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With Ancient Human DNA, Africa’s Deep History Is Coming to Light

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ancient african dna

Ancient DNA can reveal much about the genetic history of Africa because it predate major events like slavery and colonialism, which upended African populations and territories. (Credit: Zita/shutterstock)

In 2010, extraordinary circumstances allowed geneticists to reconstruct the first full genome of an ancient human: the DNA came from a hairball, frozen 4,000 years in Greenland soil. Since then, methods have improved so much in cost and efficiency that individual papers now report genomic data from hundreds of dead people (here, here, here). Ancient DNA (aDNA) has now been published from well over 2,000 human ancestors, stretching as far back as 430,000 years ago.

But around 70 percent of those sequences are from Eurasia, where cold temperatures favor DNA preservation and considerable archaeological research has occurred. For researchers interested in the genetic history of Europe and Asia, there are plenty of excavated skeletons, sitting in museums and other collections, and there’s a good chance those bones hold appreciable DNA.

The situation is different in Africa — the place where Homo sapiens originated some 300,000 years ago and has continued diversifying ever since. Despite Africa’s prominence in the human story, so far only 30 ancient genomes between 300 and 15,000 years old have been published from the continent.

Part of the reason is methodological and environmental: Hot, humid conditions destroy DNA in human remains, long before geneticists attempt to extract it. However, in 2015 scientists showed that aDNA preservation can be 100-fold higher in the petrous — dense bone surrounding the inner ear — than other skeletal parts. In 2018, researchers used this bone to recover the oldest African genomes yet, from 15,000-year-old skeletons excavated from a cave in Morocco.

It’s unlikely geneticists will capture much older African DNA than that. So, the petrous find is a “game changer,” not a miracle maker. But bones between 5,000 and 15,000 years old — surrounding the start of the Holocene, our current geologic epoch — can reveal much about the genetic history of Africa. That’s because they predate major events that upended African populations and territories. These include the slave trade and colonialism. Earlier still, there were major migrations within Africa linked to the spread of herders and farmers, starting around 5,000 years ago.

“What we see is this huge amount of noise from the past 5,000 years,” says Elizabeth Sawchuk, an archaeologist who works in East Africa.

DNA from Holocene remains would allow researchers to peer beyond this noise, to glimpse the genetic map of Africa prior to agriculture and historical migrations. And now, it’s technologically possible.

Yet there’s reason to pause, as ancient DNA studies receive criticism. Archaeologists and historians accuse geneticists of making sweeping claims based solely on DNA data, without considering the centuries of evidence and scholarship accumulated by other fields. Ethical concerns have also been raised about taking skeletal samples out of Africa and into Western laboratories for the destructive process of genetic sequencing. Moreover, the results may fuel ancestry claims over territories or cultural heritage, and therefore affect living people who did not consent to the research.

In this context, some scientists are proceeding with caution, and a number of African aDNA projects are underway. One of the largest is led by Sawchuk, archaeologist Mary Prendergast and geneticist David Reich, who runs the aDNA laboratory at Harvard Medical School.

Discover talked to Sawchuk, a post-doctoral researcher at Stony Brook University, about the potential risks and rewards of African aDNA.

Why is African aDNA important?

It’s where our species evolved, where we’ve been the longest. And as a consequence, Africa has the highest genetic diversity of anywhere else on the planet. It potentially is going to tell us the most about our species, but it’s an area that we know the least about.

Why is that?

Largely because of underfunded research. Africa is very expensive to go to. The continent is humongous. Areas are inaccessible for geographical, environmental and political reasons. As a result there are fewer skeletons and archaeological sites identified for this huge area and huge period of time. [Also aDNA] preservation is bad because high heat, humidity and water destroy the organic content of bones. Getting aDNA out of this continent was regarded to be something we would all love to do, but nobody could do.

Now that it’s technologically feasible, why should researchers be cautious?

Human remains are the only direct link we have to the past. We have far fewer skeletons in Africa than other parts of the world, so every skeleton is incredibly precious. That puts a really big burden on these genetics projects in terms of how much material they’re sampling, how many sites they’re sampling, if they’re sampling all of the sites.

There’s a fundamental tension: You don’t know which skeletons and sites will have aDNA preserved, so you just have to try them all. But if we try them all now, in 5 years, 10 years, 15 years, 50 years, the science might be completely different, and we may have limited ourselves in the future. So it’s a tight line to walk.

What are some concerns of present-day Africans?

Across a continent as big of Africa, [countries] with individual, imposed colonial histories have very different ways of approaching their own national heritage. Transporting material outside of Africa to a clean room — so we can minimize contamination and maximize the chance of getting a sequence — that kind of parallels a lot of the colonial justifications for removing artifacts out of their countries of origin to better funded European or American institutions. So there needs to be a lot of sensitivity about how human remains are approached, sampled, processed, and eventually returned.

How has your project been responsive to these concerns and other criticisms of aDNA research?

It’s taken a lot longer compared to other genetic projects to start — to get the permissions, to really get everybody on board, and to do this right. It just takes time, face-time. People who can go there, propose this research, bring on African collaborators in a senior role, and then do this project going forward together.

Many of the criticisms of other DNA projects are that it’s DNA first, Anthropology second. This was really an Anthropology first project. It’s driven by questions that myself and many other anthropologists have been asking for decades, but integrating this new line of evidence, DNA.

It’s absolutely really exciting that we might have this new line of evidence, but DNA will not be the magic key to all of these answers. It’s not to the exclusion of decades and hundreds of years of pottery studies, ancient tool studies, landscape archaeology, ethnographies. These are all just pieces of a puzzle that we need to put together. This is always going to have to be an interdisciplinary effort, where we work with other types of scientists and we work with local communities.

This is so exciting. We just have to make sure that we do it right, right now.

What have you found so far?

We’ve sampled from institutions in Tanzania and Zambia and Kenya. This will be one of the largest African DNA studies to date when it comes out. It’s blown my mind. I hope it will blow many other peoples’ minds.

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Ecology

What if a jolt of electricity could make you happy?

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Scientists found a way to literally spark joy using joly of electricity. (Credit: icon99/shutterstock)

Scientists found a way to literally spark joy using jolts of electricity. (Credit: icon99/shutterstock)

People all around the world (or at least where Netflix is available) have been exhausting themselves of late trying to “spark joy” in their lives. The urge comes from cleaning guru Marie Kondo, whose philosophy rests on the principle that we should rid our homes and minds of things that don’t inspire bursts of pleasure.

The message resonates, in part, because it ties positivity to the world of material things. Happiness is in our minds. So having a tangible mechanism for producing joy is understandably comforting.

But there’s a simpler way to spark joy, if we really want to get literal about it. Any emotion we feel has a physical cause inside our brains. Electrical charges pass from neuron to neuron, spreading ripples of thought and feeling. What we call happiness is just electricity. And now researchers say they’ve found a remarkably specific means of triggering the electrical fireworks that add up to happiness in our brains. By electrically stimulating a brain region known as the cingulum, scientists created spontaneous laughter and a sense of calm and joy in three different patients.

The find could lead to treatments for anxiety and depression, and it hints at insights into the very roots of our emotions themselves.

An artist's illustration shows how an electrode tapped into the cingulum. (Credit: From Bijanki et al, J. Clin. Invest. (2019). Courtesy of American Society for Clinical Investigation)

An artist’s illustration shows how an electrode tapped into the cingulum. (Courtesy of American Society for Clinical Investigation)

Unexpected Bliss

The young woman is clad in hospital garb, sitting upright in a bed. A white hospital cap mushrooms above her head, wires splay from its rear. She’s due for brain surgery in a few days to treat a difficult, disruptive kind of epilepsy. She’s been worried and anxious.

She breaks into a radiant smile, laughter flowing uninhibited.

“I’m kind of like smiling because I can’t help it,” she says. A bit later, “Sorry, that’s just a really good feeling. That’s awesome.”

Neuroscientists just administered a tiny jolt of electricity to wires threaded through her skull and into her brain. The wires are there to guide surgeons to the source of her seizures. But before the procedure, she’s agreed to play guinea pig to a team of Emory University researchers.

Patients like her offer an unprecedented opportunity for researchers to test the workings of various brain regions with unparalleled specificity. By delivering targeted bursts of electricity through the electrodes, they can watch what happens when specific neural circuits are activated.

The team was sending small bursts of electricity to her cingulum, a horseshoe of brain matter that links to regions associated with emotion, self-assessment, social interaction and motivation, among other things. It’s also known to regulate anxiety and depression.

This kind of research, though hardly common, is not new. The patient’s reaction is.

“It was really exciting,” says Kelly Bijanki, a neuroscientist at Emory University who studies behavioral neuromodulation. She was one of the scientists working with the young woman, whose name was not given for privacy reasons, that day. She says the kind of spontaneous joy she saw was unprecedented.

Experiments with brain stimulation have elicited laughter and smiles before. But those responses seemed mechanical. Bijanki says the patients usually described it as a purely motor response. “Their body has laughed, but there’s no content to it.”

This case was different. There was real warmth behind the laughter; true happiness in her voice. At one point, the patient reported she was “so happy she could cry,” the researchers write in their paper.

“The way she was laughing was really infectious,” Bijanki says. “The whole room felt different: she was laughing, she was having a good time, and not afraid. Just that social, emotional contagion took over.”

Further tests confirmed the response. They conducted sham trials, telling the patient that they were providing stimulation when they weren’t. She didn’t react. They tested various levels of stimulation and saw that the more electricity they delivered, the stronger the joyous reaction was. The pattern remained the same: An initial burst of exultation faded into a state of happy relaxation after several seconds.

The researchers found no drawbacks to the treatment, either, they report in a paper in the Journal of Clinical Investigation. Her language skills and memory remained perfectly intact, and they saw no ill aftereffects of the stimulation.

In a screengrab from the scientists' experiment, the patient feels overwhelming joy even while pondering her dog dying. (Credit:)

In a screengrab from the scientists’ experiment, the patient feels overwhelming joy even while pondering her dog dying. (Credit: Bijanki et al, Journal of Clinical Investigation)

Put to the Test

The woman’s impending surgery would require her to remain awake while surgeons probed inside her skull. Their goal was to cut out the tissue responsible for her epilepsy, but it’s a game of millimeters. Doctors must remove enough to ensure that seizures don’t recur, but without causing permanent harm. The patient’s seizures appeared to emanate from a region near to language processing centers. Her job was to stay awake while surgeons worked, reading and talking to ensure they wouldn’t excise anything important.

The brain stimulation turned out to work so well that doctors were able to cut out completely the drugs used to manage anxiety during this type of brain surgery. Those medications can make patients sleepy and unresponsive, so the anesthesiologist decided to stop them midway through. The young woman, her skull opened to surgical tools, breezed through.

“During the surgery … she was telling me jokes about her dad, where prior to turning on the stimulation she had been crying and hyperventilating and right on the edge of panic,” Bijanki says.

To confirm their findings, the researchers performed the same tests with two more epilepsy patients with electrodes similarly implanted in their skulls. They got the same results. Jabs of electricity literally sparking joy inside their heads.

Putting Happiness to Work

It’s too simplistic to say the researchers have stumbled upon the place where joy hides within us. The brain is complex, and emotions well up from more than just a single place. Multiple brain regions are involved, and each contributes a facet to the emotion that we come to know as happiness.

In fact, researchers have found joy in another place in the brain as well. Sameer Sheth, a neurosurgeon at the Baylor College of Medicine, says that he’s had patients report feelings of euphoria during the course of his own work with brain stimulation as well. He was working with the ventral striatum, a region separate from the cingulum, though the two are tightly connected.

Stimulation to the ventral striatum has also produced the same sort of laughter and mood elevation that Bijanki saw, Sheth says.

But just because emotions are neurologically complex doesn’t mean there’s no value to understanding their origins.

“The more we understand this circuitry, the more we can fine tune how to harness that capability within an individual and the better we’ll be able to treat patients with mood disorders,” Sheth says.

Bijanki sees a range of applications for brain stimulation aimed at specific targets, beginning with the kind of surgeries the young epileptic was undergoing. By precluding the use of sedatives, the find might give brain surgeons new options when performing the kind of procedures the young woman went through. Allowing patients to give more feedback could make brain surgeries more targeted. It might also expand the scope of neurosurgery.

“The definition of what is an inoperable tumor is in some circumstances related to what is the surgeon reasonably comfortable with removing that isn’t going to ruin the patients life,” Bijanki says. “If the surgeon could know that in real time, then the surgery could proceed a little bit differently.”

More broadly, it could also find use as a treatment for mental disorders like depression, anxiety and PTSD. Bijanki imagines electrodes powered by a pacemaker battery delivering continuous, low-grade stimulation to patients with depressive disorders.

In the future, we may not even need wires to spark such emotions. Scientists are developing means of activating brain regions with pulses of light, or with ultrasound. Flashes and vibrations could one day deliver ease to the afflicted.

There are drugs that accomplish similar things today, of course, but those often have side effects, and the treatment isn’t always as direct. Brain stimulation could offer a better path.

Banish the Sadness

Bijanki was also struck by an odd side-effect of the stimulation. Though patients had no trouble recalling sad memories during treatment, the recollections were wholly powerless to make them feel unhappy.

“I remember my dog dying, and I remember that it was a sad memory, but I don’t feel sad about it right now,” the young woman said, as reported by the researchers in their paper. Another patient concurred, unable to recollect a tragic memory without smiling. The effect is slightly jarring, but it could provide a shield of sorts to those overcoming trauma.

Those suffering from PTSD often go through what’s called exposure therapy, where they are asked to repeatedly sift through memories of a traumatic event. The goal is to drain those memories of their fearsome power over time, but it is difficult, frightening work.

Paired with temporary brain stimulation that elides sadness, Bijanki thinks PTSD patients might be far better equipped to tread through painful memories.

Finding Balance

Ultimately, however, the goal of therapies involving brain stimulation isn’t to wipe out negative emotions.

Anger, sadness and fear are not without their merits, and banishing them could have unintended consequences. Sadness sits at the other end of the spectrum from happiness, for example. Taking away any of our emotions would be removing an aspect of our humanity. What’s more, we have emotions for a reason.

“Our emotions exist for a very specific purpose, to help us understand our world, and they’ve evolved to help us have a cognitive shortcut for what’s good for us and what’s bad for us,” Bijanki says.

That’s not the goal here, of course, though discussions about the ethical use of such technologies in the future is certainly warranted. Bijanki says that we’d need to be careful about applying things like brain stimulation that could be abused.

But, she’s not very worried about electrodes and electric shocks becoming the next designer drug. It’s just too technically demanding, she says. And the potential benefits for those with depression and other conditions are great.

Sometimes the bad can outweigh the good. In those cases, sparking a little joy might be what we need.

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NASA Picks Science Experiments to Send to the Moon This Year

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Virgin Galactic’s SpaceShipTwo Just Made its Second Trip to Space

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SpaceShipTwo under rocket power

SpaceShipTwo is carried into the air on the back of a plane, but then takes off into space under its own power. (Credit: Virgin Galactic)

On Friday, Virgin Galactic’s SpaceShipTwo flew in space for the second time, taking off from Mojave, California after days of weather delay. SpaceShipTwo took off at 8:07 a.m. PST carrying two pilots, a crewmember, and a nearly full weight of science projects from NASA.

Unlike most spaceflights that fire rockets from the ground, SpaceShipTwo is carried on the belly of a plane named WhiteKnightTwo before being released to propel itself into the upper atmosphere. After being carried 45,000 feet into the air, SpaceShipTwo successfully fired its rocket engine and reached suborbital space at approximately 8:55 a.m. PST. It coasted there for only a few minutes before heading back toward the ground, where it landed much like any other plane, roughly an hour after takeoff. Like all of SpaceShipTwo’s planned flights, this one was suborbital, meaning it does not reach orbit, and attains weightlessness for only a few minutes during its trip.

SpaceShipTwo made its maiden space voyage in December 2018, and today was its fifth powered flight in total. Unlike other private spaceflight companies like SpaceX, Virgin Galactic has made their main goal ferrying private citizens into space, and have been taking reservations for years.

The third crewmember today was Virgin Galactic’s Chief Astronaut Instructor and cabin evaluation lead. Her job today was to see how SpaceShipTwo feels from the cabin. Eventually, Virgin Galactic hopes to seat six passengers in place of the science payloads – or alongside them.

The spacecraft today also carried research projects from NASA’s Flight Opportunities program, which pairs research institutions with private companies who can fly their projects into space. The combined weight of the payloads put SpaceShipTwo at close to, but just under, the requirements for the commercial launch weight that NASA has specified. One of Virgin Galactic’s goals during this flight was testing how the vehicle flies with a greater weight distribution. Details will likely come later, but the flight was successful, which bodes well for the craft’s future in ferrying cargo as well as passengers.

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