"Some animals were born to run. Others were born to burrow," says Emory paleontologist Anthony Martin, shown with the cast of a crustacean burrow from the Georgia coast. (Photo by Lisa Streib.)
By Carol Clark
The dirt flies in Emory paleontologist Anthony Martin’s new tell-all book, “The Evolution Underground: Burrows, Bunkers and the Marvelous Subterranean World Beneath Our Feet.” The book takes readers on a head-spinning tour of the underworld, from the tiny tunnels drilled by modern-day earthworms to the massive, four-meter-wide paleo-burrows excavated by the Pleistocene’s giant sloths.
“I want people to understand how the evolution of burrowing has shaped the environments we see today, from the ocean floor to high mountaintops,” Martin says. “Burrowing strategies are also key to the survival of many species – beyond just the burrowers themselves.”
Martin is a leading expert of ichnology – the study of trace fossils, including burrows, nests, tracks and feces. “The Evolution Underground,” published by Pegasus Books, is Martin’s seventh book, and his second aimed at a general audience, after 2014’s “Dinosaurs Without Bones.”
In the following interview, he reveals some of nature’s deepest, darkest secrets.
Q. When did burrowing behaviors begin in animals?
Tony Martin: The earliest evidence we have for burrowing goes back 550 million years, with marine animals. But these early burrowers, including trilobites, didn’t go very deep. If you think of the sea floor like a carpet, they were digging into the top of it or just beneath it, probably mining the sediment for food.
Around 545 million years ago, trilobites, marine worms and other invertebrates starting going deeper, burrowing vertically. They were probably both seeking organic particles for food and shelter against predators. Soon after that, predators started burrowing and the arms race was on.
Map of tunnel system made by Pleistocene giant ground sloths. U.S.S. Enterprise shuttlecraft (7 meters/23 feet long) for scale. (Figure by Anthony Martin.)
Q. How did these burrowers impact the environment?
TM: By punching down into the seabed, they put oxygen down into sediment that normally wasn’t exposed to it. That started oxidizing elements on the ocean floor, changing the carbon, phosphorous, nitrogen and sulphur cycles. So burrowing changed the ocean chemistry, which in turn had an influence on atmospheric chemistry. These early burrowers were ecosystem engineers.
They were also highly adaptable. The invasion of land by ocean life may have been facilitated by burrowing, enabling some species to make the transition to a new environment.
Q. So burrowers were the original survivalists?
TM: Yes! Burrowing enabled animals to make it through the worst that Earth threw at them – or even the worst that the solar system threw at them. A lot of animals, for example, lived after a large asteroid impact killed off the dinosaurs 66 million years ago. Why did they survive? They were in their bunkers! It’s likely there were other factors, but burrowing is definitely an advantage when you get a giant space rock dropped on you.
There are modern examples, as well. After the 1980 eruption by Mount St. Helens, scientists flew over this barren, smoldering wasteland in helicopters. All the largest animals were gone. One of the only signs of life was the tops of pocket gopher burrows. Ecologists determined that pocket gophers didn’t just survive the explosion, they helped the entire ecosystem come back. They mined the soil and brought up seeds from below, restoring vegetation. And their burrows provided microhabitats for reptiles and amphibians in the area.
Pocket gophers aren’t the only ecological heroes. Gopher tortoises dig burrows six-meters deep and create an underground zoo of diversity. Some 300-to-400 species live alongside the tortoises in their burrows, including indigo snakes, the longest snake native to North America, and rattlesnakes.
Behold an ecological hero — the pocket gopher! (Photo by Ty Smedes, Washington Department of Fish and Wildlife.)
Q. Do any animals stand out as the best burrowers?
TM: It depends on how you define “best,” but when it comes to the amount of soil overturned, ants are the rulers of the underground. Leafcutter ants create these spiral, vertical shafts that go down two meters and branch into a labyrinth of tunnels that connect to outer chambers. A recent excavation of a leafcutter colony in Brazil showed that these tiny insects had to move about 40 tons of soil to create their underground city. That’s the ant equivalent of the Great Wall of China, in terms of the effort that went into it. And that’s just a single ant colony. Especially compared to their size, ants have a disproportionate impact on ecosystems.
Q. What about human burrowing behaviors?
TM: Humans also burrow to survive predation and environmental extremes. The massive underground cities carved out of volcanic ash in Cappadocia, Turkey, during Byzantine times served as safe havens during times of war. Fears of nuclear warfare during the Cold War prompted the U.S. military to build networks of underground bunkers.
Montreal’s The Underground City was created mainly to deal with Canada’s long winters. People live, shop and go to the office while staying in a climate-controlled environment. And in the opal-mining town of Coober Pedy, in the Outback of Australia, people have adapted to the scorching heat by building underground houses.
We can learn a lot from burrowers of the geologic past, as well as the burrowing animals of today. If you want to survive a mass extinction, for example, you should probably start digging.
Related:
Bringing to life 'Dinosaurs Without Bones'
Dinosaur burrows yield clues to climate change
Lake bed trails tell ancient fish story
Thursday, February 2, 2017
Thursday, January 19, 2017
Experts warn of impending extinction of many of the world's primates
The black-and-white ruffed lemur of Madagascar is endangered due to hunting and to habitat loss. Most primates live in regions with high levels of human poverty and inequality, which contributes to the decline of the animals, says Thomas Gillespie, an Emory expert in the disease ecology of primates.
By Carol Clark
Urgent action is needed to protect the world’s dwindling primate populations, warns a group of 31 leading experts on primate conservation in Science Advances. Sixty percent of the more than 500 primate species worldwide are threatened with extinction, while more than 75 percent have declining populations, the landmark article reports. The authors include scientists and policymakers from the United States, Europe, Asia, Latin America and Africa.
“The majority of primate species are endangered now. We are at a turning point where we must take action or lose many species during the next 50 years,” says co-author Thomas Gillespie, an associate professor in Emory University’s Department of Environmental Sciences and an expert in the disease ecology of primates.
“Primates are our closest relatives and make up a large proportion of the mammals of the world,” he adds. “If we lose them, not only do we lose a lot of insights into ourselves, we lose the ecological services that they provide.”
The order primates – ranging from the tiny mouse lemurs of Madagascar to the massive mountain gorillas of Central Africa – is the third most diverse order of mammals, after rodents and bats. Primate species serve as seed dispersers, pollinators, predators and prey to keep ecosystems in balance. For instance, other rare animals – such as jaguars, leopards and harpy eagles – include monkeys in their diets.
Primates are so prevalent in zoos and in media imagery, many people are lulled into a false sense of security and do not realize how scarce they are becoming, Gillespie says.
The Science Advances article details how escalating human activities are putting unsustainable pressures on primates and their habitats, including extensive forest loss due to the expansion of industrial agriculture and large-scale catting ranching, logging, oil and gas drilling, mining, dam building and the construction of road networks for resource extraction.
In addition to habitat loss and poaching, disease is a major threat to many primate populations, and is often intertwined with the other two issues, Gillespie says. “It’s important to try to keep primate habitats as intact as possible,” he says, “because when they become fragmented primates may be forced to come out and raid agricultural crops just to get enough to eat. And crop raiding leads to all kinds of conflict, such as fights between dogs and primates, and opportunities for fecal contamination.”
A young chimpanzee in Gombe Stream National Park, where human misuse of antibiotics is putting the animals at risk for antibiotic-resistant bacterial infections. "If you help a local human population become healthier, you also reduce the potential for infectious disease in the surrounding wildlife," Gillespie says.
Disease is the main threat to the survival of the endangered chimpanzees of Tanzania’s Gombe Stream National Park, made famous by the work of primatologist Jane Goodall, who began observing them during the 1960s.
Work by Gillespie and his colleagues has found that human misuse of antibiotics is putting the Gombe chimpanzees at risk for antibiotic-resistant bacterial infections. The Gillespie lab is one of the few investigating the ecology and epidemiology of infectious disease in natural systems where domesticated animals, humans and wildlife overlap.
Among the pathogens threatening both humans and non-human primates are the malaria species Plasmodium knowlesi, which can cause disease in pigtail macaques in Southeast Asia; Ebola, which affects chimpanzees and gorillas in Africa; and yellow fever, which strikes brown howler monkeys in South America.
Most primates live in regions with high levels of human poverty and inequality, and the co-authors stress the need to improve human health and access to education, while also preserving traditional livelihoods that can contribute to food security and environmental conservation.
“If you help a local human population become healthier, you also reduce the potential for infectious disease in the surrounding wildlife,” Gillespie says.
The authors are calling on governmental officials, scientists, non-governmental organizations, businesses and individual citizens to mobilize and raise awareness of the plight of the world’s primates.
“If humans continue to alter and degrade habitats such that they are unsuitable for our primate relatives, then these habitats will eventually become unsuitable for ourselves,” they conclude.
Related:
In Madagascar, a health crisis of people and their ecosystem
Disease poses risk to chimpanzee conservation, Gombe study finds
Sanctuary chimps show high rates of drug-resistant staph
By Carol Clark
Urgent action is needed to protect the world’s dwindling primate populations, warns a group of 31 leading experts on primate conservation in Science Advances. Sixty percent of the more than 500 primate species worldwide are threatened with extinction, while more than 75 percent have declining populations, the landmark article reports. The authors include scientists and policymakers from the United States, Europe, Asia, Latin America and Africa.
“The majority of primate species are endangered now. We are at a turning point where we must take action or lose many species during the next 50 years,” says co-author Thomas Gillespie, an associate professor in Emory University’s Department of Environmental Sciences and an expert in the disease ecology of primates.
![]() |
| A young orangutan |
“Primates are our closest relatives and make up a large proportion of the mammals of the world,” he adds. “If we lose them, not only do we lose a lot of insights into ourselves, we lose the ecological services that they provide.”
The order primates – ranging from the tiny mouse lemurs of Madagascar to the massive mountain gorillas of Central Africa – is the third most diverse order of mammals, after rodents and bats. Primate species serve as seed dispersers, pollinators, predators and prey to keep ecosystems in balance. For instance, other rare animals – such as jaguars, leopards and harpy eagles – include monkeys in their diets.
Primates are so prevalent in zoos and in media imagery, many people are lulled into a false sense of security and do not realize how scarce they are becoming, Gillespie says.
The Science Advances article details how escalating human activities are putting unsustainable pressures on primates and their habitats, including extensive forest loss due to the expansion of industrial agriculture and large-scale catting ranching, logging, oil and gas drilling, mining, dam building and the construction of road networks for resource extraction.
In addition to habitat loss and poaching, disease is a major threat to many primate populations, and is often intertwined with the other two issues, Gillespie says. “It’s important to try to keep primate habitats as intact as possible,” he says, “because when they become fragmented primates may be forced to come out and raid agricultural crops just to get enough to eat. And crop raiding leads to all kinds of conflict, such as fights between dogs and primates, and opportunities for fecal contamination.”
A young chimpanzee in Gombe Stream National Park, where human misuse of antibiotics is putting the animals at risk for antibiotic-resistant bacterial infections. "If you help a local human population become healthier, you also reduce the potential for infectious disease in the surrounding wildlife," Gillespie says.
Disease is the main threat to the survival of the endangered chimpanzees of Tanzania’s Gombe Stream National Park, made famous by the work of primatologist Jane Goodall, who began observing them during the 1960s.
Work by Gillespie and his colleagues has found that human misuse of antibiotics is putting the Gombe chimpanzees at risk for antibiotic-resistant bacterial infections. The Gillespie lab is one of the few investigating the ecology and epidemiology of infectious disease in natural systems where domesticated animals, humans and wildlife overlap.
Among the pathogens threatening both humans and non-human primates are the malaria species Plasmodium knowlesi, which can cause disease in pigtail macaques in Southeast Asia; Ebola, which affects chimpanzees and gorillas in Africa; and yellow fever, which strikes brown howler monkeys in South America.
Most primates live in regions with high levels of human poverty and inequality, and the co-authors stress the need to improve human health and access to education, while also preserving traditional livelihoods that can contribute to food security and environmental conservation.
“If you help a local human population become healthier, you also reduce the potential for infectious disease in the surrounding wildlife,” Gillespie says.
The authors are calling on governmental officials, scientists, non-governmental organizations, businesses and individual citizens to mobilize and raise awareness of the plight of the world’s primates.
“If humans continue to alter and degrade habitats such that they are unsuitable for our primate relatives, then these habitats will eventually become unsuitable for ourselves,” they conclude.
Related:
In Madagascar, a health crisis of people and their ecosystem
Disease poses risk to chimpanzee conservation, Gombe study finds
Sanctuary chimps show high rates of drug-resistant staph
Tags:
Biology,
Community Outreach,
Ecology
Wednesday, January 18, 2017
Neuro-imaging maps brain wiring of extinct Tasmanian tiger
An 1862 illustration of the thylacine, or Tasmanian tiger. The extinct marsupial had dog-like features, along with tiger-like stripes and an abdominal pouch. "The thylacine brain is very different than the canine brain, despite the physical resemblance of their bodies," says Emory neuroscientist Gregory Berns.
By Carol Clark
Scientists have used an imaging technique to reconstruct the brain architecture and neural networks of the thylacine – better known as the Tasmanian tiger – an extinct carnivorous marsupial native to Tasmania. The study, published in PLOS ONE, used magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) to scan postmortem specimens of two thylacine brain specimens, both of which were about 100 years old.
The results, when compared to the Tasmanian tiger’s closest living relative, the Tasmanian devil, suggest that the larger-brained thylacine had more cortex devoted to planning and decision-making.
“The natural behavior of the thylacine was never scientifically documented,” says Gregory Berns, a neuroscientist at Emory University and the lead author of the study. “Our reconstruction of its white matter tracts, or neural wiring, between different regions of its brain is consistent with anecdotal evidence that the thylacine occupied a more complex, predatory ecological niche versus the scavenging niche of the Tasmanian devil.”
The comparative study also supports theories of brain evolution suggesting that as brains grow larger they become more modular, or divided into sections associated with discrete functions, Berns says.
Kenneth Ashwell, an anatomist at the University of New South Wales School of Medical Sciences and an expert on the brain evolution of marsupials and monotremes, co-authored the study.
“The technology for imaging the preserved brains of rare, extinct and endangered species is an exciting innovation in the study of brain evolution,” Ashwell says. “It will allow us to track pathways and study functional connections that could never be analyzed through older experimental techniques.”
Image shows the reconstruction of the neural pathways of the Tasmanian devil (left) and the Tasmanian tiger, or thylacine (right). (Image courtesy Gregory Berns).
Monotremes, such as the egg-laying platypus, are remnants of the first mammals, going back more than 150 million years. Marsupials formed a later branch of mammals, including the best-known example, the kangaroo. Instead of laying eggs, they bear relatively undeveloped young that must be carried in a mother’s pouch.
The Tasmanian tiger looked like an amalgam of several animals. It is one of only a few marsupials to have a pouch in both sexes. It was the size and shape of a medium-to-large size dog, but had tiger-like stripes running down its lower back and an abdominal pouch. Its Greek name, Thylacinus cynocephalus, means “dog-headed pouched one.”
The fossil record shows that the Tasmanian tiger appeared about four million years ago in Australia. By the 20th century it was extinct, or extremely rare, on the mainland but was still found in Tasmania, the island state off Australia’s southern coast. Its demise is attributed to loss of habitat through farming activity, coupled with a bounty scheme placed on the animal after it was suspected of killing sheep and other livestock. The last known Tasmanian tiger died in 1936, in Tasmania’s Hobart Zoo.
The Tasmanian devil, another iconic animal of Tasmania, is now the island’s largest surviving carnivorous marsupial. It is known for its powerful jaws and scream-like vocalizations. Tasmanian devils are also unique because they suffer from devil facial tumor disease – an infectious, non-viral parasitic cancer which they can transmit to one another through fighting. While the unusual disease makes the animals of interest to cancer researchers, it is threatening the survival of the remaining Tasmanian devils, whose wild population has declined by 70 percent during the past 20 years.
Berns, who was the first to conduct MRI experiments on awake, unrestrained dogs to learn more about their neural processes, was particularly intrigued by the thylacine due to its physical resemblance to dogs.
“The thylacine appears to be an example of convergent evolution, filling a similar niche that members of the canid family did elsewhere,” Berns says. “It’s interesting, however, that the thylacine brain is very different than the canine brain, despite the physical resemblance of their bodies.”
Only four surviving specimens of the brains of Tasmanian tigers exist, and the study gained access to two of them. One was provided by the Smithsonian Institution, taken from a male Tasmanian tiger after it died at the National Zoological Park in 1905. The other specimen, loaned to the researchers by the Australian Museum in Sydney, came from an animal that died during the 1930s.
The two Tasmanian devil brains used in the study included one from the Smithsonian Institution, which had been preserved around the same time as its Tasmanian tiger specimen. The other specimen came from a recently deceased animal and was supplied by the Save the Tasmanian Devil Program, a conservation initiative of the Australian and Tasmanian governments.
A male and female thylacine in the National Zoo of Washington D.C., circa 1904. (Photo by E. J. Baker, from the Smithsonian Institution archives).
MRI scans reveal information about the architecture of a brain – known as gray matter. Diffusion tensor imaging (DTI) provides information about how molecules move through biological tissues, revealing the connective pathways of a brain – known as white matter.
The technique of using DTI on a non-living brain is mainly applied to research on recently deceased humans, primates and rats. Berns is pioneering the use of a special form of DTI to digitally reconstruct the neural networks of other animals, using archived brain specimens from zoological and museum collections.
In 2015, Berns successfully used DTI on two decade-old specimens to map the sensory and motor systems of the brains of dolphins for the first time. The results showed how at least two areas of the dolphin brain are associated with the auditory system, unlike most mammals that primarily process sound in a single area.
The current digital reconstruction of the brain of the Tasmanian tiger is particularly important, Berns says, not just because the animal is extinct but because the specimens used were much older than those of the dolphins.
“While it is easier to study the brains of animals that have recently died, we’ve shown that we can successfully use our scanning techniques on specimens that are 100 years old,” Berns says. “We now have the technology available to make use of the treasure trove of museum collections around the world.”
Berns launched a project called the Brain Ark, a digital archive of high-resolution, three-dimensional brain structures of megafauna, which is publicly accessible via the web so that other researchers can contribute to and draw from the data. It currently includes the scans from the dolphins, Tasmanian tigers and Tasmanian devils.
The digital resource will allow researchers to explore questions about brain evolution, including how brain structure is related to species-specific attributes such as being primarily a predator or prey, foraging strategies, ecological niches and sexual dimorphisms.
“We know a lot about the brains of primates and rats, but there are a lot of other animal brains out there that no one has looked at in any kind of detail,” Berns says. “The Brain Ark is going to fill that gap. We are living in a time when much of the planet’s megafauna is at risk for extinction. It’s important to gather as much data as we can before many of these animals disappear.”
Related:
First images of dolphin circuitry hint at how they sense sound
Brain scans unleash canine secrets
By Carol Clark
Scientists have used an imaging technique to reconstruct the brain architecture and neural networks of the thylacine – better known as the Tasmanian tiger – an extinct carnivorous marsupial native to Tasmania. The study, published in PLOS ONE, used magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) to scan postmortem specimens of two thylacine brain specimens, both of which were about 100 years old.
The results, when compared to the Tasmanian tiger’s closest living relative, the Tasmanian devil, suggest that the larger-brained thylacine had more cortex devoted to planning and decision-making.
“The natural behavior of the thylacine was never scientifically documented,” says Gregory Berns, a neuroscientist at Emory University and the lead author of the study. “Our reconstruction of its white matter tracts, or neural wiring, between different regions of its brain is consistent with anecdotal evidence that the thylacine occupied a more complex, predatory ecological niche versus the scavenging niche of the Tasmanian devil.”
The comparative study also supports theories of brain evolution suggesting that as brains grow larger they become more modular, or divided into sections associated with discrete functions, Berns says.
Kenneth Ashwell, an anatomist at the University of New South Wales School of Medical Sciences and an expert on the brain evolution of marsupials and monotremes, co-authored the study.
“The technology for imaging the preserved brains of rare, extinct and endangered species is an exciting innovation in the study of brain evolution,” Ashwell says. “It will allow us to track pathways and study functional connections that could never be analyzed through older experimental techniques.”
Image shows the reconstruction of the neural pathways of the Tasmanian devil (left) and the Tasmanian tiger, or thylacine (right). (Image courtesy Gregory Berns).
Monotremes, such as the egg-laying platypus, are remnants of the first mammals, going back more than 150 million years. Marsupials formed a later branch of mammals, including the best-known example, the kangaroo. Instead of laying eggs, they bear relatively undeveloped young that must be carried in a mother’s pouch.
The Tasmanian tiger looked like an amalgam of several animals. It is one of only a few marsupials to have a pouch in both sexes. It was the size and shape of a medium-to-large size dog, but had tiger-like stripes running down its lower back and an abdominal pouch. Its Greek name, Thylacinus cynocephalus, means “dog-headed pouched one.”
The fossil record shows that the Tasmanian tiger appeared about four million years ago in Australia. By the 20th century it was extinct, or extremely rare, on the mainland but was still found in Tasmania, the island state off Australia’s southern coast. Its demise is attributed to loss of habitat through farming activity, coupled with a bounty scheme placed on the animal after it was suspected of killing sheep and other livestock. The last known Tasmanian tiger died in 1936, in Tasmania’s Hobart Zoo.
![]() |
| Tasmanian devil, top, and thylacine (1808) |
The Tasmanian devil, another iconic animal of Tasmania, is now the island’s largest surviving carnivorous marsupial. It is known for its powerful jaws and scream-like vocalizations. Tasmanian devils are also unique because they suffer from devil facial tumor disease – an infectious, non-viral parasitic cancer which they can transmit to one another through fighting. While the unusual disease makes the animals of interest to cancer researchers, it is threatening the survival of the remaining Tasmanian devils, whose wild population has declined by 70 percent during the past 20 years.
Berns, who was the first to conduct MRI experiments on awake, unrestrained dogs to learn more about their neural processes, was particularly intrigued by the thylacine due to its physical resemblance to dogs.
“The thylacine appears to be an example of convergent evolution, filling a similar niche that members of the canid family did elsewhere,” Berns says. “It’s interesting, however, that the thylacine brain is very different than the canine brain, despite the physical resemblance of their bodies.”
Only four surviving specimens of the brains of Tasmanian tigers exist, and the study gained access to two of them. One was provided by the Smithsonian Institution, taken from a male Tasmanian tiger after it died at the National Zoological Park in 1905. The other specimen, loaned to the researchers by the Australian Museum in Sydney, came from an animal that died during the 1930s.
The two Tasmanian devil brains used in the study included one from the Smithsonian Institution, which had been preserved around the same time as its Tasmanian tiger specimen. The other specimen came from a recently deceased animal and was supplied by the Save the Tasmanian Devil Program, a conservation initiative of the Australian and Tasmanian governments.
A male and female thylacine in the National Zoo of Washington D.C., circa 1904. (Photo by E. J. Baker, from the Smithsonian Institution archives).
MRI scans reveal information about the architecture of a brain – known as gray matter. Diffusion tensor imaging (DTI) provides information about how molecules move through biological tissues, revealing the connective pathways of a brain – known as white matter.
The technique of using DTI on a non-living brain is mainly applied to research on recently deceased humans, primates and rats. Berns is pioneering the use of a special form of DTI to digitally reconstruct the neural networks of other animals, using archived brain specimens from zoological and museum collections.
In 2015, Berns successfully used DTI on two decade-old specimens to map the sensory and motor systems of the brains of dolphins for the first time. The results showed how at least two areas of the dolphin brain are associated with the auditory system, unlike most mammals that primarily process sound in a single area.
The current digital reconstruction of the brain of the Tasmanian tiger is particularly important, Berns says, not just because the animal is extinct but because the specimens used were much older than those of the dolphins.
“While it is easier to study the brains of animals that have recently died, we’ve shown that we can successfully use our scanning techniques on specimens that are 100 years old,” Berns says. “We now have the technology available to make use of the treasure trove of museum collections around the world.”
Berns launched a project called the Brain Ark, a digital archive of high-resolution, three-dimensional brain structures of megafauna, which is publicly accessible via the web so that other researchers can contribute to and draw from the data. It currently includes the scans from the dolphins, Tasmanian tigers and Tasmanian devils.
The digital resource will allow researchers to explore questions about brain evolution, including how brain structure is related to species-specific attributes such as being primarily a predator or prey, foraging strategies, ecological niches and sexual dimorphisms.
“We know a lot about the brains of primates and rats, but there are a lot of other animal brains out there that no one has looked at in any kind of detail,” Berns says. “The Brain Ark is going to fill that gap. We are living in a time when much of the planet’s megafauna is at risk for extinction. It’s important to gather as much data as we can before many of these animals disappear.”
Related:
First images of dolphin circuitry hint at how they sense sound
Brain scans unleash canine secrets
Friday, December 16, 2016
Mind over matter: Her interest in the brain led her to computer science
"Your brain can store all of your experiences at some level. It doesn’t store every detail," says Emory computer scientist Avani Wildani. "If we can get a better idea of how information storage and reductionism
work in the brain, perhaps we could translate that to a computer
framework." (Photos by Ann Borden, Emory Photo/Video)
By Carol Clark
Avani Wildani, an Emory assistant professor of Mathematics and Computer Science, got her first computer when she was three years old. A TI-99 from Texas Instruments, it was the first 16-bit personal computer and known for its eccentricities.
“It spoke to you in this very robotic voice,” Wildani says. “It was a really hot thing at the time for the computer to talk to you.”
Wildani was born in Mechanicsburg, Pennsylvania, to immigrants from the state of Gujarat in India. The oldest of three children in a close-knit family, she did not start speaking English until she began school.
Biology fascinated her from an early age, particularly mysteries of how the brain works. “I’m interested in how we think about things,” she says, “and what information means for the mind.”
One focus of her current research is the looming problem of information storage: The disconnect between our growing ability to gather digital information – on everything from human genetics to deep space – and our limited technology and resources for keeping and managing all of that data.
Wildani originally aspired to be a physician, like her father. “He steered me into a more sedentary direction,” she says.
Her father realized that she needed a job where she could sit because she was born with osteogenesis imperfecta, or brittle bone disease. The disorder causes bones to break easily and Wildani endured hundreds of breaks and countless medical procedures as a child.
In September, she was hit by a car while crossing an Atlanta pedestrian crosswalk in her wheelchair, an incident that fractured her legs in seven places. She continued to work while recovering in her Druid Hills home.
Light streams into the modernistic home through large, plate-glass windows, which look out onto wooded terrain. Evidence of Wildani’s many hobbies is strewn about the house – a full set of drums, a telescope that she built from scratch, her pencil sketches, photos of her kayaking adventures. As she settles in for an interview in her home office, she offers a visitor a tray of Indian pastry sweets.
Below are some excerpts from the interview.
Q. What was it like to spend so much time in hospitals as a child?
Wildani: It wasn’t that bad. It would take me about 20 to 30 minutes a day to do my school homework, and I could still keep up. So the rest of the time I got to lie around, eat ice cream, and read. In fourth grade, I got through all of Nancy Drew.
It was probably harder on my parents. As a child, I just took it for granted that my parents would be at the hospital at 3 am with Indian food because I didn’t like American food. My mother would make me treats like khandvi – chickpea flour mixed with lemon and yogurt, rolled out and fried. It’s super good! Gujartis are like the Southerners of India: We fry everything.
Playing computer games "allows you to try something and fail in a safe way," says Wildani, who also plays the drums.
Q. Did you also spend a lot of time on a computer?
Wildani: Yes, I started learning about programming as soon as I learned to read, at age 3. I used LOGO, an educational programming language for children. It’s all about drawing pictures. In fact, the first time I taught Python to college students I had them integrate it with LOGO to make flowers for their mothers on Mother’s Day. People really loved that assignment and ran with it. They did all sorts of amazing animations.
Growing up, I also enjoyed computer games. I played a lot of King’s Quest, an early strategy game designed by Roberta Williams, who is one of my inspirations. King’s Quest was full of puzzles and the puzzles were hard. It teaches perseverance.
Q. So you don’t consider computer games a waste of time?
Wildani: No, not at all. They inspire a lot of people. I would say that everybody I knew during my college years played a lot of computer games as a kid. Even if you don’t go into computer science or technology for a career, computer games allow you to try something and fail in a safe way. You don’t die and you keep getting better the more you try. It also teaches team building. I think playing computer games is in some ways like playing a sport. I would be interested in studies that look at how the motor cortex changes if you play a lot of computer games.
Q. Maybe all those computer games you played account for the can-do spirit you embody in your real life.
Wildani: I’m not afraid to try things. I fail sometimes, but I have a really supportive family. I have a pretty solid mat to fall on when I screw up.
Q. How does your interest in the human brain relate to your research into computer data storage?
Wildani: Your brain can store all of your experiences at some level. It doesn’t store every detail. In fact, it forgets things on purpose, pruning data and keeping what you need to make sense of the world, stringing together related ideas and forming memories that it can then retrieve. One theory is that the hippocampus acts like a kind of card catalogue where the brain can look up the place where it has stored different pieces of data.
The brain does all this using very little power, only around 60 watts, and with a high fault rate. Neurons are dying all the time and synapses are breaking down. In fact, stroke patients can lose a significant part of their hippocampus and still function.
If we can get a better idea of how information storage and reductionism work in the brain, perhaps we could translate that to a computer framework. We’re using vision classification as a bio-model to run simulations and try to figure out how the brain makes tradeoffs between network size, power and reliability.
"We’re losing information about hidden things that we don’t already know to look for," Wildani says. "That’s why it’s critical now to come up with new ways to store large volumes of data."
Q. Why is it important to understand this?
Wildani: People are creating entire digital identities of family photos, emails, receipts – all kinds of data. Some of it is data that people want to keep and some of it is just stuff that gets saved unintentionally. You can think of all our personal collections of data like junk-filled closets that we store in “clouds.”
But what many people don’t realize is that the clouds are actually physical computer-data centers. And they require space, electricity and people to maintain them and to run them.
The centers house the physical storage devices for all the data. Disks, for instance, save data using tiny dots, called bits. But there is a limit to how close these dots can be, based on physics. They can only go to a certain resolution and no lower. Flash drives don’t rely on that sort of density, but they are not as reliable. And a disk only lasts about five years. So you have to have a plan to move data around between different devices.
We make a lot more information than we have anywhere to put it. Right now, Internet traffic is annually generating zetabytes of information and that’s projected to go up to yottabytes by 2020. [A yottabyte equals 1,000,000,000,000,000,000,000,000 bytes.]
We have this huge mess of data collected across time. How do we decide what’s important and what’s not? How long should we keep it? Who will pay for keeping it over time? There are things we archive with intention, like family photos, and things that we archive without really meaning to, like random receipts and emails.
Q. Could it just be a matter of everyone throwing out their digital “junk” and making space?
Wildani: The issue is much bigger than that. We can’t always know what is going to be important in the future. The tapes of the early “Dr. Who” episodes, for example, got written over years ago because the BBC didn’t think they were important.
In the future, if you get sick with something, it might be useful to pull up the medical records of your great grandparents. Or maybe not. You might also want to store a genome analysis of your family for the future.
My favorite example of “junk” data that became useful is a photograph that was taken in 1900 of a random patch of sky. Decades later, cosmologists found this photo in a drawer and saw that it contained a pre-supernova. By comparing it to modern-day photos of the same patch of sky, they were able to compute a more exact rate for the expansion of the universe.
We have much more powerful telescopes today but not enough storage to save all the data these instruments are capturing. The same is the case for CERN, home of the Large Hadron Collider, which is gathering large datasets on sub-atomic particles. CERN is only able to save the data that is being experimented on now.
We’re losing information about hidden things that we don’t already know to look for. That’s why it’s critical now to come up with new ways to store large volumes of data.
Q. How do you feel about the scarcity of women in computer science?
Wildani: When I was an undergraduate, I would have felt more comfortable if there had been more women in the room when I was asking a basic, technical question. But I had no choice. I was the only female in most of my computer science classes. And the default assumption for women is that you’re not competent. You have to prove yourself.
The traditional image of a computer science major is a guy with a beard who drinks a lot of Mountain Dew and spends a lot of time ranting on online forums. There are definitely some people who fit that personality type, but also many people who don’t. And some of them are so far from it that they don’t feel welcome and they leave.
I knew a woman in graduate school who was great at computer science, great at math, but she was also tall and blonde. She got tired of dealing with harassment and people who thought she was the receptionist. Eventually, she decided to go into a different field.
And yet, we need more people and different perspectives in computer science. The salaries for computer engineering are high because there are not enough people to fill the jobs.
I developed a web site (Project Hypatia) to highlight important research by women in computer science. I think it’s important to make it clear that women are not just asking for equality, but leading teams, doing impressive science and getting results.
Related:
BRAIN grant to fund study of how the mind learns
By Carol Clark
Avani Wildani, an Emory assistant professor of Mathematics and Computer Science, got her first computer when she was three years old. A TI-99 from Texas Instruments, it was the first 16-bit personal computer and known for its eccentricities.
“It spoke to you in this very robotic voice,” Wildani says. “It was a really hot thing at the time for the computer to talk to you.”
Wildani was born in Mechanicsburg, Pennsylvania, to immigrants from the state of Gujarat in India. The oldest of three children in a close-knit family, she did not start speaking English until she began school.
Biology fascinated her from an early age, particularly mysteries of how the brain works. “I’m interested in how we think about things,” she says, “and what information means for the mind.”
One focus of her current research is the looming problem of information storage: The disconnect between our growing ability to gather digital information – on everything from human genetics to deep space – and our limited technology and resources for keeping and managing all of that data.
Wildani originally aspired to be a physician, like her father. “He steered me into a more sedentary direction,” she says.
Her father realized that she needed a job where she could sit because she was born with osteogenesis imperfecta, or brittle bone disease. The disorder causes bones to break easily and Wildani endured hundreds of breaks and countless medical procedures as a child.
In September, she was hit by a car while crossing an Atlanta pedestrian crosswalk in her wheelchair, an incident that fractured her legs in seven places. She continued to work while recovering in her Druid Hills home.
Light streams into the modernistic home through large, plate-glass windows, which look out onto wooded terrain. Evidence of Wildani’s many hobbies is strewn about the house – a full set of drums, a telescope that she built from scratch, her pencil sketches, photos of her kayaking adventures. As she settles in for an interview in her home office, she offers a visitor a tray of Indian pastry sweets.
Below are some excerpts from the interview.
Q. What was it like to spend so much time in hospitals as a child?
Wildani: It wasn’t that bad. It would take me about 20 to 30 minutes a day to do my school homework, and I could still keep up. So the rest of the time I got to lie around, eat ice cream, and read. In fourth grade, I got through all of Nancy Drew.
It was probably harder on my parents. As a child, I just took it for granted that my parents would be at the hospital at 3 am with Indian food because I didn’t like American food. My mother would make me treats like khandvi – chickpea flour mixed with lemon and yogurt, rolled out and fried. It’s super good! Gujartis are like the Southerners of India: We fry everything.
Playing computer games "allows you to try something and fail in a safe way," says Wildani, who also plays the drums.
Q. Did you also spend a lot of time on a computer?
Wildani: Yes, I started learning about programming as soon as I learned to read, at age 3. I used LOGO, an educational programming language for children. It’s all about drawing pictures. In fact, the first time I taught Python to college students I had them integrate it with LOGO to make flowers for their mothers on Mother’s Day. People really loved that assignment and ran with it. They did all sorts of amazing animations.
Growing up, I also enjoyed computer games. I played a lot of King’s Quest, an early strategy game designed by Roberta Williams, who is one of my inspirations. King’s Quest was full of puzzles and the puzzles were hard. It teaches perseverance.
Q. So you don’t consider computer games a waste of time?
Wildani: No, not at all. They inspire a lot of people. I would say that everybody I knew during my college years played a lot of computer games as a kid. Even if you don’t go into computer science or technology for a career, computer games allow you to try something and fail in a safe way. You don’t die and you keep getting better the more you try. It also teaches team building. I think playing computer games is in some ways like playing a sport. I would be interested in studies that look at how the motor cortex changes if you play a lot of computer games.
Q. Maybe all those computer games you played account for the can-do spirit you embody in your real life.
Wildani: I’m not afraid to try things. I fail sometimes, but I have a really supportive family. I have a pretty solid mat to fall on when I screw up.
Q. How does your interest in the human brain relate to your research into computer data storage?
Wildani: Your brain can store all of your experiences at some level. It doesn’t store every detail. In fact, it forgets things on purpose, pruning data and keeping what you need to make sense of the world, stringing together related ideas and forming memories that it can then retrieve. One theory is that the hippocampus acts like a kind of card catalogue where the brain can look up the place where it has stored different pieces of data.
The brain does all this using very little power, only around 60 watts, and with a high fault rate. Neurons are dying all the time and synapses are breaking down. In fact, stroke patients can lose a significant part of their hippocampus and still function.
If we can get a better idea of how information storage and reductionism work in the brain, perhaps we could translate that to a computer framework. We’re using vision classification as a bio-model to run simulations and try to figure out how the brain makes tradeoffs between network size, power and reliability.
"We’re losing information about hidden things that we don’t already know to look for," Wildani says. "That’s why it’s critical now to come up with new ways to store large volumes of data."
Q. Why is it important to understand this?
Wildani: People are creating entire digital identities of family photos, emails, receipts – all kinds of data. Some of it is data that people want to keep and some of it is just stuff that gets saved unintentionally. You can think of all our personal collections of data like junk-filled closets that we store in “clouds.”
But what many people don’t realize is that the clouds are actually physical computer-data centers. And they require space, electricity and people to maintain them and to run them.
The centers house the physical storage devices for all the data. Disks, for instance, save data using tiny dots, called bits. But there is a limit to how close these dots can be, based on physics. They can only go to a certain resolution and no lower. Flash drives don’t rely on that sort of density, but they are not as reliable. And a disk only lasts about five years. So you have to have a plan to move data around between different devices.
We make a lot more information than we have anywhere to put it. Right now, Internet traffic is annually generating zetabytes of information and that’s projected to go up to yottabytes by 2020. [A yottabyte equals 1,000,000,000,000,000,000,000,000 bytes.]
We have this huge mess of data collected across time. How do we decide what’s important and what’s not? How long should we keep it? Who will pay for keeping it over time? There are things we archive with intention, like family photos, and things that we archive without really meaning to, like random receipts and emails.
Q. Could it just be a matter of everyone throwing out their digital “junk” and making space?
Wildani: The issue is much bigger than that. We can’t always know what is going to be important in the future. The tapes of the early “Dr. Who” episodes, for example, got written over years ago because the BBC didn’t think they were important.
In the future, if you get sick with something, it might be useful to pull up the medical records of your great grandparents. Or maybe not. You might also want to store a genome analysis of your family for the future.
My favorite example of “junk” data that became useful is a photograph that was taken in 1900 of a random patch of sky. Decades later, cosmologists found this photo in a drawer and saw that it contained a pre-supernova. By comparing it to modern-day photos of the same patch of sky, they were able to compute a more exact rate for the expansion of the universe.
We have much more powerful telescopes today but not enough storage to save all the data these instruments are capturing. The same is the case for CERN, home of the Large Hadron Collider, which is gathering large datasets on sub-atomic particles. CERN is only able to save the data that is being experimented on now.
We’re losing information about hidden things that we don’t already know to look for. That’s why it’s critical now to come up with new ways to store large volumes of data.
Q. How do you feel about the scarcity of women in computer science?
Wildani: When I was an undergraduate, I would have felt more comfortable if there had been more women in the room when I was asking a basic, technical question. But I had no choice. I was the only female in most of my computer science classes. And the default assumption for women is that you’re not competent. You have to prove yourself.
The traditional image of a computer science major is a guy with a beard who drinks a lot of Mountain Dew and spends a lot of time ranting on online forums. There are definitely some people who fit that personality type, but also many people who don’t. And some of them are so far from it that they don’t feel welcome and they leave.
I knew a woman in graduate school who was great at computer science, great at math, but she was also tall and blonde. She got tired of dealing with harassment and people who thought she was the receptionist. Eventually, she decided to go into a different field.
And yet, we need more people and different perspectives in computer science. The salaries for computer engineering are high because there are not enough people to fill the jobs.
I developed a web site (Project Hypatia) to highlight important research by women in computer science. I think it’s important to make it clear that women are not just asking for equality, but leading teams, doing impressive science and getting results.
Related:
BRAIN grant to fund study of how the mind learns
Tuesday, December 6, 2016
How will the shifting political winds affect U.S. climate policy?
By Carol Clark
“No U.S. president has been as vocal about climate change, or as focused on mitigating it, as Barack Obama,” says Eri Saikawa, an assistant professor in Emory’s Department of Environmental Sciences and an expert in public policy and the science of emissions linked to global warming.
President-elect Donald Trump, however, has repeatedly called climate change a hoax.
“The concern about how Trump will deal with climate change is worldwide,” Saikawa says. “We all share the same atmosphere and the United States is a leading emitter of greenhouse gases. The impacts of global warming will affect the entire planet.”
Among Obama’s initiatives is the U.S. Clean Power Plan – which established the first national carbon pollution standards for power plants. U.S. leadership was also instrumental in the historic Paris Agreement to combat climate change. The 2015 agreement, organized by the United Nations’ Framework Convention on Climate Change (UNFCC), brought more than 190 countries together to commit to a framework to reduce greenhouse gas emissions.
“The Paris Agreement is an amazing achievement, and there was so much momentum and excitement surrounding it,” Saikawa says.
On November 7, delegates from around the world gathered in Marrakech, Morocco, to hammer out details resulting from the Paris Agreement. Saikawa headed a 10-member Emory delegation to Marrakech for the two-week event, known as the U.N. 22nd Conference of the Parties (COP 22). (Emory, one of the few universities approved as an official U.N. observer by the COP, also sent a delegation to the Paris talks last year.)
Emory’s Marrakech delegation included six students and three staff members. They split into two teams, with half participating at COP 22 during the first week and the other half during the second.
Emory delegates on the ground in Marrakech, including senior Emily Li (front left), and, from upper left: Kate Lee (clinical fellow and staff attorney for the Turner Environmental Law Clinic), sophomore Maya Bornstein, senior Jennie Sun and Tyler Stern (an Emory grad who is now a Residence Life Fellow).
Emily Li, a senior majoring in environmental sciences and English, was there when the U.S. presidential election results were announced.
“Everyone was in shock,” Li says, of the surprise victory by Trump. “You could tell which delegates were from the U.S. because they just looked so tired that morning. The U.S. press office was total chaos.”
Li also struggled to take in the turn of events. “It was discouraging at first,” she says. “I’m really passionate about mitigating climate change and to have a national leader who doesn’t recognize it as an important issue is really disheartening.”
During the election campaign, Trump threatened to ax the Clean Power Plan and to pull the United States out of the Paris Agreement. After winning, Trump seemed to soften his stance somewhat, saying he would keep an “open mind” about the agreement. But he tapped Myron Ebell, a well-known climate-science denier, to lead his administration’s revamping of the Environmental Protection Agency (EPA).
Li summed up the post-election mood at COP 22 in a blog post called “Talking about the Elephant in the Room.” You can read it, along with posts by other members of the Emory delegation, on the Emory Climate Organization (ECO) web site, founded by students focused on understanding climate change.
The mood at COP 22 soon shifted from shock to a sense of renewed urgency. “A lot of the younger delegates, in particular, were saying how the Trump administration could help bring people together and motivate more engagement and action,” Li says. “We need to think about how to move forward because focusing on the negatives is ultimately not going to be useful.”
Local initiatives are more important than ever, she noted. For her senior thesis in environmental sciences, Li is zeroing in on ways that climate change may affect public health in Atlanta. “I’m doing a lot of research, looking at different studies to learn the scientific consensus. I’m also interviewing policy makers and people affected by events like the drought and the recent wildfires,” she says.
She plans to translate the science into engaging stories that she will post to a public web site, along with possible solutions. “I want to help communicate the direct effects of climate change on public health in Atlanta, so people living here can better understand the potential impact on themselves and their children,” Li explains. “I think that the more local an issue is, the more people tend to care about it.”
Geoff Martin, who is working on a master degree in environmental sciences, participated in the second week of COP 22. “In the month leading up to Morocco, I was really excited,” he recalls. “The Paris Agreement had finally gotten things moving in the right direction and I was going to this great event, COP 22, the first step towards implementation.”
The election results took the wind out of his sails, but only momentarily. “Being at the conference helped me regain my perspective,” Martin says. “People from all different levels and areas – government officials, those from the private sector and from non-governmental agencies – found reasons to still be hopeful.”
One of the major take-home messages for him is that the international community is going to continue to move forward in combating climate change, with or without the United States.
Another theme he heard repeatedly was that governing is a lot different from campaigning. “Trump will likely find that many of the things he said he was going to do during his campaign, like dismantle the EPA and cancel the Paris Agreement, may be easier said than done,” Martin says.
He also draws hope from the fact that the energy market is shifting. “The price of renewable energy keeps going down, making it increasingly competitive with fossil fuels in many places,” he says. “Regardless of government policy, the market could continue to drive a transition towards renewable energy.”
Martin is at work on a thesis, focused on analyzing the effectiveness of state-level climate and energy policies. He agrees with Li that the election of Trump could serve as a wake-up call for those concerned about climate change to take action at the local level, and not wait for the federal government to take the lead.
“Lots of talks at COP 22 were focused on sub-national efforts to mitigate climate change, not just in the United States, but throughout the world,” Martin says. He cites the Regional Greenhouse Gas Initiative, a successful cap-and-trade program for the power sector comprising nine U.S. states in the northeast.
The recent victory by the Standing Rock Sioux Tribe to block the $3.7 billion Dakota Access pipeline is another hopeful sign, Martin says. “Their victory was entirely a result of grassroots activism,” he says. “It shows how, if people really care about an issue and come out to protest and pressure government officials, they can make a difference.”
Related:
Peachtree to Paris: Emory delegation headed to U.N. climate talks
Tags:
Biology,
Chemistry,
Climate change,
Community Outreach,
Ecology,
Economics,
Health
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