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Polyfunctional Old Testament Biblical Texts: An Analogy to Molecular Biochemistry of DNA—Introduction
I love Sudoku! Some might think it odd, but working on a Sudoku number puzzle helps my brain relax enough to gently fall off to sleep, either at night or for a nap. I think that is because Sudoku is a wordless puzzle. It focuses the brain, quiets distractions, and all without mental images, narratives, or words. That’s pretty cool. For those who are unfamiliar with Sudoku, it’s a square made of a 3×3 grid of smaller squares, each of which are divided into a 3×3 grid of still smaller squares. In other words, nine squares form a larger square, and these larger squares are arranged in a 3×3 grid. There are 81 small squares all together.
Sudoku is played by filling each of the 9 grids with the digits 1 through 9. Each of these digits must be used exactly once. The trick is to fill each grid in such a way that any and all rows in either horizontal or vertical direction must contain each of the 9 digits used exactly once. In the case of a Sudoku puzzle, there can only be one solution per puzzle. The puzzle publisher provides the digits for a certain number of the smallest squares at the beginning of each game. The more numbers provided, the easier the puzzle, and vice versa.
The biological world of living things resembles a Sudoku puzzle in the following way. Living cells contain molecules which are arranged into larger units, which are then arranged into larger units, which are arranged into yet larger units. Everything from the simplest, smallest unit to the entire network of functioning parts must work together in cooperative unity in order for the biological entity, whether plant, animal, bacteria, or virus, to exist.
But the biological world greatly differs from a Sudoku puzzle. Ultimately, except for challenging the minds of some people and putting others to sleep, a Sudoku puzzle has no meaning. It makes no statements. It gives no information, and no language is involved. A living, biological organism is quite different. In the last few decades, scientists have made exciting discoveries about the organization of living entities at the cellular and molecular level.
Scientists have discovered nucleotides. A nucleotide is a micro-unit of biological chemistry in which the chemicals are linguistic letters. These letters both store and communicate information. Nucleotides get joined together in orderly arrangements to perform functions within a living cell, such as supplying instructions for other parts of the cell to build proteins.
Nucleotide packets join together in a string to form DNA strands. Individual units of a single strand of DNA are called DNA sequences. In recent decades scientists discovered that DNA sequences are polyfunctional. That means that a single DNA sequence, comprised of nucleotide packets, participates in more than one chemical network of information and function. A simple analogy is an individual letter at an intersection of two words in a crossword puzzle. That single letter participates in both a vertical and horizontal direction whose resultant products are completely distinct one from another (two different words). Another example is a single Sudoku digit, which must participate in three addition equations simultaneously: its own square, a vertical line, and a horizontal line.
When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. (1)
Most DNA sequences are polyfunctional… This means that DNA sequences have meaning on several different levels (polyfunctional) … For example, imagine a sentence which has a very specific message in its normal form but with an equally coherent message when read backwards. Now let’s suppose that it also has a third message when reading every other letter, and a fourth message when a simple encryption program is used to translate it. Such a message would be polyfunctional…(2)
In the last decade, we have discovered still another aspect of the multidimensional genome. We now know that DNA sequences are typically “polyfunctional” . Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” . The ENCODE project  has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes . So not only are there many “knobs” in Fisher’s microscope analogy, each one can affect multiple traits simultaneously and interactively. (3)
Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). Several codes of nucleotide sequences are discussed including: (1) the translation framing code, responsible for correct triplet counting by the ribosome during protein synthesis; (2) the chromatin code, which provides instructions on appropriate placement of nucleosomes along the DNA molecules and their spatial arrangement; (3) a putative loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. (4)
Sudoku puzzles, crossword puzzles, and polyfunctional DNA sequences provide examples of how the same piece of information can possess multiple meanings in the real world. We can think of countless further examples in human languages, where context provides signals that change meanings of an identical information unit. For example, a change in emotive expression (anger, sarcasm, nostalgia, etc.) can change a word’s meaning tremendously. We can also think of figures of speech, such as puns, metaphors, similes, and so forth. Much sexual humor is based upon multiple meanings of words and phrases. Would it be a stretch to say that most human speech is context-dependent?
Even physical objects can convey polyfunctional information. For example, take an empty can of tomato soup. Left lying on a kitchen counter, it might indicate that the cook is still busy. Found in an enormous pile of similar objects the same can might mean that a recycling plant or garbage dump is near. On a long stretch of beach or in an alleyway outside a restaurant, the very same can could indicate improperly discarded trash. Placed in an art gallery with a title and someone’s name nearby, one and the same empty can of tomato soup might convey a profound artistic statement.
The more we consider polyfunctional information units, the more we discover that our world is permeated with them.
Next Time: Polyfunctional Text: Authorship
1 David C. Krakauer, Stability and Evolution of Overlapping Genes, Evolution: International Journal of Organic Evolution, first published May 9, 2007. Available at https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2000.tb00075.x, accessed April 22, 2020.
2 John Sanford, Genetic Entropy & the Mystery of the Genome, p. 131–3, FMS Publications, Third Edition 2008.
3 George Montañez, Robert J. Marks II, Jorge Fernandez and John C. Sanford, “Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation” in Biological Information: New Perspectives, edited by George Montañez, Robert J. Marks II, Jorge Fernandez and John C. Sanford, published by World Scientific Company: Hackensack, New Jersey, 2011, p 141.
4 E.N. Trifonov, The Multiple Codes of Nucleotide Sequences, Bulletin of Mathimatical Biology 51, 417–432 (1989). https://doi.org/10.1007/BF02460081.