Susumu Ohno and Midori Ohno
David Deamer and Susan Alexjander
Brent D. Hugh
Aurora Sanchez Sousa and Richard Krull
John Dunn and KW Bridges
Mary Anne Clark and John Dunn
LY Han and YZ Chen
Erik Jensen and Ronald Rusay
DNA and PROTEIN:
Kenshi Hayashi and Nobuo Munakata
Charles Strom and Peter Gena
Ross King and Colin Angus
Other reference websites:
1986 Susumu Ohno and Midori Ohno have transformed DNA sequences into musical scores based on an eight note scale. Their project was based on the principle of repetitious recurrence and redundancy that is found in nature, for example genome duplication, and within human inventions such as music. They ordered the nucleotides, AGCT, based on the molecular weight of each nucleotide. Using each nucleotide twice, a scale beginning on the note D can be assigned the following nucleotide sequence (note=nucleotide): D=A, E=A, F=G, G=G, A=T, B=T, C=C, D=C, etc. The A and G (purines) have heavier molecular masses than the C and T (pyrimidines) so the former nucleotides were placed at the lower end of the scale.
They used the human X-linked phosphoglycerate kinase (PGK) coding sequence as an example to show the resulting musical conversion. Secondly, they used their coding assignment to translate the Chopin Nocturne Op. 55 No. 1 into a DNA sequence. The sequence was compared to the large subunit of the mouse DNA polymerase II and the mouse sequence encoded a similar sequence to that found in the Nocturne: CAACCTCTC. The sequence occurs four times in the Nocturne and differs from the Chopin sequence by one nucleotide.
Susumu Ohno also converted both strands of the mouse H1 histone variety-1 DNA into music according to the previously established rules in order to hear the peptide palindromes, which are commonly found in DNA-binding proteins.
Susumo Ohno and Midori Ohno. The all prevasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition. Immunogenetics 24: 71-78. 1986.
Susumo Ohno. A song in praise of peptide palindromes. Leukemia 7 (Supplement 2, August 1993): S157-9
1988 David Deamer (biologist) and Susan Alexjander (musician) measured and converted the molecular vibrations of DNA into music. An infrared spectrophotometer was used to measure the wavelength of the light absorbed by the DNA after begin exposed to infrared light. The ratios of light frequencies were converted into ratios of sound. Spectrophotometer wavenumbers were converted into hertz (Hz)=velocity x wavenumber. The resulting frequency value is out of the audible range for humans and therefore the resulting hertz value was divided by 236. In total, the four bases yielded 60 unique frequencies. After the frequencies were converted into hearing range, the frequencies were programmed into a Yamaha DX7 IID synthesizer. The resulting sounds were microtones, which are frequencies or sounds that occur in between the half tone notes traditionally used in the harmonic scale.
2002 David Lindsay (musician) has converted DNA sequences into rhythmic elements based on DNA dissociation and replication. Because three H-bonds require more energy to break, Lindsay assigned three beats to Guanine and Cytosine each, while assigning two beats for Adenine and Thymidine. Based on the data that H-bonds break in groups of four bases, the rhythmic conversions were broken into groups of four nucleotides. The bidirectionality of DNA dissociation can also be incorporated into the translation by simultaneously playing both rhythms outward from the origin of replication.
Another variation on the original conversion uses stressed and unstressed beats. The C and G are represented by stressed beats and the A and T are represented by unstressed beats. The rhythmic display of DNA sequences can reveal differences between repetitive and non-repetitive sequences in non-coding DNA vs. coding DNA, for example.
Brent D. Hugh (professor of music) translated genomic data into music by dividing the DNA sequences into four-letter segments: the first two letters of a segment represented the pitch and the latter two nucleotides determined the duration of the specified pitch. He then ran the derived themes through a computer program that would generate melodies and rhythm. Based on the software output, Hugh would compose harmonies, counterpoints, and various phrasings. Hugh calls his work “Music of the Human Genome”.
Robert Thomason. DNA the way to San Jose?. Wired News. 12 March 2001.
2001 Todd Barton (composer) assigned each nucleotide to a note and elaborated on the basic theme by shifting the pitches up or down an octave, still maintaining the integrity of the sequence-derived melody. He uses a MIDI sequencer, Xx program, and the graphic music synthesizer, Metasynth, to derive his rhythmic and pitch patterns according to his original nucleotide-to-note assignment. Based on the MIDI output, Barton creates expansions and contractions of the original pattern.
Barton has modified the length of the pitches or assigned different instrumentation to certain parts of the DNA sequence. For example, Barton has assigned the percussion section to perform the beginning segment of Chromosome 1. By taking the beginning segments of all chromosomes, Barton can combine the various musical translations to create “Genome Music”, the title of his project. Barton has also translated the amino acid sequence of proteins, such as insulin, into a musical sequence based on his set of rules.
Robert Thomason. DNA the way to San Jose?. Wired News. 12 March 2001.
Genome Music: The Human Genome Project Presentation. Smithsonian National Museum of Nautral History, Washington, DC, USA. 9 June 2001.
2001 Aurora Sanchez Sousa (microbiologist) and Richard Krull (composer) converted DNA sequences into music by assigning a note (do, re, mi, etc) to each nucleotide. For example, thymine=re, guanine=so, adenine=la, cytosine=do. The conversion of a DNA sequence into music would serve as an underlying bass line to accompany a melody that was composed by Krull and Sousa.
CBS News. DNA Makes Sweet Music!. 18 Jan 2003.
Jonathan Middleton (musician) has created an interactive computer program called Musical Algorithms in order to allow users to create their own algorithmic conversions based on DNA sequences and mathematical patterns. The user is free to decide the range of notes, pitch assignments, and rhythmic values of the notes based on their preferences that can be specified into the program webpage.
1989 John Dunn (computer musician) and KW Bridges (botanist) created a software that converts protein sequences into music based on the characteristics and frequency of each amino acid. The 20 amino acids were grouped according to acidity, basicity, and polarity. A frequency analysis was conducted on the amino acids to find the most abundant amino acid within each group. The most common amino acid within a group would be assigned the middle C and then the second most common amino acid would be assigned the next note on the keyboard, D, and so forth. Each amino acid within a chemical group will have a unique note, but across groups, there may be overlap of common notes for two different amino acids from distinct groups.
Other aspects of the music, such as instrumentation, would be left to the discretion of the composer. Each of the groups is assigned an instrument and the importance of the each instrument can be controlled by the volume. The genes can be read sequentially or they can also be read randomly. The overall intention of such creative contributions is to mimick the biological process of transcribing the DNA sequences into proteins. Furthermore, Dunn and Bridges added their own creative component by adjusting the instrumentation and tempo to match the biological characteristics of the protein such as starfish being “relatively simple and quite mechanical”. Dunn continued from 1992 through 1995 to convert DNA sequences from organisms such as starfish, slime mould, sea urchins, etc. using his algorithm.
1996 Mary Anne Clark (biologist) and John Dunn (computer musician) converted protein sequences into music. Clark created a system used to assign amino acids to musical notes and the coding assignment was then computer programmed by Dunn, creator of Algorithmic Arts. The twenty amino acids were assigned to a 20-note scale based on relative hydrophobicity. The range of notes spanned three octaves for a diatonic scale. Taking into consideration the ultimate harmony of the conversion, Dunn and Clark set amino acids with similar R groups to consonant intervals. The length of each note depends on the number of DNA codons associated with the specific amino acid. Clark uses various instruments to signify certain known aspects of the protein: vibraphone for the calcium binding sites, harp plays the DNA codons, secondary structure characteristics (alpha helix, beta sheets, turns) are played by the flute. Different voice ranges represent the hydrophobic and hydrophilic R groups: lower voices represent the hydrophobic amino acids and higher voices represent the hydrophilic amino acids. Clark points out numerous assignments can be made simply by reversing the amino acid to note assignment or by having the same note represent several amino acids with similar solubilities.
The conversion has been applied to listen to evolutionary homologies and divergence. Hemoglobin sequences were taken from the tree shrew, human, Sumatran tiger, and African elephant and converted to hear evolutionary similarities. Lastly, large proteins can be played at a quicker tempo in order to understand the large size of the protein structure.
Sean Henahan. Protein Preludes. Access Excellence. http://www.accessexcellence.com/WN/SUA12/genemusic398.html
John Dunn and Mary Anne Clark. “Life Music”: The Sonification of Proteins. Leonardo, vol. 32, No. 1. (1999), pp. 25-32
Herb Moore used John Dunn’s computer software from Algorithmic Arts in order to convert the acid sphingomyelinase (ASM) enzyme into music. A functional form of this enzyme is lacking in a neurologic disorder known as Niemann Pick Type-A disease.
2001 Linda Long (researcher) founder of Molecular Music, generated music based on the x-ray crystallography (3-D structure) of proteins. Certain points on the protein structure map to musical parameters such as pitch and amplitude. Long also focuses on hearing secondary structure patterns such as helices (expressed as arpeggios) and beta-sheets (expressed as a succession of similar notes).
Clare Sansom. DNA makes protein—makes music?. The Biochemist. December 2002.
David Lane (musician) created a twenty note musical scale based on amino acid properties. Lane was initially a student when he began the project of converting genetic sequences to music. He used a Kurtzweil synthesizer and Yahama sequencer in order to facilitate the translation from protein sequence to music. Translations can be accessed under the title GenSong.
Bryan D. Hance. Art exhibit to showcase musical works based on genetic sequences. Arizona Daily Wildcat. 31 Jan 1996.
Larry Lang converted amino acid sequences to music based on the codons. The notes span a range of three octaves. He primarily focused on oxytocin to demonstrate his conversion: the 27 nucleotides that compose the oxytocin protein are accompanied by the entire oxytocin DNA sequence in the bass line.
LY Han (scientist) and YZ Chen (scientist) converted protein sequences into music based on structural and physiochemical properties. The tone, pitch, intensity, and instrumentation were based on five amino acid properties. Han and Chen have created a computer program called PROM that directly converts amino acid sequences into music.
Erik Jensen and Ronald Rusay converted amino acid sequences to music based on the physical and chemical properties of amino acids. A pitch and note duration was assigned to each amino acid. The amino acids were assigned to two scales based on the polarity of each molecule. Each scale contains a designation for the pitch assignment as well as the note duration. A higher pitch corresponds to an increasingly complex amino acid side chain (R group).
Erik Jensen and Ronald Rusay.Musical and Graphic Representations of the Fibonacci String and Proteins using Mathematica. The Mathematica Journal. Volume 8, Issue 2, 2001.
1984 Kenshi Hayashi and Nobuo Munakata assigned DNA and amino acid sequences to musical instrument digital interface (MIDI) notes in order to obtain an auditory display of genetic sequences. MIDI notes are a standard mode of communicating musical notes in the form of digital data (rather than sound) from computers to other electronic devices such as synthesizers. They also aimed to further enhance the original translation from genetic sequences to music using MIDI-sequencer programs. Hayashi and Munakata assigned one of four notes spanning a five-note interval range to the DNA bases (adenine=A, thymine=G, cytosine=E, guanine=D). The range was chosen to be a fifth based on the human voice range that occurs in daily speech patterns. The notes were chosen from the middle of the C Major scale (rather than from the ends) for reasons of symmetry.
The amino acids were assigned to notes based on twenty pitches starting from the note D# in the first octave (D1#) to the note B in the fourth octave (B4). The notes span nearly four octaves. The scope of notes was based on choral orchestrations that typically include voices ranging from bass to soprano. The amino acids were ordered according to hydrophobicity and other characteristics. Ultimately, each amino acid was classified into one of six groups: acidic, basic, polar, small nonpolar, aromatic, and hydrophobic. A synthesizer was used for its microtuning capabilities.
K. Hayashi and N. Munakata, Basically Musical. Nature, 310, 96 (1984).
N. Munakata, Gene Sequence Analysis with Auditory Display.
Peter Gena and Charles Strom. Musical Synthesis of DNA Sequences.
Charles Strom (geneticist) and Peter Gena (composer) used physical properties of amino acids and individual bases in order to convert DNA sequences into music. For pitch, the dissociation constant (pKa), purine/pyrimidine content, and number of hydrogen bonds were taken into account using a two formulas (one for amino acids above pKa 7.0 and another for below pKa 7.0). The intensity (or velocity) of each pitch was determined by codon melting temperature (number of hydrogen bonds per codon). The duration of each note was determined by the pKa and atomic weights of each amino acid. Again, the intensity and duration of each note was based on two formulae: one for acidic amino acids and another for basic amino acids, similar to the formulae used to determine pitch. All of these specifications were used to yield the final MIDI note. The genomes of certain organisms were scanned by a MAX/MSP patch (called DNA Mixer) and DSP language and then played in MIDI note format on a Yamaha TX802 digital synthesizer. A second series of algorithms scan the raw DNA for start and stop codons from different starting points, analogous to the scanning of mRNA by ribosomes. Using this system, Gena and Strom have converted blood and liver cells, polio virus, botulinin toxin, measles, rubella, common cold viruses, and the HIV virus.
Peter Gena and Charles Strom. A Physiological Approach to DNA Music.
Ross King (biologist) and Colin Angus (musician) incorporated aspects of the DNA sequence and protein sequence of a gene into music. The translation is based on a C Major scale and the DNA and protein sequences are played simultaneously. The top line of music is coded by the DNA sequence according to the following assignment: A=A4 submediant, T=E3 mediant, C=C3 tonic, G=G3 dominant (where E indicates the note and the 3 indicates the octave, for example). The bass line is coded by the amino acid sequence where each physical property, such as polarity and size, are indicated by a particular note. Polar=A2 mediant, hydrophobic=C1 tonic, charged=F1 subdominant, positive=E1 mediant, aliphatic=G1 dominant, aromatic=D1 supertonic, tiny=all+1 octave. Therefore, the number of notes per amino acid varies based on the properties the amino acid has. The total range of notes is nearly two octaves in the bass-line (excluding tiny amino acids, which would make three octaves). The top line spans the same number of notes as the bass line (about two octaves). The time signature is in ¾ based on three nucleotides per codon. The initial program was written in C on a Macintosh computer and then later re-written in Java for wider computer compatibility by Andreas Karwath.
Ross King and Colin Angus. PM—Protein Music. CABIOS Applications Note. Vol. 12 No. 3 (1996). pp. 251-252. http://bioinformatics.oxfordjournals.org/cgi/reprint/12/3/251
Ross King, Colin Angus, and Andreas Karwath. Protein Music. Applications note for Java PM program. January 2001.
Wayne Ford. Setting DNA to Music. Online Athens.
Alexandra Pajak was a music student when she converted amino acid and DNA sequences to music. In one of her pieces, she used chords played by string instruments to signify the amino acids. The amino acids were grouped according to hydrophobicity: major chords were assigned to hydrophilic amino acids and minor chords were assigned to hydrophobic amino acids. The DNA sequence was incorporated into the orchestration using the piano. In another movement of her orchestration, she used chords for her DNA sequence instead of single notes.
Kristin Kallaher. Music in Your Blood. Agnes Scott College Alumnae Magazine.
Mark Gresham. In the Key of Life: Decatur-based composer finds musical inspiration in DNA. Creating Loafing Atlanta. http://atlanta.creativeloafing.com/gyrobase/PrintFriendly?oid=oid%3A12797
Alexander Mihalic (composer) converted amino acid sequences into music by assigning each of the twenty amino acids to a musical group or melody. Beginning with his composition Atoms, the composer assigned certain musical parameters, such as pitch and duration, to each of the five atoms: hydrogen, carbon, nitrogen, oxygen, and sulfur based on the chemical and physical properties of the atom. The result is a “musical representation” for each atom. The combination of these atomic melodies, based on the atomic composition of an amino acid, results in the composition DNA. A unique musical theme represents each amino acid in this second composition. The form and duration of the resulting music depends on the tastes of the performer.
Mihalic began a project titled “Encyclopaedia Musicalis” in 1991 where a collection of pieces based on DNA can be found.
Mihalic, Alexander. DNA and composition. galileo.cincom.unical.it/esg/Music/workshop/articoli/mihalic.pdf