Related papers: Physical constraints on epistasis
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…
We investigate the relationship between the average fitness decay due to single mutations and the strength of epistatic interactions in genetic sequences. We observe that epistatic interactions between mutations are correlated to the…
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…
Every now and then the cultural paradigm of a society changes. Human history can be regarded as a sequence of long periods of cultural stasis punctuated by paradigm shifts that transform culture upside-down over the turn of a few…
Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are `simple'…
While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult to reproduce in silico. Known as open-endedness, we've been…
The class of epistatic fitness landscapes is much more diverse than the class of non-epistatic landscapes, and so it stands to reason that there exist dynamical phenomena that can only be realized in the presence of epistasis. Here, we…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
The environment in which a population evolves can have a crucial impact on selection. We study evolutionary dynamics in finite populations of fixed size in a changing environment. The population dynamics are driven by birth and death…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
When complex systems are driven to extinction by some external factor, their non-stationary dynamics can present an intermittent behaviour between relative tranquility and burst of activity whose consequences are often catastrophic. To…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Kinetically constrained spin systems play an important role in understanding key properties of the dynamics of slowly relaxing materials, such as glasses. So far kinetic constraints have been introduced in idealised models aiming to capture…
Environmental science almost invariably proposes problems of extreme complexity, typically characterized by strongly nonlinear evolution dynamics. The systems under investigation have many degrees of freedom - which makes them complicated -…