Protein music

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Protein music or, more broadly, genetic music (including DNA music) is a musical technique where music is composed by converting protein sequences or DNA sequences to musical notes. The earliest published references to genetic music in the scientific literature include a short correspondence by Hayashi and Munakata in Nature in 1984, [1] a publication by geneticist Susumu Ohno and Midori Ohno (his wife and a musician) in Immunogenetics, [2] and a paper in the journal Bioinformatics (then called Computer Applications in the Biosciences) co-authored by Ross D. King and Colin Angus (a member of the British psychedelic band The Shamen) in 1996, [3]

Contents

Shortly before the King and Angus publication the French physicist and composer Joël Sternheimer (a singer also known by his stage name, Évariste) applied for a patent to use protein music to affect protein synthesis. [4] The idea that music can affect protein synthesis is generally viewed as pseudoscientific by the molecular biology community, although the methods proposed by Sternheimer form the basis for software called Proteodyne. Applications for genetic music proposed in the scientific literature include aids to memorization and education.

Theory

The idea that genes and music exhibit similarities was noted even earlier than the scientific publications in the area by Douglas Hofstadter in Gödel, Escher, Bach . [5] Hofstadter even proposes that meaning is constructed in protein and in music. [6]

The ideas that supports the possibility of creating harmonic musics using this method are:

Musical renditions of DNA and proteins is not only a music composition method, but also a technique for studying genetic sequences. Music is a way of representing sequential relationships in a type of informational string to which the human ear is keenly attuned. The analytic and educational potential of using music to represent genetic patterns has been recognized from secondary school to university level. [13]

Susumu Ohno and DNA music

Susumu Ohno, one of the referents in the development of protein music, proposed in the early 80s that repetition is a fundamental to the evolution of proteins. [14] This idea was fundamental to his notion that the repetition in biological sequences would have parallels in music composition, leading Ohno to state that the "...all-pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition." [15]

By implementing the concept of musical transformation in DNA sequences, and changing the fragments into musical scores, researchers are allowed to explore the repetitions in the sequences in terms of musical periodicities. The approach consists of assigning musical notes to nucleotide sequences, unveiling hidden patterns of relationship within genetic coding. Music and DNA share similarities in their structure by exhibiting repeating units and motifs. [16]

Musical Patterns

Periodicities and the principle of repetitious recurrences govern many aspects of life on this earth, including musical compositions and coding base sequences in genomes. [2] This inherent similarity resulted in the effort to interconvert the two. One of music’s uses, from its creation by the primitive Homo sapiens to the modern day, is as a time-keeping device. In Ohno’s rendition, a space and a line on the octave scale are assigned to each base, A, G, T, and C. His work compares and identifies parallels in genomic sequences and notable music from the early Baroque and Romantic periods. [15] Beyond the parallels that can be found rhythmically in music and peptide sequences, musical patterns can be a valuable tool for identifying sequence patterns of interest. For example, work done by Robert P. Bywater and Jonathan N. Middleton has used melody generation software to identify protein folds from sequence data. [17]

Periodicities in genes and proteins

Given the importance of repetition in music it is logical to assume that deviations from purely random patterns are likely to be necessary to produce aesthetically pleasing sonic patterns. Indeed, the idea that repetition is key in the formation of functional proteins [16] was central to Ohno's early work in the area of genetic music. The question of randomness in protein sequences has received substantial attention, with early work suggesting that protein sequences are effectively random [18] (at least when viewed at the scale of proteomes). However, subsequent work suggests the existence of statistically important regularities in protein sequences [19] [20] and experimental work has shown that periodicities can play a role in the origin of ordered proteins. [21] Presumably, these periodicities are responsible for the aesthetically pleasing nature of music based on at least some proteins.

Ohno suggested that one important deviation from randomness is palindromic amino acid sequences ("peptide palindromes" [22] ) in DNA-binding proteins, such as the H1 histone. [23] Another example of these periodic sequences are the dipeptidic repeats found in the per locus coding sequences in Drosophila melanogaster have been found in the mouse as well. [15] Ohno argues that the coding sequences behave periodically not merely as unique products of pure randomness and understanding this is a key feature to unraveling the complexity behind the genetic information challenging the notion of randomness in biological processes and comparing it more proximate with music. [16] Although peptide palindromes are important deviations from randomness, they are distinct from palindromic sequences in nucleic acids, which are sequences that read identically to the sequence in the same direction on complementary strands. Peptide palindromes, as defined by Ohno, are actually much more similar to palindromes in other contexts. For example, the mouse H1 histone palindrome highlighted by Ohno is KAVKPKAAKPKVAK (letters correspond to the standard one-letter amino acid codes); note that this sequence simply reads identically when written forwards or backwards and is unrelated to nucleic acid complementarity. Large-scale surveys of peptide palindromes indicate that they are present in many proteins but they are not necessarily associated with any specific protein structures. [24] The relationship between peptide palindromes and protein music has not been studied at a large scale.

Practice

Related Research Articles

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<span class="mw-page-title-main">Nucleic acid</span> Class of large biomolecules essential to all known life

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References

  1. ↑ Hayashi, Kenshi; Munakata, Nobuo (1984). "Basically Musical". Nature. 310 (5973): 96. Bibcode:1984Natur.310...96H. doi: 10.1038/310096a0 . PMID   6738718.
  2. 1 2 3 Ohno, Susumu; Ohno, Midori (1986). "The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition". Immunogenetics. 24 (2): 71–8. CiteSeerX   10.1.1.455.1625 . doi:10.1007/BF00373112. PMID   3744439. S2CID   31738506.
  3. ↑ King, Ross; Angus, Colin (1996). "Protein Music". CABIOS. 12 (3): 251–2. doi: 10.1093/bioinformatics/12.3.251 . PMID   8872396.
  4. ↑ Joel Sternheimer. "Method for the epigenetic regulation of protein biosynthesis by scale resonance." European Patent Office EP0648275B1 https://patents.google.com/patent/EP0648275B1/en
  5. ↑ Hofstadter, Douglas (1999). Gödel, Escher, Bach (1980 ed.). Vintage Books. p. 519. ISBN   978-0-465-02656-2. Imagine the mRNA to be like a long piece of magnetic recording tape, and the ribosome to be like a tape recorder. As the tape passes through the playing head of the recorder, it is "read" and converted into music, or other sounds...When a 'tape' of mRNA passes through the 'playing head' of a ribosome, the 'notes' produced are amino acids and the pieces of music they make up are proteins.
  6. ↑ Hofstadter (1980) p525: "Music is not a mere linear sequence of notes. Our minds perceive pieces of music on a level far higher than that. We chunk notes into phrases, phrases into melodies, melodies into movements, and movements into full pieces. similarly proteins only make sense when they act as chunked units. Although a primary structure carries all the information for the tertiary structure to be created, it still 'feels' like less, for its potential is only realized when the tertiary structure is actually physically created."
  7. ↑ "Proteomusic". Proteomusic. Retrieved October 22, 2016.
  8. ↑ "Proteomusic album by TWISTED HELICES". Proteomusic. Retrieved April 5, 2022.
  9. ↑ Greenwood, Priscilla; Ward, Lawrence (2007). "1/f noise". Scholarpedia. 2 (12): 1537. Bibcode:2007SchpJ...2.1537W. doi: 10.4249/scholarpedia.1537 .
  10. ↑ Li, Wentian (1991). "Expansion-modification systems: A model for spatial 1/f spectra". Physical Review A. 43 (10): 5240–60. Bibcode:1991PhRvA..43.5240L. doi:10.1103/PhysRevA.43.5240. PMID   9904836.
  11. ↑ Sansom, Clare (2002), DNA makes protein — makes music? (PDF), The Biochemical Society, retrieved March 22, 2014
  12. ↑ "DNA Music", The Robert S. Boas Center for Genomics and Human Genetics. Archived November 30, 2012, at the Wayback Machine
  13. 1 2 3 Clark, M. A. (November 2, 2005). "Genetic Music: An Annotated Source List".
  14. ↑ Ohno, Susumu (August 1984). "Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes". Journal of Molecular Evolution. 20 (3–4): 313–321. doi:10.1007/BF02104737. ISSN   0022-2844.
  15. 1 2 3 Ohno, S. (1987). "Repetition as the Essence of Life on this Earth: Music and Genes". In Neth, Rolf; Gallo, Robert C.; Greaves, Melvyn F.; Kabisch, Hartmut (eds.). Modern Trends in Human Leukemia VII. Haematology and Blood Transfusion / Hämatologie und Bluttransfusion. Vol. 31. Berlin, Heidelberg: Springer. pp. 511–519. doi:10.1007/978-3-642-72624-8_107. ISBN   978-3-642-72624-8. PMID   3443409.
  16. 1 2 3 Ohno, S. (August 1988). "On periodicities governing the construction of genes and proteins". Animal Genetics. 19 (4): 305–316. doi:10.1111/j.1365-2052.1988.tb00822.x. ISSN   0268-9146. PMID   2852906.
  17. ↑ Bywater, Robert P.; Middleton, Jonathan N. (October 2016). "Melody discrimination and protein fold classification". Heliyon. 2 (10): e00175. Bibcode:2016Heliy...200175B. doi: 10.1016/j.heliyon.2016.e00175 . ISSN   2405-8440. PMC   5079661 . PMID   27812548.
  18. ↑ Nevill-Manning, C.G.; Witten, I.H. (1999). "Protein is incompressible". Proceedings DCC'99 Data Compression Conference (Cat. No. PR00096). IEEE: 257–266. doi:10.1109/dcc.1999.755675. ISBN   0-7695-0096-X.
  19. ↑ Hategan, A., & Tabus, I. (2004). Protein is compressible. In Proceedings of the 6th Nordic Signal Processing Symposium, NORSIG 2004, Espoo, Finland, 9–11 June 2004 (pp. 192-195)
  20. ↑ Adjeroh, D.; Fei Nan (2006). "On Compressibility of Protein Sequences". Data Compression Conference (DCC'06). IEEE. pp. 422–434. doi:10.1109/DCC.2006.56. ISBN   978-0-7695-2545-7.
  21. ↑ Shiba, Kiyotaka; Takahashi, Yuki; Noda, Tetsuo (July 2002). "On the Role of Periodism in the Origin of Proteins". Journal of Molecular Biology. 320 (4): 833–840. doi:10.1016/S0022-2836(02)00567-3. PMID   12095259.
  22. ↑ Ohno, Susumu (December 1992). "Of palindromes and peptides". Human Genetics. 90 (4). doi:10.1007/BF00220455. ISSN   0340-6717.
  23. ↑ Ohno, S. (August 1993). "A song in praise of peptide palindromes". Leukemia. 7 (Suppl 2): S157–159. ISSN   0887-6924. PMID   8361224.
  24. ↑ Sridhar, Settu; Nagamruta, Mallapragada; Guruprasad, Kunchur (2015-10-14). Permyakov, Eugene A. (ed.). "Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins". PLOS ONE. 10 (10): e0139568. doi: 10.1371/journal.pone.0139568 . ISSN   1932-6203. PMC   4605511 . PMID   26465610.
  25. ↑ examples from Nucleic acid database Archived June 7, 2013, at the Wayback Machine
  26. ↑ de la Cruz, Joanna. "Plain Melody & Composition". Neucleic acid database. Archived from the original on 9 March 2004. Retrieved 13 September 2011.
  27. ↑ "Genetic Music From DNA and Protein ", AlgoArt.com.
  28. ↑ whozoo.org/mac/Music/samples.htm
  29. ↑ Vanhoose, Joe (30 November 2010). "Sounds of HIV". Athens Banner-Herald. Archived from the original on 16 January 2014. Retrieved 17 January 2014.

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