PlanetPhysics/Complex Systems Biophysics

Complex Systems Biophysics

Introduction

Complex Systems Biophysics ($CSB$) or Complex systems biology ($CSB$) is generally described as a non-reductionist, mathematical theory of emergent living organisms or biosystems in terms of a network, [[../Bijective/|graph]] or [[../Cod/|category]] of integrated interactions between their structural and functional components or [[../GenericityInOpenSystems/|subsystems]]. This is often abbreviated to systems biology in entries that should be described in fact as complex systems biology .

Categorical ontology: theories of existence levels

A \htmladdnormallink{categorical ontology {http://planetphysics.us/encyclopedia/CategoricalOntology.html} theory of levels} is often defined as the [[../TrivialGroupoid/|classification]] of ontology, or theory of existence of items (objects--in the mathematical sense) by means of the mathematical theory of categories into three levels of [[../GenericityInOpenSystems/|dynamic systems]] pertaining to: the physical/chemical level, the biological level, and the psychological level (or human mind). Connections between the three levels of reality and their transformations are represented, respectively, by [[../TrivialGroupoid/|morphisms/]] and [[../VariableCategory2/|natural transformations]] defined for [[../CategoryOfMolecularSets/|categories of molecular sets]], categories of $(M,R)$-systems and [[../SuperCategory6/|organismic supercategories]].

From a categorical ontology theory of levels viewpoint, however, the term complex is misplaced because \htmladdnormallink{systems {http://planetphysics.us/encyclopedia/SimilarityAndAnalogousSystemsDynamicAdjointnessAndTopologicalEquivalence.html} with chaos}, or chaotic [[../MathematicalFoundationsOfQuantumTheories/|dynamics]], are currently defined by physicists as `complex systems' , which may have placed a role in the emergence of living systems that are, in fact, super-complex . Therefore, the more appropriate classification of this relatively new area in mathematical or theoretical biology and Biophysics is super-complex systems biology, $s$-complex systems biology, or simply "systems biology"--as a more general approach where the focus may be not on the super-complexity aspects of living systems but on [[../SupercomputerArchitercture/|computer]] modeling of physiological, or functional genomics, integration of physiological flows, signaling pathways or interactomics. However, unlike the case of purely functional $(M,R)$-systems theory in abstract relational biology ([[../RSystemsCategory/|ARB]]), complex systems biology (or systems biology) proponents are primarily concerned with the integration of data from a multitude of bioinformatics and genomic/proteomic/post-genomic (primarily structural) data; $CSB$ scientists also aim to study interactomics or metabolomics primarily through computer-based data analysis, and often Bayesian-based attempts at integration. branches of mathematics that find applications in $CSB$ are, for example: computer modeling, colored graphs, graph-theoretical based approaches, biotopology, genetic, metabolic and signaling network theories, [[../GeneNetDigraph/|Bayesian models]], biostatistics, correlation techniques, and less frequently: [[../PAdicMeasure/|abstract algebra]], [[../TrivialGroupoid/|group]] theory, [[../QuantumOperatorAlgebra5/|groupoid]] and [[../TrivialGroupoid/|category theory]] modeling of cell-cell interactions and biodynamics.