He did the math for his country

A bill in the Senate could open the door to the chance for Puerto Rico to become the 51st state. So where should we put the 51st star on the American flag?

Slate columnist Chris Wilson put the question to Emory mathematician Skip Garibaldi, who wrote a computer program for all possible combinations for flags of any number of stars. Slate used the code to make an interactive flag calculator:



Related:
The math of rock climbing
Lottery story zeros in on risk

Gulf oil mess fuels interest in green energy

Oil floats on the surface of the Gulf of Mexico. Photo: BP p.l.c.

“The spill in the Gulf, which is just heartbreaking, only underscores the necessity of seeking alternative fuel sources,” President Obama said in a recent speech.

As thousands of barrels of oil gush daily into the waters of the Gulf of Mexico, Emory inorganic chemist Craig Hill has been spending time in Washington, speaking about the University’s green energy research.

“The Gulf oil mess affects everybody,” Hill said. “I think there’s no question that it’s having a significant impact on how we view the risks for offshore drilling as we seek ever more fossil fuel.”

Louisiana beach clean-up, below. Photo by Patrick Kelly, U.S. Coast Guard/Marine Photobank.

On May 2, Hill addressed the Council of Scientific Society Presidents in Washington on his lab’s recent breakthrough in sustainable solar energy research. Work by Hill’s lab on water oxidation catalysis, a crucial component of converting solar energy into clean hydrogen fuel, was recently published in Science, and is the centerpiece of the Emory Bio-inspired Renewable Energy Center.

“Emory is becoming a focal point for a lot of interest in the efforts to confront the problems of fossil fuel consumption and global climate change,” Hill said. “Our team really does have the best water oxidation catalyst on the planet.”

Hill is back in Washington this week and next, for Department of Energy meetings on catalysis and solar energy.

Carol Browner, Obama’s top energy advisor, has called the Gulf oil gusher “probably the biggest environmental disaster this country has ever faced,” and the president is pushing Congress to pass a climate change bill this year.

“Federal funding is substantial for green energy, but it’s still far below what it should be,” Hill said. “Everything is pointing to the fact that we’re going to need alternative energy to power society. It’s really a global imperative that affects health and security worldwide.”

Related:
Water oxidation advance aims at solar fuel
Bringing new energy to solar quest
Doing chemistry with the sun
Oil spill may reshape environmental law
Can whales and dolphins adapt to oily Gulf?

Peptides may hold 'missing link' to life

Emory scientists have discovered that simple peptides can organize into bi-layer membranes. The finding suggests a “missing link” between the pre-biotic Earth’s chemical inventory and the organizational scaffolding essential to life.


“We’ve shown that peptides can form the kind of membranes needed to create long-range order,” says chemistry graduate student Seth Childers, lead author of the paper recently published by the German Chemical Society’s Angewandte Chemie. “What’s also interesting is that these peptide membranes may have the potential to function in a complex way, like a protein.”

Chemistry graduate student Yan Liang captured images of the peptides as they aggregated into molten globular structures, and self-assembled into bi-layer membranes. The results of that experiment were recently published by the Journal of the American Chemical Society.

“In order to form nuclei, which become the templates for growth, the peptides first repel water,” says Liang, who is now an Emory post-doctoral fellow in neuroscience. “Once the peptides form the template, we can now see how they assemble from the outer edges."

Click here to watch the movies.

In addition to providing clues to the origins of life, the findings may shed light on protein assemblies related to Alzheimer’s disease, Type 2 diabetes, and dozens of other serious ailments.

“This is a boon to our understanding of large, structural assemblies of molecules,” says Chemistry Chair David Lynn, who helped lead the effort behind both papers, which were collaborations of the departments of chemistry, biology and physics. “We’ve proved that peptides can organize as bi-layers, and we’ve generated the first, real-time imaging of the self-assembly process. We can actually watch in real-time as these nano-machines make themselves.”


Chemistry grad student Seth Childers, left, discovered that if you just add water to simple peptides, you get the scaffold for life. Fellow graduate student Yan Liang, right, made the first real-time images of the peptides self-assembling into nano-machines. Photo by Bryan Meltz.

The ability to organize things within compartments and along surfaces underpins all of biology. From the bi-layer phospholipids of cell membranes to information-rich DNA helices, self-assembling arrays define the architecture of life.

But while phospholipids and DNA are complicated molecules, peptides are composed of the simple amino acids that make up proteins. The Miller-Urey experiment demonstrated in 1953 that amino acids were likely to be present on the pre-biotic Earth, opening the question of whether simple peptides could achieve supra-molecular order.

To test how the hollow, tubular structure of peptides is organized, the researchers used specialized solid-state nuclear magnetic resonance (NMR) methods that have been developed at Emory during the past decade.


Working with Anil Mehta, a chemistry post-doctoral fellow, Childers tagged one end of peptide chains with an NMR label, and then allowed them to assemble to see if the ends would interact. The result was a bi-layer membrane with inner and outer faces and an additional, buried layer that localized functionality within the interior.

“The peptide membranes combine the long-range structure of cell membranes with the local order of enzymes,” Childers said. “Now that we understand that peptide membranes are organized locally like a protein, we want to investigate whether they can function like a protein.”

The goal is to direct molecules to perform as catalysts and create long-range order. “We’d really like to understand how to build something from the bottom up,” Childers says. “How can we take atoms and make molecules? How can we get molecules that stick together to make nano-machines that will perform specific tasks?”

The research is part of “The Center for Chemical Evolution,” a center based at Emory and Georgia Tech, for integrated research, education and public outreach focused on the chemistry that may have led to the origin of life. The National Science Foundation and the U.S. Department of Energy have funded the research.

Many groups studying the origins of life have focused on RNA, which is believed to have pre-dated living cells. But RNA is a much more complicated molecule than a peptide. “Our studies have now shown that, if you just add water, simple peptides access both the physical properties and the long-range molecular order that is critical to the origins of chemical evolution,” Childers says.

Related:
Synthetic cell: A step closer to 'recipe for life'
2010: A Science Odyssey
A new twist on an ancient story

How we learn language

From the Quadrangle magazine:

“Humans have evolved with some general capacities to do things like remember, pay attention, recognize patterns,” says psychologist Laura Namy, who heads the Language and Learning Lab at Emory’s Child Study Center.

"Pattern recognition, for example, can help you see a tiger in the grass, which would have helped early humans, but that same cognitive capacity can lend itself to lots of other skills, including the trick of discovering how language works."

Early on, children use gestures spontaneously, Namy says. "They might make one hand motion for ‘more,’ another for ‘juice,’ or ‘up.’ Then as verbal vocabulary develops, the gestures sort of fall by the wayside. While it’s not anything we teach our kids, we want to learn what parents do to encourage this, either with their own gestures or by their responses.”



Our sensitivity to tone of voice is remarkable, too. “When we stress words in certain ways, for instance by saying ‘eNORmous’ or ‘teeny-weeny,’ we’re doing with our voice what we would call an iconic gesture with our hands. And kids get that,” Namy says. “Even with made-up words, pre-schoolers can reliably infer from these cues whether a word should mean big or small, hot or cold. We can even filter speech so that content is gone and all that’s left is tone of voice. And even then, people can guess.”

Sound symbolism goes further. In English, for example, sl words often refer to slippery or slimy things, and sn words to nasal things (think sniffle and snort). “And while that’s not true for all words in every language, there is something about certain sound clusters that makes them common carriers of meaning across languages,” Namy says. “If you play an Urdu word to native English speakers who’ve never heard Urdu and ask them to say if it means tall or short, they guess right more often than chance would allow.”

Emory recently brought together leading scholars in the emerging field of sound symbolism for a conference: “Sound Symbolism: Challenging the Arbitrariness of Language.”

Related:
Uncovering secrets of sound symbolism
Gestures may point to speech origins
What is your baby thinking?

Water oxidation advance aims at solar fuel

Liquid sunlight: Bubbles form during water oxidation, catalyzed by the new tetra-cobalt WOC. Photo by Benjamin Yin.

Emory chemists have developed the most potent homogeneous catalyst known for water oxidation, considered a crucial component for generating clean hydrogen fuel using only water and sunlight. The breakthrough, to be published in the journal Science, was made in collaboration with the Paris Institute of Molecular Chemistry.

The fastest, carbon-free molecular water oxidation catalyst (WOC) to date "has really upped the standard from the other known homogeneous WOCs," said Emory inorganic chemist Craig Hill, whose lab led the effort. "It's like a home run compared to a base hit."

In order to be viable, a WOC needs selectivity, stability and speed. Homogeneity is also a desired trait, since it boosts efficiency and makes the WOC easier to study and optimize. The new WOC has all of these qualities, and it is based on the cheap and abundant element cobalt, adding to its potential to help solar energy go mainstream.

Benjamin Yin, an undergraduate student in Hill’s lab, is the lead author on the Science paper. Emory chemists who are co-authors include Hill, Yurii Gueletii, Jamal Musaev, Zhen Luo and Ken Hardcastle. The U.S. Department of Energy funded the work.

The WOC research is a component of the Emory Bio-inspired Renewable Energy Center, which aims to mimic natural processes such as photosynthesis to generate clean fuel. The next step involves incorporating the WOC into a solar-driven, water-splitting system.

The long-term goal is to use sunlight to split water into oxygen and hydrogen. Hydrogen becomes the fuel. Its combustion produces the by-product of water – which flows back into a clean, green, renewable cycle.Three main technical challenges are involved: developing a light collector, a catalyst to oxidize water to oxygen and a catalyst to reduce water to hydrogen. All three components need improvement, but a viable WOC may be the most difficult scientific challenge. “We are aiming for a WOC that is free of organic structure, because organic components will combine with oxygen and self-destruct,” Hill says. “You’ll wind up with a lot of gunk.”

Enzymes are nature’s catalysts. The enzyme in the oxygen-evolving center of green plants “is about the least stable catalyst in nature, and one of the shortest lived, because it’s doing one of the hardest jobs,” Hill says.

"We've duplicated this complex natural process by taking some of the essential features from photosynthesis and using them in a synthetic, carbon-free, homogeneous system. The result is a water oxidation catalyst that is far more stable than the one we found in nature."

For decades, scientists have been trying to imitate Mother Nature and create a WOC for artificial photosynthesis. Nearly all of the more than 40 homogeneous WOCs developed by labs have had significant limitations, such as containing organic components that burn up quickly during the water oxidation process.

Two years ago, Hill’s lab and collaborators developed the first prototype of a stable, homogenous, carbon-free WOC, which also worked faster than others known at the time. The prototype, however, was based on ruthenium, a relatively rare and expensive element.

Building on that work, the researchers began experimenting with the cheaper and more abundant element cobalt. The cobalt-based WOC has proved even faster than the ruthenium version for light-driven water oxidation.

Related:
Bringing new energy to solar quest
Shining a light on green energy
Chemistry's crucial catalyst
Doing chemistry with the sun

Bringing new energy to solar quest

The search for clean, cheap energy sources is the biggest problem of our age, says chemist Brian Dyer, director of the Emory Bio-inspired Renewable Energy Center (EBREC). eScienceCommons interviewed Dyer about how the new center is carving out a unique niche in the development of solar energy solutions, through its work at the intersection of chemistry, physics and biology, and its outreach to the broader community.

Q: How is EBREC tackling the technical problems of clean energy?

Dyer: We want to create a completely green, cheap and sustainable energy cycle, using just sunlight and water to generate hydrogen fuel. We are trying to mimic the way that plants use photosynthesis to capture sunlight and store it as fuel, and also harness the power of anaerobic bacteria to generate hydrogen.

Q. Is Emory competitive with other institutions at work on these problems?

Dyer: Emory brings together leading expertise in key areas: quantum dot technology, to absorb light and drive reactions; water oxidation catalysis, to split water into oxygen and protons; microbial catalysis by the protein hydrogenase, to convert protons into hydrogen; and protein re-engineering, to evolve the needed properties in hydrogenase.

All of these areas need a lot more refinement in order to cheaply and efficiently produce hydrogen fuel, but a water oxidation catalyst, or WOC, is considered the most difficult and crucial piece of the puzzle. Craig Hill’s inorganic chemistry lab just led the development of the best homogeneous WOC known, with the highest potential for getting hydrogen fuel from water, using only solar energy. This breakthrough puts Emory and our energy center in a very strong position.

Emory has a good track record of bringing together interdisciplinary teams, and tremendous strengths in the biological sciences, as well as the physical sciences. Most of the advances in renewable energy are going to be made at that interface.

But we’re not just a bunch of nerdy scientists tinkering in our labs. We’re thinking about the human implications of our work.

Q. How do you view your role beyond the lab?

Dyer: We realize that renewable energy is much more than just a science problem. It’s a political problem, an economic problem, an environmental problem, a health problem, a cultural problem and even a peace problem.

EBREC needs to engage resources throughout the University to further the cause of clean energy, as well as local, national and international communities. You can come up with great technology, but it doesn’t do any good if you don’t change the way people think. We need political will, economic incentives and public outreach to help people understand that our collective future depends on clean, renewable energy.

So in addition to building on our foundation of interdisciplinary science, EBREC plans to leverage Emory’s tremendous strengths in community engagement and global initiatives that span disciplines.

Q: How urgent is this issue?

Dyer: Energy underlies everything, from the quality of our daily lives, to our industrial capacity, our transportation and our security. Our current worldwide energy use is equivalent to about 100 billion 100-watt light bulbs that are on all the time: 24/7, 365 days of the year. Our energy use is expected to double within the next 40 years. So how are we going to get there without running out of fossil fuels, further warming our climate and destroying the environment?

While the United States is distracted by the health care debate, China is building coal-fired plants as fast as it can. At the same time, China is investing billions of dollars in renewable energy technology, in an attempt to dominate that market. In 10 years, I believe that it will. The United States is falling behind in this critical area, which in the long run could endanger our economy as well as the fate of the planet.

It’s going to take an enormous collective effort to solve the scientific and social problems surrounding renewable energy. EBREC is working to make a difference in both of these areas.

Related:
Water oxidation advance aims at solar fuel
A biochemical path to solar energy
Shining a light on green energy
Chemistry's crucial catalyst

Tiny aphids hold big surprises in genome

Pea aphids, expert survivors of the insect world, appear to lack major biological defenses, according to the first genetic analysis of their immune system.

“It’s surprising,” says Emory biologist Nicole Gerardo, who led the study, published this week in Genome Biology. "Aphids have some components of an immune system, but they are missing the genes that we thought were critical to insect immunity."

Pea aphids are major agricultural pests and also important biological models for studies of insect-plant interactions, symbiosis, virus vectoring and genetic plasticity. These resilient insects thrive despite a host of enemies, including parasitic wasps, lady bugs, fungal pathogens and frustrated farmers and gardeners the world over.


The immune-system analysis is among a group of findings generated by the International Aphid Genomics Consortium, which just published the full sequence of the pea aphid genome, and sponsored dozens of in-depth analyses of different areas of the sequence.

"This is the first look at the genome of a whole group of insects we know little about," says Gerardo, an evolutionary biologist who focuses on host-parasite interactions.

All insects previously sequenced belong to a group that undergoes metamorphosis. Pea aphids, however, belong to an insect group known as basel hemimetablous – meaning they are born looking like tiny adults.
"We went into this expecting to find the same set of immune-system genes that we've seen in the genomes of flies, mosquitoes and bees," Gerardo says. “Given these missing genes, it seems that aphids have a weak immune system. Our next step is to figure out how they protect themselves.” One hypothesis is that aphids may compensate for their lack of immune defenses by focusing on reproduction. From birth, a female aphid contains embryos that also contain embryos.

“She is born carrying her granddaughters,” Gerardo says. “In a lab, a female aphid can produce up to 20 copies of herself per day. About 10 days later, those babies will start producing their own offspring.”

Over 50 million years, aphids have evolved complex relationships with beneficial bacteria that supply them with nutrients or protect them from predators and pathogens. It’s possible that the weak immune response in aphids developed as a way to keep from killing off these beneficial microbes, Gerardo says. “A key question is whether these microbes could have changed the aphid genome, or changed how the aphid uses its genes.”

Further study of how the aphid immune system interacts with microbes could yield better methods for controlling them in agriculture.

Aphids are not just pests, Gerardo says. They are also potential resources for questions related to human health.

"Humans need beneficial bacteria for proper digestion in the gut and to protect against cavities in the teeth," she says. "Some people feel sick when they take antibiotics because the drug kills off all the beneficial bacteria. If we can study the process of how to keep beneficial bacteria while clearing out harmful bacteria across several organisms, including aphids, we might be able to understand it better."

Related:
Are depressed people too clean?
The monarch butterfly's medicine kit
Farming ants reveal evolution secrets

Biology may not be so complex after all

By Carol Clark

Centuries ago, scientists began reducing the physics of the universe into a few, key laws described by a handful of parameters. Such simple descriptions have remained elusive for complex biological systems – until now.

Emory biophysicist Ilya Nemenman has identified parameters for several biochemical networks that distill the entire behavior of these systems into simple equivalent dynamics. The discovery may hold the potential to streamline the development of drugs and diagnostic tools, by simplifying the research models.

The resulting paper, now available online, will be published in the March issue of Physical Biology.

"It appears that the details of the complexity of these biological systems don't matter, as long as some aggregate property, which we've calculated, remains the same," says Nemenman, associate professor of physics and biology. He conducted the analysis with Golan Bel and Brian Munsky of the Los Alamos National Laboratory.

The simplicity of the discovery makes it “a beautiful result,” Nemenman says. “We hope that this theoretical finding will also have practical applications.”

He cites the air molecules moving about his office: “All of the crazy interactions of these molecules hitting each other boils down to a simple behavior: An ideal gas law. You could take the painstaking route of studying the dynamics of every molecule, or you could simply measure the temperature, volume and pressure of the air in the room. The second method is clearly easier, and it gives you just as much information.”


Nemenman wanted to find similar parameters for the incredibly complex dynamics of cellular networks, involving hundreds, or even thousands, of variables among different interacting molecules. Among the key questions: What determines which features in these networks are relevant? And if they have simple equivalent dynamics, did nature choose to make them so complex in order to fulfill a specific biological function? Or is the unnecessary complexity a “fossil record” of the evolutionary heritage?

For the Physical Biology paper, Nemenman and co-authors investigated these questions in the context of a kinetic proofreading (KPR) scheme.

KPR is the mechanism a cell uses for optimal quality control as it makes protein. KPR was predicted during the 1970s and it applies to most cellular assembly processes. It involves hundreds of steps, and each step may have different parameters.

Nemenman and his colleagues wondered if the KPR scheme could be described more simply. "Our calculations confirmed that there is, in fact, a key aggregate rate," he says. "The whole behavior of the system boils down to just one parameter."

That means that, instead of painstakingly testing or measuring every rate in the process, you can predict the error and completion rate of a system by looking at a single aggregate parameter.


Charted on a graph, the aggregate behavior appears as a straight line amid a tangle of curving ones. “The larger and more complex the system gets, the more the aggregate behavior is visible,” Nemenman says. “The completion time gets simpler and simpler as the system size goes up.”

Nemenman is now collaborating with Emory theoretical biologist Rustom Antia, to see if the discovery can shed light on the processes of immune cells. In particular, they are interested in the malfunction of certain immune receptors involved in most allergic reactions.

"We may be able to simplify the model for these immune receptors from about 3,000 steps to three steps," Nemenman says. "You wouldn't need a supercomputer to test different chemical compounds on the receptors, because you don't need to simulate every single step, just the aggregate."

Just as the discovery of an ideal gas law led to the creation of engines and automobiles, Nemenman believes that such simple biochemical aggregates could drive advancements in health.

Related:
Biochemical cell signals quantified for first time

A brainy time traveler

By Carol Clark

Anthropologist James Rilling, founder of Emory's Laboratory for Darwinian Neuroscience, is mapping the evolution of our minds.

"It's like the space program," he explains. "We believe that we should be trying to understand the universe around us. I feel the same way about exploring the brain to learn who we are and how we got here."

The Milwaukee native came to Emory as a graduate student, drawn by the anthropology department's emphasis on human biology. "It's a definite strength," says Rilling, citing the department's access to the Yerkes National Primate Research Center and the quality of the faculty.

For his dissertation, Rilling used fMRI to compare the neuroanatomy of humans and 10 other primate species at Yerkes. The 1998 study was the first in-depth look at whether the human brain is merely a scaled-up version of the brains of other primates.

“We found that human temporal lobes are larger than you would expect for a primate of our brain size,” Rilling says. “We’ve done subsequent work that shows this larger size is likely due to the evolution of language pathways in humans.”

The Laboratory for Darwinian Neuroscience is a leader in the use of non-invasive imaging technology to compare the neuroanatomy of living primates.

Much previous work has focused on the gray matter of brains. Rilling's group is the only one in the world using diffusion tensor imaging (DTI) to compare the white matter connections of monkeys, humans and our closest relative, chimpanzees. White matter contains the fiber tracts that connect and "wire" the brain.

“We’ve discovered a difference in both the size and the trajectory of the fiber tract that runs between Wernicke’s area in the left temporal lobe and Broca’s area in the left inferior frontal cortex,” Rilling says. Broca’s area is involved in speech production and Wernicke’s in understanding language. In humans, the pathway that connects the two areas is much more massive, and projects beyond Wernicke’s area down to the ventral part of the temporal lobe.

“There’s something special going on in the human brain with that pathway,” Rilling says. “It’s organized differently than in other primates.”

The lab is also exploring the neural basis of human cognition and behavior. One of its studies showed that reciprocation in humans is tied to activation of a reward pathway in the brain. “The magnitude of that reaction correlated to how likely the person was to cooperate in the future,” Rilling says.

Why are some people more cooperative than others? How does the brain change with age? What promotes social bonding and attachment? These are just a few of the many research questions the lab is tackling.

"We want to start to understand individual human differences in social behavior, at both the genetic and neurological levels," Rilling says.

He's particularly interested in understanding why some men are more nurturing as fathers than others. “It’s important to have someone besides the mother involved in a child’s care. I think one way that we could improve childhood development is to have more committed dads,” says Rilling, who is married to a psychiatrist and hopes to one day become a father.

Related:
Brain expert explores human dawn
Inside the chimpanzee brain
Give your mind a hand
Exploring our brains: The internal frontier
The science of love

Grounded cognition gives your mind a hand

Before you read this, pour yourself a cup of hot tea.

Now, sit up straight. Smile. Hold that warm cup in your hand. Research is showing that these kinds of actions can positively influence what you think about a piece of writing.

"All the states of your body affect how you think. So does the environment," says Lawrence Barsalou, an Emory psychologist and a leading researcher of grounded cognition -- the idea that thought is shaped by bodily states. And vice-versa.

For instance, you may feel anxious about an upcoming presentation. Just thinking about forgetting your speech can produce the same physical stress reactions that occur when you actually are standing in front of a group of people and draw a blank.

"We're just barely beginning to understand the mechanisms, at a detailed and specific level, that operate to produce these experiences," Barsalou says.

We are entering a new era in psychology research, says Barsalou, who is especially interested in how meditation might be used to alleviate stress reactions.

Related:
New thoughts on cognition
Gestures may point to speech origins
2010: A science odyssey

2010: A Science Odyssey

Crystal ball courtesy of Crystal Blue in Little Five. Photo by Carol Clark.

Anyone remember the Y2K scare? Fears that a fluke of technology would cause our entire digital world to crash with the 2000 calendar rollover were a mere distraction. As we enter 2010, we're hoping technology can save us from climate change.

The first decade of the 21^st century flew by, with changes coming at breakneck speed. It's a good time to peer into the crystal ball of research. eScienceCommons asked Emory scientists for their views on key advances during the past 10 years, and what may be in store by 2020.

"The most important thing that's happened is the recalibration of our perception of the world, and a clarification of the real challenges," says David Lynn, chair of chemistry. "That relates to everything from how we understand the origins of life, to the emerging focus on predictive health, and our increased understanding of the need for renewable energy."

Lynn cited the sequencing of the human genome and the identification of new planets as two events that shook the foundations of our social structure.

NASA photo

“The existence of other planets was predicted decades ago, but now we’ve accumulated hard evidence that we’re clearly not alone – our solar system is not the only one,” he says. “And what are we going to look for on these other planets that could allow life to emerge and evolution to start? I think that is where the fun begins.”

The fast pace of discovery contributed to a polarization of views on research, particularly in areas such as stem cells and evolution.

“The theme of our recent Evolution Revolution conference was that the world is changing very quickly, and we need to understand what that means so we can make better informed decisions,” Lynn says. “The important problems, and the fact that many are interconnected, have become more clearly defined. This clarification attracts people’s attention, and means the chance of finding viable solutions goes way up.”

Emory chemists are using “directed evolution” to study ways to reprogram bacteria to perform useful tasks, from fighting disease to producing renewable hydrogen fuel.

"We are taking principles that are central to evolution and probing them to use in different ways," Lynn says.  "It's a great time to be a scientist -- the sky is no longer the limit."

For neuroscientist Elaine Walker, one of the biggest breakthroughs was the growing awareness of genetic plasticity, or the idea that DNA is not necessarily destiny. "In the past, it was generally assumed that with only a few exceptions the individual genotype was fixed at conception, and that its effects on human health and disease were relatively fixed across the life span," Walker says.

In recent years, however, we've learned that genetic mutations in the form of copy number variations and microdeletions occur much more frequently than was previously assumed. "It now appears that these mutations can occur in embryogenesis, and that they can confer risks for autism, schizophrenia and a range of other disorders," Walker says.

Adding to this paradigm shift is our understanding of epigenetics: changes in the expression of genes due to a person's physical and psycho-social environment. "I think during the next decade, we're going to see more focus on applications of epigenetics for the treatment of everything from cancer to heart disease," says Victor Corces, chair of biology and one of the pioneers of the field.

We have also learned that the brain changes significantly across the life span, a finding that overlaps with genetic plasticity. "These developments have made our research much more complex," Walker says, "but they also provide us with much more optimism about our opportunities to prevent illness."

Walker is studying whether it might be possible to identify the changes in gene expression occurring in some young people that are causing a change in brain funciton that can put them at risk for psychotic disorders.

The theory of grounded cognition has revolutionized studies of the mind during the past decade, says psychologist Larry Barsalou, a leading researcher in this field. "Previously, it was argued that you could study the cognitive system in isolation. Now we realize that you cannot understand cognition without grounding it into the body and the sensory motor system and the world," he explains.

Watch a video of Barsalou explaining grounded cognition.

When you think about walking, for instance, your brain fires the same parts that operate when you are actually walking.

Research is increasingly showing the impact of social processes, culture, development and emotion on cognition, he adds. “I think that during the next 10 to 30 years, theories and research of cognition processes and social processes will be increasingly integrated.”

Everything needs to be studied from an interdisciplinary perspective, Barsalou says. "A big question is how to build programs that foster this kind of work. Psychology departments are becoming very strange beasts."

Deboleena Roy’s research spans women’s studies, philosophy, neuroscience and bioethics. During the past decade, the long struggle of women and minorities to be included in clinical trials began paying off, she says. Studies of biological differences can raise thorny issues about race and gender, she adds, stressing that we need to move forward with knowledge of the mistakes of history.

"People who are the subject of research need to be involved in generating the research questions," Roy says. "The day of the scientist in a white coat working alone in a lab is over. Scientists have to learn to connect to the broader community."

Biologists Nicole Gerardo and James Taylor are taking DNA sequencing to the next level, by tapping cutting-edge technology to analyze the sequence of a complex system, the world of agricultural ants.

“We’re entering completely new territory,” says Taylor, a computer scientist specialized in bioinformatics. “DNA sequencing technology is becoming faster and cheaper, but this transition is just happening.”

Within five years, he adds, the complex data sets he is mining through a grant will likely become much cheaper and more easily obtainable.

Psychologist Joe Manns, whose work focuses on the biology of memory, views the use of genetically engineered mice and functional magnetic resonance imaging (fMRI) as transformational. While both these technologies were developed prior to the past decade, they matured and hit their stride during the past 10 years, he says.

He believes that the emerging technology of optogenetics – using high-speed optics to control genetically targeted neurons – will likely help fuel memory discoveries in the coming decade.
 
“Now we can put a wire into a brain and induce neurons within a region of the brain to fire, but we can’t control which neurons,” Mann says. “Optogenetics gives you anatomical precision, allowing you to target a specific neuron, along with temporal precision, because the pulses of light operate in milliseconds.”

The past decade saw wireless devices like iPods and iPhones become almost physical extensions of the human body. Google became a household word – both as a noun and a verb – as search engine technology connected our collective digital mind.

Search personalization, coupled with advances in wireless handheld devices and biometrics such as eye-tracking, will further speed changes in Web search, predicts Eugene Agichtein, who directs the Emory Intelligent Information Access Lab. “Ten years from now, computerized searches will look much different than they do today — you won’t be just typing words into a box on a screen,” he says.

Related:
Give your mind a hand
Daily pot smoking may hasten psychosis onset
DNA is not destiny
Can neuroscience read your mind?

Her math adds up to a brilliant career

Emory math professor R. Parimala has received one of the highest honors in her field: Selection as a plenary speaker for the International Congress of Mathematicians, set for Aug. 19–27, 2010, in Hyderabad, India. The ICM is held only every four years, and is the most important activity of the International Mathematical Union. The 20 plenary speakers are chosen from top talent throughout the world.

It may be a lofty honor, but Parimala remains decidedly down to earth. “I’ve always been very comfortable with math,” she says, relaxing in her office after teaching a class. Her hair hangs down her back in a long dark braid and she looks casually elegant in a cotton tunic, shawl and pants.

The outfit is called a “salwar-kameez,” she explains, and is from northern India. She grew up in the southern tip of the country, in the state of Tamil Nadu, where the saree is the traditional dress. “I love to wear a saree, but it’s six yards of fabric and hard to maintain,” she says. “Ironing is a bit boring.”

When she graduated from high school, her father sat her down and asked her what she wanted to do. “I said, ‘I want to continue with math. Period,’” Parimala recalls, adding that it was an unusual path for a female. “My father knew I had an aptitude for math and was very supportive of my higher studies.”

At Stella Maris College in Chennai, India, she says that she briefly considered focusing her studies on Sanskrit poetry, but math won out. “Math has the beauty of poetry. Its abstractions are combined with perfect rigor.”

For her doctorate, Parimala attended the Tata Institute of Fundamental Research in Mumbai, one of the top institutes in India for the basic sciences. She spent most of her career on the faculty there, until she joined Emory in 2005.

“I’ve always enjoyed teaching,” Parimala says, “and it’s fun to work with undergraduate students. They are so enthusiastic.”

She also looks forward to new research challenges, primarily in algebraic groups, and quadratic forms. “There are many interesting questions that keep my attention,” she says. “Math is dynamic, not only internally dynamic, but across disciplines.”

Parimala was recently invited to speak at Nehru University in Delhi, during a conference aimed at inspiring more female students to focus on math.

“Most bright students in India choose another career over basic sciences,” Parimala says. “It’s a global phenomenon, actually, because they think there are more attractive jobs in other areas. But math offers a challenging and rewarding profession. If you have a love and a talent for it, you should come to math. That is my plea.”

Celebrating Darwin's legacy

What is it that makes the human brain different from the brain of our closest relative, the chimpanzee, besides the larger size? What are the origins of empathy, fairness and cooperation? What constitutes culture in humans and other species, and how far back can we trace it?

Some of the world’s leading scholars of evolution – including many from Emory – will gather to discuss these questions during the conference on the Evolution of Brain, Mind and Culture Nov. 12-13. The free, public event – held in honor of the 200th anniversary of Charles Darwin’s birth – will give an overview of the latest discoveries in biological, cognitive and cultural studies of evolution.

“We are taking the conceptual and theoretical tools that Darwin gave us and putting them in the midst of contemporary thought and controversies,” said Robert McCauley, director of the Emory Center for Mind, Brain and Culture, which is hosting the event. “We’re taking a forward look at Darwin’s legacy.”

Award-winning science writer Matt Ridley, author of “Francis Crick: Discoverer of the Genetic Code” and “Nature via Nurture,” will give the keynote, “Darwin in Genes and Culture,” at 1 p.m. on Thursday.

Click here for more details of the two-day event.

Related stories:
Getting a grip on cultural evolution
Ape murder-suicide leads to human drama
Icons of evolution

No bones about it: A great place to work

The Scientist magazine's readers ranked Emory as the 5th Best Place to Work in Academia in the United States. The ranking was based on a survey of more than 2,350 life scientists with a permanent position in an academic, hospital, government or research organization. The scientists represented 94 US institutions and 25 institutions from the rest of the world.

Emory ranked especially high in the categories of "peers" and "job satisfaction." The top four institutions were Princeton University, University of California-San Francisco, Albert Einstein College of Medicine, and University of Oklahoma Health Sciences Center. The top international institution was the Max Planck Institute of Molecular Cell Biology and Genetics.

Read the full survey results.

Bug splatter study is data driven

The next time you take a road trip, think before you clean the bug splatter off your car. Those insect remains may actually be more interesting than your vacation photos.

“It turns out that your car is a sampling device for understanding the biodiversity of all the places you’ve been,” says James Taylor, a computational biologist at Emory.

Genome Research recently published a paper by Taylor and collaborators that applied advanced DNA sequencing techniques that are traditionally used on microbial samples to look at insect biodiversity. “We were curious whether these techniques would work for more complex organisms,” Taylor says.

To collect genetic material for the study they used the bumper and windshield of a moving vehicle. Two samples were collected: on a drive from Pennsylvania to Connecticut, and on a trip from Maine to New Brunswick, Canada.

“We found that there is a huge amount of insect diversity, but what was really surprising was to see the enormous amount of novel sequence,” Taylor says. “It’s indicative of how poorly we have sampled the whole tree of life in genome research so far. There’s an enormous amount of species out there.”

Road tested

Taylor is a co-developer of Galaxy, an open-source software system for analyzing genetic data. The Galaxy developers recently refined the system, creating the Galaxy metagenomic pipeline that allows a research team to integrate all of the data, analyses and workflows of a study, and then publish this material as a live online supplement.

The bug splatter paper served as the first test of the metagenomic pipeline.
“I believe that this study is one of the most transparent and reproducible bioinformatics papers ever,” Taylor says. “Anyone can go online, follow links and see every step of our analysis and exactly what parameters were used. And they can take our data and do their own analysis of other questions.”

No computational experience is required to use the free Galaxy system, Taylor says. “All of science is becoming computationally intensive, so tools like this are needed to improve transparency.”

DNA sequencing technology is getting cheaper, opening more doors for research by small investigators, and Taylor is focused on serving this niche.

“Nowadays, you can have a crazy idea like studying bug splatter and without a lot of money or work, you can go out and do it just to see what’s there,” he says.

Related story:
Mapping genomics of complex ant system
Plug your data into the Galaxy

Fish vision makes waves in natural selection

Emory researchers have identified the first fish known to have switched from ultraviolet vision to violet vision, or the ability to see blue light. The discovery is also the first example of an animal deleting a molecule to change its visual spectrum.

Their findings on scabbardfish, linking molecular evolution to functional changes and the possible environmental factors driving them, are in the current issue of the Proceedings of the National Academy of Sciences.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says evolutionary geneticist Shozo Yokoyama, who led the study. “Building on this framework will take studies of natural selection to the next level.”

The research team included Takashi Tada, a post-doctoral fellow in biology, and Ahmet Altun, a post-doctoral fellow in biology and computational chemistry.

For two decades, Yokoyama has done groundbreaking work on the adaptive evolution of vision in vertebrates. Vision serves as a good study model, since it is the simplest of the sensory systems. For example, only four genes are involved in human vision.

"It's amazing, but you can mix together this small number of genes and detect a whole color spectrum," Yokoyama says. "It's just like a painting."

The common vertebrate ancestor possessed UV vision. However, many species, including humans, have switched from UV to violet vision, or the ability to sense the blue color spectrum.


Fish provide clues for how environmental factors can lead to such vision changes, since the available light at various ocean depths is well quantified. All fish previously studied have retained UV vision, but the Emory researchers found that the scabbardfish has not. To tease out the molecular basis for this difference, they used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.

“Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted,” Yokoyama says.

“The finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” he adds. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet vision.”

Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light.

"Evolutionary biology is filled with arguments that are misleading, at best," Yokoyama says. "To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment." 

Last year, Yokoyama and collaborators completed a comprehensive project to track changes in the dim-light vision protein opsin in nine fish species, chameleons, dolphins and elephants, as the animals spread into new environments and diversified over time. The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes.

Their results provided a reference framework for further research, and helped bring to light the limitations of studies that rely on statistical analysis of gene sequences alone to identify adaptive mutations in proteins.

Related stories:
A fish-eye view of natural selection

Exploring our brains: 'The internal frontier'

“I’m a great fan of physics and astronomy. I think of that as the great external frontier. One can really say that brain science is the great internal frontier,’’ says Dennis Choi, director of Emory’s Neuroscience, Human Nature and Society Initiative.

How does the mind emerge from the brain?

That question particularly intrigues Choi: "As we really begin to understand the biology of the brain, one has to hit this question. So, okay, we know what this molecule is doing, we know what this cell is doing and we know what this circuit is doing – how do I come out of that? Where does my sense of being come from? How do I develop a consciousness? Where are my thoughts, where are my memories?"

Watch the video interview with Choi, known for his groundbreaking research into brain and spinal cord injuries, and his insights into the mind-brain relationship.

Plug your data into the Galaxy

A report from Genome Web: Data-intensive bioinformatics tasks that were once relatively rare are now "permeating every aspect of biology," says James Taylor, a computational biologist at Emory and co-developer of Galaxy, an open-source software system that allows anyone with a normal laptop to analyze genomic data. Read more of the Genome Web article.

An Earthling from the unsequenced genome files:
Malaysian long-tongued nectar bat: Photo by Robert Baker.

Taylor's lab is working with biologist Nicole Gerardo to analyze the first sequencing of the ant genome, as well as the genomics of agricultural ant societies. A key part of the project is bringing genomics into classrooms, by giving high school and college students experience at analyzing genomic data.

"We hope to build up a public research community around this project to facilitate broader analysis," says Taylor, a leading expert in bio-informatics. "We will provide supporting infrastructure to allow people to discover new things. This project is novel – and it's going to be fun."

Related:
Bug splatter study is data driven
Mapping genomics of complex ant system

What genome would you most like to see analyzed?