Author: Ashley Yeager Page 6 of 7

Your brain on memories

On November 15, 2011

In Behavior/Psychology, Neuroscience, Science Communication & Education, Students, Visualization

By Ashley Yeager

Students map the molecules associated with memory and how they flow through a brain cell. Courtesy of Craig Roberts, Duke.

9/11. JFK’s assassination. A man on the moon.

These words probably evoke a memory of where you were and how you reacted, if you were alive when the events occurred.

The exact molecules and brain processes that form memories and make some memories stronger than others haven’t been worked out yet. But by “walking” through our brain cells, a team of Duke students is taking a more vivid look at how we remember the past.

With Duke computer science faculty, neuroscientist Craig Roberts and his students have created and tested a virtual representation of our brain cells. In this world, students move around a virtual neuron, rearranging and organizing molecules to express their understanding of our memories.

In this 3-D environment of a neuron, students can mock how molecules flow through the brain to make memories. Courtesy of Craig Roberts, Duke.

Working in a shared digital space from individual computers, the students collaborate in both real life and cyberspace to model the flow of molecules from brain cell to brain cell. Computer scientists Julian Lombardi and Mark McCahill designed the neuronal landscape on Open Cobalt, a community-based, open-source web page for developing virtual, 3-D workspaces.

Roberts, the assistant director of education of the Duke Institute for Brain Sciences, says he trying to harness the “eventuality of the Internet,” where we’ll explore ideas and solve scientific problems on media-rich, multi-dimensional websites.

Roberts says he wanted to teach students about learning and memory. But he also wanted to experiment with whether 2-D or 3-D environments affected how different types of learners participated in class and retained what they were supposed to be studying.

He and undergrad student Daniel Wilson assessed the learning types of the students in the neurobiology class and then gauged their reactions to the 3-D environment compared to the 2-D work done in a collaborative Google document.

A 2-D Google doc mapping molecule movements for making memories. Courtesy of Craig Roberts, Duke.

“We’re finding that active learners perceive greater benefit from the 2-D environment than reflective learners. Visual learners perceive greater benefit than verbal learners from the 3-D environment,” Robert says. He presented the 3-D neuronal environment, his research results and other learning media he has been experimenting with at the 2011 Society for Neuroscience meeting in Washington D.C. on Sat. Nov. 12

By developing different environments in which students can learn, teachers may be able to engage all their students, independent of learning style, Roberts says.

He also said he “sees it as icing on the cake” that in a neurobiology course on learning and memory, students are working in a “learner-centric,” non-lecturing environment to expand their understanding of how they remember and recall the past.

Particles on Ice

By Ashley Yeager

On November 10, 2011

In Field Research, Lecture, Physics

By Ashley Yeager

Protons, neutrinos and photons take different paths toward Earth. Physicists have to figure out their paths to determine where the particles came from. Credit: Deutsches Elektronen-Synchrotron.

Imagine nabbing the cover of the journal Science. Now, imagine doing it without making a single discovery. For University of Wisconsin physicist Francis Halzen, those dreams came true in 2007.

“We hadn’t done anything by then,” he said during a Nov. 9 physics colloquium as he described the experiment called IceCube.

IceCube is a neutrino detector buried deep in the ice of Antarctica. It did not begin full scientific operations until May 2011. So why did it claim prime Science real estate four years earlier?

Because Halzen and his team were the clear winners in a race, which began in the 1970s, to build a kilometer-wide bucket to capture particles called neutrinos.

To cover just over a half mile of Antarctica with such a detector, Halzen’s team engineered 5,000 neutrino buckets to sit on 86 electronic wires, a bit like strings of Christmas lights. The team then fed each string a mile and a half into the ice near the South Pole.

The idea was that the instrument would detect blue light coming from the reaction of a single neutrino crashing into an ice atom. From that reaction, the physicists could start to tease apart where neutrinos and other high-energy showers of particles, called cosmic rays, come from. Now, the team has also begun adding to the instrument so it can probe what dark matter and dark energy are.

This diagram, superimposed on an aerial photo of the South Pole Station, shows where the 86 detector strands sit. Courtesy of: Tom Gaisser, Univ. of Delaware.

Halzen said studying neutrinos is a lot like taking an X-ray, rather than a normal photo, of the galaxy and the universe. He added that even though there are some promising data points in IceCube’s preliminary scans, no one should get too excited. The neutrino buckets haven’t really seen anything, yet.

It’s a bit like the Large Hadron Collider not seeing the Higgs boson, he said. If scientists don’t see what they are looking for, it will be really interesting and may call for a re-write of the physics textbooks.

But, Halzen said, “I can tell you, we want to see something,” and, doing it before next year, when the discovery of cosmic rays turns a century old, would fulfill another of his physics dreams.

Prescription lens brings spinning black holes into focus

By Ashley Yeager

On November 4, 2011

In Physics, Visualization

This computer generated image highlights how strange space would look if you could fly right up to a black hole. The effect of gravity on light causes some very unusual visual distortions. Credit & Copyright: Alain Riazuelo.

By Ashley Yeager

If a black hole is the eye of a galaxy, then Duke mathematician Arlie Petters is its optometrist.

Petters along with his colleagues, visiting scholar Amir Aazami and Rutgers astronomer Charles Keeton, have written the prescription, or mathematical equation, to describe the lens of a spinning black hole.

The new equation provides astronomers with an easier way of calculating what’s going on around a spinning black hole, says Harvard astrophysicist Avi Loeb, who was not involved in the research.

Astronomers typically classify black holes into two types, static or spinning.

Static black holes are easier to describe mathematically, which is why most previous studies describing a black hole’s action on light did not include a spin variable.

In reality, though, everything is in motion. Stars, planets, even black holes, spin. “As scientists, we need to add that spin into the equation if we are going to try to explain spinning black holes as an element of nature and how they work on a grand scale,” Petters says.

To describe black holes mathematically, Petters and his team had to first consider how elements of nature distort light. On Earth, air, water, glass and even our eyes alter how we interpret patterns of light.

In the case of our eyes, doctors can describe the distortion with a “lensmakers equation,” which underlies how they write precise prescriptions for our contacts or glasses.

In space, it’s gravity that bends light. Black holes have so much gravity due to their extreme mass that they can pull particles of light onto new paths. That bending and pulling of light acts as a cosmic lens creating cosmic mirages like Einstein rings.

The mirages or effects of the lensing can convey a lot of information about the universe, such as its age and the nature of dark matter. They also reveal details about the black holes themselves, Petters says.

This Hubble Space Telescope image shows a double Einstein ring. Credit: NASA

But, to the decode the mirages, astronomers need a precise prescription of the lenses creating them, just like we need prescription lenses to see our world more clearly.

In the past, astronomers would calculate the characteristics of a black hole lens using the equation for a static black hole. Or, they would use heavy-duty computer simulations or other painstakingly difficult methods to track particle trajectories and describe the lensing effects.

The new prescription Petters and his team has written, however, allows astronomers to calculate certain characteristics of a black hole by observing it and recording its mass and lensing effects. The researchers can then solve the lensmakers equation for the spin of the black hole. Petters and his colleagues describe the equation in two papers published in the Journal of Mathematical Physics.

Aside from making it easier to study black holes, the new equation also gives scientists another way to test Albert Einstein’s theory of gravity.

It is important to test Einstein, just as scientists continued to test Newton’s theory of gravity, Petters says. “We need to find any discrepancies in Einstein’s theory in order to push beyond it and to continue to comprehend and to appreciate the structure of the universe around us.”

Citations

A. B. Aazami, C. R. Keeton, and A. O. Petters. Lensing by Kerr Black Holes. I. General Lens Equation and Magnification Formula. J. Math. Phys., vol 52, (2011). doi:10.1063/1.3642614

A. B. Aazami, C. R. Keeton, and A. O. Petters. Lensing by Kerr Black Holes. II. Analytical Study of Quasi-Equatorial Lensing Observables J. Math. Phys., vol 52, (2011). doi:10.1063/1.3642616

Shaping and shattering theories of glass

By Ashley Yeager

On October 25, 2011

In Chemistry, Faculty, Physics

By Ashley Yeager

An artist shapes a piece of molten glass. Credit: Sarah Weiser / The Herald

The nature of a glass is a debate that runs far deeper than whether one appears half empty or half full.

For years scientists have known that the atoms and molecules in glasses arrange themselves randomly, like the non-uniform pattern of particles in a liquid.

What’s puzzling, though, is that while the molecules in a glass are arranged like in a liquid, the overall structure is solid.

“We’re close to understanding why certain materials do not crystallize, but it’s still an open challenge to explain how these materials then become viscous and form glasses,” says Patrick Charbonneau, a theoretical chemist at Duke.

In other words, scientists do not yet have an accurate theory to describe both the liquid and solid characteristics of glass.

Instead, there’s just an old joke that says there are more explanations about how glasses form and behave than there are theorists to propose the ideas.

Click the graphic to learn more about the molecular intricacies of glass. Credit: Jonathan Corum, The New York Times.

Using new computer simulations, Charbonneau has begun to wipe away some of the less influential theories, and with his collaborators Atsushi Ikeda, Giorgio Parisi and Francesco Zamponi, he has identified serious flaws in one of the leading explanations describing the nature of glass.

The results of the research appear in the Oct. 28 issue of the journal Physical Review Letters.

In the study, Charbonneau tested the glass theories using simulations designed to look at a material’s atomic and molecular interactions in up to 12 dimensions. If scientists can make sense of how glass particles interact in these higher dimensions, then “we’ll be in a better position for understanding two and three-dimensional glass formation,” he says.

One of the leading theories of glass works, sometimes, but for it to hold more water, it needs to be modified so that its predictions match what the 12-dimensional simulations are showing.

If scientists can’t corroborate the predictions and simulated results, they may need to completely overhaul all they think they know about the nature of glasses — empty or full.

Citation: Charbonneau et al. Phys. Rev. Lett. 107, 185702 (2011).
DOI: 10.1103/PhysRevLett.107.185702

Changing American science and engineering education

By Ashley Yeager

On October 20, 2011

In Behavior/Psychology, Environment/Sustainability, Science Communication & Education, Students

Students in India work on a forensics experiment. Image courtesy of Duke TIP.

By Viviane Callier, graduate student in Duke Biology

It’s no secret that primary and secondary education in the U.S. falls behind when compared to many other developed countries.

David Kahler, a recent Ph.D. graduate from Duke’s Environmental Engineering program, has been involved in several education and outreach programs that aim to address this problem.

During his graduate career at Duke, Kahler participated in a National Science Foundation (NSF) Graduate Fellows program, which provides support for graduate students in science, technology, engineering, and mathematics, also known as STEM. The program is called NSF GK-12.

In exchange for funding for their graduate studies, Kahler and other fellows contribute to the science curriculum in local primary and secondary schools from kindergarten through grade 12. Kahler taught science at Rogers-Herr Middle School in Durham.

He also taught for two summers in India, and in Texas, as part of Duke TIP, the Talent Identification Program, which identifies academically gifted students and provides them with intellectually stimulating opportunities.

Through these teaching experiences in different locations and cultures, Kahler observed several factors that affect the quality of education in American schools. One important factor is the training of teachers. Unfortunately, teachers are sometimes expected to teach science without having received an adequate background in the subject.

STEM fellows helped to address this problem by contributing their expertise and by helping to increase the scientific literacy of students and their teachers.

Another issue is that parents in the U.S. are often not involved in their children’s education and do not support the mission of both schools and teachers. As a result, children are not engaged in or committed to their own education. In contrast, Kahler found that in India, children are taught by their parents to value and take responsibility for learning.

Because of this difference in attitude toward education, too many American high school graduates are inadequately prepared for college.

Kahler says that NSF GK-12 has a strong, positive impact to change this because it simultaneously improves the educational experience of students in primary and secondary school and trains graduate students to communicate and teach effectively.

Unfortunately, the NSF GK-12 program is no longer in the NSF budget for 2012.

Exploring the "last frontier" of our genome

By Ashley Yeager

On September 22, 2011

In Biology, Cancer, Genetics/Genomics, Students

In this image of a human cell, the centromeres are the pink spots and the blue "sticks" are chromosomes. Image courtesy of Karen Hayden, Duke.

Guest post by Viviane Callier, Duke biology

The human genome first appeared in print in 2001. But scientists aren’t done yet. There’s part of our DNA that geneticists have yet to assemble a sequence for: the centromeres.

Centromeres are necessary for chromosomes to segregate during cell division so that each new cell receives a complete copy of the genome. If chromosome segregation does not occur correctly, the resulting cells could die or become cancerous.

The sequence of centromeres remains one of the mysterious regions in the human genome because these areas are made of highly repetitive DNA sequences called satellite DNAs, said Karen Hayden, a recent graduate of Hunt Willard’s lab in Duke’s IGSP.

Centromere sequences are currently represented as gaps or spaceholders in the genome. Hayden, however, has developed a new strategy to study these elusive arrangements of DNA.

To study genomic material, scientists first break it into small pieces and sequence them. Then, much like a puzzle, they reassemble the pieces into the full sequence.

But when highly repetitive DNA, such as is found in centromeres, is broken into pieces, the parts of the puzzle look strikingly similar. As a result, scientists have trouble knowing if they have truly reassembled the pieces into the original sequence.

Using computational methods and studying the centromere sequences in the lab, however, Hayden was able to solve the puzzle and determine sequence arrangement in human centromeres. She also created a database to analyze the variations in among centromere sequences in the human genome.

Hayden said she hopes that the experiments she designed, along with the database of sequences, will provide the tools to study whether certain centromere sequences are more highly associated with diseases, such as cancer and birth defects.

This fall she will go to the Segal Lab at the Weizmann Institute in Israel to model the physical properties of centromeric sequences and study if centromeric sequences play a role in the centromere function. She then plans to continue her work in David Haussler’s lab at UC Santa Cruz.

Human brain isn't so special, neurobiologist says

By Ashley Yeager

On September 21, 2011

In Behavior/Psychology, Biology, Lecture, Neuroscience

Mark Changizi argues that speech, writing and music evolved from our brain's interactions with nature.Image courtesy of changizi.com.

By Ashley Yeager

Mark Changizi says there’s no “special sauce” in the human brain. Instead, he argues that our way of thinking is just the brain’s ability to recognize and mimic visual and sound patterns found in nature.

Changizi, an evolutionary neurobiologist and director of Human Cognition at 2ai Labs, spoke about his research during Duke’s first neurohumanities research group seminar on Sept. 20. The group is co-organized by the Franklin Humanities Institute and the Duke Institute for Brain Sciences.

During his talk, Changizi explored with the audience of both scientists and artists his investigations between shapes and sounds, nature and the fundamental elements of speech, music and writing.

He said that our brains didn’t evolve to have language and music instincts. Instead, language and music shaped themselves to be tailored to our brains. Because our brains were cut for nature, language and music mimicked it to transform ape to man.*

Comparing letter structures, with simple opaque, object positions like fallen trees, for example, Changizi explained that there are 36 topological shapes that form the basis for the letters found in 100 different writing systems across the world.

He showed the audience how these different structures could be made by crossing his arms. Most would think that this makes an X, but based on the position of the two objects, the shapes are ultimately two T intersections, he said.

By dropping objects and listening to the thunks and bangs, he explained the origin of sounds that have become words. And, by walking across the room, he pointed out elements in music such as pitch, loudness and melody.

Changizi's latest book explores how speech, music and writing evolved. Credit: changizi.com

“If you have a dog, you know exactly where he is in the house and probably what he is doing, just by listening to his movements,” Changizi said. The same goes for kids banging drawers in the kitchen.

Changizi explores this idea and more of his research in his latest book, Harnessed: How Language and Music Mimicked Nature and Transformed Ape to Man (Benbella 2011).

He said he has drawn a lot of inspiration from art, adding that artists and those in the humanities are the true experimentalists that must shape the complicated structures to affect human minds.

It’s these experimentalists who really know “what minds like or don’t like,” he said, adding that he turns to their work to explore the “universal regularities” that are being discovered about the mind.

*This passage is adapted from Changizi’s book. To read an excerpt, click here.

Lemur film features future Duke post-doc

By Ashley Yeager

On September 8, 2011

In Animals, Biology, Environment/Sustainability, Field Research, Lemurs

Primatologist Erik Patel studies the endangered silky sifaka, seen here. Credit: Erik Patel.

Primatologist Erik Patel is trying to study and save a cute lemur called the silky sifaka (Propithecus candidus).

In a recent online documentary, he takes viewers through Marojejy National Park, a 148,387-acre area of jungle with rugged mountainous terrain, and gives them a rare, up-close look at the silky in its wild habitat.

These lemurs are most at risk of extinction, which is one of the reasons Patel studies them, and, as the documentary shows, the illegal logging and bushmeat trade are likely accelerating the loss of the lemurs’ habitat and their overall population.

Patel, who will join Duke’s Lemur Center in January, told the New York Times that “stopping illegal logging in Madagascar will be impossible until the government stabilizes and some measure of accountability is put in place.”

“It’s about money,” as the individuals in government are now “organizing and profiting from the problem,” he told the Times reporter.

One of Patel’s roles when he joins Duke will be to oversee the Lemur Center’s new conservation initiative to help individuals in cities near Marojejy understand and value the distinct environment and animals found only in their country.

Watch the full feature here.

A Witness to AIDS

By Ashley Yeager

On September 8, 2011

In Behavior/Psychology, Global Health, Lecture, Medicine

Edwin Cameron is the only South African public figure to speak openly about his infection with HIV. Credit: witnesstoaids.com

By Ashley Yeager

Telling young people to use a condom or to stop having sex won’t prevent the spread of HIV in South Africa.

It’s like telling the one in five people in the U.S. who still smoke to simply stop, said Judge Edwin Cameron, a sitting justice in the South African Constitutional Court and an HIV-positive public figure.

Cameron spoke to a standing-room only crowd during a Global Health Seminar in the John Hope Franklin Center on Sept. 8.

His message was that the biggest barrier to preventing the spread of HIV and deaths from AIDS in his country was not access to anti-viral drugs or even the spread of information about the disease.

The barrier is self-stigma and our inability to talk candidly about sex.

In South Africa, 300,000 new HIV infections are diagnosed each year. For every two individuals treated, three more become infected, Cameron said.

Yet, women found with condoms in their purses can be harassed and arrested as suspected sex workers.

What’s even more of an issue is that both heterosexual and homosexual individuals still have difficulty talking openly about HIV and its transmission through sex, a natural part of human biology.

Having condoms and medication to prevent and treat the disease is not enough, Cameron said. “We need to understand the genetic cofactors of the disease,” to figure out why it spreads like “wildfire” in southern parts of Africa but not in west Africa, he said.

Cameron also argued that young activists, health practitioners, parents, basically all individuals, need to work as a civil society to normalize HIV and have open discussions about intimacy and the misconception that the virus “can’t touch me.”

Getting infected people to come forward and not be ashamed to admit they are sick because they fear being stigmatized has been, and remains, pivotal to the social understanding, acceptance and prevention of this disease, he said.

In 2005, Cameron published a book about his own issues dealing with self-stigma and his journey to speaking openly about his battle with HIV.

Lemurs leap in back-to-school lessons

By Ashley Yeager

On August 30, 2011

In Animals, Biology, Environment/Sustainability, Lemurs, Science Communication & Education

Mr. Gimod, an education specialist, reads notes taken from the Malagasy Teacher's Guide, a teaching tool to help preserve the country's lemurs and biodiversity. Courtesy of Lanto Andrianandrasana.

By Ashley Yeager

Halfway around the world, in Madagascar’s northeastern city of Sambava, 30 students crowded into a classroom to start lessons in biology and conservation.

These students weren’t your average school children, however.

They were mostly Chefs ZAP, officials from the local school districts in Sambava and another nearby city, Andapa.

People in these cities “are not yet conscious” that it’s urgent to protect the biodiversity in this region, says Lanto Andrianandrasana, a Malagasy field assistant and who helped organize the lessons.

The lessons are to help individuals there to appreciate and understand the importance of the environment through a new Duke Lemur Center conservation initiative.

One reason the center chose to develop a new conservation education initiative in Sambava is because the nearby national parks are experiencing devastating effects from illegal logging and lemur trapping.

In 2009, armed gangs began harvesting rosewood trees worth hundreds of millions of dollars and trapping and killing critically endangered lemur species after a military coup overthrew democratically elected president, Marc Ravalomanana. The illegal activity continues, with the wood being shipped to China for use in high-end furniture and the lemurs eaten or sold as bushmeat.

Andrianandrasana, who is the on the ground coordinator for the DLC conservation initiative, says that to protect the lemurs and the rosewood trees in the region, the people must learn to love them. He says they need to understand the importance of the environment, and that’s why it is essential to give them basic biology knowledge, particularly in primary and secondary school.

Through the initiative, he and others will train the Chefs ZAP to use a Malagasy-prepared Teacher’s Guide, which discusses the biology of the rosewood and lemur populations and the environmental strategies to preserve them, along with other conservation topics.

The Chefs ZAP will then share the guide with the directors of the schools in the region. The directors are then to train their teachers to use the guide so they can share it with their students. This is a training cascade technique that has worked in schools in other eastern Madagascar cities to encourage enthusiasm for environmental issues not only among teachers and students, but also adults in the community, says Duke Lemur Center conservation coordinator Charlie Welch.

Welch worked with Andrianandrasana and other Malagasy conservationists to plan and implement the new initiative. The lessons and the Teacher’s Guide are borrowed from an already successful conservation initiative run by the MFG, or Madagascar Fauna Group. The Duke Lemur Center, or DLC, is a founding and managing participant of this 27-member group, which for the past ten years has sponsored Malagasy education specialists to train teachers in the Tamatave region in environmental education.

The Chefs Zap from Andapa and Sambava after their biology and conservation training. Courtesy of Lanto Andrianandrasana.

But Welch and others at DLC thought the center could “do more” to broaden the efforts of the MFG, he says. Using DLC grants and donations, Welch arranged for the most experienced MFG trainers, along with Andrianandrasana, to work with the local Chefs ZAP in Sambava and Andapa.

The first session was on Aug. 15, and the trainings will continue through the school year.

Welch, meanwhile, has been working with other Duke departments, including four masters students in the Nicholas School who will evaluate the trainings, to further develop the education initiative.