The Road to a Tastier Tomato

This week, I discovered that I’ve lived life deprived of a good tomato.

As a tomato-lover, I was surprised to learn from Professor Harry Klee of the University of Florida that the supermarket tomatoes I’ve enjoyed throughout my 18-year existence are all flavorless compared to the tomatoes of the past. He spoke at Duke as a guest of the University Program in Genetics and Genomics on Feb. 28.

It turns out that commercial tomato growers, by breeding more profitable (i.e. higher-yield, redder-color, larger-fruit) tomato varieties over the past 50 years, inadvertently excluded what Klee believes is the most important tomato trait of all:

Commercial tomato growers have bred larger, redder tomatoes that are less flavorful than heirloom and older varieties. Image courtesy of Harry Klee.

Flavor.

Apparently, I was one of very few people unaware of this issue. The public outcry in response to the increasing flavorlessness of commercial tomatoes began over a decade ago, when Klee first began to study tomato genetics.

From his research, Klee has drawn several important, unexpected conclusions, chief among them:

1: Flavor has more to do with smell than taste;

2: Lesser-known biochemical compounds called “volatiles” influence the flavor of tomatoes more than sugars, acids, and other well-known, larger compounds;

3: These “volatiles” are less present in modern tomato varieties than in tastier, older, and heirloom varieties;

But fear not—

4: Tomatoes can be back-bred to regain the genes that code for volatile compounds.

In other words, Klee has mapped the way back to the flavorful tomatoes of the past. His work culminated in a cover story of the Jan. 27 issue of Science. The corresponding paper describing the analysis of over 300 tomato strains to identify the chemicals associated with “good” and “bad” tomatoes.

Dr. Harry Klee and collaborators in his lab at the University of Florida. Image courtesy of Harry Klee.

To prove that modern tomatoes have less of the compounds that make them tasty, Klee and his team recruited a panel of 100 taste-testers to rank 160 representative tomato varieties. According to Klee, the team “developed statistical models to explain the chemistry of ‘liking’ [tomatoes],” then narrowed down the list of compounds that correlated with “liking” from 400 to 26. After tracing these 26 compounds to genetic loci, they used whole-genome sequencing to show that these loci are less expressed in modern tomatoes than in “cerasiforme” (i.e. old) and heirloom tomato varieties.

Further studies showed that tomato weight is inversely correlated with sugar content—in other words, “a gigantic fruit doesn’t taste as good,” Klee said.

If Klee can convince tomato growers that consumers value flavor over size, color, and quantity, then he might just single-handedly put flavorful tomatoes back on the shelves. Nevertheless—and despite the publicity surrounding his work—Klee understands it make take a while before commercial tomato growers see the light.

Klee and his team of scientists have genetically mapped the way back to the tasty tomatoes of the past. Image courtesy of Harry Klee.

“Growers get no more money if the tomato tastes good or bad; they’re paid for how many pounds of red objects they put in a box…[but] we can’t just blame the modern breeders. We’ve been selecting bigger and bigger fruit for millennia, and that has come at the cost of reducing flavor,” Klee said.

Post by Maya Iskandarani

The Man Who Knew Infinity, and his biggest fan

Ken Ono, a distinguished professor of mathematics at Emory University, was visibly thrilled to be at Duke last Thursday, January 26. Grinning from ear to ear, he announced that he was here to talk about three of his favorite things: math, movies, and “one of the most inspirational figures in my life”: Srinivasa Ramanujan.

Professor Ken Ono of Emory University poses with a bust of Newton and one of Ramanujan’s legendary notebook pages. Source: IFC Films.

Ramanujan, I learned, is one of the giants of mathematics; an incontestable genius, his scrawls in letters and notebooks have spawned whole fields of study, even up to 100 years after his death. His life story continues to inspire mathematicians around the globe—as well as, most recently, a movie which Ono helped produce: The Man Who Knew Infinity, featuring Hollywood stars Dev Patel and Jeremy Irons.

I didn’t realize until much too late that this lecture was essentially one massive spoiler for the movie. Nevertheless, I got to appreciate the brains and the heart behind the operation in hearing Ono express his passion for the man who, at age 16, inspired him to see learning in a new light. Ramanujan’s story follows.

Ramanujan was born in Kambakunam, India in 1887, the son of a cloth merchant and a singer at a local temple. He was visibly gifted from a young age, not only an outstanding student, but also a budding intellectual: by age 13, he had discovered most of modern trigonometry by himself.

Ramanujan’s brilliance earned him scholarships to attend college, only for him to flunk out not once, but twice: he was so engrossed in mathematics that he paid little heed to his actual schoolwork and let his grades suffer. His family and friends, aware of his genius, supported him anyway.

Thus, he spent the daytime in a low-level accounting job that earned him barely enough income to live, and spent the night scribbling groundbreaking mathematics in his notebooks.

A photo portrait of Srinivasa Ramanujan, a brilliant Indian mathematician born in the late 19th century. Source: IFC Films.

Unable to share his discoveries and explain their importance to those around him, Ramanujan finally grew so frustrated that, in desperation, he wrote to dozens of prominent English mathematics professors asking for help. The first of these to respond was G. H. Hardy (for any Biology nerds, this is the Hardy of the Hardy-Weinberg equilibrium), who examined the mathematics Ramanujan included in his letters and was so astounded by what he found that, at first, he thought it was a hoax perpetrated by his friend.

Needless to say, it wasn’t a hoax.

Ramanujan left India to join Hardy in England and publish his discoveries. The meat of the movie, according to Ono, is “the transformation of the relationship between these two characters:” one, a devout Hindu with no formal experience in higher education; the other, a haughty English professor who happened to be an atheist.

The two push past their differences and manage to jointly publish 30 papers based on Ramanujan’s work. Overcoming impossible odds—poverty, World War I, and racism in particular—Ramanujan’s discoveries finally found the light of day.

Sadly, Ramanujan’s story was cut short: a lifelong vegetarian, he fell ill of malnutrition while working in England, returning to India for the last year of his life in the hopes that the warmer climate would improve his health. He died in 1920, at 32 years old.

He continued writing to Hardy from his deathbed, his last letter including revolutionary ideas, which, like much of his work, were so far ahead of his time that mathematicians only began to wrap their minds around them decades after his death.

“Ramanujan was a great anticipator of mathematics, writing formulas that seemed foreign or random at the time but later inspired deep and revolutionary discoveries in math,” Ono said.

Ono’s infatuation with Ramanujan began when he was 16 years old, himself the son of a mathematics professor at Johns Hopkins University. Upon receiving a letter from Ramanujan’s widow, Ono’s father—by Ono’s account, a very stoic, stern man—was brought to tears. Shocked, Ono began to research the origin of the letter, discovering Ramanujan’s story and reaching a turning point in his own life when he realized that there were aspects to learning that were far more important than grades.

That seems to have worked out quite well for Ono, considering his success and expertise in his own area of study—not to mention that he now has “Hollywood producer” under his belt.

Professor Ken Ono chats with actor Dev Patel on the set of The Man Who Knew Infinity. Photo credit: Sam Pressman.

 

Post by Maya Iskandarani

Starting Your Own Business in Social Entrepreneurship? Lessons from Four Founders

Interested in starting your own jazz festival? Or creating hydrogen-rich water to boost your circulation and improve muscle recovery?

These are the accomplishments of Cicely Mitchell and Gail Levy, who were among four inspiring leaders at the evening panel discussion in the Fuqua School of Business this past Wednesday. Excited students and faculty gathered in the Kirby Reading room to learn about the leaders’ unique perspectives as founders of non-profit and for-profit solutions to various social impact and sustainability issues.

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Students and faculty gathered for dinner and networking before the panel discussion.

Organized by the Duke Innovation & Entrepreneurship Initiative and the Center for the Advancement of Social Entrepreneurship (CASE), the panel served to enlighten the audience about the challenges the women have faced and the lessons they learned in starting and scaling their social ventures. Panel moderator Erin Worsham, the Executive Director of CASE, opened the discussion with a few statistics.

In the non-profit sector, women make up 75% of the workforce, but in leadership positions, this ratio drops to 45%. As of 2013 in the for-profit sector, only 2.7% of venture capital investments went to fund companies with a female CEO. While black women own 1.5 million businesses in the U.S., they receive only 0.2% of venture funding. Undoubtedly, Worsham concluded, there is a lot of work to do in terms of women getting funded and represented as leaders.

Erin Worsham opened up the panel with statistics about women in the workforce. Worsham is the Executive Director of the award-winning CASE based at Duke University’s Fuqua School of Business

To commence the discussion, Worsham asked the panelists to speak about the gender discrimination they faced while starting their own companies. Gail Levy, founder of H Factor Water, a health-focused company producing hydrogen-infused water in environmentally friendly packaging, answered with a time she was challenged to a drinking match in order to close a deal. “The lesson I learned is to not go and drink your way into making a deal,” Levy joked. “But more importantly, you need to have grit and tenacity. Let our presence be known, because eventually we will be heard.”

Gail

Gail Levy was the founder of the White House Millennium Green Committee under the Clinton Administration in 1999. She is passionate about advocating for women worldwide and is also the founder of H Factor Water.

Founder of The Art of Cool, a Durham nonprofit promoting music education to Durham-area youth, Cecily Mitchell remarked that she would be charged significantly more money than a male counterpart to work with the same artist.

Cicely Mitchell is co-founder of The Art of Cool, a Durham nonprofit promoting music education to Durham-area youth

Cicely Mitchell is co-founder of The Art of Cool, a Durham nonprofit promoting music education to Durham-area youth

Rebecca Ballard, lawyer and founder of Maven Women, a sustainability-focused fashion company dedicated to making professional wear for women, noted that “we live in a visual world, but we need to start looking at a person’s character rather than solely focusing on how they look.” Based on her experience with her medical real estate development company ACCESS Medical Development, angel investor Stephanie Wilson expanded on the comment, adding that the best thing to do about the prejudice against women is to know that it’s there and fight for it.

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Rebecca Ballard told the audience, “The most challenging thing about being a working woman is that appearance is considered ‘relevant.’” She started her career as a public interest lawyer and was previously the Executive Director of Social Impact 360.

I asked the founders to share their experiences in building a successful customer base. Wilson noted that to institute her company, she “determined who was the top real estate agent in our area and sought them out. I discussed my idea with them and asked for their advice on segueing into the market.” She suggested sending handwritten thank you notes to build relationships with your customers.

Stephanie Wilson founded ACCESS Medical Development and is also the co-founder of MillennialsMovingMillions.org.

Stephanie Wilson founded ACCESS Medical Development and is also the co-founder of MillennialsMovingMillions.org.

Mitchell added that The Art of Cool held the first few concerts for relatives and friends, and later partnered up with other small entrepreneurs. “Make sure what you do connects with people enough that they want to go and tell other people about what you’re doing,” she advised.

Cecily Mitchell talked about her experience with The Art of Cool. She handles the booking, contracts, networking, pitching for sponsorships and assisting in writing grants for the company.

Maven Woman founder Rebecca Ballard commented on the importance getting support from women in other sustainable industries, since “you are all driven by the same mission in the social entrepreneurship space.”

Rebecca

Rebecca Ballard is the founder of Maven Women, a sustainability-focused fashion company dedicated on making professional wear for women.

Worsham’s final question for the panel asked for any last pieces of advice. Ballard concluded the conversation with a reason why she started her company: “Social entrepreneurship exists because the status quo is not okay. There are externalities happening and people being treated badly; the status quo doesn’t have to be the way it is.”

From left to right:

Posing with the panelists! From left to right: Anika Radiya-Dixit (author), Gail Levy, Cecily Mitchell, Rebecca Ballard, and Stephanie Wilson.

By Anika Radiya-Dixit

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Mapping the Brain With Stories

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Dr. Alex Huth. Image courtesy of The Gallant Lab.

On October 15, I attended a presentation on “Using Stories to Understand How The Brain Represents Words,” sponsored by the Franklin Humanities Institute and Neurohumanities Research Group and presented by Dr. Alex Huth. Dr. Huth is a neuroscience postdoc who works in the Gallant Lab at UC Berkeley and was here on behalf of Dr. Jack Gallant.

Dr. Huth started off the lecture by discussing how semantic tasks activate huge swaths of the cortex. The semantic system places importance on stories. The issue was in understanding “how the brain represents words.”

To investigate this, the Gallant Lab designed a natural language experiment. Subjects lay in an fMRI scanner and listened to 72 hours’ worth of ten naturally spoken narratives, or stories. They heard many different words and concepts. Using an imaging technique called GE-EPI fMRI, the researchers were able to record BOLD responses from the whole brain.

Dr. Huth explaining the process of obtaining the new colored models that revealed semantic "maps are consistent across subjects."

Dr. Huth explaining the process of obtaining the new colored models that revealed semantic “maps are consistent across subjects.”

Dr. Huth showed a scan and said, “So looking…at this volume of 3D space, which is what you get from an fMRI scan…is actually not that useful to understanding how things are related across the surface of the cortex.” This limitation led the researchers to improve upon their methods by reconstructing the cortical surface and manipulating it to create a 2D image that reveals what is going on throughout the brain.  This approach would allow them to see where in the brain the relationship between what the subject was hearing and what was happening was occurring.

A model was then created that would require voxel interpretation, which “is hard and lots of work,” said Dr. Huth, “There’s a lot of subjectivity that goes into this.” In order to simplify voxel interpretation, the researchers simplified the dimensional subspace to find the classes of voxels using principal components analysis. This meant that they took data, found the important factors that were similar across the subjects, and interpreted the meaning of the components. To visualize these components, researchers sorted words into twelve different categories.

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The Four Categories of Words Sorted in an X,Y-like Axis

These categories were then further simplified into four “areas” on what might resemble an x , y axis. On the top right was where violent words were located. The top left held social perceptual words. The lower left held words relating to “social.” The lower right held emotional words. Instead of x , y axis labels, there were PC labels. The words from the study were then colored based on where they appeared in the PC space.

By using this model, the Gallant could identify which patches of the brain were doing different things. Small patches of color showed which “things” the brain was “doing” or “relating.” The researchers found that the complex cortical maps showing semantic information among the subjects was consistent.

These responses were then used to create models that could predict BOLD responses from the semantic content in stories. The result of the study was that the parietal cortex, temporal cortex, and prefrontal cortex represent the semantics of narratives.

meg_shieh_100hedPost by Meg Shieh

Does Digital Healthcare Work?

Wearable technologies like Fitbit have been shown to provide a short-term increase in physical activity, but long-term benefits are still unclear, even if recent studies on corporate wellness programs highlight the potential healthcare savings.

Headshot of Luca Foschini

Luca Foschini, PhD is a co-founder and head of data science at Evidation Health, and a visiting research scientist at UCSB. Source: Network Science IGERT at UCSB.

To figure out the effects of these technologies on our health, we need ways to efficiently mine through the vast amounts of data and feedback that wearable devices constantly record.

As someone who has recently jumped on the Fitbit “band” wagon, I have often wondered about what happens with all the data collected from my wrist day after day, week after week.

Luca Foschini, a co-founder and head of data science at Evidation Health, recently spoke at Duke’s Genomic and Precision Medicine Forum where he explained how his company uses these massive datasets to analyze and predict how digital health interventions — Fitbits and beyond — can result in better health outcomes.

California-based Evidation health uses real-life data collected upon authorization from 500,000-plus users of mobile health applications and devices. This mobile health or “mHealth” data is quickly becoming a focus of intense research interest because of its ability to provide such a wealth of information about an individual’s behavior.

Foschini and Evidation Health have taken the initiative to design and run clinical studies to show the healthcare field that digital technologies can be used for assessing patient health, behavioral habits, and medication adherence, just to name a few.

Foschini said that the benefits of mobile technologies could go far beyond answering questions about daily behavior and lifestyle to formulate predictions about health outcomes. This opens the door for “wearables and apps” to be used in the realm of behavior change intervention and preventative care.

Foschini speaks at Duke’s Genomic and Precision Medicine Forum

Foschini explains how data collected from thousands of individuals wearing digital health trackers was used to find a associations between activity tracking patterns and weight loss.

Evidation Health is not only exploring data based on wearable technologies, but data within all aspects of digital health. For example, an interesting concept to consider is whether devices create an opportunity for faster clinical trials. So-called “virtual recruiting” of participants for clinical studies might use social media, email campaigns and online advertising, rather than traditional ads and fliers. Foschini said a study by his firm found this type of recruitment is up to twelve times faster than normal recruitment methods for clinical trials (Kumar et al 2016). 

While Foschini and others in his field are excited about the possibilities that mHealth provides for the betterment of healthcare, he acknowledges the hurdles standing in the way of this new approach. There is no standardization in how this type of data is gathered, and greater scrutiny is needed to ensure the reliability and accuracy of some of the apps and devices that supply the data.

amanda_cox_100 Post by Amanda Cox

Diabetes — and Privacy — Meet ‘Big Data’

“Click here to consent forever.”

If consent to participate in medical research were that simple, Joanna Radin of Yale University would have to find a new focus for her research, and I would never have found the Trent Center for Bioethics, Humanities & History of Medicine.

Luckily for us both, this is not the case. Medical consent is a very complex issue that can, as Radin’s research attests, traverse generations.

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Joanna Radin’s reserach focuses on the intersection of medical history, anthropology and ethics at Yale University. Source: Yale School of Medicine

Radin is an Associate Professor of Medical History at Yale, the perfect fit for the Humanities in Medicine Lecture Series taking place this month at the Trent Center. Her research nails the narrow intersection of medical history, anthropology, bioethics and data analytics. In fact, Radin’s appeal is so broad that her visit to Duke was sponsored by no less than six Duke departments, including the Departments of Computer Science, History, Electrical and Computer Engineering, Cultural Anthropology and Statistical Science.

Radin’s lecture honed in on a well-known case in the realm of bioethics and medical history: the Pima Native American tribe in Arizona, which is known for unusually high rates of diabetes and obesity. The Pima were the first Native American tribe to be granted a reservation in Arizona—30,000 acres—at the beginning of the California Gold Rush. In 1963, following nearly half a century of mass famine among the Pima, the National Institute of Health (NIH) conducted a survey for rheumatoid arthritis in the Pima tribe, instead discovering a frighteningly high frequency of diabetes.

In 1965, the NIH initiated a long-term observational study of the Pima that continued for about 40 years, though it was meant to last no more than 10. The goal of the study was to learn about diabetes in the “natural laboratory” of sorts that the Pima reservation unwittingly provided. The data collected in this study came to be known as the Pima Indian Diabetes Data set (PIDD).

Machine learning enters the story around 1987, when David Aha and colleagues at the University of California, Irvine (UCI) created the UCI Machine Learning Repository, an archive containing thousands of data sets, databases and data generators. The repository is still active today, virtually a gold mine for researchers in machine learning to test their algorithms. The PIDD is one of the oldest data sets on file in the UCI archive, “a standard for testing data mining algorithms for accuracy in predicting diabetes,” according to Radin.

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A Pima farmer in Pima, Arizona, circa 1900. Source: Wikimedia Commons

Generations’ worth of data on the Pima tribe have been publicly accessible in the UCI archive for over two decades, creating ethical controversy around the accessibility of information as personal as blood pressure, body mass index (BMI) and number of pregnancies of Pima Native Americans. Though the PIDD can help refine machine learning algorithms that could accurately predict—and prevent—diabetes, the privacy issues provoked by the publicness of the data are impossible to ignore.

This is where “eternal” medical consent enters the equation: no researcher can realistically inform a study participant of what their medical data will be used for 40 years in the future.

These are the interdisciplinary questions that Radin brought forth in her lecture, weaving together seemingly opposite fields of study in an engaging, thought-provoking presentation. No one who left that room will look at the Apple Terms & Conditions the same way again.

 

Post by Maya Iskandarani iskandarani_maya_100hed