Protein music explained

Protein music (DNA music or genetic music) is a musical technique where music is composed by converting protein sequences or genes to musical notes. It is a theoretical method made by Joël Sternheimer, who is a physicist, composer and mathematician.^[1]

The first published references to protein music in the scientific literature are a paper co-authored by a member of The Shamen in 1996,^[2] and a short correspondence by Hayashi and Munakata in Nature in 1984.^[3]

Theory

In Gödel, Escher, Bach, Douglas Hofstadter draws similarities and analogies between genes and music.^[4] It even proposes that meaning is constructed in protein and in music.^[5]

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

• The repetition process governs both the musical composition and the DNA sequence construction.^[6]
• The conformations and energetics of the protein secondary and tertiary structures at the atomic level.^[7] See also^[8] for full compositions made using this concept.
• Pink noise (the correlation structure "1/f spectra") have been found in both musical signals and DNA sequences.^[9]
• Models with duplication and mutation operations, such as the "expansion-modification model" are able to generate sequences with 1/f spectra.^[10]
• When DNA sequences are converted to music, it sounds musical.^[11]
• Human Genome Project has revealed similar genetic themes not only between species, but also between proteins.^[12]

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.^[12]

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 process that not only influences the DNA but also music composition. "The all-pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition."^[13]

By implementing the concept of musical transformation in DNA sequences, and changing the fragments into musical scores, researchers are allowed to explore the patterns of 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.^[14]

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. This inherent similarity resulted in the effort to interconvert the two. One of music’s uses, from its creation by the primitive Homo sapien 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. 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.^[15]

Periodicities in genes and proteins

The universe and its phenomena are subject to various periodicities, it is erroneous to exclude the coding sequence and see it as an exclusive random combination. Instead, the four bases evolve in a combination of primitive and repetitive units. For instance, repetition is key in the formation of functional proteins. Palindromic sequences, nucleic acid sequences that read identically to the sequence in the same direction on the complementary strand, are found in peptide palindromes and are particularly abundant in DNA-binding proteins such as the H1 histone.^[16] Dipeptidic repeats found in the per locus coding sequences in Drosophila melanogaster have been found in the mouse as well.^[17] 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.

Practice

• Examples of simple protein structures converted to midi music file^[18] show the independence of protein music from musical instrument, and the convenience of using protein structures in music composition.^[19]
• The software Algorithmic arts can convert raw genetic data (freely available for download on the web) to music. There are many examples of musics generated by this software, both by designer^[20] and by others.
• Several people have composed musics using protein structure, and several students and professors have used music as a method to study proteins.^[12] The recording Sounds of HIV is a musical adaptation of the genetic material of HIV/AIDS.^[21]

Further reading

Journal articles, Arranged by post date:

• Ohno . S . 1993 . A song in praise of peptide palindromes . Leukemia . 7 . Suppl 2. S157–9 . 8361224 .
• Book: Ohno . Susumu . Repetition as the Essence of Life on this Earth: Music and Genes . 1987 . Modern Trends in Human Leukemia VII . Haematology and Blood Transfusion . Haematology and Blood Transfusion / Hämatologie und Bluttransfusion . 31 . 511–8 . 10.1007/978-3-642-72624-8_107 . 3443409 . 978-3-540-17754-8 .
• Ohno . S . 2009 . On periodicities governing the construction of genes and proteins . Animal Genetics . 19 . 4. 305–16 . 10.1111/j.1365-2052.1988.tb00822.x . 2852906 .
• Dunn . John . Clark . Mary Anne . 1999 . Life Music: The Sonification of Proteins . Leonardo . 32 . 1 . 25–32 . 10.1162/002409499552966 . 1576622. 57562936 .
• Takahashi . Rie . Miller . Jeffrey H . 2007 . Conversion of amino-acid sequence in proteins to classical music: Search for auditory patterns . Genome Biology . 8 . 5. 405 . 10.1186/gb-2007-8-5-405 . 17477882 . 1929127 . free .
• Mannone . M . 2018 . Knots, Music and DNA . Journal of Creative Music Systems . 2 . 2 . 10.5920/jcms.2018.02 . 64956325 . free .

External links

• Clark, M. A. "A Protein Primer: A Musical Introduction to Protein Structure", WhoZoo.org. See: Henahan, Sean (03/20/98) "Protein Preludes", AccessExcellence.com.
• Your DNA Song "Protein Code to Music Translation",
• Music and DNA http://nsmn1.uh.edu/dgraur/
• Susumu Ohno: Music Based on part of a Immunoglobulin Gene https://www.youtube.com/watch?v=9Q1EkWtff2I&list=PLgONlyj5hSN9z2ephX5AhLZJKVE0QmNXH&index=1

Notes and References

1. [:fr:Jo%C3%ABl Sternheimer]
2. Protein Music . CABIOS . 12 . 3 . 251–2 . 10.1093/bioinformatics/12.3.251 . 1996 . King . Ross . Angus . Colin . 8872396 . free .
3. Basically Musical . Nature . 310 . 5973 . 96 . 10.1038/310096a0 . 1984 . Hayashi . Kenshi . Munakata . Nobuo . 6738718 . 1984Natur.310...96H . free .
4. Book: Hofstadter, Douglas. Gödel, Escher, Bach. Vintage Books. 978-0-465-02656-2. 519. 1980. Douglas Hofstadter. 1999. 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..
5. 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."
6. 71–8 . 10.1007/BF00373112 . The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition . 1986 . Susumu Ohno . Ohno . Susumu . Ohno . Midori . Immunogenetics . 24 . 2 . 3744439. 10.1.1.455.1625 . 31738506 .
7. Web site: Proteomusic . Proteomusic . October 22, 2016.
8. Web site: Proteomusic album by TWISTED HELICES . Proteomusic . April 5, 2022.
9. 1/f noise . Scholarpedia . 2 . 12 . 1537 . 10.4249/scholarpedia.1537 . 2007 . Greenwood . Priscilla . Ward . Lawrence . 2007SchpJ...2.1537W . free .
10. 10.1103/PhysRevA.43.5240 . Expansion-modification systems: A model for spatial 1/f spectra . 1991 . Li . Wentian . Physical Review A . 43 . 10 . 5240–60 . 9904836. 1991PhRvA..43.5240L .
11. "DNA Music", The Robert S. Boas Center for Genomics and Human Genetics.
12. Web site: Clark. M. A.. Genetic Music: An Annotated Source List. November 2, 2005.
13. Book: Ohno, S. . Repetition as the Essence of Life on this Earth: Music and Genes . Haematology and Blood Transfusion / Hämatologie und Bluttransfusion . 1987 . 31 . Neth . Rolf . Gallo . Robert C. . Greaves . Melvyn F. . Kabisch . Hartmut . Modern Trends in Human Leukemia VII . https://link.springer.com/chapter/10.1007/978-3-642-72624-8_107 . en . Berlin, Heidelberg . Springer . 511–519 . 10.1007/978-3-642-72624-8_107 . 3443409 . 978-3-642-72624-8.
14. Ohno . S. . August 1988 . On periodicities governing the construction of genes and proteins . Animal Genetics . en . 19 . 4 . 305–316 . 10.1111/j.1365-2052.1988.tb00822.x . 2852906 . 0268-9146.
15. Bywater . Robert P. . Middleton . Jonathan N. . October 2016 . Melody discrimination and protein fold classification . Heliyon . 2 . 10 . e00175 . 10.1016/j.heliyon.2016.e00175 . free . 2405-8440 . 5079661 . 27812548. 2016Heliy...200175B .
16. Ohno . S. . August 1993 . A song in praise of peptide palindromes . Leukemia . 7 . Suppl 2 . S157–159 . 0887-6924 . 8361224.
17. Book: Ohno, S. . Repetition as the Essence of Life on this Earth: Music and Genes . Haematology and Blood Transfusion / Hämatologie und Bluttransfusion . 1987 . 31 . Neth . Rolf . Gallo . Robert C. . Greaves . Melvyn F. . Kabisch . Hartmut . Modern Trends in Human Leukemia VII . https://link.springer.com/chapter/10.1007/978-3-642-72624-8_107 . en . Berlin, Heidelberg . Springer . 511–519 . 10.1007/978-3-642-72624-8_107 . 3443409 . 978-3-642-72624-8.
18. http://ndbserver.rutgers.edu/atlas/music/musica.html examples from Nucleic acid database
19. Web site: de la Cruz. Joanna. Plain Melody & Composition. Neucleic acid database. 13 September 2011. https://web.archive.org/web/20040309080946/http://ndbserver.rutgers.edu/atlas/music/proj.1.html. 9 March 2004. dead.
20. "Genetic Music From DNA and Protein ", AlgoArt.com.
21. News: Sounds of HIV. Athens Banner-Herald. Vanhoose, Joe. 30 November 2010. 17 January 2014. https://web.archive.org/web/20140116071602/http://onlineathens.com/stories/113010/liv_743149831.shtml. 16 January 2014. dead.