Scientist describes the dynamics of signs when reading genetic information
Scientist suggests viewing genetic code not as a static "manual" that determines how organisms function, but a dynamic process of the birth of meaning and signs—semiosis. As part of this approach, the "letters" (signs) in the DNA molecule acquire significance only after a number of biochemical operations, just as words acquire particular meaning when combined in a specific sentence. This way of looking at the genetic code allows for a better understanding of the information transmission processes that underlie life. The results of the study supported by a grant from Russian Science Foundation (RSF) were published in the BioSystems journal.
Many terms that describe processes related to DNA are borrowed from philology: the "letters" (DNA nucleotides), "transcription" (a written notation of sounds and at the same time reading genetic information from DNA), "synonym" (in the context of synonymous or representing the same thing codons—nucleotides in DNA that have a triadic relationship) and others. These terms were simply convenient analogies for a long time, and biologists did not attach much importance to their original meaning.
Previously, a scientist from Immanuel Kant Baltic Federal University (Kaliningrad) suggested a model where the genetic code is considered as a language with its own alphabet, grammar and vocabulary. This approach allowed to describe how the nucleic acid (DNA and RNA) and protein building blocks (DNA and RNA) turn into a meaningful instruction for building and functioning of a living organism.
In his new research the scientist focused on the process of emergence of the signs and their meaning during gene expression. The author analyzed the process of DNA doubling (replication), transcription (DNA and RNA molecule reading). In doing so the scientist regarded each stage not as a simple set of biochemical reactions, but as a sequence of semiotic acts—the process of creating, transmitting and transitioning of signs and meanings.
As part of this approach, the nucleotide triplets—codons—in the DNA gain meaning (which is reflected on its designated amino acid) only after going through a cascade of transformations. Biochemically, it means reading the DNA and RNA "letters" according to the complementarity principle, meaning alignment, similar to a key and a lock, as it is usually regarded. But there is an additional measurement such as a code based on the the difference between the amount of hydrogen bonds (two or three) and carbon nucleuses (one or two) inside a nucleotide. In this way a nucleotide functions as a binary information unit. At the same time, the "letter" itself (the nucleotide) does not have a meaning as it depends on its position inside the "word" (codon) and the context.
The main new development was the redefining the role of transfer RNA (tRNA)—the molecules that carry amino acids to the ribosome (a "factory" that synthesizes proteins). The scientist described the stages how the tRNA works in terms of creating and transmitting information. At first the tRNA is "empty"—it is ready to function but hasn't yet attached an amino acid. Then the tRNA gets "charged" and starts carrying information, meaning it becomes a sign. When a complex of transfer RNA and the amino acid interacts with ribosome, the tRNA becomes a complex two-level sign: one sign (codon—anticodon) builds into another (tRNA—amino acid). After the amino acid detaches and becomes part of a new protein, the tRNA once again returns back to its "uninformative" state.
Thus, the signs aren't stored in the genes as a given; they are constantly "born" and then "die off" in the course of genetic coding. It is this process that the author considers as semiosis in terms of molecular biology, and that, namely, it can be regarded as prototypical, including language.
"Consideration of semiotic relationships and operations in genetic coding allows us to reconsider the common understanding of a sign as something permanent, necessarily linked to a specific object. The suggested concept gives an opportunity to represent more broadly the sign manufacturing (semiosis) as an inherent property of systems that control the information processes not only in biology but in the field of "human being—artificial intelligence" interaction"—says the main performer of the project, supported by a grant from RSF, Suren Zolyan, doctor of philology, professor, leading researcher at Immanuel Kant Baltic Federal University.
"In the future we are planning to expand this approach up to the field of gene activity control processes. That is a wide number of signaling molecules and motive signals in the regulatory regions of the genes, signallig cascades from outside the cells and up to the target genes turning on and off levels at which these signals are eventually aimed at. So we expect remarkable cross-disciplinary generalizations"—concludes the head of the project, supported by a grant from RSF, Alexander Spirov, Ph.D. in Biology and Senior Researcher at the Evolution Modeling Laboratory at the Institute of Evolutionary Physiology and Biochemistry RAS.
More information:
doi.org/10.1016/j.biosystems.2025.105602
Provided by Immanuel Kant Baltic Federal University
