Related papers: Genetic code evolution as an initial driving force…
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…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
The holographic bound in physics constrains the complexity of life. The finite storage capability of information in the observable universe requires the protein linguistics in the evolution of life. We find that the evolution of genetic…
To synthesize peptides alongside the RNAs making the so-called RNA world, some genetic coding involving RNA had to develop. Herein, it is proposed that the first real-coding setup was a direct one, made up of continuous poly-tRNA-like…
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…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
We present a scenario for the origin of biological coding. In this context, coding is a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding…
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…
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
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…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
The origin of life is often framed primarily as a chemical problem, yet life's defining feature is evolution. Advances in geochemistry, prebiotic chemistry, and molecular biology have produced diverse scenarios for the emergence of genomes,…
This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…
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 grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…