相关论文: Molecular Labor Division: Its Cause and Consequenc…
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…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
Organisms have increased in complexity through a series of major evolutionary transitions, in which formerly autonomous entities become parts of a novel higher-level entity. One intriguing feature of the higher-level entity after some major…
A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as…
In the theoretical biology framework one fundamental problem is the so-called error catastrophe in Darwinian evolution models. We reexamine Eigen's fundamental equations by mapping them into a polymer depinning transition problem in a…
In previous work I proposed a framework for thinking about open-ended evolution. The framework characterised the basic processes required for Darwinian evolution as: (1) the generation of a phenotype from a genetic description; (2) the…
Ecology and evolution are inherently linked, and studying a mathematical model that considers both holds promise of insightful discoveries related to the dynamics of cooperation. In the present article, we use the prisoner's dilemma (PD)…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
The advent of new experimental genomic technologies and the massive increase of DNA sequence information is helping researchers better understand how our genes work. Recently, experiments on mRNA abundance (gene expression) have revealed…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
The origin of cellular life can be described in terms of the transition from inorganic matter: solids, liquids and gases, to the emergence of cooperative assemblies of organic matter, DNA and proteins,capable of replication and metabolism.…