Related papers: Darwinian Evolution of Taste
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…
We propose, in this article, an analysis of the Darwin's approach to sociality. Sociality is perfectly integrated into the selective model, and is caused by the same process as struggle for existence. Thus, the selective process does not…
Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically…
The scheme of a unified Darwinian evolutionary theory for physical and biological systems is described. Every physical system is methodologically endowed with a classical information processor what turns every system into an agent being…
Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic…
We study the Fisher model describing natural selection in a population with a diploid structure of a genome by differential- geometric methods. For the selection dynamics we introduce an affine connection which is shown to be the…
Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach…
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of…
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
It is a widespread belief among musicians that a violin's sound ``opens up'' or improves through regular playing. However, physical evidence for this ``playing-in'' effect remains elusive. This study revisited the phenomenon by testing two…
Two evolutionary lineages: Machiavellian and Bohrian intelligence Mutation and natural selection are the two most basic processes of evolution, yet the study of their interplay remains a challenge for theoretical and empirical research.…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression,…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…