Changes in rat size reveal habitat of 'Hobbit' hominin

At the Liang Bua cave site, paleoanthropologist Matthew Tocheri, left, measures a modern giant rat with the assistance of Bonefasius Sagut. At right is a reconstruction of Homo floresiensis carrying a giant rat, by paleo artist Peter Schouten.

By Carol Clark

A study of rat body sizes shifting over time gives a glimpse into the habitat of the mysterious hominin Homo floresiensis — nicknamed the “Hobbit” due to its diminutive stature.

The Journal of Human Evolution is publishing the study, based on an analysis of thousands of rodent bones, mainly fore- and hind-limbs, from an Indonesian cave where H. floresiensis was discovered in 2003. The results indicate that the local habitat was mostly open grasslands more than 100,000 years ago, but began shifting rapidly to a more closed environment 60,000 years ago.

“Our paper is the first that we know of to use the leg bones of rats in this way to interpret ecological change through time, and it provides new evidence for the local environment during the time of Homo Floresiensis,” says Elizabeth Grace Veatch, a PhD candidate at Emory University and a first author of the study.

Veatch with an H. floresiensis skull.

H. floresiensis stood only about 3 feet 6 inches tall and was known to have lived about 190,000 to 50,000 years ago on the oceanic island of Flores in eastern Indonesia. The tiny hominin shared the island with animals that could have come from the pages of a Tolkien novel, including giant Komodo dragons, six-foot-tall storks, vultures with a six-foot wingspan, and pygmy Stegodons — herbivores that looked like small elephants with swooping, oversized tusks.

It was the rats, however, that most interested Veatch.

Murids, as the rat family is known, are more taxonomically diverse than any other mammal group and are found in nearly every part of the world. “They exhibit an incredible range of behaviors occupying many different ecological niches,” Veatch says. “And because small mammals are typically sensitive to ecological shifts, they can tell you a lot about what’s going on in an environment.”

The study was based on remains recovered from the limestone cave known as Liang Bua, where partial skeletons of H. floresiensis have been found, along with stone tools and the remains of animals — most of them rats. In fact, out of the 275,000 animal bones identified in the cave so far, 80 percent of them are from rodents.

Veatch came to Emory to work with paleoanthropologist Jessica Thompson, a leading expert in using taphonomy — the study of what happens to bones after an organism dies — to learn more about the evolution of the human diet. Although Thompson has now moved to Yale University, she continues to mentor Veatch in her graduate studies at Emory.

Veatch became part of the Liang Bua project while doing an internship with the Human Origins Program of the Smithsonian Institution’s National Museum of Natural History. Her mentor there was paleoanthropologist Matthew Tocheri (now with Lakehead University in Ontario) who shares first-authorship of the current paper with Veatch.

“Matthew asked me if I wanted to analyze some rat bones and I said, ‘Sure,’” Veatch recalls. “I had no idea what I was getting into.”

A graphic of the rat species included in the study.

The study encompassed about 10,000 of the Liang Bua rat bones. The remains spanned five species with distinct sizes, from the mouse-sized Rattus hainaldi up to the housecat-sized Papagomys armandvillei — commonly known as the Flores giant rat. After categorizing the bones, the researchers could then directly link them to both species and environmental types.

While rats can adjust to new environments, the morphologies of different species tend to be adaptive to their preferred environment. For example, the habitat of the medium-sized Komodomys rintjanus, included in the study, is primarily open grasslands intermittent with patches of forest. In contrast, the tiny R. hainaldi and the giant P. armandvillei both prefer more closed or semi-closed forested habitats.

Tracking the relative abundances of the different rat species over time indicated that the local ecology was mostly open grassland 100,000 years ago, transitioning to a more-closed, forested habitat around 60,000 years ago. That is around the same time that skeletal elements belonging to Homo floresiensis, the pygmy Stegodon, giant storks, vulture and Komodo dragons disappear from Liang Bua.

“The evidence suggests that Homo floresiensis may have preferred more open habitats where they may have been a part of this scavenging guild of Stegodons, storks and vultures,” Veatch says. “We think that when the habitat changed, becoming more forested, Homo floresiensis probably left the Liang Bua area, tracking these animals to more open habitats elsewhere on the island.”

Veatch looks at piles of sediment excavated from Luang Bua as it is being wet sieved using the irrigation system of a rice paddy near the cave site.

Many more mysteries remain regarding H. floresiensis, Veatch says, and the Liang Bua rat bones may help solve some of them. One key question is whether H. floresiensis hunted small game.

“Our early ancestors adapted to consuming large amounts of big game through hunting or scavenging — or both,” Veatch says. “Big game undoubtedly became a critical food source, resulting in numerous social and physiological adaptations, including social cooperation and brain expansion. It’s much less known, however, what role small-game hunting may have played in our early evolution — if any at all.”

Liang Bua, she says, offers an ideal opportunity to study what a small-brained hominin, like H. floresiensis, might hunt if it had both sources of big game, like the Stegodon, and small game, like the giant Flores rat and other rat species.

Veatch is conducting field studies at the Liang Bua site, including running experiments to determine how difficult it would be to capture wild Flores rats. She is also doing research at the Pusat Penelitian Arkeologi Nasional (ARKENAS) Museum in the Indonesian capital of Jakarta where many of the bones from the cave site are now stored. She is analyzing a large sample of the bones to determine if any have cut marks — indicating butchering with tools — or pitted marks that would indicate they were digested by owls or other raptors that may have deposited them in the cave.

“In Indonesia, my nickname is Miss Tikus, which means ‘Miss Rat,’” Veatch says. “I’m perfectly fine with that because rats are really intelligent and extraordinary animals. We see them through the entire sequence in the archeology of Liang Bua and we will continue to use them in future studies to learn more about what went on in the cave.”

Co-authors of the current paper include Thomas Sutikna, E. Wahyu Saptomo and Jamiko, who are all from ARKENAS and the University of Wollongong in Australia; Kate McGrath from the University of Bordeaux, France; and Kristofer Helgen from the University of Adelaide in Australia.

Photo credits: All images courtesy of the Liang Bua research team. Photo of Veatch with skull was taken by Kristofer Helgen. The photo of Veatch and sediment was taken by Hanneke Meijer.

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From Stone Age chips to microchips: How tiny tools made us human

Tiny stone flakes such as the one above, from a site in South Africa called Boomplaas, may have helped some humans survive the last period of rapid climate change, 17,000 years ago, says Emory anthropologist Justin Pargeter.

Anthropologists have long made the case that tool-making is one of the key behaviors that separated our human ancestors from other primates. A new paper, however, argues that it was not tool-making that set hominins apart — it was the miniaturization of tools.

Just as tiny transistors transformed telecommunications a few decades ago, and scientists are now challenged to make them even smaller, our Stone Age ancestors felt the urge to make tiny tools. “It’s a need that we’ve been perennially faced with and driven by,” says Justin Pargeter, an anthropologist at Emory University and lead author of the paper. “Miniaturization is the thing that we do.”

The journal Evolutionary Anthropology is publishing the paper — the first comprehensive overview of prehistoric tool miniaturization. It proposes that miniaturization is a central tendency in hominin technologies going back at least 2.6 million years.

Learn more by clicking here.

Computer scientist explains 'Dangers of the Coded Gaze'

Watch a video of Joy Buolamwini discussing her work.

As a master’s student at MIT, Joy Buolamwini discovered that her own face read as male in many facial-analysis software systems — if her face was detected at all. And, no, it was not a personal slight; it turns out that many darker-skinned women of color also read as male. If you were what Buolamwini terms a “pale male,” though, most systems could categorize you with a high rate of accuracy. 

Buolamwini, a computer scientist and digital activist, went on to found the Algorithmic Justice League, raising awareness to the problem of any company refusing to acknowledge bias in its facial-recognition software. She recently spoke at Emory as part of the Provost Lecture Series, which is designed to inspire the Emory community to think about big questions and collaborate on innovative solutions.

As Deboleena Roy, chair of Emory’s Department of Women’s, Gender, and Sexuality Studies and faculty in Neuroscience and Behavioral Biology, said in introducing Buolamwini, “Rather than sit back and see the creation of new technologies that work to reinforce dominant and discriminatory gender and racial norms, she instead is using her expertise as a scientist to envision a more socially just technological future. Applying her awareness of gender and race issues, she has dedicated her research and her career to creating more inclusive code and more inclusive coding practices.”

Click here to read more about Buolamwini's Emory talk, entitled "Dangers of the Coded Gaze."

Atlanta Science Festival to launch at Emory with the power of WOW!

Wow in the World host Mindy Thomas, center, will kick off the Atlanta Science Festival with the help of musical duo The Pop Ups (Jacob Stein, left, and Jason Rabinowitz).

By Carol Clark

Watch for serious fun to spring up all around town as part of the 2019 Atlanta Science Festival, March 9 to March 23. The festival begins with a Wow in the World Pop Up Party on Saturday, March 9 from 11 am to noon on the Emory University campus. Mindy Thomas, a host of the popular NPR science-themed podcast Wow in the World, will engage curious kids and their grown-ups in games and skits with mad musical accompaniment by the Pop Ups — creators of the children’s music album Giants of Science.

A "Wow in the World" launch

“Wow in the World is an excellent program for kids and we really wanted to bring the energy of its team to Atlanta,” says Meisa Salaita, co-director of the Atlanta Science Festival. “They tie new and relevant research into interesting topics for kids, everything from ants that explode to seaweed that might boost your brain power. Kids are our future and getting them excited about science is so important.”

Kids will enjoy skits and games inspired by topics from the podcast like “Contagion Alert: The Science of Trying Not to Laugh” and “It SNOT What You Think.” Tickets are required for the launch event, set at Emory’s Glenn Memorial United Methodist Church, and it is expected to sell out.

The Atlanta Science Festival, or ASF, will feature more than 100 events throughout the metro area hosted by school districts, universities, museums, businesses and civic and community groups. Delta Air Lines is the presenting sponsor for 2019.

This year, Emory scientists will lead a walk with Mesozoic dinosaurs, discuss how neuro-engineering is blurring the lines between mind and machine and describe the physics of how babies learn to talk. Click here to see a full list of events connected to Emory.

Hundreds of visitors are expected on the Emory campus on Friday, March 22 for the perennial festival favorites, "Chemistry Carnival" and "Physics Live!"

“Science on Stage: The Forgotten Organ,” stars the bacteria, fungi and viruses within the human microbiome that shapes every one of us from birth. The Emory Center for the Study of Human Health teamed up with Theater at Emory to have playwrights quickly produce short plays about the microbiome. The playwrights drew their inspiration from a New York Times bestselling book by science writer Ed Yong, “I Contain Multitudes: The Microbes Within Us and a Grander View of Life.”

Yong will join the playwrights for readings of their works and a panel discussion of this unique collaboration between art and science. This event is set for Wednesday, March 20, at 6:30 pm at the Carter Presidential Library and Museum.

The Emory event “Become an Archaeologist” returns on Thursday, March 21 from 6 to 8 pm. This year the faculty and students involved are taking their bones off campus, to Brownwood Park in East Atlanta Village. The Emory experts will teach community members how to extract DNA and put pieces of ancient objects back together like a puzzle. “It’s a great example of the festival taking events that we know are popular and setting them in other parts of the city so that we can continue to reach new audiences and connect in different ways,” Salaita says. “Our goal is to keep broadening access to our programming.”

Two perennial festival favorites — Chemistry Carnival and Physics Live! — return this year to the Emory campus on Friday, March 22 from 3:30 to 7 pm. Emory science faculty and students will explain their research, give lab tours, and entertain with games like Peptide Jenga, a chance to play with giant soap bubbles and tastings of liquid nitrogen ice cream. Hundreds of visitors are expected to turn out for the events, held in the Mathematics and Science Center and Atwood Chemistry Center.

Oxford hosts "Ada and the Engine"

A highlight on Emory’s Oxford campus will be performances of the play “Ada and the Engine,” portraying the groundbreaking career of Ada Lovelace — a mathematician, poet and the first computer programmer. The play was written by Lauren Gunderson, an acclaimed playwright who graduated from Emory in 2004. During the festival, the play will be performed Friday and Saturday, March 21 and 22, at 7:30 pm. Performances will be followed by talks on the themes of women working in a field dominated by men, and a chance to walk through a special interactive exhibition, "Reviving Ada," curated by Oxford students to celebrate women's contributions to STEM fields from throughout history.

The festival culminates on Saturday, March 23 with the Exploration Expo at Piedmont Park — a day-long, free carnival of science with hundreds of hands-on activities. More than a dozen booths will feature Emory faculty and students, who will engage crowds in activities with names like “Air Pollution Particle Toss,” “Opening a Can of Worms: Exploring Biomaterials and Nanotechnology with Alginate Gummy Worms,” “Smell the World,” and “Can You Guess What Your Brain is Thinking?”

Founded in 2014 by Emory University, Georgia Tech and the Metro Atlanta Chamber, the ASF celebration of local science, technology, engineering and math has brought programming to more than 200,000 people in the metro region, reaching a diverse audience of a wide variety of ages. 

Special funding from sponsors such as Delta, the Arthur M. Blank Family Foundation and others is helping ASF soar to new heights and extend some of its programming and events year-round. A chief science officer program charges student representatives from middle schools and high school to foster science communities at their schools.

“These chief science officers, who are elected by their student bodies, receive leadership training, meet with state legislators and learn about the role of science and policy,” Salaita says. “We launched the program this year with 22 students and we plan to grow exponentially over the next three years to 200 students.”

Another program piloted this past year by the ASF is a science communication training fellowship for graduate students and post-doctoral fellows. “We’ve started with eight students who met monthly to learn about narrative in science communication, data visualization and other communication techniques,” Salaita says. “They will use their new skills to create events for the science festival and give informal talks to the general public.”

Another new component of the ASF is a year-round calendar of STEM-themed activities. “We want people to stay connected to science,” Salaita explains. “Our new events calendar is a guide for family friendly activities in the metro Atlanta area when the festival’s not happening.”

A new spin on computing: Chemist leads $3.9 million DOE quest for quantum software

"Quantum computers are not just exponentially faster, they work in a radically different way from classical computers," says chemist Francesco Evangelista, who is leading a project to develop quantum software.

By Carol Clark

When most people think of a chemistry lab, they picture scientists in white coats mixing chemicals in beakers. But the lab of theoretical chemist Francesco Evangelista looks more like the office of a tech start-up. Graduate students in jeans and t-shirts sit around a large, round table chatting as they work on laptops.

“A ‘classical’ chemist is focused on getting a chemical reaction and creating new molecules,” explains Evangelista, assistant professor at Emory University. “As theoretical chemists, we want to understand how chemistry really works — how all the atoms involved interact with one another during a reaction.”

Working at the intersection of math, physics, chemistry and computer science, the theorists develop algorithms to serve as simulation models for the molecular behaviors of atomic nuclei and electrons. They also develop software that enables them to feed these algorithms into “super” computers — nearly a million times faster than a laptop — to study chemical processes.

The problem is, even super computers are taxed by the mind-boggling combinatorial complexity underlying reactions. That limits the pace of the research.

“Computers have hit a barrier in terms of speed,” Evangelista says. “One way to make them more powerful is to make transistors smaller, but you can’t make them smaller than the width of a couple of atoms — the limit imposed by quantum mechanics. That’s why there is a race right now to make breakthroughs in quantum computing.”

Evangelista and his graduate students have now joined that race.

The Department of Energy (DOE) awarded Evangelista $3.9 million to lead research into the development of software to run the first generation of quantum computers. He is the principal investigator for the project, encompassing scientists at seven universities, to develop new methods and algorithms for calculating problems in quantum chemistry. The tools the team develops will be open access, made available to other researchers for free.

Watch a video about Francesco Evangelista's work, 
produced by the Camille & Henry Dreyfus Foundation:


While big-data leaders — such as IBM, Google, Intel and Rigetti — have developed prototypes of quantum computers, the field remains in its infancy. Many technological challenges remain before quantum computers can fulfill their promise of speeding up calculations to crack major mysteries of the natural world.

The federal government will play a strong supporting role in achieving this goal. President Trump recently signed a $1.2 billion law, the National Quantum Initiative Act, to fund advances in quantum technologies over the next five years.

“Right now, it’s a bit of a wild west, but eventually people working on this giant endeavor are going to work out some of the current technological problems,” Evangelista says. “When that happens, we need to have quantum software ready and a community trained to use it for theoretical chemistry. Our project is working on programming codes that will someday get quantum computers to do the calculations we want them to do.”

The project will pave the way for quantum computers to simulate chemical systems critical to the mission of the DOE, such as transition metal catalysts, high-temperature superconductors and novel materials that are beyond the realm of simulation on “classical” computers. The insights gained could speed up research into how to improve everything from solar power to nuclear energy.

Unlike objects in the “classical” world, that we can touch, see and experience around us, nature behaves much differently in the ultra-small quantum world of atoms and subatomic particles.

“One of the weird things about quantum mechanics is that you can’t say whether an electron is actually only here or there,” Evangelista says.

He takes a coin from his pocket. “In the classical world, we know that an object like this quarter is either in my pocket or in your pocket,” Evangelista says. “But if this was an electron, it could be in both our pockets. I cannot tell you exactly where it is, but I can use a wave function to describe the likelihood of whether it is here or there.”

To make things even more complicated, the behavior of electrons can be correlated, or entangled. When objects in our day-to-day lives, like strands of hair, become entangled they can be teased apart and separated again. That rule doesn’t apply at the quantum scale where entangled objects are somehow intimately connected even if they are apart in space.

“Three electrons moving in three separate orbitals can actually be interacting with one another,” Evangelista says. “Somehow they are talking together and their motion is correlated like ballerinas dancing and moving in a concerted way.”

Graduate students in Evangelista's lab are developing algorithms to simulate quantum software so they can run tests and adapt the design based on the results.

Much of Evangelista’s work involves trying to predict the collective behavior of strongly correlated electrons. In order to understand how a drug interacts with a protein, for example, he needs to consider how it affects the hundreds of thousands of atoms in that protein, along with the millions of electrons within those atoms.

“The problem quickly explodes in complexity,” Evangelista says. “Computationally, it’s difficult to account for all the possible combinations of ways the electrons could be interacting. The computer soon runs out of memory.”

A classical computer stores memory in a line of “bits,” which are represented by either a “0” or a “1.” It operates on chunks of 64 bits of memory at a time, and each bit is either distinctly a 0 or a 1. If you add another bit to the line, you get just one more bit of memory.

A quantum computer stores memory in quantum bits, or qubits. A single qubit can be either a 0 or a 1 — or mostly a 0 and part of a 1 — or any other combination of the two. When you add a qubit to a quantum computer, it increases the memory by a factor of two. The fastest quantum computers now available contain around 70 qubits.

“Quantum computers are not just exponentially faster, they work in a radically different way from classical computers,” Evangelista says.

For instance, a classical computer can determine all the consequences of a chess move by working one at a time through the chain of possible next moves. A quantum computer, however, could potentially determine all these possible moves in one go, without having to work through each step.

While quantum computers are powerful, they are also somewhat delicate.

“They’re extremely sensitive,” Evangelista says. “They have to be kept at low temperatures to maintain their coherence. In a typical setup, you also need a second computer kept at very low temperatures to drive the quantum computer, otherwise the heat from the wires coming out will destroy entanglement.”

The potential error rate is one of the challenges of the DOE project to develop quantum software. The researchers need to determine the range of errors that can still yield a practical solution to a calculation. They will also develop standard benchmarks for testing the accuracy and computing power of new quantum hardware and they will validate prototypes of quantum computers in collaborations with industry partners Google and Rigetti.

Just as they develop algorithms to simulate chemical processes, Evangelista and his graduate students are now developing algorithms to simulate quantum software so they can run tests and adapt the design based on the results.

Evangelista pulled together researchers from other universities with a range of expertise for the project, including some who are new to quantum computing and others who are already experts in the field. The team includes scientists from Rice University, Northwestern, the University of Michigan, CalTech, the University of Toronto and Dartmouth.

The long-range goal is to spur the development of more efficient energy sources, including solar power, by providing detailed data on phenomena such as the ways electrons in a molecule are affected when that molecule absorbs light.

“Ultimately, such theoretical insights could provide a rational path to efforts like making solar cells more efficient, saving the time and money needed to conduct trial-and-error experiments in a lab,” Evangelista says.

Evangelista also has ongoing collaborations with Emory chemistry professor Tim Lian, studying ways to harvest and convert solar energy into chemical fuels. In 2017, Evangelista won the Dirac Medal, one of the world’s most prestigious awards for theoretical and computational chemists under 40.

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