Audio Pandemic by Ali Choudhry and Dr. Matthew Latif

Artist Statement

The first case of infection caused by COVID-19 was reported in Wuhan City, China, in December 2019. Since then COVID-19 has evolved into a global pandemic impacting our financial, educational, and social systems – including how we create and exhibit artworks.

Audio Pandemic” by Ali Choudhry and Dr. Matthew Latif is a novel, timely, and innovative project that uses the processes of “data sonification”, “data visualisation”, and “algorithmic composition” in a creative context to create audio-visual representations of the COVID-19 virus. Each of the audio-visual pieces is composed using statistical information and genomic data gathered from the World Health Organisation and the Shanghai Public Health Clinical Center, China. Firstly, audible representations of mortality and genomic data for the DNA and protein structure of COVID-19 are made with each note algorithmically correlated to every point in each data set. Secondly, a visualisation technique that uses multi-colored nested rectangles is used to display the hierarchical data that underlies each composition.

The results are a collection of mesmerising, haunting, and unique pieces of contemporary art that challenge audience preconceptions of the COVID-19 pandemic.

1. Spike Glycoprotein

This song was created from the spike protein “S”. The spike glycoprotein is the most important surface protein of COVID-19, mediating the entrance to human respiratory epithelial cells by interacting with cell surface receptor angiotensin-converting enzyme 2 (ACE2). The spike glycoprotein includes two regions, S1 and S2, where S1 is responsible for binding to the host cell receptor while S2 is responsible for membrane fusion. The spike glycoprotein is the key target for vaccines, therapeutic antibodies, and diagnostics.

Molecular simulations reveal that the spike protein is shaped like a knight’s lance. And just as the lance was used during the periods of classical and medieval warfare, COVID-19’s spike protein has evolved into being the leading weapon in its arsenal in its cellular battle. Once the spike protein contacts its cellular target it drives itself through the host cell membrane, fusing the membranes of both the viral and target cell and allowing entry of the virus so that it can begin the viral infection process.

The deep tones of the song give the impression of an incoming threat, a warrior stalking its prey that is punctuated by short sharp bursts of high piercing notes as its lance penetrates the enemy’s defences.

The song that results from the data sonification process lends support to the function of the S spike protein. It resonates with higher tones which correspond to residues whose function is to act as the “spike” or lance as the virus particle attacks the delicate cellular membrane.

Similarly, lower tones permeate the song which correspond to residues that anchor the spike to the viral capsid. The lower tones suggest a threat, a warrior stalking its prey that is punctuated by short sharp bursts of high piercing tones as its lance penetrates the enemy’s defences.

The gene corresponding to the S spike protein was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 1273 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the amino acids that make up the S spike protein as it exists when interacting with the host cell. Amino acids that are more highly represented in the spike protein appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

2. Nucleocapsid Protein

This song was created from the nucleoprotein “N” which packages the positive strand viral genome RNA into the helical-shaped nucleocapsid. In COVID-19 the N protein plays a fundamental role in protecting the fragile nucleic acid that constitutes the COVID-19 genome.

The sound that results from the data sonification process lends support to the inherent function of the N protein. The hauntingly beautiful tones generated are reminiscent of a calm, soothing, lullaby – where the N protein safely cocoons its precious genetic cargo on its journey through both space and time.

This song was created from the “N” membrane protein. The gene corresponding to the M protein was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 419 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived. Therefore, the tonal sequences from the string of 419 residues that make up the N protein is an organised, audio representation of the data.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the amino acids that make up the N protein as it exists when interacting with the lipid bi-layer of the host cell. Amino acids that are more highly represented in the sequence appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

3. Membrane Protein

This song was created from the membrane protein “M” of the COVID-19 genome. The M protein is a component of the viral envelope and plays a central role in virus morphogenesis and intracellular assembly formation of virus particles following infection of the host cell.

The song that results from the data sonification process lends support to the function of the M protein. It resonates with lower tones which correspond to residues whose function is to structurally support the delicate viral envelope. Similarly, higher tones occasionally permeate the song which correspond to residues that interact with other proteins of the interior of the viral capsid.

This song was created from the “M” membrane protein. The gene corresponding to the M protein was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 222 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived. Therefore, the tonal sequences from the string of 222 residues that make up the M protein is an organised, audio representation of the data.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the M protein as it exists when interacting with the lipid bi-layer of the host cell. Amino acids that are more highly represented in the sequence appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

4. Helicase

This song was created from the “helicase protein” of the COVID-19 genome. A helicase is an enzyme whose main function is to unpack the viral genome. Helicases are motor proteins that separate DNA and RNA strands as they move directionally along a nucleic acid backbone.

The song that results from the data sonification process lends support to the function of the helicase protein. As the song evolves a torturous, tearing, and twisting sense is evoked as the helicase forces the nucleic acid strands apart in order for the replication machinery to copy the viral genome.

This song was created from the “helicase” protein. The gene corresponding to the helicase enzyme was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 601 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived. Therefore, the tonal sequences from the string of 601 residues that make up the helicase protein is an organised, audio representation of the data.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the helicase protein. Amino acids that are more highly represented in the sequence appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

5. Envelope Small Membrane Protein

This song was created from the envelope small membrane protein “E” of the COVID-19 genome. The E protein is the tiniest of the major structural proteins, but also the most enigmatic. It is involved in several aspects of the virus’ life cycle, such as assembly, budding, and envelope formation. During the viral replication cycle, the E protein is abundantly expressed inside an infected cell, but only a small portion is eventually incorporated into the virion envelope. The COVID-19 E protein also acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport.

The song that results from the data sonification process lends support to the function of the envelope E protein. The higher notes suggest the function of the E protein might dictate its membrane topology, depending on whether it is required to function as an ion channel or its involvement in the viral envelope during assembly.

This song was created from the “E” small membrane E protein. The gene corresponding to the E protein was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 75 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived. Therefore, the tonal sequences from the string of 75 residues that make up the E protein is an organised, audio representation of the data.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the envelope E protein as it exists when interacting with the lipid bi-layer of the host cell. Amino acids that are more highly represented in the sequence appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

6. RNA-dependent RNA-polymerase (RdRp)

This song was created from the RNA-dependent RNA polymerase “RdRp” protein of the COVID-19 genome. The RdRp protein is the central component of the COVID-19 viral replication and transcription machinery.

The song that results from the data sonification process lends support to the function of the RdRp protein. There is a fluidity to the piece that gives the impression of the enzyme moving through the liquid environment of the infected cell as it replicates its genome.

This song was created from the RNA-dependent RNA polymerase protein. The gene corresponding to the RdRp protein was first translated into its corresponding protein sequence. This sequence was then analysed to calculate the free energies for each of the 933 amino acid residues in a “window” of a defined length and values assigned to the middle residue within each window. The “biological scale” used assigned each individual residue a free energy value based in part on a its relative position in relation to a normal to a lipid bilayer (i.e., cell membrane). The resultant free energy values were then used to assign each of the 20 unique amino acids a tone with the pitch of each tone proportional to the free energy of the amino acid from which the tone was derived. Therefore, the tonal sequences from the string of 933 residues that make up the RdRp protein is an organized, audio representation of the data.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of the residual free energies of the envelope protein as it exists when interacting with the lipid bi-layer of the host cell. Amino acids that are more highly represented in the sequence appear as larger rectangles, with rectangles of a similar size representing identical amino acids which only differ in their residual free energy as represented by their different colours.

7. Flattening the Curve – Australia

This song was created to give an audible representation of the rate of infections of COVID-19 in Australia.

The song used data from December 31st 2019 through June 3rd 2020 for the number of new cases reported per day.

The song that results from the data sonification process allows the listener to hear the increase in COVID-19 cases as they occur in Australia over time. The song begins with a single note corresponding to zero cases between December 31st 2019 until January 24th 2020. On January 25th 2020 the first case of COVID-19 was identified and can be heard as an increase in the tone of the song at 19 seconds. From that date until March 23rd 2020 new COVID-19 cases increased, peaking at 611 infections per day.

From that date the number of new COVID-19 infections decreased – flattening the curve.

This song was created using data from the European Center for Disease Prevention and Control (ECDC).

The song used data from December 31st 2019 through June 3rd 2020 for the number of new cases reported per day in Australia. Data was used in line with ECDC’s copyright policy.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of new COVID-19 cases per day in Australia. Days with larger increases in COVID-19 cases appear as larger rectangles, with rectangles of a smaller size representing days where fewer new cases of COVID-19 were identified.

For example, the light pink rectangle in the upper left corner is the largest and corresponds to March 23rd 2020 when new cases of COVID-19 peaked at 611 per day. If you compare the Australian picture against the one for the USA you can see that Australia has a few larger rectangles, corresponding to a few days where COVID-19 cases peaked with most of the rectangles being smaller corresponding to the decrease in new infections. In contrast, the USA is predominantly composed of rectangles of a similar size indicative that the rate of infections is not decreasing.

8. Flattening the Curve – USA

This song was created to give an audible representation of the rate of infections of COVID-19 in the United States of America.

The song used data from December 31st 2019 through June 3rd 2020 for the number of new cases reported per day.

The song that results from the data sonification process allows the listener to hear the increase in COVID-19 cases as they occur in the USA over time. The song begins with a single note corresponding to zero cases between December 31st, 2019 until January 20th 2020. On January 21st 2020 the first case of COVID-19 in the USA was identified and from that date new COVID-19 cases have been increasing.

In contrast to Australia, where we were able to flatten the curve – the United States has not been as successful – with daily infections still in the tens of thousands per day.

This song was created using data from the European Center for Disease Prevention and Control (ECDC).

The song used data from December 31st 2019 through June 3rd 2020 for the number of new cases reported per day in the USA. Data was used in line with ECDC’s copyright policy.

The picture was created using a visualisation technique that uses nested rectangles to display hierarchical data of new COVID-19 cases per day in the USA. Days with larger increases in COVID-19 cases appear as larger rectangles, with rectangles of a smaller size representing days where fewer new cases of COVID-19 were identified.

For example, the light blue rectangle in the upper left corner is the largest and corresponds to April 26th 2020 when new cases of COVID-19 peaked at 48,529 per day in the USA. In contrast to Australia, the USA picture is predominantly composed of rectangles of a similar size indicative that the rate of infections is not decreasing.

About Ali Choudhry and Dr. Matthew Latif

Ali Choudhry is an emerging visual artist in Melbourne. He sits at a unique intersection of identity, being a person of color, refugee, Pakistani immigrant, and queer. Since 2019 Ali has been studying year studying at RMIT for a Bachelor of Fine Arts. He has had numerous group shows since 2012; and is planning his second solo show for Midsumma 2020/2021. He has also won numerous awards including: Silver placement at the Australian Professional Photography Awards, two-time finalist for Incinerator Award, and semi-finalist for HeadOn.
Instagram: @ali.choudhry.photo

Dr. Latif is a bio-artist, synthetic biologist, and biohacker. He is known for creating music using living brain cells and genetically engineering his own stem cells to create fluorescent works of art. In his artistic practice he embraces the concepts of scientific democracy by attempting to directly connect, resonate, and challenge the way audiences think about science and the natural world. Throughout his career, he has used the concepts of “timeliness” and “relevance” as the source of inspiration for his bio-art projects. As Nina Simone once said, “It’s an artist’s duty to reflect the times in which we live.”

Audio Pandemic by Ali Choudhry and Dr Matthew Latif is created for Shelter 2020.

Featured Image 
Title: Flattening the Curve: Australia
Photo credit: Matthew Latif

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