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The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
Motivated by present activities in (statistical) physics directed towards biological evolution, we review the interplay of three evolutionary forces: mutation, selection, and genetic drift. The review addresses itself to physicists and…
Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is…
We investigate the evolution of populations of random Boolean networks under selection for robustness of the dynamics with respect to the perturbation of the state of a node. The fitness landscape contains a huge plateau of maximum fitness…
The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
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,…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
It has been proposed that, since the origin of life and the ensuing evolution of biological species, a second evolutionary process has appeared on our planet. It is the evolution of culture-e.g., ideas, beliefs, and artifacts. Does culture…
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?…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
A tendency in biological theorizing is to formulate principles above or equal to Evolution by Variation and Selection of Darwin and Wallace. In this letter I analyze one such recent proposal which did so for the developmental ascendency. I…
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression,…
We interpret the Moran model of natural selection and drift as an algorithm for learning features of a simplified fitness landscape, specifically genotype superiority. This algorithm's efficiency in extracting these characteristics is…
Mutation and drift play opposite roles in genetics. While mutation creates diversity, drift can cause gene variants to disappear, especially when they are rare. In the absence of natural selection and migration, the balance between the…
Evolution by natural selection can be seen an algorithm for generating creative solutions to difficult problems. More precisely, evolution by natural selection is a class of algorithms that share a set of properties. The question we address…