IV. Ecosmomics: A Survey of Genomic Complex Network System Sources
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.
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?
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.
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.
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.
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.
Aschwanden, Markus, et al. Order Out of Randomness: Self-Organization Processes in Astrophysics. arXiv:1708.03394. Reviewed at length in Systems Cosmology, this is an 18 author, 97 page treatise which could be seen as a premier affirmation of an inherently nonlinear, lively, complexifying cosmic genesis.