Algebraic computation of genetic patterns related to three-dimensional evolution algebras

The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic Geometry to determine the distribution of three-dimensional evolution algebras over any field into isotopism classes and hence, to describe the spectrum of genetic patterns of three distinct genotypes during a mitosis process. Their distribution into isomorphism classes is also determined in case of dealing with algebras having a onedimensional annihilator

An Application of Total-Colored Graphs to Describe Mutations in Non-Mendelian Genetics

Any gene mutation during the mitotic cell cycle of a eukaryotic cell can be algebraically represented by an isotopism of the evolution algebra describing the genetic pattern of the inheritance process. We identify any such pattern with a total-colored graph so that any isotopism of the former is uniquely related to an isomorphism of the latter. This enables us to develop some results on graph theory in the context of the molecular processes that occur during the S-phase of a mitotic cell cycle. In particular, each monochromatic subset of edges is identified with a mutation or regulatory mechanism that relates any two statuses of the genotypes of a pair of chromatids.Junta de Andalucía FQM-016Junta de Andalucía FQM-32

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation

Mutation graphs of asexual diploid organisms

The mutation graph of an asexual diploid organism is introduced as an edgecolouredgraph derived from the genetic pattern by isotopisms of an evolution algebraover a finite field. We describe the step-by-step construction of this graph and establishsome of its basic properties. In order to illustrate this construction, we focus on thespectrum of genetic patterns of two distinct genotypes during a mitosis process

A historical perspective of Tian’s evolution algebras

Even if it has been less than a decade and a half since Tian introduced his concept of evolution algebras to represent algebraically non-Mendelian rules in Genetics, their study is becoming increasingly widespread mainly due to their applications to many scientific disciplines. In order to facilitate further research on the topic, this paper deals with the past and present research on these kind of algebras, together with the most relevant topics regarding themJunta de Andalucía FQM-01