Genomes contain relics of a triplet code connecting the origins of primordial RNA synthesis to the origins of genetically coded protein synthesis

Life on earth relies on three types of information polymers- DNA, RNA and proteins. In all organisms and viruses, these molecules are synthesized by the copying of pre-existing templates. A triplet-based code known as the genetic code guides the synthesis of proteins by complex enzymatic machines that decode genetic information in RNA sequences. The origin of the genetic code is one of the most fundamental questions in biology. In this study, computational analysis of about 5,000 species level metagenomes using techniques for the analysis of human language suggests that the genomes of extant organisms contain relics of a distinct triplet code that potentially predates the genetic code. This code defines the relationship between adjacent triplets in DNA/RNA sequences, whereby these triplets predominantly differ by a single base. Furthermore, adjacent triplets encode amino acids that are thought to have emerged around the same period in the earth's early history. The results suggest that the order of triplets in primordial RNA sequences was associated with the availability of specific amino acids, perhaps due to a coupling of a triplet-based primordial RNA synthesis mechanism to a primitive mechanism of peptide bond formation. Together, this coupling could have given rise to early nucleic acid sequences and a system for encoding amino acid sequences in RNA, i.e. the genetic code. Thus, the central role of triplets in biology potentially extends to the primordial world, contributing to both the origins of genomes and the origins of genetically coded protein synthesis.

Functional Domains in the Encrypted Inverse Fine-Structure Constant

The inverse fine-structure constant 1/α = 137.035999… … is encrypted by a numerical 137 035 999 … … triplet code, and functional domains of this code are separated from each other by 999 triplets.

Astronomical Significance of the 137.035 999 Part of the Inverse Fine-Structure Constant

The inverse fine-structure constant 1/α= 137.035 satisfies 1/α = 112 + 42 + 0.035 = 121 + 16 + 0.035 = 137.035, with 11 being the 11 dimensions of M-theory, 4 the number of dimensions of Einstein’s space-time, and 0.035 the 3.5 percent visible Universe. Cosmological information appears to be encrypted linearly as a triplet code in 1/α.

Free Triplet Conjecture and Equivalence Classes Derived Using Group Theory

All proteins are made up of 20 different amino acids which contain 4 kinds of nucleotides . Three consecutive nucleotides on the gene, called triplet codons, are used to code an amino acid, and 64 triplet codons comprise the genetic code table. Central dogma (DNA-RNA-protein) has been acknowledged, but the process and mechanism of mRNA passing through the nuclear membrane still require further investigation. For these two problems mentioned above, this paper proposed a conjecture of nucleotide free triplet and obtained 20 equivalence classes of mapping from free triplet vertex set to nucleotide set using group theory. Whether the four numbers 3, 4, 20 and 64 have relevance are taken into consideration here. Subsequently, the numbers 3, 4, 20 and 64 were connected together which was important for the analysis of triplet code and protein composition.

Macrodynamic Cooperative Complexity of Information Dynamics

The introduced concept and measure of macrocomplexity (MC) arise in an irreversible macrodynamic cooperative process and determine the process components ability to assemble into an integrated system. MC serves as a common indicator of the origin of the cooperative complexity measured by the specific entropy speed per assembled volume, rather than the entropy, as it has been accepted before. The MC cooperative mechanism is studied using the variation principle (VP) of information macrodynamics (IMD), applied to a complex system with the macrolevel dynamics and random microlevel stochastics and different forms of physical and virtual transitions of information. This principle describes a transition from a local unstable process movement to a local stable process — the former is associated with the current influx of information that precedes cooperation, and the latter is continued after the cooperation with incoming information and its accumulation. This transition enables the production of the cooperative phenomena and, in particular, the contributions from different superimposing processes, which are measured by the MC. MC, arising as an indicator of these phenomena at the unification (or decomposition) of the system processes, is defined by the invariant information measure, allowing for both analytical formulation and computer evaluation. An optimal multi-dimensional consolidation process, satisfying the VP, forms the information hierarchical network (IN) consisting of the model eigenvalues sequential cooperation in triples. The MC of such an optimal cooperative triplet structure is measured by the IN triplet code (as an algorithm of the minimal program, which evaluates the IN hierarchical structure by the triplet information contributions in bits of information). The distributed IN allows for the automatic arrangement and measurement of the MC-local complexities in a multi-dimensional cooperative process, taking into account the MC time-space locations and mutual dependencies, and providing the MC hierarchical invariant information measure by quantity and quality in the triplet code. The MC is connected to Kolmogorov (K) complexity, which measures a deterministic order over a stochastic disorder by a minimal program. The MC specific consists of providing a computable complexity measure of a cooperative dynamic irreversible process, as an opposite to the K incomputability.