Related papers: System-Level Genetic Codes: An Explanation for Bio…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
Complex evolving systems such as the biosphere, ecosystems and societies exhibit sudden collapses, for reasons that are only partially understood. Here we study this phenomenon using a mathematical model of a system that evolves under…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…
Ongoing progress in computational intelligence (CI) has led to an increased desire to apply CI techniques for the purpose of improving software engineering processes, particularly software testing. Existing state-of-the-art automated…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
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…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
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…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…