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

A. A Procreative Ecode: An Ecosmome to Geonome Complementary Hereditary Endowment

Ge, Xiaofei, et al. Self-Organized Critical Dynamics of RNA Virus Evolution. arXiv:2204.08627. We cite this entry by Tsinghua University, Beijing and University of Paris researchers amongst a rush of nonlinear COVID studies which show how its etiologies can be deeply modeled complex network science. Once again, even in highly stressed, variegated disease pandemic, these mathematic dynamics seek and reside at a default condition poised between more or less relative order. A payoff would be that the past two intense years of such findings could result in methods to identify, prevent and control future epidemics

Studies of RNA virus (e.g., SARS-CoV-2) evolution are vital for understanding molecular evolution and medicine development but so far remain insufficient. Here, we characterize the RNA virus evolution as a physical system with absorbing states and avalanche behaviors. This approach maps biological data (e.g., phylogenetic tree and infection) to a general stochastic process which enables researchers to verify a self-organized criticality underlying RNA virus evolution. We find that SARS-CoV-2 exhibits scale-invariant avalanches as mean-field theory predicts. The lineages that emerge from such critical evolution coincidentally also match the Delta variant. (Abstract excerpt)

Guan, Shaohua. Universal scaling relation and criticality in bacterial metabolism and growth. arXiv:2308.04776. Four Chinese Academy of Sciences system theorists deftly apply the latest criticality findings so to perceive their optimum invariant occasion across life's earlier phases. Into mid 2923, the evidence grows broadly stronger by the weekly postings

The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. In this study, we employ a maximum entropy approach to investigate the universality in various constraint-based metabolic networks of Escherichia coli. Our findings reveal the existence of universal scaling relations across different nutritional environments and metabolic network models, similar to the universality observed in physics. By analyzing single-cell data, we confirm that bacterial metabolism operates close to the state with maximum Fisher information, which serves as a signature of criticality. This critical state provides functional advantages such as high sensitivity and long-range correlation. Moreover, we demonstrate that a metabolic system operating at criticality achieves an optimal balance between growth and adaptation, thereby serving as a survival strategy in fluctuating environments. (Abstract)

Hancock, Fran, et al. Metastability Demystified—The Foundational Past, the Pragmatic Present, and the Potential Future. preprints202307.1445.v1.pdf.. King's College London, University of Sussex, University of Newcastle, Australia, Florida Atlantic University, Oxford and Montreal Neurological Institute including Fernando Rosas, Scott Kelso and Andrea Luppi provide a latest comprehensive survey of wide and deep tendencies to arrange and optimize cerebral functions as a best bicameral balancing act between chimera-like more or less coherent states. Once again into 2024 these many findings, aka self-organized criticalities, approach a proven mathematical veracity which contribute to manifold discoveries of a natural universality across the infinities. See also The Squiggle Sense: The Complementary Nature and the Metastable Brain~Mind by Scott Kelso and David Engstrom (Springer, 2024) for another version.

Healthy brain functioning depends on stable integration between areas for coordinated functioning to reconfigure and express localization. Metastability, a concept that joins statistical physics and dynamical systems theory, could be a key signature of this trait. In regard, the neuroscience literature has used markers of metastability to attribute brain functions such as cognitive performance, healthy ageing, meditation, sleep, and pharmacological issues to psychiatric disorders. In this paper we review metastability neuroscience, covering its scientific and historical foundations and to estimate it in empirical data. (Excerpts)

The notion of “metastability” has been increasingly employed in neuroscience investigations.1 Metastability has been associated with coexisting tendencies in neuronal populations (e.g., brain regions) to work collectively by coordinating the activity across multiple brain regions while also exhibiting segregated activity to allow the performance of specialised functions. Thus, metastability is said to reflect a mixture of cooperation and relative independence between brain areas in response to inputs from the environment; it is considered to be a fundamental signature of high brain functions. (!)

Jensen, Henrik. Brain, Rain and Forest Fires: What is Critical about Criticality: In Praise of the Correlation Function. Journal of Physics: Complexity. 2/032002, 2021. The veteran Imperial College London mathematician (search) reviews the field of self-organized criticality studies form Per Bak in 1987 to the later global 2010s, which are now seen as entering a new phase of robust veracity. A vital nuance is then distilled that such natural propensities, especially for cerebral activities, tend more to oscillate around a poise point rather than be set in place. (But I must say that a definition of Correlation Function also seems quite malleable.)

We present a brief review of power laws and correlation functions as measures of criticality and the relation between them. By comparing phenomenology from rain, brain and the forest fire model we discuss the relevant features of self-organisation to the vicinity about a critical state. We conclude that organisation to a region of extended correlations and approximate power laws may be behaviour of interest shared between the three considered systems. (Abstract)

The similar behaviour shared between so Many different systems indicates that the basic ingredients of dynamics driven by load, spreading and relaxation will tend to organize towards configurations poised near some kind of onset of (correlated) percolation. The buildup of spatially extended structures, which then abruptly collapse through release of precipitation, neuronal firing or fires respectively in the three cases discussed, keeps turning “over critical” configuration into under “under critical” ones. (9)

It is often suggested that the reason the brain operates at or near a critical point is the hypersensitivity of this state, indicated by the divergence of the susceptibility. This seems reasonable, but there may even be reasons why the brain does not sit exactly in a critical state. It has been suggested that operating in the region across the critical point may have a computational advantages for the brain in terms of combining high data storage capability in the sub-critical region with increased information transfer in the super-critical region. (9)

Kagaya, Katsushi, et al.. Self-organized Criticality of Dendritic Readiness Potential. arXiv:2209.09075. University of Tokyo neuroresearchers report the latest sophisticated experimental proofs of nature’s widely ubiquitous avail and preference for this best balance optimum condition.

Self-organized criticality is a principle explaining avalanche-like phenomena obeying power-laws in integrate-and-fire type dynamical systems. Here, we demonstrate that the behaviorally relevant brain neurons, mediating voluntary and reflexive behaviors in crayfish show signatures of self-organized criticality. The dendritic activities reside at critical states with power-laws and scaling functions, in line with the extracellular neuronal avalanches in vertebrate species which provide similar evidence of the critical brain. Our intracellular data extend the "from crayfish to human" universality of the hypothesis. Thus the nervous systems can exploit the universal dynamics for volition across the phylogenetic tree. (Abstract)

Katsnelson, Mikhail, et al. Self-Organized Criticality in Neural Networks. arXiv:2107.03402. As MK and Tom Westerhout, Radboud University and Vitality Vanchurin, NIH, Bethesda (search VV and MK) continue to propose that such cognitive connectivities have a common natural prevalence, they advance that this SOC optimum condition ought to be appreciated for its definitive advantage. If taken to a farthest implication, the whole ecosmic uniVerse might take on the cerebral semblance of a neural net learning process. See also Emergent Quantumness in Neural Networks at 2012.05082 for another entry by the authors.

We demonstrate, both analytically and numerically, that learning dynamics of neural networks is generically attracted towards a self-organized critical state. The effect can be modeled with quartic interactions between non-trainable variables (e.g. states of neurons) and trainable variables (e.g. weight matrix). Non-trainable variables are rapidly driven towards stochastic equilibrium and trainable variables are slowly driven towards learning equilibrium described by a scale-invariant distribution on a wide range of scales. Our results suggest that the scale invariance observed in many physical and biological systems might be due to some kind of learning dynamics and support the claim that the universe might be a neural network. (Abstract)

Kauffman, Stuart, et al, eds.. The Principle of Dynamical Criticality.. Entropy. December, 2022. This is a special issue to collect a current flow of evident findings about nature’s deep propensity across the universe to seek and reside at this optimum resolve. It is edited by SK, Roberto Serra, University of Modena, Italy, and Ilya Shmulevich and Sui Huang, Institute of Systems Biology, Seattle. Among the six papers so far are Emergent Criticality in Coupled Boolean Networks by Chris Kang, et al, and Robustness and Flexibility of Neural Function through Dynamical Criticality by Marcel Magnasco (see review herein).

While life, as Darwin noted, displays “endless forms most beautiful” at a macroscopic scale, it appears much more uniform at a microscopic level, where living systems share many common structural and functional features. There are, however, few “operating principles” at a macroscale that seem to hold for large classes of organisms. A promising candidate is the “criticality” principle, whereby evolution would have driven living beings towards critical states, since they are should be favorably selected over those that are chaotic or ordered. Moreover, since dynamically critical states are endowed with computational properties, they are interesting outside the domain of biology, such as artificial designs. (Excerpt)

Li, Xiu-Juan and Yu-Peng Yang. Signatures of the Self-organized Criticality Phenomenon in Precursors of Gamma-ray bursts. arXiv:2308.14281. Qufu Normal University and Nanking University astro-cybernetics researchers describe still another instance of nature's common avail of this optimum balance.

Precursors provide important clues to the nature of gamma-ray burst (GRB) central engines and can be used to contain GRB physical processes. In this letter, we study the self-organized criticality in precursors of long GRBs in the third Swift/BAT Catalog. We investigate the differential and cumulative size distributions with the Monte Carlo method. All of the distributions can be well described by power-law models within the physical framework of a self-organized criticality. The results show that both precursors and main bursts can be attributed to an self-organized criticality system.

Li, Xiu-Juan, et al. Evidence for Self-Organized Criticality Phenomena in Prompt Phase of Short Gamma-Ray Bursts. arXiv:2303.06667. Qufu Normal University, China physicists report a further notice of how this insistent propensity distinguishes all manner of atomic activities.

The prompt phase of gamma-ray burst (GRB) contains essential information about the physical nature and central engine, which is yet unknown. In this paper, we investigate the self-organized criticality (SOC) in GRBs as done in X-ray flares of GRBs, which can be well described by power-law models. Our findings show that GRB prompt phases and X-ray flares possess the very same magnetically dominated stochastic process and mechanism. (Excerpt)

Lopez, Roberto, et al.. The Excitatory-Inhibitory Branching Process: Cortical Asynchronous States, Excitability, and Criticality.. arXiv:2203.16374. RL and Miguel Munoz, University of Granada, Spain and Victor Buendia, University of Tubingen provide a current update on the widening evidence and propensity for an optimum cerebral and maybe “cosmobral” self-organized balance between activity and sedentary.

The branching process is the minimal model for propagation dynamics, avalanches and criticality, broadly used in neuroscience. Adding inhibitory nodes then induces a richer phenomenology, including between quiescence and saturation to reveal the features of "asynchronous states" in cortical networks which allows us to rationalize striking empirical findings within a common and parsimonious framework. (Excerpt)

The idea that information-processing systems, both biological and artificial, can extract important functional advantages from operating near the edge of a phase transition was already suggested by A. Turing in 1950. Beggs and Plenz, pioneering the experimental search for signatures of criticality in neural systems in the 2010s, found scale-free outbursts of neuronal activity occurring in between consecutive periods of quiescence, i.e.neuronal avalanches. These avalanches have sizes and durations distributed as power laws with exponents consistent with those of a critical branching process and often exhibit a parabolic shape on average [1)

Magnasco, Marcelo. Robustness and Flexibility of Neural Function through Dynamical Criticality. Entropy. 24/5, 2022. In a special issue on this title subject into the 2020s, a Rockefeller University integrative neuroscientist (view his RU website) writes one of the strongest theoretical confirmations of this common phenomena to date. After an extensive review of earlier notices back to Stuart Kauffman in 1970s and Leo Szilard before, as this site section reports, it has lately become well known that this preferred poise actually occurs from celestial, quantum and material phases all through life’s cellular and communal development. A natural propensity thus seems to seek, prefer and reside at an optimum middle way via a reciprocity of more or less order, conserve or create, tradition and innovation options, and so on. Into 2023, after decades and years of complexity studies, by a combined virtue of structural and vitality features our Earthuman acumen may at last have reached a true discovery which can be affirmed and announced. As a horrific war rage close to the lands of Mendel and Galileo, this grand fulfillment need take on a guise as an epochal, crucial, revolutionary realization.

In theoretical biology, robustness refers to the ability of a biological system to function even under a stress of basic parameters (temperature or pH); flexibility refers to the ability of a system to switch functions or behaviors easily when necessary. While there are extensive explorations of the concept of robustness and what it requires mathematically, understanding flexibility has proven elusive, as well as also elucidating the opposite mathematical models for either mode. In this paper we consider a numberof neuroscience theories that show both robustness and flexibility can be attained by systems that poise themselves at the onset of dynamical bifurcations, which can influence the integration of information processing and function. (Abstract)

Long-term survival requires surviving many short terms. Thus species need to do “well enough” in the short term, but able ability to change when the niche shifts. In physiology, these two conflicting demands are identified with “robustness”, the ability of a physiological system to perform the same task correctly, and “flexibility”, so to adjust when as conditions change. While studies have explored robustness most often in molecular cell biology, the theoretical bases of biological flexibility are still obscure. One of the most striking forms of flexibility in neural function is integration. This phenomenon occurs at various scales, from the input-dependent changes in the range of intracortical functional connectivity, all the way up to entire brain areas working together to form associations. (1, 2)

Conclusion A large number of biological systems have shown dynamics that are linked to a system state which spontaneously poises itself at the boundary of dynamical transitions. We have reviewed the evolution of these ideas over many years and their firm rootings in experimental evidence. We have derived from this a family of models, the critically coupled map lattices. We have here shown the direct similarity and many connections to a related notion of criticality, that of “edge of chaos” dynamics, which altogether become a cellular automaton Turing universality. (15)

Marcelo Magnasco’s neuropsychology group uses living beings as a source of inspiration for creating new mathematical descriptions of nature. The lab’s focus is on computational and experimental methods to model the complexity, organization, and information-processing properties of living organisms. A primary interest is auditory function along with studies of vision, memory, olfaction, and sensory processing. Human beings are the main subject but dolphin communication in aquaria and the wild is also undertaken. (RU synopsis)

Mondal, Suman, et al. Self-Organized Criticality of Magnetic Avalanches in Disordered Ferrimagentic Material. arXiv:2210.05183. Indian Association for the Cultivation of Science researchers posted in Kolkata and Bangalore proceed to report the universal presence of this “golden mean” optimum state even across these substantial domains. (Once again, our intent is to document SOC occurrences everywhere across a genesis nature so that public politics might finally also become healed by a bicameral complementarity.)

We observe multiple step-like jumps in a Dy-Fe-Ga-based ferrimagnetic alloy in its magnetic hysteresis curve. The observed jumps have a stochastic character with respect to their magnitude and critical field of occurrence.. The jump size distribution follows a power law indicating the scale invariance nature of the jumps. The flipping of coupled Dy and Fe clusters is responsible for the observed discrete avalanche-like features in the hysteresis loop. These characteristics indicate that the present phenomenon can be well described within the realm of self-organized criticality. (Abstract)

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