ARCS Scholar Spotlights
Kimberly Lau: Unearthing the Roots of Extinction
The most productive research areas often arise at the overlapping edges between different fields. Geobiologist Kimberly Lau, an ARCS scholar at Stanford University, works at such an intersection. She incorporates chemistry, biology, and Earth science to better understand the times in our planet’s past when most living things went extinct.
Lau grew up in Cupertino and, like many kids, was captivated by dinosaurs. She recalls a formative trip with her parents to Canada, where they visited the Royal Tyrell Museum of Paleontology in Alberta. The dino exhibits sparked her imagination, creating visions in her mind of what the world looked like before humans came on the scene. This fascination continued during her undergraduate Earth history classes at Yale University, where she began to think more broadly about “the evolution of Earth and the environment, and how they’re inter linked.”
Life on Earth took an unusually long time to recover its previous bio diversity after the Permian-Triassic extinction. Even 5 million years after the event, the fossil record shows only creatures with small body sizes and low biological complexity, and an overall low level of diversity. Because the recovery was so slow, many scientists suspect that some environmental factor repressed life’s comeback.
Lau uses uranium isotopes in ancient rocks---previously deposited on ancient seafloors but now exposed in mountains---as her window into the past. She examines each sample’s ratio of uranium-235 to uranium-238, isotopes that are chemically reduced at different rates in the presence or absence of oxygen. By comparing her findings to the modern-day uranium isotope ratio, she can estimate the chemistry of the environment in which the older rocks formed. The work suggests that after the Siberian eruptions, as much as 20 percent of the global ocean was anoxic—meaning it was completely depleted in oxygen. In comparison, only 0.2 percent of the modern-day ocean is anoxic. Those extremely low oxygen conditions persisted for roughly 5 million years, a number that matches up well with the absence of diverse lifeforms in the fossil record. It’s a strong clue that the two were linked.
For another part of her research, Lau studies ocean chemistry during the Cryogenian Era, a period that spanned 630 million to 720 million years ago. This era was bracketed by the two most extreme ice ages in our planet’s history. Scientists believe glaciers covered the entire globe, creating a “snowball Earth. ”While her results are preliminary, Lau’s work suggests that the oceans became rich in oxygen just after the first snowball Earth, and then reverted back to predominantly anoxic conditions. Because the earliest fossils of animals (in the form of marine sponges) appear during the Cryogenian, many scientists have wondered about the connection between different oxygen levels and the evolution of complex life. Lau is focused in this direction as well.
“Linking environmental to evolutionary change is, I think, one of the really big challenging questions in this field,” she says.
The ARCS Scholar Award has given Lau the freedom to spend more time in lab, measuring data samples important to her research.
But on a more personal level, she says receiving the award has boosted her confidence. “Someone beyond your advisor and your parents thinks you’re doing a good job,” she says. “It’s this nice affirmation that what I’m doing is valuable.”
After completing her degree, Lau plans to pursue a post-doctoral research position in geology, ideally in an area that allows her to extend her current research. When not in the lab, she enjoys camping along the beautiful California coast and skiing in the Sierras.
Saahil Shenoy: Predicting the Extreme
Mathematics has always captivated ARCS Scholar Saahil Shenoy. “It’s just amazing to build a logical system and see what comes out of it,” he says. In his current research at Stanford University, he applies this mathematical fascination toward analyzing large data sets, incorporating rare data points to improve our predictions of when extreme events might occur.
Shenoy grew up in San Jose and, given his love of numbers and calculations, thought he would become an economist, a career he considered practical and pragmatic. But one day in high school his physics teacher showed the documentary The Elegant Universe to the class. Based on the best-selling book of the same name by Brian Greene, the film explores string theory, a model that seeks to explain many deep questions in fundamental physics.
Upon arriving at Stanford, Shenoy was introduced by one of his professors to a research group working on the statistics of extreme events bringing an exciting – and timely - new focus.
“People often use information from the past to predict whether a certain region will experience a major flood, fire, hurricane, or other natural disaster in a given time period,” he notes. “But as climate change worsens, environmental data from the past 50 years has started to lose its relevance in forecasting. How do you fit a model to data it has never seen before?”
Shenoy asks. “When there are errors, and in particular when you have very large errors, you’ll get hit the hardest.”
Many statistical models rely on Gaussian distributions, the familiar bell-shaped curves that can describe everything from variations in height within a population to the range of scores on a test. But Gaussians struggle to incorporate data points that fall far outside what the normal distribution predicts. Shenoy instead uses exponential distributions—which rise on one side toward infinity to include large but rare data points—to make better forecasts.
In recent work, Shenoy built a model to tell electricity providers how much power they can expect to need 24 hours in advance. Electricity is sold on open markets one day ahead of time. Providers must walk a fine line between buying too much power and seeing some of it go to waste, or buying too little power and risk seeing heavy use that might overtax their system. Electricity demand is generally steady, but a freak heat wave could make everyone turn on their air conditioners and send demand soaring. Using a branch of statistics called extreme value theory, Shenoy has now included such scenarios to improve forecasts.
Real-world data from the east coast utility PJM suggest that his model could save the company more than $600 million each year.
Before receiving the ARCS scholarship, Shenoy often took on teaching responsibilities to help fund his research, creating a hectic schedule. “Paper deadlines don’t wait just because I have a teaching shift,” he says. By allowing him to pare back on conflicting tasks, the ARCS Foundation Award has made his research much more enjoyable and productive.
In the future, he foresees himself working in the energy sector, where he can put his statistical prediction abilities to good use.
Shenoy also enjoys salsa dancing and DJ’ing salsa music at clubs. “It’s a positive feeling to share music you like with other people,” he says.“I find the same joy in sharing research.”
ARCS Scholar Claudia Corona: Following the Water
As California copes with its fourth straight year of drought, its stores of surface water are disappearing at an alarming rate and groundwater has become a vital resource.
ARCS Scholar Claudia Corona of San Francisco State University is working hard to understand the past and present of the state’s aquifers to help managers predict and plan for their future.
The key difference, she found, was that the more vegetated basin was fed by a subsurface spring , which had higher ion concentrations, while the less-vegetated stream was fed by a melting snowfield with low ion concentrations. A greater presence of ions in the spring-water was the result of water-mineral mixing over previous decades and centuries. Streams with greater ion concentrations allow more plant life to bloom, due to the greater than normal presence of nitrates.
Working in the field taught Corona the methods of hands-on science as she developed an appreciation for the opportunity to step beyond the classroom and develop her own research questions.
Corona is now working toward her master’s degree in geosciences at San Francisco State University, where she studies the influence of climate on groundwater recharge rates.
“Surface water and groundwater are connected”, she says.
California’s drought, and below-average snowpack levels have led to the pumping of billions and billions of groundwater, due to the lack of surface water resources. California’s agricultural power-house, the heavily agrarian Central Valley, has been especially hard-hit, and farmers now depend on groundwater to sustain their crops. Corona is helping to create a national database which catalogues i) the composition of the vadose zone—the variably saturated layer between the ground surface and the water table that water must travel through in order to recharge aquifers, and ii) how water flow behaves in the subsurface, through time.
Differences in soil texture and other characteristics govern how quickly water percolates through soils composed of a variety of textures like clay, silt or sand. An understanding of the rates of flow through these different soils remains unknown but critical. Corona’s data will help scientists improve calculations of groundwater extraction in the present and the future.
Corona is also working to address how global climate change and major climate patterns like El Niño, influence aquifer levels and recharge rates.
“Identifying natural climate variability signals in the vadose zone are important to understand how groundwater levels fluctuate, especially in times of drought,” she says.
Communication is central to Corona’s work. She says the ARCS Foundation Award has been key in helping her collaborate with other scientists as the database grows. In the future, she plans to get a Ph.D. in environmental or civil engineering and eventually focus on California’s water management strategies.
She also looks forward to directly engaging the public around water issues.
“Our livelihoods are becoming more and more affected by climate change, our dwindling water resources and extreme weather events…I want my family, your family, and everyone to be informed”.
Corona played softball, basketball and rugby in college. She now enjoys hiking and running; she ran the Los Angeles Marathon last year and San Francisco Marathon this summer, with some races and hikes in between.
She also enjoys mentoring younger students about the wonders of science. For more than 10 years, she’s engaged elementary, middle school, and high school student groups, specifically kids in challenging urban environments who have not yet had a chance to step outside of the cityscape.
“The talks are meant to inspire. I want these kids to be unafraid to follow their dreams, and I want to introduce them to the beauty of science. They are our future, and we need to cultivate their sense of ecosystem and water conservation stewardship now, so that they may build a sustainable, healthy, and prosperous future for our beautiful state of California.”
Willie Mae Reese: Improving the Capabilities of Implantable Medical Devices
Biomedical researchers are always on the lookout for new techniques to heal us when we break down. As part of this pursuit, ARCS Scholar Willie Mae Reese of the University of California, Berkeley is improving the capabilities of implantable medical devices and helping them stay where they’re most needed.
Reese knew from a young age that she wanted to study science. But growing up in rural Carlsbad, New Mexico, she didn’t see many local options for her future studies. In her junior year of high school, she applied for and was accepted to the Leadership Enterprise for a Diverse America (LEDA) program, which gives underprivileged youths access to resources that can help them realize their potential. The eight-week program flew her to Princeton, New Jersey, where she took classes on ethics, learned about historical leadership, and studied grass-roots empowerment. One of the main themes instilled by LEDA, Reese recalls, was the concept of “always giving back and pulling the next person up.” She has carried this ideal with her throughout her career.
Encouraged and assisted by LEDA, Reese applied to the Massachusetts Institute of Technology to study Materials Science and Engineering. During her undergraduate years at MIT, she worked on a research team that was trying to develop bio-compatible screws to reattach tendons to bones after an injury. Current medical practice usually involves inserting metal screws into the body, which are then permanently responsible for holding bones and tendons together. Reese and her collaborators tried to foster the healing process by creating a screw made from polylactic acid—a natural substance produced in muscles during a workout—to encourage the bone to regrow. Over time, the screw would dissolve, leaving behind healed bones and tendons.
After an internship for Intel in a manufacturing plant in Albuquerque, New Mexico, Reese came to UC Berkeley to study Materials Science and Engineering with a focus on biomaterials. Her current project aims to tamp down some of the immune responses employed by the human body so that doctors can better treat patients. From the perspective of our bodies, implantable devices are foreign invaders. Cells known as fibroblasts, which are similar to skin cells, often grow a protective capsule around implanted devices to cordon them off. Reese and her lab group at Berkeley are working to counter this response with an ingenious trick: nanometer-sized pits etched onto a device’s surface using a laser beam.
Reese’s earlier research showed that cells tend to avoid growing on surfaces covered with microscopic craters. Though why this happens is unknown, her hypothesis is that the cells have trouble reaching down into the pits to anchor themselves. In this way, a cratered surface should provide fibroblasts with fewer places to stick and flourish. An implantable device textured with nano-pits on its surface should be easier for the body to accept, preventing complications and multiple surgeries.
Reese says she’s always interested in learning new things and expanding her perspective. Alongside her implantable device research, she’s also involved in several organ-on-a-chip projects, which seek to reprogram groups of skin cells into simplified versions of human organs—such as hearts, kidneys, or lungs—so that doctors can test cancer treatments and other personalized medicine techniques.
After completing her Ph.D., she hopes to work in biomedical device consulting, helping shepherd new life-saving devices from the laboratory bench to the consumer.
Throughout all her pursuits, Reese remains mindful of working with and assisting others. She is involved in several college social groups, such as the Black Graduate Engineering and Science Students Association (BGESS) and the UC Berkeley Graduate Social Club. She enjoys taking her two dogs, Coco and Chewy, for walks and adventures around the Bay Area.
More on Willie Mae Reese’s work, as published in Nature Materials (July 2015): Directing cell migration and organization via nanocrater-patterned cell-repellent interfaces
Myka Estes: Tracing a Mother’s Influence
We all learn in school that the different systems of the human body have different functions. The nervous system, for instance, governs our behavior and senses, while the immune system keeps us healthy. “And never the twain shall meet,” says ARCS Scholar Myka Estes of UC Davis. “Well, actually it turns out that’s not true.” In fact, her research shows just how complicated and multifarious the interactions of these two systems can be.
Intending to become a lawyer, Estes enrolled at Mount Holyoke College in Massachusetts but was forced to drop out after her first year when she was diagnosed with lupus, an auto-immune disorder. It was a major setback, but it spurred her to read scientific literature about her disease, gain a better understanding of it, and consider a future in research. “I thought, ‘Science has made a huge impact on my life,’” she says. “So maybe I can add to it a little bit.” She went on to complete her undergraduate degree in molecular biology from the University of Colorado, Boulder, and after graduating decided she wanted to study neuro-immunology full time.
In her current work at the Center for Neuroscience at UC Davis, Estes studies how infections contracted by a mother during pregnancy might contribute to mental issues in her offspring. Previous data from Scandinavian countries has suggested that when some pregnant women experience a sustained high-temperature fever, their children can go on to develop behavioral disorders such as autism and schizophrenia. The extended families of these children also tend to have many cases of allergic reactions and auto-immune diseases.
Though much of the research remains preliminary, evidence now suggests that the timing of the immune response determines the outcome. An infection hitting a mother very early in pregnancy might cause a miscarriage; one during mid-gestation could give rise to autism and schizophrenia; while later-stage infections might contribute to cerebral palsy. Such things happen in only a small percentage of pregnancies, Estes notes. “Many women get fevers and flus and their babies are perfectly fine,” she says.
Instead, she describes what’s going on as an interplay of genetic and environmental factors: family background combining with lifestyle, diet, and immune stress to create a susceptibility for certain behavioral disorders. Considering how complex the different processes are in her research, Estes says she often wants to explore every possible angle. Sometimes she has trouble deciding where the cut-off line is and condensing it down into a single publishable paper. “My boss said, ‘Stop doing experiments,’” she says jokingly. “The more information I add, the more the model disintegrates before my eyes.”
Her research might one day open the door to new therapeutic drugs for autism and schizophrenia. It’s already known that when a person gets sick, their behavior changes. “That’s IL-1β having an effect on you,” Estes says. And in a subset of autistic children, fevers actually seem to improve some behaviors, indicating that immune molecules could alter mental functioning. Cytokines might therefore offer a sort of back door across the blood-brain barrier, gaining entry in ways that current drugs cannot.
The ARCS Scholarship has given Estes the freedom to focus solely on research. If she didn’t have this funding source, she’d probably need to teach and then, she says, she wouldn’t have time to carry on many different projects at once. Estes feels fortunate that she hasn’t had to take on this extra burden during her graduate experience.
Because the early developmental issues that she examines are exacerbated by environmental stress and trauma, Estes’ research has also sparked an awareness of social justice within her. “There are populations in our country where every baby is cooked in that environment,” she says. “So they’re starting off already without the capacity to have a lot of what we call executive control.” Such kids tend to do worse in schools and often end up in jail. Estes has volunteered at San Quentin State Prison to teach English classes to inmates. In the future, she hopes to use her neuroscience research to help underprivileged communities.
Allison Hoch: Rebuilding Bones Naturally
One day, patients with broken bones could be rushed to a hospital and injected with stem cells from their own body. These cells would take hold and mend the fracture, naturally regrowing the skeleton’s healthy structure. Though such therapies remain a dream, ARCS Scholar Allison Hoch of UC Davis is working to make them a reality.
Hoch is from the Lehigh Valley of Pennsylvania, north of Philadelphia, and did her undergraduate work in biomedical engineering at Bucknell University in nearby Lewisburg. For an undergraduate project, she studied the physics underlying bio-mechanical injuries relating to the eyes. The work was germane to toy manufacturers, such as Nerf, that need to know how to safely produce their plastic guns and foam missiles for kids.
Recently, Hoch completed her biomedical engineering Ph.D. at UC Davis, where she researched therapies based on mesenchymal (pronounced MEzen-KY-mal) stem cells. Unlike the embryonic stem cells formed shortly after conception, mesenchymal cells are produced in the fatty marrow within adult bones. As a type of stem cell, mesenchymal cells are what’s known as multipotent, which means they may differentiate into a variety of bodily tissues, including bone, muscle, cartilage, and fat. As Hoch explains, “They can wear a lot of hats.”
Such materials may last just 15 to 20 years, which is why such procedures are typically reserved for the elderly. For younger patients, a hospital might harvest another piece of bone in the body (usually from the hip). But that technique is painful and requires extra surgery, and losing a mass of bone can be harmful. Instead, Hoch and many other researchers would like to get the body to grow a new piece of bone in the place of the broken one.
At the laboratory in Basel, Hoch worked with a bioreactor in which blood-like fluid washed over the cells as they grew. Her work showed that these cells were much more potent, mainly because they could divide and spread on a three-dimensional scaffold—a much better simulation of the perforated nooks and crannies within human bone than offered by a plastic 2-D platform. Within the bioreactor, the mesenchymal cells could also be joined by hematopoietic stem cells, which give rise to blood cells. These “little buddies,” as Hoch describes them, undergo all sorts of chemical cross-talk with the mesenchymal stem cells to nurture them.
Hoch has been striving to get the mesenchymal stem cells to more fully commit to being bone producers. With the current chemical cocktail, the cells sometimes revert from bone cells back into mesenchymal stem cells when placed at the fracture site. So Hoch has coerced the cells to produce an extra-cellular matrix, composed mostly of proteins and collagen fibrils—similar to the material surrounding cells when they reside in the body. Using mice, she’s shown that adding this material decreases the rate at which the bone cells revert back into stem cells once inside a body.
Science is experimental, and often require performing tests with unknown outcomes. But traditional funding sources, seeking to mitigate risk, see a need to justify every trial. The ARCS Award has given Hochan opportunity to unleash her “creative side” in science, she says. It’s enabled her to delve deeper into her data to try to figure out the most interesting questions to ask about it.
“The ARCS Award has enabled me to perform the most rigorous experiment to test my hypothesis,” she says, “rather than compromise the ideal technique due to cost.”
Having completed her Ph.D., Hoch now works in biotechnology in the Bay Area where she utilizes significant business acumen to align objectives of account plans and field teams. Furthermore, she engages customers in transitions of care/population health management models. When she’s not at work, Hoch enjoys travelling internationally, hiking in the Bay Area, and attending performances at the San Francisco Opera.
Cade Fox: Delivering Drugs Without a Shot
On a list of fun things, getting a shot at the doctor’s office probably ranks pretty low for most people. But for patients with diabetes and other hormone disorders, injections are a daily necessity. ARCS Scholar Cade Fox of UC San Francisco wants to replace these shots with something much easier: swallowing a pill.
Fox received his undergraduate degree in chemistry from George Fox University near Portland, Oregon. Afterwards, he worked in a biomedical research laboratory that was trying to combat cancer using a molecule found in some viruses called small interfering RNA (siRNA). True to its name, this molecule binds to and silences RNA—specifically, the messenger RNA that cells use to transcribe DNA into proteins.
Fox was targeting a protein called HER2 that’s overproduced in certain aggressive forms of breast cancer. By loading up siRNA into silica nanoparticles and delivering them into cancer cells, the research aimed to disrupt the production of HER2, making the cells easier to kill off.
Now as a third-year pharmaceutical science student at UCSF, Fox is looking at new techniques for treating diseases like diabetes. Insulin and certain other drugs can’t be administered orally because the harsh environment of the gastrointestinal tract degrades them before the body absorbs the drugs. To get around this , Fox has figured out a way to mass-produce tiny medicine-carrying microdevices. The disk-shaped devices are printed atop a silicon wafer that is then scraped away, leaving 10,000 dots each slightly larger than the width of a human hair. The manufacturing process also coats each disk with nano-scale wires and fibers, which allows them to stick to the epithelial cells lining the GI tract.
Fox envisions placing as many as 100,000 of the microdevices inside a pill. This process would deliver drugs in higher doses than normal oral pills can attain. Though researchers do not yet know how the devices work in the gut, Fox says the nano-wires seem to open up the tight junctions between epithelial cells.
They also appear to ruffle the cell surfaces, providing more entry points for the drugs. And because they’re made of biodegradable materials, the devices dissolve once they’ve delivered their medicine. Along with diabetes, the treatment could replace any regimen that requires taking many shots, such as certain chemotherapy treatments or growth hormone therapy for teenagers.
Though he was building on knowhow from nearby Silicon Valley, Fox says he spent a lot of time figuring out the best way to manufacture the microdevices so they had all the properties he wanted.
He says he often wanted to “try some crazy new idea” in the lab, but traditional funding models required that his research have specific goals in mind. The ARCS Scholarship has given him the opportunity to explore unconventional ideas, he says, helping to push his research forward.
When he’s done with his Ph.D., Fox says it would be fun to join the San Francisco startup scene. The Bay Area is a hotbed of biomedical research, and Fox thinks he can take his nanofabrication and drug-delivery techniques to either an existing small company or start his own. Outside the lab, he likes to snowboard and work on graphic design.
Caroline Morley: Probing Alien Clouds
Sometimes when Caroline Morley flies on a plane, she gazes out the window and daydreams about the clouds on alien planets. This isn’t idle fantasy, but rather part of her scientific research as an ARCS Scholar at UC Santa Cruz.
While an undergraduate at MIT, Morley found herself drawn to astrophysics because of the field’s focus on big questions: How does the universe work? What is it made of? One of her MIT professors, the celebrated astrophysicist Sara Seager, was a leader in the search for planets around other stars. Morley’s time in Seager’s class coincided with the launch of NASA’s Kepler Space Telescope, a dedicated observatory that has since discovered more than 1,000 extrasolar worlds. Getting a front-row seat for this new frontier in astronomy helped solidify Morley’s desire to go to graduate school to study exoplanets.
For her senior thesis at MIT, she used 14-inch telescopes to watch for the periodic diminishing of a star’s brightness—indicating that a planet was passing in front and eclipsing its light. She participated in a network of collaborators around the world who maintained a 24/7 watch of the night sky; Caroline would know what was happening in real time, even when it was daytime or cloudy in Massachusetts. At one point, she and her colleagues in Spain, Arizona, and Hawaii observed a long-duration 12-hour transit of a distant world as it traversed the face of its parent star.
Morley is now a sixth-year graduate student , enrolled in the Ph.D. program in Astronomy and Astrophysics at UC Santa Cruz. Incorporating physics, chemistry, and atmospheric science, she creates computer simulations of the types of clouds that might form on alien worlds.
Some of the speculations are truly exotic: A giant planet close to its parent star might be heated to 1,000 or 2,000 degrees Fahrenheit, meaning that rather than clouds made from condensed water droplets the atmosphere would contain billowing patches of vaporized rock.
Morley’s models predict how the light reflecting off these outlandish worlds might appear to astronomers on Earth, which could one day give researchers insight into the composition of real-life exoplanets.
Because we cannot yet send probes to such distant places, the only window scientists have onto these worlds is through their atmospheres. Should organisms exist on another planet, they will likely alter its atmospheric chemistry, just as life on Earth has infused our atmosphere with oxygen. Morley looks forward to the day when simulations like hers include such biological factors. Perhaps in the future, an astronomer will know whether a distant world harbors life simply by looking at its light.
Because the field of exoplanet research is so young and dynamic, Morley loves her work. She says that new discoveries are so frequent that if she stopped paying attention for six months, she’d come back to find that everything had changed. That’s why she’s grateful for the ARCS Scholarship, which will help her attend conferences and stay connected to the latest research. And, as she will soon be on the market for a post-doctoral research position, traveling will serve a second purpose: meeting with colleagues outside her immediate field and perhaps finding her next career opportunity.
Outside of the lab, Morley indulges her adventurous side by skiing and hiking in California’s scenic places, such as Lake Tahoe. In the past year, she’s also taken up mountain biking. She and her boyfriend brew their own beer at home, often a variety of IPA. While studying at Santa Cruz, Morley has received an award for excellence in teaching and looks forward to being a professor one day. She likes to cultivate inquiry-based learning, where students develop their own questions to understand a process. “I think it’s very important in our society—where science is often being questioned—to give people a sense of how the scientific process works,” she says.
Adam Novak: Mapping Human Genetic Variation
Most people start to get dizzy when thinking about complex systems, but not ARCS Scholar Adam Novak of UC Santa Cruz. “They’re very exciting,” he says. “Sometimes I go out and intentionally find very difficult and complex systems to learn about for fun.”
Originally from Illinois, Novak completed his undergraduate degree at Harvey Mudd College in Claremont, California. There, he helped design a program that used virtual enzymes to transform food chemicals into specific products. As the simulation ran, the artificial enzymes evolved, trying to find the optimal way to generate their product. The idea was to model how certain protein subunits—like those making up the hemoglobin in our blood—work together to produce better results than an individual protein alone. Novak says the hardest part of the research was just getting the virtual enzymes to stop “cheating”: Instead of stumbling toward the best solutions, they would tweak their own settings, increasing the speed at which they worked, or maxing out the term controlling how well they cooperated.
So Novak is building software that can say: In this place, on chromosome 6, here’s what the reference genome expects to find, and here are seven or eight other possibilities that could be found there. This is an incredibly complex task, given that an individual human genome is 3 billion base pairs long, and this software needs to be a good representation of any of the 7 billion plus genomes out there. So far, he has created a program to map variation in the major histocompatibility complex, a section of our DNA controlling our immune response. That piece of our genetic code is 4 million base pairs long—still far from the goal, but showing that the approach is feasible.
Novak has also been working on a related venture, called the Global Alliance for Genomics and Health. He and his collaborators hope to adopt technological standards for exchanging information about genetic variation. This could be useful in a hospital of the future, where the DNA of all patients is sequenced as they come in for treatment. While scientists would like access to this data, a hospital would consider it highly sensitive.
With the Global Alliance's common standards, a researcher could run an online request asking a hospital database whether it has any genomes with some particular variation. Rather than hand over all the information and have the scientist comb through it herself, the database could simply respond yes or no, and then provide the number of genomes with that variation. Such common standards could help tie together many different genetic databases. This would allow researchers to statistically analyze large populations of people, helping to pinpoint what parts of our DNA correlate with which genetic diseases.
Novak hopes to use the ARCS Scholarship in part to travel to conferences. Science works only when researchers share their ideas, and Novak would like to discuss both his genome maps and genetic data standards with other teams. By talking with colleagues and figuring out how they might employ these tools, he hopes to expand the tools and make them more useful. In his spare time, Novak enjoys social dances such as blues dancing. He is an active amateur radio operator, and founded the Santa Cruz Meshnet Club, which aims to create free access public computer networks as an alternative to those offered at a fee by private companies.