Related papers: The genome is software and evolution is a software…
Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural…
The current theory of evolution is almost the one Darwin and Wallace proposed two centuries ago and the following discoveries e.g., Mendelian genetics and neutral mutation theory have not made significant modifications. The current…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Testing provides means pertaining to assuring software performance. The total aim of software industry is actually to make a certain start associated with high quality software for the end user. However, associated with software testing has…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
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…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Currently it is widely accepted that the language of science is mathematics. This book explores an alternative idea where the future of science is based on the language of algorithms and programs. How such a language can actually be…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact…
Living things, computers, societies, and even books are part of a grand evolutionary struggle to survive. That struggle shapes nature, nations, religions, art, science, and you. What you think, feel, and do is determined by it. Darwinian…
We formulate genome assembly problem as an optimization problem in which the objective function is the likelihood of the assembly given the reads.
Modern science is relying on software more than ever. The behavior and outcomes of this software shape the scientific and public discourse on important topics like climate change, economic growth, or the spread of infections. Most…
Here we propose an evolutionary algorithm that self modifies its operators at the same time that candidate solutions are evolved. This tackles convergence and lack of diversity issues, leading to better solutions. Operators are represented…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
The nature of software re-engineering is to improve or transform existing software so it can be understood, controlled and reused as new software. Needs, the necessity of re-engineering software has greatly increased. The system software…