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Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…

This paper reviews predictive coding, from theoretical neuroscience, and variational autoencoders, from machine learning, identifying the common origin and mathematical framework underlying both areas. As each area is prominent within its…

The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…

New analyses of the organization of the genetic code system together with their relation to the two classes of aminoacyl-tRNA synthetases are reported in this work. A closer inspection revealed how the enzymes and the 20 amino acids of the…

Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and…

In a certain way, this paper presents the continuation of the previous one which discussed the harmonic structure of the genetic code (Rakocevic, 2004). Several new harmonic structures presented in this paper, through specific unity and…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…

We propose a novel definition of life in terms of which its emergence in the universe is expected, and its ever-creative open-ended evolution is entailed by no law. Living organisms are Kantian Wholes that achieve Catalytic Closure,…

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can…

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…

Chirality or the property that distinguishes lefthandedness from righthandedness is an important aspect of the universe, starting from neutrinos, which are lefthanded. Fifteen years ago the author had proposed that life on the earth was…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the…

In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within…

The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides and cofactors. At the origin of metabolism there were no enzymes--how did it start? Empirical…

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…

It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and…

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…