Related papers: Evolution: Life has Evolved to Evolve
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes,…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome…
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…
Life is a discrete, stochastic phenomena : for a biological organism, the time of the two most important events of its life (reproduction and death) is random and these events change the number of individuals of the species by single units.…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…
This chapter begins by outlining a promising, new theoretical framework for the process by which human culture evolves inspired by the views of complexity theorists on the problem of how life began. Elements of culture, like species, evolve…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
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…
Biological evolution is realised through the same mechanisms of birth and death that underlie change in population density. The deep interdependence between ecology and evolution is well-established, and recent models focus on integrating…
Based on statistical analysis of the complete genome sequences, a remote relationship has been observed between the evolution of the genetic code and the three domain tree of life. The existence of such a remote relationship need to be…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Various features of the development of individual living species, including individual humans, are programmed. Is death also programmed, and if yes, how is it implemented and what can be the underlying mechanism providing the inevitability…
We attempt to provide a comprehensive model of evolution of science across millennia taking into account the contributions of other intellectual traditions, cultural value system and increasing in sophistication of humans in their study of…
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly…
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…