daily herald science & research THE BROWN
SCIENCE & RESEARCH ROUNDUP BY PHOEBE DRAPER, SCIENCE & RESEARCH EDITOR
Human odometer Humans continually estimate distances — whether while guessing if there is enough time to cross the street before a car passes by, calculating how far a Frisbee should be thrown or pondering how long it will take to walk to the mall. The internal human odometer was the subject of a recent study conducted by researchers in the Department of Cognitive, Linguistic and Psychological Sciences. The researchers sought to discover whether a human’s ability to estimate distances was internal or based on external inputs. Subjects of the study first traveled an “outbound” distance and then attempted to travel the same distance they initially traveled. The researchers used a variety of locomotive methods — subjects walked, galloped and threw objects to estimate distances. Subjects estimated distances more accurately when the distance input was the same as the output used to estimate that distance. For example, subjects were better at estimating distances originally galloped when they galloped to replicate it rather than walking. The findings support what the researchers called the “intrinsic model” of human distance estimation: the idea that humans can more accurately predict distances when they can embody the distance, rather than objectively estimate it.
Cancer genetics Dendrix, a computer-based algorithm designed by Brown computer scientists, offers much promise for untangling the genetic mapping that may lay the foundation for 12 different types of cancer, including breast, lung, colon and kidney. Dendrix scours genetic codes to pinpoint spots in the human genome where mutations can predispose people to certain cancers. Ben Raphael, associate professor of computer science, Fabio Vandin, adjunct assistant professor of computer science, and a host of graduate students designed the algorithm. The program has identified numerous locations on the genome common to many forms of cancer where, if mutation occurs, the individual is predisposed to cancer. Along with a preexisting algorithm also developed by Brown computer scientists, Dendrix has helped scientists map out the genetic infrastructure of a blood cancer called Acute Myeloid Leukemia. The algorithm is part of a project called The Cancer Genome Atlas, which works to increase understanding of the genetic basis of cancers.
Econometric recognition The Econometric Society named Roberto Serrano, chair of the economics department, as a new fellow Nov. 3. Serrano, who specializes in microeconomic theory and game theory, has worked in areas such as bargaining theory and the economics of risk, according to his Brown research profile. He has taught numerous undergraduate and graduate courses such as ECON 0110: “Principles of Economics,” ECON 1110: “Intermediate Microeconomics” and ECON 1870: “Game Theory and Applications to Economics.” He has also published two books: “A Short Course in Intermediate Microeconomics with Calculus” and “Welfare Economics and Social Choice Theory.” As a fellow, Serrano will meet with other international leaders in the field throughout the year at numerous conferences around the world. The society’s members aim to unite the fields of statistics and mathematics with economic theory.
WEDNESDAY, NOVEMBER 13, 2013
U. research shapes science startups
The Science Coalition recognized four companies developing products based on Brown research By STEVEN MICHAEL SENIOR STAFF WRITER
Academics have escaped the ivory tower and are using research findings in attempts to better the world. A recent report from the Science Coalition, an advocacy group of research universities including Brown, highlighted nearly 200 startup companies that were directly inspired by academic research. The report included four companies founded based on research done at Brown. “Given the times, we are in for tight funding at the national level. We want to show Washington the bang for the buck they’re getting” from federally funded university research, said Tim Leshan, president of the Science Coalition. To compile the list, member universities submitted the names of companies whose products stem directly from university research, Leshan said. Research to drug development Researchers often first seek to understand basic mechanisms in life sciences that do not have obvious business implications. But discoveries can lead to commercial ventures, as was the case for Professor of Neuroscience Justin Fallon and former Professor of Neuroscience Mark Bear PhD’84, who is now a professor of neuroscience at the Massachusetts Institute of Technology. Fallon researches how muscular memory works through neural synapses. His work led to the discovery of a protein that could potentially serve as a treatment for Duchene’s muscular dystrophy, he said. “It was a lot of basic science with an eye toward what we know about disease,” he said. Once Fallon showed that the protein can be delivered throughout the body, it opened the door for the development of a commercial therapy. Fallon co-founded Tivorsan Pharmaceuticals with John Nicholson ’72 and Joel Braunstein, and currently serves as its chief scientific advisor. Bear’s story mirrors Fallon’s. He was investigating changes in neural synapses when his team discovered
a mechanism that might play a role in Fragile X syndrome. Fragile X is a leading cause of inherited mental disabilities, including autism, Bear said. The discovery of the mechanism behind Fragile X enabled them to develop novel treatments for the disorder, he said. Bear found an outside investor and an executive to co-found and run Seaside Therapeutics, a pharmaceutical company of which he became the scientific advisor. When professors commercialize their research, outside investors and executives are frequently brought in to run these startup companies. “I have insights into how synapses work, but I have a lot to learn about drug development,” Bear said. “My full time job is a professor.” Both companies are still testing their new drugs. Though big pharmaceutical companies initially balked at Seaside Therapeutics’ approach to targeting Fragile X, the startup is now partnering with pharmaceutical giant Roche on the phase two clinical trials of a medication, Bear said. Tivorsan is still waiting on approval from the Food and Drug Administration on their new drug before clinical trials, which they hope to begin next year, Fallon said. Though Tivorsan plans to conduct its own clinical trials,,the company is also open to forming a partnership with a larger company, Fallon said.
Producing patents Professors’ academic pursuits can also catalyze business ventures through patenting new inventions. The Technology Ventures Office handles patents produced by University researchers and works with startups, said Katherine Gordon, managing director of the office. In order to develop a product based on University research, a company must sign a licensing agreement with the office. About one company per year is founded based on ideas or developments from Brown research, a number that does not include companies started by alums, she said. After expenses, the inventor receives one-third of the royalties from a licensing agreement, according to the Brown University Patent and Invention Policy and Copyright Policy. “I strongly believe that patenting is
an important thing for the University to be pursuing,” said Harvey Silverman MS’68 PhD’71, professor of engineering. “In the long run, it can be a very good income stream for the University.” Silverman developed microphone arrays — groups of microphones that record sound together — that were licensed by both Polycom, a large telecom company, to protect itself from a patent lawsuit brought by a competitor, and Acoustic Magic, a startup building the devices. Though Silverman has no involvement in Acoustic Magic, the company, which is currently producing and selling microphone arrays, was included on Science Coalition’s list. ‘Unpleasant disputes’ Nabsys, a company developing DNA sequencing technology, claimed the final spot on Science Coalition’s list of Brown-based companies. The company has currently raised $41 million on venture capital, including $20 million this year — but not without ruffling a few feathers. Two different research projects led by University faculty merged to form Nabsys, which is based in the Jewelry District. Professor of Physics Xinsheng Sean Ling developed a better method of DNA sequencing, using an electrical current to force DNA through a small hole called a nanopore to “proofread” it, he said. “I think it’s possible to sequence DNA using physics alone,” Ling added. Ling founded Nabsys to commercialize the technology with his former student Barrett Bready ’99 MD ’03, who serves as the company’s president and CEO. In 2004, Nabsys merged with GeneSpectrum, another DNA sequencing company founded on University research. GeneSpectrum commercialized algorithms to compile DNA sequencing data developed by Professors of Computer Science Eli Upfal and Franco Preparata and former Assistant Professor of Chemistry John Oliver, Bready said. Sequencing techniques employed by other companies were like mapping a city based on Facebook photos, Bready said, while Nabsys’ approach to sequencing was comparable to a satellite map with a big picture view. Nabsys has yet to commercialize its technology, but Upfal said the company has developed prototypes. Startups begin with a certain idea that changes » See STARTUPS, page 5
Study links high school violence, standardized test scores Violent crime may disrupt the learning environment, preventing the curriculum from covering key material By ALEXANDRA SAALI CONTRIBUTING WRITER
High school students’ standardized test scores are adversely affected by violent crime’s presence in Chicago schools, according to new research by Julia Burdick-Will, a postdoctoral researcher in Brown’s Population Studies and Training Center. By linking high schools with the location of violent incidents from 2002 to 2010 — data made publicly available by the Chicago Police Department — Burdick-Will found an inverse relationship between violent crime rates in Chicago schools and
student test scores, but not between crime rates and grades. Violent crime likely affects learning through “cognitive stress and classroom disruption,” rather than through “changes in perceived safety, general school climate or discipline practices,” Burdick-Will wrote in her paper, which was published in the journal Sociology of Education last month. Crime likely affects test scores but not grades because the metrics reflect “different kinds of achievement,” she said. “Grades are more subjective
— they come from teachers. They are a more global measure of more than actual content knowledge,” BurdickWill said. Test scores, she said, reflect a student’s knowledge and ability to concentrate. “Some kids will be doing ‘A’ quality work, but their class will only have gotten halfway through the textbook, leading to low standardized test scores,” she added, which suggests that “violent crime is an indicator of disruptive instruction.” In her paper, Burdick-Will also offered alternate, non-causal explanations for the relationship between violent crime and student performance. For example, lower-achieving students are likelier to commit violent crimes, she said, meaning
crime itself might not cause lower test scores. “Perhaps the association between violent crime at school and achievement is really caused by students from disadvantaged neighborhoods bringing the violence they experience around their homes onto school grounds,” Burdick-Will wrote in her paper. “Her research gets us thinking about educational policy in a broader and more sophisticated way. How do we address community problems not just schools?” said Josh Pacewicz, an assistant professor of sociology who was not involved in the research. Burdick-Will also investigated the “influence of neighborhood poverty” on violence and school performance,
finding “a lot of variation in highpoverty schools and neighborhoods,” she said. She examined past research on students’ perception of the safety of their school environment, finding little connection between how safe students felt and the level of reported crime. She found that nonviolent crime has a much smaller effect on student performance and does not influence students’ perceptions of their schools’ climates. Burdick-Will said she now plans to further investigate how violent crime affects school choice and student achievement in certain neighborhoods, examining “patterns across the country.”