The Quantum Workings of the Rotating 64-Grid Genetic Code

Abstract

In this article, the pattern learned from the classic or conventional rotating circular genetic code is transferred to a 64-grid model. In this non-static representation, the codons for the same amino acid within each quadrant could be exchanged, wobbling or rotating in a quantic way similar to the electrons within an atomic orbit. Represented in this 64-grid format are the three rules of variation encompassing 4, 2, or 1 quadrant, respectively: 1) same position in four quadrants for the essential hydrophobic amino acids that have U at the center, 2) same or contiguous position for the same or related amino acids in two quadrants, and 3) equivalent amino acids within one quadrant. Also represented is the mathematical balance of the odd and even codons, and the most used codons per amino acid in humans compared to one diametrically opposed organism: the plant Arabidopsis thaliana, a comparison that depicts the difference in third nucleotide preferences: a C/U exchange for 11 amino acids, a G/A exchange for 2 amino acids, and G/U or C/A exchanges for one amino acid, respectively; by studying these codon usage preferences per amino acid we present our two hypotheses: 1) A slower translation in vertebrates and 2) a faster translation in invertebrates, possibly due to the aqueous environments where they live. These codon usage preferences may also be able to determine genomic compatibility by comparing individual mRNAs and their functional third dimensional structure, transport and translation within cells and organisms. These observations are aimed to the design of bioinformatics computational tools to compare human genomes and to determine the exchange between compatible codons and amino acids, to preserve and/or to bring back extinct biodiversity, and for the early detection of incompatible changes that lead to genetic diseases.

Golden and Harmonic Mean in the Genetic Code

“…It is expected that all these uniqueness correspond to the same, or similar uniqueness, found by other authors ( [16], [17], [18], [19]), what in future researches should be checked.…”

Matrix Genetics and Algebraic Properties of the Multi-Level System of Genetic Alphabets

“…Generally speaking, we suppose that in the phenomenological field of molecular genetics and inherited physiological systems, the 8-dimensional genetic algebras (which have been revealed in our works) can be a natural genetic basis to simulate numeric regularities in inherited families of information elements. In our opinion, these genetic algebras can be used also in development of "science of consciousness" (Penrose, 1996) and in solving many other questions of the genetic system and inherited physiological functions (see for example (Castro-Chavez, 2011)). …”

Most Used Codons per Amino Acid and per Genome in the Code of Man Compared to Other Organisms According to the Rotating Circular Genetic Code

“…From this point on, the differences increase dramatically if we compare the most used codons in humans per amino acid to an amphibian (frog Xenopus laevis ) or a reptile (cobra Naja naja ) [data not shown]; and even more abundant differences were seen when comparing the most used codons in humans to the most used codons of a plant ( Arabidopsis thaliana , which will be compared elsewhere within this journal, in my topic of the quantum workings of the genetic code) (Castro-Chavez, 2011), except for the most abundant Lys AA G 51.5% and Arg AGA 35.19%. Unexpectedly, the differences between humans and bacteria ( E. coli K12), in relation to the most used codons, are less notable than the ones for the last three mentioned organisms (frog, cobra and plants).…”