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8 levels of harmony and 8 concepts of Complex Systems  [PDF]
D. B. Saakian
Physics , 2001,
Abstract: A set of general physical principles is proposed as the structural basis for the theory of complex systems. First the concept of harmony is analyzed and its different aspects are uncovered. Then the concept of reflection is defined and illustrated by suggestive examples. Later we propose the principle of (random) projection of symmetrically expanded prereality as the main description method of complex systems.
Using graph concepts to understand the organization of complex systems  [PDF]
Claire Christensen,Reka Albert
Quantitative Biology , 2006, DOI: 10.1142/S021812740701835X
Abstract: Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the topologies of different systems. Attempts to explain these similarities have led to the ongoing development and refinement of network models and graph-theoretical analysis techniques with which to characterize and understand complexity. In this tutorial, we demonstrate through illustrative examples, how network measures and models have contributed to the elucidation of the organization of complex systems.
Intelligibility in microbial complex systems: Wittgenstein and the score of life  [PDF]
Fernando Baquero,Andrés Moya
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00088
Abstract: Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the “score of life” metaphor is more accurate to express the complexity of living systems than the classic “book of life.” Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.
Life in Silico - Simulation of Complex Systems by Enzymatic Computation  [PDF]
Gerhard Mack,Jan Wuerthner
Physics , 2000,
Abstract: We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from ``atomic constituents'' called enzymes.The notion is abstracted from biochemistry. The software can be used to simulate physical systems as well as basic life processes. Systems can be constructed and manipulated by mouse click and there is an automatic translation of all operations into a LISP-like scripting language, so that one may compose code by mouse click.
Categorial Ontology of Complex Systems, Meta-Systems and Levels: The Emergence of Life, Human Consciousness and Society  [cached]
Ion C. Baianu,James F. Glazebrook
Brain. Broad Research in Artificial Intelligence and Neuroscience , 2010,
Abstract: Relational structures of organisms and the human mind are naturally represented in terms of novel variable topology concepts, non-Abelian categories and Higher Dimensional Algebra{ relatively new concepts that would be defined in this tutorial paper. A unifying theme of local-to-global approaches to organismic development, evolution and human consciousness leads to novel patterns of relations that emerge in super- and ultra- complex systems in terms of compositions of local procedures [1]. The claim is defended in this paper that human consciousness is unique and should be viewed as an ultra-complex, global process of processes, at a meta-level not sub{summed by, but compatible with, human brain dynamics [2]-[5]. The emergence of consciousness and its existence are considered to be dependent upon an extremely complex structural and functional unit with an asymmetric network topology and connectivities{the human brain. However, the appearance of human consciousness is shown to be critically dependent upon societal co-evolution, elaborate language-symbolic communication and `virtual', higher dimensional, non{commutative processes involving separate space and time perceptions. Theories of the mind are approached from the theory of levels and ultra-complexity viewpoints that throw new light on previous semantic models in cognitive science. Anticipatory systems and complex causality at the top levels of reality are discussed in the context of psychology, sociology and ecology. A paradigm shift towards non-commutative, or more generally, non-Abelian theories of highly complex dynamics [6] is suggested to unfold now in physics, mathematics, life and cognitive sciences, thus leading to the realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. The presence of strange attractors in modern society dynamics gives rise to very serious concerns for the future of mankind and the continued persistence of a multi-stable Biosphere.
Life as Complex Systems --- Viewpoint from Intra-Inter Dynamics  [PDF]
Kunihiko Kaneko
Physics , 1998,
Abstract: Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach for a biological system is proposed. As a construction in a computer, intra-inter dynamics is presented for cell biology, where the following five general features are drawn from our model experiments; intrinsic diversification, recursive type formation, rule generation, formation of internal representation, and macroscopic robustness. Significance of the constructed logic to the biology of existing organisms is also discussed.
Complex networks: the key to systems biology
Costa, Luciano da F.;Rodrigues, Francisco A.;Cristino, Alexandre S.;
Genetics and Molecular Biology , 2008, DOI: 10.1590/S1415-47572008000400001
Abstract: though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. the current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. the main concepts and models of complex networks are presented and illustrated in an accessible fashion. three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. the key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.
Entropy-Based Model for Interpreting Life Systems in Traditional Chinese Medicine  [PDF]
Guo-lian Kang,Shao Li,Ji-feng Zhang
Evidence-Based Complementary and Alternative Medicine , 2008, DOI: 10.1093/ecam/nem026
Abstract: Traditional Chinese medicine (TCM) treats qi as the core of the human life systems. Starting with a hypothetical correlation between TCM qi and the entropy theory, we address in this article a holistic model for evaluating and unveiling the rule of TCM life systems. Several new concepts such as acquired life entropy (ALE), acquired life entropy flow (ALEF) and acquired life entropy production (ALEP) are propounded to interpret TCM life systems. Using the entropy theory, mathematical models are established for ALE, ALEF and ALEP, which reflect the evolution of life systems. Some criteria are given on physiological activities and pathological changes of the body in different stages of life. Moreover, a real data-based simulation shows life entropies of the human body with different ages, Cold and Hot constitutions and in different seasons in North China are coincided with the manifestations of qi as well as the life evolution in TCM descriptions. Especially, based on the comparative and quantitative analysis, the entropy-based model can nicely describe the evolution of life entropies in Cold and Hot individuals thereby fitting the Yin–Yang theory in TCM. Thus, this work establishes a novel approach to interpret the fundamental principles in TCM, and provides an alternative understanding for the complex life systems.
Universal Dynamics, a Unified Theory of Complex Systems. Emergence, Life and Death  [PDF]
Gerhard Mack
Mathematics , 2000, DOI: 10.1007/s002200100397
Abstract: A universal framework is proposed, where all laws are regularities of relations between things or agents. Parts of the world at one or all times are modeled as networks called SYSTEMS with a minimum of axiomatic properties. A notion of locality is introduced by declaring some relations direct (or links). Dynamics is composed of "atomic" constituents called mechanisms. They are conditional actions of basic local structural transformations (``enzymes''): indirect relations become direct (friend of friend becomes friend), links are removed, objects copied. This defines a kind of universal chemistry. I show how to model basic life processes in a self contained fashion as a kind of enzymatic computation. The framework also accommodates the gauge theories of fundamental physics. Emergence creates new functionality by cooperation - nonlocal phenomena arise out of local interactions. I explain how this can be understood in a reductionist way by multiscale analysis (e.g. renormalization group).
How do life, economy and other complex systems escape the heat death?  [PDF]
Sorin Solomon,Natasa Golo
Physics , 2014, DOI: 10.3390/e16031687
Abstract: The primordial confrontation underlying the existence of our universe can be conceived as the battle between entropy and complexity. The law of ever-increasing entropy (Boltzmann H-theorem) evokes an irreversible, one-directional evolution (or rather involution) going uniformly and monotonically from birth to death. Since the 19th century, this concept is one of the cornerstones and in the same time puzzles of statistical mechanics. On the other hand, there is the empirical experience where one witnesses the emergence, growth and diversification of new self-organized objects with ever-increasing complexity. When modeling them in terms of simple discrete elements one finds that the emergence of collective complex adaptive objects is a rather generic phenomenon governed by a new type of laws. These 'emergence' laws, not connected directly with the fundamental laws of the physical reality, nor acting 'in addition' to them but acting through them were called by Phil Anderson 'More is Different', 'das Maass' by Hegel etc. Even though the 'emergence laws' act through the intermediary of the fundamental laws that govern the individual elementary agents, it turns out that different systems apparently governed by very different fundamental laws: gravity, chemistry, biology, economics, social psychology, end up often with similar emergence laws and outcomes. In particular the emergence of adaptive collective objects endows the system with a granular structure which in turn causes specific macroscopic cycles of intermittent fluctuations.
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