Category Archives: Human Genetics

The genetic code to alllife on Earth, both simple and complex, comes down to four basic letters: A, C,T and G.

Untangling the role thatthese letters play in lifes blueprint has allowed scientists to understandwhat makes everything from bacteria to people the way they are. But as researchershave learned more, they have also sought ways to tinker with this blueprint,bringing ethical dilemmas into the spotlight. The Gene, a two-part PBS documentary from executive producer Ken Burnsairing April 7 and 14, explores the benefits and risks that come withdeciphering lifes code.

The film begins with oneof those ethical challenges. The opening moments describe how biophysicist HeJiankui used the gene-editing tool CRISPR/Cas9 to alter the embryos of twin girls who were born in China in 2018 (SN: 12/17/18). Worldwide, criticscondemned the move, claiming it was irresponsible to change the girls DNA, asexperts dont yet fully understand the consequences.

This moment heraldedthe arrival of a new era, narrator David Costabile says. An era in whichhumans are no longer at the mercy of their genes, but can control and evenchange them.

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The story sets the stagefor a prominent theme throughout the documentary: While genetics holdsincredible potential to improve the lives of people with genetic diseases,there are always those who will push science to its ethical limits. But thedriving force in the film is the inquisitive nature of the scientistsdetermined to uncover what makes us human.

The Gene, based on the book of the same name by Siddhartha Mukherjee (SN:12/18/16), one of the documentarys executive producers, highlights many ofthe most famous discoveries in genetics. The film chronicles Gregor Mendels classicpea experiments describing inheritance and how experts ultimately revealed inthe 1940s that DNA a so-called stupid molecule composed of just four chemicalbases, adenine (A), thymine (T),cytosine (C) and guanine (G) is responsible for storing geneticinformation. Historical footage, inBurns typical style, brings to life stories describing the discovery of DNAshelical structure in the 1950s and the success of the Human Genome Project indecoding the human genetic blueprint in 2003.

The film also touches ona few of the ethical violations that came from these discoveries. The eugenicsmovement in both Nazi Germany and the United States in the early 20th century aswell as the story of the first person to die in a clinical trial for genetherapy, in 1999, cast a morbid shadow on the narrative.

Interwoven into thistimeline are personal stories from people who suffer from genetic diseases.These vignettes help viewers grasp the hope new advances can give patients asexperts continue to wrangle with DNA in efforts to make those cures.

In the documentarysfirst installment, which focuses on the early days of genetics, viewers meet a family whose daughter is grappling with arare genetic mutation that causes her nerve cells to die. The family searchesfor a cure alongside geneticist Wendy Chung of Columbia University. The secondpart follows efforts to master the human genome and focuses on AudreyWinkelsas, a molecular biologist at the National Institutes of Health studyingspinal muscular atrophy, a disease she herself has, and a family fighting tosave their son from a severe form of the condition.

For science-interested viewers, the documentary does not disappoint. The Gene covers what seems to be every angle of genetics history from the ancient belief that sperm absorbed mystical vapors to pass traits down to offspring to the discovery of DNAs structure to modern gene editing. But the stories of the scientists and patients invested in overcoming diseases like Huntingtons and cancer make the film all the more captivating.

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The PBS documentary The Gene showcases genetics promise and pitfalls - Science News

The World Health Organisation (WHO), in its quest to find efficacious therapies to treat COVID-19, plans to conduct a multi-arm, multi-country clinical trial. The trials have yet to begin, but ten countries have already signed up. Only one of them, South Africa, is on the African continent.

Of course, the WHO isnt the only organisation trying to find treatments or even a vaccine for COVID-19. The United States National Institutes of Health maintains an online platform that lists all registered, ongoing clinical trials globally. On March 26, a quick search of the platform using the term coronavirus revealed 157 ongoing trials; 87 of these involve either a drug or a vaccine, while the rest are behavioural studies. Only three are registered in Africa all of them in Egypt.

This low representation of African countries in clinical trials is not unusual. Poor visibility of existing sites, limited infrastructure and unpredictable clinical trial regulatory timelines are some of the key issues hindering investments in this area.

Africas virtual absence from the clinical trials map is a big problem. The continent displays an incredible amount of genetic diversity. If this diversity is not well represented in clinical trials, the trial findings cannot be generalised to large populations.

The same goes for the outcomes of the COVID-19 studies. They too may not be relevant for people in African countries unless conducted locally. This is because responses to drugs or vaccines are complicated and can be influenced by, among other things, human genetics: different people will respond differently to different drugs and vaccines.

More countries on the African continent must urgently get involved in clinical trials so that the data collected will accurately represent the continent at a genetic level.

Time is of the essence. The usual approach, of developing site or country specific protocols, wont work. Instead, African governments need to look at ways to harmonise the response towards COVID-19 across the continent. Now, more than ever, African countries need to work together.

Africa does have clinical trial infrastructure and capabilities. But the resources remain unevenly distributed. The vast majority are in Egypt and South Africa. Thats because these countries have invested more heavily in research and development than others on the continent.

Traditionally, clinical trials are conducted at centres of excellence, which are sites that have the appropriate infrastructure and human skills necessary to conduct good quality trials. These can be located at a single university or research organisation, or work can be split between a few locations. But setting up these centres requires significant time and financial investment. Most that I am aware of on the continent have developed over the years with heavy support from external partners or sponsors. In many cases, African governments have not been involved in these efforts.

Once such centres are set up, the hard work continues to maintain these centres and to ensure theyre able to attract clinical trial sponsors. They require continuous funding, the establishment of proper institutional governance and the creation of trusted, consistent networks.

Usually African scientists leading clinical trial sites can apply for funding to conduct a trial; if the site is well known the scientists may be approached by a sponsor such as a pharmaceutical company interested in conducting a trial.

Clearly this approach takes time and usually benefits well-known sites or triallists. So what alternatives are available in the face of an epidemic thats moving as fast as COVID-19?

Key stakeholders should work together to expedite the rollout of trials in different countries. This would include inter-country collaborations such as working with different governments and scientists in co-designing trials; and providing harmonised guidelines on patient management, sample collection and tracking and sharing results in real time.

African governments, meanwhile, should provide additional funding to clinical research institutions and clinical trial sites. This would allow the sites to pull resources together and rapidly enrol patients to answer various research questions.

Because of the uneven distribution of skills and resources the continent should also adopt a hub-and-spoke model in its efforts. This would involve countries that dont have much capacity being able to ship samples easily across borders for analysis in a centralised well-equipped laboratory, which then feeds back data to the country of sample origin.

Governments should also form a task force to quickly engage with key pharmaceutical companies with drug candidates for COVID-19. This team should establish the companies appetite for collaborations in conducting relevant trials on the continent.

Through all of this, it is necessary for stakeholders to identify and address key ethical issues that may arise. Ethics should not be compromised by haste.

Every countrys epidemic preparedness kit should contain funds set aside for clinical trials during epidemics or pandemics.

This would require governments on the continent to evaluate their role and level of investment in the general area of clinical trials. This will augment the quality and quantity of clinical trials in the face of the constant challenge of emerging and re-emerging infectious diseases as well as a steady rise in non-communicable diseases.

On top of this, clinical trial centres, clinical research institutions and clinical triallists on the continent should strive to increase their visibility in the global space. This will make them easy to find in times of crisis, and enhance both south-south and north-south collaborations.

The African Academy of Sciences is currently building an online platform to facilitate this visibility and encourage greater collaboration.

More:
Few clinical trials are done in Africa: COVID-19 shows why this urgently needs to change - The Conversation Africa

Leticia Ortiz |April 7, 2020

Newswise A team of UCLA researchers has launchedStop COVID-19 Together, a web-based app that will enable the public to help fight the spread of the coronavirus.

Through the site, anybody can take a brief survey that covers basic demographics, whether they have symptoms and their possible exposure to COVID-19. The system aggregates users responses to help the UCLA team find ways to reduce the spread of the virus, and to try to protect the health system from being overloaded.

The key contributors to Stop COVID-19 Together are the members of the public who contribute data to the effort, which is designed to predict the spread of COVID-19 throughout the community and to assess the effectiveness of current measures in that community, including physical distancing, said Dr. Vladimir Manuel, a clinician, medical director of urgent care at UCLA Health and one of the projects leaders. We are extremely grateful to everyone who is contributing.

The app was created by UCLA experts from a range of fields, including engineering, data science, clinical medicine, epidemiology and public health. The project is an initiative of the AI in Medicine program at theUCLA Department of Computational Medicine, which is part of UCLA Health.

One of the most pressing challenges with the coronavirus pandemic is the lack of information, said Eran Halperin, a UCLA professor of computational medicine, computer science, human genetics and anesthesiology, and another leader of the project. We do not have a clear understanding of how many people are infected, where they are or how effective the measures that we are taking to slow the spread have been. And we dont know how much strain the virus will put on our local hospitals in the near and more distant future.

The system will build a map of possible hotspots where there may be a higher risk for accelerated spread of the disease. Identifying hotspots will be critical for helping hospitals and medical centers reduce the risk of becoming overloaded as the number of people with COVID-19 increases. The system will also inform the public where hotspots are located, and it is using artificial intelligence to predict where and when the disease will spread. That information could be useful to public officials letting them know, for example, how effective physical distancing is in slowing the spread.

Our system will use machine learning tools to answer these questions and make predictions that will help us as a society be more prepared to fight this disease, said Jeff Chiang, a data scientist on the team.

Follow #TeamLA and #stopcovid19together on social media.

Link:
UCLA web app will enlist publics help in slowing the spread of COVID-19 - Newswise

GINA FERAZZI / LOS ANGELES TIMES Riverside County medical personnel administer a coronavirus test to a motorist at a drive-thru testing facility at Diamond Stadium in Lake Elsinore, California, on March 21. Those tested have symptoms or have had a risk of exposure.

SAN JOSE, Calif. Monica and Adrian Arima both were infected by COVID-19 at the same time on the same Nile River cruise, probably during a shared dinner buffet between the Egyptian cities of Aswan and Luxor. As they traveled home to Palo Alto, California, the couples early symptoms body aches and low-grade fever were identical.

But then, mysteriously, their experiences suddenly diverged. Monica spent 13 days at Stanford Hospital; Adrian was there for just three days. She needed extra oxygen and an experimental drug; he didnt.

Now, weeks later, she still has a cough. He is fully recovered, healthy enough to go food shopping and do other errands. Meanwhile, two of their traveling companions in their 70s and 80s tested positive but never suffered symptoms.

Their experience illustrates one of the many puzzling questions raised by the lethal new disease: Why is COVID-19 so inexplicably and dreadfully selective? The difference between life and death can depend on the patients health and age but not always.

To understand, scientists are scrutinizing patients medical histories, genomes and recoveries for any clues to explain this mystery.

Why are some people completely asymptomatic, some have mild disease, others have severe disease but recover and others have fatal disease? We are still trying to figure this out, said Dr. Brian Schwartz, vice chief for clinical affairs in UC San Franciscos Division of Infectious Diseases.

For most, not severe

It is a small subset of people that will go on to develop serious disease. Most will not, he said. We want to learn how to prevent people from developing serious disease and if they do, figure out how to treat it the right way.

Its well-known that death rates are higher among older people. Only 0.2% of people younger than 19 die. But for people between the ages of 60 and 69, the death rate is 3.6%. It jumps to 8% to 12.5% for those between ages 70 and 79, and 14.8% to 20% for those older than 80.

But theres more to it than that. Monica Arima is age 64; her husband, Adrian, is 70. But she has asthma and diabetes, while his underlying health is good.

Emerging U.S. data confirms trends seen in China and Italy: Rates of serious COVID-related symptoms are higher in those with other medical problems and risk factors, such as diabetes, hypertension, chronic obstructive pulmonary disease, coronary artery disease, cerebrovascular disease, chronic renal disease and smoking. In a U.S. Centers for Disease Control report released Tuesday, higher percentages of patients with underlying conditions were admitted to the hospital and to an ICU than patients without other health issues.

There may also be a genetic influence.

One of the things that weve learned from human genetics is that there are extremes at the human phenotype distribution, and pathogen susceptibility is no different, Stanford geneticist Carlos Bustamante told the journal Science. Stanford is part of a COVID-19 Host Genetics Initiative, a Finnish effort to link genetic variants associated with COVID-19 susceptibility and severity.

There are going to be people who are particularly susceptible, and there are going to be those who are particularly resistant, he said.

At the cellular level

Biologically, whats going on?

One leading theory is focused on the doors of a cell that permit the virus to enter. We know that the virus enters the body through epithelial cells in the respiratory tract. To get inside the cell, the virus uses a door a receptor called ACE-2 (angiotensin converting enzyme 2) on the cells surface.

Individual variations in this receptor could make it harder or easier for the virus to enter, cause infection and burrow deep into the lungs. In some of us, the cell door may open easily; in others, it may stay closed.

Or perhaps some people simply have more of these receptors on their cells. With more doors, the virus may enter more readily, so patients suffer worse infection and more serious disease, said Schwartz.

Theres an abundance of this ACE-2 receptor in cells in the lower lung, which may explain the high incidence of pneumonia and bronchitis in those with severe COVID-19 infection.

Once someone is infected, their immune systems response to that infection is likely the next big decider of their fate.

Doctors are discovering that nine or 10 days into the illness, theres a fork in the road. In most people, the immune system launches a carefully calibrated and effective response, so they recover. But in others, the immune response is too aggressive, triggering massive inflammation in whats called a cytokine storm. Immune cells are overproduced and flood into the lungs, making it hard to breathe and leading to often fatal acute respiratory distress syndrome. Those people develop sepsis, then acute kidney and heart damage. By day 20, they may be dead.

Why does the immune system misbehave? One reason may be age. As we get older, our immune response grows less accurate. It doesnt respond as effectively, and it is not as well-regulated. Genetics may also play a role.

Finally, other preexisting illnesses seem to elevate our risk, although the precise mechanisms arent known.

There may be something about these illnesses that causes them to have an abundance of ACE-2 open doors on the cell surface, Schwartz speculated.

Or perhaps the viral infection worsens the underlying diseases.

Not just the lungs

While typically considered a threat to the lungs, the virus also presents a significant threat to heart health, according to recently published research.

Cardiovascular disease, for example, is an inflammatory condition; so is COVID-19, said cardiologist Dr. Michelle A. Albert of UC San Francisco and president of the Bay Area American Heart Associations board of directors.

New research shows that the inflammatory response of a cytokine storm can lead to heart failure.

The circulating cytokines released during a severe systemic inflammatory stress can lead to atherosclerotic plaque instability and rupture. And infections can trigger an increase in myocardial demand.

Against the backdrop of existing inflammation, it could set off a cascade that results in a worsened underlying biological system, she said.

Some cancer treatments including chemotherapy, targeted therapies, immunotherapy and radiation can weaken the immune system, making a patient more vulnerable.

And if the airways of the lungs already are impaired by illnesses such as cystic fibrosis, asthma, emphysema or surgery, that person is much more susceptible to a pathogen that enters and infects the injured tissue.

People living with cystic fibrosis particularly need to be cautious because they already have compromised lung function and are susceptible to chronic infections, said Ashley Mahoney of the Cystic Fibrosis Foundation.

That likely explains the different courses of illness experienced by singer songwriter John Prine and his wife, Fiona, both infected during a recent tour in Europe. Fiona has recovered. But Prine, a survivor of lung cancer surgery, is hospitalized and critically ill.

Also at risk is anyone who must take medication to suppress their immune systems, such as organ transplant recipients.

Viral infections are always hard on people with diabetes, according to the American Diabetes Association. Thats because infection can cause the body to produce higher levels of certain hormones, such as adrenaline or cortisol, which counter the effects of insulin. Patients may develop a dangerous condition called diabetic ketoacidosis.

Patients come in all different kinds, said Monica Arima.

Some, like my husband, recover at home, without much help, she said. But I got knocked down.

More:
Why does the new coronavirus kill some people and barely affect others? - Wilkes-Barre Citizens Voice

People walk along Harajuku's famous Takeshita Street in Tokyo's Shibuya Ward, on March 28, 2020. (Mainichi/Kimi Takeuchi)

Experts in Japan have been simulating how the spread of the novel coronavirus can be tamped down, but in areas where the national government has declared a state of emergency, people's behavior must be firmly restricted, which is a task that, realistically speaking, is extremely difficult.

Akihiro Sato, a professor of data science at Yokohama City University, analyzed the numbers of 15 prefectures, including the seven where the state of emergency was declared. Based on the number of newly infected people announced by local governments, and the proportion of people who recover after being infected and showing symptoms, Sato calculated the shift in the numbers of people who were infected. Setting behavior before the period in which newly infected people increased by a large margin at 100%, Sato calculated the target percentage at which people must refrain from direct contact with others in the following two weeks for no new infections to be detected in the long term.

The results showed that in the case of Tokyo, every individual would have to cut back on the time spent on public transportation and the people they meet by 98%. For example, if one person rides on trains and buses for a total of seven hours per week, and has direct contact with a total of 100 people through work and leisure activities, that person must cut back their time on public transport to 8.4 minutes and their contact to two people per week to prevent new infections from being detected in the long term.

Fukuoka Prefecture requires the greatest behavioral restrictions, at 99.8%. Professor Sato emphasized, "Similar to evacuating from floods and tsunami, the current infection requires behavior that avoids people."

Meanwhile, Jun Ohashi, an associate professor at the University of Tokyo who specializes in human genetics, took particular note of the behavior of those infected with the new coronavirus who have symptoms and those who do not. Based on global infection data, Ohashi postulated that one person infects, on average, 2.5 people. He then calculated that in a city of 100,000 people, when there is one person who tests positive for the virus, the number of newly infected people in a day will reach 15,700 people at its peak. However, if the person who tests positive for the virus reduces their contact frequency with others by 55% of their usual behavior, newly infected people would drop to 430 people per day.

"Unless everyone, including those who are asymptomatic and those who are not infected, suppress the frequency with which they come into contact with people, the number of people who are infected will continue to rise, possibly causing the collapse of the health care system," Ohashi said. "Until we come up with vaccines and therapeutic medications, a long-term vision is essential, and it is important to change the awareness of each and every individual.

Hiroshi Nishiura, a professor specializing in theoretical epidemiology at Hokkaido University, has also calculated that if person-to-person contact can be reduced by 80%, the number of newly infected people would decline.

(Japanese original by Ryo Watanabe and Ayumu Iwasaki, Science & Medical News Department)

Follow this link:
'Behavioral suppression' needed to decrease coronavirus infections in Japan: experts - The Mainichi

The World Health Organisation (WHO), in its quest to find efficacious therapies to treat COVID-19, plans to conduct a multi-arm, multi-country clinical trial. The trials have yet to begin, but ten countries have already signed up. Only one of them, South Africa, is on the African continent.

Of course, the WHO isnt the only organisation trying to find treatments or even a vaccine for COVID-19. The United States National Institutes of Health maintains an online platform that lists all registered, ongoing clinical trials globally. On March 26, a quick search of the platform using the term coronavirus revealed 157 ongoing trials; 87 of these involve either a drug or a vaccine, while the rest are behavioural studies. Only three are registered in Africa all of them in Egypt.

This low representation of African countries in clinical trials is not unusual. Poor visibility of existing sites, limited infrastructure and unpredictable clinical trial regulatory timelines are some of the key issues hindering investments in this area.

Africas virtual absence from the clinical trials map is a big problem. The continent displays an incredible amount of genetic diversity. If this diversity is not well represented in clinical trials, the trial findings cannot be generalised to large populations.

The same goes for the outcomes of the COVID-19 studies. They too may not be relevant for people in African countries unless conducted locally. This is because responses to drugs or vaccines are complicated and can be influenced by, among other things, human genetics: different people will respond differently to different drugs and vaccines.

More countries on the African continent must urgently get involved in clinical trials so that the data collected will accurately represent the continent at a genetic level.

Time is of the essence. The usual approach, of developing site or country specific protocols, wont work. Instead, African governments need to look at ways to harmonise the response towards COVID-19 across the continent. Now, more than ever, African countries need to work together.

Centres of excellence

Africa does have clinical trial infrastructure and capabilities. But the resources remain unevenly distributed. The vast majority are in Egypt and South Africa. Thats because these countries have invested more heavily in research and development than others on the continent.

Traditionally, clinical trials are conducted at centres of excellence, which are sites that have the appropriate infrastructure and human skills necessary to conduct good quality trials. These can be located at a single university or research organisation, or work can be split between a few locations. But setting up these centres requires significant time and financial investment. Most that I am aware of on the continent have developed over the years with heavy support from external partners or sponsors. In many cases, African governments have not been involved in these efforts.

Once such centres are set up, the hard work continues to maintain these centres and to ensure theyre able to attract clinical trial sponsors. They require continuous funding, the establishment of proper institutional governance and the creation of trusted, consistent networks.

Also read: COVID-19: What Are Serological Tests, and How Can They Help India?

Usually African scientists leading clinical trial sites can apply for funding to conduct a trial; if the site is well known the scientists may be approached by a sponsor such as a pharmaceutical company interested in conducting a trial.

Clearly this approach takes time and usually benefits well-known sites or triallists. So what alternatives are available in the face of an epidemic thats moving as fast as COVID-19?

How to change direction

Key stakeholders should work together to expedite the rollout of trials in different countries. This would include inter-country collaborations such as working with different governments and scientists in co-designing trials; and providing harmonised guidelines on patient management, sample collection and tracking and sharing results in real time.

African governments, meanwhile, should provide additional funding to clinical research institutions and clinical trial sites. This would allow the sites to pull resources together and rapidly enrol patients to answer various research questions.

Because of the uneven distribution of skills and resources the continent should also adopt a hub-and-spoke model in its efforts. This would involve countries that dont have much capacity being able to ship samples easily across borders for analysis in a centralised well-equipped laboratory, which then feeds back data to the country of sample origin.

Governments should also form a task force to quickly engage with key pharmaceutical companies with drug candidates for COVID-19. This team should establish the companies appetite for collaborations in conducting relevant trials on the continent.

Through all of this, it is necessary for stakeholders to identify and address key ethical issues that may arise. Ethics should not be compromised by haste.

Beyond COVID-19

Every countrys epidemic preparedness kit should contain funds set aside for clinical trials during epidemics or pandemics.

This would require governments on the continent to evaluate their role and level of investment in the general area of clinical trials. This will augment the quality and quantity of clinical trials in the face of the constant challenge of emerging and re-emerging infectious diseases as well as a steady rise in non-communicable diseases.

On top of this, clinical trial centres, clinical research institutions and clinical triallists on the continent should strive to increase their visibility in the global space. This will make them easy to find in times of crisis, and enhance both south-south and north-south collaborations.

The African Academy of Sciences is currently building an online platform to facilitate this visibility and encourage greater collaboration.

Jenniffer Mabuka-Maroa isProgramme Manager, African Academy of Sciences.

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

Continued here:
COVID-19: Few Clinical Trials are Done in Africa. This Needs to Change ASAP. - The Wire

Sam Williams Macaw Recovery Network in Costa Rica rewilds captivity-hatched fledgling scarlet and great green macaws. But introducing young birds into a complex forest world bereft of the cultural education normally provided by parents is slow and risky.

For 30 years or so scientists have referred to the diversity of life on Earth as biological diversity, or just biodiversity. They usually define biodiversity as operating at three levels: the diversity of genes within any particular species; the diversity of species in a given place; and the diversity of habitat types such as forests, coral reefs, and so on. But does that cover it? Not really. A fourth level has been almost entirely overlooked: cultural diversity.

Culture is knowledge and skills that flow socially from individual to individual and generation to generation. Its not in genes. Socially learned skills, traditions and dialects that answer the question of how we live here are crucial to helping many populations survive or recover. Crucially, culturally learned skills vary from place to place. In the human family many cultures, underappreciated, have been lost. Culture in the other-than-human world has been almost entirely missed.

We are just recognising that in many species, survival skills must be learned from elders who learned from their elders. Until now, culture has remained a largely hidden, unrecognised layer of wild lives. Yet for many species culture is both crucial and fragile. Long before a population declines to numbers low enough to seem threatened with extinction, their special cultural knowledge, earned and passed down over long generations, begins disappearing. Recovery of lost populations then becomes much more difficult than bringing in a few individuals and turning them loose.

Many young birds learn much by observing their parents, and parrots probably need to learn more than most. Survival of released individuals is severely undermined if there are no free-living elder role models. Trying to restore parrot populations by captive breeding is not as easy as training young or orphaned creatures to recognise what is food while theyre in the safety of a cage then simply opening the door. In a cage, Williams says, you cant train them to know where, when and how to find that food, or about trees with good nest sites. Parents would normally have done exactly that.

A generational break in cultural traditions hampered attempts to reintroduce thick-billed parrots to parts of south-west America, where theyd been wiped out. Conservation workers could not teach the captive-raised parrots to search for and find their traditional wild foods, skills they would have learned from parents.

Landscapes, always complex, are under accelerated change. Culture enables adaptation far faster than genes alone can navigate hairpin turns in time. In some places, pigeons and sparrows have learned to use motion-sensors to get inside enclosed shopping malls and forage for crumbs. Crows have in some locales learned to drop nuts on the road for cars to crack. In at least one area they do this at intersections, so they can safely walk out and collect their cracked prizes when the light turns red and the cars stop. Theyve developed answers to the new question: How can we survive here, in this never-before world?

Because the answers are local, and learned from elders, wild cultures can be lost faster than genetic diversity. When populations plummet, traditions that helped animals survive and adapt to a place begin to vanish.

In a scientific article on the vocabulary of larks living in north Africa and Spain titled, Erosion of animal cultures in fragmented landscapes, researchers reported that as human development shrinks habitats into patches, isolation is associated with impoverishment. They write: Song repertoires pass through a cultural bottleneck and significantly decline in variety.

Unfortunately, isolated larks are not an isolated case. Researchers studying South Americas orange-billed sparrow found that sparrow song complexity the number of syllables per song and song length deteriorated as humans continued whittling their forests into fragments. When a scientist replayed 24-year-old recordings of singing male white-crowned sparrows at the same location shed recorded them, they elicited half the responses they had when first recorded. The birds responses show that changes in the dialect lead to changes in listener preference, a bit analogous to pop music. And as with humans, preferences can affect whether a particular bird will be accepted as a mate. White-crowned sparrows singing a local dialect become fathers of more offspring than do singers of unfamiliar dialects, indicating females prefer a familiar tune.

Im not just talking about a few songs. Survival of numerous species depends on cultural adaptation. How many? Were just beginning to ask such questions. But the preliminary answers indicate surprising and widespread ways that animals survive by cultural learning. Regionally different vocalisations are sometimes called song traditions but the more commonly used word is dialects. More than a hundred studies have been published on dialects in birds. And its not just birds but a wide array of animals Including some fish.

Cod particularly, said Steve Simpson of the University of Exeter, have very elaborate calls compared with many fish. You can easily hear differences in recorded calls of American and European Atlantic cod. This species is highly vocal with traditional breeding grounds established over hundreds or even thousands of years. Many fish follow elders to feeding, resting and breeding areas. In experiments, introduced outsiders who learned such preferred locales by following elders continued to use these traditional routes after all the original fish from whom they learned were gone.

Cultural survival skills erode as habitats shrink. Maintaining genetic diversity is not enough. Weve become accustomed to a perilous satisfaction with precariously minimal populations that not only risk genetic viability of populations but almost guarantee losing local cultural knowledge by which populations have lived and survived.

In all free-living parrots that have been studied, nestlings develop individually unique calls, learned from their parents. Researchers have described this as an intriguing parallel with human parents naming infants. Indeed, these vocal identities help individuals distinguish neighbours, mates, sexes and individuals; the same functions that human names serve.

Williams tells me that when he studied Amazon parrots, he could hear differences between them saying, essentially, Lets go, Im here, where are you? and Darling, I just brought breakfast. Researchers who develop really good ears for parrot vocalisation and use technology to study recordings show that parrot noise is more organised and meaningful than it sounds to beginners like me. In a study of budgerigars, for instance, birds who were unfamiliar with each other were placed together. Groups of unfamiliar females took a few weeks for their calls to converge and sound similar. Males copied the calls of females. Black-capped chickadees flock members calls converge, so they can distinguish members of their own flock from those of other flocks. The fact that this happens, and that it takes weeks, suggests that free-living groups must normally be stable, that groups have their own identity, and that the members identify with their group.

Group identity, we see repeatedly, is not exclusively human. Sperm whales learn and announce their group identity. Young fruit bats learn the dialects of the crowds theyre in. Ravens know whos in, whos out. Too many animals to list know what group, troop, family or pack they belong with. In Brazil, some dolphins drive fish toward fishermens nets for a share of the catch. Other dolphins dont. The ones who do, sound different from the ones who dont. Various dolphin groups who specialise in a food-getting technique wont socialise with other groups who use different techniques. And orca whales, the most socially complex non-humans, have layered societies of pods, clans and communities, with community members all knowing the members of all their constituent pods, but each community scrupulously avoiding contact with members of another community. All this social organisation is learned from elders.

Elders appear important for social learning of migratory routes. Various storks, vultures, eagles and hawks all depend on following the cues of elders to locate strategic migration flyways or important stopover sites. These could be called their migration cultures. Famously, conservationists have raised young cranes, geese and swans to follow microlight aircraft as a surrogate parent on first migrations. Without such enculturation, they would not have known where to go. The young birds absorbed knowledge of routes, then used them in later seasons on their own self-guided migrations. Four thousand species of birds migrate, so Andrew Whiten of the University of St Andrews in Scotland speculates that following experienced birds may be an underappreciated but very significant realm of cultural transmission.

When you look at free-living animals, you dont usually see culture. Culture makes itself visible when it gets disrupted. Then we see that the road back to reestablishing cultures the answers to the questions of how we live in this place is difficult, often fatal.

Young mammals too moose, bison, deer, antelope, wild sheep, ibex and many others learn crucial migration routes and destinations from elder keepers of traditional knowledge. Conservationists have recently reintroduced large mammals in a few areas where theyve been wiped out, but because animals released into unfamiliar landscapes dont know where food is, where dangers lurk, or where to go in changing seasons, many translocations have failed.

Williams describes his procedure with the macaws as very much a slow release. First his team trains the birds to use a feeder. With that safety net, they can explore the forest, gain local knowledge, begin dispersing and using wild foods.

Some rescue programmes declare success if a released animal survives one year. A year is meaningless for a bird like a macaw that doesnt mature until its eight years old, says Williams.

I ask what theyre doing for those eight long years.

Social learning, Williams replies immediately. Working out whos who, how to interact, like kids in school.

To gain access to the future, to mate and to raise young, the birds Williams is releasing must enter into the culture of their kind. But from whom will they learn, if no one is out there? At the very least they must be socially oriented to one another. Ex-pets are the worst candidates for release; they dont interact appropriately with other macaws, and they want to hang around near humans.

To assess the social abilities of 13 scarlet macaws who were scheduled for release, Williams and his crew documented how much time they spent close to another bird, how often they initiated aggression, things like that. When the bird scoring lowest for social skills was released, he flew out the door and was never seen again. The next-to-lowest didnt adapt to the free-living life and had to be retrieved. The third-lowest social scorer remained at liberty but stayed alone a lot. The rest did well.

All of the above adds up to this: a species isnt just one big jar of jellybeans of the same colour. Its different smaller jars with differing hues in different places. From region to region, genetics can vary. And cultural traditions can differ. Different populations might use different tools, different migration routes, different ways of calling, courting and being understood. All populations have their answers to the question of how to live where they live.

Sometimes a group will be foraging in a tree, Williams says. A pair will fly overhead on a straight path. Someone will make a contact call, and the flying birds will loop around and land with the callers. They seem to have their friends. Bottom line, said Williams, there is much going on in the social and cultural lives of his macaws and other species, much that they understand but we dont. We have a lot of questions. The answers must lurk, somewhere, in their minds.

As land, weather and climate change, some aspects of cultural knowledge will be the tickets necessary for boarding the future. Others will die out. Across the range of chimpanzees, cultures vary greatly, as do habitats. All populations but one use stick tools. Some use simple probes, others fashion multi-stick toolsets. Only one population makes pointed daggers for hunting small nocturnal primates called bush-babies hiding in tree holes. Only the westernmost chimpanzees crack nuts with stones.

As researchers have noted, distinctive tool-using traditions at particular sites are defining features of unique chimpanzee cultures. Whiten wrote: Chimpanzee communities resemble human cultures in possessing suites of local traditions that uniquely identify them A complex social inheritance system that complements the genetic picture.

Some chimpanzee populations have learned to track the progress of dozens of specific trees ripening in their dense forests. Others live in open semi-savannah. Some are more aggressively male-dominated, some populations more egalitarian. Some almost never see people; some live in sight of human settlements and have learned to crop-raid at night. For a long, long time chimpanzees have been works in progress. Weve learned, writes Craig Stanford, not to speak of The Chimpanzee. Chimpanzees vary and chimpanzee culture is variable at every level.

Its not just the loss of populations of chimps that worries me, Cat Hobaiter emphasised when I spent several weeks with her studying chimpanzees in Uganda. I find terrifying the possibility of losing each populations unique culture. Thats permanent.

Diversity in cultural pools perhaps more crucially than in gene pools will make species survival more likely. If pressures cause regional populations to blink out, a species odds of persisting dim.

Williams goal is to re-establish macaws where they range no longer, in hopes that they, and their forests, will recover. (Most of the central American forests that macaws need have been felled and burned, largely so fast-food burger chains can sell cheap beef.) It often takes a couple of generations for human immigrant families to learn how to function effectively in their new culture; it may take two or three generations before an introduced population of macaws succeeds. In other words, macaws are born to be wild. But becoming wild requires an education.

So whats at stake is not just numbers. Whats at stake is: ways of knowing how to be in the world. Culture isnt just a boutique concern. Cultural knowledge is what allows many populations to survive. Keeping the knowledge of how to live in a habitat can be almost as important to the persistence of a species as keeping the habitat; both are needed. Cultural diversity itself is a source of resilience and adaptability to change. And change is accelerating.

This is an edited extract from Becoming Wild: How Animals Learn to be Animals by Carl Safina, which published in the UK by Oneworld on 9 April and in the US by Henry Holt and Co on 14 April

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The secret call of the wild: how animals teach each other to survive - The Guardian

A new study into badger genetics has shown those from thenorth-eastern and south-eastern counties of Ireland share genetics with badgers in Britain.

The study, just published in the journal Royal Society Open Science, was carried out by scientists from the Agri-food and Biosciences Institute (AFBI) in Northern Ireland and suggests people may have played a role in bringing badgers to Ireland.

The team worked with colleagues from the Department of Agriculture, Food and the Marine and the Waterford Institute of Technology in the Republic of Ireland, to assemble a larger, island-wide set of 545 badger samples.

Badgers from the island of Ireland have previously been the subject of several genetic studies which compared their heritage to those of badgers from other European countries.

However, previous studies were based on small numbers of animals from only a few Irish locations. The extent of the influence of British animals on the Irish population, and the timing and mechanism of any potential import events remained unclear.

Ireland has fewer mammal species than Britain and continental European neighbours because of its geological history.

Ireland became an island around 15,000 years ago, at a time when glaciers were retreating from northern Europe, permitting recolonisation by animals that had retreated to more temperate, southern climes at the height of the last ice age.

Consequently, natural colonisation routes for animals into Ireland were barred for all but those species that could fly.

As a result, how Ireland came to acquire the fauna it possesses in modern times, is one of the great puzzles of modern biology.

These revealed that Irish badgers had a mixed genetic profile sharing similarities with animals from Britain and Scandinavia and suggesting they may have been moved from those territories into Ireland by human agency.

The new study by AFBI looked into a much bigger sample size than typical before. Aside from the 545 local samples, collaborators at the Universities of Glasgow, Oxford and Exeter and the Animal and Plant Health Agency (APHA) provided a further 91 samples from badgers from Britain.

The population genetic analyses revealed that badgers with British genetic heritage are localised in north-eastern and south-eastern counties in Ireland and that human-aided import of badgers from Great Britain, around 700 years ago, is the most probable explanation.

Although anecdotal, it is notable that humans from these same regions in Ireland also exhibit genetic and genealogical links to Great Britain, an observation thought to result from the Plantations of Ireland that occurred in the 13th and 16th centuries.

The findings improve scientists knowledge of how Irelands modern mammal populations have been formed as well as the population structure of badgers in Ireland.

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Study suggests humans transported badgers from Britain to Ireland - Agriland

An opinion piece published on Livemint by Sandipan Deb claimed that COVID-19 will not affect Indians as they have the genetics for a sturdier immune system.

When questioned on Twitter, the author, also a founder of Swarajya Magazine, cited a Nature Asia article titled, More immunity in Indian genes, as his source.

The Nature Asia article (2008), based on the research study by Du and colleagues (2008), published in the journal Genes & Immunity was conducted by a team of scientists from the University of California in Los Angeles (UCLA), USA, All India Institute of Medical Sciences, India (AIIMS), and National Marrow Donor Program (NMDP), USA.

More immunity in Indian genes The title of Nature Asia magazine article.

Our bodies have one of the toughest immune systems in the world. We have grown up surrounded by so much filth and pollution that our natural resilience is much stronger than people in the developed world. Sandipan Deb in Livemint.

False.

1. The Livemint article is based on a superficial understanding of the title of the Nature Asia, not its text.

The Nature Asia article is titled More immunity genes in Indians. However, the article itself does not make any such claims that, on the basis of the research study quoted, that Indians will be protected from the coronavirus pandemic or other infections due to their biologically inherited resilience. It simply states that Indians may have more genes linked with immunity as per the data. Also, one of the authors of the article and the research study Rajalingam Raja wrote, Whether having more activating KIR genes is an advantage or disadvantage for Indians remains to be elucidated.

This means that the genes tested through this study are not a piece of conclusive evidence that the contested tougher immunity will be an advantage for Indians in any way.

2. The Nature Asia article is based on a research study based on a single gene polymorphism in various ethnicities.

The Nature Asia article is based on a research study which relies upon a single gene KIR2DL5 polymorphism in many ethnicities including Indian, East Asian, white (Caucasian) and black (African Americans), suggesting that the gene is not unique to Indians only. Also, no evidence suggests that the presence of gene translates to gene expression or phenotypic change (e.g. higher immunity) in this case.

Nature Asia article based its claim on a gene polymorphism study by Du and colleagues (2008). Genetic polymorphism is the occurrence of multiple forms of a single gene which is expressed in the same population as a trait or a phenotype (Bull, 2004). It is similar, but not the same, as varying levels of pigmentation in eyes, hair or skin colour.

The study quoted showed the nature of polymorphism of one gene KIR2DL5 in four ethnic groups: Caucasians (European race, mostly white), Asian-Indians (South Asians), African-Americans and Asians (East Asians, i.e. Korean, Vietnamese, Japanese and Filipino).

KIR2DL5 (or CD158f) is the last identified KIR gene (the inhibitory receptor expressed on the surface of immune cells), with KIR2DL4, it makes up a structurally divergent lineage conserved in different primate species such as humans. The percentage frequency of this KIR2DL5 gene in Indians is used as an indicator of higher immunity.

The graph from the research study illustrates that the percentage frequency of KIR2DL5 (A and B, polymorphic forms of KIR2DL5 gene) is higher in Asian Indians than the other ethnic populations studied. However, the graph below from the same study suggests that the Individuals carrying the KIR2DL5 gene vary substantially among populations ranging in frequency from 35-85%. Thus, as per the authors conclusions, higher immunity can be found in every ethnicity ranging from 35-85% population, not just in Indians.

Hence, with such large variability in genes in each population, it is impossible to deduce that the researchers certainly found the KIR2DL5 gene more frequently in Indian ethnicities, as compared to other ethnicities.

Also, the research paper doesnt claim that this higher frequency in Asian-Indians population is linked to a better immune system or more natural killer cells in the body. In fact, there are no conclusions drawn on any ethnic group being genetically superior or inferior regarding immunity.

3. Is the occurrence of genes (KIR2DL5 gene) linked with immunity synonymous with its traits (tougher immunity)?

The occurrence of more genes in a population isnt always synonymous with better traits. This is mainly because a greater amount of genes doesnt always translate to a protein abundance, which consequently becomes a trait. That is, the presence of genes doesnt always lead to the presence of characteristic traits related to the expression of the gene.

Sometimes, polymorphic changes in natural killer cells can also be associated with a susceptibility towards certain diseases (Orange, 2002). Thus, more correlative studies should be conducted where a higher frequency of KIR2DL5 gene results in an increased immunity regardless of ethnicity.

4. Smaller sample size

The beneficial effects of higher frequency of a polymorphic gene in a population can only be established after detailed protein, genomics and evolutionary studies with large sample size. But in this study, only 96 Indian genomes were studied as opposed to 250 Caucasians. Hence, these higher percent frequencies of polymorphs KIR2DL5 gene could also be an artefact resulting from a smaller sample size.

Only 96 non-randomised samples for the Asian-Indian group were sourced from New Delhi, which is a minuscule representation for the Indian population. These sample sizes were further reduced after identification of KIR2DL5 positive individuals.

Also, the Nature Asia article further claims that Indians gained the activating KIR (killer cell immunoglobulin-like receptors) genes because of natural selection to survive the environmental challenges during their pre-historic coastal migrations from Africa. This conclusion is not based on any evidence.

Dr Mehra, former Dean of AIIMS, in his opinion piece in The Print mentions the results from the same study that includes SK Sharma of AIIMS, to make his claims about the genetic advantage of Indians over Caucasians with respect to immunity against the coronavirus. Additionally, Dr Mehra also included other factors that may give Indians advantage broad-based immunity due to overexposure to other pathogens, and epigenetic factors such as environment and consumption of Indian spices in cuisine. However, since the novelty of the virus and the increasing pathogenesis of SARS-CoV-2 in India, these claims remain without any research or evidence in Science.

The Nature Asia article published a misleading title on the basis of a genetics study which was termed inconclusive by the authors in their own research study. This title formed the basis of the Livemint article by Mr Deb.

The Nature Asia authors generalised their misleading article about Natural Killer cells (NK) to immunity genes. Natural killer cells are a small component of what makes up human immunity, not the expansive immune system.

Later, in the Livemint article, the Nature Asia article was used to claim a blanket superiority of the immune system of Indians. Mr Deb stated that Indians immune system is more robust than the people in the developed world to tackle the coronavirus pandemic.

Such dangerous opinion pieces with no understanding of the genetics of immunity have the potential to drive people to be careless with the protocols issued by the government on social distancing and other precautions or to encourage reckless behaviour during a critical situation.

Du, Z., Sharma, S. K., Spellman, S., Reed, E. F., & Rajalingam, R. (2008). KIR2DL5 alleles mark certain combination of activating KIR genes. Genes & Immunity, 9(5), 470-480.

Bull, L. (2004). Genetics, Mutations, and Polymorphisms. Molecular Pathogenesis of Cholestasis, 77-95.

Estefana, E., Flores, R., Gmez-Lozano, N., Aguilar, H., Lpez-Botet, M., & Vilches, C. (2007). Human KIR2DL5 is an inhibitory receptor expressed on the surface of NK and T lymphocyte subsets. The Journal of Immunology, 178(7), 4402-4410.

Orange, J. S. (2002). Human natural killer cell deficiencies and susceptibility to infection. Microbes and infection, 4(15), 1545-1558.

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Indians do not have genetic protection against coronavirus, published research incorrectly interpreted - Alt News

A patient in Italy receives intensive care for COVID-19. Human geneticists are coming together to look for genes that make some people more vulnerable to the disease.

By Jocelyn KaiserMar. 27, 2020 , 3:25 PM

Sciences COVID-19 reporting is supported by the Pulitzer Center.

COVID-19, caused by the new pandemic coronavirus, is strangelyand tragicallyselective. Only some infected people get sick, and although most of the critically ill are elderly or have complicating problems such as heart disease, some killed by the disease are previously healthy and even relatively young. Researchers are now gearing up to scour the patients genomes for DNA variations that explain this mystery. The findings could be used to identify those most at risk of serious illness and those who might be protected, and they might also guide the search for new treatments.

The projects range from ongoing studies with DNA for many thousands of participants, some now getting infected with the coronavirus, to new efforts that are collecting DNA from COVID-19 patients in hard-hit places such as Italy. The goal is to compare the DNA of people who have serious cases of COVID-19 (which stands for coronavirus disease 2019)but no underlying disease like diabetes, heart or lung diseasewith those with mild or no disease. We see huge differences in clinical outcomes and across countries. How much of that is explained by genetic susceptibility is a very open question, says geneticist Andrea Ganna of the University of Helsinkis Institute for Molecular Medicine Finland (FIMM).

Its hard to predict what will pop out from these gene hunts, some researchers say. But there are obvious suspects, such as the gene coding for the cell surface protein angiotensin-converting enzyme 2 (ACE2), which the coronavirus uses to enter airway cells. Variations in the ACE2 gene that alter the receptor could make it easier or harder for the virus to get into cells, says immunologist Philip Murphy of the National Institute of Allergy and Infectious Diseases, whose lab identified a relatively common mutation in another human cell surface protein, CCR5, that makes some people highly resistant to HIV.

Ganna heads up a major effort to pool COVID-19 patients genetic data from around the world. The idea came quite spontaneously about 2 weeks ago when everyone was sitting at their computers watching this crisis, says Ganna, who is also affiliated with the Broad Institute, a U.S. genomic powerhouse.

He and FIMM Director Mark Daly quickly created a website for their project, the COVID-19 Host Genetics Initiative, and reached out to colleagues who run large biobank studies that follow thousands of volunteers for years to look for links between their DNA and health. At least a dozen biobanks, mostly in Europe and the United States, have expressed interest in contributing COVID-19 data from participants who agreed to this. Among them are FinnGen, which has DNA samples and health data for 5% of the 5 millionperson Finnish population, and the 50,000-participant biobank at the Icahn School of Medicine at Mount Sinai.

The UK Biobank, one of worlds largest with DNA data for 500,000 participants, also plans to add COVID-19 health data from participants to its data set, the project tweeted this month. And the Icelandic company deCODE Genetics, which is helping test much of the nations population to see who is infected with the new coronavirus, has received government permission to add these data and any subsequent COVID-19 symptoms to its database, which contains genome and health data on half of Icelands 364,000 inhabitants, says its CEO Kri Stefnsson. We will do our best to contribute to figuring this out, Stefnsson says.

Another effort to identify protective or susceptibility DNA variants is the Personal Genome Project led by Harvard Universitys George Church, which recruits people willing to share their full genome, tissue samples, and health data for research. Earlier this month, it sent questionnaires to its thousands of participants, asking about their COVID-19 status. More than 600 in the United States responded within 48 hours. It seems that most people want to do their part, says Church, whose group isnt yet part of Gannas collaboration.

Other researchers working with Gannas initiative are recruiting COVID-19 patients directly within hospitals for such genomics studies. Italian geneticist Alessandra Renieri of the University of Siena expects at least 11 hospitals in the nation to give ethics approval for her team to collect DNA samples from willing patients. It is my opinion that [host] genetic differences are a key factor for susceptibility to severe acute pneumonia, Renieri says.

Pediatrics researcher Jean-Laurent Casanova at the Rockefeller University, who specializes in identifying rare genes that can make healthy young people susceptible to certain serious diseases, is drawing on a network of pediatricians around the world to look for the relatively few young people who develop COVID-19 serious enough to get admitted to intensive care. We study exclusively patients who were previously healthy and under 50, as their serious COVID-19 illness is more likely to have a genetic basis, he explains.

In addition to genetic variants of the ACE2 receptor, scientists want to see whether differences in the human leukocyte antigen genes, which influence the immune systems response to viruses and bacteria, affect disease severity. And some investigators want to follow up a finding, which a Chinese team reported in a preprint: that people with type O blood may be protected from the virus. Were trying to figure out if those findings are robust, says Stanford University human geneticist Manuel Rivas, who is contributing to Gannas initiative.

The catastrophic spread of the coronavirus should soon increase the number of COVID-19 patients available to these gene hunts. And that could speed findings. Ganna expects the first susceptibility genes could be identified within a couple of months.

With reporting by Elizabeth Pennisi.

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How sick will the coronavirus make you? The answer may be in your genes - Science Magazine