Related papers: Quantifying the Emergence of Selection Prior to Bi…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
We present an algebraic approach to evolutionary accumulation modelling (EvAM). EvAM is concerned with learning and predicting the order in which evolutionary features accumulate over time. Our approach is complementary to the more common…
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…
This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the…
If evolution can be connected to the principle of least action, and if it is depicted in evolution space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate…
We develop a nonparametric Bayesian modeling framework for clustered ordinal responses in developmental toxicity studies, which typically exhibit extensive heterogeneity. The primary focus of these studies is to examine the dose-response…
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…
In Bayesian nonparametric inference, random discrete probability measures are commonly used as priors within hierarchical mixture models for density estimation and for inference on the clustering of the data. Recently, it has been shown…
Species sampling processes have long served as the fundamental framework for modeling random discrete distributions and exchangeable sequences. However, data arising from distinct but related sources require a broader notion of…
We define a novel quantitative strategy inspired by the ecological notion of nestedness to single out the scale at which innovation complexity emerges from the aggregation of specialized building blocks. Our analysis not only suggests that…
Significant galaxy mergers throughout cosmic time play a fundamental role in theories of galaxy evolution. The widespread usage of human classifiers to visually assess whether galaxies are in merging systems remains a fundamental component…
The non-selective and selective measurements of a self-adjoint observable $A$ in quantum mechanics are interpreted as `jumps' of the state of the measured system into a decohered or pure state, respectively, characterized by the spectral…
The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures for a given chemical composition. Here we extend this method to predict the crystal structure of polymers by…
Evolutionary algorithms (EAs), a large class of general purpose optimization algorithms inspired from the natural phenomena, are widely used in various industrial optimizations and often show excellent performance. This paper presents an…
Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…
The environment plays a critical role in galaxy evolution, with galaxy clusters and their infall regions offering diverse conditions that shape galaxies before they enter the dense cluster core, a process known as ``pre-processing''.…
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…