Wednesday, October 1, 2014

Former Pres. Carter celebrates 90th birthday with butterfly garden dedication

Garden party: On his 90th birthday, former U.S. President Jimmy Carter and his wife, Rosalynn, celebrated in their new pollinator garden. Among the guests was Emory evolutionary ecologist Jaap de Roode, bottom right, and his children Jakob and Ella.

By Megan McRainey

Former U.S. President Jimmy Carter celebrated his 90th birthday at The Carter Center today with a tour of a new butterfly garden created in his honor.

The Jimmy and Rosalynn Carter Pollinator Garden created with the help of Emory University evolutionary ecologist Jaap de Roode, is filled with flowers and plants native to Georgia and is part of the Rosalynn Carter Butterfly Trail, developed by the former first lady to draw attention to the plight of diminishing numbers of migrating monarch butterflies. The garden is certified by Monarch Watch as an official monarch way station, and is listed as a certified wildlife habitat of the National Wildlife Federation.

De Roode and undergraduate students from his lab worked with volunteers from Trees Atlanta to provide seedlings for the garden and to plant them over the summer. They will continue to help monitor and maintain the plants.

The garden features two species of milkweed, the host plants monarch caterpillars need to complete their life cycle, and a variety of plants that can host Georgia’s state butterfly, the Tiger Swallowtail. An array of nectar plants also will appeal to other pollinator species, particularly bees and wasps, and to birds. Visitors are welcome to drop by the garden, which also features two Japanese-style arbors made by local artist Jesse Reep.

De Roode’s lab is one of only a few labs in the world devoted to the study of monarch butterflies and their parasites. In 2010, the lab discovered that monarchs use the toxic chemicals in certain species of milkweed to rid themselves of harmful parasites.

Jaap de Roode and his children at work in the garden last June, along with students from his lab, including, from left: Michelle Tsai, Kevin Hoang, Camden Gowler and Itai Doron.

Nature published de Roode's latest paper on monarchs today, involving the genomic analysis of monarch butterflies from around the world. The researchers traced the ancestral lineage of monarchs to a migratory population that likely originated in the southern United States or Mexico, instead of South America, as was previously hypothesized.

Every year, millions of monarchs from Canada and the United States fly south to overwinter in Mexico. Due to declining amounts of milkweed, from pesticide use and development of land, the number of monarchs making the migration has dropped dramatically, from an estimated180-900 million in 1996-1997 to an estimated 6.7-33 million in 2013-2014.

“The whole migrating population could be gone over the next decade,” de Roode says. “It’s an amazing natural phenomenon in danger of disappearing.”

Initiatives such as the Rosalynn Carter Butterfly Trail can help reverse the trend, he adds, and encourage individual gardeners to lend more support to monarchs by planting milkweed. The trail, which begins in Plains, Georgia, now includes registered sites extending as far as Canada.

Born on Oct. 1, 1924, Jimmy Carter served as the 39th President of the United States from 1977 to 1981 and joined Emory’s faculty in 1982, the same year he established The Carter Center. He is the University Distinguished Professor at Emory.

Pumping wings: Muscles make migrating monarchs unique

Pumping wings: Muscles make migrating monarchs unique

Genes related to muscle function distinguish the monarchs that migrate over thousands of miles.

By Carol Clark

A major study that sequenced the genomes of monarch butterflies from around the world identified a gene related to muscle function that appears central to the monarch’s spectacular annual mass migration across North America.

The findings, published in Nature October 1, also traced the evolutionary origins of monarchs to North America, instead of South America as was previously hypothesized, and identified a gene related to the butterfly’s distinctive orange-and-black coloration.

“Our findings add several interesting twists to our understanding of these iconic insects,” says Jaap de Roode, an evolutionary ecologist at Emory and a co-author of the paper.

Evolutionary geneticist Marcus Kronforst from the University of Chicago led the sequencing of the genomes of 101 monarchs, which involved scientists from five other universities, in addition to Emory. De Roode, who runs one of a handful of labs in the world focused on monarch butterflies, assisted in the design of the project and the analysis of the results.

The researchers traced the ancestral lineage of monarchs to a migratory population that likely originated in the southern United States or Mexico. The evolutionary tree created from the sequencing showed that the monarch’s current worldwide distribution appears to stem from three separate dispersal events – to Central and South America; across the Atlantic; and across the Pacific. In all three cases, the butterfly independently lost its migratory behavior.

In addition to better muscle function, migrating monarchs have more efficient metabolisms than populations of monarchs that have not evolved the ability for long migrations. Photo by Jaap de Roode.

The monarch’s North American origin runs counter to a long-standing hypothesis that the butterfly originated from a non-migratory tropical species.

“Previously, it was widely thought that after spreading from the tropics through North America, the evolution of migration enabled monarchs to fly south and survive the winter,” de Roode says. “It turns out that we had that upside down.”

To better understand the genetic basis for the butterfly’s migratory behavior, the researchers compared the genomes of migratory and non-migratory monarch populations from around the world. A disparity between the two groups among genes related to muscle function stood out, including one in particular: collagen IV alpha-1. The migratory butterflies expressed greatly reduced levels of this gene, which is involved in muscle function.

Humans have a similar gene that is associated with a muscle disease known as myopathy, de Roode notes.

“The data clearly show that muscles are the main thing that enables monarchs to migrate over thousands of miles,” he says. “We also found that the migrating monarchs have much more efficient metabolisms.”

The researchers identified a gene mutation underlying the lack of color in the Hawaiian white monarch.

By comparing the genome of mutant white monarchs, found in Hawaii, with other monarchs the researchers identified a gene clearly correlated with the butterfly’s beautiful orange color.

A similar gene found in mice, myosin 5a, is associated with a dilute phenotype: Instead of the black fur, mice with a mutation in this gene are light brown or beige. “Myosin 5a is a gene that regulates transport of pigment within a cell, moving color to a hair shaft in the case of mice, or apparently to scales in the case of monarchs,” de Roode says. The gene has never before been implicated in insect coloration, he adds.

In 2010, de Roode’s lab discovered that monarchs use a toxic chemical in certain species of milkweed to rid themselves of harmful parasites, providing some of the best evidence that animals use medication.
“Monarchs are a fascinating system to study,” he says.

“There is so much that we don’t yet know about these insects, and we may never know because they are now in decline.”

Monarch larvae feed on milkweed, which is becoming rarer due to pesticide use and development of land. As a result, the number of monarchs making the annual migration from Canada and the United States to Mexico has dropped dramatically: From an estimated 180 million-900 million in 1996-1997 to an estimated 6.7 million-33 million this past year.

“The whole migrating population could be gone over the next decade,” de Roode says. “It’s an amazing natural phenomenon in danger of disappearing.”

De Roode and his students helped create the Jimmy and Rosalynn Carter Pollinator Garden at The Carter Center, which opened October 1 in honor of President Carter’s 90th birthday. The garden is filled with milkweed and flowers and plants native to Georgia and is part of the Rosalynn Carter Butterfly Trail, developed by the former first lady to draw attention to the plight of the monarchs.

Credits: Top and bottom photos via ThinkStock; center photo by Jaap de Roode.

Monarch butteflies use drugs
Mystery of monarch migration takes new turn

Monday, September 29, 2014

Biology students aim for fast, portable Ebola test

Rostam Zafari and Brian Goldstone have made a video appeal to support their idea.

By Kimber Williams, Emory Report

Two Emory freshmen have turned a classroom challenge into an exercise in real-life social entrepreneurship, advancing their idea to create a new method of testing for the Ebola virus into an online crowdfunding campaign that is already gaining steam.

The result? A student-powered proposal to develop REDS, Rapid Ebola Detection Strips, a portable, fast, less expensive, user-friendly approach to detecting the virus in the field.

It was on the first day of classes this semester, during an Introduction to Biology course, that Brian Goldstone and Rostam Zafari heard Senior Biology Lecturer Rachelle Spell mention a way to earn extra-credit: Learn how doctors currently test for the Ebola virus and come up with a faster, more affordable idea.

Read the full story.

Thursday, September 25, 2014

Doing math with movie stars

Emory mathematician Ken Ono, left, coaches actor Dev Patel for his portrayal of the math genius Ramanujan, on the set of "The Man Who Knew Infinity." (Photos by Sam Pressman.)

By Carol Clark

Emory mathematician Ken Ono did not plan for his career to veer into the movie business. Unexpected paths can open, however, when your work involves unraveling the trail of mysteries left by Srinivasa Ramanujan. The Indian math genius had little formal education, but filled notebook after notebook with fantastic formulas that he said were visions from a Hindu goddess.

While British colonialism was still at its height, English mathematician G.H. Hardy helped Ramanujan become a scholar at Cambridge University, where he bedazzled and baffled professors. Ramanujan died in 1920 at the age of 32, leaving behind many extraordinary contributions to math, along with big questions about the proofs underlying his work.

The film is based on a 1991 book
Ono is among those who’ve cracked some of these questions: Most notably, the realization in 2011 that partition numbers are fractals, an insight that opened a theoretical window onto “seeing” their infinitely repeating superstructure. Ono’s team also devised the first finite formula for calculating the partitions of any number.

In July, Ono received a request from film director Matt Brown in London to chat over Skype about a biopic he was working on. “The Man Who Knew Infinity,” produced by Stillwater Pictures, will feature Dev Patel as Ramanujan and Jeremy Irons as Hardy.

Ono happily agreed to the Skype session. The next thing he knew, he was flying to London to serve as an on-the-scene consultant during filming at Pinewood Studios.

In the following Q&A, eScienceCommons talks with Ono about what it’s like for a mathematician to get swept up into the production of a major motion picture.

eScienceCommons: What did you and Matt Brown talk about during that Skype session? 

Ken Ono: I had gone to India in 2012 to work on a docu-drama about Ramanujan by an Indian film company. Matt had seen that short movie, and he knew that as part of that project I had gotten to actually hold Ramanujan’s original notebooks and go through them. For his movie, Matt wanted me to advise the art department to ensure the props were accurate. And also to make sure that the script had all the math details right. The problem with the partition numbers raised by Ramanujan is a key part of the script and Matt said he found it fascinating that mathematicians still hadn’t cracked that mystery. I told him, “Actually, I led the team that solved that problem a couple of years ago.”

His response was: “You need to come to England tomorrow, if you can!”

I was already planning to compete in the World Triathlon Championships in Germany in two weeks, so I agreed to just go to Europe early and spend that time in London.

Working with the art department to get every detail right. "All of the math in this movie will be absolutely accurate," Ono says. 

eSC: What was your first day of work like? 

Ono: A driver came and picked me up from my London hotel in a BMW. I’m definitely not accustomed to having my own personal driver! Pinewood Studios is in a rural area. We traveled through pastures with cows grazing in them and then, out of nowhere, you see these gigantic buildings. 

The art department for the film is amazing. They were reproducing artifacts related to Ramanujan in fanatical detail, including 100-year-old issues of mathematical journals and an 11-page letter he wrote to Hardy. One person’s job was to master Ramanujan’s handwriting and replicate it. They had more than 400 photos taken from reconnaissance trips to various places and they asked me what it was like to be in Ramanujan’s home, which I had visited when I was in India.

Kevin McNally, left, is portraying British mathematician Major McMahon. "McNally played Mr. Gibbs in 'Pirates of the Caribbean' and he would do this pirate fist bump," Ono says. "I'm not sure what it means."

eSC: How did you wind up actually working with the actors? 

Ono: The second day when I arrived at the studio Matt Brown said, “We need you to come to rehearsal.” So suddenly I found myself in a room witnessing two world-class actors, Dev Patel and Jeremy Irons, recreating one of the greatest stories of math, and one that has been the basis of my career. It was a huge thrill.

I was the only mathematician present and I was helping to both get the math right and tweak the dialog to maximize the impact of each scene. A big part of the movie is how Ramanujan and Hardy learn to understand each other so they can work together. Their cultures and their methods of doing math are in conflict.

In a scene soon after Ramanujan arrives in England, Hardy is trying to get him to write down a proof to one of his formulas. But Ramanujan received his formulas as complete visions and thought it was a waste of time to write down proofs of things he already knew. I explained to the actors that there is a difference between a claim, or a formula, and a proof. For trained mathematicians, a proof is necessary, it gives value to a statement. Ramanujan eventually realized why it’s important to prove things, that even he can make a mistake.

Taking a break from filming, from left: Producer Ed Pressman, Jeremy Irons, Dev Patel, Ken Ono, Matt Brown and actress Sorel Carradine.

Another key part of the movie is Ramanujan and Hardy working together to find a good approximation for the partition numbers. These numbers grow at an astronomical rate. I described what it’s like for two mathematicians to be working at a board, trying to figure something out. I wanted the actors to know that when you finally are confident that you have a method to find the answer, that’s the “aha” moment, not the dotting of the i’s that comes later. We wanted the audience to really feel what it meant to get closer and closer to a theorem. Ramanujan had an idea and Hardy had the technical expertise required to write it out.

It's pivotal when Hardy realizes that they have found a way to approximate the partition numbers. We needed a line of dialogue to describe his excitement over this insight into these numbers that keep growing so rapidly. We couldn’t use the word “trillions” because it wasn’t part of the British vernacular in the early 18th century.

I suggested the line, “Ramanujan, you are truly the man who knows infinity.” It both makes mathematical sense and it worked the name of the name of the movie into the script.

When we finally got all of the details of the scene right, and Jeremy Irons read that line in his magical voice, the feeling was electric!

A letter from Ramanujan to Hardy is among the many props painstakingly reproduced by the art department for the film.

eSC: What’s your favorite scene of those that you worked on? 

Ono: One scene that I am quite fond of shows Ramanujan sitting in a class of students at Cambridge looking absolutely bored as a professor discusses a math problem. The professor resents having this lowly Indian in his class. And Ramanujan is not even taking notes, which is infuriating to him. So he challenges Ramanujan to complete a formula. Ramanujan walks to the board and instantly writes it out. 

My job was to come up with a formula for the scene that makes sense in terms of the topic of the class. It also had to be complex enough to be impressive, but simple enough so that it would not be too difficult for Dev Patel to easily remember it and write it down quickly.

I chose a special decimal expansion for Pi, which involves having the odd numbers in order by means of a special fraction that Ramanujan knew. Ramanujan saw beautiful patterns in numbers and I wanted the math for the scene to reflect that. The formula had to look pleasing to the eye, so whether you were an expert or not you could sense this beautiful symmetry that represents Ramanujan’s talent.

Between takes: "Jeremy Irons' attention to detail is amazing," Ono says.

eSC: How did the actors react to having a mathematician working with them? 

Ono: I was referred to as “the guy who cracked partitions” all over the set. Dev Patel did a hilarious, over-the-top impression of me talking about math. I didn’t realize I got so excited.

He is only 24, very humble and super smart, although he’ll tell you that he’s bad at math. He’s a great actor and fun person. Someone took a video of he and I running across a campus green, and then kept playing it backwards.

It was mostly, however, very serious hard work and really long days. The actors were really down-to-earth and focused.

Jeremy Irons’ attention to detail is amazing. He now knows that Pi(x) is not always less than Li(x). We discussed partitions, Skewe’s number, PNT and the Old English ways of pronouncing huge numbers. 

For one scene, Hardy barges into the vice chancellor of the university’s office, to tell him that he must not reject Ramanujan for a Royal Society fellowship. Irons was wearing a top coat and a hat and before each take for this 15-second scene he would walk fast in a circle about 20 times. Then he knocks on the door.

When I asked why he did that, he explained that walking in circles changed his face slightly and said, “Acting angry is the easy part. Convincing the audience that I just ran across campus in a huff is much harder.”

Irons even practiced Hardy’s handwriting using a 1930s-era fountain pen. The movie opens with Hardy writing this very special speech about Ramanujan that he delivered at Harvard: “I’m charged with the task today of telling you one of the most romantic and peculiar stories in the history of math.”

I almost cried when we were filming that. I knew the speech well and, on top of that, to hear it spoken in Jeremy Irons’ voice was incredible.

eSC: Now that you have your own IMDb page, will you be leaving math for the movies? 

Ono: I’ll definitely be sticking to math. Making movies is a lot harder! It’s grueling work but I also had a wonderful time. I signed some autographs one night just because I was sitting next to Dev Patel and Jeremy Irons in a swanky restaurant. I still can’t believe that they are making this movie and that I got to be involved. It’s so awesome that math is now hip!

New theories reveal the nature of numbers
Math formula gives new glimpse into the magical mind of Ramanujan

Wednesday, September 24, 2014

'I first became a scientist in my backyard'

That’s me, climbing a flagpole just outside my house when I was about seven years old, circa 1967. The rest of my family was standing below watching, cheering me on, and documenting the event. Little did I know at the time that other kids were told they couldn’t climb flagpoles, let alone make it to the top. Yes, that’s a metaphor.

By Anthony Martin

Emory paleontologist Anthony Martin wrote a moving, personal piece about his path from poverty to a PhD for his blog "Life Traces of the Georgia Coast." Below is an excerpt from Martin's article:

"I first became a scientist in my backyard. This path to life-long inquiry began when I was four years old, as soon as my family moved to a larger house, and one with a larger yard. This small, outdoor patch of land with a few large trees, bushes, and grass soon became my field area, laboratory, classroom, and all-purpose place for conducting experiments in nature. Even better, my proclivity for observing this world outside of myself was encouraged – or at least tolerated – by my mother and father.

"At the time, I had no idea just how important of a role this backyard and parental support would play in my scientific career. Yet now I look back on it with a mix of gratitude and wistfulness, especially as both of my parents have departed this earth I have studied for most of my life. ...

"For about nine months of any given year during my childhood, starting in the spring, I could step out the back door of my house and watch ants, bees, wasps, butterflies, moths, spiders, and praying mantises. Plant-insect interactions in particular – such as pollination, herbivory, and wound responses in plants – drew me in, teaching me those ecological principles long before I ever heard the words 'pollination,' 'herbivory, and 'wound response.'"

Read the whole article on "Life Traces of the Georgia Coast." It's an amazing story.

Bringing to life "Dinosaurs Without Bones"