Related papers: Selective advantage for multicellular replicative …
We describe a simple model of evolution which incorporates the branching and extinction of species lines, and also includes abiotic influences. A first principles approach is taken in which the probability for speciation and extinction are…
We consider the problem of regulating by means of external control inputs the ratio of two cell populations. Specifically, we assume that these two cellular populations are composed of cells belonging to the same strain which embeds some…
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…
We point out that a simple and generic strategy to lower the risk for extinction consists in the developing a dormant stage in which the organism is unable to multiply but may die. The dormant organism is protected against the poisonous…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…
When users can benefit from certain predictive outcomes, they may be prone to act to achieve those outcome, e.g., by strategically modifying their features. The goal in strategic classification is therefore to train predictive models that…
It has been suggested that major transitions in evolution require the emergence of novelties, often associated to the cooperative behaviour of previously existing objects or agents. A key innovation involves the first cooperative…
The large scale behaviour of a population of cells that grow and interact through the concentration field of the chemicals they secrete is studied using dynamical renormalization group methods. The combination of the effective long-range…
Data scarcity drives the need for more sample-efficient large language models. In this work, we use the double descent phenomenon to holistically compare the sample efficiency of discrete diffusion and autoregressive models. We show that…
A microscopic agent dynamical model for diploid age-structured populations is used to study evolution of polymorphism and sympatric speciation. The underlying ecology is represented by a unimodal distribution of resources of some width.…
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of…
Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…
We examine a model of biological evolution of Eigen's quasispecies in a holey fitness landscape, where the fitness of a site is either 0 (lethal site) or a uniform positive constant (viable site). So, the evolution dynamics is determined by…
Numerous living systems are hierarchically organised, whereby replicating components are grouped into reproducing collectives -- e.g., organelles are grouped into cells, and cells are grouped into multicellular organisms. In such systems,…
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…
In any ecosystem, the conditions of the environment and the characteristics of the species that inhabit it are entangled, co-evolving in space and time. We introduce a model that couples active agents with a dynamic environment, interpreted…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The dynamical behavior of two types of non-equilibrium systems is discussed: $(a)$ two-dimensional cellular structures, and $(b)$ living polymers. Simple models governing their evolution are introduced and steady state distributions (cell…
Tumor development is characterized by a compromised balance between cell life and death decision mechanisms, which are tighly regulated in normal cells. Understanding this process provides insights for developing new treatments for fighting…
The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully…