Related papers: Origin and evolution of the genetic code: The univ…
By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…
An equation describing the evolution of phenotypic distribution is derived using methods developed in statistical physics. The equation is solved by using the singular perturbation method, and assuming that the number of bases in the…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
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…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
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…
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…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
Languages across the world exhibit Zipf's law of abbreviation, namely more frequent words tend to be shorter. The generalized version of the law - an inverse relationship between the frequency of a unit and its magnitude - holds also for…
We consider the problem of the evolution of a code within a structured population of agents. The agents try to maximise their information about their environment by acquiring information from the outputs of other agents in the population. A…
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,…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Recent experimental and theoretical work on neural populations belonging to two separate early sensory systems, olfaction and vision, has challenged the notion that the two operate under different computational paradigms by providing…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
Significant fraction (about 98.5% in humans, 24% in microbe Rickettsia prowazekii) of most animal genomes is non-coding DNA. Although recent studies established functions of its certain portions, it remains genomic dark matter. The paper…
The standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.
Predictive coding offers a potentially unifying account of cortical function -- postulating that the core function of the brain is to minimize prediction errors with respect to a generative model of the world. The theory is closely related…