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In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
`Entropy' appears as driving force in many different evolution equations, both deterministic and stochastic, and in these equations this `entropy' also takes different forms. We show how all these examples can be understood as different…
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…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
Evolution depends on the fitness of organisms, the expected rate of reproducing. Directly getting offspring is the most basic form of fitness, but fitness can also be increased indirectly by helping genetically related individuals (such as…
During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
We study the coevolutionary dynamics of the diversity of phenotype expression and the evolution of cooperation in the Prisoner's Dilemma game. Rather than pre-assigning zero-or-one interaction rate, we diversify the rate of interaction by…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
There are two contrasting explanations of sleep: as a proximate, essential physiological function or as an adaptive state of inactivity and these hypotheses remain widely debated. To investigate the adaptive significance of sleep, we…
Adaptive dynamics is a widely used framework for modeling long-term evolution of continuous phenotypes. It is based on invasion fitness functions, which determine selection gradients and the canonical equation of adaptive dynamics. Even…
Environmental and genetic mutations can transform the cells in a co-operating healthy tissue into an ecosystem of individualistic tumour cells that compete for space and resources. Various selection forces are responsible for driving the…
The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the…
Deep Learning (DL) is a surprisingly successful branch of machine learning. The success of DL is usually explained by focusing analysis on a particular recent algorithm and its traits. Instead, we propose that an explanation of the success…
The possibility of complicated dynamic behaviour driven by non-linear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility…
We consider the dynamics imposed by natural selection on the populations of two competing, sexually reproducing, haploid species. In this setting, the fitness of any genome varies over time due to the changing population mix of the…