biology. Theoretical work focusing on the changes over time of self-organizing networks can provide key information about these natural systems. Particularly, network theory provides us with a highly insightful systems-level perspective to extremely complicated biological problems, which has helped advance knowledge in fields such as neuroscience, ecology and epidemiology. The study of information processing in living systems has greatly benefited from this network perspective, complementing parallel endeavours for the analysis of single pathways, and providing a much richer understanding of collective phenomena emerging from a large number of basic inter-related units. (1)

Visentin-Bugoni, Jeferson, et al. Structure, Spatial Dynamics and Stability of Novel Seed Dispersal Mutualistic Networks in Hawai’i. Science. 364/78, 2019. Eight systems ecologists posted in Illinois, Wyoming, New Hampshire, and Honolulu report the presence of common topological forms as alien fauna and flora proceed to invade complex ecosystems. We thus record the presence of an independent mathematical source in universal formative effect.

Increasing rates of human-caused species invasions and extinctions may reshape communities and modify the structure, dynamics, and stability of species interactions. To investigate how such changes affect communities, we performed multiscale analyses of seed dispersal networks on Oahu, Hawaii. Networks consisted exclusively of novel interactions, were largely dominated by introduced species, and exhibited specialized and modular structure at local and regional scales, despite high interaction dissimilarity across communities. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide. Our findings suggest that the emergence of complex network structure, and interaction patterns may be highly conserved, regardless of species identity and environment. (Abstract)

Vitiello, Giuseppe. On the Isomorphism between Dissipative Systems, Fractal Self-Similarity and Electrodynamics: Toward an Integrated Vision of Nature. Systems. 2/203, 2014. In this online journal, the University of Salerno theoretical physicist summarizes two decades of studies, with colleagues, upon a universal form and theme that seems to be exemplified and repeated in kind everywhere. The project is to achieve a unified, viable “living matter physics” situated in and aligned with a conducive quantum cosmos. See also Fractals, Coherent States and Self-Similarity Induced Noncommutative Geometry by GV at arXiv:1206.1854.

One more aspect which is related with the discussion here presented concerns with the description of fractal-like structures with self-similarity properties in terms of non-homogeneous Bose condensation. Indeed, in the present scheme they appear to be generated by coherent SU(1; 1) quantum condensation processes at the microscopic level, similar to “extended objects” or macroscopic quantum systems. The macroscopic appearances (forms) of the fractals seems to emerge out of a process of morphogenesis as the macroscopic manifestation of the underlying dissipative, coherent quantum dynamics at the elementary level. An integrated vision of Nature resting, in its essence, on the paradigm of coherence and dissipation thus emerges. Nature appears to be modulated by coherence, rather than being hierarchically layered in isolated compartments, in multi-coded collections of isolated systems and phenomena. (213)

The DNA genetic code appears in conclusion to be the output of the coherent dynamics. In this way, it is subtracted from its purely phenomenological characterization, which is sometimes at the origin of dogmatic or even miraculous beliefs. In this view, DNA appears to be the vehicle through which the laws of form express themselves in living systems and coherence and its deformations propagate through duplication and multiplication processes. (214)

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