Related papers: The genome is software and evolution is a software…
A deductive program synthesis tool takes a specification as input and derives a program that satisfies the specification. The drawback of this approach is that search spaces for such correct programs tend to be enormous, making it difficult…
A historical dispute in the conceptual underpinnings of evolution is the validity of the gene centered view of evolution. \cite{dawkins,lewontin} We transcend this debate by formalizing the gene centered view as a dynamic version of the…
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…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Darwin's theory of evolution is considered to be one of the greatest scientific gems in modern science. It not only gives us a description of how living things evolve, but also shows how a population evolves through time and also, why only…
Gene expression is a biochemical process, where stochastic binding and un-binding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin…
It is impossible to separate the human factors from software engineering expertise during software development, because software is developed by people and for people. The intangible nature of software has made it a difficult product to…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Molecular evidence regarding the genetic code has been examined and the findings on the nature of the early events responsible for the amino acid distribution in the code are reported.
The natural evolution of life seems to proceed through steps characterized by phases of relatively rapid changes, followed by longer, more stable periods. In the light of the string-theory derived physical scenario proposed in [1], we…
Automatic software generation based on some specification is known as program synthesis. Most existing approaches formulate program synthesis as a search problem with discrete parameters. In this paper, we present a novel formulation of…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
Generative AI enables rapid ``vibe coding," where natural language prompts yield working software systems. While this lowers barriers to software creation, it also collapses the boundary between prototypes and engineered software, leading…
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…