A viral hit? The sequence of coronavirus makes surprisingly lovely music

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Mark Temple, Western Sydney University

All my life I’ve been involved in music and molecular biology. At the crossroads between science and art, I see great scope for insight.

My latest research, published in the journal BMC Bioinformatics, reveals how music can be used to reveal functional properties of the coronavirus genome.

This project followed earlier work I had done generating audio from human DNA sequences; this time, I wanted to apply those techniques to the virus sweeping the world to see what might be revealed. In other words, this was the difficult second album!

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Read more:
What does DNA sound like? Using music to unlock the secrets of genetic code

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Assigning notes to the ‘words’ in the genome

Genes of the coronavirus are like biological book chapters; they hold all the words that describe the virus and how it might function. These “words” are made from strings of chemical letters scientists refer to as G, A, U and C.

This viral “book” is over 30,000 characters long. Some of these characters come together to form what scientists call a codon, which is a sequence of RNA that corresponds to a specific amino acid. But to stick with our analogy, let’s just say they come together to form “words”.

In my work, I assigned notes to these words to generate audio; I had wondered if this might helps us understand what the words mean.

I devised an online tool to hear the sound of coronavirus doing two things most genomes do: the first is called “translation”, which is where the virus makes new proteins. The second is called “transcription”, which is where the genome of the virus copies itself.

Sounds of the coronavirus genome.

There are several things you can hear: the start and end of genes, the regions between genes and the parts of the genome that control how genes are expressed.

Other researchers have written about this extensively in the coronavirus scientific literature but this is the first time you can distinguish between these regions by listening.

Revealing relationships between structure and function

So, what’s the point of all this?

As a research tool the audio helps supplement some of the many visual displays that exist to represent genomic information. In other words, it helps scientists understand even more about the virus and how it operates. Recently, UK-based composer and researcher Eduardo Miranda at the University of Plymouth used DNA sequence data for music composition and to better understand synthetic biology. Researcher Markus Buehler at MIT has been working with musical representations of proteins to enquire about novel protein structures.

I think an equally valid question is: does the audio sound musical? Now that I have finished the scientific research part of this project, I listen to the coronavirus genome with fresh ears, and from a musician’s perspective I been surprised as to how musical it sounds.

I don’t mean to trivialise the pandemic by thinking about the virus in musical terms.

As a molecular biologist at Western Sydney University, when I think about the virus I see RNA sequences, and it’s my job to see relationships between structure and function. I don’t see patients in the clinic and I’m not researching a cure — these things are not my domain.

Taking the genome to the recording studio

As a musician, I have also taken the audio data into the recording studio, away from the research lab, to reveal other perspectives on the coronavirus.

The coronavirus audio is pulsating and incessant, but, working with other musicians, we have tried to tame the sequence; to make it subservient to our musical knowledge, ideas and human spirit.

I returned to the trusty drum kit that once drove my old band The Hummingbirds and this now beats the viral sequence into submission. With guitar by Mike Anderson, who is in Sydney-based instrumental surf twang band Los Monaros, we have reached an understanding of its jagged rhythms and syncopated pulses to create some music.

Sonification can reveal new perspectives on the function and structure of the coronavirus genome.
Author provided, Author provided

We mixed the computer-generated audio from the coronavirus genome with real guitars and drums played by real people. The result sounds more musical than I thought it would and it reminds me of the pulsing music of US composer Steve Reich. I still hear genes and other viral characteristics within the science data but music wins out in the rehearsal studio.

As a musician, this project has been rewarding but as a scientist, I hope sonifying the coronavirus genome helps people think about its function in new and helpful ways.

I was also challenged to create something almost beautiful out of something so awful. Let’s hope we will soon be able to return to work and live music more “normally”, to the parts of life that engage us intellectually and creatively.

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Read more:
Music-making brings us together during the coronavirus pandemic

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Mark Temple, Senior Lecturer in Molecular Biology, Western Sydney University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

INDIA: ORISSA BRACES FOR MORE VIOLENCE AFTER ANOTHER MURDER

Suspecting cover-up, Communist investigators say 500 people may have been killed.

NEW DELHI, November 5 (Compass Direct News) – Terrified Christians already ravaged by more than two months of violence in Orissa state’s Kandhamal district braced for more carnage as suspected Maoists today gunned down a local worker of the Hindu extremist Rashtriya Swayamsevak Sangh (RSS).

Dhanu Pradhan was an RSS activist said to be on the Maoists’ hit list. Police said he was shot by three suspected Maoists in Kumharigaon village under Brahmanigaon jurisdiction in Kandhamal at 1 p.m., reported The Indian Express. Modern India’s worst-ever spate of violence began in the forest district of Kandhamal on Aug. 24, a day after a leader of the Hindu extremist Vishwa Hindu Parishad (World Hindu Council or VHP), Laxmanananda Saraswati, was killed.

Although a Maoist group admitted killing Saraswati and four of his aides, the VHP blamed local Christians for the assassinations. The wave of violent attacks carried on unabated for more than two months, destroying at least 4,500 houses and churches in the district.

More than 500 people, mostly Christian, might have been killed in the past few months’ violence in Kandhamal district, according to a report by a Communist Party fact-finding team. The report also suggested that the state government downplayed and covered up evidence of unreported deaths.

“The official figure for deaths has been reported to be 31, however, a senior government official on the condition of anonymity informed that he himself consigned two hundred dead bodies – found from the jungle – to flames after getting them collected in a tractor,” said the report by the Communist Party of India-Marxist-Leninist (CPI-ML).

The unnamed official estimated that, based on the intensity and pace of killings, the number of those killed was more than 500, according to the report. The fact-finding team visited Kandhamal district on Oct. 15-16 and published its report in the Oct. 27 issue of the party’s official publication, Liberation.

The report, signed by CPI-ML member J.P. Minz, also said that Hindu extremists might have used state government machinery to “minimize the evidence and possibly destroy dead bodies.”

Dr. John Dayal, a member of the National Integration Council of the Government of India, told Compass the report was startling but not surprising.

“I have been tabulating the data from independent church groups,” he said. “Even the Bishop’s House in Bhubaneswar has maintained that tens of thousands of refugees are hiding in forests, many of them with injuries of various degrees of grievousness.”

Dayal said that people must have been killed in the forests. “Even in villages, bodies have been discovered in neighboring fields,” he added.

The fact-finding team reported that the numerous attacks, acts of vandalism and killings took place “in full view of police, and the police remained mute spectators.” At least 200 Christian villages and 127 church and prayer halls were either destroyed or burned, it added.

Victims in numerous relief camps told the fact-finding team that the VHP and its youth wing, Bajrang Dal, were responsible for the tensions and violence.

“They used to organize meetings of the Kandha tribals and incite them to attack the Christian hamlets and also provided funds for doing this,” the report said.

Dayal said the Supreme Court of India should act on the report’s findings.

 

‘Great Terror’

The CPI-ML reported that Christians continued to experience “great terror,” and that Hindu nationalist groups were demanding the withdrawal of security personnel sent by the federal government to contain the violence.

“Riot victims are frightened to go back to their villages because they have been threatened that if they return they will be cut into pieces,” said the report. “The rioters are also proclaiming that only Hindu converts will be allowed to return. On the other hand, those in charge of the relief camps are pressuring the riot victims to return to their villages, saying that the life has returned to normalcy and peace has returned.”

The Indian Express yesterday reported that about 250 riot victims who had taken shelter in the Meliaputti and Mandasa areas of Srikakulam district in neighboring Andhra Pradesh state were refusing to go back to their villages “out of fear.”

“As many as 109 persons of 35 families of Sarlaguda, Raikia, Nuagaon, Baliguda, Bataguda, Barkhama, G. Udaygiri, Tikabali and Suraballi areas have been residing at Sourakaligam village of Meliaputti area, Andhra Pradesh, since the Kandhamal violence,” said the newspaper, adding that 140 others had taken shelter in Kumudhisingi village of the Mandasa area.

There are 12,641 violence-affected people in seven relief camps in Kandhamal, according to the district authorities.

 

Violence in Another District

The violence in Kandhamal has led to tensions in several other districts of Orissa. Yesterday a mob of around 400 people surrounded and beat five Christian men in the Bindha area of Bhadrak district’s Tihidi Block, according to the Christian Legal Association.

The incident took place when five men and two women, all staff of the Discipleship Centre, were returning from a few villages where that Christian organization has projects. A cyclist suddenly appeared before them and had an accident, incurring minor injuries. Soon a mob of about 300 people gathered and began beating the men, accusing them of converting Hindus, as if such activity were illegal in India.

The mob dragged the Christians to a Hindu nationalist rally where slogans against them were chanted. Police arrived and took the Christians to a police station, charging them under laws against forcible or fraudulent conversion. The seven Christians remained in jail at press time.

Police also filed a counter-complaint against the attackers, but no one was arrested at press time.

 

Nun’s Rape Case

In the case of a Catholic nun raped on Aug. 25 during the initial violence, the Kandhamal district court today issued a notice summoning her to appear for identification of the culprits, reported the Press Trust of India news agency.

The victim, who said she was raped in K. Nuagaon in Baliguda, had refused to cooperate with police, demanding that a federal agency investigate her case. On Oct. 24, she appeared before media and blamed police for not coming to her rescue. She said she was raped while police did nothing, and that later she saw a policeman talking congenially to one of the rapists.

Previously she had filed a complaint at the Baliguda police station, but officers did not make any arrests until a national newspaper, The Hindu, highlighted the case on Sept. 30. When the nun initially went to the police station to file her complaint, an officer had warned her of possible negative consequences of doing so.

 

One-Man Investigation

While Christians are demanding that a federal agency take over investigation of the violence in Orissa, the state government has appointed a one-man panel, the Justice S.C. Mohapatra judicial commission, to carry out the probe.

The commission placed an advertisement in a local newspaper, Sambad, on Nov. 3 seeking affidavits of victims by Nov. 15. It also said that people could appear before the commission on Nov. 28 in its office in Bhubaneswar, the state capital.

The commission will analyze the sequence of events and circumstances leading to the killing of Saraswati on Aug. 23 and the subsequent violence. It will also probe the role, conduct and responsibility of individuals, organizations, groups and agencies in precipitating and committing the crimes and investigate whether the measures that followed were adequate.

Mohapatra is a retired judge of the Orissa High Court.

Orissa is ruled by a coalition of a local party, the Biju Janata Dal, and the Hindu nationalist Bharatiya Janata Party, which has close ties with the VHP.

Report from Compass Direct News

INDIA: FAITHFUL MOURN DEATH OF PRIEST ATTACKED IN ORISSA

Hindu extremists beat Fr. Bernard Digal unconscious, leaving him bleeding in forest.

NEW DELHI, October 31 (Compass Direct News) – More than 3,000 people today attended the funeral in Bhubaneswar, Orissa of a Catholic priest who died on Tuesday (Oct. 28) from injuries sustained in anti-Christian violence that began in August.

Father Bernard Digal died in Chennai, Tamil Nadu, after an operation to remove a blood clot that developed in his brain due to a head injury from Hindu extremists attacking him on Aug. 25-26 in Kandhamal district, Orissa state. He was 46.

“He was smashed like a pulp,” Raphael Cheenath, archbishop of Cuttack-Bhubaneswar, told Compass. “Because of the hate campaign of the [Hindu extremist] Sangh Parivar, the attackers lost their humanity and they became devils. Human beings can’t do what they have done.”

Archbishop Cheenath flew with Fr. Digal’s remains from Chennai to Orissa. Treasurer of Cuttack-Bhubaneswar archdiocese in Orissa, Fr. Digal was visiting Sankarakhole parish when violence flared after Maoists killed Hindu leader Laxmanananda Saraswati and his disciples on Aug. 23.

Though police suspected Maoists from the start and the outlawed Marxists had claimed responsibility for the murders by Sept. 1, Hindu extremists bent on stoking anti-Christian flames continued to publicize that Christians had committed the crime – and have not stopped doing so.

Fr. Digal and Father Alexander Chandy, along with driver Sisir Pradhan, had taken shelter in a forest after a furious mob gathered outside the parish shouting slogans to kill all missionaries. After spending two days in the forest, they left the forest after Fr. Chandy became ill, moving from village to village.

They finally took refuge in a gutted church building in Dudukangia village. It had been torched and only its walls were standing. Legs swollen from walking, the refugees hoped that the enraged Hindu mobs would not come, Archbishop Cheenath said.

But the mob tracked them down by midnight, the archbishop said, and the clerics and driver ran. The crowd caught hold of Fr. Digal, who later told Archbishop Cheenath, “The mob shouted to each other to kill me. I pleaded for my life, but in vain.”

Stripping Fr. Digal naked, the Hindu mob then hit him with crowbars, iron rods, cycle chains, axes, sticks and other weapons, the archbishop said.

“They made a bonfire to burn him alive,” he said.

Seeing the fire, Fr. Digal managed to escape and run through some thorny bushes but was caught shortly after. The intolerant Hindus continued to hammer him until blood flowed from his head and he lost consciousness, and they left him for dead, Archbishop Cheenath said.

“He lay there on the wet ground and in the cool breeze for six to seven hours,” he added. Two villagers who found him in the forest carried him to Phulbani.

After much pressure, the state administration took Fr. Digal to a private hospital in Bhubaneswar, under security cover, and from there he was taken to Holy Spirit Hospital in Mumbai.

Discharged the first week of October after more than a month in the hospital, he reached Chennai, Tamil Nadu on Oct. 12 to visit his friend the vicar general of the archdiocese, who was undergoing a heart treatment in St. Thomas Hospital.

“Fr. Digal, after coming to Chennai, complained of high fever, blood in the urine and headache, and lastly his lungs collapsed,” Archbishop Cheenath told Compass.

Tests revealed he had a blood clot in the brain, and he underwent emergency surgery on Sunday evening (Oct. 26), reported The Times of India. The next day, he developed acute respiratory disorder and slipped into a coma.

Kandhmal district Police Chief Pravin Kumar told the national daily that he had no knowledge of the attack on Digal.

“So many incidents took place,” he reportedly said. “I don’t know whether there was any formal complaint pertaining to the attack on him. The police can begin an enquiry into the incident if a complaint is lodged even now.”

The Orissa state government has ordered a probe into the death of Fr. Digal, according to The Statesman News Service.

Fr. Digal was ordained on May 29, 1992. He was a native of the village of Tiangia in Kandhamal.

 

Orissa Rape Victim’s Plea

Two months after a nun was raped and paraded half-naked on Aug. 25 in the anti-Christian violence in Orissa, the victim went before the media in New Delhi on Oct. 24 and recounted her traumatic experience.

Her head and face covered by a black scarf, Sister Meena Lalita Barwa accused police of being “friendly” with the attackers and of not being responsive to her plea. Expressing her distrust in Orissa police for failing to protect her from those who raped her and other attackers, she demanded a Central Bureau of Investigation (CBI) probe.

The nun had gone into hiding after the attack but decided to come forward after the Supreme Court turned down her initial request for a CBI investigation last week.

Sr. Barwa read from her handwritten statement, giving stark details of the incident. Archbishop Cheenath accompanied her in the press conference.

“Two of them were holding my neck to cut off my head with an axe,” she said. “Others told them to take me out to the road; I saw Fr. [Thomas] Chellan also being taken out and being beaten.”

The 40 to 50 men were armed with axes, spades, crowbars, iron-rods and sickles, Sr. Barwa added. She said she was taken to a building full of ashes and broken glass and raped there, with the mob subsequently parading her and Fr. Chellan for about a half a kilometer. Upon reaching a market she asked about a dozen Orissa police to help her, she said, “but they did not move.”

“This hate campaign,” Archbishop Cheenath said, “is done under the very nose of the authorities, and they are mere spectators of these shameful deeds.”

At the Balliguda police station, the nun recounted, she told the inspector in charge and other government officers how she was attacked, raped, taken away from policemen and paraded half-naked, and how the officers did nothing as she wept bitterly. The inspector asked her, she said, if she knew “what will be the consequence” of filing a First Information Report (FIR).

On Aug. 26, as she was writing the FIR, the inspector told her to hurry and not write it in detail, she said.

“State police failed to stop the crimes, failed to protect me from the attackers, they were friendly with the attackers,” she said. “They tried their best that I did not register an FIR, not make complaints against police, [and] police did not take down my statement as I narrated in detail and they abandoned me half of the way. I was raped and now I don’t want to be victimized by the Orissa police. I want a CBI enquiry.”

Since her press conference, Orissa Chief Minister Naveen Patnaik has called for a detailed report on the sequence of events from the district collector and superintendent of police.  

Report from Compass Direct News