Related papers: Non-coding DNA programs express adaptation and its…
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…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
Object detection and recognition are fundamental functions underlying the success of species. Because the appearance of an object exhibits a large variability, the brain has to group these different stimuli under the same object identity, a…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the…
Biological intelligence is inherently adaptive -- animals continually adjust their actions based on environmental feedback. However, creating adaptive artificial intelligence (AI) remains a major challenge. The next frontier is to go beyond…
Various features of the development of individual living species, including individual humans, are programmed. Is death also programmed, and if yes, how is it implemented and what can be the underlying mechanism providing the inevitability…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Neutral landscapes and mutational robustness are believed to be important enablers of evolvability in biology. We apply these concepts to software, defining mutational robustness to be the fraction of random mutations that leave a program's…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
While Neutral Theory famously describes the number of discrete genetic differences in populations, we consider the number of genetic backgrounds under which such differences are observed - setting limits to the generalizability of their…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
An algorithm is described that adaptively learns a non-linear mutation distribution. It works by training a denoising autoencoder (DA) online at each generation of a genetic algorithm to reconstruct a slowly decaying memory of the best…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…