Wednesday, September 28, 2011

Virtual reality helps Marine fight PTSD

“It was killing me,” Joshua Musser told CNN about the effects of post-traumatic stress disorder (PTSD). Musser, a Marine Corps veteran who fought in the battle of Fallujah in Iraq, realized that he needed help. He turned to Emory clinical psychologist Maryrose Gerardi, who uses virtual reality to treat PTSD.

The treatment required Musser to relive the sights and sounds of war through computer simulation, as Gerardi talked him through the experience.

“They put you back in Iraq where you kind of have one foot here and one foot there,” Musser told CNN. “The only thing outside of Iraq that you hear is her voice. I would shake really bad and I would sweat, but she would be in my ear and pull me back.”

“People often try not to think about what happened to them, and what we’ve found is that’s the worst thing that you can do when you experience a trauma,” Girardi said. “If you don’t process it and deal with it, that’s what can eventually cause PTSD and a chronic problem.”

Tuesday, September 27, 2011

'Galaxy' makes genomics more user-friendly


Kevin Davies writes in Bio-IT World about an open-source platform for computational analysis:

Enter the term “galaxy” in a Web search engine, Penn State’s Anton Nekrutenko muses, and the top hits are likely to be an astrophysical entity or “a very bad soccer team.” But making fast strides up the web charts is the Galaxy open-source tool, which is coming into its own as more and more researchers seek ways to easily handle and manipulate next-gen sequencing (NGS) and other large datasets.

“Galaxy allows you to do analyses you cannot do anywhere else, without the need to install or download anything,” says Nekrutenko. “We can make genomics better, easier and more efficient. You can analyze multiple sequence alignments, compare genomic annotations, profile metagenomic samples and much, much more.” Galaxy was originally developed by Nekrutenko, who is based in the Center for Comparative Genomics and Bioinformatics at Penn State, and his former Penn State colleague James Taylor, who is now an assistant professor in biology and math and computer science at Emory University. Both are quick to cite the many contributions to Galaxy’s evolution from the genomics community.

Taylor was finishing his Ph.D. when the pair started to develop Galaxy, and they have devoted much of their time to that effort ever since. Nekrutenko is the more biologically inclined of the pair. “I can script a bit,” he says, “but Galaxy could only be developed with proper software engineering practices, which was only possible after James got involved.”

Galaxy is primarily a platform for making computational tools accessible. Nekrutenko and Taylor observed “a huge disconnect” between computer science development tools and algorithms on the one hand, and the researchers wanting to use them on the other. Galaxy is designed to fill that gap. …

Most of the Galaxy tools are in the genomics and gene evolution space, but researchers are also adapting the platform to proteomics and other areas. “When this started, NGS didn’t exist,” says Nekrutenko. “Initially, we were addressing problems with whole genome sequence, comparative genomics, etc. In reality, very few people can use this information. We’re still the only resource to meaningfully manipulate genome alignments on a large scale.”

The basic model is a Web-based platform. “We believe that’s really important for collaboration and communication,” says Taylor. “Having no barrier to using Galaxy other than a Web browser is very important.”

Read the whole article at

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

Monday, September 26, 2011

Jewish law in the era of bio-engineering

Mary Loftus writes in the Huffington Post:

Cats with bits of luminescent jellyfish DNA. Sheep-goat hybrids, "geep," with furry legs and floppy ears. Human stem cells inserted into the brains of newborn mice. Embryonic screening that allows parents to choose to implant an embryo without the breast cancer gene. Human-human chimeras that allow gay couples to have children that belong, biologically, to both of them.

To paraphrase Dickens, these are not things that will happen in time, these are things that are happening.

Speaking from a Jewish law perspective about the ethics of reproductive technologies, Rabbi Michael Broyde, a law professor at Emory University and a member of the Beth Din of America, the largest Jewish law court in the country, is just getting warmed up in his delivery of the Decalogue Lecture for Emory's Center for the Study of Law and Religion Sept. 13.

He's enjoying the reaction this bioethically edgy information, complete with slides of an adorable glowing kitten and a geep, is getting from his audience.

Broyde has covered artificial insemination: "No adultery is associated with AI. The dominant Jewish law view doesn't look at misplaced paternity, absent sexual conduct, as a moral or religious wrong... It's even discussed in the Talmud."

And cloning: "When people think of cloning, they think of Star Wars, or The Boys from Brazil. They are opposed to cloning because they think it will allow creation of armies or will be used in some way that's dehumanizing. But cloning could be a form of assisted reproduction for profoundly infertile people."

Broyde moves on to reproductive xenotransplants -- the placing of a fertilized embryo of one species into the uterus of another species.

"Like human-animal chimeras, when cells of a human are mixed with cells of another mammal, basic ideas of human identity come into play," Broyde says.

"Of course, one definition of humanity is, that which comes from a human mother is human," he adds. "Yet, if you put a human fetus in a gorilla and it gives birth to a human being who, six years later, is playing chess or reading or engaging in other human activity, there's no doubt at all that Jewish thought would label that a human being even if the mother is not."

Broyde says these frightful, fascinating visions are no reason to halt the advance of assisted reproduction, no matter how rapidly the biotech may be slip-sliding into areas that make us uncomfortable.

Read the whole article in the Huff Post.

Blurring the lines between life forms
The science and ethics of X-Men

Friday, September 23, 2011

Mary Anning and the art of fossil hunting

Robey Tapp loves history and science and has served as a docent at Emory’s Carlos Museum for the past six years. She is also an independent artist who works in fiber. When she was invited to create a piece for the Fernbank Museum’s special Darwin exhibit, opening on Saturday, Sept. 24, Tapp started reading up on the England of Darwin’s time. That’s how she stumbled across Mary Anning.

Anning was a contemporary of Darwin’s, a self-taught paleontologist, who made key findings that supported Darwin’s theory of evolution. She grew up poor on the southern England coast and did not receive full scientific credit for her work during her lifetime, due to her gender and working-class status.

A painting of Mary Anning, left, hangs in the Natural History Museum of London.

“Every day she walked along the water in Lyme Regis where she lived,” Tapp says. “She saw things in the rocks and she dug them out.”

In 1811, when Anning was just 12 years old, she and her brother Joseph discovered the fossil of an entirely new animal, later named Ichthyosaurus. Throughout her life, Anning continued to make discoveries, working tirelessly along the rugged coastline.

“What inspires me about her is that she believed in herself and her findings despite the fact that it went against the religion of the time,” Tapp says. “She was really upsetting the apple cart. And she didn’t stop because she was a woman, and people told her that women couldn’t be scientists.”

Anning died poor but “her work lives on,” Tapp says. In 2010 the Royal Society included Anning in a list of the 10 British women who have most influenced the history of science.

Tapp’s fiber art inspired by Anning is part of the “Selections” show at Fernbank. Local artists, including scientists from Emory’s department of environmental studies, have created pieces influenced by evolution. The art will remain on display during the museum’s special exhibit commemorating the life and mind of Darwin, which continues through January 1.

Teaching evolution enters new era
Polar dinosaur tracks open new trail to past
Dinosaur burrows yield clues to climate change

Thursday, September 22, 2011

In the Congo, a secret world of bonobos

Anthropologist Amy Cobden's fieldwork is challenging stereotypical ideas about chimpanzees, left, and bonobos, right. Photos copyrighted by Frans de Waal.

Journalist Kate Roach writes in New Scientist about the research of an Emory graduate student of anthropology:

A dark, chiseled face looks at us from way up in the branches of a vast rainforest tree. Deep-set, inky eyes peer suspiciously through the foliage, throwing an occasional glance towards movement in a tree beyond. This is Ruby, a mature female bonobo. She lingers, almost as if to separate us from the rest of her party, who are moving on in search of more fruit. Then she leaps away.

Such encounters are typical of the pleasure and frustration of studying bonobos in their natural habitat. Found only in the heart of the Democratic Republic of the Congo, these were the last great apes to be discovered and are the least studied. Their range, beneath a huge arc made by the Congo river, is fragmented across a region of lowland rainforest that approximates 350,000 square kilometres, about the size of Germany. It is a hauntingly beautiful landscape, encompassing both swamp and dry forest, all of it inaccessible, with travel mostly restricted to following forest trails by foot or trail bike, or navigating the rivers in unsteady flat-bottomed pirogues.

But physical remoteness is not the only reason why bonobos are so elusive. A succession of wars in the Democratic Republic of the Congo between 1996 and 2003 has severely disrupted research. In 1998, scientists were forced to leave the area where I am staying with primatologist Amy Cobden from Emory University in Atlanta. … Cobden knows it will be many months, possibly years, before the apes once again become sufficiently used to humans to behave naturally. With so much still to learn about these animals, she is hopeful that her patience will be rewarded.

Click here to read the whole article. You will have to log in to access it, but it’s free to do so.

Chimps, bonobos yield clues to social brain
A wild view of apes of the planet
Mountain gorillas cope with people in their midst

Tuesday, September 20, 2011

The monarch defense: In chess and in life

Emory evolutionary biologist Jaap de Roode has had some strange assignments in his academic career. In his early days as a researcher, for example, his job was to measure the penis size of Malaysian dung beetles.

So it was no big deal when a photographer for Popular Science magazine asked de Roode to pose at a chessboard, pretending to watch two opponents: A butterfly and a bio-hazard bottle that was standing in for a parasite. The photo shoot was to illustrate the Popular Science “Brilliant 10,” top scientists under 40 from across the nation recognized by the editors of the magazine.

De Roode was declared “Brilliant” for his discovery of how monarch butterflies treat themselves and their offspring for parasites, using medicinal plants.

“I liked the concept of the chess game,” says de Roode. “That really is how scientists view the co-evolutionary process of a host and its parasites. One makes a move, and the other responds with a defense or attack.”

Many scientists have argued that animal medication requires great cognitive ability, memory and learning behaviors, and that self-medication may be restricted to a handful of animals, such as chimpanzees and gorillas. Research by the de Roode lab, however, clearly shows that very simple and small-brained animals can use “natural” medicine.

De Roode’s findings, which were published in Ecology Letters, suggest that animal medication is probably much more widespread than originally thought, opening the door for many new discoveries of medication in nature.

Currently, de Roode is studying different populations of monarchs, to determine whether they use medication only therapeutically, when they are already infected with parasites, or as a preventative, when they live in areas with a higher risk of infection.

He explains the hypothesis with a human analogy: “If we travel to Africa, we may take anti-malaria drugs prophylactically, but while we’re at home in the United States we don’t use them. You don’t want to take drugs when you don’t need them.”

In previous work, de Roode provided a new perspective on another long-standing question in evolutionary ecology: How do parasites strike the balance between living off of their hosts and killing them?

A prevalent theory – still proclaimed by most medical doctors – was that over time, parasites become less virulent and evolve a capacity to be nearly harmless to their hosts.

De Roode’s work revealed a different underlying strategy, showing that instead of becoming kinder, parasites may actually be selected to be virulent and deadly. By doing so, they produce more offspring, which increases the chances of the parasite jumping to new hosts.

The monarch butterfly's medicine kit

Monday, September 19, 2011

Artist brings original 'warm pond' to life

For her latest work, including "Warm Pond," above, Atlanta artist Terri Dilling is drawing her inspiration from Earth's primordial soup, where chemical reactions may have created life on the planet some 3.5 billion years ago. Her exhibit "Assembly" opens at the Portal Gallery with a reception on Friday, September 23 at 7 p.m. and continues through October 30.

The prints and paintings were informed by conversations with scientists from the Center for Chemical Evolution during the past seven months. "Although their research is complex, I think scientists are asking very basic questions about what the world is made of and how it works," Dilling says. "As an artist, I'm asking similar questions."

The NSF/NASA Center for Chemical Evolution involves scientists from Emory, Georgia Tech and other institutions, stretching from California to Italy. The visiting artist program is an educational initiative of the CCE to raise awareness about research in chemical evolution, the process of how simple atoms and molecules might form bigger and more complex structures.

"Chemistry has been an interesting influence, causing me to look at my art in a new way," Dilling says.

An artistic spin on renewable energy
Prepare to flash your intelligence
Teaching evolution enters new era

Thursday, September 15, 2011

Biochemical cell signals quantified for first time

Can you hear me now? When you feel symptoms of a nasty bug, you phone the doctor. Cells in your body are also receiving “calls,” through a biochemical signaling pathway that turns out to have surprisingly low data capacity. 

By Carol Clark

Just as cell phones and computers transmit data through electronic networks, the cells of your body send and receive chemical messages through molecular pathways. The term “cell signaling” was coined more than 30 years ago to describe this process.

Now, for the first time, scientists have quantified the data capacity of a biochemical signaling pathway and found a surprise – it’s way lower than even an old-fashioned, dial-up modem.

“This key biochemical pathway is involved in complex functions but can transmit less than one bit – the smallest unit of information in computing,” says Ilya Nemenman, an associate professor of physics and biology at Emory University. “It’s a simple result, but it changes our view of how cells access chemical data.”

The journal Science is publishing the discovery by Nemenman and colleagues from Johns Hopkins University, including Andre Levchenko, Raymond Cheong, Alex Rhee and Chiaochun Joanne Wang.

During the 1980s, cell biologists began identifying key signaling pathways such as nuclear factor kappa B (NF-kB), known to control the expression of genes in response to everything from invading pathogens to cancer. But the amount of information carried by chemical messengers along these pathways has remained a mystery.

“Without quantifying the signal, using math and computer analysis to attach a number to how much information is getting transmitted, you have a drastically incomplete picture of what’s going on,” says Nemenman, a theoretical biophysicist.

He and Levchenko, a biomedical engineer, began discussing the problem back in 2007 after they met at a conference.

Click on NF-kB graphic, below, to enlarge it:

NF-kB is a protein complex that is a key element of a biochemical signaling pathway involved in cellular responses to a range of stimuli. Graphic: Wikipedia Commons.

Levchenko provided the experimental framework to measure the transmissions occurring on the pathway in many thousands of cells at one time. Nemenman formulated the theoretical framework to analyze and quantify the results of the experiments. Graduate student Raymond Cheong developed and conducted the experiments and performed much of the analysis.

“It was a shock to learn that the amount of information getting sent through this pathway is less than one bit, or binary digit,” Nemenman says. “That’s only enough information to make one binary decision, a simple yes or no.”

And yet NF-kB is regulating all kinds of complex decisions made by cells, in response to stimuli ranging from stress, free radicals, bacterial and viral pathogens and more. “Our result showed that it would be impossible for cells to make these decisions based just on that pathway because they are not getting enough information,” Nemenman says. “It would be like trying to send a movie that requires one megabit per second through an old-style modem that only transmits 28 kilobits per second.”

They analyzed the signals of several other biochemical pathways besides NF-kB and got a similar result, suggesting that a data capacity of less than one bit could be common. So if cells are not getting all the information through signaling pathways, where is it coming from?

“We’re proposing that cells somehow talk with each other outside of these known pathways,” Nemenman says. “A single cell doesn’t have enough information to consider all the variables and decide whether to repair some tissue. But when groups of cells talk to each other, and each one adds just a bit of knowledge, they can make a collective decision about what actions to take.”

He compares it to a bunch of people at a cocktail party, with cell phones that have weak signals pressed to their ears. Each person is receiving simple messages via their phones that provide a tiny piece to a puzzle that needs to be solved. When the people chatter together and share their individual messages, they are able to collectively arrive at a reliable solution to the puzzle.

A similar phenomenon, called population coding, had been identified for the electrical activity of neural networks, but Nemenman and his colleagues are now applying the idea to bio-chemical pathways.

They hope to build on this research by zeroing in on the role of cell signaling in specific diseases.

In particular, Nemenman wants to analyze and compare the signaling capacities of a cancerous cell versus a normal cell.

“Cancerous cells divide when they shouldn’t, which means they are making bad decisions,” he says. “I would like to quantify that decision-making process and determine if cancer cells have reduced information transduction capacities, or if they have the same capacities as healthy cells and are simply making wrong decisions.”

Nemenman uses a malfunctioning computer as an example. “If you push the ‘a’ key on your computer and a ‘d’ always shows up, that means the computer is misprogrammed but the information from your keystroke gets through just fine,” he says. “But if you keep pressing the letter ‘a’ and different, random letters show up, that indicates a problem with the way the information is being transmitted.”

Biology may not be so complex after all

Wednesday, September 14, 2011

CDC disease detectives to chat live online

Epidemics have been with us since people began living in cities. “An almost inevitable accompaniment to the fevers, and the coughs and other symptoms of these epidemics has been fear,” says Jeffrey Koplan, director of the Emory Global Health Institute and a former director of the CDC.

The hit movie “Contagion” begs the question, how will the CDC control the next outbreak and the public panic? You can ask CDC experts, including members of the elite Epidemic Intelligence Service, during two live Twitter chats, on Friday, Sept. 16 and Monday, Sept. 19 from 2 to 3 p.m.

You can follow #CDCcontagion live on Twitter, and you can also submit questions in advance to @CDCgov.

Contagion: The cough heard around the world
CDC turns into movie set for 'Contagion'

Monday, September 12, 2011

Rare mummy gets new lease on the afterlife

Conservators put the finishing touches on what was a major makeover for the 4,000-year-old mummy, one of only half-a-dozen in the world dating back to Egypt's Old Kingdom.

By Margie Fishman, Emory Report

The mummy from 2300 B.C. was in a sorry state when he arrived at Emory in 1921. Headless, his neck bones had tumbled into his abdominal cavity. Gaping holes and sagging linens marred vague remnants of shoulders, hips and knees. One conservator likened his physique to a crushed bag of potato chips.

Today, the oldest Egyptian mummy in North America has a new lease on the afterlife and is featured in a Michael C. Carlos Museum exhibit, thanks to a patient group of Emory conservation experts, anthropologists and doctors.

"Life and Death in the Pyramid Age: The Emory Old Kingdom Mummy" places the mummy in the context of ancient Egypt's burial rites and rituals, along with exploring the social and political changes at the end of the Pyramid Age. Approximately 120 objects from the Carlos Museum's collection and borrowed from other museums and private collectors will be on display through Dec. 11.

They include a life-size replica of an Old Kingdom tomb, "magic" vessels and wands used to recite spells on the dead, and a rare statue of Pharaoh Pepi, who ruled during the mummy's lifetime.

"This mummy is a very important piece. We've finally been able to conserve it and put it on display," says Peter Lacovara, the Carlos Museum's senior curator of ancient Egyptian, Nubian and near Eastern art.

Listen to leading Egyptologists discuss the history of the mummy and the site where it originated:

It was a long road to get the mummy ready for prime time.

Acquired by Emory theology professor William A. Shelton in 1920, the mummy was the first inventoried object in what was then the Emory University Museum of Art and Archaeology.

Dismissed as a massive reconstruction effort, the mummy was squirreled away in two crates in storage (one for his body and one for his head, that had fallen off).

At Lacovara's nudging, the mummy identified as "1921.1" was retrieved about a year ago and carefully transported to Emory University Hospital for X-ray and CT radiographic imaging.

Modern technology revealed much about the early mummification process, which used a combination of salts, oils and resin. It also permitted the conservation team to peer inside the mummy to assess the body's condition without actually unwrapping him. Exposing the body would have been disrespectful as well as damaging, notes Carlos conservator Renee Stein.

"The overarching goal of the project was to restore some structural integrity to the body and dignity to human remains," she says.

The mummy predates the period when the brain was removed during the embalming process, and the head contained a walnut-sized piece of material that appears to be the dessicated brain.

With the help of radiology professor William Torres, who has examined several Carlos mummies, the conservation team learned that the mummy's bones were well-mineralized, it hadn't suffered any major head trauma and it hadn't been prone to ear infections. Although his pelvis was obscured, the group determined that the mummy was most likely a male, given the size and shape of his skull.

All in all, "this was a pretty healthy individual," says Emory anthropologist George Armelagos, who was involved in the examination effort.

In light of the physical evidence and that the mummy had been buried at a holy site, conservators safely assumed that the mummy had access to a good diet and other social advantages. The cause of death, however, remained a mystery.

The Carlos Museum called on Mimi Leveque, a freelance conservator from Boston. Leveque has lent her expertise to several of the dozen mummies in the Carlos collection, the youngest of which is 2,000 years old.

One of the most glaring issues with the Old Kingdom mummy was his displaced head. The mummy originally was laid on his right side (a common burial position at the time), his head supported by a headrest. Over time, the headrest had been lost, along with the bulk of his coffin, leaving the head unsupported.

In the slideshow below, see images of the mummy before the makeover, and listen to Egyptologists discuss mummy science:

As a solution, Leveque relied on low-tech methods, carving out a piece of archival-quality foam and wedging it in the hollow between the mummy's collar bones and shoulder blades. She then threaded a padded dowel in the foam and through the hole at the base of the skull.

The mummy's jaw was cast from a mold from a similarly-sized, more modern jaw from Armelagos' lab. Two undergraduate interns used an epoxy putty to form missing bones for the hands and feet. They placed the bones inside padded papier-mache forms, wrapped in modern linen that was dyed to match the ancient wrappings.

Once intact, the mummy appeared lifelike, as if he had just lain down to sleep.

Eventually the mummy, one of only a half-dozen from that period who have survived, will be a permanent fixture at the Carlos. Due to his fragility, he will not tour.

Ancient Egyptians believed that by visiting tombs and actively remembering the dead through images, mummies were kept alive in the afterlife, explains Lacovara.

"In recreating the tomb and restoring the Old Kingdom mummy, we are fulfilling his wish," he says.

Mummies tell history of 'modern' plague

Friday, September 9, 2011

Contagion: The cough heard round the world

It all started with what seemed like a simple cold. The new movie “Contagion” vividly portrays how society could unravel in the face of a deadly pandemic.

Many health officials say a major pandemic in real life is more a matter of when, not if. We’ve been lucky in recent years, says Emory physician Phyllis Kozarsky, an infectious disease expert who specializes in travel medicine.

The H5N1 virus, more commonly known as bird flu, is one recent scare. The virus kills about 60 percent of infected people. “It’s a very serious disease, and we hope it doesn’t obtain the ability to be easily transmitted,” Kozarsky says.

Related: Wired blogger Maryn McKenna separates fact from fiction in "Contagion."

H5N1 is just one of many diseases on the radar of health officials concerned with pandemics. A critical aspect of controlling an outbreak will be getting out accurate information, making social media both a potential asset and nightmare.

Bursting media's bubble: Jude Law portrays a social media maverick in San Francisco who is obsessed with both freedom of information and conspiracy theories. Warner Brothers photo.

In “Contagion,” Jude Law plays crazed blogger Alan Krumwiede. The paranoid character is driven by conspiracy theories, and yet he uncovers some facts that journalists from traditional media miss, scooping them all. He later leverages his wide Internet following to hawk a "cure" for the disease and tell people not to take a government-made vaccine.

Elliot Gould plays a scientist who also goes a bit rogue, in his rush to isolate the virus. He brushes off Krumwiede with the line: “Blogging is not writing, it’s graffiti with punctuation.”

Law told Philadelphia Inquirer columnist Steven Rea that he researched the blogosphere to prepare for his role:

"I don't want to list anyone in particular," he says, asked to cite a couple of influential bloggers. "I'd rather people see it and draw on their own imagination, but yeah, I certainly looked at an awful lot of blogs, and bloggers who have been interviewed and who have made a bit of a name for themselves, who have become personalities. ... I drew on a few and tried to create someone that seemed to fit that particular persona.

"And yet, what was most exciting was that [director Steven Soderbergh] didn't want to judge him, he didn't want him to necessarily be a bad guy. ... Maybe this guy was correct all along, who knows?"

Some of the scenes from “Contagion” were shot around the Emory campus and the Centers for Disease Control and Prevention. Click here to watch some of the videos of the crew and cast in action.

Thursday, September 8, 2011

Hominid skull hints at later brain evolution

An endocast of the A. sediba skull was created using synchrotron radiation, giving scientists a high-resolution, 3-D view of life 2 million years ago. Photo courtesy of Kristian Carlson/University of the Witwatersrand.

By Carol Clark

An analysis of a skull from the most complete early hominid fossils ever found suggests that the large and complex human brain may have evolved more rapidly than previously realized, and at a later time than some other human characteristics.

While some features of Australopithecus sediba were more human-like, most notably the precision-grip hand, the brain was more ape-like, says Emory University anthropologist Dietrich Stout. “It’s basically a primitive brain that looks a lot like other austrolopiths, although you can see what could be the first glimmerings of a reorganization to a more human pattern.”

Stout is a member of the team that analyzed a virtual endocast of the skull, which dates back nearly 2 million years, to the pivotal period when the human family emerged. The resulting paper will be among those on A. sediba appearing in a special issue of Science on September 9.

If A. sediba is a human ancestor, as some have proposed, then its fossils could help resolve long-standing debates about human brain evolution, Stout says.

“The brain defines humanity, leading early anthropologists to expect that the brain changed first, and then the rest of the body followed,” Stout says. “More recently, it has been assumed that the brain and other human traits evolved together.”

The A. sediba find suggests a more “mosaic” pattern of evolution, he says. “The more modern hand paired with a primitive brain is a cautionary tale for what inferences can be drawn about a whole body from fossil fragments.”

A 60 Minutes video of Lee Berger, showing how the endocast was made:

The new species was discovered in a region of South Africa known as the Cradle of Humanity, by paleontologist Lee Berger of University of the Witwatersrand (Wits) in Johannesburg. After announcing the find in 2010, Berger and colleagues began making the case that A. sediba may be the bridge between more primitive austropiths and the human genus, Homo. The debate over whether A. sediba is a human ancestor will likely continue, even as more material is excavated from a limestone cave called Malapa, one of the richest hominid fossil sites ever found.

“The site is especially exciting because the A. sediba skeletons are nearly complete,” Stout says. “We can relate the face to the hand and the body and the brain of a single individual. A. sediba is represented by the most complete hominid skeletons we have, until we get up to the Neanderthals.”

Stout studies the relationship between stone tools and brain evolution, and is an expert in functional adaptation of neuroanatomy. He was invited to assist in the analysis of the cranium of a young A. sediba male, estimated to be 12 to 13 years old at the time of death, with brain growth essentially complete. The research was led by Kristian Carlson of Wits and also included other researchers from Wits; Indiana University; the Georgian National Museum of Tibilisi, Georgia; the University of Zurich; Texas A&M University; and the European Synchroton Radiation Facility.

The brain of A. sediba can be seen in incredible detail, including blood vessels, in this transparent image of the virtual endocast. Photo courtesy of Kristian Carlson/University of Wits.

The virtual endocast gives a three-dimensional view of the surface features of the cranium, which was missing only part of the right side and the back. The high-resolution images reveal bumps and ridges and even impressions from blood vessels.

“You can actually see the morphology of the brain inside a skull,” Stout says. “Bone is a lot more alive and plastic than many people realize. It’s constantly being remodeled and shaped and the growing brain does a lot to shape the skull around it.”

The researchers estimate that the brain was 420 cubic centimeters, around the size of a grapefruit. “That’s tiny and about what you’d expect for a chimpanzee,” Stout says.

The face, however, of A. sediba was far less protruded than that of a chimpanzee. “We don’t fully understand how the human face got smaller and tucked under the brain case, although that may have a lot to do with diet and chewing,” Stout says. “That further complicates matters. The relationship of human brain evolution to cognitive changes and other biological and behavioral changes is something we have to keep looking at.”

Click here to see an artist's representation of the face of A. sediba.

The researchers took a band of measurements on the underside of the A. sediba frontal lobes and did a comparative analysis with humans, chimpanzees and other hominids.

While the A. sediba brain clearly was not a human configuration, a surface bump shows possible foreshadowing of Broca’s area, a region of the human brain associated with speech and language, Stout says. “It’s a big leap, however, to go from a surface bump to really understanding what the cells were doing beneath it,” he adds.

The researchers plan to expand the analysis, gathering data from more scans of chimpanzee skulls and more hominid fossil specimens from East and South Africa. “We want to put as many dots on a comparative graph as we can, to help show us where A. sediba fits in,” Stout says.

Use of simple stone tools by hominids began about 2.5 million years ago. Was A. sediba a toolmaker? Its hands appear associated with that activity, Stout says, but the evidence is still incomplete. “For now, A. sediba raises more questions than it answers.”

Brain trumps hand in Stone Age tool study
Brain expert explores realm of human dawn

Wednesday, September 7, 2011

West Nile virus up in Atlanta mosquitoes

The West Nile virus rate in mosquitoes is way up in metro Atlanta this summer compared to last year, and health officials are warning residents to take precautions.

“The hot temperatures and relatively dry conditions probably contributed to the spike in infected mosquitoes,” says Rebecca Levine, a graduate student in Emory’s department of environmental studies. “This may be due to the fact that the heat allows the mosquitoes to develop faster and the lack of rain prevents developing larvae from being flushed out of the system, so they are more likely to
survive to adulthood.”

During Dekalb County’s entire 2010 May-to-October mosquito surveillance, 26 samples of mosquitoes tested positive for WNV, according to the Dekalb Board of Health. This year, with a month-and-a-half remaining for surveillance, the county already reports nearly 80 positive test results. “That’s a remarkable increase,” Levine says.

The peak season for WNV begins in August and continues until the weather gets cooler. Last week, Dekalb County reported the first human case of WNV this year, in a 79-year-old resident of Tucker.

Protect your peeps: Environmental studies students are doing the painstaking work of mist-netting birds and testing them for WNV, to track how the virus moves through an urban environment. Photos by Ryan Huang, above, and Rebecca Levine, below.

To reduce your risk, Levine advises wearing long sleeves and pants and using insect repellant if you are outdoors from dusk through dawn, when the species of mosquitoes that carry WNV are active. For more information about WNV and how to prevent it, call the Dekalb Board of Health, 404-508-7900, or visit its Web site.

The current soaking of metro Atlanta by the remnants of Hurricane Lee may dampen down the mosquito activity a bit, “but they’ll be back, for sure,” Levine says.

Emory’s department of environmental studies is studying the transmission risk of WNV in metro Atlanta. Mosquitoes are the vectors for WNV and birds are the amplifying hosts.

For her dissertation, Levine is monitoring how WNV moves among mosquitoes and birds in an urban environment. At nine different parks and forested areas in metro Atlanta, Emory researchers are capturing birds in mist nets, then tagging them and taking blood samples before releasing them.

“Our preliminary results are showing that the sites where humans are most active have significantly higher transmission rates in birds than in undisturbed urban forests and more secluded portions of parks,” Levine says.

Mosquito monitoring saves lives and money
Sewage raises West Nile virus risk

Opposable 'thumbs up' for ape animation

Anne Eisenberg writes in the New York Times about movie animation:

The chimpanzees, gorillas and orangutans that star in the hit film “Rise of the Planet of the Apes” are all computer animations. But they look a lot like the real thing, even to a primatologist.

“It’s astonishing how far the technology has come,” said Frans de Waal, a professor of primate behavior at Emory University in Atlanta and director of the Living Links Center at the Yerkes National Primate Research Center at Emory.

“We have the illusion we are looking at chimpanzees,” Dr. De Waal said of the computer-generated figures. “They are remarkably convincing.”

Producing computer-animated chimps that people will accept as realistic is a signal accomplishment, said Chris Bregler, an associate professor of computer science at New York University.

“It’s easier to fool us when you animate a dragon or another mythical or fairy tale creature,” Dr. Bregler said of characters created in earlier movies using the technology, called performance capture. “But humans or their closest relatives, chimps — that’s more difficult to do. Our human eyes are finely tuned to detecting problems with those depictions, and the illusion breaks down.”

Read the whole article in the New York Times.

A wild view of 'Planet of the Apes'
Computers breathe life into 'Toy Story'

Thursday, September 1, 2011

Fantastic light, from science fiction to fact

By Carol Clark

Next time you switch on a light, consider the enormity of this everyday phenomenon. Light allows us to travel back in time to explore the origins of the universe. Even after thousands of years of study, we still don’t fully understand light, yet we are harnessing its powers in ways that transform our daily lives and turn science-fiction fantasies into real possibilities.

“The technology of light keeps getting more and more amazing,” says Emory physicist Sidney Perkowitz.

Perkowitz’ new book is called “Slow Light: Invisibility, Teleportation and other Mysteries of Light.”
NASA is using laser technology to map longitude and latitude positions on the moon. Credit: Tom Zagwordzki/Goddard Space Flight Center.

“Only three percent of your brain is needed to figure out what you’re hearing, while 30 percent is needed to figure out the meaning of what you’re seeing. So if you want one number to explain how important and complex light is, that’s it,” Perkowitz says.

He describes Isaac Newton’s use of a prism, to demonstrate that white light contains a spectrum of colors, as the single most important experiment in the history of light. By the end of the 19th century, it was clear that light is an electromagnetic wave defined by its wavelength.

Physics started getting more complicated when Albert Einstein showed that light comes in discrete packets or particles of energy, which were later named photons. That discovery helped give birth to quantum mechanics.
Beam me up! It seemed magical the way the crew from Star Trek was "teleported," but light photons also appear to travel via teleportation. Credit: Paramount Pictures.

“Like Dr. Frankenstein’s creature, Einstein’s creation was remarkable but troublesome to its creator and others,” Perkowitz says. The photon was at odds with the wave theory of light, and Einstein himself was baffled by it.

Light can travel the way Star Trek’s Captain Kirk did when he’d say, “Beam me up, Scotty.”

“You can take a particle of light and mysteriously transport it from point A to point B, apparently without it traveling through the space in between,” Perkowitz says. “I find that the weirdest single thing that we know about light.”

Related: The top 10 Star Trek technologies, now available in the real world, by

Light's dual nature, as wave and particle, is one of the biggest mysteries in science. Infrared portrait of the Seven Sisters star cluster by NASA, JPL-Caltech, J. Stauffer.

Even though we don’t fully understand the quantum nature of light, we’re able to use it for remarkable technology, like lasers and optical fiber networks that channel photons around the world. When you communicate by Internet or phone, your message is carried by light, Perkowitz says. “If you stop and think about it, that’s truly amazing.”

Harry Potter’s invisibility cloak seemed like a child’s fantasy when the fictional character debuted in 1997. An actual cloak began taking shape about a decade later, however, when engineers at Duke University deflected microwave beams so they flowed around a small object, making it appear as if nothing was there. Since then, the race to perfect invisibility technology has heated up.

(Here's a related study, recently published by Science: Weird quantum effect can make materials transparent.)

Light lies at the heart of one of the biggest mysteries of science. If we could merge the theory of relativity and quantum mechanics into a so-called “theory of everything,” all kinds of things could break loose, Perkowitz says. “For instance, the fact that the speed of light is the ultimate speed limit might turn out to no longer be true. And if that were the case, then the universe opens up because you might be able to go to the furthest reaches in a reasonable time.”

Decatur Book Festival adds science track
Physics flies off the rails in 'Unstoppable'
Movies go under the microscope