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Geneticists reverse engineer DNA of the first black Icelander, who left no remains
Scientists can now virtually reconstruction certain long-dead individuals, without the need for DNA samples from physical remains.
It’s no wonder Iceland is a country obsessed by genealogy.
The majority of its 330,000 inhabitants descend from a small group of Vikings and Celts who settled some 1,100 years ago, and immigration to the island country has been rare ever since. Icelanders keep exceptional genealogical records on almost every single citizen, a longstanding practice done partly out of ancestral reverence, but also to avoid the very real possibility of bedding down with a not-too-distant relative.
Case in point: In 2013, a group of engineering students at the University of Iceland released an incest prevention app that lets users tap their phones together to see if they share a common ancestor. Its slogan? “Bump in the app before you bump in bed.”
The country’s genealogical records can be found in the Islendingabok, “the book of Icelanders,” which contains detailed genealogical information for about 95 percent of Icelanders who have lived over the past three centuries. It’s this database and the country’s unique demographic history that have made Iceland ideal for genetics research.
deCODE, an Icelandic genetics firm, has for years been using the genealogical records to study how genetic mutations can affect people’s chances of having everything from cancer to blond hair. Most recently, the firm used the records, along with well-known DNA markers, to reconstruct a substantial part of the genome of an 18th-century man.
“To our knowledge, this study demonstrates the first use of genotype data from contemporary individuals, along with information about their genealogical relationships, to reconstruct a sizeable portion of the genome from a single ancestor born more than 200 years ago,” the team wrote in an article published in Nature.
The reconstructed genome belonged to Hans Jonatan, a mixed-race man who escaped slavery in 1802 by sailing to Iceland where he was accepted “with open arms,” as Kári Stefánsson of deCODE told New Scientist. Before his death in 1827, Jonatan married an Icelandic woman and raised two children, marking the introduction of African DNA into the country’s gene pool.
“There was no African ancestry in Iceland, apart from Hans Jonatan, prior to around 1920,” Stefánsson told New Scientist.
Lúðvík Lúðvíksson, grandchild of Hans Jonatan. Credit: Helga Tomasdottir
To reconstruct part of Jonatan’s genome sequence, the team identified 182 of his living descendants in Iceland and searched their genetic code for well-known African DNA markers, under the assumption that these bits of DNA could have only been inherited from Jonatan. The researchers found in the descendants 593 fragments of African DNA that they used to re-create 38 percent of Jonatan’s mother’s genome, which represents 19 percent of his own. They also were able to determine that his mother’s family likely originated from the African countries of Benin, Cameroon, or Nigeria.
Diagram representing Jonatan's descendants.
“Ancestor genome reconstruction of this kind can be viewed as a virtual ancient DNA study, whereby genotype information is retrieved from a long-dead individual without the need for DNA samples from physical remains,” the team wrote.
There are a few of proposals of what “virtual ancient DNA” might be used for in the future.
“It’s the sort of study that could, for instance, be used to recover genomes of explorers who had interbred with isolated native communities,” Robin Allaby, a biologist at the University of Warwick, told Futurism.
Agnar Helgason of deCODE said in the same piece that scientists could use the process to reconstruct the genome of “any historic figure born after 1500 who has known descendants” —noting the year 1500 due to lack of genealogical information and because the expected genetic contribution of an ancestor to a single descendant is very small after 10 generations.
The team also suggested genome reconstruction could be used by medical researchers “in cases where valuable phenotype data is available for ancestors who can no longer be sampled for DNA and directly genotyped.”
In any case, the team wrote, the study highlights the ongoing genetic story “of a resourceful refugee from the Danish transatlantic slave trade, who was able to prosper in a culturally homogeneous and insular community of early-nineteenth-century Icelanders.”
Innovation in manufacturing has crawled since the 1950s. That's about to speed up.
Health officials in China reported that a man was infected with bubonic plague, the infectious disease that caused the Black Death.
- The case was reported in the city of Bayannur, which has issued a level-three plague prevention warning.
- Modern antibiotics can effectively treat bubonic plague, which spreads mainly by fleas.
- Chinese health officials are also monitoring a newly discovered type of swine flu that has the potential to develop into a pandemic virus.
Bacteria under microscope
needpix.com<p>Today, bubonic plague can be treated effectively with antibiotics.</p><p style="margin-left: 20px;">"Unlike in the 14th century, we now have an understanding of how this disease is transmitted," Dr. Shanthi Kappagoda, an infectious disease physician at Stanford Health Care, told <a href="https://www.healthline.com/health-news/seriously-dont-worry-about-the-plague#Heres-how-the-plague-spreads" target="_blank">Healthline</a>. "We know how to prevent it — avoid handling sick or dead animals in areas where there is transmission. We are also able to treat patients who are infected with effective antibiotics, and can give antibiotics to people who may have been exposed to the bacteria [and] prevent them [from] getting sick."</p>
This plague patient is displaying a swollen, ruptured inguinal lymph node, or buboe.
Centers for Disease Control and Prevention<p>Still, hundreds of people develop bubonic plague every year. In the U.S., a handful of cases occur annually, particularly in New Mexico, Arizona and Colorado, <a href="https://www.cdc.gov/plague/faq/index.html" target="_blank">where habitats allow the bacteria to spread more easily among wild rodent populations</a>. But these cases are very rare, mainly because you need to be in close contact with rodents in order to get infected. And though plague can spread from human to human, this <a href="https://www.healthline.com/health-news/seriously-dont-worry-about-the-plague#Heres-how-the-plague-spreads" target="_blank">only occurs with pneumonic plague</a>, and transmission is also rare.</p>
A new swine flu in China<p>Last week, researchers in China also reported another public health concern: a new virus that has "all the essential hallmarks" of a pandemic virus.<br></p><p>In a paper published in the <a href="https://www.pnas.org/content/early/2020/06/23/1921186117" target="_blank">Proceedings of the National Academy of Sciences</a>, researchers say the virus was discovered in pigs in China, and it descended from the H1N1 virus, commonly called "swine flu." That virus was able to transmit from human to human, and it killed an estimated 151,700 to 575,400 people worldwide from 2009 to 2010, according to the Centers for Disease Control and Prevention.</p>There's no evidence showing that the new virus can spread from person to person. But the researchers did find that 10 percent of swine workers had been infected by the virus, called G4 reassortant EA H1N1. This level of infectivity raises concerns, because it "greatly enhances the opportunity for virus adaptation in humans and raises concerns for the possible generation of pandemic viruses," the researchers wrote.
So far, 30 student teams have entered the Indy Autonomous Challenge, scheduled for October 2021.
- The Indy Autonomous Challenge will task student teams with developing self-driving software for race cars.
- The competition requires cars to complete 20 laps within 25 minutes, meaning cars would need to average about 110 mph.
- The organizers say they hope to advance the field of driverless cars and "inspire the next generation of STEM talent."
Indy Autonomous Challenge<p>Completing the race in 25 minutes means the cars will need to average about 110 miles per hour. So, while the race may end up being a bit slower than a typical Indy 500 competition, in which winners average speeds of over 160 mph, it's still set to be the fastest autonomous race featuring full-size cars.</p><p style="margin-left: 20px;">"There is no human redundancy there," Matt Peak, managing director for Energy Systems Network, a nonprofit that develops technology for the automation and energy sectors, told the <a href="https://www.post-gazette.com/business/tech-news/2020/06/01/Indy-Autonomous-Challenge-Indy-500-Indianapolis-Motor-Speedway-Ansys-Aptiv-self-driving-cars/stories/202005280137" target="_blank">Pittsburgh Post-Gazette</a>. "Either your car makes this happen or smash into the wall you go."</p>
Illustration of the Indy Autonomous Challenge
Indy Autonomous Challenge<p>The Indy Autonomous Challenge <a href="https://www.indyautonomouschallenge.com/rules" target="_blank">describes</a> itself as a "past-the-post" competition, which "refers to a binary, objective, measurable performance rather than a subjective evaluation, judgement, or recognition."</p><p>This competition design was inspired by the 2004 DARPA Grand Challenge, which tasked teams with developing driverless cars and sending them along a 150-mile route in Southern California for a chance to win $1 million. But that prize went unclaimed, because within a few hours after starting, all the vehicles had suffered some kind of critical failure.</p>
Indianapolis Motor Speedway
Indy Autonomous Challenge<p>One factor that could prevent a similar outcome in the upcoming race is the ability to test-run cars on a virtual racetrack. The simulation software company Ansys Inc. has already developed a model of the Indianapolis Motor Speedway on which teams will test their algorithms as part of a series of qualifying rounds.</p><p style="margin-left: 20px;">"We can create, with physics, multiple real-life scenarios that are reflective of the real world," Ansys President Ajei Gopal told <a href="https://www.wsj.com/articles/autonomous-vehicles-to-race-at-indianapolis-motor-speedway-11595237401?mod=e2tw" target="_blank">The Wall Street Journal</a>. "We can use that to train the AI, so it starts to come up to speed."</p><p>Still, the race could reveal that self-driving cars aren't quite ready to race at speeds of over 110 mph. After all, regular self-driving cars already face enough logistical and technical roadblocks, including <a href="https://www.bbc.com/news/technology-53349313#:~:text=Tesla%20will%20be%20able%20to,no%20driver%20input%2C%20he%20said." target="_blank">crumbling infrastructure, communication issues</a> and the <a href="https://bigthink.com/paul-ratner/would-you-ride-in-a-car-thats-programmed-to-kill-you" target="_self">fateful moral decisions driverless cars will have to make in split seconds</a>.</p>But the Indy Autonomous Challenge <a href="https://static1.squarespace.com/static/5da73021d0636f4ec706fa0a/t/5dc0680c41954d4ef41ec2b2/1572890638793/Indy+Autonomous+Challenge+Ruleset+-+v5NOV2019+%282%29.pdf" target="_blank">says</a> its main goal is to advance the industry, by challenging "students around the world to imagine, invent, and prove a new generation of automated vehicle (AV) software and inspire the next generation of STEM talent."
A new Harvard study finds that the language you use affects patient outcome.
- A study at Harvard's McLean Hospital claims that using the language of chemical imbalances worsens patient outcomes.
- Though psychiatry has largely abandoned DSM categories, professor Joseph E Davis writes that the field continues to strive for a "brain-based diagnostic system."
- Chemical explanations of mental health appear to benefit pharmaceutical companies far more than patients.
Challenging the Chemical Imbalance Theory of Mental Disorders: Robert Whitaker, Journalist<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="41699c8c2cb2aee9271a36646e0bee7d"><iframe type="lazy-iframe" data-runner-src="https://www.youtube.com/embed/-8BDC7i8Yyw?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>This is a far cry from Howard Rusk's 1947 NY Times editorial calling for mental healt</p><p>h disorders to be treated similarly to physical disease (such as diabetes and cancer). This mindset—not attributable to Rusk alone; he was merely relaying the psychiatric currency of the time—has dominated the field for decades: mental anguish is a genetic and/or chemical-deficiency disorder that must be treated pharmacologically.</p><p>Even as psychiatry untethered from DSM categories, the field still used chemistry to validate its existence. Psychotherapy, arguably the most efficient means for managing much of our anxiety and depression, is time- and labor-intensive. Counseling requires an empathetic and wizened ear to guide the patient to do the work. Ingesting a pill to do that work for you is more seductive, and easier. As Davis writes, even though the industry abandoned the DSM, it continues to strive for a "brain-based diagnostic system." </p><p>That language has infiltrated public consciousness. The team at McLean surveyed 279 patients seeking acute treatment for depression. As they note, the causes of psychological distress have constantly shifted over the millennia: humoral imbalance in the ancient world; spiritual possession in medieval times; early childhood experiences around the time of Freud; maladaptive thought patterns dominant in the latter half of last century. While the team found that psychosocial explanations remain popular, biogenetic explanations (such as the chemical imbalance theory) are becoming more prominent. </p><p>Interestingly, the 80 people Davis interviewed for his book predominantly relied on biogenetic explanations. Instead of doctors diagnosing patients, as you might expect, they increasingly serve to confirm what patients come in suspecting. Patients arrive at medical offices confident in their self-diagnoses. They believe a pill is the best course of treatment, largely because they saw an advertisement or listened to a friend. Doctors too often oblige without further curiosity as to the reasons for their distress. </p>
Image: Illustration Forest / Shutterstock<p>While medicalizing mental health softens the stigma of depression—if a disorder is inheritable, it was never really your fault—it also disempowers the patient. The team at McLean writes,</p><p style="margin-left: 20px;">"More recent studies indicate that participants who are told that their depression is caused by a chemical imbalance or genetic abnormality expect to have depression for a longer period, report more depressive symptoms, and feel they have less control over their negative emotions."</p><p>Davis points out the language used by direct-to-consumer advertising prevalent in America. Doctors, media, and advertising agencies converge around common messages, such as everyday blues is a "real medical condition," everyone is susceptible to clinical depression, and drugs correct underlying somatic conditions that you never consciously control. He continues,</p><p style="margin-left: 20px;">"Your inner life and evaluative stance are of marginal, if any, relevance; counseling or psychotherapy aimed at self-insight would serve little purpose." </p><p>The McLean team discovered a similar phenomenon: patients expect little from psychotherapy and a lot from pills. When depression is treated as the result of an internal and immutable essence instead of environmental conditions, behavioral changes are not expected to make much difference. Chemistry rules the popular imagination.</p>