Related papers: Design principles of multi-map variation in biolog…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
We propose a model for co-evolving ecosystems that takes into account two levels of description of an organism, for instance genotype and phenotype. Performance at the macroscopic level forces mutations at the microscopic level. These, in…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
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…
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?…
Fitness landscapes are mappings between genotypes, phenotypes, and fitness that shape evolution. In recent years, empirical work and theoretical models have greatly advanced our understanding of how populations navigate rugged fitness…
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…
The capacity to adapt can greatly influence the success of systems that need to compensate for damaged parts, learn how to achieve robust performance in new environments, or exploit novel opportunities that originate from new technological…
In a highly simplified view, a disease can be seen as the phenotype emerging from the interplay of genetic predisposition and fluctuating environmental stimuli. We formalize this situation in a minimal model, where a network (representing…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
Self-organization of complex morphological patterns from local interactions is a fascinating phenomenon in many natural and artificial systems. In the artificial world, typical examples of such morphogenetic systems are cellular automata.…
Developmental bias plays a major role in phenotypic evolution. Some researchers have argued that phenotypes, regulated by development, can only evolve along restricted trajectory under certain scenarios, such as the case for mammalian molar…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
Both external environmental selection and internal lower-level evolution are essential for an integral picture of evolution. This paper proposes that the division of internal evolution into DNA/RNA pattern formation (genotype) and protein…
A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…