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.

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?

Emory seniors Emily Li (left) and Jennie Sun were part of an Emory delegation to Marrakech, Morocco, in November for a U.N. Climate Change Conference. Shortly after the event began, Donald Trump, who has called climate change a hoax, won the U.S. presidential election. “We need to think about how to move forward," Li says, "because focusing on the negatives is ultimately not going to be useful.”

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.”

Peachtree to Paris: Emory delegation headed to U.N. climate talks

Thursday, November 24, 2016

The top 10 policies needed now to protect pollinators

Bee thankful: “If you enjoyed a bountiful Thanksgiving Day dinner, you should give thanks to pollinators,” says Emory biologist Berry Brosi.

By Carol Clark

Scientific experts from eight different countries developed a list of the top 10 policies needed to reverse the decline of pollinators crucial to the world’s food supply.

The journal Science is publishing the recommendations for the global community in a forum article, “10 Policies for Pollinators.” The recommendations will be presented at the United Nations Convention of the Parties on Biological Diversity (CoP13), to take place in Mexico December 4 to 17.

“If you enjoyed a bountiful Thanksgiving Day dinner, you should give thanks to pollinators,” says Berry Brosi, a biologist and ecologist in Emory University’s Department of Environmental Sciences and a co-author of the article.

Brosi cites the first policy recommendation on the list as the most concrete and actionable: Better pesticide regulatory standards.

He adds that several of the recommendations related to sustainable agriculture more broadly include making chemical control for insects and other pests a last resort.

“Especially in light of the emergence of the Zika virus, and widespread public concern about mosquito-borne diseases, we are likely to see increased demands for pesticide use,” Brosi says. “Mosquito control is, of course, important, but we also need to be thoughtful about what kinds of pesticides we use and how we use them. We should carefully consider the impact on pollinators and other biodiversity.”

The Environmental Protection Agency is currently reviewing a class of insecticides commonly used in agriculture, neonicotinoids, which have been linked to wide-scale bee declines and impacts to other pollinator species by a range of scientific studies.

"Neonicotinoids are known to kill bees and other insect pollinators in very low doses, and to cause behavioral disruptions in even minute concentrations, measured in parts-per-billion," says Brosi, whose research focuses on both managed honeybees and wild bees.

In 2014, Emory began taking steps to eliminate the use of neonicotinoid-based pesticides and pre-treated plants on its campus grounds, the first university to do so worldwide.

The EPA’s review of the safety of neonicotinoids is not due until 2017.

The complete list of recommended policies for pollinators is as follows:

1. Raise pesticide regulatory standards
2. Promote integrated pest management
3. Include indirect and sublethal effects in GM crop risk assessments
4. Regulate movement of managed pollinators
5. Develop insurance schemes to help farmers
6. Recognize pollination as agricultural input in extension services
7. Support diversified farming systems
8. Conserve and restore “green infrastructure” (a network of habitats that pollinators can move between) in agricultural and urban landscapes
9. Develop long-term monitoring of pollinators and pollination
10. Fund participatory research on improving yields in organic, diversified and ecologically intensified farming

The policy recommendations follow a United Nations warning in February that pollinators were under threat. Brosi was among 77 international experts who worked on that report, the first global pollinator assessment for the U.N.’s Intergovernmental Panel for Biodiversity Ecosystem Services (IPBES).

The assessment found that more than 40 percent of invertebrate pollinator species, particularly bees and butterflies, face extinction. And 16 percent of vertebrate pollinators are under threat. The issue is critical to agricultural, economics and the health of humans and ecosystems: 75 percent of the world’s food crops depend on pollination by at least one of 20,000 species of pollinators, including bees, butterflies, moths, wasps, beetles, birds, bats and other vertebrates.

Pollinators vital to food supply facing extinction, U.N. report warns 
Emory to ban bee-harming pesticides, protect pollinators

Monday, November 21, 2016

Learning to love our bugs

Each of us is a mobile ecosystem, teeming with trillions of living organisms. (Illustration by Giula Ghigini) 

By Jerry Grillo
Emory Medicine

They live on us and inside us, surround us like an invisible cloud, maintain and sustain us, ignore us, occasionally attack and kill us, and, ultimately, define us.

The human microbiome is made up of bacteria, fungi, viruses, and the like, and they cover every surface of our bodies.

"These microbiota are mostly in your gut, but also in your mouth, on your skin, in your lungs," says Emory biologist Nicole Gerardo. "They're playing critical roles in how you interact with the environment, how you process food, how you fight off pathogens, how you interact with drugs.

"Some of our remarkably fertile microbes are identical to those that live in other humans. But many are a distinct reflection of our individual experiences, shaped by who or what we've touched, where we've been, what we've breathed, and what we've consumed.

"Research interest in the human microbiome is exploding now," says Gerardo, who gave the introductory presentation at Emory's first microbiome symposium in November.

Spurred on by ambitious efforts like the National Institutes of Health's Human Microbiome Project, such research is demystifying the role of our myriad microbial passengers.

"It's like we're entering a new frontier of science, something that was basically ignored by medicine for a long time," says infectious disease researcher David Weiss, director of Emory's Antibiotic Resistance Center. "We're really at the beginning of studying all this, but I do think that in our lifetime, we'll be able to monitor each person's microbiome and intervene to improve their health. Looking at what type of bacteria we have and how resistant or sensitive they are to drugs will be an important part of health care. Most of the bugs we tote around are helpful, but they can also be ticking time bombs."

We may be able to someday diffuse the situation, replacing pathogenic microbes with a friendlier variety.

"There's great promise in manipulating the microbiome, in actually changing it," says geneticist Michael Zwick. "Actually, it's already happening."

Read the whole article in Emory Medicine.

What aphids can teach us about the microbiome and the immune system

Monday, November 14, 2016

Companies pushing 'toddler milk' for 'growth' need oversight, experts warn

"Parents are commonly concerned about the size of their children and how well they are doing developmentally," says Emory's Michelle Lampl, MD, PhD, adding: "Not all kids who are smaller than average have a problem."

By Carol Clark

Liquid-based nutritional supplements, originally formulated for malnourished or undernourished children, need more regulatory oversight as they are increasingly marketed to promote growth in children generally, warn researchers at Emory University.

The journal Healthcare published their commentary article, citing the lack of scientific evidence to support marketing claims of the benefits for growth of giving healthy children liquid-based nutritional supplements, commonly known as “toddler milks.”

“A plumper baby is not necessarily a healthier baby,” says Michelle Lampl, who is the lead author of the article, director of the Center for the Study of Human Health at Emory University and an internationally recognized expert in human growth.

In fact, toddler milk supplements may actually be doing harm by fueling rapid, unnecessary weight gain in young children in the midst of a global obesity epidemic, she adds.

She notes that the liquid supplements may have as much as 240 calories per serving and have the potential to turn a healthy, lean toddler into an overweight one. “Healthy developmental growth does not mean gaining weight and getting fat,” she says. “It is primarily measured by whether a child is growing a stronger, longer skeleton.”

Liquid-based nutritional supplements fall into a regulatory loophole, because the Food and Drug Administration (FDA) does not consider supplements to be a drug or a “conventional” food. “When a mother goes into a store and sees a toddler milk supplement on a shelf, she has no idea that it falls into a less rigorous FDA category than those covering so-called conventional food and medicine,” Lampl says. “We have a product aimed at a vulnerable population – infants and young children – that does not have adequate oversight.”

Co-authors of the commentary article are: Meriah Schoen, a research assistant at Emory’s Center for the Study of Human Health and a graduate student focused on nutrition at Georgia State University; and Amanda Mummert, who recently received a PhD in Anthropology from Emory's Laney Graduate School.

The commentary appears in a special issue of Healthcare, dedicated to the physician-scientist David Barker, who died in 2013. He originated the Barker Hypothesis, also known as the Developmental Origins of Health and Disease model, linking fetal and early infant experiences to an individual’s health status across the lifespan.

“David Barker opened the door to the importance of early influences, including nutrition and other environmental factors, for lifelong health,” Lampl says. “He believed that we have an ethical responsibility to ensure that the next generation is as healthy as it can be.”

Companies have marketed infant formulas for decades. In 1981, however, the World Health Organization (WHO) voted to recommend banning marketing of formulas for babies under six months, since the formulas were associated with lower rates of breastfeeding, and increased disease and malnutrition in the developing world.

Countries around the world adopted the rules and breastfeeding rates went up globally. The formula industry responded by focusing on toddler milk supplements, aimed at children ages six months and up.

Liquid-based supplements containing vitamins and minerals may be beneficial to children that are malnourished, or suffering from chronic diseases that prohibit their ability to consume solid foods, Lampl says. The problem, she adds, is that toddler milks have grown into a multi-billion-dollar industry that is expanding internationally to encompass healthy children.

Rapidly boosting the weight of children who are simply smaller than average but healthy could have lifelong consequences, she says. Barker, for instance, found a direct link to higher rates of metabolic disorders among individuals who were born relatively small and grew rapidly in the first few years of life.

“Parents are commonly concerned about the size of their children and how well they are doing developmentally,” Lampl says, adding that the growth charts used in pediatrician offices are often misunderstood. “Not all kids who are smaller than average have a problem.”

Busy mothers on the go, who may be consuming “energy drinks” and liquid supplements themselves, are primed to buy toddler milk for young children under the assumption that they are healthy choices, particularly for children who may be picky eaters.

“Although it can take a picky eater up to 20 times of trying a food to decide if they like it, most mothers offer a food fewer than five times before switching to something more convenient,” Lampl says. “It’s much easier to hand your child a sugary ‘toddler milk,’ thinking it’s healthy and it helps them grow.”

The WHO is set to consider recommendations concerning calorie amounts and ingredients for liquid-based nutritional supplements marketed to toddlers and older children during a meeting in early December.

Those recommendations will not have teeth, however, and it will be up to individual governments whether they decide to adopt them and enforce them.

“We are really behind when it comes to regulatory oversight for the marketing of these supplements, and for rigorous scientific research showing the impact of their widespread use on children,” Lampl says.

Support mothers to curb the global rise in chronic diseases
Grandma was right: Infants wake up taller