Related papers: The genome is software and evolution is a software…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
Evolutionary computing (EC) is an exciting development in Computer Science. It amounts to building, applying and studying algorithms based on the Darwinian principles of natural selection. In this paper we briefly introduce the main…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the…
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
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…
Computer programs are part of our daily life, we use them, we provide them with data, they support our decisions, they help us remember, they control machines, etc. Programs are made by people, but in most cases we are not their authors, so…
Information theoretic analysis of large evolved programs produced by running genetic programming for up to a million generations has shown even functions as smooth and well behaved as floating point addition and multiplication loose entropy…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…
A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…
Nowadays, software has become a complex piece of work that may be beyond our control. Understanding how software evolves over time plays an important role in controlling software development processes. Recently, a few researchers found the…
This paper introduces a new concept. We intend to give life to a software agent. A software agent is a computer program that acts on a user's behalf. We put a DNA inside the agent. DNA is a simple text, a whole roadmap of a network of…
Automatic Programming is one of the most important areas of computer science research today. Hardware speed and capability have increased exponentially, but the software is years behind. The demand for software has also increased…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Programming languages serve a dual purpose: to communicate programs to computers, and to communicate programs to humans. Indeed, it is this dual purpose that makes programming language design a constrained and challenging problem.…
Programming is the activity of modifying a program in order to bring about specific changes in its behaviour. Yet programming language theory almost exclusively focuses on the meaning of programs. We motivate a "change-oriented" viewpoint…