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Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
Species sharing a prey or a predator species may go extinct due to exploitative or apparent competition. We examine whether evolution of the shared species acts as a coexistence mechanism and to what extent the answer depends on the genetic…
In the field of evolutionary robotics, choosing the correct encoding is very complicated, especially when robots evolve both behaviours and morphologies at the same time. With the objective of improving our understanding of the mapping…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
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…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
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?…
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
All possible phenotypes are not equally accessible to evolving populations. In fact, only phenotypes of large size, i.e. those resulting from many different genotypes, are found in populations of sequences, presumably because they are…
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes,…
The problem of unicellular-multicellular transition is one of the main issues that is discussing in evolutionary biology. In [1] the fitness of a colony of cells is considered in terms of its two basic components, viability and fecundity.…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…