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

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

Mumford,, David, et al. Indra’s Pearls. Cambridge: Cambridge University Press, 2002. A visually impressive book to convey how fast computers can now give colorful exposition to the intricate mathematics of the early 20th century, especially those of Felix Klein. By these insights and methods, an intricate fractal self-similarity seems to pervade nature at every scale. These findings are next seen to affirm the ancient Buddhist vision of reality as a net or web of jewels whence the entire universe is reflected in each pearl. These equations and images convey a universally repeated interrelationship, a mutual identity, among every domain and member of the cosmos.

Making a statement equally faithful to both mathematics and religion, we can say that each part of our pictures contains within itself the essence of the whole. (xix)

Nacher, Jose and T. Ochiai. Emergent Principles in Gene Expression Dynamics. Open Bioinformatics Journal. 5/34, 2011. We place this online contribution by Future University-Hakodate, Complex and Intelligent Systems, and Toyama Prefectural University, Japan, bioengineers in Universal Principles as an example of how complex network phenomena is being found to infuse this genomic domain, and as many papers today wherein the authors trace their exemplary presence and role to an implied independent, archetypal source. By so doing, akin to more articles in Nature Scientific Reports and such journals, a once and future doubleness is verified of a manifest phenotype, and these waxing admissions of an informative genotype.

Rapid advances in data processing of genome-wide gene expression have allowed us to get a first glimpse of some fundamental laws and principles involved in the intra-cellular organization as well as to investigate its complex regulatory architecture. However, the identification of commonalities in dynamical processes involved in networks has not followed the same development. In particular, the coupling between dynamics and structural features remains largely uncovered. Here, we review several works that have addressed the issue of uncovering the gene expression dynamics and principles using micro-array time series data at different environmental conditions and disease states as well as the emergence of criticality in gene expression systems by using information theory. Moreover, we also describe the efforts done to explore the question of characterizing gene networks by using transcriptional dynamics information. The combination of the emergent principles uncovered in the transcriptional organization with dynamic information, may lead to reconstruct, characterize and complete gene networks. (Abstract)

Universality in Systems Biology The molecular interactions within a cell are very complex and their direct study poses enormous difficulties from experimental and theoretical view point. However, the cell is not the only example of complexity. We are surrounded by many disparate complex systems like, for example, financial systems, social networks, fluid dynamics and Internet evolution. In these cases, it is simply impracticable to solve and predict the behavior of single stock prices, individuals, water atoms and web pages, respectively. In spite of that, these systems often show a remarkably simple behavior and commonalities. (35)

Criticality If we think in terms of atomic matter, fluids or even larger-scales like social networks, populations, cities or ecosystems, we observe that these systems are composed of multiple fundamental elements or individuals that interplay by means of physical forces, social relationships or information exchange. While these interactions are originated by intrinsic features of the systems, external forces, like electromagnetic and gravitational fields, social rules as well as drastic and severe climate changes, may also drive the evolution of the system. An intriguing phenomena is that even though intrinsic and extrinsic forces co-exist, it seems that systems share a high degree of commonality and behavior, which seems to be independent of the nature and details of the system itself. (36)

Nakamura, Eita and Kunihiko Kaneko. Statistical Evolutionary Laws in Music Styles. arXiv:1809.05832. Kyoto University and University of Tokyo complexity theorists perceive and quantify the same stochastic motifs and movements within musical compositions as those that are constantly present across life’s developmental course. See also Higor Sigaki, et al (below) for similar appearances throughout artistic schools.

If a cultural feature is transmitted over generations and exposed to stochastic selection when spreading in a population, its evolution may be governed by statistical laws, as in the case of genetic evolution. Music exhibits steady changes of styles over time, with new characteristics developing from traditions. Recent studies have found trends in the evolution of music styles, but little is known about quantitative laws and theories. Here we analyze Western classical music data and find statistical evolutionary laws.. The model reproduces the observed statistical laws and its predictions are in good agreement with real data. We conclude that some trends in music culture can be formulated as statistical evolutionary laws and explained by the evolutionary model incorporating statistical learning and the novelty-typicality bias. (Abstract)

Norris, Vic. What Properties of Life Are Universal? Substance-Free, Scale-Free Life. Origins of Life and Evolution of Biospheres. Online March, 2015. The University of Rouen biologist posts a succinct list of eight properties that serve to distinguish living systems. As the Abstract notes, they are a balance of stability and change, diversity, dual survival and growth, complementary biomolecules, nested hierarchies, pervasive networks, sensory perceptions, and subjective experience. The especial point is made that these qualities appear repeatedly for every sequential stage or species entity. In regard, the paper is a good instance of an ability to specify life’s constant lineaments, which can then be seen to have a common independence of their own. So these insights are another advance to realizations of a natural genetic endowment which would be present and exemplify in just this fashion.

One approach to answering the question of what properties of life are universal is to try to answer the question of what are the essential properties of biology’s best understood model organism, Escherichia coli. One of these properties is competitive coherence whereby E. coli reconciles the generation of a coherent cell state with the generation of a coherent sequence of cell states. The second property is differentiation which occurs ineluctably when E. coli divides. The third property is dualism which is how E. coli navigates between the two main attractors of phenotypes – survival and growth – which are based on quasi-equilibrium and non-equilibrium structures, respectively. The fourth property is complementarity: the interactions between the molecules and macromolecules that constitute E. coli protect them from degradation and confer new properties. The fifth property is multi-scale existence: E. coli exists at levels extending from the bacterium to the global super-organism.

The sixth property is maintenance of connectivity; growth alters connectivity and, in the case of E. coli, alters the phenotype. The seventh property is the combination of intensity sensing (the constituents can work no harder) and quantity sensing (too much unused material has been made); this combination is used by E. coli to drive its cell cycle and thereby generate an environmentally adapted population of cells. The eighth property is subjective experience which exists even at the level of a single E. coli but which only becomes important at higher levels of organisation. I propose that the search for life at other times and in other places be based on the above eight universal properties and be independent of both particular substances and spatio-temporal scales. (Abstract)

Competitive coherence is a universal property of life insofar as the systems in which competitive coherence occurs are either alive themselves or comprise elements that are alive. At the level of a bacterium, growth and survival require selection of an active subset of macromolecules in response to external and internal conditions; such responses entail both the generation of a coherent cell state, in which the cell’s content work together efficiently and harmoniously, and the generation of a coherent sequence of cell states. (2)

Nowak, Martin. Evolutionary Dynamics. Cambridge: Harvard University Press, 2006. An array of technical chapters by the Harvard mathematical biologist which collect and expand on applications of game theory, broadly conceived, to fitness strategies in evolving populations from microbes to language-based societies. As noted in a New York Times article for July 31, 2007, by these insights an innate propensity for cooperation can be added to mutation and selection. Nowak is also co-director with Sarah Coakley of the Evolution and Theology of Cooperation Project at Harvard, Google name to reach its Templeton Foundation website.

Oborny, Beata. The Plant Body as a Network of Semi-Autonomous Agents. Philosophical Transactions of the Royal Society B. April, 2019. A Lorand Eotvos University, Budapest systems botanist shows how even life’s flora phase is distinguished and enabled by agent/link network modularities as they sense, process and convey vital information. See also Percolation Theory Suggests Some General Features Across Environmental Gradients by BO and Robert Juhasz at arXiv:1909.00585.

Plants can solve many difficult tasks while adjusting their growth and development to the environment. They can explore and exploit several resources, even when their distributions vary in space and time. Current research has found that the functional use of modular features enables the plant to adjust a flow of information and resources to ever changing conditions. Experiments have yielded many results about these processes but a theoretical model to encompass the high number of components and interactions has lagged behind. In this paper, I propose a framework on the basis of network theory, viewing the plant as a group of connected, semi-autonomous agents. I review some characteristic plant responses to the environment through changing the states of agents and/or links. (Abstract excerpt)

Oltvai, Zoltan and Albert-Laszlo Barabasi. Life’s Complexity Pyramid. Science. 298/763, 2002. A synoptic report on new research results and evidence about how nature is arrayed in an emergent scale where the same form and dynamics are in effect everywhere.

At the lowest level, these components form genetic-regulatory motifs or metabolic pathways (level 2), which in turn are the building blocks of function modules (level 3). These modules are nested, generating a scale-free hierarchical architecture (level 4). Although the individual components are unique to a given organism, the topologic properties of cellular networks share surprising similarities with those of natural and social networks. This suggests that universal organizing principles apply to all networks, from the cell to the World Wide Web. (763)

Palese, Luigi and Fabrizio Bossis. The Human Extended Mitochondrial Metabolic Network. BioSystems. Online April, 2012. University of Bari, Italy, physicians find an organism’s broad class of lipid biochemicals, in their systemic physiology, to similarly exhibit nature’s universal interactive geometries.

One of the most striking aspects of complex metabolic networks is the pervasive power-law appearance of metabolite connectivity. However, the combinatorial diversity of some classes of compounds, such as lipids, has been scarcely considered so far. In this work, a lipid-extended human mitochondrial metabolic network has been built and analyzed. It is shown that, considering combinatorial diversity of lipids and multipurpose enzymes, an intimate connection between membrane lipids and oxidative phosphorilation appears. This finding leads to some biomedical considerations on diseases involving mitochondrial enzymes. Moreover, the lipid-extended network still shows power-law features. Power-law distributions are intrinsic to metabolic network organization and evolution. (Abstract, 1)

Perez Velazquez, Jose. Finding Simplicity in Complexity: General Principles of Biological and Nonbiological Organization. Journal of Biological Physics. 35/209, 2009. As many disparate scientific fields converge on the same patterns and processes, a University of Toronto, Hospital for Sick Children, neurophysician muses that a common, infinite iteration must inhere as their source. To illustrate it is shown that neuronal dendrites, tree branches, river beds, lung bronchioles, gene phylogenies, blood capillaries, and lightning strikes exhibit the same network structure. See Towards a Statistical Mechanics of Consciousness at arXiv:1606.00821 with JPV as a coauthor for a further entry.

What differentiates the living from the nonliving? What is life? These are perennial questions that have occupied minds since the beginning of cultures. The search for a clear demarcation between animate and inanimate is a reflection of the human tendency to create borders, not only physical but also conceptual. It is obvious that what we call a living creature, either bacteria or organism, has distinct properties from those of the normally called nonliving. However, searching beyond dichotomies and from a global, more abstract, perspective on natural laws, a clear partition of matter into animate and inanimate becomes fuzzy. Based on concepts from a variety of fields of research, the emerging notion is that common principles of biological and nonbiological organization indicate that natural phenomena arise and evolve from a central theme captured by the process of information exchange. Thus, a relatively simple universal logic that rules the evolution of natural phenomena can be unveiled from the apparent complexity of the natural world. (Abstract)

Perez-Mercader, Juan. Scaling Phenomena and the Emergence of Complexity in Astrobiology. Gerda Horneck and Christa Baumstark-Khan, eds. Astrobiology. Berlin: Springer, 2002. Deep in the scientific literature a new universe is being described which arises by emergent, nested sequential stages. Perez-Mercader contends that these phases from biomolecules to human persons to galactic networks are distinguished by a universality whereby the same, invariant form and process recurs over and over.

Finally, among the main patterns we can identify a systematic presence of systems within systems, within systems: planetary systems, within galaxies, within clusters of galaxies, or bases within DNA molecules, within chromosomes, within cell nuclei, within cells, etc. (339)

Picoli, S., et al. Scale-Invariant Structure of Size Fluctuations in Plants. Scientific Reports. 2/Article 328, 2012. Universidade Estadual de Maringá, Brazil, physicists untangle nature’s floral profusion by way of complex systems science to lately decipher this recurrent, recursive, “analogy of proper proportion” (Aquinas) scripture. See also Picoli and Mendes in Religion and Science.

A wide range of physical and biological systems exhibit complex behaviours characterised by a scale-invariant structure of the fluctuations in their output signals. In the context of plant populations, scaling relationships are typically allometric. In this study, we analysed spatial variation in the size of maize plants (Zea Mays L.) grown in agricultural plots at constant densities and found evidence of scaling in the size fluctuations of plants. The findings indicate that the scaling of the probability distribution of spatial size fluctuation exhibits non-Gaussian behaviour compatible with a Lévy stable process. The scaling relationships were observed for spatial scales spanning three orders of magnitude. These findings should provide additional information for the selection and development of empirically accurate models of pattern formation in plant populations.

Potirakis, Stelios, et al. Dynamical Analogy between Economical Crisis and Earthquake Dynamics within the Nonextensive Statistical Mechanics Framework. Physica A. Online February, 2013. University of Athens physicists drawn upon these thermodynamic theories of Constantino Tsallis to discern across disparate realms the presence of deep similarities, which are extended to seizures, magnetic storms and solar flares. So are we closing on a great historic realization, as other ages and cultures long aver, of an infinitely recurrent natural creation which so springs as if by universally applicable, genetic-like code. See also in regard “The Earth as a Living Planet” at arXiv:1210.4804 (October 2012) by Y. Contoyiannis, with Potirakis, whence more analogies are noted between geological criticalities and human physiology.

The field of study of complex systems considers that the dynamics of complex systems are founded on universal principles that may be used to describe a great variety of scientific and technological approaches of different types of natural, artificial, and social systems. Several authors have suggested that earthquake dynamics and the dynamics of economic (financial) systems can be analyzed within similar mathematical frameworks. We apply concepts of the nonextensive statistical physics, on time-series data of observable manifestations of the underlying complex processes ending up to these different extreme events, in order to support the suggestion that a dynamical analogy exists between a financial crisis (in the form of share or index price collapse) and a single earthquake. (Abstract)

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