- The Geometry -

On DNA codons, which codons codes for which protein?   In DNA, codons are specific sequences of three nucleotides that encode for particular amino acids during protein synthesis. The genetic code is degenerate, meaning that multiple codons can code for the same amino acid. The genetic code is nearly universal, meaning that the same codons typically code for the same amino acids across different organisms. Here is a basic table showing the DNA codons and the amino acids they code for (using the single-letter amino acid code): Codon (DNA) Amino Acid AAA Lysine (K) AAC Asparagine (N) AAG Lysine (K) AAU Asparagine (N) ACA Threonine (T) ACC Threonine (T) ACG Threonine (T) ACU Threonine (T) AGA Arginine (R) AGC Serine (S) AGG Arginine (R) AGU Serine (S) AUA Isoleucine (I) AUC Isoleucine (I) AUG Methionine (M) (Start codon) AUU Isoleucine (I) CAA Glutamine (Q) CAC Histidine (H) CAG Glutamine (Q) CAU Histidine (H) CCA Proline (P) CCC Proline (P) CCG Proline (P) CCU Proline (P) CGA Arginine (R)

National Center for Biotechnology Information (NCBI) - Gene database: Website: https://www.ncbi.nlm.nih.gov/gene/ Ensembl Genome Browser: Website: https://www.ensembl.org/ UCSC Genome Browser: Website: https://genome.ucsc.edu/ GeneCards - Human Gene Database: Website: https://www.genecards.org/ GenBank - DNA sequence database: Website: https://www.ncbi.nlm.nih.gov/genbank/ NCBI Map Viewer: Website: https://www.ncbi.nlm.nih.gov/mapview/ Gene Expression Omnibus (GEO): Website: https://www.ncbi.nlm.nih.gov/geo/ The Human Protein Atlas: Website: https://www.proteinatlas.org/ Reactome - A curated knowledgebase of biological pathways: Website: https://reactome.org/ KEGG - Kyoto Encyclopedia of Genes and Genomes: Website: https://www.genome.jp/kegg/  

On average how many nucleotide pairs do each the other 23 pairs of chromosomes hold? Are the 3 billion pairs or so of nucleotide pairs more or less evenly distributed among all 23 pairs? Are the x and y gender chromosomes longer or shorter than the others?   As of my last update in September 2021, humans have 23 pairs of chromosomes, for a total of 46 chromosomes. Among these pairs, 22 pairs are called autosomes, and the remaining pair determines an individual's sex, known as the sex chromosomes. The sex chromosomes are labeled as X and Y. Females have two X chromosomes (XX), and males have one X and one Y chromosome (XY). Regarding the number of nucleotide pairs, it is essential to clarify that a nucleotide pair consists of two nucleotides, one from each strand of the DNA double helix, held together by hydrogen bonds. However, it is more common to refer to the total number of nucleotides rather than pairs. The human genome contains approximately 3.2 billion nucleotide base pairs.

Analyzing the DNA molecule from the perspective of complexity theory allows us to understand its structure, functions, and information processing in the context of computational complexity. Complexity theory is a branch of computer science that studies the resources required to solve computational problems. In this context, we can consider DNA as a "molecular machine" that processes genetic information and carries out complex biological functions. Let's explore some aspects of DNA in terms of complexity theory: Information Storage and Representation: DNA is a remarkable molecule capable of storing and representing vast amounts of genetic information. It uses a four-letter alphabet (A, T, C, G) to encode the instructions necessary for the development, functioning, and reproduction of living organisms. From a complexity theory perspective, the alphabet size is important because it influences the amount of information that can be encoded in a given length of DNA. Computation

  The schematic diagram above shows some detail about the DNA molecule. Deoxyribonucleic acid is a mouthful to pronounce so scientists just say DNA. The most outstanding feature of the DNA molecule is its shape. This is the crux of DNA and yet its shape is ignored.  Semiotically, the DNA double helix structure signifies love of beauty. Two long strands of nucleotides in taut embrace is the most significant aspect of the molecule. DNA is an aesthetic phenomenon with functional features thrown in for good measure. It's overall structure reflect sophisticated aesthetic principles. With less than 1% of nucleotide pairs coding for anything at all, geneticists are wondering what to make of human DNA. Clearly, as humans are at the top of the pyramid of organisms, we hold the rights to being the most complex as well. No such luck. Why Onions Have More DNA Than You Do: https://news.harvard.edu/gazette/story/2000/02/why-onions-have-more-dna-than-you-do/ Potatoes have more genes than humans:

Using concepts in semiotics in as great detail as possible, how to measure the DNA molecule for its aesthetic value and the extent that principles of aesthetics play a part before its formation? Measuring the aesthetic value of a DNA molecule and determining the extent to which principles of aesthetics play a part before its formation involves applying concepts from semiotics, which is the study of signs and symbols. While semiotics is traditionally concerned with the analysis of human communication, we can adapt its principles to explore the aesthetics of the DNA molecule. However, it is important to note that assessing the aesthetic value of a DNA molecule is highly subjective and speculative, as aesthetic judgments are typically rooted in human perception and cultural contexts. Nevertheless, I will provide a conceptual framework that can be used for this analysis. Signs and Symbols: Semiotics recognizes signs as entities that convey meaning. In the context of DNA, we can consider th

DNA is an aesthetic phenomenon that incorporates function rather than a functional phenomenon that incorporates aesthetic elements. Aesthetic principles takes precedence over functional principles in the metaphysical universe we live in.

https://ideas-monger.blogspot.com/2023/04/the-semiotics-of-dna-structure.html  

Pseudorandomness as an artistic theme  - https://ideas-monger.blogspot.com/p/pseudorandomness-as-artistic-theme.html  

  Measuring the correlation between DNA pseudorandomness and aesthetic principles in a way that yields a definitive number between 0 and 1 can be a complex task. It involves several steps and considerations. Here's a detailed outline of a possible approach: Define Aesthetic Principles: Begin by clearly defining the aesthetic principles you want to assess in the DNA sequence. This can include factors such as symmetry, proportion, complexity, or any other qualities relevant to aesthetics. Select a Pseudorandomness Measure: Choose a specific pseudorandomness measure that can capture the randomness or pattern characteristics of the DNA sequence. There are various measures available, such as entropy, autocorrelation, or spectral analysis. Select a measure that suits your analysis. DNA Segmentation: Divide the DNA sequence into smaller segments to analyze the pseudorandomness within each segment. The size of the segments will depend on the specific analysis requirements and the scale at

If the measure of pseudorandomness applied to human DNA shows a high correlation to aesthetic principles and, to a lesser extent, a correlation to functional principles, it would imply that there are patterns or structures in the DNA sequence that align with aesthetic preferences more strongly than with functional considerations. This would suggest an intriguing relationship between the genetic code and aesthetic qualities. In terms of how this would present itself in the measure of pseudorandomness, it would manifest as a higher value for the correlation measure of aesthetic principles compared to the correlation measure of functional principles. The correlation measure quantifies the strength of the relationship between the DNA sequence and a particular principle, such as aesthetics or functionality. A high correlation to aesthetic principles would indicate that the DNA sequence exhibits patterns or characteristics that align with what is typically considered aesthetically pleasing.

Applying measures of pseudorandomness to the entire length of human DNA can provide insights into the presence or absence of patterns or randomness within the DNA sequence. However, it's important to note that human DNA is a complex and highly organized structure, with various regions serving specific functions. The DNA sequence itself exhibits patterns and structures, such as genes, regulatory elements, and repetitive sequences. These patterns are not random but have specific biological functions. Therefore, when evaluating the entire length of human DNA using measures of pseudorandomness, we would generally expect to find deviations from randomness due to the presence of these functional elements. However, there are regions within the human genome that are considered non-coding or have unknown functions. These regions may exhibit characteristics of randomness, and measures of pseudorandomness can help assess their level of randomness. It's worth noting that even in these non-

Measures of pseudorandomness showing binary sequence with small correlation measure of order k up to a sufficiently large k cannot have a large arithmetic correlation applying the result to several classes of sequences including Legendre sequences defined with polynomials. Measures of Pseudorandomness: Arithmetic Autocorrelation and Correlation Measure - https://www.semanticscholar.org/paper/Measures-of-Pseudorandomness%3A-Arithmetic-and-Hofer-M%C3%A9rai/5d721da76d6867f97d309d681669f73f0d0c4299    Consider a simplified example to illustrate the phenomenon described in the paper. Imagine we have a binary sequence: 0101010101010101. This sequence alternates between 0s and 1s. If we calculate the correlation measure of order 1 for this sequence, it will be small because adjacent elements are different. Now, let's calculate the arithmetic autocorrelation for the same sequence. The arithmetic autocorrelation measures the correlation between the elements at different positions in the