DNA sequences carry biological information, DNA molecules (double-stranded helix) obey physical laws, DNA genomes are products of generations of evolution, and DNA texts can be read as a string of symbols. All these different aspects of DNA sequences (and, to some extent, protein sequences) make their analysis a multi-disciplinary topic, which touches on biochemistry, biophysics, evolutionary biology, as well as mathematics, statistics, computer science, and statistical physics.
DNA and protein texts contain a variety of features, patterns, and correlations that are important for understanding the structure and function of these molecules. Some examples include:
- Base pair correlations: The sequence of base pairs in DNA is important for determining the three-dimensional structure of the molecule and the specific sequences of amino acids that are encoded. There are known patterns of base pair correlations that are important for DNA structure and function, such as the presence of GC-rich or AT-rich regions or the occurrence of specific base pair sequences that are involved in DNA replication or transcription.
- Protein motifs: Proteins are composed of amino acids that are arranged in specific patterns and structures, known as protein motifs, that are important for their function. Protein motifs can include specific amino acid sequences, such as zinc fingers or helix-turn-helix motifs, or specific three-dimensional structures, such as alpha helices or beta sheets.
- Protein-DNA interactions: The interactions between proteins and DNA are important for regulating gene expression and maintaining the integrity of the genome. These interactions can be mediated by specific protein motifs that bind to specific DNA sequences or structural features of the DNA molecule.
- Protein-protein interactions: Proteins can interact with each other through specific amino acid sequences or structural features, such as binding domains or interface residues. These interactions are important for a variety of cellular processes, including signal transduction, enzyme activity, and protein folding.
Overall, the features, patterns, and correlations in DNA and protein texts are important for understanding the structure and function of these molecules and their role in cellular processes.
Protein Texts and ED
Erectile dysfunction (ED) is a common problem that affects men of all ages. It is defined as the inability to achieve or maintain an erection sufficient for satisfactory sexual performance. ED can have a number of causes, including physical conditions such as diabetes, heart disease, and low testosterone levels, as well as psychological conditions such as stress, anxiety, and depression.
Proteins play a role in the development and function of the male reproductive system, including the corpus cavernosum, the spongy tissue in the penis that fills with blood during an erection. Dysregulation of protein expression or function in the corpus cavernosum may contribute to the development of ED. For example, studies have shown that the expression of certain enzymes, such as phosphodiesterase type 5 (PDE5), can affect the ability of the corpus cavernosum to relax and fill with blood during an erection. Inhibitors of PDE5, such as sildenafil (e.g., Viagra and telehealth service BlueChew), are commonly used to treat ED.
Other proteins that have been studied in relation to ED include endothelial nitric oxide synthase (eNOS), which is involved in the production of nitric oxide (NO), a signaling molecule that plays a role in erectile function; and matrix metalloproteinases (MMPs), which are enzymes that can break down the structural proteins in the corpus cavernosum. Dysregulation of eNOS or MMPs may contribute to the development of ED.
Overall, proteins are important molecules in the development and function of the male reproductive system, and the study of protein expression and function may provide insight into the underlying molecular mechanisms of ED and help to identify potential targets for new treatments or therapies.
Quotes
… But I am very much excited by your article in May 30th [1953] Nature, and think that bring Biology over into the group of “exact” sciences. I plan to be in England through most of September, and hope to have a chance to talk to you about all that, but I would like to ask a few questions now. If your point of view is correct [,] each organism will be characteristized by a long number written in quadrucal (?) system with figures 1, 2, 3, 4 standing for different bases … This would open a very exciting possibility of theoretical research based on combinatorix [sic] and the theory of numbers! … I have a feeling this can be done. What do you think?
George Gamow (1904-1968), in a letter to Watson and Crick (1953).
From the point of view of the theory of information, the works of Shakespeare, with the same number of letters and signs aligned at random by a monkey, would have the same value. It is this lack of definition of the value of information that makes it difficult to use in biology. What could be considered as “objective” in the Shakespearean information that would distinguish it from the monkey's information? Essentially the transmissibility. The value of influence, therefore of evolution. …
Jacques Monod (1910-1976), notesbook (1959).
“Whereas ordinary mortals are content to mimic others, creative geniuses are condemned to plagiarize themselves” is my shorter, albeit inarticulate, version of what Van Veen said in Ada by Vladimir Nobokov. Indeed, it seems that vaunted geniuses seldom invented more than one modus operandi during their lifetimes, and even civilization has largely been dependent upon plagiarizing a small number of creative works; e.g., the multitudes of Gothic churches can be viewed as pan European plagiarism of the abbey church of St. Denis and/or the cathedral at Sens. This is not surprising for new genes sensu stricto has seldom been invented. Evolution rather relies on palgiarizing an old and tested theme; the mechanism of evolution by gene duplication. … this principle of repetitious recurrence pervades both the construction of coding sequences in the genome, which can be regarded as being representative of nature, and musical composition which can be regarded as the most abstract and therefore the most intellectual expression of nature.”
Susumu Ohno (1928-2000) and Midori Ohno, Immunogenetics, 24:71-78 (1986).
Searching for an objective reconstruction of the vanished past must surely be the most challenging task in biology. I need to say this because, today, given the powerful tools of molecular biology, we can answer many questions simply by looking up the answer in Nature – and I do not mean the journal of the same name. … In one sense, everything in biology has already been ‘published' in the form of DNA sequences of genomes; but, of course, this is written in a language we do not yet understand. Indeed, I would assert that the prime task of biology is to learn and understand this language so that we could then compute organisms from their DNA sequences. … We are at the dawn of proper theoretical biology.
Sidney Brenner, in Evolution of Life, eds. S Osawa and T Honjo (Springer-Verlag) (1991).
While … human genome projects … were launched only in the past decade, the technoscientific imaginary and the discursive practices that have animated them, specifically the textual and linguistic representations of the genome, are quite old. In their (post?) modern form they first emerged in the late 1940s and were then fully elaborated within the work on the genetic code in the 1950s and 1960s.
Lily Kay (science historian, 1947-2000), in Who Wrote the Book of Life? (2000).