Wednesday, April 29, 2015

What literature can teach us about sleep

"I never met a man who was quite wide awake," Thoreau wrote in "Walden." The sketch shows the cabin where he withdrew from society.

By Maria Lameiras, Emory Report

As a winner of the prestigious Guggenheim Fellowship for 2015, Emory English professor Benjamin Reiss will spend the upcoming academic year working on his third book, a cultural and literary study of modern sleep and its almost-obsessive management by society and the medical profession.

Reiss's Guggenheim project is "Thoreau's Bed: How Sleep Became a Problem in the Modern World," a book whose idea germinated in a course Reiss co-taught with Emory neurologist David Rye on "Sleep in Science and Culture." The book "asks how sleep became a nightly ordeal in need of micromanagement, medical attention and pervasive worry."

In his Guggenheim proposal, Reiss states, "Far from a simple biological constant, sleep actually is one of the most rule-bound and tightly regimented activities of our society — and yet the rules we adhere to (sleep in one unbroken stretch for roughly eight hours; do so in a private, sealed room with at most one other consenting adult; train your children to sleep alone through the night from a very young age) seem particularly maladaptive to the waking worlds we inhabit."

While teaching a course on Thoreau's "Walden," Reiss says he realized the book was "a rich record of sleeping and waking." "When I began to pull out that thread of sleep in his writing, his understanding of what had gone wrong with sleep seemed very contemporary to me," Reiss says.

"In 'Walden,' there is a famous chapter, 'Where I Lived and What I Lived For,' in which he says 'I have never met a man who was quite wide awake.' He also talks about people being addicted to news and gossip, writing 'Hardly a man takes a half-hour's nap after dinner, but when he wakes he holds up his head and asks, 'What's the news?' as if the rest of mankind had stood his sentinels.'

"Part of what he was witnessing was the birth of the modern world and he was recording how that affected people's rhythms."

"Thoreau's Bed" is scheduled to be published in 2017, the 200th anniversary of Thoreau's birth.

Read more in Emory Report.

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Thursday, April 23, 2015

Her father’s trip to the moon showed her the power of evidence

Commander David Scott emerges from a hatch during the Apollo 9 mission. The 10-day flight in 1969 provided vital information on the operational performance, stability and reliability of lunar module propulsion and life support systems. NASA photo.

“When I was a kid, I didn’t think flying into space was a big deal. All my friends’ dads went into space,” says Tracy Scott, senior lecturer in sociology and director of Emory’s Quality Enhancement Plan (QEP).

The goal of Emory’s QEP topic, “The Nature of Evidence,” is to empower students as independent scholars capable of supporting arguments with different types of evidence. Scott’s interest in the topic was formed while growing up immersed in the culture of NASA.

Her father, Commander David Scott, was an astronaut who flew on Gemini 8, Apollo 9 and Apollo 15. He’s one of only 12 people who’ve ever set foot on the moon.

“The thing that was exciting for me was the chance to discover new evidence on the moon,” Scott recalls of her father’s lunar trip. “Here was a new environment that humans had never experienced before and there was a huge amount of knowledge to be gained. My dad took a lot of time before the Apollo 15 mission to explain the scientific goals to me. And particularly the experiment he was going to do on the moon. He helped to find new evidence to confirm a very old theory.”

Watch the video, above, to see Commander Scott conduct his famous hammer and feather experiment while standing on the moon. In a vacuous space, without air resistance, they fell at the same rate, just as Galileo predicted in 1589. It was a striking visual demonstration of what we now know as the equivalence principle: The influence of gravity and the influence of inertia are exactly the same.

“I thought it was really cool that my dad was able to do an experiment that linked all the way back to Galileo,” Scott says. “Learning about the power of evidence when I was a child inspired me. I developed a keen sense of seeking out evidence to deepen what I was being taught, and to support my own arguments and to create new knowledge.”

Thursday, April 16, 2015

Field notes: Attack of the siafu ants

Militant siafu ants form colonies in the millions and can take over an entire house within hours. Photo by Alexander Wild,

Ever wonder what it’s like to do science in the field? As an Emory graduate student, Michele Parsons spent three months in Tanzania’s Gombe Stream National Park to research the disease ecology of people, wild primates and livestock. Gombe is where Jane Goodall conducted her pioneering chimpanzee behavioral research, beginning in 1960, and Parsons got to meet the famed primatologist during her stay. 

She also came face-to-face with wild baboons that ransacked her room at the research station. But that was nothing compared to an invasion of militant ants. 

Below is a condensed version of the ant incident that Parsons sent to her friends and family while she was in Tanzania. Parsons received her PhD this month from Emory’s departments of Environmental Sciences and Environmental Health. She is a research microbiologist at the Centers for Disease Control and Prevention.

By Michele Parsons
It snacks on rats.

Sunday evening following dinner, I headed over to my side of the research station house and my little room to check on my charging GPS units, as we had plans to deploy them on livestock the following day. Satisfied that they were working, I went through my usual habit of preparing for bed, brushing my teeth and arranging my bed net. I settled in for sleep at about 10:30 pm.

The final World Cup game was available for watching on an older, 10-inch TV down in the main camp (my roommate Emma had gone to watch it with others from the field team). But I knew Monday was to be a busy day, as we were launching more sampling components, and I wanted to get a good night’s sleep.

Emma came in around midnight. She whispered, “Michele, are you awake?”

“I can hear you,” I said, “are you okay?”

“Sorry to bother you,” she replied, “but I think we have some ants in the house.”

Now, in most countries, ants wouldn’t raise a major alarm bell. Ants in your sandwich, on your picnic cake, in the maple syrup or on the counter top are annoying, but not a big deal.

Parsons spent two six-week periods in the field at Gombe.

In sub-Sahara Africa, however, ants can cause a stir. Specifically, the Dorylus genus, more commonly known as safari ants or “siafu” in Swahili. The siafu are so militant and invasive they can take over an ENTIRE house in just a few hours.

I sat up and, still inside my bed net, shined my headlamp around the room. It was like a scene from a horror movie. Ants were streaming into the room, from below the door and along the walls. They were literally pouring in from the windows. Clumps of thousands of them formed these little balls that appeared to be dripping from the makeshift curtains. It was both amazing and toe-curling to witness.

The space competition was over fast because Emma and I high-tailed it out of there. The siafu have a nasty sting to them if you sit around and wait for it. Their colonies number in the millions and they are by definition meat eaters: They love insects, rats and reptiles and can gobble one up quickly.

So while Emma and I were running from the house, pretty much everything else was, too. Fleeing out the door with us were spiders, scorpions, geckos and centipedes. It was in some respect hilarious, as if I instantly forgot the years of evolution and understanding that separated me from these creatures, for we were suddenly on the same team, fighting for survival. I imagined that if I could have looked into the eyes of one of those centipedes, I could have read the same thought going through my mind: “It’s time to get the hell out of here!”

The lake's rocky shore served as an emergency bed, and its waters were always handy for a bracing "shower dip."

Well, it was after midnight and our departure wasn’t exactly planned, so we headed for the lake shore with what we had managed to grab before running out the door. I had my headlamp, a towel and my backpack, which held a CLIF bar, my laptop and a jacket. Two other members of the research team staying in the house joined us on the beach.

Initially, we tried to sleep. That was unsuccessful due to the hard rocks and general feeling of unrest. So Emma and I entertained the crew with a sing-along of Disney show tunes and easy favorites like “Stand By Me” and “Lean On Me.”

The night was lit with kerosene lanterns that dotted the lake, as Tanzanian fishermen were up and working in their boats. And above us were the stars. We were far from any bustling city so there were tons of them, and shooting stars, too! I found myself looking for familiar sights – Orion’s Belt and the Big Dipper. For a moment, Atlanta didn’t seem so far away.

By dawn, the siafu had begun to recede from the house so we could return to our rooms. The good thing about the siafu is they clean house. We noticed substantially fewer “insect stowaways” in the corners and under the bed. About the only thing the siafu leave behind is cobwebs.

I crashed for a couple of hours. But, as I had mentioned, Monday was “a big day” so I tumbled out of bed to head to the office/lab before 7 am to meet the chimp and baboon teams and set up for the day. After breakfast, around 9:30 am, I considered taking a nap, but the baboons were playing on our roof again and the noise was deafening. Instead, I headed to the lake for a refreshing “shower dip” and that kept me going for the rest of the day.

Gombe photos courtesy of Michele Parsons.

Disease poses risk to chimpanzee conservation 
Farming ants reveal evolution secrets

Wednesday, April 15, 2015

Complex cognition shaped the Stone Age hand axe, study shows

Even with extensive training, the modern mind finds it challenging to make an Acheulean hand axe. "We should have respect for Stone Age tool makers," says experimental archeologist Dietrich Stout. Photo by Carol Clark.

By Carol Clark

The ability to make a Lower Paleolithic hand axe depends on complex cognitive control by the prefrontal cortex, including the “central executive” function of working memory, a new study finds. 

PLOS ONE published the results, which knock another chip off theories that Stone Age hand axes are simple tools that don’t involve higher-order executive function of the brain.

“For the first time, we’ve showed a relationship between the degree of prefrontal brain activity, the ability to make technological judgments, and success in actually making stone tools,” says Dietrich Stout, an experimental archeologist at Emory University and the leader of the study. “The findings are relevant to ongoing debates about the origins of modern human cognition, and the role of technological and social complexity in brain evolution across species.”

The skill of making a prehistoric hand axe is “more complicated and nuanced than many people realize,” Stout says. “It’s not just a bunch of ape-men banging rocks together. We should have respect for Stone Age tool makers.”

The study’s co-authors include Bruce Bradley of the University of Exeter in England, Thierry Chaminade of Aix-Marseille University in France; and Erin Hecht and Nada Khreisheh of Emory University.

Stone tools – shaped by striking a stone “core” with a piece of bone, antler, or another stone – provide some of the most abundant evidence of human behavioral change over time. Simple Oldowan stone flakes are the earliest known tools, dating back 2.6 million years. The Late Acheulean hand axe goes back 500,000 years. While it’s relatively easy to learn to make an Oldowan flake, the Acheulean hand axe is harder to master, due to its lens-shaped core tapering down to symmetrical edges.

“We wanted to tease apart and compare what parts of the brain were most actively involved in these stone tool technologies, particularly the role of motor control versus strategic thinking,” Stout says.

The researchers recruited six subjects, all archeology students at Exeter University, to train in making stone tools, a skill known as “knapping.” The subjects’ skills were evaluated before and after they trained and practiced. For Oldowan evaluations, subjects detached five flakes from a flint core. For Acheulean evaluations, they produced a tool from a standardized porcelain core.

At the beginning, middle and end of the 18-month experiment, subjects underwent functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) scans of their brains while they watched videos. The videos showed rotating stone cores marked with colored cues: A red dot indicated an intended point of impact, and a white area showed the flake predicted to result from the impact.

The subjects were asked the following questions: “If the core were struck in the place indicated, is what you see a correct prediction of the flake that would result?” “Is the indicated place to hit the core a correct one given the objective of the technology?”

The subjects responded by pushing a “yes” or “no” button.

Answering the first question, how a rock will break if you hit it in a certain place, relies more on reflexive, perceptual and motor-control processes, associated with posterior portions of the brain. Stout compares it to the modern-day rote reflex of a practiced golf swing or driving a car.

The second question – is it a good idea to hit the core in a certain spot if you want to make a hand axe – involves strategic thinking, such as planning the route for a road trip. “You have to think about information that you have stored in your brain, bring it online, and then make a decision about each step of the trip,” Stout says.

This so-called executive control function of the brain, associated with activity in the prefrontal cortex, allows you to project what’s going to happen in the future and use that projection to guide your action. “It’s kind of like mental time travel, or using a computer simulation,” Stout explains. “It’s considered a high level, human cognitive capacity.”

The researchers mapped the skill level of the subjects onto the data from their brain scans and their responses to the questions. Greater skill at making tools correlated with greater accuracy on the video quiz for predicting the correct strategy for making a hand axe, which was itself correlated with greater activity in the prefrontal cortex.

“These data suggest that making an Acheulean hand axe is not simply a rote, auto pilot activity of the brain,” Stout says. “It requires you to engage in some complicated thinking.”

Most of the hand axes produced by the modern hands and minds of the study subjects would not have cut it in the Stone Age. “They weren’t up to the high standards of 500,000 years ago,” Stout says.

A previous study by the researchers showed that learning to make stone tools creates structural changes in fiber tracts of the brain connecting the parietal and frontal lobes, and that these brain changes correlated with increases in performance. “Something is happening to strengthen this connection,” Stout says. “This adds to evidence of the importance of these brain systems for stone tool making, and also shows how tool making may have shaped the brain evolutionarily.”

Stout recently launched a major, three-year archeology experiment that will build on these studies and others. Known as the Language of Technology project, the experiment involves 20 subjects who will each devote 100 hours to learning the art of making a Stone Age hand axe, and also undergo a series of MRI scans. The project aims to hone in whether the brain systems involved in putting together a sequence of words to make a meaningful sentence in spoken language overlap with systems involved in putting together a series of physical actions to reach a meaningful goal.

Top 10 reasons to learn to make Stone Age tools
Brain trumps hand in Stone Age tool study

WaterHub recycles wastewater to heat and cool buildings

Click here if video does not appear on screen.

Emory's WaterHub replicates the natural system of a wetland to recycle and treat sewer water so that it can be used to heat and cool the campus buildings. The facility is the first of its kind in the nation. You can take a tour of the facility this Friday, located behind the sorority houses on Eagle Row, as part of the grand opening of the WaterHub. Watch the video to learn more.

Tapping nature to clean wastewater

Tuesday, April 14, 2015

Climate@Emory: Change is in the air

Steve Sclar, left, recently demonstrated on the Emory campus how he gathers indoor air quality data. (Emory Photo/Video)

By Carol Clark

Steve Sclar traveled to Golog Tibetan Autonomous Prefecture in China last summer to research the indoor air quality of nomads, who burn yak dung in their stoves for warmth and to cook their food. His measurements showed high levels of fine particulate matter in the smoked-filled tents and homes of some of the nomads. But Sclar also caught a glimpse of how global pollutants from industrialization may be impacting the isolated realm of the Tibetan plateau.

"The Tibetans are noticing changes in their climate and they're worried about the effects," says Sclar, an MPH student in Rollins School of Public Health's Department of Environmental Health. "Their grassland is getting poorer in the summer months and they see the snow pack getting smaller on the holiest mountain range in the region, known as Amnye Machen.

"I asked one nomad, 'What happens if Amnye Machen loses all of its snow?' He told me, 'Then it's the end of the world.'"

Climate change "is the biggest environmental health problem we face," Sclar says, "and yet it is so hard to pin down. There's no one country or entity to blame, and there is no one field of study that has the solution. We need to figure out how to reconcile all this."

Climate@Emory is an initiative made up of more than 50 faculty and staff from 20 departments across the university. Its goal is to harness Emory's strengths to help it play a leading role in the global response to perhaps the most complicated and pressing problem of our time. Since its launch last fall, the initiative has worked to support, connect and expand Emory's climate-related scholarship, teaching and community engagement.

"It's really not possible to understand climate change from the standpoint of any one discipline," says Eri Saikawa, who is Sclar's adviser and one of the founders of Climate@Emory. She is an assistant professor at Rollins and in the Department of Environmental Sciences. "We want to connect the dots to improve the quality and impact of Emory's research and provide a platform for intellectual engagement on climate change."

Read more in Emory Report.

Creating an atmosphere for change

Thursday, April 2, 2015

How zinnias shaped a budding biologist, and other fun facts about plants

"We're tied into plants in myriad and intricate ways," says biologist Roger Deal, who studies how plants build and adapt their bodies.

By Carol Clark

“I’ve always been really fascinated by plants, even from a young age,” says Emory biologist Roger Deal. “Their lives are so interesting, even though they are stuck where they are born.”

Deal's roots are in Columbia, South Carolina, where his father was a physician and his mother loved to garden.

“My first plants were zinnias,” he recalls. “I was about 10 and my mom and I went to the garden store where I picked out a packet of seeds. You have these little dry things that look like pieces of dust. All you have to do is put them in the ground and get them wet, and then you have a whole organism. I thought, ‘Wow, what an amazing life cycle! How does it work?’”

Roger Deal
Plants go back millions of years, when the Earth’s atmosphere contained very little oxygen. “Where did all that extra oxygen come from? It’s a byproduct of plants,” Deal says. “All the energy that we need to live also comes from plants. And they’re beautiful – they’re an important part of our aesthetic. We are basically tied into plants in myriad and intricate ways.”

As an undergraduate at the University of South Carolina, Deal worked in a lab that studied phytoremediation, or the process of using plants to clean up pollution. “A lot of plants are tolerant of heavy metals,” he explains. “I worked on a project that was exploring how to use Spartina, the grass you see growing along salt marshes on the coast, to suck mercury pollution up out of the soil.”

Deal became interested in how genes are controlled in plant development during his graduate school years at the University of Georgia.

In his lab at Emory, he’s continuing this focus on how plants build and adapt their bodies. By digging deep into the developmental biology and genetics of plant systems, he hopes to unearth secrets that could benefit both agriculture and human health.

“A big question in studying the genome of any organism is figuring out where all the genes are, and how you put all the parts together to build an organism,” he explains. “Humans have a parts list of about 30,000 different genes, for example, but only 2 percent of our genome is genes. The rest was once considered junk DNA, but we now know that it’s not junk.”

Watch a video of Roger Deal:

DNA is not just floating around by itself in the nucleus of a cell. It’s wrapped up in little globules of proteins called histones. By wrapping tightly around histones, a six-meter long strand of DNA can cram into a cell nucleus.

“This complex of histones and DNA is called chromatin,” Deal says. “The chromatin is used to turn genes on or off, which determines the function of a cell. So chromatin is part of the system that differentiates the cells when an embryo is growing. Chromatin is also involved in establishing and maintaining cell proliferation. If cell proliferation gets turned on inappropriately, the result can become a tumor.”

One of the model organisms Deal’s lab uses is Arabidopsis thaliana, a small flowering plant that is a member of the mustard family. “It’s just a lowly little weed that you’ve probably stepped on and not noticed,” Deal says of Arabidopsis. “It grows all over the northern hemisphere.”

The Arabidopsis genome is about one-twentieth the size of the human genome. “It’s sort of streamlined,” Deal says. “It has about the same number of genes as we do, but it has way less ‘intergenic’ DNA. So in terms of finding the regulatory parts, we have a lot less stuff to look at. When it comes to lab research, Arabidopsis is like the fruit fly of the plant world.”

Arabidopsis thaliana (NIH)
Arabidopsis plants begin their life as the fusion of a sperm and an egg: A single cell, which develops into an embryo inside of a seed. “This little embryo can sit there for decades,” Deal says. “But once it gets wet, the whole thing kicks into action. Suddenly, it starts growing, pops a root, develops leaves.”

At some point, the plant switches from vegetative growth to reproductive growth. “Something in the environment, the length of the day, the quality of light, tells these plants it’s time to stop making leaves and start making flowers,” Deal says. “A really important question is how this switch operates at the molecular level.”

A key part of the puzzle appears to be a histone protein called H2AZ, which is an important component of chromatin in plants, animals and fungi.

“The H2AZ gene is essential for life in animals,” Deal says. “If an embryo doesn’t have it, the embryo stops developing and dies. But an overproduction of an H2AZ molecule appears to drive the genesis of several types of cancer, including breast and prostate cancer.”

Plants, unlike laboratory rats, can survive without the H2AZ gene. “If you knock out the H2AZ gene in Arabidopsis plants they don’t die, it just messes them up,” Deal says. “The lack of H2AZ affects the leaf size, flowering time and their susceptibility to pathogens and other stresses.”

That makes Arabidopsis an easily accessible model to study this particular gene and its on-and-off switch. “We can mess with Arabidopsis in pretty extreme ways, removing this critical regulator of a process, and then study what happens at the molecular level,” Deal says. “We’re hoping that our research will help us understand something about the biology of cancer and the biology of animal and plant development all in one fell swoop.”

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