IV. Ecosmomics: An Independent, UniVersal, Source Code-Script of Generative Complex Network Systems

Biocomplexity Institute. http://www.indiana.edu/~bioc/. Accessed June 2011, this is an interdisciplinary endeavor of Indiana University at the leading edge of these lively sciences. Biophysicist James Glazier is director, members include biophysicist John Beggs, information visionary Katy Borner, psychologist Robert Goldstone, Allessandro Flammini and Luis Rocha, bioinformatics, and neuroscientist Olaf Sporns. We quote the Institute’s main definition, along with a statement for Goldstone’s Percepts and Concepts Laboratory, as they convey this revolutionary engagement with and discovery of a radical genesis nature.

Biocomplexity is the study of the emergence of self-organized, complex behaviors from the interaction of many simple agents. Such emergent complexity is a hallmark of life, from the organization of molecules into cellular machinery, through the organization of cells into tissues, to the organization of individuals into communities. The other key element of biocomplexity is the unavoidable presence of multiple scales. Often, agents organize into much larger structures; those structures organize into much larger structures, etc. A classic example is the primary, secondary, tertiary, and quaternary folding of DNA into chromosomes that allows a strand of a length of several centimeters to fold, without tangling or losing function, into a chromosome about one micron long. Biocomplexity is a methodology and philosophy as well as a field of study. It focuses on networks of interactions and the general rules governing such networks.

Typically, complex adaptive system models are applied to natural phenomena, such as the pattern of stripes on zebras or seeds on sunflowers. Our research goal is to apply these models to understanding how individual people learn and perceive, and how groups of people organize themselves into emergent structures which none of the individuals in the group may understand or even perceive. Our laboratory is currently exploring interactions between perceptual and conceptual learning, methods for learning abstract concepts using computer simulations, the perception of similarity and analogy, and group behavior from a complex systems perspective. Our typical modus operandi is to simultaneously conduct psychological experiments on humans and develop computational models of the observed behavior. The results from the experiments help to constrain and inform our computational models, and the computational models serve to organize and explain our empirical results. (R. Goldstone)

Center for Models of Life. www.cmol.nbi.dk. A graphically informative website for this endeavor located at the Niels Bohr Institute, University of Copenhagen and directed by Kim Sneppen. Research is pursued such areas as: Physics of Gene Regulation, Models of Biological Circuits, Networks and Communication, and Evolution and Dynamical Systems, each with referenced publications. If our extant nature from cell to city is found to exhibit these pervasive innate and invariant phenomena, by what sufficient proof, might it prompt and allow us to realize a greater genesis?

Complexity Digest. www.comdig.org. Founded by the late Gottfried Mayer, the present Editor-in-Chief is Carlos Gershenson who with international collaborators and audience, suggest and post new citations apropos the wavefront of the complex systems revolution. The engaging site enters the latest advances in articles, books, presentations and conferences, along with university programs, and more. Complexity Digest represents a premier resource for learning about and keeping up with the frontiers of a self-organizing universe and sustainable future.

New England Complex Systems Institute. www.necsi.org. Founded and run by systems scholar Yaneer Bar-Yam and colleagues, this multifaceted site is a rich resource for general and specific content all about the nonlinear systems revolution from evolution to economies. The group has run a biannual International Conference on Complex Systems in the Boston area since the late 1990s. I went to four of these incredible events to which luminaries such as Edward Lorenz, Stephen Wolfram, Stuart Kauffman, Gene Stanley, and everyone else it seems presents or attends. The Proceedings for the 2011 gala are accessible from the home page, click ICCS under Events.

The New England Complex Systems Institute (NECSI) is an independent academic research and educational institution with students, postdoctoral fellows and faculty. In addition to the in-house research team, NECSI has co-faculty, students and affiliates from MIT, Harvard, Brandeis and other universities nationally and internationally.

NECSI has been instrumental in the development of complex systems science and its applications. We study how interactions within a system lead to its behavioral patterns, and how the system interacts with its environment. Our new tools overcome the limitations of classical approximations for the scientific study of complex systems, such as social organizations, biological organisms and ecological communities. NECSI's unified mathematically-based approach transcends the boundaries of physical, biological and social sciences, as well as engineering, management, and medicine (see Complex Systems Resources).

NECSI research advances fundamental science and its applications to real world problems, including social policy matters. NECSI researchers study networks, agent-based modeling, multiscale analysis and complexity, chaos and predictability, evolution, ecology, biodiversity, altruism, systems biology, cellular response, health care, systems engineering, negotiation, military conflict, ethnic violence, and international development. (see NECSI Research).

NECSI conducts classes, seminars and conferences to assist students, faculty and professionals in their understanding of complex systems. NECSI sponsors postdoctoral fellows, provides research resources online, and hosts the International Conference on Complex Systems. Through its education, NECSI strives to contribute to science and the betterment of society (see NECSI Education).

Plamen Ch. Ivanov website. physics.bu.edu/people/show/plamen. We cite this home page of the Bulgarian-American, Boston University research professor as an example of the creative, worldwide frontiers of nonlinear, self-organizing complex network theories. From this site, the Keck Laboratory for Network Physiology which Ivanov directs, can be accessed with its rich array of projects, people, and publications. A recent contribution is the discovery of non-equilibrium critical dynamics in bursts of cortical dynamics in sleep/wake cycles (search for 2019 paper). His collegial research across a wide range from condensed matter to cardiac, neural, somatic onto societies well attests to nature’s universally recurrent manifestation of the same mathematical dynamics everywhere.

My research group has introduced several innovative approaches to analyze physiologic data by adapting concepts from modern statistical physics, nonlinear dynamics, and applied mathematics. These methods have been successfully applied to cardiac, respiratory, locomotion, and brain systems, along with sleep-stage transitions and circadian rhythms. Those data-driven approaches enabled us to discover basic laws of physiologic regulation of individual systems whose results were published in leading journals such as Nature, PNAS and Physical Review Letters. Our overall research objective is to develop a new interdisciplinary field, Network Physiology, integrating efforts across statistical and computational physics, biomedical engineering, human physiology, and medicine.

Santa Fe Institute. www.santafe.edu. The original, innovative center since 1984 for the theoretical and practical study of complex, dynamical system insights into natural and social worlds. Typical subject areas include the Physics of Complex Systems, Emergence and Innovation in Evolutionary Systems, Information Processing and Computation in Nature and Society, and Emergence, Organization and Dynamics of Living Systems. For publications, the SFI Bulletin, (e.g., Volume 24, 2009), a long list of Working Papers each year, and under Research, a Bibliography of papers by SFI members cited on the website convey the leading edge of nonlinear studies.

Mission The Santa Fe Institute is a transdisciplinary research community that expands the boundaries of scientific understanding. Its aim is to discover, comprehend, and communicate the common fundamental principles in complex physical, computational, biological, and social systems that underlie many of the most profound problems facing science and society today.

Vision Many of society’s most pressing problems fall far from the confines of disciplinary research. Complex problems require novel ideas that result from thinking about non-equilibrium and highly connected complex adaptive systems. We are dedicated to developing advanced concepts and methods for these problems, and pursuing solutions at the interfaces between fields through wide-ranging collaborations, conversations, and educational programs. SFI combines expertise in quantitative theory and model building with a community and infrastructure able to support cutting-edge, distributed and team-based science. At the Santa Fe Institute, we are asking big questions that matter to science and society.

One of the grand challenges of 21st century science is the search for fundamental principles beyond the genetic code and Darwinian evolutionary process that govern how the complexity of life emerges from its underlying simplicity.

Altan-Bonnet, Gregoire, et al. Quantitative Immunology for Physicists. Physics Reports. Online January, 2020. Veteran complexity theorists G A-B, National Cancer Institute, USA, with Thierry Mora Aleksandra Walczak, CNRS Sorbonne University, Paris post a 70 page tutorial which reviews the latest perceptions of this important biological process. It then shows how much the immune system has become understood as another vital manifestation of nature’s universal complexities. Some sections are Ligand-Receptor Interaction, Antigen Diiscrimination, Cel to Cell Communication, and Populations Dynamics of Pathogens and Hosts.

The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules and sub-systems is often also petrifying. Despite this complexity, as experiments on different scales of the adaptive immune system become more quantitative, many physicists have made both theoretical and experimental contributions that help predict the behaviour of ensembles of cells and molecules that participate in an immune response. Here we review some recent contributions with an emphasis on quantitative questions and methodologies. We also provide a more general methods section that presents some of the wide array of theoretical tools used in the field. (Abstract)

Altmann, G. and Walter Koch, eds. Systems: New Paradigms for the Human Sciences. Berlin: de Gruyter, 1998. A European compendium which situates and contemplates the human phase within a self-developing universe.

Amaral, L. and J. Ottino. Augmenting the Framework for the Study of Complex Systems. European Physics Journal B. 38/2, 2004. An introduction to a special issue on the ubiquitous presence of scale-free dynamic networks from food webs and epidemics to neural phenomena and especially the worldwide Internet. In this regard a generic definition of complex systems is attempted, see the quote below. These elemental units and interactions then self-organize into a universal, nested self-similarity.

A complex system is a system with a large number of elements, building blocks or agents, capable of interacting with each other and with their environment. The common characteristic of all complex systems is that they display organization without any external organizing being applied. The whole is much more than the sum of its parts. (148)

Anderson, Philip. More Is Different - One More Time. N. Phuan Ong and Ravin Bhatt, eds. More Is Different. Princeton: Princeton University Press, 2001. The Nobel laureate physicist revisits his landmark 1967 paper which helped turn science from a fixation on subatomic domains to the complexity revolution.

The actual universe is the consequence of layer upon layer of emergence, and the concepts and laws necessary to understand it are as complicated, subtle and, in some cases, as universal as anything the particle folks are likely to come up with. (7)

Anderson, Philip, et al, eds. Downward Causation. Arrhus, Denmark: Arrhus University Press, 2000. Papers that explore how self-organizing, agent-based systems lead to an increasing influence by ‘higher,’ more consciously informed levels, over lower or prior stages, which is present from physical theory to literary genres.

Araujo, Nuno, et al.. Steering Self-Organization through Confinement. arXiv:2204.10059. This entry is a composite synopsis of a June 2021, Leiden University Lorentz Center workshop on the title topic, which can serve as an overview of the 21st century scientific revolution to date. Some 29 attendees from Europe and the USA included Liesbeth Janssen, Simon Garnier, and Audrey Dussutour. A novel agenda went on to consider how certain system boundaries can have a formative effect on this dynamic development process. As the quotes allude, from our late vantage, the broad field of complexity studies over 50 years (which this site seeks to report) can be seen as a singular, WorldWise revolutionary endeavor which is just coming a convergent, self-similar synthesis from uniVerse to wumanVerse.

In regard, at this consummate moment, the outlines of a general scenario that is much akin to life’s developmental genotype and phenotype basis can become quite evident. Physical models, for example, cite implicate/explicate and informative bit/it versions. Altogether the whole ecosmic genesis appears to be suffused by an independent, universally present, mathematic code-script which serves to engender and self-organize at each and every scale and beingness. As a consequence, astro biochemicals, evolutionary organisms, entities in groups, communicative mores, societal processes and all else arise, complexity, and quicken in an oriented fashion wherever they can. As life’s emergence thus goes forth, these myriad phenotypes come to exemplify the familial source in their complementary bigender, whole occasion. So into this fraught 2022 year, an epochal, once and future true universality can at last be affirmed.

Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has found that self-organisation is mediated and controlled by local boundaries which then steer the emergence or suppression of collective phenomena. Here we consider a common framework for future research and scientific challenges across disciplines. We hope this endeavor will advance deeper appreciations of natural self-organisation for novel material, biological and societal benefits. (Abstract excerpt)

From molecular aggregates to groups of animals and human crowds, from microswimmers to granular materials and robotic swarms, systems that self-organise can be found across a wide diversity of length and time scales. The dynamic concept arose in the later 20th century and defines the spontaneous emergence of large-scale collective structures and patterns from the interaction of many individual units, such as molecules, colloidal particles, cells, animals, robots, pedestrians or even astronomical objects. These units can be heterogeneous in size, shape, composition and function. (3-4)

We can thus define confinement in self-organisation as anything which causes units to localise to a region of space at a given time. The variety of self-organising systems influenced by confinement spans s wide range of length scales from active filaments driven by microscopic molecular motors enclosed within living cells, to the emergence of macroscopic coherent flow structures confined by Earth’s atmosphere, to the formation of entire galaxies under the pull of the gravitational potentials of black holes. While confinement is not always required for a system to self-organise [17], it can play a pivotal role as either a catalyst or inhibitor for self-organisation. (5)

In conclusion, steering self-organisation through confinement is a very active and rapidly evolving field of research, which is intrinsically multidisciplinary. To push the field forward, the scientific community working on self-organisation should increasingly take advantage of the cross-fertilisation of ideas that results from sharing hypotheses, theoretical approaches and experimental methods among experts from different fields and disciplines. This perspective article provides a first step in this direction. (11)

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