Related papers: Evolution of genetic organization in digital organ…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
We represent a process of learning by using bit strings, where 1-bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial-and-error; and social learning by copying knowledge…
Self-organisation lies at the core of fundamental but still unresolved scientific questions, and holds the promise of de-centralised paradigms crucial for future technological developments. While self-organising processes have been…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
This chapter investigates the evolutionary ecology of software, focusing on the symbiotic relationship between software and innovation. An interplay between constraints, tinkering, and frequency-dependent selection drives the complex…
Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population…
Understanding the complex dynamics of communities of software developers requires a view of such organizations as a network of interacting agents involving both goals and constraints. Beyond their special features, these systems display…
The selection pressures that have shaped the evolution of complex traits in humans remain largely unknown, and in some contexts highly contentious, perhaps above all where they concern mean trait differences among groups. To date, the…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Although information theory has found success in disciplines, the literature on its applications to software evolution is limit. We are still missing artifacts that leverage the data and tooling available to measure how the information…
We have performed a statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. The analysis reveals that operons that regulate each other and operons that are coregulated tend…
The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…