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

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

Wurthner, Laeschkir, et al. Bridging Scales in a Multiscale Pattern-Forming System. arXiv:2111.12043. Ludwig-Maximilians-Universitat, Munchen and Delft University of Technology theorists including Erwin Frey advance studies of self-organizing structural qualities of from proteins to organisms. Their purpose is thus to reveal and express the occurrence of general, ultimately physical, principles and forces which serve as an independent source-code for life’s evolutionary and metabolic occasion.

Self-organized pattern formation is vital for many biological processes. Mathematical modeling using reaction-diffusion models has advanced our understanding of how biological systems develop spatial structures. However, biological processes inherently involve multiple spatial and temporal scales and transition from one pattern to another over time. Here, we describe mass-conserving reaction-diffusion systems that can reconstruct information about patterns across the large-scale dynamics. We illustrate by the Min protein system which produces multiscale patterns in a spatially heterogeneous geometry. Since conservation laws are inherent in many different physical environs, our general approach can uncover underlying principles in pattern-forming systems. (Abstract excerpt)

Yang, Ang and Yin Shan, eds. Intelligent Complex Adaptive Systems. Hershey, PA: IGI Publishing, 2008. This technical volume illustrates a revolution in conceptual modeling as applied across a wide range from computational processes to international conflicts. All such phenomena can now be expressed as universally manifest multi-agent, interactive, modular, information-driven dynamic networks.

Yang, Haiqian, et al. Configural Fingerprints of Multicellular Living Systems. Proceedings of the National Academy of Sciences. 118/44, 2021. Seven bioengineers from MIT, University of Ottawa, and Northeastern University quantify deeper rootings of life’s evolutionary sequential course into invariant physical phenomena such as dynamic state transitions. As substantial matter is found to possess an active spontaneity, it becomes a fertile soil for regnant flora and fauna.

Cells cooperate as groups to achieve structure and function at the tissue level, during which specific material characteristics emerge. Analogous to phase transitions in classical physics, transformations in multicellular assemblies are essential for a variety of vital processes including morphogenesis, wound healing, and cancer. In this work, we develop configurational fingerprints of particulate and multicellular assemblies and extract volumetric and shear order parameters to quantify the system disorder. These two parameters form a complete and unique pair of signatures for the structural disorder of a multicellular system. (Abstract excerpt)

Tissues are composed of many cells that coordinate in space, through which structural formations emerge. While recent progress has shown that many biological processes are analogous to material phase transitions, a systematic framework to describe the spatial order of complex living systems has not yet occurred. We develop a unified method to quantify the evolution of spatial order across different types of disordered systems, including jammed thermal systems, 2D cell monolayers, 3D epithelial spheroids, and Drosophila embryos. Using scaling analysis, we show successful differentiation of gas-like, liquid-like, and solid-like phases in various living systems. (Significance)

Yeung, Chi Ho, et al. From the Physics of Interacting Polymers to Optimizing Routes on the London Underground. Proceedings of the National Academy of Sciences. 110/13717, 2013. As the Abstract and Synopsis detail, Aston University, Birmingham, UK, and Hong Kong University of Science and Technology, systems physicists quantify nature’s universal preference for metabolic movement from biochemicals to biocities, so as carry it forth for a better organic design of our human scale dynamic systems.

Optimizing paths on networks is crucial for many applications, ranging from subway traffic to Internet communication. Because global path optimization that takes account of all path choices simultaneously is computationally hard, most existing routing algorithms optimize paths individually, thus providing suboptimal solutions. We use the physics of interacting polymers and disordered systems to analyze macroscopic properties of generic path optimization problems and derive a simple, principled, generic, and distributed routing algorithm capable of considering all individual path choices simultaneously. We demonstrate the efficacy of the algorithm by applying it to: (i) random graphs resembling Internet overlay networks, (ii) travel on the London Underground network based on Oyster card data, and (iii) the global airport network. (Abstract)

From Polymer Physics to Quicker Commuter Travel. Whether planning water distribution routes, military convoy movements, internet traffic, or simply the best way to the airport, path optimization algorithms are essential for everyday logistics. Global optimization techniques that consider all path choices simultaneously are computationally difficult. As a result, most existing routing algorithms choose paths individually, but these methods tend to favor the shortest path regardless of the choice’s impact on other routes. Chi Ho Yeung et al. have borrowed from the physics of polymers to create a simple, generic, and distributed global path optimizing algorithm. The researchers tested their statistical physics-based technique on large real-world data sets, including the London Underground subway system and global air traffic. Compared to current methods, the algorithm decreased overall congestion at the cost of a slightly longer path length. (PNAS Summary)

Yu, Haiyuan and Mark Gerstein. Genomic Analysis of the Hierarchical Structure of Regulatory Networks. Proceedings of the National Academy of Sciences. 103/14724, 2006. Genomic systems employ a consistent network motif to achieve viable translation, which is found to be the same organization as present in human societies. Another contribution to the discovery of a natural genesis that recycles a common pattern and process from atom to cosmos.

A fundamental question in biology is how the cell uses transcription factors (TFs) to coordinate the expression of thousands of genes in response to various stimuli. The relationship between TFs and their target genes can be modeled in terms of directed regulatory networks. These relationships, in turn, can be readily compared with commonplace “chain-of-command” structures in social networks, which have characteristic layouts. (14724) In general, our results show that there is a pyramid-shaped hierarchical structure in regulatory networks, which is well organized in a clearly nonrandom manner. The decision making scheme in this hierarchy is a cogitation-like multistep process. (14730)

Zhang, Mengsen, et al. Connecting Empirical Phenomena and Theoretical Models of Biological Coordination across Scales. Journal of the Royal Society Interface. Online August, 2019. By way of sophisticated procedures, Center for Complex Systems and Brain Sciences, Florida Atlantic University researchers MZ, Chris Beetle, Scott Kelso and Emmanuelle Tognoli (search SK & ET) uncover intrinsic mathematic reciprocities which seem to imbue and guide small group social interactions. These patterns are then seen to suffuse organic and cerebral behaviors so at to reveal a broader scale-invariance. See also Critical Diversity: Divided or United States of Social Coordination by this group in PLoS One (April 4, 2018) which alludes to a chimeric dynamics.