Related papers: Evolution of genetic organization in digital organ…
Can intelligence optimise Digital Ecosystems? How could a distributed intelligence interact with the ecosystem dynamics? Can the software components that are part of genetic selection be intelligent in themselves, as in an adaptive…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the…
In this work we model the dynamics of a population that evolves as a continuous time branching process with a trait structure and ecological interactions in form of mutations and competition between individuals. We generalize existing…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…
The model of interaction between learning and evolutionary optimization is designed and investigated. The evolving population of modeled organisms is considered. The mechanism of the genetic assimilation of the acquired features during a…
Jim Shapiro synthesizes a great many observations about the mechanisms of evolution to reach the remarkable conclusion that large-scale modification, exchange, and rearrangement of the genome are common and should be viewed as fundamental…
When dealing with evolving or multi-dimensional complex systems, network theory provides with elegant ways of describing their constituting components, through respectively time-varying and multi-layer complex networks. Nevertheless, the…
The dynamical evolution of many economic, sociological, biological and physical systems tends to be dominated by a relatively small number of unexpected, large changes (`extreme events'). We study the large, internal changes produced in a…
In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some initial time. We deduce the time translational matrix for…
A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
We consider a Moran-type model of cultural evolution, which describes how traits emerge, are transmitted, and get lost in populations. Our analysis focuses on the underlying cultural genealogies; they were first described by Aguilar and…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…