genetic nets
0.1 Introduction
Genetic ‘nets’, or networks, $GN$ – that represent a living organism’s genome –are mathematical models of functional^{} genes linked through their non-linear, dynamic interactions.
A simple genetic (or gene) network $G{N}_{s}$ may be thus represented by a directed graph^{} ${G}_{D}$ whose nodes (or vertices) are the genes ${g}_{i}$ of a cell or a multicellular organism and whose edges (arcs) are arrows representing the actions of a gene ${a}_{g}^{i}$ on a linked gene or genes; such a directed graph representing a gene network has a canonically associated biogroupoid ${\mathcal{G}}_{B}$ which is generated or directly computed from the directed graph ${G}_{D}$.
0.2 Boolean vs. N-state models of genetic networks in $L{M}_{n}$- logic algebras
The simplest, Boolean, or two-state models of genomes represented by such directed graphs of gene networks form a proper subcategory^{} of the category^{} of n-state genetic networks, ${\text{\mathbf{G}\mathbf{N}}}_{\u0141{M}_{n}}$ that operate on the basis of a Łukasiewicz-Moisil n-valued logic algebra^{} $L{M}_{n}$. Then, the category of genetic networks, ${\text{\mathbf{G}\mathbf{N}}}_{\u0141{M}_{n}}$ was shown in ref. [2] to form a subcategory of the algebraic category^{} of Łukasiewicz algebras (http://planetmath.org/AlgebraicCategoryOfLMnLogicAlgebras), $\mathcal{L}\mathcal{M}$ [1, 2]. There are several published, extensive computer simulations of Boolean two-state models of both genetic and neuronal networks (for a recent summary of such computations see, for example, ref. [2]. Most, but not all, such mathematical models are Bayesian, and therefore involve computations for random networks that may have limited biological relevance as the topology of genomes, defined as their connectivity, is far from being random.
The category of automata^{} (or sequential machines based on Chrysippean or Boolean logic) and the category of $(M,R)$-systems (which can be realized as concrete metabolic-repair biosystems of enzymes, genes, and so on) are subcategories of the category of gene nets ${\text{\mathbf{G}\mathbf{N}}}_{\u0141{M}_{n}}$. The latter corresponds to organismic sets of zero-th order ${S}_{0}$ in the simpler, Rashevsky’s theory of organismic sets.
References
- 1 Baianu, I.C. (1977). A Logical Model of Genetic Activities in Łukasiewicz Algebras: The Non-linear Theory., Bulletin of Mathematical Biology, 39:249-258.
- 2 Baianu, I.C., Brown, R., Georgescu, G., Glazebrook, J.F. (2006). Complex nonlinear biodynamics in categories, higher dimensional algebra^{} and Łukasiewicz-Moisil topos: transformations^{} of neuronal, genetic and neoplastic networks. Axiomathes 16(1-2):65-122.
- 3 Baianu, I.C., J. Glazebrook, G. Georgescu and R.Brown. (2008). A Novel Approach to Complex Systems Biology based on Categories, Higher Dimensional Algebra and Łukasiewicz Topos. Manuscript in preparation, 16 pp.
- 4 Georgescu, G. and C. Vraciu (1970). On the Characterization^{} of Łukasiewicz Algebras., J. Algebra, 16 (4), 486-495.
Title | genetic nets |
Canonical name | GeneticNets |
Date of creation | 2013-03-22 18:11:28 |
Last modified on | 2013-03-22 18:11:28 |
Owner | bci1 (20947) |
Last modified by | bci1 (20947) |
Numerical id | 50 |
Author | bci1 (20947) |
Entry type | Topic |
Classification | msc 55U99 |
Classification | msc 92D15 |
Classification | msc 03B50 |
Classification | msc 92B20 |
Classification | msc 92B05 |
Synonym | genome network |
Synonym | genome |
Synonym | entity of all interacting genes in a living organism |
Related topic | DirectedGraph |
Related topic | AlgebraicCategoryOfLMnLogicAlgebras |
Related topic | OrganismicSets3 |
Related topic | OrganismicSets2 |
Related topic | JanLukasiewicz |
Related topic | SupercategoriesOfComplexSystems |
Related topic | MolecularSetTheory |
Related topic | CategoryTheory |
Related topic | OrganismicSetTheory |
Related topic | FunctionalBiology |
Defines | gene net |
Defines | Bayesian model |
Defines | genetic network |
Defines | N-state net models |
Defines | two-state models |
Defines | genome Boolean models |
Defines | category of genetic nets |