相关论文: An Illustrated Introduction to the Basic Biologica…

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…

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…

We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…

The concept of fitness is introduced, and a simple derivation of the Fundamental Theorem of Natural Selection (which states that the average fitness of a population increases if its variance is nonzero) is given. After a short discussion of…

In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…

Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…

At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge {\it de novo} with relative ease. At early times of molecular evolution,…

We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…

Different classes of phenomenological universalities of environment dependent growths have been proposed. The logistic as well as environment dependent West-type allometry based biological growth can be explained in this proposed framework…

The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…

One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…

Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like "adaptive zones", "punctuated equilibrium" and "blunderbuss patterns", require more elaborate explanations than a…

We introduce a new model for large scale evolution and extinction in which species are organized into food chains. The system evolves by two processes: origination/speciation and extinction. In the model, extinction of a given species can…

Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…

Darwinian evolution is driven by random mutations, genetic recombination (gene shuffling) and selection that favors genotypes with high fitness. For systems where each genotype can be represented as a bitstring of length $L$, an overview of…

Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…

A simple model of macroevolution is proposed exhibiting both the property of punctuated equilibrium and the dynamics of potentialities for different species to evolve towards increasingly higher complexity. It is based on the phenomenon of…

We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…

Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will…

The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…