An electron micrograph shows a red blood cell, an activated platelet (in yellow) and a white blood cell. The ability to map the magnitude and orientation of forces on a
cell provides a new tool for investigating not just blood clotting
but a range of biomechanical processes. (NCI photo)
By Carol Clark
Platelets are cells in the blood whose job is to stop bleeding by sticking together to form clots and plug up a wound. Now, for the first time, scientists have measured and mapped the key molecular forces on platelets that trigger this process.
The extensive results are published in two separate studies, in the Proceedings of the National Academy of Sciences (PNAS) and in Nature Methods.
“We show conclusively that, in order to activate clotting, the cell needs a targeted force of a magnitude of just a few piconewtons — or a force about a billion times less than the weight of a staple,” says Khalid Salaita, associate professor in Emory University’s Department of Chemistry and the lead author of the studies. “The real surprise we found is that platelets care about the direction of that force and that it has to be lateral. They’re very picky. But they should be picky because otherwise they might accidentally create a clot. That’s what causes strokes.”
Fibrinogen, the third most abundant protein in blood, acts like glue to stick platelets together as a clot forms. Each platelet has about 70,000 copies of a receptor for fibrinogen on its surface. These receptors can work like grappling hooks to latch onto fibrinogen.
“What was puzzling,” Salaita explains, “is that platelets, despite having all these receptors, do not normally latch onto the abundant fibrinogen. They keep flowing past it until you have an injury and fibrinogen becomes anchored. Then the platelets rapidly bind to fibrinogen allowing platelets to aggregate and for clotting to proceed.”
The Salaita lab is a leader in visualizing and mapping the mechanical forces applied by cells. In order to explore the biomechanics of blood clotting, the lab teamed up with physician and biomedical engineer Wilbur Lam, an expert in hematology at Emory’s School of Medicine. Both Salaita and Lam are also affiliated with Emory’s Winship Cancer Institute and the Wallace H. Coulter Department of Biomedical Engineering at Emory and Georgia Tech.
In initial experiments, for the PNAS paper, the Salaita lab anchored fibrinogen ligands onto a lipid membrane. On this surface, the ligands could slip and slide laterally, but resisted motion perpendicular to the surface — similar to the way a hockey puck slides easily over the surface of an ice rink but is harder to lift off of the plane of ice. The researchers then introduced platelets to this surface and experiments showed that the platelets failed to activate and stick together.
In contrast, when the fibrinogen ligands were anchored to a glass slide and unable to move laterally, the platelets rapidly activated. Using tension-imaging technology it developed, the Salaita lab showed that the platelets applied forces between five and 20 piconewtons to initiate activation.
“Platelets have to walk this tightrope between stopping bleeding quickly and accurately during an injury but avoiding unnecessary clotting. Mistakes could be fatal,” Salaita says. “We think they use this lateral force signal like a safety lock to prevent unnecessary clotting.”
Blood vessels are lined with endothelial cells and an injury exposes the fibrous matrix underneath these cells, Salaita explains. Platelets and fibrinogen in the blood can then stick to the injury site.
Salaita theorizes that when a platelet encounters stuck fibrinogen molecules, the platelet tugs on this fibrinogen as a way to test it. The resulting force generates a potent signal to activate platelets and that allows them to grab the fibrinogen from the blood, driving the process of clumping with other platelets.
The abnormal clotting that leads to strokes, and the uncontrollable bleeding of hemophilia, may be related to malfunctions in this biomechanical mechanism, he adds.
In 2011, the Salaita lab developed a fluorescence-sensor method for mapping cell mechanics. Alexa Mattheyses, a cell biologist at Emory’s School of Medicine and Winship Cancer Institute, teamed with the lab to test whether fluorescence polarization could be applied to map the direction of cell forces and provide further insights into the biomechanics of blood clotting.
The results, published in the Nature Methods paper, showed that they could.
Mattheyses “is a guru of fluorescence polarization,” Salaita says. She built a dedicated microscope that allowed mapping force direction at piconewton resolution. She also worked with Joshua Brockman and Aaron Blanchard, graduate students in the Salaita lab, to develop the new imaging technology.
The technique uses DNA molecules as force probes, which behave like molecular ropes and extend in the direction that a cellular force pulls. A series of microscopy images captures the orientation of the DNA, which can then be used to calculate the orientation of piconewton cell forces.
“We got really good at measuring and mapping magnitude, using fluorescence to see how stretched a polymer was,” Salaita says. “Now we can also see which direction a polymer is pointing, in three dimensions.”
Experiments revealed that as platelets begin sticking together to form a clot they contract toward a line, or central axis, in each cell. They do not, however, pull together toward a shared central axis. “It’s similar to having a group of people in a room that are all facing different directions,” Salaita explains. “When they join hands and everybody pulls inward you still get a cluster but the direction that each person is pulling is randomly oriented.”
The ability to map both the magnitude and orientation of forces on a cell provides a powerful tool for investigating not just blood clotting but a range of biomechanical processes, from immune cell activation and embryo development to the replication and spread of cancer cells.
“We’ve developed a completely new way to see things that were not visible before,” Salaita says. “It’s a basic tool with broad applications to help understand why cells are doing things and maybe predict what they’re going to do next.”
The Goldwater Rule takes its name from a 1964 incident during the failed presidential bid of Barry Goldwater. An article in a now defunct magazine declared, "1,189 Psychiatrists Say Goldwater is Psychologically Unfit to be President."
By Carol Clark
The rationale for the Goldwater Rule — which prohibits psychiatrists from publicly commenting on the mental health of public figures they have not examined in person — does not hold up to current scientific scrutiny, a new analysis finds.
Perspectives on Psychological Science is publishing the analysis, which concludes that the Goldwater Rule is not well-supported scientifically and is outdated in today’s media-saturated environment. A preprint of the article is available online.
“We reviewed a large body of published scientific literature and it clearly showed that examining someone directly is often not necessary if you compile other valid sources of information,” says Scott Lilienfeld, lead author of the analysis and a professor of psychology at Emory University.
As examples of those sources, the authors cite interviews with family members, friends and others who know a person well, and extensive public records such as media interviews, biographies, YouTube videos, social media accounts and other material that may reveal a person’s longstanding behavioral patterns. The authors also report that direct interviews are subject to a host of biasing factors that are difficult to eliminate, including efforts on the part of interviewees to create positive impressions.
“Even though it is often possible to make a reasonably valid psychiatric diagnosis at a distance, that doesn’t necessarily mean that a mental health professional should,” Lilienfeld cautions. “Such a diagnosis should only be made with great discretion and after a thorough investigation.”
The Goldwater Rule takes its name from an incident during the failed presidential bid of Barry Goldwater. A 1964 article in a now defunct magazine declared, “1,189 Psychiatrists say Goldwater is Psychologically Unfit to be President.” Many of the psychiatrists described the candidate in terms such as “emotionally unstable,” “cowardly,” “grossly psychotic,” “paranoid,” “delusional” and a “dangerous lunatic.” Some of the psychiatrists went so far as to offer diagnoses of Goldwater, including schizophrenia and obsessive-compulsive disorder.
Goldwater lost the election to Lyndon B. Johnson, but went on to successfully sue the magazine for libel.
“Many psychiatrists who commented on Goldwater in that article crossed an ethical line,” Lilienfeld says. “A lot of unfair statements were made about him that were poorly supported or unwarranted.”
The APA later responded by passing what came to be known as the Goldwater Rule, in part to protect public figures from humiliation and in part to safeguard the integrity of the psychiatric profession.
The Goldwater Rule may have been more defensible at the time it was implemented, Lilienfeld says, because much less information was available on public figures.
Times have changed, however, particularly with the advent of the Internet and social media.
“If someone is running for the most powerful position in the world, behavioral professionals should be able to speak out if they take the time to properly investigate a candidate,” Lilienfeld says. “There should be a high threshold for doing so, but psychologists and psychiatrists should not feel gagged if they want to contribute to a national conversation about a presidential candidate or current president.”
While the authors of the analysis recommend abandoning the Goldwater Rule, they add that mental health professionals should avoid making diagnoses of celebrities in general, simply for the sake of prurient interest.
Lilienfeld’s co-authors are Joshua Miller from the University of Georgia and Donald Lynam from Purdue University.
"Anthropological genetics is a huge and growing field," says Kendra Sirak. The Emory graduate student has developed a specialized technique for drilling into ancient skulls to remove DNA samples. (Photo by Kristin Stewardson.)
By Carol Clark
“Wherever I travel, I take my bone drill with me,” says Kendra Sirak.
An Emory PhD candidate in anthropology, Sirak has developed a specialized technique for drilling into ancient skulls to remove DNA samples. She’s flown to more than a dozen countries and drilled more than 1,000 skulls, perfecting the technique.
“No one at customs has ever questioned me about why I’m carrying a gigantic drill in my suitcase,” she notes.
Sirak has the distinction of being the last graduate student of the late George Armelagos, Goodrich C. White Professor of Anthropology. Armelagos, who died in 2014 at the age of 77, was one of the founders of the field of paleopathology.
He spent decades working with graduate students to study the bones of ancient Sudanese Nubians to learn about patterns of health, illness and death in the past. The only piece missing in studies of this population was genetic analysis. So in 2013, Armelagos sent Sirak to one of the best ancient DNA labs in the world, University College Dublin, with samples of the Nubian bones.
“I had no interest in genetics,” says Sirak, who was passionate about studying human bones and paleopathology. “But George believed DNA was going to become a critical part of anthropological research.”
Sirak drills the base of an ancient skull.
Sirak soon became hooked when she saw how she could combine her interest in ancient bones with insights from DNA. She formed collaborations not just in Dublin but at Harvard Medical School’s Department of Genetics and elsewhere, working on unsolved mysteries surrounding deaths going back anywhere from decades to ancient times.
As genetic sequencing techniques keep improving, anthropology and DNA analysis are becoming increasingly complementary. In 2015, another breakthrough occurred when researchers realized that the petrous bone consistently yielded the most DNA from ancient skeletons. This pyramid-shaped bone houses several parts of the inner ear related to hearing and balance.
But the way the petrous bone is wedged into the skull makes it difficult to access without shattering the cranium. Understandably, museum curators were reluctant to allow DNA researchers to tamper with rare, fragile ancient skulls.
So Sirak set about developing a technique to drill into a skull and reach the petrous bone in the most non-invasive way possible, while also getting enough bone powder for DNA analysis. The journal Biotechniques recently published her method, which involves drilling through the cranial base, where the spinal cord enters the skull.
“Hopefully, it will become the gold standard for both anthropology stewardship as well as DNA analysis,” Sirak says.
Sirak herself has the most experience in using the technique and her services have been in demand, as researchers seek to unlock secrets of ancient skeletons in museums and other collections.
Sirak’s trusty bone drill is a more modern version of the electric drill her father kept in the garage for household projects. Hers, however, has a foot pedal giving her precision control over the drill’s speed, and a flexible extension cord similar to what you might encounter in a dentist’s chair. The drill bits she uses range from 3.4 to 4.8 millimeters in diameter.
“Drilling an ancient skull can be nerve wracking,” Sirak says, “because you don’t want to be responsible for ruining a specimen. I’ve had museum curators watch me over my shoulder. Sometimes they are so close you can feel their breath on your neck.”
Besides drilling for DNA, she speaks at conferences, gives demonstrations and trains other researchers in her technique. “It’s a lot of fun to work with others who want to learn,” says Sirak, who has helped set up ancient DNA labs in India and China.
She is now finishing up her dissertation, a bioethnography of the ancient Nubians, and expects to graduate from Emory in June.
“Anthropological genetics is a huge and growing field,” Sirak says, acknowledging Armelagos for setting her on the path. “He was a good mentor. He introduced me to something that I didn’t know existed and let me run with it.”
Every day, the average American throws away about 4.4 pounds of waste, about the weight of one chihuahua. Multiple that by every day of the year and over 300 million Americans and you get 167,000,000 tons of trash a year — or the equivalent of 76 billion chihuahuas.
Meggie Stewart, a senior majoring in Environmental Sciences, did the math for her two-minute video about landfills (above) — the first place winner for the Emory Office of Sustainability Initiatives 2017 Waste Video Competition. Emory is striving to achieve zero landfill waste on campus, since landfills have negative social, economic and environmental impacts.
A side view of the new catalyst. The dirhodium, shown in blue, "is the engine that makes the catalyst work," says Emory chemist Huw Davies. "The shape of the scaffold around the dirhodium is what controls which C-H bond the catalyst works on." (Graphic image by Kuangbiao Liao)
By Carol Clark
Chemists have developed another catalyst that can selectively activate a carbon-hydrogen bond, part of an ongoing strategy to revolutionize the field of organic synthesis and open up new chemical space.
The journal Nature is publishing the work by chemists at Emory University, following on their development of a similar catalyst last year. Both of the catalysts are able to selectively functionalize the unreactive carbon-hydrogen (C-H) bonds of an alkane without using a directing group, while also maintaining virtually full control of site selectivity and the three-dimensional shape of the molecules produced.
“Alkanes have a lot of C-H bonds and we showed last year that we can bring in one of our catalysts and pluck out a particular one of these bonds and make it reactive,” says Huw Davies, an Emory professor of organic chemistry whose lab led the research. “Now we are reporting a second catalyst that can do the same thing with another C-H bond. We’re building up the toolbox, and we’ve got more catalysts in the pipeline that will continue to expand the toolbox for this new way of doing chemistry.”
Selective C-H functionalization holds particular promise for the pharmaceutical industry, Davies adds. “It’s such a new strategy for making chemical compounds that it will opens up new chemical space and the possibility of making new classes of drugs that have never been made before.”
Alkanes are the simplest of molecules, consisting only of hydrogen and carbon atoms. They are cheap and plentiful. Until the recent development of the catalysts by the Davies lab, however, alkanes were considered non-functional, or unreactive, except in uncontrollable situations such as when they were burning.
The first author of the Nature paper is Emory chemistry graduate student Kuangbiao Liao.
The CCHF is leading a paradigm shift in organic synthesis, which has traditionally focused on modifying reactive, or functional, groups in a molecule. C-H functionalization breaks this rule for how to make compounds: It bypasses the reactive groups and does synthesis at what would normally be considered inert carbon-hydrogen bonds, abundant in organic compounds.
“Twenty years ago, many chemists were calling the idea of selectively functionalizing C-H bonds outrageous and impossible,” Davies says. “Now, with all of the results coming out of the CCHF and other research groups across the world they’re saying, ‘That’s amazing!’ We’re beginning to see some real breakthroughs in this field.”
Many other approaches under development for C-H functionalization use a directing group — a chemical entity that combines to a catalyst and then directs the catalyst to a particular C-H bond.
The Davies lab is developing a suite of dirhodium catalysts that bypass the need for a directing group to control the C-H functionalization. The dirhodium catalysts are encased within a three-dimensional scaffold.
“The dirhodium is the engine that makes the chemistry work,” Davies says. “The shape of the scaffold around the dirhodium is what controls which C-H bond the catalyst works on.”
Additional co-authors of the Nature paper include Thomas Pickel, Vyacheslav Boyarskikh and John Basca (from Emory’s Department of Chemistry) and Djamaladdin Musaev (from Emory’s Department of Chemistry and the Cherry L. Emerson Center for Scientific Computation).
The tortoise beetle, which eats thistle leaves, has evolved a symbiotic relationship with bacteria that allows it to have such a specialized diet. Photo by Hassan Salem.
By Carol Clark
A leaf-eating beetle has evolved a symbiotic relationship with bacteria that allows the insect to break down pectin — part of a plant’s cell wall that is indigestible to most animals.
The journal Cell published the findings on the novel function of the bacterium, which has a surprisingly tiny genome — much smaller than previous reports on the minimum size required for an organism not subsisting within a host cell.
“This insect is a leaf eater largely because of these bacteria,” says Hassan Salem, lead author of the study and a post-doctoral fellow in Emory University’s Department of Biology. “And the bacteria have actually become developmentally integrated into the insect’s body.”
Two organs alongside the foregut of the beetle Cassida rubiginosa house the bacteria and appear to have no other function than to maintain these microbes. “The organs are equivalent to the liver in humans, in the sense that they contain the tools to break down and process food,” Salem says.
The newly characterized bacterium has only 270,000 DNA base pairs in its genome, compared to the millions that are more typical for bacterial strains. That makes its genome closer to that of intracellular bacteria and organelles than to free-living microbes. Mitochondria, for example, the organelles that regulate metabolism within cells, have 100,000 base pairs.
The two symbiotic organs of the tortoise beetle, dyed a fluorescent green, are shown on either side of the insect's foregut. Microscopy image by Hassan Salem.
Salem is a researcher in the lab of Emory biologist Nicole Gerardo, an associate professor who specializes in the evolutionary ecology of insect-microbe interactions. The lab combines genomic and experimental approaches to learn how both beneficial and harmful microbes establish and maintain relationships with their hosts.
A human gut holds about 10,000 species of bacteria. These microbial communities, which can be genetically characterized as microbiomes, are transferred generationally but are also dynamic and respond to environmental changes. The microbiome of an urbanite, for example, has different characteristics from that of a hunter-gatherer.
Unlike humans, insects tend to have specialized feeding ecologies. They offer simple models to study symbiotic relationships between microbes and their hosts.
Salem with Buchner's book
Salem became fascinated by Cassida rubiginosa, more commonly known as the tortoise beetle, while he was a graduate student at the Max Planck Institute for Chemical Ecology in Jena, Germany. He was leafing through a 1953 edition of a book by the late Paul Buchner, a German scientist and one of the pioneers of systematic symbiosis research in insects. Buchner referenced a paper published in 1936 by one of his students, Hans-Jurgen Stammer, on Cassida rubiginosa.
“Stammer wrote that, unlike most leaf-eating beetles that he had studied, this one had sac-like organs that he had never seen before and the organs were filled with micro-organisms,” says Salem, who looked up Stammer’s original paper in a now-obscure journal. “He didn’t have the high-powered microscopes that we have now, or genome sequencing technology, so he wasn’t able to comment on the functionality of the mysterious microbes. At that point, the idea that microbes could do anything beneficial for an animal was mushy science.”
Intrigued by the article, Salem went to a nearby woodland to collect some of the leaf beetles. “To find these beetles, you don’t go looking for them,” he explains. “You go looking for the plants they eat.”
The tortoise beetle feeds on the tough, spiny leaves of the Californian thistle (Asteraceae). This prolific weed grows throughout much of the world and is difficult to control. “It pops up in a lot of areas where sheep are maintained,” Salem says. “In fact, it’s a huge pest to New Zealand sheep farmers. The more thistles covering a farmland, the less food the sheep have to eat and the lower the yield. But the thistle is hard to get rid of because its roots run so deep.”
Salem followed the trail of his curiosity to New Zealand, spending time with an agricultural researcher, Michael Cripps, who breeds the tortoise beetle as a bio-control model for thistles. “You drop 100 beetles on a thistle plant and the insects will just drain the plant metabolically until it dies,” Salem explains.
As an herbivore that specializes in eating leaves, the tortoise beetle must consume large amounts of plant cell walls, made of hard-to-digest materials like pectin. One of nature’s most complex polysaccharides, pectin is a gelatinous substance that gives plant cell walls their shape and rigidity. While it was unclear how the beetle obtained needed nutrients of amino acids and vitamins from such a diet, Salem suspected that symbiotic bacteria played a role.
In this cross-section of the symbiotic organ the bacteria it contains are lit up in fluorescent green dye. Microscopy image by Hassan Salem.
When he joined the Gerado lab at Emory, Salem continued to study the tortoise beetle and its micro-organisms with the help of fellow post-doc Aileen Berasategui, a co-author of the Cell paper.
They used genome sequencing technology to characterize the microorganisms as a new species of bacterium. Despite its tiny genome, the bacterium has the power to degrade pectin.
“Just as an apex predator has claws and strong mandibles to obtain the nutritional value that it needs from its prey, the bacterium has pectin-digesting genes that enable the beetle host to deconstruct a plant cell,” Salem says.
After the bacterium breaks down the pectin, the beetle’s digestive system can then access all of the amino acids and vitamins within the plant’s cells for its nutrients.
Salem christened the new bacterium Candidatus Stammera capleta, after Hans-Jurgen Stammer, the ecologist who first glimpsed it and wondered about it more than 80 years ago.
“The most amazing thing to me is that we made this discovery because I read a really old book,” Salem says. “It speaks to the importance of natural history collections and libraries for old journals. We truly stand on the shoulders of giants, extending the work of those who came before us.”
Additional co-authors of the paper are from the Max Planck Institute for Chemical Ecology, the University of Luxembourg, the Lincoln Research Centre in New Zealand, Johannes Gutenberg University in Germany and the National Institute for Advanced Industrial Science and Technology in Japan.
The Lying Conference will unmask the many factors involved in deception, including evolution, culture and the human affinity for storytelling and make believe.
By Carol Clark
We grow up with this notion that we should always tell the truth. But can we live without lying?
That’s one of the questions to be explored in a day-long event, “The Lying Conference,” on Friday, November 17, from 8:30 am to 6:30 pm at Emory Conference Center. Emory’s Department of Psychology is bringing together scientists from psychology, neuroscience and anthropology — along with a leading journalist, a theater director and a professional magician — to discuss their insights into lying and deception. The conference is free and open to the public, but registration is requested.
Topics to be covered include: The deep, evolutionary roots of lying. How children learn to tell lies. Cultural differences in lying. How we decide whether someone is trustworthy. How technology and the changing media and political landscapes are affecting our collective beliefs. The role of deception in the arts and entertainment.
“Lying is kind of a hot topic right now, with all the buzz about fake news and accusations of cover-ups and deception,” says Emory developmental psychologist Philippe Rochat, lead organizer of the event. “When we talk about lying, what we are indirectly trying to understand is, what is the truth? It can be a profound question.”
Science uses probabilities to approximate the truth, Rochat notes. “It’s a never-ending journey and you keep trying to get closer.”
In day-to-day interactions, we regularly negotiate the truth with one another, trying to convince others of a point of view. “People put on makeup to exaggerate their features,” Rochat says. “We amplify some things about ourselves and hide others. We make believe. We seduce.”
People can lie maliciously, in an anti-social way. Or they can tell white lies, to be polite and avoid hurting another person’s feelings.
Rochat is particularly interested in the developmental trajectory of lying. Between the ages of two and three, children begin to engage in pretend play. By around age four, when children start to have ideas about what other people are thinking, lying emerges. “They can be explicit at this stage, because they can understand that someone can be deceived,” Rochat says. “But they still cannot lie very well. They tend to leak the truth.” By the age of six or seven, he adds, “we become much better at concealing the truth and keeping a secret tight.”
Whatever the reasons for lying, one thing is clear: “We’ve evolved to lie,” Rochat says. “It’s deeply rooted in our nature and somehow important to our survival.”
Following are the seven speakers of the conference and brief summaries of their topics.
“Perspective-taking and Dishonest Communication in Primates and Other Animals,” by Emory primatologist Frans de Waal: While there is plenty of evidence for functional deception in animals — such as the way a butterfly might use mimicry as camouflage — but tactical deception requires anticipating the reaction of others. Tactical deception is clearly more developed in apes than most other species, although there is also evidence for corvids.
“Lying, American Style,” by Emory anthropologist Bradd Shore: He will discuss the role of culture in lying and how it differs across cultures. Shore will also touch on the some of the ways the American cultural model has been politically deployed and manipulated in recent decades.
“Little Liars — How Children Learn to Tell Lies,” by Kang Lee a developmental psychologist from the University of Toronto: Lee will use scientific evidence from his lab to show how lying begins early in life, what factors contribute to the development of lying, why children lie and whether adults can easily detect children’s lies. He will also discuss recent developments in technology that may help in detecting lies.
“Face Value — The Irresistible (and Misleading) Influence of First Impressions,” by neuroscientist Alexander Todorov from Princeton University: People form instantaneous impressions from faces and act on these impressions. In the last 10 years, data-driven computational methods allow scientists to visualize the configurations of face features leading to specific impressions such as trustworthiness. But these appearance stereotypes are not often accurate. So why do we form first impressions?
“What Happened to the News? Technology, Politics and the Vanishing Truth,” by Johnathan Mann, former CNN International anchor: Many American believe that the news media intentionally lie to them. President Donald Trump is the best-known detractor of “fake news,” though he himself has been accused of lying more than any other public figure in recent memory. Mann will address the overlapping changes to technology, politics and business that have crippled our national conversation with deception and distrust.
“Onions and Identities — Theater and the True Self,” by Emory dramatist Tim McDonough: Drama is densely populated by duplicitous schemers, by power figures whose lies maintain the sociopolitical status quo, and by characters in search of themselves, who mirror to us our confusions and self-deceptions. Theater provides a template for understanding identity and insight into existentially and socially necessary forms of deceit.
“The Science of Magic and the Art of Deception,” by professional magician Alex Stone: Magicians trick our brains into seeing what isn’t real, and for whatever reason our brains let them get away with it. Through a mix of psychology, storytelling and sleight-of-hand, Stone will explore the cognitive underpinnings of misdirection, illusion, scams and secrecy, pulling back the curtain on the many curious and powerful ways our brains deceive us not just when we’re watching a magician but throughout our everyday lives.
“Due to the current void in national leadership on the issue of climate change, efforts at the state and local level are more important than ever,” says Eri Saikawa, an assistant professor of Environmental Sciences. Saikawa is part of an Emory delegation to the U.N. Climate Change Conference talks in Bonn, Germany, which includes two faculty and 12 students.
By Carol Clark
U.S. state policies aimed at mitigating power plant emissions vary widely in effectiveness, finds a new study by researchers at Emory University.
Nature Climate Change published the analysis, which shows that policies with mandatory compliance are associated with the largest reductions in power plant emissions.
“Based on the results of our study, we recommend that states adopt a policy of mandatory greenhouse gas emissions registry and reporting for power plants,” says Eri Saikawa, an assistant professor in Emory’s Department of Environmental Sciences. “We also found a significant impact in states that adopt public benefit funds aimed at energy efficiency and renewable energy programs. These two policies not only are effective in reducing power-plant emission levels but also emissions intensity.”
Saikawa, an expert in public policy and the science of emissions linked to global warming, co-authored the study with Emory graduate Geoff Martin, whose thesis project focused on the topic. Martin received his master’s degree in environmental sciences in May and now works as an energy coordinator for the town of Hartford, Vermont.
Their findings were released today as the U.N. Climate Change Conference (COP23) opens in Bonn, Germany. Delegates from around the world are gathering to hammer out details for meeting the goals of the 2015 Paris Agreement.
The United States was among the 195 countries that committed to this framework to reduce greenhouse gas emissions — although the Trump administration has said it plans to withdraw from this historic accord.
“Due to the current void in national leadership on the issue of climate change, efforts at the state and local level are more important than ever,” Saikawa says. “U.S. cities and states need to step up and do what they can.”
Emory is one of 50 universities from around the country to hold official U.N. observer status for COP23. Saikawa and Sheila Tefft, senior lecturer from the Department of English, will be on the ground in Bonn — leading a delegation of 11 Emory undergraduates and one graduate student as part of their co-taught class, “Climate Change and Society.”
The students will report news live from the event on Twitter under the hashtag #EmoryCOP23. They will also post longer reports, podcasts and videos on a web site they created for the event, Climate Talks Emory University.
Global atmospheric CO2 levels increased at record speed last year, to reach a level not seen for more than three million years, the U.N. warned in a report released last week. The U.S. government’s National Climate Assessment, also released last week, affirmed that climate change is driven almost entirely by human action and detailed how the country is already experiencing more extreme heat and rainfall events, more large wildfires and more flooding due to the warming climate.
About 30 percent of U.S. greenhouse gas emissions come from the electric power sector. For the Nature Climate Change paper, the researchers started out to review the potential impact of President Obama’s Clean Power Plan — which established the first national carbon pollution standards for power plants. When President Trump took office, and announced plans to repeal the Clean Power Plan, the researchers shifted focus.
They analyzed 17 policies adopted by various states relating to climate and energy. States that adopted a mandatory policy for power plants to register and report greenhouse gas emissions, along with three to four other policies, showed the largest reductions, at an average of 2.6 million metric tons of carbon dioxide (CO2) emissions per year.
The second most significant policy involved public benefit funds allotted for energy efficiency and renewable energy programs. That policy was associated with a reduction of about 1.5 million tons of CO2 emissions from power plants, when adopted with three to four other policies.
It’s unclear whether one of these single policies was the actual driver of the reduction in emissions, or an indicator that a state takes climate change mitigation seriously and is attacking the issue on many fronts, Saikawa says.
For instance, three states — New York, Connecticut and Oregon — have each adopted both of the top two most effective policies, along with at least eight other policies.
In 2007, China surpassed the United States as the largest emitter of greenhouse gases globally. “But the per capita emissions in the United States are more than double that of China,” Saikawa notes.
The Obama administration played a key role in securing the Paris Agreement, to keep global warming to no more than 2 degrees Celsius since the start of the Industrial Revolution.
“It will be interesting to hear the take of officials from the Trump administration this year,” Saikawa says.
“U.S. coalitions from the state and city level are forming and they will likely have a strong presence at side events for COP23,” she adds. “Many groups are working at the local level around the world to try to meet the goal of the Paris Agreement.”
Emory is co-hosting an event on Thursday, November 16 at COP23, focused on ways to mitigate climate change impacts in the developing world. Saikawa will appear on a panel, along with John Seydel, director of sustainability for the city of Atlanta.
“We’ll be discussing how efforts at the city and state level in the United States might be replicated in other parts of the world,” Saikawa says.
This marks the third year in a row that Emory has sent a delegation to the U.N. climate talks.
Emory graduate student Guga Gogia slowly “salted” micron-sized particles into a vacuum chamber filled with plasma, creating a single layer of particles levitating above a charged electrode. He kept a low gas pressure, so the particles could move freely. “After a few minutes I could see with my naked eye that they were acting strangely," Gogia says.
By Carol Clark
Physicists have shown how a system of lifeless particles can become “life-like” by collectively switching back and forth between crystalline and fluid states — even when the environment remains stable.
Physical Review Letters recently published the findings, the first experimental realization of such dynamics.
“We’ve discovered perhaps the simplest physical system that can consistently keep changing behavior over time in a fixed environment,” says Justin Burton, Emory assistant professor of physics. “In fact, the system is so simple we never expected to see such a complex property emerge from it.”
Many living systems — from fireflies to neurons — switch behaviors collectively, firing on and then shutting off. The current paper, however, involved a non-living system: Plastic particles, tiny as dust specks, that have no “on” or “off” switches.
“The individual particles cannot change between crystalline and fluid states,” Burton says. “The switching emerges when there are collections of these particles — in fact, as few as 40. Our findings suggest that the ability for a system to switch behaviors over any time scale is more universal than previously thought.”
Watch a video to learn more and see the particles in action:
The Burton lab studies the tiny, plastic particles as a model for more complex systems. They can mimic the properties of real phenomena, such as the melting of a solid, and reveal how a system changes when it is driven by forces.
The particles are suspended in a vacuum chamber filled with a plasma — ionized argon gas. By altering the gas pressure inside the chamber, the lab members can study how the particles behave as they move between an excited, free-flowing state into a jammed, stable position.
The current discovery occurred after Emory graduate student Guram “Guga” Gogia tapped a shaker and slowly “salted” the particles into the vacuum chamber filled with the plasma, creating a single layer of particles levitating above a charged electrode. “I was just curious how the particles would behave over time if I set the parameters of the chamber at a low gas pressure, enabling them to move freely,” Gogia says. “After a few minutes I could see with my naked eye that they were acting strangely.”
From anywhere between tens of seconds to minutes, the particles would switch from moving in lockstep, or a rigid structure, to being in a melted gas-like state. It was surprising because the particles were not just melting and recrystallizing but going back and forth between the two states.
“Imagine if you left a tray of ice out on your counter at room temperature,” Gogia says. “You wouldn’t be surprised if it melted. But if you kept the ice on the counter, you would be shocked if it kept turning back to ice and melting again.”
Gogia conducted experiments to confirm and quantify the phenomenon. The findings could serve as a simple model for the study of emerging properties in non-equillibrium systems.
“Switching is an ubiquitous part of our physical world,” Burton says. “Nothing stays in a steady state for long — from the Earth’s climate to the neurons in a human brain. Understanding how systems switch is a fundamental question in physics. Our model strips away the complexity of this behavior, providing the minimum ingredients necessary. That provides a base, a starting point, to help understand more complex systems.”
"The ultimate goal is making it possible to devise all-optical computers and telecommunications," says Hayk Harutyunyan, left, with Ajit Srivastava. (Ann Borden, Emory Photo/Video)
By Carol Clark
The National Science Foundation awarded two Emory physicists a $2 million Emergent Frontiers grant, for development of miniaturized optical transistors to take computers and telecommunications into a new era.
“We are working to change some properties of light — such as making it travel in only one direction — by using atomically thin, two-dimensional materials,” says Ajit Srivastava, assistant professor of physics and principal investigator for the grant. “These novel materials are being touted as the next silicon. They could open the door to even smaller and more efficient electronics than are possible today.”
Srivastava’s co-investigators include Hayk Harutyunyan, also an assistant professor of physics at Emory, as well as scientists from Georgia State and Stanford universities.
“The ultimate goal is making it possible to devise all-optical computers and telecommunications,” Harutyunyan says.
A major revolution in telecommunications occurred in the 1950s, driven by the development of silicon semiconductors as miniature transistors to control the flow of electrical current. These transistors led to smaller, faster computers and paved the way for everything from flatscreen TVs to cell phones.
“They changed civilization,” Harutyunyan says. “Every year new computers would come out with faster processors as the transistors got tinier and more efficient. But about a decade ago this progress stopped, because these transistors cannot be made any smaller than about 15 nanometers and still function well.”
Meanwhile, the gradual replacement of copper wiring with fiber optics is speeding up transmissions between computers and other electronic devices and allowing for greater bandwidth. “When you send an email from Atlanta to Europe, the information is encoded into light and relayed by fiber optic cables running under the ocean,” Srivastava explains. “It’s super fast, because light is the fastest thing that you can imagine.”
Unlike in our everyday life, however, where the arrow of time moves in one direction, light photons operate at the quantum scale and can move back and forth. This lack of a fixed direction is called reciprocity. “Reciprocity in optics,” Srivastava says, “can best be described by a familiar observation: ‘If I can see you, you can see me.’”
Fiber optic cables use magnetic fields to break reciprocity and prevent light from reflecting off surfaces and creating “noise” in a signal. The required magnetic devices, known as optical isolators, are typically bulky and heavy because tiny magnets are not strong enough to do the job.
The Emory project aims to develop powerful nonreciprocal optical devices that are not based on magnets and can function at the nanoscale.
Srivastava’s lab is investigating the potential of transition metal dichalcogenides, or TMDs. TMDs are semiconductors within a new family of two-dimensional, extraordinarily thin materials. While the smallest feature of a current computer processor is 14 nanometers thick, a TMD monolayer is smaller than a single nanometer.
Harutyunyan’s lab, meanwhile, is exploring ways to make interactions between light and matter stronger through the use of metallic nano particles. Metals are shiny because of their free electrons that easily interact with light. The oscillations of these free electrons, called plasmons, allow metallic nano-particles to funnel large amounts of light into tiny dimensions.
A long-term goal of the project is to hybridize TMDs and metallic particles into nanomaterials that use laser fields to create the same light-guiding effects of magnetic fields. Such devices have the potential to be faster and cheaper and offer more precise control of the light-directing process. They would also be much smaller than existing optical isolators and transistors.
“Nano-science is an exciting area,” Srivastava says. “You can imagine the possibility of flexible cell phones or even wearable electronic membranes that would take the shape of your body.”
More powerful computers could also ramp up the ability of scientists to analyze massive datasets faster, Harutyunyan notes.
The Emory grant will also fund public outreach projects in Atlanta area schools. “We want people to understand the importance of fundamental science research,” Harutyunyan says. “And we want to inspire young people to think about science careers.
An electron micrograph shows human immune system cells attacking methicillin-resistant Staphylococcus aureus (MRSA). MRSA is an example of antibiotic-resistant bacteria that can occur in multiple strains in an infection, further complicating diagnosis, treatment and interventions.
By Carol Clark
The Centers for Disease Control and Prevention (CDC) awarded $380,000 to three Emory University faculty to develop and refine a promising technique to detect and respond to threats from drug-resistant pathogens.
The grant investigators include Lars Ruthotto and Ymir Vigfusson — both assistant professors in the Department of Mathematics and Computer Science — and Rebecca Mitchell, a visiting professor with a joint appointment in the Department of Mathematics and Computer Science and the Nell Hodgson Woodruff School of Nursing.
The trio is developing a method to quickly and cost-effectively diagnose multiple strains of antibiotic-resistant bacteria within a single biological sample.
“This project harmonizes our different scientific specialties,” Vigfusson says. He is a computer scientist who develops software and programming algorithms that work at scale, while Ruthotto is a mathematician who focuses on solving inverse problems. Mitchell is a veterinarian and epidemiologist experienced in gathering biological samples and testing them for pathogens.
Antibiotic-resistant infections are a growing national and global problem, causing at least two million illnesses and 23,000 deaths in the United States annually, according to the CDC.
The Emory grant is part of a $9 million package of CDC funding announced today, including awards to projects at 25 leading research institutions around the country that are exploring gaps in knowledge about antibiotic resistance and piloting innovative solutions in the healthcare, veterinary and agriculture industries. The work complements broader CDC efforts to support known strategies for protecting people and slowing antibiotic resistance, collectively known as the CDC Antibiotic Resistance Solutions Initiative.
The Emory project seeks to tame the complexity of analyzing multiple infections within a biological specimen, from a drop of blood to a fecal sample.
In the case of a widespread outbreak of antibiotic-resistant E. coli for instance, it would be useful to quickly determine whether fecal samples contained multiple strains of the bacteria and what those strains were, in order to more rapidly trace the sources of the outbreak and design effective interventions.
It is costly and labor-intensive, however, to culture biological samples at the local level, and then send them to the CDC for testing. And if multiple strains of a pathogen are within a single sample, only some strains that are present may grow in the culture while other strains may be missed.
“It’s a challenge to deal with samples containing mixed strains of a pathogen in a lab setting,” Mitchell says. “You have to do a large amount of work to get the finer gradations of what species of pathogens are present, and in what proportions.”
The Emory researchers are striving to balance accuracy with the need to simplify and streamline the process. Their method eliminates labor-intensive, technical steps, such as culturing the sample. “We want to automate the process so that you need less expertise at the local level, and so that data coming from individual states can be easily integrated into a central system,” Mitchell explains.
They use multiple short polymorphic regions in the genome to look for genetic variations among the DNA templates present within a biological sample. In the case of antibiotic-resistant bacteria, the number of reference sites ranges between the hundreds to the thousands, depending on the specific bacteria targeted.
“We’ve developed an algorithm and software and mathematical models to rapidly run these comparisons and estimate the number of strains in a single sample, and the percentage of each,” Ruthotto says. “Now we are trying to quantify the accuracy of this estimate, which is a mathematical challenge. The grant gives us the resources to refine our method for real-world applications.”
The ultimate goal is to develop a system that will work not just on antibiotic-resistant bacteria, but for mixed-strains of any pathogen within a biological sample. In a separate project, for example, Mitchell and Vigfusson are applying the method to test for multiple strains of the malaria parasite within a blood sample.
“Quickly teasing apart mixed-strain samples is a big challenge in public health, and it’s essential in order to plan effective interventions,” Mitchell says.
“We’re using math and computer science to draw more information from a single biological sample than was previously practical,” Vigfusson says. “We hope that our method could turn into a work engine that helps to understand multiple-strain infections and makes an impact on public health.”
Climate change. Partisan politicians debate its reality, and many citizens see it as a faraway threat, something that endangers the future of polar bears but not them personally.
The health effects of global warming, however, are already being felt. Extreme weather events such as wildfires, droughts, and flooding are becoming more frequent, resulting in more injuries, deaths, and relocations. Heat and air pollution are sending people with asthma and other respiratory ailments to the emergency room. Diseases carried by mosquitoes, fleas, and ticks are expanding their territory—dengue has become endemic in Florida, Lyme disease has worked its way up to Canada and over to California, and some fear that malaria may re-emerge in the U.S.
Tie these health burdens—which are only likely to worsen—with the current administration’s decision to pull out of the Paris climate agreement and dismantle environmental regulations, and the call to action becomes more urgent. “The federal government’s actions might be a headwind from a funding perspective, but they are also very much a tailwind from an inspiration and motivation perspective,” says Daniel Rochberg, an instructor in environmental health who worked for the U.S. State Department as special assistant to the lead U.S. climate negotiators under presidents Bush and Obama. “As others have said, ‘We are the first generation to feel the sting of climate change, and we are the last generation that can do something about it.’ We have to get busy doing something about it.”
Rollins School of Public Health has gotten busy. Faculty researchers are building the science of climate impacts, strategies for reducing greenhouse gas emissions, and approaches for increasing resilience to climate change. Climate@Emory, a university-wide organization of concerned students, faculty, and staff, is partnering with other academic institutions, industries, and governments to support education and climate remediation efforts. Through Climate@Emory’s initiative, Emory University is an accredited, official observer to the UN climate talks and has sent students and faculty to the climate conferences in Paris in 2015 and in Marrakech in 2016. And, of course, Rollins is educating the next generation of scientists who will be dealing with the fallout of today’s climate decisions.
“For environmental scientists, it’s a challenging climate,” says Paige Tolbert, O. Wayne Rollins Chair of Environmental Health. “That means we have to be creative, because we can’t step aside and wait four years. It’s more critical than ever that we keep moving forward and make whatever contributions we possibly can.”
"We’ve developed advanced catalysts that allow us to control which carbon-hydrogen bond within a molecule will react and when," says Huw Davies, director of the Center for Selective C-H Functionalization. (Graphic/photo by Stephen Nowland and Dan Morton)
By Carol Clark
The National Science Foundation has awarded another $20 million to Emory University’s Center for Selective C-H Functionalization, to fund the next phase of a global effort to revolutionize the field of organic synthesis.
“Our center is at the forefront of a major shift in the way that we do chemistry,” says Huw Davies, professor of chemistry at Emory and the director of the Center for Selective C-H Functionalization (CCHF). “This shift holds great promise for creating new pathways for drug discovery and the production of new materials to benefit everything from agriculture to electronics.”
The CCHF began as an NSF Center for Chemical Innovation in 2009, with a seed grant of $1.5 million and four collaborating universities. In 2012, the NSF awarded the CCHF its first $20 million, enabling it to grow to encompass 16 U.S. institutions and seven industrial affiliates, including six major pharmaceutical companies and one of the largest U.S. chemical suppliers. The center also built global connections with major players in C-H functionalization in Japan, South Korea and the U.K.
The CCHF has led the way for explosive growth in the field of C-H functionalization, publishing more than 200 papers on the topic through its collaborators. It has developed dozens of new catalysts for C-H functionalization, including four major classes from the Huw Davies group.
“The past five years we’ve developed the fundamentals for C-H functionalization and documented that the concept is viable,” Davies says. “Now we’re ideally positioned to maximize the further development of this chemistry and move forward to apply it.”
Huw Davies, right, in his lab with Emory post-doctoral fellow Sidney Wilkerson-Hill, left, and Emory junior Patricia Chi Lin. The CCHF has developed dozens of new catalysts for C-H functionalization, including four major classes from the Davies group. (Photo by Stephen Nowland, Emory Photo Video)
Traditionally, organic chemistry has focused on the division between reactive, or functional, molecular bonds and the inert, or non-functional bonds carbon-carbon (C-C) and carbon-hydrogen (C-H). The inert bonds provide a strong, stable scaffold for performing chemical synthesis with the reactive groups. C-H functionalization flips this model on its head.
“We’ve devised ways to make C-H bonds react so that they become functional,” Davies says. “And we’ve reached the stage where it is no longer the molecule itself that determines the process of the reaction — we’ve developed advanced catalysts that allow us to control which carbon-hydrogen bond within a molecule will react and when.”
C-H functionalization opens unexplored chemical space by taking petroleum byproducts, which have a lot of carbon-hydrogen bonds, and transforming them from waste into useful materials. It also strips out steps from the linear process of traditional organic synthesis, making it faster and more efficient.
The CCHF is not only transforming organic synthesis — it’s also creating new models for the way that organic chemistry is taught and that labs conduct research. Where previously individual labs tended to work in isolation to tackle problems, the CCHF has broken down walls across specialties, institutions and even countries to collectively take on the remaining challenges of selective C-H functionalization.
“We’ve got this incredible collaborative environment where organic chemists aren’t just sharing results — they’re sharing ideas,” Davies says. “That’s rare. And we’ve expanded that environment beyond our network of universities to also engage the pharmaceutical industry.”
In 2015, the CCHF launched an online symposia on recent advances in C-H functionalization. More than 1,000 graduate students and chemistry faculty from up to 45 countries join the symposia, held about four times a year, via the Internet.
“We have leading voices in the field give these free talks that are easy to join live and participate in,” Davies says. “The aim is to further expand the field of C-H functionalization by introducing it to graduate students and other chemists around the world.”
In the simplest terms, an elliptic curve is a doughnut shape with carefully placed points, explain Emory University mathematicians Ken Ono, left, and John Duncan, right. “The whole game in the math of elliptic curves is determining whether the doughnut has sprinkles and, if so, where exactly the sprinkles are placed,” Duncan says. (Photos by Stephen Nowland, Emory Photo/Video)
By Carol Clark
Mathematicians have opened a new chapter in the theory of moonshine, one which begins to harness the power of the pariahs – sporadic simple groups that previously had no known application.
“We’ve found a new form of moonshine, which in math refers to an idea so farfetched as to sound like lunacy,” says Ken Ono, a number theorist at Emory University. “And we’ve used this moonshine to show the mathematical usefulness of the O’Nan pariah group in a way that moves it from theory to reality. It turns out that the O’Nan group knows deep information about elliptic curves.”
Nature Communications published the representation theory for the O’Nan group developed by Ono, John Duncan (also a number theorist at Emory) and Michael Mertens (a former post-doctoral fellow at Emory who is now at the University of Cologne).
“We’ve shown that the O’Nan group, a very large pariah group, actually organizes elliptic curves in a beautiful and systematic way,” Duncan says. “And not only does it organize them, it allows us to see some of their deepest properties. It sees infinitely many curves, which allows us to then use our moonshine to make predictions about their general behavior. That’s important, because these objects underlie some of the hardest questions at the very horizon of number theory.”
Elliptic curves may sound esoteric, but they are part of our day-to-day lives. They are used in cryptography – the creation of codes that are difficult to break.
An elliptic curve is not an ellipse, rather it is a complex torus, or doughnut shape.
“You can think of it as a doughnut together with specific, delicate configurations of rational points that are very carefully placed,” Duncan says. “So, in the simplest of terms, it’s like a doughnut that you eat, that may have sprinkles on it. The whole game in the math of elliptic curves is determining whether the doughnut has sprinkles and, if so, where exactly the sprinkles are placed.”
Unlike an edible doughnut, however, these mathematical doughnuts are not visible.
“Imagine you are holding a doughnut in the dark,” Ono says. “You wouldn’t even be able to decide whether it has any sprinkles. But the information in our O’Nan moonshine allows us to ‘see’ our mathematical doughnuts clearly by giving us a wealth of information about the points on elliptic curves.”
The findings are especially surprising since none of the pariahs, as six of math’s sporadic simple groups are known, had previously appeared in moonshine theory, or anywhere else in science.
Math’s original moonshine theory dates to a 1979 paper called “Monstrous Moonshine” by John Conway and Simon Norton. The paper described a surprising connection between a massive algebraic object known as the monster group and the j-function, a key object in number theory. In 2015, a group of mathematicians – including Duncan and Ono – presented proof of the Umbral Moonshine Conjecture, which revealed 23 other moonshines, or mysterious connections between the dimensions of symmetry groups and coefficients of special functions.
In theoretical math, symmetry comes in groups. Symmetrical solutions are usually optimal, since they allow you to divide a large problem into equal parts and solve it faster.
The classification of the building blocks of groups is gathered in the ATLAS of Finite Groups, published in 1985. “The ATLAS is like math’s version of the periodic table of the elements, but for symmetry instead of atoms,” Duncan explains.
Both the ATLAS and the periodic table contain quirky characters that may – or may not – exist in nature.
Four super heavy elements with atomic numbers above 100, for example, were discovered in 2016 and added to the periodic table. “People have to work hard to produce these elements in particle accelerators and they vanish immediately after they are constructed,” Ono says. “So you have to wonder if they really are a part of our everyday chemistry.”
The pariah groups pose a similar question in math. Are they natural or simply theoretical constructs?
“Our work proves, for the first time, that a pariah is real,” Ono says. “We found the O’Nan group living in nature. Our theorem shows that it’s connected to elliptic curves, and whenever you find a correspondence between two objects that are seemingly not related, it opens the door to learning more about those objects.”
Emory anthropologist Jessica Thompson next to Malawi rock art paintings, likely made by hunter-gatherers. Thompson's work in Malawi is part of a major new paper in the journal Cell, filling in thousands of years of human prehistory of hunter-gatherers in Africa. (Photo by Suzanne Kunitz)
By Carol Clark
Emory anthropologist Jessica Thompson was at a human origins conference years ago when she heard a presenter lament: “Of course, there is no ancient DNA from Africa because of the poor preservation there.”
That’s when it clicked in Thompson’s mind: She had visited a place in Africa — the highlands of northern Malawi — that had neither extremes of heat or wetness — two main environmental factors that degrade DNA. She also knew that scant archaeological research had been done in the region, although a team had unearthed several ancient skeletons there decades ago.
“It’s a strange and fascinating landscape,” says Thompson, who made that 2005 visit as a tourist and was struck by the surreal beauty of the high mountain grassland.
It’s also remote and off the radar of most of the world. “We saw maybe three other tourists while we were there,” she recalls.
That fateful trip laid the groundwork for discoveries of the oldest-known DNA from Africa. The journal Cell just published an analysis of the new discoveries, filling in thousands of years of human prehistory of hunter-gatherers in Africa, led by Harvard geneticist David Reich.
Thompson is second author of the paper. She contributed and described the cultural context for nearly half of the 15 new DNA finds, including the oldest samples. Her fieldwork in Malawi uncovered human remains that yielded DNA ranging in age from about 2,500 to 6,100 years old. And her work is ongoing at a site where a skeleton recovered in 1950 was just dated to 8,100 years old and also yielded DNA.
The other DNA in the Cell paper ranges in age from 3,000-to-500 years ago and comes from South Africa, Tanzania and Kenya.
“Malawi is positioned in between where living hunter-gatherers survive,” Thompson says. “For the first time, we can see the distribution of ancient hunter-gatherer DNA across Africa, showing how these populations were connected in the past.”
Ancient hunter-gatherers do not have a lot of living representatives in Africa today, and they occur as remnants of people scattered across the continent. The remains of Malawi hunter-gatherers that Thompson is studying may represent a population that was once thriving but subsequently pushed into marginal areas during the expansion of agriculturalists and pastoralists during the past 3,000 years.
Some of this population may have survived until much more recently.
“There are legends in Malawi of the original people who came there, passed down through oral histories,” Thompson says. “They are described as hunters and little people, short in stature. There is also a story of a last, epic battle — that occurred about 200 years ago — when these people got eradicated.”
Mount Hora, where the oldest DNA included in the Cell paper was obtained, from a woman who lived more than 8,000 years ago. (Photo by Jessica Thompson)
Malawi captivated Thompson during that first visit as a tourist, in 2005. She was a graduate student when she spent a summer working on a dig in the Serengeti. She and two companions decided to make a road trip before returning to the United States, including a stop in Malawi.
The landlocked country is located in southeast Africa, bordered by Zambia, Tanzania and Mozambique. It is one of the least-developed and smallest countries in Africa, about the size of the state of Tennessee, and runs north to south along the Rift Valley. An enormous body of water, Lake Malawi, makes up about one-third of the country.
“My traveling companies wanted to relax by the lake in the lowlands,” Thompson recalls. “I had read about the Malawi highlands and really wanted to see this unique ecosystem, so I convinced them to go there instead.”
Her companions complained of the cold — it’s windy and regularly freezes in the highlands of Malawi and summer temperatures peak at around 65 or 70 degrees Fahrenheit. Despite the cold, Thompson admired the rugged, isolated beauty of rocky outcrops and grasslands studded with orchids and fairy ferns where zebra and shaggy antelope grazed.
Thompson, who joined Emory as an assistant professor of anthropology in 2015, dug through the archaeological literature surrounding Malawi and started making exploratory trips there in 2009. She learned of two digs in the Malawi highlands — in 1950 and 1966 — that revealed human skeletons alongside rich cultural evidence of an extinct hunting-and-gathering lifeway.
Dancers at a festival in Malawi. The people living in the country today are the descendants of the Iron Age agriculturalists and pastoralists who swept across the African continent about 3,000 years ago. (Photo by Jessica Thompson)
The 1950 dig turned out to be led by the renowned archaeologist J. Desmond Clark, who Thompson calls her “academic grandfather.” Although Clark died before Thompson could meet him, he served as the mentor to her mentor, Curtis Marean.
On the slopes of Mount Hora — a striking 1,500-meter peak and a major landmark in the highlands — Clark uncovered two skeletons: A woman who had died at around age 22 and a nearby male, who had died in his 40s. The skeletons had been taken out of the country, to the Livingstone Museum in Zambia, and were never dated.
“It was impossible to accurately do radiocarbon dating on bone in 1950,” Thompson explains. “The skeletons became, quite frankly, forgotten over time.”
Guided by the clues from the previous excavations, Thompson began heading digs in the Malawi highlands. A site at a landmark outcrop, known as Fingira Rock, is particularly isolated, requiring the team to hike up a mountainside to more than 2,000 meters on the Nyika Plateau. “Working there you feel the wind, you feel the chill,” Thompson says.
Poachers are a hazard in the area, along with the occasional black mamba — one of the world’s deadliest snakes.
The Fingira site had not been excavated since 1966. “We were appalled to discover that it had been heavily disturbed since then,” Thompson says. Her team uncovered two human leg bones, from two different adult males, which yielded DNA that was about 6,100 years old.
The leg bone of a hunter-gatherer that lived 6,100 years ago, found at the Fingira Rock site. (Photo by Jessica Thompson)
In the back of a cave, they found fragments of a child’s skull in a termite mound. A tiny leg bone next to it indicated that the remains were from a baby younger than age one. DNA analysis revealed that she had been a girl and radiocarbon dating showed that she had died about 2,500 years ago. The analysis also showed that the bones from the infant and the two men were from the same hunter-gatherer population — even though they were separated by thousands of years of time.
The archaeological sediments suggest that Fingira was a place where the dead were buried, although the skeletal material has become scattered over time. Human bones are mixed with the bones of animals that they hunted and ate, as well as with stone tools and shell beads that they used for ornaments.
“When you visit the site,” Thompson says, “you wonder, why were these people living up here when it’s not the most comfortable conditions you can imagine? What was bringing them here? Why were they burying their dead, over and over again, for many thousands of years, in the same place?”
Meanwhile, Thompson tracked down the skeletons that Clark had discovered at Mount Hora in 1950. She learned they had been moved from Zambia to the University of Cape Town in South Africa.
Here’s where Emory graduate student Kendra Ann Sirak enters the story. Sirak had the distinction of being the last graduate student of Emory anthropologist George Armelagos, one of the founders of the field of paleopathology. He spent decades working with graduate students to study the bones of ancient Sudanese Nubians to learn about patterns of health, illness and death in the past. Armelagos sent Sirak to one of the best ancient DNA labs in the world, at University College Dublin (UCD), in Ireland, with samples of the Nubian bones.
After Armelagos died in 2014, at age 77, Thompson stepped in as one of Sirak’s mentors.
Thompson,
left, examines fragments of artifacts from the Malawi excavations in her
lab with Emory graduate student Kendra Ann Sirak. Sirak helped with the
radiocarbon dating and DNA extraction of the "forgotten" 8,100-year-old
skeleton from Mount Hora. (Photo by Ann Borden, Emory Photo/Video)
Thompson contacted the curator of the two skeletons from Mount Hora, to ask about the possibility of getting DNA from them. Alan Morris, now Professor Emeritus at the University of Cape Town, had had the same idea. A sample from the female skeleton was already slated to be sent to the UCD lab where Sirak was working. So Thompson, Morris and Sirak teamed up on the quest.
The petrous bone, which contains components of the inner ear, is the most promising site to drill for ancient DNA. The skeleton's petrous bone had already broken away from the skull, so only this tiny, triangular-shaped piece of the skeleton was sent to Dublin.
"It was extremely fragile," says Sirak, whose job was to drill into the petrous bone and get about 200 millimeters of bone powder without shattering the specimen.
She drank a cup of coffee, donned a hair cover, overalls, a face mask, two pairs of gloves and shoe covers, then entered a small, sterile room where the petrous bone awaited. "I said to myself, 'Here we go, I've got this!'" Sirak recalls.
Sirak was successful. Her colleagues in Dublin processed the sample and then sent it to the genetics team at Harvard Medical School for DNA analysis, which was also successful.
Meanwhile, radiocarbon dating revealed that the skeleton was 8,100 years old.
"It was like Christmas," Sirak says, "knowing that we had DNA data on such an ancient specimen."
The skeleton's genetics connected her to the same population of hunter-gatherers who died thousands of years later and were found 70 kilometers away at Fingira.
Another surprise revealed by the genetic analysis of the Malawi hunter-gatherers: They did not contribute any detectable ancestry to the people living in Malawi today, the descendants of the Iron Age agriculturalists and pastoralists who began sweeping across the African continent about 3,000 years ago.
“In most parts of Africa, you see quite a bit of admixture,” Thompson says. “When you take genetic samples from modern people who are living today, you find that they are a combination of the folks who were expanding into a region and also the folks who were living there before. In Malawi we see that’s not the case. It appears that there was a complete replacement of the original hunter-gatherer people. They are not just gone as a lifeway, they are actually gone as a people as well.”
One of the mysteries Thompson hopes to solve is how that replacement happened. Was it violent? Was it a sudden or a slow process? Did the entrance of strange new technologies, like pottery and iron working, play a role?
“We can’t use genetics to answer these questions,” Thompson says. “We have to use the archaeology.”
Emory anthropology undergraduates assisting with the Malawi excavations this past summer included, from left: Alexa Rome, Alexandra Davis, Suzanne Kunitz and Aditi Majoe. Graduate student Grace Veatch is on the far right.
She continues to excavate in Malawi, aided by local technicians and other collaborators. This summer, five Emory anthropology students accompanied her in the field: Graduate student Grace Veatch, senior Alexandra Davis, juniors Aditi Majoe and Suzanne Kunitz, and sophomore Alexa Rome. They uncovered more human remains at Mount Hora — a charred bone from a human arm and parts of two legs. These bones, recently dated to between 9,500 and 9,300 years old, show that the Hora site still has many secrets to reveal.
While radiocarbon dating of charcoal samples from just above and below the bones establishes their age, it is not clear whether they will yield DNA. “We don’t have high hopes,” Thompson says, “as they were burned and that tends to create even more preservation problems.”
The students assisted in the tedious work of carefully sifting through grey dust and ash, marking coordinates through GPS and other surveying tools, and recording the data into a computer.
Back in her lab at Emory, Thompson uses the data to generate three-dimensional images of the digs and pinpoint where each bone fragment, shell bead or stone tool was found. Her digital model for the this summer’s Mount Hora dig uses different-colored dots to give a glimpse of how hunter-gatherers were depositing both human remains and ordinary objects from their day-to-day lives over time.
“And then at this point,” Thompson says as she moves her cursor on her computer screen, “you see the introduction of pottery and iron technology. And right after that you see this fundamental change in the way that the site was used. People are no longer going there frequently. They’re no longer making these big bonfires. And they’re no longer interring their dead there.”
Thompson and her students are also sorting through hundreds of gallon-sized Ziploc plastic bags containing fragments from the Malawi sites. “As you excavate,” she explains, “you clean away the dirt and you’re left with all these tiny pieces of stone and bone artifacts. The bones are mostly animals. But every once in a while you find something that looks like it might be human. Any one one of them could be a new individual, a new piece to the story.”
She pulls out a small plastic bag labeled “Human distal phalanx.” It contains a piece of bone about the size of a Tic-Tac. “In this case, we think we have a finger bone, most likely from a child,” Thompson says.
Ultimately, Thompson seeks to understand how and when the earliest members of our species — Stone Age Homo sapiens — interacted with one another and with their environments in Africa.
“One thing that’s really easy to forget, when we look at the way people live today, is that for most of our evolution we lived as hunter-gatherers,” she says. “So if we want to understand our own origins as a species, we have to know what those lifeways looked like in the past.”
