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Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
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…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
In this paper, we introduce a model of evolution and learning in robots that co-optimizes a distribution of latent design vectors (genotypes) and a mixture of control experts (neural modules), which are gated by the latent coordinates of…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
This study facilitates the understanding of evolutionary transitions in individuality (ETIs) through a novel artificial life framework, named VitaNova, that intricately merges self-organization and natural selection to simulate the…
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…
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
The evolutionary process has been modelled in many ways using both stochastic and deterministic models. We develop an algebraic model of evolution in a population of asexually reproducing organisms in which we represent a stochastic walk in…
An object-oriented combinator chemistry was used to construct an artificial organism with a system architecture possessing characteristics necessary for organisms to evolve into more complex forms. This architecture supports modularity by…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…