Related papers: Degeneracy in the genetic code and its symmetries …
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
We have used the sexual Penna ageing model to show that the relation between dominance and recessiveness could be a force which optimizes the genome size. While the possibility of complementation of the damaged allele by its functional…
A historical dispute in the conceptual underpinnings of evolution is the validity of the gene centered view of evolution. \cite{dawkins,lewontin} We transcend this debate by formalizing the gene centered view as a dynamic version of the…
A general theory of quantum error avoiding codes is established, and new light is shed on the relation between quantum error avoiding and correcting codes. Quantum error avoiding codes are found to be a special type of highly degenerate…
Solving Quadratic equation is one of the intrinsic interests as it is the simplest nonlinear equations. A novel approach for solving Quadratic Equation based on Genetic Algorithms (GAs) is presented. Genetic Algorithms (GAs) are a technique…
A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon…
Genetic programming is the practice of evolving formulas using crossover and mutation of genes representing functional operations. Motivated by genetic evolution we develop and solve two combinatorial games, and we demonstrate some…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
A quantum code is a subspace of a Hilbert space of a physical system chosen to be correctable against a given class of errors, where information can be encoded. Ideally, the quantum code lies within the ground space of the physical system.…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Any permutation has a disjoint cycle decomposition and concept generates an equivalence class on the symmetry group called the cycle-type. The main focus of this work is on permutations of restricted cycle-types, with particular emphasis on…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…
The current theory of evolution is almost the one Darwin and Wallace proposed two centuries ago and the following discoveries e.g., Mendelian genetics and neutral mutation theory have not made significant modifications. The current…
Decoding of convolutional codes poses a significant challenge for coding theory. Classical methods, based on e.g. Viterbi decoding, suffer from being computationally expensive and are restricted therefore to codes of small complexity. Based…