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A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
The performance of evolutionary algorithms can be heavily undermined when constraints limit the feasible areas of the search space. For instance, while Covariance Matrix Adaptation Evolution Strategy is one of the most efficient algorithms…
Phenotypically structured equations arise in population biology to describe the interaction of species with their environment that brings the nutrients. This interaction usually leads to selection of the fittest individuals. Models used in…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
The relationship between intelligence and evolution is bidirectional: while evolution can help evolve intelligences, the degree of intelligence itself can impact evolution (Baldwin, 1896). In the field of Evolutionary Computation, the…
A key challenge to make effective use of evolutionary algorithms is to choose appropriate settings for their parameters. However, the appropriate parameter setting generally depends on the structure of the optimisation problem, which is…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two…
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…
Evolutionary model merging provides a powerful framework for the automated, training-free composition of LLMs through parameter-space search. However, existing methods predominantly rely on stochastic, hand-crafted operators that overlook…
Agent harness evolution improves frozen language-model agents by modifying the executable structures around them. We study this paradigm as a form of sample-efficient fast adaptation: instead of updating model weights, an agent can acquire…
Adaptive therapy is a recent paradigm in cancer treatment aiming at indefinite, safe containment of the disease when cure is judged unattainable. In modeling this approach, inherent limitations arise due to the structure of the vector…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…
The importance of mutator clones in the adaptive evolution of asexual populations is not fully understood. Here we address this problem by using an ab initio microscopic model of living cells, whose fitness is derived directly from their…
Biological living systems in general exhibit complex and diverse dynamics. The latter, in particular, is essential, since diversification increases the odds of survival of an organism while reducing the risk of extinction of the population.…
An important transition after the origin of life was the first emergence of a Darwinian population, self-reproducing entities exhibiting differential reproduction, phenotypic variation, and inheritance of phenotypic traits. The simplest…