Related papers: Are there laws of genome evolution?
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…
The discovery of two fundamental laws concerning cellular dynamics with recursive growth is reported. First, the chemical abundances measured over many cells are found to obey a log-normal distribution and second, the relationship between…
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
We develop a ``unified'' model that describes both ``micro'' and ``macro'' evolutions within a single theoretical framework. The eco-system is described as a dynamic network; the population dynamics at each node of this network describes…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
We present significantly advanced studies of the previously introduced physical growth mechanism and unite it with biochemical growth factors. Obtained results allowed formulating the general growth law which governs growth and evolutional…
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…
Time evolution of number of species (genera, families, and others), population of them, and size distribution of present ones and life times are studied in terms of a new model, where population of each genetic taxon increases by a (random)…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented. Physical approach, which takes advantage of their extensively quantified mortality, establishes that its dominant fraction yields…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
By measuring or calculating coalescence times for several models of coalescence or evolution, with and without selection, we show that the ratios of these coalescence times become universal in the large size limit and we identify a few…
Concepts rooted in physics are becoming increasingly important in biology as we transition to an era in which quantitative descriptions of all processes from molecular to cellular level are needed. In this essay I discuss two unexpected…
Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the validity of MC but also have shown that MC is…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…