Related papers: The genome is software and evolution is a software…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
We live in a world brimming with uncertainty, where we constantly have to make a lot of decisions under incomplete information. We are firm believers that our subjective belief cannot be computed by rigorous mathematical formula; instead…
Evolution is the process of optimal adaptation of biological populations to their living environments. This is expressed via the concept of fitness, defined as relative reproductive success. However, it has been pointed out that this…
Uncertain, unpredictable, real time, and lifelong evolution causes operational failures in intelligent software systems, leading to significant damages, safety and security hazards, and tragedies. To fully unleash the potential of such…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…
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…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
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 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…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
The development of scientific software is often a partnership between domain scientists and scientific software engineers. It is especially important to embrace these collaborations when developing advanced scientific software, where…
Changes, they use to say, are the only constant in life. Everything changes rapidly around us, and more and more key to survival is the ability to rapidly adapt to changes. This consideration applies to many aspects of our lives. Strangely…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Biological evolution continuously refines the design of species, resulting in highly optimised organisms over hundreds of millennia. Intuitively, we expect that random changes-evolution's primary mechanism-are more likely to be harmful than…
Software is a field of rapid changes: the best technology today becomes obsolete in the near future. If we review the graduate attributes of any of the software engineering programs across the world, life-long learning is one of them. The…
Software automation has long been a central goal of software engineering, striving for software development that proceeds without human intervention. Recent efforts have leveraged Artificial Intelligence (AI) to advance software automation…
A key mission of computer science is to enable people realize their creative ideas as naturally and painlessly as possible. Software engineering is at the center of this mission -- software technologies enable reification of ideas into…
Software engineering concepts and processes are worthy of formal study; and yet we seldom formalize them. This "research ideas" article explores what a theory of software engineering could and should look like. Software engineering research…