Thursday, February 22, 2018

Frankenstein and robots rise up for Atlanta Science Festival

Hair-raising, spine-tingling fun! A young visitor to the Emory campus during last year's Atlanta Science Festival experiences the thrill of static electricity.

By Carol Clark

From the lumbering, 200-year-old Frankenstein to sleek, modern-day robots, this year’s Atlanta Science Festival — set for March 9 to 24 — highlights creations that spark wonder and fun, giving glimpses of the past and the future.

The five-year-old festival expanded to more than two weeks, encompassing 120 events sponsored by 90 different partners at 70 venues across metro Atlanta, including many on the Emory campus.

The festival culminates with a day-long “Exploration Expo” on Saturday, March 24, set in Piedmont Park. “Rise Up, Robots!” kicks off the festival on the evening of Friday, March 9 at the Ferst Center, when three robots and their inventors will take the stage.

“We thought about how we could possibly top last year’s featured speaker, astronaut Mark Kelly — someone so inspirational to children and adults all over the planet,” says Meisa Salaita, co-director of the Atlanta Science Festival. “We finally realized that no human could match him, and we would have to resort to artificial intelligence.”

Heather Knight, professor of robotics at Oregon State University, will demonstrate the interactive quips of “Data,” the world’s first robotic comedian. Georgia Tech’s Gil Weinberg will jam with “Shimon,” a marimba playing robotic musician. And Stewart Coulter, from DEKA Research and Development, will show how a bionic arm named LUKE (Life Under Kinetic Evolution) changed an amputee’s life.

Tickets are required for the event, which starts at 7 pm. Door open early with an Interactive Robotic Petting Zoo, starting at 6 pm.

Frankenstein rises up on the Emory campus on Thursday, March 22. Three Atlanta playwrights will reanimate Mary Shelley’s creation, which turns 200 this year, in the context of scientific research ongoing at Emory. Following the short plays join ethicists, scientists and the playwrights to discuss the work over refreshments. The event, titled “Frankenstein Goes Back to the Lab,” begins at 5:30 pm in Emory’s Science Commons.

On Friday, March 23, from 3:30 to 7 pm, Emory will host “Chemistry Carnival,” where visitors can join scientists in carnival games like Peptide Jenga and Bacterial Telepathy, in the Atwood Chemistry Center. On the same day and time, the ever-popular “Physics Live!” will again feature giant soap bubbles and liquid nitrogen ice cream, among other treats in the Math and Science Center.

A new Emory event this year, “Science.Art.Wonder,” will run concurrently with the chemistry and physics events, in the same venues. For the past year, the program has paired local artists and scientists to explore ideas of research through the visual arts. You can stroll through an exhibit of the resulting artwork and meet some of the artists and scientists involved in the project.

Adult fare is featured on Monday, March 19, including “The Science of ‘Motherese,’” an overview of early vocal development in infants at the Marcus Autism Center, and “CDC in the Scene,” which features CDC scientists sorting fact from fiction surrounding movies like “Outbreak,” in the Mathematics and Science Center.

On Tuesday, March 20, “Become an Archeologist” lets you in on secrets revealed by ancient skeletons and artifacts, while “Mock Climate Change Negotiation” turns you into an international policymaker for a day.

During “Unveiling the Internet,” on Wednesday, March 21, Emory computer scientists will give interactive lessons on everything from the workings of YouTube to Snapchat.

“STEM Gems: Giving Girls Role Models in STEM Careers,” on Saturday, March 10, is an interactive discussion where panelists offer advice and guidance specific to girls and young women intrigued by science, technology, engineering and math. “Women and Minorities in STEM: Surprises, Setbacks and Successes,” set for the evening of Thursday, March 22 at the Oxford campus, is a panel discussion with voices from a diverse set of scientific fields who will share their stories and take questions.

Click here for more details of Emory campus events, and events throughout the city featuring members of the Emory community.

Among the dozen Emory booths at “Exploration Expo” will be chemistry students running their non-Newtonian fluid dance pit. The Center for the Study of Human Health will explore the human gut microbiome in a booth called “Your Hundred Trillion Best Friends.” And the “Science.Art.Wonder” team will display art from the program and invite you to help create a mural.

The Atlanta Science Festival was founded by Emory, Georgia Tech and the Metro Atlanta Chamber and is a collaboration among diverse community partners and sponsors.

'The Enlightened Gene' bridges Buddhism and biology

Tibetan monk Geshe Yungdrung Konchok (left) and Emory biologist Arri Eisen (right) pose with the Dalai Lama, who wrote an introduction for their new book, "The Enlightened Gene." The book explores how dialogue between scientists and monastics enriches understandings of biology, physics and other sciences. 

By April Hunt, Emory Report

For nearly a decade, the Emory-Tibet Science Initiative has done more than challenge the idea that religion and science don’t mix by developing and successfully launching a comprehensive science curriculum for thousands of Tibetan monks and nuns.

The first major change to Tibetan Buddhist monastic education in six centuries also demonstrated how insights and information from both the monastics and professors could enrich each other’s understanding of biology, physics and other sciences.

Arri Eisen, an Emory College professor of pedagogy in biology and the Institute for Liberal Arts, explores those connections in “The Enlightened Gene,” a book he co-wrote with one of the monks, Geshe Yungdrung Konchok.

“He grew up on the Tibetan plateau herding yaks. I grew up one of about five Jewish guys in North Carolina in the 1970s,” Eisen says. “We had different experiences, but we could use them to develop a common approach, to try to better understand our world.”

Emory has woven Western and Tibetan Buddhist intellectual traditions together since founding the Emory-Tibet Partnership in 1998. His Holiness the Dalai Lama has been a Presidential Distinguished Professor at Emory since 2007.

Read more in Emory Report.

Related:
Emory Tibet Science Initiative rolls out bridges to inner and outer worlds

Friday, February 16, 2018

'Divine Felines' showcases Egypt's exaltation of cats

From ancient Egypt to modern times, cats rule many peoples' lives. Photo by Stephen Nowland, Emory Photo/Video.

By Leslie King
Emory Report

“In ancient Egypt, cats and dogs were gods, and they have not forgotten this!” says Melinda Hartwig, curator of Ancient Egyptian, Nubian and Near Eastern Art at the Michael C. Carlos Museum.

That exalted stature is illuminated in the exhibition “Divine Felines: Cats of Ancient Egypt,” which opened Feb. 10 at the museum and will be on view through Nov. 11.

The exhibit showcases cats and lions, plus dogs and jackals, as domesticated pets, creatures of the wild or mythic symbols of divinities, in ancient Egyptian mythology, kingship and everyday life. Animal burial practices and luxury items decorated with feline and canine features are also on display.

“Cats and dogs reveal so much about ancient Egyptian culture,” says Hartwig. “These animals were just as important to the ancient Egyptians as they are to us today.”

The kings of Egypt were associated with the lion, thus, the human head on the lion’s body or the sphinx.

“Cats were first domesticated in Egypt around 4000 BC. They were lovable pets, hunters of vermin and divine embodiments of fertility and protection. Lions and jungle cats were admired for their power, and were linked with royalty and divinity,” Hartwig continues. “Dogs were also kept as pets. Their loyalty and hunting abilities were keenly valued. Often found roaming the ancient necropolises, dogs and jackals became embodiments of the gods who protected the dead.”

Read more in Emory Report.

Monday, February 5, 2018

Twitter reveals how future-thinking Americans are and how that affects their decisions


By Carol Clark

Individuals who tend to think further into the future are more likely to invest money and to avoid risks, finds a new paper by psychologists at Emory University. The Proceedings of the National Academy of Sciences (PNAS) published the research, which tapped big data tools to conduct text analyses of nearly 40,000 Twitter users, and to run online experiments of behavior of people who provided their Twitter handles.

The researchers also found an association between longer future-sightedness and less risky decision-making at a U.S. state population level.

“Twitter is like a microscope for psychologists,” says co-author Phillip Wolff, an Emory associate professor of psychology. “Naturalistic data mined from tweets appears to give insights not just into tweeters’ thoughts at a particular time, but into a relatively stable cognitive process. Using social media and big-data analytical tools opens up a new paradigm in the way we study human behavior.”

Co-author Robert Thorstad, an Emory PhD candidate in the Wolff lab, came up with the idea for the research, worked on the design and analyses, and conducted the experiments.

“I'm fascinated by how peoples’ everyday behavior can give away a lot of information about their psychology,” Thorstad says. “Much of our work was automated, so we were able to analyze millions of Tweets from thousands of individuals’ day-to-day lives.”

The future-sightedness found in individuals’ tweets was short, usually just a few days, which differs from prior research suggesting future-sightedness on the order of years.

“One possible interpretation is that the difference is due to a feature of social media,” Wolff says. Another possible reason, he adds, is that prior studies explicitly asked individuals how far they thought into the future while the PNAS paper used the implicit measure of previous tweets.

While the relationship between future-sightedness and decision-making may seem obvious, the researchers note that previous findings on the subject have not been consistent. Those inconsistencies may be due to factors such as observer bias in a laboratory setting and small sample sizes.

The PNAS paper used a suite of methods (such as the Stanford CoreNLP natural language processing toolkit and SUTime, a rule-based temporal tagger built on regular expression patterns) to automatically analyze Twitter text trails previously left by individual subjects. Experimental data was gathered using the Amazon crowdsourcing tool Mechanical Turk, a web site where individuals can complete psychology experiments and other internet-based tasks. Participants in the Mechanical Turk experiments were asked to supply their Twitter handles.

In one experiment for the PNAS paper, Mechanical Turk participants answered a classic delay discounting question, such as: Would you prefer $60 today or $100 in six months? The participants’ Tweets were also analyzed. Future orientation was measured by the tendency of participants to tweet about the future compared to the past. Future-sightedness was measured based on how often tweets referred to the future, and how far into the future.

The results showed that future orientation was not associated with investment behavior, but that individuals with far future-sightedness were more likely to choose to wait for future rewards than those with near future-sightedness. That indicates that investment behavior depends on how far individuals think into the future and not their tendency to think about the future in general.

A second Mechanical Turk experiment used a digital Balloon Analogue Risk Task (BART). Participants’ could earn real money every time they inflated a balloon, but each inflation could lead to the balloon popping, resulting in no money earned for that trial. If participants stopped inflating before the balloon popped, they could bank the money that they have earned and proceed to the next trial.

The BART participants’ tweets were also analyzed. The results showed that those with longer future-sightedness were less likely to take the risk of fully inflating the balloon.

Another study in the PNAS paper focused on Twitter users whose profiles tied them to a particular state. About eight million of their tweets were analyzed for future-sightedness.

The researchers measured a state’s risk-taking behaviors at the population level using the proxy of publicly available statistics, such as seat-belt compliance rates, drunken driving rates and teen-aged pregnancy rates. The results showed that shorter future-sightedness measures for tweets from individual states correlated closely to higher rates of risky behaviors, in a pattern similar to the results of the individual experimental studies.

To measure a state’s investment behavior, the researchers used state statistics for spending on state parks, pre-kindergarten education, highways and per-pupil education. The researchers found that states that invested more in these areas were associated with tweets from individuals with longer future-sightedness, but not at a statistically significant level.

The researchers controlled for state demographics such as political orientation, per capita income, household income and GDP. “We found that, while demographics are important, they couldn’t explain away the effects of future-thinking,” Wolff says.

The estimated 21 percent of American adults who use Twitter tend to be younger and more technologically literate than the general population, Thorstad concedes. But he adds that Twitter’s demographics are not that far off from the general population in terms of gender, economic status and education levels. And the percentages of Twitter users living in rural, urban and suburban areas are virtually the same.

“Twitter can provide a much broader participant pool than many psychology experiments that primarily use undergraduates as subjects,” Thorstad notes. “Big-data methods may ultimately improve generalizability for psychology results.”

“Through social media, we’re amassing huge amounts of data on ourselves, behaviorally and over time, that is leaving behind a kind of digital phenotype,” Wolff adds. “We’re now in an age where we have big-data analytical tools that can extract information to tell us something indirectly about an individual’s cognitive life, and to predict what an individual might do in the future.”

Monday, January 29, 2018

New method calculates equilibrium constant at the small scale

Mixing computational chemistry and theoretical math proved a winning formula for Emory chemist James Kindt (center), his graduate students (from left) Xiaokun Zhang and Lara Patel, and mathematics graduate students Olivia Beckwith and Robert Schneider. Photo by Stephen Nowland, Emory Photo/Video.

By Carol Clark

Computational chemists and mathematicians have developed a new, fast method to calculate equilibrium constants using small-scale simulations — even when the Law of Mass Action does not apply.

The Journal of Chemical Theory and Computation published the resulting algorithm and software, which the researchers have named PEACH — an acronym for “partition-enabled analysis of cluster histograms” and a nod to the method’s development in Georgia at Emory University.

“Our method will allow computational chemists to make better predictions in simulations for a wide range of complex reactions — from how aerosols form in the atmosphere to how proteins come together to form amyloid filaments implicated in Alzheimer’s disease,” says James Kindt, an Emory professor of computational chemistry, whose lab led the work.

Previously it would require at least a week of computing time to do the calculations needed for such predictions. The PEACH system reduces that time to seconds by using tricks derived from number theory.

“Our tool can use a small set of data and then extrapolate the results to a large-system case to predict the big picture,” Kindt says.

“What made this project so fun and interesting is the cross-cultural aspects of it,” he adds. “Computational chemists and theoretical mathematicians use different languages and don’t often speak to one another. By working together we’ve happened onto something that appears to be on the frontiers of both fields.”

The research team includes Lara Patel and Xiaokun Zhang, who are both PhD students of chemistry in the Kindt lab, and number theorists Olivia Beckwith and Robert Schneider, Emory PhD candidates in the Department of Mathematics and Computer Science. Chris Weeden, as an Emory undergraduate, contributed to early stages of the work.

The equilibrium constant is a basic concept taught in first-year college chemistry. According to the Law of Mass Action, at a given temperature, no matter how much of a product and a reactant are mixed together — as long as they are at equilibrium — a certain ratio of product to reactant will equal the equilibrium constant.

“That equation always holds true at equilibrium for huge numbers of molecules,” Kindt says. “It doesn’t matter if it’s applied to a bucket of water or to a single drop of water — which consists of about a billion trillion molecules.”

At much smaller scales of around dozens of molecules, however, the Law of Mass Action breaks down and does not apply.

The Kindt lab uses computers to simulate the behavior of molecules, in particular how they self-assemble into clusters. Sodium octyl sulfate, or SOS, is one of the compounds the lab uses as an experimental model. SOS is a surfactant that can act as a detergent. It forms little clusters in water that can encapsulate oil and grease. Simulations of how SOS molecules come together can predict the distribution of sizes of clusters formed under different conditions, in order to improve the design of soaps and detergents, and to better understand biological processes such as how bile salts break down globules of fat during the digestive process.

In a key test of their model, the lab needed to make sure that the equilibrium for the assembly reaction of SOS molecules into clusters matched up with experiments.

“If we were to run simulations with huge numbers of molecules, we could count the clusters that were formed of each size, count the molecules that remained free of the clusters, and use this information to calculate the equilibrium constant for forming each size cluster,” Kindt says. “The challenge we faced was that it would take too long for the computers to perform simulations of sufficiently huge numbers of molecules to get this to work, and for the numbers of clustering molecules we could practically handle — around 50 — the Law of Mass Action wouldn’t work.”

Kindt decided to approach the problem by considering all the different ways the molecules in a reaction could group into clusters of different sizes in order to arrive at an average. After doing some reading, he realized that these different ways of molecules grouping were what number theorists call integer partitions.

A partition of a number is a sequence of positive integers that add up to that number. For instance, there are five partitions of the number 4 (4 = 3+1 = 2+2 = 2+1+1 = 1+1+1+1). The partition numbers grow at an incredible rate. The amount of partitions for the number 10 is 42. For the number 100, the partitions explode to more than 190,000,000.

That same explosion of possibilities occurs for the ways that molecules can cluster.

Lara Patel and Xiaokun Zhang worked on a “brute force” method to get a computer to run through every single way to combine 10 molecules of one type with 10 molecules of another type. The problem was it took one computer working a couple of days to do a single analysis. And the computational time needed if just a few more molecules were added to the analysis went up exponentially.

The computational chemists had hit a wall.

Kindt reached out to Ken Ono, a world-renowned number theorist in Emory's Mathematics and Computer Science Department, to see if any of his graduate students would be interested in taking a crack at the problem.

Olivia Beckwith and Robert Schneider jumped at the chance.

“The Kindt lab’s computer simulations show that classical theorems from partition theory actually occur in nature, even for small numbers of molecules,” Schneider says. “It was surprising and felt very cosmic to me to learn that number theory determines real-world events.”

“It was definitely unexpected,” adds Beckwith. “In theoretical math we tend to work in isolation from physical phenomena like the interaction of molecules.”

The chemists and mathematicians began meeting regularly to discuss the problem and to learn one another’s terminology. “I had to pull out my son’s high school chemistry book and spend a weekend reading through it,” Schneider says.

“It happened so organically,” Patel says of the process of blending their two specialties. “Olivia and Robert would write equations on the board and as soon as a formula made sense to me I’d start thinking in my head, ‘How can we code this so that we can apply it?’”

The two mathematicians suggested a strategy that could make the problem much easier to calculate, based on a theorem known as FaĆ  di Bruno’s Formula.

“It was surprising,” Zhang says, “because it was an idea that never would have occurred to me. They helped us get unstuck and to find a way to push our research forward.”

“They helped us find a shortcut so that we didn’t have to generate all the partitions for ways that the molecules could clump together,” Kindt adds. “Their algorithm is a much more elegant and simple way to find the entire average overall.”

Patel and Zhang used this new algorithm to put together a piece of software to analyze data from the computer simulations. The resulting system, PEACH, speeds up calculations that previously took two hours to just one second. After demonstrating how PEACH simplifies simulations of SOS assemblages, the research team is moving on to simulate this process for a range of other molecules.

“We’re interested in describing how molecular structures dictate assembly in any type of scenario, such as the early stages of crystal formation,” Kindt says. “We’re also working on quantifying just where the Law of Mass Action breaks down. We could then refine the PEACH strategy to make it even more efficient.”

Related:
New theories reveal the nature of numbers