Thursday, June 13, 2019

The whisper of schizophrenia: Machine learning finds 'sound' words predict psychosis

"Machine learning technology is advancing so rapidly that it's giving us tools to data mine the human mind," says Emory psychologist Phillip Wolff, senior author of the study.

By Carol Clark

A machine-learning method discovered a hidden clue in people’s language predictive of the later emergence of psychosis — the frequent use of words associated with sound. The journal npj Schizophrenia published the findings by scientists at Emory University and Harvard University.

The researchers also developed a new machine-learning method to more precisely quantify the semantic richness of people’s conversational language, a known indicator for psychosis.

Their results show that automated analysis of the two language variables — more frequent use of words associated with sound and speaking with low semantic density, or vagueness — can predict whether an at-risk person will later develop psychosis with 93 percent accuracy.

Even trained clinicians had not noticed how people at risk for psychosis use more words associated with sound than the average, although abnormal auditory perception is a pre-clinical symptom.

“Trying to hear these subtleties in conversations with people is like trying to see microscopic germs with your eyes,” says Neguine Rezaii, first author of the paper. “The automated technique we’ve developed is a really sensitive tool to detect these hidden patterns. It’s like a microscope for warning signs of psychosis.”

Rezaii began work on the paper while she was a resident at Emory School of Medicine’s Department of Psychiatry and Behavioral Sciences. She is now a fellow in Harvard Medical School’s Department of Neurology.

“It was previously known that subtle features of future psychosis are present in people’s language, but we’ve used machine learning to actually uncover hidden details about those features,” says senior author Phillip Wolff, a professor of psychology at Emory. Wolff’s lab focuses on language semantics and machine learning to predict decision-making and mental health.

“Our finding is novel and adds to the evidence showing the potential for using machine learning to identify linguistic abnormalities associated with mental illness,” says co-author Elaine Walker, an Emory professor of psychology and neuroscience who researches how schizophrenia and other psychotic disorders develop.

The onset of schizophrenia and other psychotic disorders typically occurs in the early 20s, with warning signs — known as prodromal syndrome — beginning around age 17. About 25 to 30 percent of youth who meet criteria for a prodromal syndrome will develop schizophrenia or another psychotic disorder.

Using structured interviews and cognitive tests, trained clinicians can predict psychosis with about 80 percent accuracy in those with a prodromal syndrome. Machine-learning research is among the many ongoing efforts to streamline diagnostic methods, identify new variables, and improve the accuracy of predictions.

Currently, there is no cure for psychosis.

“If we can identify individuals who are at risk earlier and use preventive interventions, we might be able to reverse the deficits,” Walker says. “There are good data showing that treatments like cognitive-behavioral therapy can delay onset, and perhaps even reduce the occurrence of psychosis.”

For the current paper, the researchers first used machine learning to establish “norms” for conversational language. They fed a computer software program the online conversations of 30,000 users of Reddit, a social media platform where people have informal discussions about a range of topics. The software program, known as Word2Vec, uses an algorithm to change individual words to vectors, assigning each one a location in a semantic space based on its meaning. Those with similar meanings are positioned closer together than those with far different meanings.

The Wolff lab also developed a computer program to perform what the researchers dubbed “vector unpacking,” or analysis of the semantic density of word usage. Previous work has measured semantic coherence between sentences. Vector unpacking allowed the researchers to quantify how much information was packed into each sentence.

After generating a baseline of “normal” data, the researchers applied the same techniques to diagnostic interviews of 40 participants that had been conducted by trained clinicians, as part of the multi-site North American Prodrome Longitudinal Study (NAPLS), funded by the National Institutes of Health. NAPLS is focused on young people at clinical high risk for psychosis. Walker is the principal investigator for NAPLS at Emory, one of nine universities involved in the 14-year project.

The automated analyses of the participant samples were then compared to the normal baseline sample and the longitudinal data on whether the participants converted to psychosis.

The results showed that higher than normal usage of words related to sound, combined with a higher rate of using words with similar meaning, meant that psychosis was likely on the horizon.

Strengths of the study include the simplicity of using just two variables — both of which have a strong theoretical foundation — the replication of the results in a holdout dataset, and the high accuracy of its predictions, at above 90 percent.

“In the clinical realm, we often lack precision,” Rezaii says. “We need more quantified, objective ways to measure subtle variables, such as those hidden within language usage.”

Rezaii and Wolff are now gathering larger data sets and testing the application of their methods on a variety of neuropsychiatric diseases, including dementia.

“This research is interesting not just for its potential to reveal more about mental illness, but for understanding how the mind works — how it puts ideas together,” Wolff says. “Machine learning technology is advancing so rapidly that it’s giving us tools to data mine the human mind.”

The work was supported by grants from the National Institutes of Health and a Google Research Award.

Related:
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Risk calculator for psychosis gives clinicians a valuable new tool
How chronic inflammation may drive down dopamine and motivation

Wednesday, June 12, 2019

A focus on fathers: The science of dads

Anthropologist James Rilling with his son Toby, 8, and daughter Mia, 2. (Photo by Becky Stein)

Want to do something special for a father on June 16? Try asking him what he finds most rewarding — and most challenging — about being a dad.

James Rilling, an anthropologist at Emory University, recently completed in-depth interviews on that topic with 120 new fathers. Rilling and his colleague Craig Hadley, also an anthropologist at Emory, are still analyzing data from the interviews for a comprehensive study.

One result, however, is already clear. A positive-and-negative-affect scale administered to the subjects before and after the interviews shows how talking about fatherhood influenced their moods. “Most of them experienced an increase in how enthusiastic, proud and inspired they felt after talking about their experience as a father,” Rilling says. “They seemed to find it therapeutic to talk about their feelings surrounding being a father, particularly if they were struggling with some things. The challenges of being a mother are often much greater. So fathers may think that nobody really wants to hear about the things they are dealing with as a new parent.”

Read more about Rilling's work here, and learn five surprising facts about fathers.

Related:
How dads bond with toddlers
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Tuesday, June 4, 2019

How chronic inflammation may drive down dopamine and motivation

“If our theory is correct, then it could have a tremendous impact on treating cases of depression and other behavioral disorders that may be driven by inflammation,” says co-author Andrew Miller, an Emory professor of psychiatry. (Getty Images)

By Carol Clark

Growing evidence shows that the brain’s dopamine system, which drives motivation, is directly affected by chronic, low-grade inflammation. A new paper proposes that this connection between dopamine, effort and the inflammatory response is an adaptive mechanism to help the body conserve energy.

Trends in Cognitive Sciences published the theoretical framework developed by scientists at Emory University. The authors also provided a computational method to experimentally test their theory.

“When your body is fighting an infection or healing a wound, your brain needs a mechanism to recalibrate your motivation to do other things so you don’t use up too much of your energy,” says corresponding author Michael Treadway, an associate professor in Emory’s Department of Psychology, who studies the relationship between motivation and mental illness. “We now have strong evidence suggesting that the immune system disrupts the dopamine system to help the brain perform this recalibration.”

The computational method will allow scientists to measure the effects of chronic inflammation on energy availability and effort-based decision-making. The method may yield insights into how chronic, low-grade inflammation contributes to motivational impairments in some cases of depression, schizophrenia and other medical disorders.

Co-author Andrew Miller, William P. Timmie Professor of Psychiatry and Behavioral Sciences in Emory’s School of Medicine and the Winship Cancer Institute, is a leader in this field and is pioneering the development of immunotherapeutic strategies for the treatment of psychiatric disorders.

“If our theory is correct, then it could have a tremendous impact on treating cases of depression and other behavioral disorders that may be driven by inflammation,” Miller says. “It would open up opportunities for the development of therapies that target energy utilization by immune cells, which would be something completely new in our field.”

Co-author Jessica Cooper, a post-doctoral fellow in Treadway’s lab, led the development of the computational model.

It has previously been shown that inflammatory cytokines — signaling molecules used by the immune system — impact the mesolimbic dopamine system. And recent research has revealed more insights into how immune cells can shift their metabolic states differently from most other cells.

The researchers built on these findings to develop their theoretical framework.

An immune-system mechanism to help regulate the use of energy resources during times of acute stress was likely adaptive in our ancestral environments, rife with pathogens and predators. In modern environments, however, many people are less physically active and may have low-grade inflammation due to factors such as chronic stress, obesity, metabolic syndrome, aging and other factors. Under these conditions, the same mechanism to conserve energy for the immune system could become maladaptive, the authors theorize.

Studies by Miller and others have provided evidence of an association between an elevated immune system, reduced levels of dopamine and motivation, and some diagnoses of depression, schizophrenia and other mental disorders.

“We’re not proposing that inflammation causes these disorders,” Treadway says. “The idea is that a subset of people with these disorders may have a particular sensitivity to the effects of the immune system and this sensitivity could contribute to the motivational impairments they are experiencing.”

The researchers are now using their computational method to test their theory in a clinical trial on depression.

The work for the current paper was supported by the National Institute of Mental Health.

Related:
Study reveals how the brain decides to make an effort

Thursday, May 23, 2019

Civil War plant medicines blast drug-resistant bacteria

Micah Dettweiler gathered samples for the study from Lullwater Forest on the Emory campus. He began the project for his honors thesis as an Emory undergraduate majoring in biology.

During the height of the Civil War, the Confederate Surgeon General commissioned a guide to traditional plant remedies of the South, as battlefield physicians faced high rates of infections among the wounded and shortages of conventional medicines.

A new study of three of the plants from this guide — the white oak, the tulip poplar and the devil’s walking stick — finds that they have antiseptic properties. Scientific Reports published the results of the study led by scientists at Emory University. The results show that extracts from the plants have antimicrobial activity against one or more of a trio of dangerous species of multi-drug-resistant bacteria associated with wound infections: Acinetobacter baumannii, Staphylococcus aureus and Klebsiella pneumoniae.

Read more about the study here.

Tuesday, May 21, 2019

Mathematicians revive abandoned approach to the Riemann Hypothesis

The idea for the paper was sparked by a "toy problem" that Emory mathematician Ken Ono (left) presented as a "gift" to entertain Don Zagier (right), of the Max Planck Institute of Mathematics, to celebrate Zagier's 65th birthday. The toy problem is seen on the whiteboard behind them.

By Carol Clark

Many ways to approach the Riemann Hypothesis have been proposed during the past 150 years, but none of them have led to conquering the most famous open problem in mathematics. A new paper in the Proceedings of the National Academy of Sciences (PNAS) suggests that one of these old approaches is more practical than previously realized.

“In a surprisingly short proof, we’ve shown that an old, abandoned approach to the Riemann Hypothesis should not have been forgotten,” says Ken Ono, a number theorist at Emory University and co-author of the paper. “By simply formulating a proper framework for an old approach we’ve proven some new theorems, including a large chunk of a criterion which implies the Riemann Hypothesis. And our general framework also opens approaches to other basic unanswered questions.”

The paper builds on the work of Johan Jensen and George Pólya, two of the most important mathematicians of the 20th century. It reveals a method to calculate the Jensen-Pólya polynomials — a formulation of the Riemann Hypothesis — not one at a time, but all at once.

“The beauty of our proof is its simplicity,” Ono says. “We don’t invent any new techniques or use any new objects in math, but we provide a new view of the Riemann Hypothesis. Any reasonably advanced mathematician can check our proof. It doesn’t take an expert in number theory.”

Read a commentary on the paper by Fields Medalist Enrico Bombieri.

Although the paper falls short of proving the Riemann Hypothesis, its consequences include previously open assertions which are known to follow from the Riemann Hypothesis, as well as some proofs of conjectures in other fields.

Co-authors of the paper are Michael Griffin and Larry Rolen — two of Ono’s former Emory graduate students who are now on the faculty at Brigham Young University and Vanderbilt University, respectively — and Don Zagier of the Max Planck Institute of Mathematics.

“The result established here may be viewed as offering further evidence toward the Riemann Hypothesis, and in any case, it is a beautiful stand-alone theorem,” says Kannan Soundararajan, a mathematician at Stanford University and an expert on the Riemann Hypothesis.

"Math at a research level is often more art than calculation and that was certainly the case here," says co-author Michael Griffin, an Emory grad who is now on the faculty at Brigham Young University.

The idea for the paper was sparked two years ago by a “toy problem” that Ono presented as a “gift” to entertain Zagier during the lead-up to a math conference celebrating his 65th birthday. A toy problem is a scaled-down version of a bigger, more complicated problem that mathematicians are trying to solve. Zagier described the one that Ono gave him as “a cute problem about the asymptotic behavior of certain polynomials involving Euler’s partition function, which is an old love of mine and of Ken’s — and of about pretty much any classical number theorist.”

“I found the problem intractable and I didn’t really expect Don to get anywhere with it,” Ono recalls. “But he thought the challenge was super fun and soon he had crafted a solution.”

Ono’s hunch was that such a solution could be crafted into a more general theory. That’s what the mathematicians ultimately achieved.

“It’s been a fun project to work on, a really creative process,” Griffin says. “Math at a research level is often more art than calculation and that was certainly the case here. It required us to look at an almost 100-year-old idea of Jensen and Pólya in a new way.”

The Riemann Hypothesis is one of seven Millennium Prize Problems, identified by the Clay Mathematics Institute as the most important open problems in mathematics. Each problem carries a $1 million bounty for its solvers.

The method outlined in the PNAS paper "has a shocking sense of being universal, in that it applies to problems that are seemingly unrelated," says co-author Larry Rolen, an Emory grad now on the faculty at Vanderbilt University.

The hypothesis debuted in an 1859 paper by German mathematician Bernhard Riemann. He noticed that the distribution of prime numbers is closely related to the zeros of an analytical function, which came to be called the Riemann zeta function. In mathematical terms, the Riemann Hypothesis is the assertion that all of the nontrivial zeros of the Zeta function have real part ½.

“His hypothesis is a mouthful, but Riemann’s motivation was simple,” Ono says. “He wanted to count prime numbers.”

Bernhard Riemann
The hypothesis is a vehicle to understand one of the greatest mysteries in number theory — the pattern underlying prime numbers. Although prime numbers are simple objects defined in elementary math (any number greater than 1 with no positive divisors other than 1 and itself) their distribution remains hidden.

The first prime number, 2, is the only even one. The next prime number is 3, but primes do not follow a pattern of every third number. The next is 5, then 7, then 11. As you keep counting upwards, prime numbers rapidly become less frequent.

“It’s well known that there are infinitely many prime numbers, but they become rare, even by the time you get to the 100s,” Ono explains. “In fact, out of the first 100,000 numbers, only 9,592 are prime numbers, or roughly 9.5 percent. And they rapidly become rarer from there. The probability of picking a number at random and having it be prime is zero. It almost never happens.”

In 1927, Jensen and Pólya formulated a criterion for confirming the Riemann Hypothesis, as a step toward unleashing its potential to elucidate the primes and other mathematical mysteries. The problem with the criterion — establishing the hyperbolicity of the Jensen-Pólya polynomials — is that it is infinite. During the past 90 years, only a handful of the polynomials in the sequence have been verified, causing mathematicians to abandon this approach as too slow and unwieldy.

For the PNAS paper, the authors devised a conceptual framework that combines the polynomials by degrees. This method enabled them to confirm the criterion for each degree 100 percent of the time, eclipsing the handful of cases that were previously known.

“The method has a shocking sense of being universal, in that it applies to problems that are seemingly unrelated,” Rolen says. “And at the same time, its proofs are easy to follow and understand. Some of the most beautiful insights in math are ones that took a long time to realize, but once you see them, they appear simple and clear.”

Despite their work, the results don’t rule out the possibility that the Riemann Hypothesis is false and the authors believe that a complete proof of the famous conjecture is still far off.

The work was supported by grants from the National Science Foundation and the Asa Griggs Candler Fund.

Related:
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Monday, May 13, 2019

Artificial intelligence and 'deep ethics'

In the sci-fi film “2001: A Space Odyssey,” astronauts go into a soundproof pod to discuss their concerns about some of the decisions made by the supercomputer Hal (seen through the window) without realizing that Hal knows how to lip read.

Advances in neurotechnology, genetics and artificial intelligence are not only going to change society as a whole, they are actually going to challenge what it means to be human and change our ethics, argues Paul Root Wolpe, director of the Emory Center for Ethics, in a recent TEDx Atlanta talk.

He uses self-driving cars as just one example.

“These vehicles are going to be going down the road and in a crisis they’re going to have to make decisions about what to do,” Wolpe says. “Do I crash into the wall and endanger my passengers or do I turn left and hit those pedestrians? For the first time we’re going to have to create ethical algorithms. That is, we’re going to have to teach a vehicle to make ethical decisions. For the first time, machines will be making ethical decisions that will have a profound impact on human beings.” 

Watch Wolpe’s talk in the video below to learn what he means by the term “deep ethics,” and how artificial intelligence may someday help us navigate through the ethical complexities raised by technology itself.



Related:
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Thursday, April 18, 2019

Ginkgo seed extracts show antibacterial activity on skin pathogens

The fan-shaped leaves of a ginkgo tree on the Emory campus, just off the Quad on the west end of Carlos Hall. The tree led a student to an ancient Chinese text and a laboratory discovery. (Photo by Ann Watson)

Extracts from the seeds of the Ginkgo biloba tree show antibacterial activity on pathogens that can cause skin infections such as acne, psoriasis, dermatitis and eczema, a study at Emory University finds. Frontiers in Microbiology is publishing the results of laboratory experiments showing that the extracts inhibit the growth of Cutibacterium acnes, Staphylococcus aureus and Streptococcus pyogenes.

A nearly 200-year-old copy of a 16th-century text on traditional Chinese medicine, the Ben Cao Gang Mu, guided the researchers in their experiments. “It was like blowing the dust off knowledge from the past and rediscovering something that had been there all along,” says Xinyi (Xena) Huang, co-first author of the paper.

Huang, a native of China, began the project for her senior thesis as a biology major at Emory. She has since graduated from Emory and is now a student at the University of Maryland School of Pharmacy.

“To the best of our knowledge, this is the first study to demonstrate the antibacterial activity of ginkgo seeds on skin pathogens,” says Cassandra Quave, senior author of the paper and assistant professor at Emory’s Center for the Study of Human Health and the School of Medicine’s Department of Dermatology. “This paper is just one more example of how much we still have to learn about the pharmacological potential of the complex chemistry of plants.”

Quave is an ethnobotanist, studying how indigenous people use plants in their healing practices, to uncover promising candidates for new drugs. Read more about the discovery.

Click here to read more about the discovery.

Thursday, April 11, 2019

When do children alter behavior to please others?


“I have spent the past four years at Emory University investigating how an infant, who has no problem walking around the grocery store in her onesie, develops into an adult that fears public speaking for fear of being negatively judged,” says Sara Botto in her newly released TEDxAtlanta talk.

Botto is a doctoral candidate in the Cognition and Development program of Emory’s Department of Psychology. Together with Emory psychologist Philippe Rochat, she designed experiments to investigate when in development we become sensitive to others’ evaluations — a big part of being human.

Watch the TEDxAtlanta video below to see young children reacting to the opinions of others during the experiments, which take the form of a game called “The Robot Task.”

Botto’s research showed that, even before they can form a simple sentence, children are sensitive to the evaluations of others, and alter their behavior accordingly.

“Whether we’re aware of it or not, we’re constantly communicating values to others,” Botto says. “We’re communicating a value when we mostly compliment girls for their pretty hair or their pretty dress but boys for their intelligence. Or when we choose to offer candy as opposed to nutritious food as a reward for good behavior.”

Visit Botto’s web site, AdultingWithKids.com, to learn more about credible, science-based child development research.




Related:
Sensitivity to how others evaluate you emerges by 24 months

Gender gap in spatial reasoning starts in elementary school, meta-analysis finds

"We're interested in the origins of gender differences in spatial skills because of their potential role in the gender gap we see in math and science fields," says Jillian Lauer, who is set to graduate from Emory in May with a PhD in psychology. (Getty Images)

By Carol Clark

It is well-established that, on average, men outperform women on a spatial reasoning task known as mental rotation — imagining multi-dimensional objects from different points of view. Men are not, however, born with this advantage, suggests a major meta-analysis by psychologists at Emory University. Instead, males gain a slight advantage in mental-rotation performance during the first years of formal schooling, and this advantage slowly grows with age, tripling in size by the end of adolescence.

The Psychological Bulletin, a journal of the American Psychological Association, is publishing the findings.

“Some researchers have argued that there is an intrinsic gender difference in spatial reasoning — that boys are naturally better at it than girls,” says lead author Jillian Lauer, who is set to graduate from Emory in May with a PhD in psychology. “While our results don’t exclude any possibility that biological influences contribute to the gender gap, they suggest that other factors may be more important in driving the gender difference in spatial skills during childhood.”

Co-authors of the paper include Stella Lourenco, associate professor of psychology at Emory, whose lab specializes in the development of spatial and numerical cognition. Co-author Eukyung Yhang worked on the paper as an Emory undergraduate, funded by the university’s Institute for Quantitative Theory and Methods. Yhang graduated in 2018 and is now at Yale University School of Medicine.

The meta-analysis included 128 studies of gender differences in spatial reasoning, combining statistics on more than 30,000 children and adolescents aged three to 18 years. The authors found no gender difference in mental-rotation skills among preschoolers, but a small male advantage emerged in children between the ages of six and eight.

While differences in verbal and mathematical abilities between men and women tend to be small or non-existent, twice as many men as women are top performers in mental rotation, making it one of the largest gender differences in cognition.

Mental rotation is considered one of the hallmarks of spatial reasoning. “If you’re packing your suitcase and trying to figure out how each item can fit within that space, or you’re building furniture based on a diagram, you’re likely engaged in mental rotation, imagining how different objects can rotate to fit together,” Lauer explains.

It takes most of childhood and adolescence for the gender gap in spatial skills to reach the size of the difference seen in adulthood.

Prior research has also shown that superior spatial skills predict success in male-dominated science, technology engineering and math (STEM) fields, and that the gender difference in spatial reasoning may contribute to the gender disparity in these STEM fields.

“We’re interested in the origins of gender differences in spatial skills because of their potential role in the gender gap we see in math and science fields,” Lauer says. “By determining when the gender difference can first be detected in childhood and how it changes with age, we may be able to develop ways to make educational systems more equitable.”

It takes most of childhood and adolescence for the gender gap in spatial skills to reach the size of the difference seen in adulthood, Lauer says. She adds that the meta-analysis did not address causes for why the gender gap for mental rotation emerges and grows.

Lauer notes that previous research has shown that parents use more spatial language when they talk to preschool sons than daughters. Studies have also found that girls report more anxiety about having to perform spatial tasks than do boys by first grade, and that children are aware of gender stereotypes about spatial intelligence during elementary school.

“Now that we’ve characterized how gender differences in spatial reasoning skills develop in children over time we can start to hone in on the reasons for those differences,” Lauer says.

Meanwhile, she adds, parents may want to be aware to encourage both their daughters and sons to play with blocks and other construction items that might help in the development of spatial reasoning skills, since evidence shows that these skills can be improved with training.

“Giving both girls and boys more opportunities to develop their spatial skills is something that parents and educators have the power to do,” Lauer says.

Lauer has accepted a post-doctoral fellowship position at New York University. Her PhD advisor is Patricia Bauer, a professor of psychology at Emory focused on cognition and child development.

Related:
Babies' spatial reasoning predicts later math skills
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Wednesday, March 27, 2019

Machine learning used to understand and predict dynamics of worm behavior

The roundworm C. elegans is a well-established laboratory model system. While the worm is a fairly simple living system, it is complicated enough to serve as "a kind of sandbox" for testing out methods of automated inference, says Emory biophysicist Ilya Nemenman. (Getty Images)

By Carol Clark

Biophysicists have used an automated method to model a living system — the dynamics of a worm perceiving and escaping pain. The Proceedings of the National Academy of Sciences (PNAS) published the results, which worked with data from experiments on the C. elegans roundworm.

“Our method is one of the first to use machine-learning tools on experimental data to derive simple, interpretable equations of motion for a living system,” says Ilya Nemenman, senior author of the paper and a professor of physics and biology at Emory University. “We now have proof of principle that it can be done. The next step is to see if we can apply our method to a more complicated system.”

The model makes accurate predictions about the dynamics of the worm behavior, and these predictions are biologically interpretable and have been experimentally verified.

Collaborators on the paper include first author Bryan Daniels, a theorist from Arizona State University, and co-author William Ryu, an experimentalist from the University of Toronto.

The researchers used an algorithm, developed in 2015 by Daniels and Nemenman, that teaches a computer how to efficiently search for the laws that underlie natural dynamical systems, including complex biological ones. They dubbed the algorithm “Sir Isaac,” after one of the most famous scientists of all time — Sir Isaac Newton. Their long-term goal is to develop the algorithm into a “robot scientist,” to automate and speed up the scientific method of forming quantitative hypotheses, then testing them by looking at data and experiments.

While Newton’s Three Laws of Motion can be used to predict dynamics for mechanical systems, the biophysicists want to develop similar predictive dynamical approaches that can be applied to living systems.

For the PNAS paper, they focused on the decision-making involved when C. elegans responds to a sensory stimulus. The data on C. elegans had been previously gathered by the Ryu lab, which develops methods to measure and analyze behavioral responses of the roundworm at the holistic level, from basic motor gestures to long-term behavioral programs.

C. elegans is a well-established laboratory animal model system. Most C. elegans have only 302 neurons, few muscles and a limited repertoire of motion. A sequence of experiments involved interrupting the forward movement of individual C. elegans with a laser strike to the head. When the laser strikes a worm, it withdraws, briefly accelerating backwards and eventually returning to forward motion, usually in a different direction. Individual worms respond differently. Some, for instance, immediately reverse direction upon laser stimulus, while others pause briefly before responding. Another variable in the experiments is the intensity of the laser: Worms respond faster to hotter and more rapidly rising temperatures.

For the PNAS paper, the researchers fed the Sir Isaac platform the motion data from the first few seconds of the experiments — before and shortly after the laser strikes a worm and it initially reacts. From this limited data, the algorithm was able to capture the average responses that matched the experimental results and also to predict the motion of the worm well beyond these initial few seconds, generalizing from the limited knowledge. The prediction left only 10 percent of the variability in the worm motion that can be attributed to the laser stimulus unexplained. This was twice as good as the best prior models, which were not aided by automated inference.

“Predicting a worm’s decision about when and how to move in response to a stimulus is a lot more complicated than just calculating how a ball will move when you kick it,” Nemenman says. “Our algorithm had to account for the complexities of sensory processing in the worms, the neural activity in response to the stimuli, followed by the activation of muscles and the forces that the activated muscles generate. It summed all this up into a simple and elegant mathematical description.”

The model derived by Sir Isaac was well-matched to the biology of C. elegans, providing interpretable results for both the sensory processing and the motor response, hinting at the potential of artificial intelligence to aid in discovery of accurate and interpretable models of more complex systems.

“It’s a big step from making predictions about the behavior of a worm to that of a human,” Nemenman says, “but we hope that the worm can serve as a kind of sandbox for testing out methods of automated inference, such that Sir Isaac might one day directly benefit human health. Much of science is about guessing the laws that govern natural systems and then verifying those guesses through experiments. If we can figure out how to use modern machine learning tools to help with the guessing, that could greatly speed up research breakthroughs.”

Related:
Biophysicists take small step in quest for 'robot scientist'
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Biology may not be so complex after all

Friday, March 15, 2019

A nod to World Sleep Day

World Sleep Day is March 15 this year. The annual event is a celebration of sleep and a call to action on issues related to sleep, including medicine, education and social aspects.

In Emory anthropologist Carol Worthman's research around the world, "sleep has emerged as both more flexible and more social than one would think from the perspective of the West," writes Todd Pitock in Aeon Magazine.

"When Worthman started exploring the anthropology of sleep more than a decade ago," the article continues, "the topic was way below the radar of colleagues who believed that culture was something you did while awake. But she found otherwise."

Read the whole article here.

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Thursday, March 14, 2019

The importance of puberty: A call for better research models

“Due to the global slowdown in fertility, this is probably the biggest cohort of young people we will ever see,” says anthropologist Carol Worthman. “If we are ever going to get serious about helping adolescents reach their full potential, now is the time.”

By Carol Clark

Puberty is much more than just a time of biological overdrive, propelled by sexual maturation. Progress in developmental science has greatly broadened the perspective of this critical maturational milestone.

“We’ve moved beyond thinking of puberty as simply raging hormones,” says Carol Worthman, professor of anthropology at Emory University. “Major advances in understanding of brain development clearly show that the sociological and psychological impacts during puberty are just as important as the hormones.”

What’s needed now, Worthman argues as lead author on a new paper, is to integrate this understanding into more comprehensive research models. The Journal of Research on Adolescence published the paper, which reviews key theories and methods that are relevant to studies of puberty.

“Puberty was once thought of as the biological process of teen development and adolescence was considered the cultural process,” Worthman says. “We want to raise awareness that bracketing research in this way is no longer a useful approach.”

For decades, researchers have focused on improving the health of infants and children, resulting in substantial declines in child mortality worldwide.

While babies and children are labeled as cute and positive, full of possibility, adolescents are more often seen as problems. They have generally been less studied, Worthman says, even though the second decade of life is a critical time when risks spike for the development of mental illness, substance abuse and the escalation of injuries. And what happens in puberty, she adds, impacts health and well-being across the lifespan.

The global population is now bulging with young people aged 10 to 19, who today number more than 1.2 billion, or 17 percent of humanity. These young people must deal with finding their way into adulthood amid massive, rapid social transformations.

“Due to the global slowdown in fertility, this is probably the biggest cohort of young people we will ever see,” Worthman says. “If we are ever going to get serious about helping adolescents reach their full potential, now is the time.”

In her own research, Worthman uses a biocultural approach to conduct comparative interdisciplinary studies of human development. Samatha Dockray, a co-author of the paper from University College Cork, studies psychobiological mechanisms to understand their effects on adolescent health and behavior. The third co-author, Kristine Marceau from Purdue University, integrates genetics, prenatal risk, neuroendocrine development and the family environment into her developmental research.

The paper outlines minimally invasive methods to study different aspects of puberty. For instance, hair and fingernail clippings can be used to track stress levels and hormones over time. Changes in the microbiome, immune function and brain are other critical aspects of puberty that can be measured, along with cognition, behavior and ecological contexts.

“By taking advantage of new methods, and working in interdisciplinary teams, developmental scientists can explore more questions about adolescent development and welfare in more integrated ways,” Worthman says.

The review paper is part of a special section on puberty published by the Journal of Research on Adolescence. Topics covered include emerging genetic-environmental complexities of puberty, the role of puberty in the developing brain, how puberty impacts health and well-being across the lifespan and the need to explore puberty in understudied populations.

Related:
Scientists zeroing in on psychosis risk factors

Wednesday, March 13, 2019

Changes in rat size reveal habitat of 'Hobbit' hominin

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

By Carol Clark

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

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

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

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

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

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

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

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

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

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

A graphic of the rat species included in the study.

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

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

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

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

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

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

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

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

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

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

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

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

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Tuesday, March 12, 2019

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

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

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

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

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

Learn more by clicking here.

Wednesday, February 20, 2019

Computer scientist explains 'Dangers of the Coded Gaze'


Watch a video of Joy Buolamwini discussing her work.

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

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

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

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

Monday, February 11, 2019

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

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

By Carol Clark

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Tuesday, February 5, 2019

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

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

By Carol Clark

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

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

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

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

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

Evangelista and his graduate students have now joined that race.

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Related:
$2 million NSF grant funds physicists' quest for optical transistors
Chemists find new way to do light-driven reactions
Physicists devise method to reveal how light affects materials

Monday, February 4, 2019

Take a 60-minute tour of space, time and spacetime



“I’ll begin with Saint Augustine,” says Emory physicist Erin Bonning, referring to the 4th-century philosopher and theologian who wrote some of the earliest known reflections on time and how humans perceive it. He summed time up: “I know well enough what it is, provided that nobody asks me; but if I am asked what it is, and try to explain, I am baffled.”

Bonning, director of the Emory Planetarium and a lecturer in the Department of Physics, collapses centuries of ideas and discovery about the universe into a mind-bending, 60-minute talk, “Space, Time and Spacetime,” that you can watch in the video above.

Bonning explains the ongoing quest for our understanding of time and how it relates to space: From recognition of the regular appearances of the sun, to the sense of time flowing through an hour glass, to the ticking of the first mechanical clocks, and on through the insights of Newton, Copernicus, Galileo, Michelson, Einstein and more. She even gives the perspective of aliens whizzing by Earth in a spaceship.

She winds up her talk, a recently delivered Emory Williams Lecture in the Liberal Arts, by discussing explorations of gravitational waves, dark matter and the drive to manipulate spacetime deliberately.

Related:
Fantastic light: From science fiction to fact

Wednesday, January 23, 2019

Growing knowledge and healthy food

Oxford student Gratia Sullivan unearths a bunch of radishes destined for the campus kitchens and community consumers. Photo by Kay Hinton.

From Emory Magazine

As an undergraduate biology major at Clemson University, Daniel Parson recognized the disconnect between environmental sustainability and traditional agriculture. He went on to get a masters degree in plant and environmental science from Clemson and spent more than a dozen years working in organic farming in Georgia and South Carolina.

"We look at nature as wilderness, but we also need things from nature and we need to learn how to get them without destroying it," says Parson.

He joined Emory's Oxford campus in 2014 to run the Oxford Organic Farm, an 11-acre piece of land that provides produce for the university's dining halls and farmers markets and unique learning opportunities for students.

"We try to match the seasons with when students are on campus so our work-student students who are here every day have the best experience possible and so we can work with faculty to connect course curriculum to the farm," says Parson, whose official title is farmer-educator. "For economics classes I might talk about how we set prices and interact with markets, but for other classes I may just be talking about the experiences I've had and how that connects with what they are discussing in class."

Click here to read more.