Related papers: A Model on Genome Evolution
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
We investigate quantum effects in the evolution of general systems. For studying such temporal quantum phenomena, it is paramount to have a rigorous concept and profound understanding of the classical dynamics in such a system in the first…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
Using the fact that any linear representation of a group can be embedded into permutations, we propose a constructive description of quantum behavior that provides, in particular, a natural explanation of the appearance of complex numbers…
I propose to treat quantum evolution as a stochastic process consisting from a sequence of doubly stochastic matrices, which naturally arise in the generalized quantum evolution. Then it is proved that the law of non-decreasing entropy is…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
It is shown that a coherent understanding of all quantized phenomena, including those governed by unitary evolution equations as well as those related to irreversible quantum measurements, can be achieved in a scenario of successive…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Darwinian evolution requires (i) heritable records, (ii) repeatable copying with variation, and (iii) routine irreversibility. Categorical quantum mechanics (CQM) makes precise why ``copy'' and ``delete'' are not generic quantum operations:…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…
The evolution equations of quantum observables are derived from the classical Hamiltonian equations of motion with the only additional assumption that the phase space is non-commutative. The demonstration of the quantum evolution laws is…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
We construct a descriptive toy model that considers quantum effects on biological evolution starting from Chaitin's classical framework. There are smart evolution scenarios in which a quantum world is as favorable as classical worlds for…