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

1. Network Physics: A Vital Interlinked Anatomy and Physiology

Kenett, Dror, et al. Networks of Networks. Chaos, Solitons, & Fractals. 80/1, 2015. With coauthors Matjaz Perc and Stefano Boccaletti, an introduction to an issue in preparation on this latest expansion of network science. As the second quotes notes, akin to other current work such as Scott Tremaine’s study of planetary systems, an endeavor is made to situate, and interpret such ubiquitous organic phenomena by way of statistical physics theory.

Recent research and reviews attest to the fact that networks of networks are the next frontier in network science. Not only are interactions limited and thus inadequately described by well-mixed models, it is also a fact that the networks that should be an integral part of such models are often interconnected, thus making the processes that are unfolding on them interdependent. From the World economy and transportation systems to social media, it is clear that processes taking place in one network might significantly affect what is happening in many other networks. Within an interdependent system, each type of interaction has a certain relevance and meaning, so that treating all the links identically inevitably leads to information loss. Networks of networks, interdependent networks, or multilayer networks are therefore a much better and realistic description of such systems, and this Special Issue is devoted to their structure, dynamics and evolution, as well as to the study of emergent properties in multi-layered systems in general. Topics of interest include but are not limited to the spread of epidemics and information, percolation, diffusion, synchronization, collective behavior, and evolutionary games on networks of networks. (Abstract)

Ever since the discovery of network reciprocity by Nowak and May (1992), who showed that in social dilemmas cooperators can survive by forming compact clusters in structured populations, the evolution of cooperation on lattice, networks and graphs has been a vibrant topic across social and natural sciences. The emergence of cooperation and the phase transitions leading to other favorable evolutionary outcomes depend sensitively on the structure of the interaction network and type of competing strategies. Studies making use of statistical physics and network science have led to significant advances in our understanding of the evolution of cooperation. (3-4)

Kepes, Francois, ed. Biological Networks. Singapore: World Scientific, 2008. Over the past decade within the field of complexity studies, the ubiquitous presence of scale-free, web-like, systems of weighted nodes and links has been well quantified and found across natural and societal kingdoms. This volume of international players such as Ricard Sole and Neo Martinez surveys their common, recurrent properties.

Khanra, P., et al. Endowing Networks with Desired Symmetries and Modular Behavior. arXiv:2302.10548. Ten system scientists in the USA, India, Spain, and Italy including Stefano Boccaletti post a latest example of on-going theoretical distillations of an actual independent, universal, genetic domain with these additional life-friendly, anatomy/physiological attributes.

Symmetries in a network regulate its organization into functional clustered states. Given a generic ensemble of nodes and a desirable cluster (or group of clusters), we exploit the direct connection between the elements of the eigenvector centrality and the graph symmetries to generate a network equipped with the desired cluster(s), with such a synthetical structure being furthermore perfectly reflected in the modular organization of the network's functioning. Our results solve a relevant problem of reverse engineering, and are of generic application in all cases where a desired parallel functioning needs to be blueprinted.

Synchronization of networked units is a behavior observed far and wide in natural and man made systems: from brain dynamics and neuronal firing, to epidemics, or power grids, or financial networks [1–10]. It may either correspond to the setting of a state in which all units follow the same trajectory [11–13], or to the emergence of structured states where the ensemble splits into different subsets each one evolving in unison. This latter case is known as cluster synchronization (CS) [14–30], and is the subject of many studies in both single-layer [20, 21] and multilayer networks [31, 32]. Swarms of animals, or synchrony (within sub units) in power grids, or brain dynamics are indeed relevant examples of CS (1)

Kiani, Narsis, et al, eds. Networks of Networks in Biology: Concepts, Tools and Applications.. Cambridge: Cambridge University Press,, 2021. Into the 2020s, this collection is indicative of a nascent phase of a convergent commonality across a wide array of living system phenomena.

Biological systems are very complex with emergent properties that cannot be explained by their individual parts. As the amount of available data grows, it becomes important to be able to analyse and integrate large data sets. This book introduces novel approaches and solutions to the Big Data problem in biomedicine, and presents new techniques in the field of graph theory. By discussing relevant problems and techniques, researchers will gain insights in the life sciences through the concept of 'network of networks'.

Kitsak, Maksim. Latent Geometry for Complementary Driven Networks. arXiv:2003.06665. A Northeastern University, Network Science Institute physicist elucidates another innate proclivity that networlds everywhere commonly appear to possess. As the abstract notes, reciprocal forms and/or actions seem to be drawn together so as to conceive a beneficial, more effective whole.

Networks of interdisciplinary teams, biological interactions as well as food webs are examples of networks that are shaped by complementarity principles: connections in these networks are preferentially established between nodes with complementary properties. We propose a geometric framework for this property by first noting that traditional methods which embed networks into latent metric spaces are not applicable. We then consider a cross-geometric representation which (i) follows naturally from the complementarity rule, (ii) is consistent with the metric property of the latent space, (iii) reproduces structural properties of real complementarity-driven networks and (iv) allows for prediction of missing links with accuracy surpassing similarity-based methods. (Abstract excerpt)

Kivela, Mikko, et al. Multilayer Networks. Journal of Complex Networks. 2/3, 2014. In this new Oxford journal, systems mathematicians from the UK, Spain, France and Ireland, including Mason Porter, post a 59 page introductory survey with 376 references that has become, along with Stefano Boccaletti’s work (search), a prime document for this latest expansion of nature’s intrinsic vitalities.

In most natural and engineered systems, a set of entities interact with each other in complicated patterns that can encompass multiple types of relationships, change in time, and include other types of complications. Such systems include multiple subsystems and layers of connectivity, and it is important to take such "multilayer" features into account to try to improve our understanding of complex systems. The origins of such efforts date back several decades and arose in multiple disciplines, and now the study of multilayer networks has become one of the most important directions in network science. In this paper, we discuss the history of multilayer networks (and related concepts) and review the exploding body of work on such networks. To unify the disparate terminology in the large body of recent work, we discuss a general framework for multilayer networks, construct a dictionary of terminology to relate the numerous existing concepts to each other, and provide a thorough discussion that compares, contrasts, and translates between related notions such as multilayer networks, multiplex networks, interdependent networks, networks of networks, and many others. (Abstract)

Kleineberg, Kij-Kolja, et al. Hidden Geometric Correlations in Real Multiplex Networks. Nature Physics. 12/11, 2016. University of Barcelona and Cyprus University of Technology researchers including Martin Boguna tease out nature’s intricate orderliness by way of deeply persistent topological interconnections. In this regard, such phenomena serves as an independent source which becomes exemplified in kind across every cosmos to creature scale and instance.

Real networks often form interacting parts of larger and more complex systems. Examples can be found in different domains, ranging from the Internet to structural and functional brain networks. Here, we show that these multiplex systems are not random combinations of single network layers. Instead, they are organized in specific ways dictated by hidden geometric correlations between the layers. We find that these correlations are significant in different real multiplexes, and form a key framework for answering many important questions. Specifically, we show that these geometric correlations facilitate the definition and detection of multidimensional communities, which are sets of nodes that are simultaneously similar in multiple layers. They also enable accurate trans-layer link prediction, meaning that connections in one layer can be predicted by observing the hidden geometric space of another layer. And they allow efficient targeted navigation in the multilayer system using only local knowledge, outperforming navigation in the single layers only if the geometric correlations are sufficiently strong. (Abstract)

Klimm, Florian, et al. Individual Node’s Contribution to the Mesoscale of Complex Networks. New Journal of Physics. 16/125006, 2014. After much identification and study of modules, hubs, and communities in living, interconnective systems, Humboldt University, Qatar Computing Research Institute, and Universitat Pompeu Fabra, Barcelona researchers including Jurgen Kurths, can now technically describe the place, importance and contribution of each discrete node, element, entity, in their relative dynamic network setting.

The analysis of complex networks is devoted to the statistical characterization of the topology of graphs at different scales of organization in order to understand their functionality. While the modular structure of networks has become an essential element to better apprehend their complexity, the efforts to characterize the mesoscale of networks have focused on the identification of the modules rather than describing the mesoscale in an informative manner. Here we propose a framework to characterize the position every node takes within the modular configuration of complex networks and to evaluate their function accordingly. For illustration, we apply this framework to a set of synthetic networks, empirical neural networks, and to the transcriptional regulatory network of the Mycobacterium tuberculosis. We find that the architecture of both neuronal and transcriptional networks are optimized for the processing of multisensory information with the coexistence of well-defined modules of specialized components and the presence of hubs conveying information from and to the distinct functional domains. (Abstract)

The representation of real systems as complex networks has become a successful practice in the literature across different scientific disciplines: biology, technology, sociology, climatology, etc. Graph analysis allows us to describe the topological organization of the constituents of a multi-component system and uncover their functional implications. This is of particular relevance in physiology whose central aim is to understand the biological function of the observed anatomical structures. For example, recent studies indicated that such networks are highly complex in terms of dynamic reorganization in multiple hierarchical levels, highlighting the necessity to treat the system in an integrative manner. Brain networks, both anatomical and functional, have properties supporting brains function. There is also growing evidence of how alterations in connectivity lead to brain malfunction or disease, and vice versa. (1)

Kojaku, Sadamori and Naoki Masuda. Finding Multiple Core-Periphery Pairs in Networks. arXiv:1702.06903. University of Bristol engineering mathematicians describe this common topological phenomena (search Porter) and then evince its presence across social, infrastructure and political settings.

With a core-periphery structure of networks, core nodes are densely interconnected, peripheral nodes are connected to core nodes to different extents, and peripheral nodes are sparsely interconnected. Core-periphery structure composed of a single core and periphery has been identified for various networks. However, analogous to the observation that many empirical networks are composed of densely interconnected groups of nodes, i.e., communities, a network may be better regarded as a collection of multiple cores and peripheries. For example, we find distinct core-periphery pairs with different political leanings in a network of political blogs and separation between international and domestic subnetworks of airports in some single countries in a world-wide airport network. (Abstract)

Kostic, Daniel. Mechanistic and Topological Explanations. Synthese. 195/1, 2018. An introduction by a University of Paris Sorbonne scholar to this special issue, coedited by DK and Philip Huneman. We earlier entered in 2016 Kostic’s full paper, The Topological Realization, online in 2016, which argued that this current relational, network turn need be given a proper philosophical appreciation. With a notice of gene regulatory, physiological, neural nets, and more it is averred that such a basis is vital so to move beyond a prior particulate emphasis. See also herein Diversifying the Picture of Explanations in Biological Sciences by P. Huneman, Mechanisms Meet Structural Explanation by Laura Felline, and Network Representation and Complex Systems by Charles Rathkopf.

Kostic, Daniel. The Topological Realization. Synthese. Online October, 2016. A University of Paris philosopher attempts to give full notice to these heretofore unappreciated interconnective, network structural properties of natural and social systems, along with their prior nodal, discrete components. The special Synthese issue this paper is included in is now available as 195/1 January 2018, search DK for his Introduction and its contents.

In this paper, I argue that the newly developed network approach in neuroscience and biology provides a basis for formulating a unique type of realization, which I call topological realization. Some of its features and its relation to one of the dominant paradigms in the sciences, i.e. the mechanistic one, are already being discussed in the literature. But the detailed features of topological realization, its explanatory power and its relation to another prominent view, namely the semantic one, have not yet been discussed. I argue that topological realization is distinct from mechanistic and semantic ones because this framework is not based on local realisers, regardless of the scale but on global realizers. Furthermore, topological realization enables us to answer the “why” questions, which make it explanatory. (Edited Abstract)

Kostic, Daniel, et al. Unifying the Essential Concepts of Biological Networks. Philosophical Transactions of the Royal Society B. February, 2020. DR, University of Bordeaux, Claus Hilgetaf, University Medical Center Hamburg, and Marc Tittgemeyer, MPI Metabolism Research introduce a special issue with this integrative title. Its content is composed of both life science and philosophical considerations since both views need join together. For example, see General Theory of Topological Explanations and Explanatory Asymmetry by D. Kostic, Hierarchy and Levels by William Bechtel, Exploring Modularity by Maria Serban, and Network Architectures Supporting Learnability by Perry Zurn and Danielle Bassett, From Inert Matter to Global Society by David Chavalarias and Evolving Complexity by Richard Sole and Sergi Valverde (search for these last three).

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organizational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels and network hierarchies. (Abstract)

Our organism constantly integrates information about the internal state with external environmental cues to adapt behavioural and autonomic responses to ensure physiological homeostasis. The Translational Neurocircuitry Group investigates how the human brain represents, integrates and prioritizes these internal and external signals to initiate adequate behavioural and physiological responses with a special focus on circuit-level models, metabolic mechanisms and human cognition. (Marc Tittgemeyer)

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