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The Gaia hypothesis considers the life-environment coupled system as a single entity that acts to regulate and maintain habitable conditions on Earth. In this paper we discuss three mechanisms which could potentially lead to Gaia: Selection…
The stacked contact process is a three-state spin system that describes the co-evolution of a population of hosts together with their symbionts. In a nutshell, the hosts evolve according to a contact process while the symbionts evolve…
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
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.…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
The paper contains the attempt to integration of the classical evolutionary game theory based on replicator dynamics and the state based approach of Houston and Mcnamara. In the new approach, individuals have different heritable strategies,…
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…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
In the present work, a geometrical method to generate a two dimensional random walk by means of a bidimensional Cellular Automaton is presented. We illustrate it by means of Conway's Game of Life with periodical borders, with a large…
Biological evolution in a sequence space with random fitnesses is studied within Eigen's quasispecies model. A strong selection limit is employed, in which the population resides at a single sequence at all times. Evolutionary trajectories…
This paper demonstrates the use of genetic algorithms for evolving: 1) a grandmaster-level evaluation function, and 2) a search mechanism for a chess program, the parameter values of which are initialized randomly. The evaluation function…
We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of…
Given a large population of players, each player has three possible choices between option 1 or 2 or no option. The two options are equally favorable and the population has to reach consensus on one of the two options quickly and in a…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
In this study, we provide a relatively simple simulation framework for constructing artificial life (ALife) with both autonomous and evolutionary aspects by extending chemoton model. While the original chemoton incorporates metabolism,…
In this paper we experiment with a 2-player strategy board game where playing models are evolved using reinforcement learning and neural networks. The models are evolved to speed up automatic game development based on human involvement at…