Related papers: The Genetic Code Paradox: Extreme Conservation Des…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
We introduce the simple parametrization for the space of codons (triples of nucleotides) by 8\times 8 table. This table (which we call the dyadic plane) possesses the natural 2-adic ultrametric. We show that after this parametrization the…
Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented, and their survival far beyond reproductive age may be a byproduct rather than tool of evolution. Physical approach, which takes…
The common understanding of protein evolution has been that neutral or slightly deleterious mutations are fixed by random drift, and evolutionary rate is determined primarily by the proportion of neutral mutations. However, recent studies…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
The Great Filter hypothesis proposes that the emergence of technological societies capable of interstellar travel depends on a small number of exceptionally hard and highly improbable steps. Traditional versions of this hypothesis enumerate…
The theory of evolution by natural selection cannot be used to evaluate the truth value of the following proposition: Through evolution, there exists at least one species that can adapt to any one given environment. To address this issue,…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid…