Participants of last year's Human Library event.
Photo by Rachael Eyler, Stony Brook University
By Daniel Dunaief
Stony Brook University is providing another opportunity for students and the community to venture beyond the labels that define and, at times, limit our views and understanding of each other.
Chris Kretz
For the second year, the university is hosting the Human Library, which gives participants an opportunity to learn about other people’s lives.
Started in 2000 in Denmark, the Human Library brings “books” (people from different walks of life, which has included a refugee, disabled parent, and person with bipolar disorder) with “readers,” who have a chance to ask questions for 30 minutes with each book.
The chapters these books share has surprised readers and given them a chance to reconsider how they view people whose lives or life experiences are different from their own.
“It’s not meant to teach people something or have them leave being converted to some new thought process,” said Chris Kretz, Head of Academic Engagement at Stony Brook University Libraries. “It gives [readers] an opportunity to speak with someone they may never normally encounter or have a conversation they may not get to have.”
The Human Library event occurs on Wednesday, Nov. 20 from noon to 3 p.m. and from 5 p.m. to 7 p.m. at the Frank Melville Jr. Memorial Library’s Central Reading Room. Participants don’t need to pre-register and can show up at the library, where about 110 readers visited last year.
Kretz recommended the latter session for interested community members, which would allow them to park for free to attend the event.
Following the defined structure created by the original Human Library, attendees won’t know about the specific backgrounds of the books until they arrive. The people that represent the books will all sit at desks wearing the same black t- shirts.
“In the conversation, the colors come out,” Kretz said.
Indeed, Richard Tomczak, Director of Faculty Engagement in the Division of Undergraduate Education at SBU and a reader at last year’s Human Library, can attest to that. Tomczak spoke with a book who grew up in the outer boroughs of New York as a member of the working class.
“When you’re having a conversation about shared experiences or experiences that are new to you, it brings out the human characteristics,” said Tomczak. “I wanted to listen and absorb it all.”
Choosing a book
When readers sit down, the book offers a prologue about their lives, providing some details about their experiences. Readers who aren’t sure where to start asking questions or perusing through different chapters in the book can use prompts at each desk to begin their interaction. Readers who stay for an entire sessionwill be able to interact with three or four books.
Participants of last year’s Human Library event. Photo by Rachael Eyler, Stony Brook University
“This is an opportunity for people to hone their conversational skills,” said Kretz, as well as to learn about the lives of the books who are offering details that may surprise and move the readers.
Indeed, this year, the university is stocking tissues near each book for those readers who may feel particularly touched by the stories they hear.
The university would like to ensure that the conversation is respectful and that both sides are comfortable with the discussion.
“We have rules for readers,’ said Kretz. “When they sit down with the book, the pages are in mint condition. We want to make sure everyone is on the same page. Books don’t necessarily have to answer every question.”
Kretz urged attendees to recognize that the interaction is not a debate, but presents ways for people to understand more about their own judgments and, as the Human Library website suggests, to “unjudge” each other. In addition to speaking and asking questions, readers and the books will have a chance to process what they’ve heard.
“By design, it’s a session where you have to listen,” said Kretz. “One of the values is that people get a chance to practice this muscle.”
Second year
In the second iteration of the Human Library, Stony Brook added the later time so people could come after work. The administrators have also reached out to journalism classes and to people in international programs.
Students from other countries will “have a chance to meet people they wouldn’t have met” during their time abroad, Kretz added.
After speaking with the people who served as books last year, Stony Brook heard that the books also wanted to serve as readers of some of the other people’s lives.
University officials were pleased with the exercise last year.
“I’m impressed by how open our community was,” said Kretz. “People learned a great deal from listening to each other.”
The university is considering making this an ongoing annual tradition and might even bring people together each semester.
Other New York schools and libraries have embraced the Human Library process, including Adelphi and SUNY Albany. The Human Library has also caught on globally, as people in 85 countries on six continents have helped facilitate these conversations.
While the participants engage in meaningful discussion, the exchange isn’t designed to create a lasting social network or lead to ongoing connections between the readers and the books.
“It’s not meant for them at the end of the reading to shake hands and exchange business cards,” explained Kretz.
The event is sponsored by the University Libraries and the DEIA (Diversity, Equity, Inclusion, Accessibility) Team with the Division of Student Affairs, Office of Diversity Inclusion and Intercultural Initiative, Office of Military and Veteran Affairs, and Diversity, Intercultural and Community Engagement, and the Program in Public Health.
A male mouse embryo surrounded by a group of female embryos during development in some cases is protected against developmental delays caused by a viral infection of their mother.
That’s one of a host of intriguing observations and findings from a recent set of experiments conducted by postdoctoral researcher Irene Sanchez Martin, who works in the lab of Assistant Professor Lucas Cheadle at Cold Spring Harbor Laboratory.
Irene Sanchez Martin and Lucas Cheadle at Cold Spring Harbor Laboratory. Photo by Justin Park
Sanchez Martin is studying how maternal exposure to viruses triggers immune responses, particularly inflammation, which can contribute to developmental delays characteristic of autism.
In mice as in humans, males are much more susceptible to the onset of the kinds of neurological developmental behaviors that are characteristic of autism than their female counterparts.
“The advantage of our model is that it helps us understand why this happens, providing insights into the underlying mechanisms driving this increased vulnerability in males,” Sanchez Martin explained.
Researchers have been studying viral exposure and developmental disorders for a while. The new element in Sanchez Martin’s research is that she can observe phenotypic changes as early as 24 hours after a pregnant mouse is exposed to a virus, providing a much earlier window into how maternal immune activation affects development.
At an early stage of gestation, when sensory organs, the head, spine and other organs are starting to develop, the male mice demonstrate disruptions in normal development, which affects these structures in different ways. Sanchez Martin hopes these kinds of studies help uncover the pathways through which environmental factors contribute to the development of some cases of autism.
Sanchez Martin’s work is part of a broader effort in Cheadle’s research.
“My lab is interested in understanding how interactions between the nervous system and the immune system shape the development and plasticity of the brain,” Cheadle explained. One goal is to understand how systemic inflammation during prenatal stages leads to heightened risk of autism in offspring.
To be sure, the genetic component suggests that inflammation is not necessary for the development of autism. Nevertheless, exposure to prenatal inflammation can increase autism risk by about three times, making inflammation a likely “key contributor to the development of autism in some, but not all, individuals,” said Cheadle.
Sanchez Martin found that female mice did not develop the same changes as males. She believes this is one of the most valuable applications of the model she’s working on with Cheadle, as it can reveal the biological and developmental differences that contribute to this gender disparity.
Timing
Sanchez Martin studied mice that were exposed to a virus between 12 to 13 days after fertilization, which is similar to the end of the first trimester in a human embryo. Mice develop more rapidly, so the process doesn’t track exactly the same as it would in humans.
About a day after the maternal exposure, some males looked different through ultrasound than they would during typical development. The differences are subtle and it is still too early to assume these changes could serve as a diagnostic marker for autism spectrum disorder.
A host of disruptions could affect the growth of the embryo. The placenta serves as a bridge between the mother and the developing embryo, allowing communication, filtering substances, and protecting the embryo during development. Each mouse embryo has its own placenta and its own amniotic fluid in its amniotic sac, creating a unique microenvironment.
In her lab work, Sanchez Martin is collaborating with Dr. Brian Kalish at Boston Children’s Hospital, who is helping to analyze molecular changes in the placentas of affected and unaffected embryos. Sanchez Martin has data indicating differences between the placentas of affected and healthy individuals, as well as in the amniotic fluid.
“This suggests a dysfunction in the placenta in affected cases” indicating it is not adequately performing its protective and filtering function, she explained.
Female mouse embryos may be more protected in part because of their more active immune response. Other studies have shown that female immune systems, as early as the developmental stage, express higher levels of interferon-stimulated genes and have stronger responses to infections, which may offer better protection than males.
While male mice in some cases benefit from the protection provided by their nearby sisters, Sanchez Martin and Cheadle are “still working to fully understand the underlying mechanism,” she explained.
Epidemiology
By looking at the prevalence of conditions such as autism in the aftermath of larger viral infections, researchers have demonstrated that these illnesses can and do have impacts on the incidence of autism and schizophrenia, among other conditions. It’s not only the pathogen that is responsible, but also the immune response triggered by the infection, as well as the timing of the infection during pregnancy.
Covid, which infected over 100 million Americans, may cause an increase in the number of children born with autism.
“There is precedent from studies of other viral infections during pregnancy, which suggest that maternal immune activation can contribute to altered neurodevelopment in offspring,” Sanchez Martin said. “There is some evidence that male children exposed to SARS-CoV-2 during pregnancy might have a slightly elevated risk of other neurodevelopmental disorders.”
Additional research with longer-term follow up is necessary to confirm these findings. The timing and the immune response during pregnancy could be key factors in determining the outcomes.
Cheadle appreciated the effort and dedication of Sanchez Martin, whom he described as being “bright, talented, motivated and an excellent experimentalist. Her work is among the most important projects in the lab.”
From Madrid to CSHL
Born and raised in Madrid, Spain, Sanchez Martin has been a master of motion. During her final years of her Veterinary Medicine studies at Universidad Alfonso X El Sabio in Madrid, she moved to the University of Helsinki to complete her clinical rotations.
She later earned her PhD at the Centre National de la Recherche Scientifique in Marseille, France and defended her thesis at the Aix- Marseille University. During her PhD, she was a visiting student at Biocenter Oulu in Finland.
Her first job was at Laboklin in Bad Kissingen, Germany, where she worked in a clinical laboratory.
She did her first postdoctoral research in the Microbiology Department at Mount Sinai. During the pandemic, she was involved in studying innate and adaptive immune responses in different in vitro models, focusing on vaccine candidates for Covid-19 and influenza.
A resident of Manhattan, Sanchez Martin has contributed to Cheadle’s lab for two years.
She enjoys listening to classical music, reading, and swimming, which she likes to do several times a week as she has some of her best ideas when she’s in the water.
As for her work, Sanchez Martin appreciates the opportunity to conduct her research as a part of Cheadle’s team that is hoping to identify the molecular mechanisms that contribute to autism in mice.
“It’s an ongoing effort and we hope that with time and collaboration, we can gain more insight,” she explained.
In the nucleus of the cell, researchers often focus on the genetic machinery, as the double-helical DNA sends signals that enable the creation of everything from my fingers that are typing these words to your brain that is processing what you’ve read.
But DNA, which occupies most of the nucleus, is not alone. Scattered through the nucleus are protein and RNA filled structures that have an influence on their important gene-bearing nuclear cohabitants, including speckles.
One of the newest members of the Cold Spring Harbor Laboratory team, Assistant Professor Kate Alexander, who joined the lab in August, is focused on a range of questions about these speckles, which represent about 10 to 30 percent of the nuclear volume.
Preliminary data from Alexander’s lab support the idea that speckles can signal how a person responds to various types of therapy, although careful extensive follow up studies are needed, Alexander explained. She would like to know how the speckles are affecting the genetic machinery.
While speckles have been known since 1910, the ways they affect healthy cells and diseased cells remains a mystery. In some cases, normal or aberrant speckles can signal how a person responds to various types of therapy.
Normal speckles are in the center of the cell nucleus, while aberrant speckles are more scattered. Aberrant speckles can activate some of the surrounding DNA.
At this point, Alexander and her colleagues have “found that normal or aberrant speckle states correlate with survival of clear cell renal cell carcinoma. This accounts for over 80 percent of all kidney cancers.”
Medical choices
After a patient with clear cell renal cell carcinoma receives a cancer diagnosis, the first line of treatment is usually surgery to remove the tumor in the kidney. In addition, doctors could treat the tumor with a systematic anti-cancer therapy. The treatments themselves can and often do cause difficult side effects, as therapies can harm healthy cells and can disrupt normal biological functioning.
Normal speckles look something like the face of the man on the moon and are more centrally located.
Alexander is hoping speckles will help predict the state of the tumor, offering clues about how it might respond to different types of treatments. She could envision how aberrant speckles could correlate with better responses to one drug, while normal speckles might correlate with better responses to another treatment.
In her research, Alexander is exploring how DNA is organized around speckles, as well as how the speckles affect DNA.
“Speckles can change and impact what’s happening to all the DNA that’s surrounding them,” she said.
Over 20 tumor types show evidence for both normal and aberrant speckles. Aberrant tumors can occur in many types of cancer.
“The consequence of [speckles] becoming normal or aberrant are starting to become more clear,” she said, although there is “still a lot to learn.”
Alexander is trying to figure out how to alter the conformation of these speckles. During cancer, she suspects these speckles may get trapped in a particular state.
In one of the first experiments in her lab, she’s culturing cells in an incubator and is trying to predict what cues may cause speckles in those cells to switch states.
‘Speckle club’ leader
Alexander previously did postdoctoral research at the University of Pennsylvania in the laboratory of Shelley Berger, where she was also a Research Associate. She led a subgroup in the lab known as the “speckle club.”
Charly Good, who is now Senior Research Investigator in Berger’s lab, worked with Alexander at Penn from 2017 until this summer.
Aberrant speckles are scattered throughout the nucleus.
Alexander “helped recruit me to the postdoc I ended up doing,” said Good who appreciated Alexander’s computational skills in analyzing big data sets. Speckles represent an “up and coming area” for research, which Alexander and Berger are helping lead, Good suggested.
Alexander’s quick thinking meant she would go to a talk and would email the speaker as soon as she got back to her desk. “Her brain is always spinning,” said Good.
Alexander is building her lab at CSHL. Sana Mir is working as a technician and is helping manage the lab. Recently, Hiroe Namba joined the group as a postdoctoral researcher. In the next few years, Alexander would like to add a few graduate students and, within five years, have about eight people.
Originally from Tigard, Oregon, Alexander attended Carleton College in Northfield, Minnesota. In her freshman year, she tried to get into a physics class that was full and wound up taking a biology class. She was concerned that biology classes were mostly memorization. When she started the course, she appreciated how the science involved searching for missing pieces of information.
Cold Spring Harbor Laboratory appealed to her because she could go in whatever direction the research took her.
For Alexander, scientific questions are like a layer of cloth with a few threads sticking out.
“You see one sticking out and you start to pull,” Alexander said. “You don’t necessarily know what’s going to come out, but you keep getting the urge to pull at that thread. You realize that it is connected to all these other things and you can look at those, too.”
She is excited to cross numerous disciplines in her work and is eager to think about how her research might “interplay across those fields and boundaries.”
Speckle origins
As for speckles, Alexander observed during her postdoctoral research how one factor seemed to influence a neighborhood of genes.
For that to occur, she realized that something had to affect those genes at the same time in the physical space. She hadn’t known about speckles before. A few of her colleagues, including Good, came across speckles in their analysis. That made Alexander curious about what these speckles might be doing.
She saw an opening to pursue connections between changes in these potential gene activators and illnesses.
Researchers know that viruses can use speckles to help them copy themselves.
If they are used by viruses “they must be important” and they “probably go wrong in a lot of diseases,” Alexander said. There are a series of neurodevelopmental disorders called “speckleopathies” that involve mutations in proteins found inside speckles.
“We have the computational and experimental tools to start investigating them across a wide variety of conditions,” she said.
Stony Brook University researchers Fusheng Wang and Dr. Richard Rosenthal
By Daniel Dunaief
Health care providers can use all the help they can get amid an ongoing opioid epidemic that claims the lives of 130 Americans each day.
In a cross-disciplinary effort that combines the computer science skills of Fusheng Wang and the clinical knowledge and experience of doctors including Dr. Richard Rosenthal, Stony Brook University is developing an artificial intelligence model that the collaborators hope will predict risk related to opioid use disorder and opioid overdose.
Fusheng Wang
Wang, a Professor in the Department of Biomedical Informatics and Computer Science at Stony Brook and Rosenthal, a Professor in the Department of Psychiatry and Behavioral Health in the Renaissance School of Medicine, received a $1.05 million, three-year contract from the independent funding organization Patient-Centered Outcomes Research Institute (PCORI).
“We have patients, clinical stakeholders, clinician scientists and community-based people within the system of care that have an interest at the table in the development cycle of this AI mechanism from day one,” Rosenthal said. The PCORI required that the scientists identify these stakeholders as a part of the research strategy.
The Stony Brook researchers are combining data from Cerner, a major electronic health record vendor under an institutional data usage agreement, with an awareness of the need to create a program that doctors can use and patients can understand.
Traditional public health studies rely on analyzing incidents that occurred. This approach, however, can be applied to population health management through early interventions, Wang explained.
With artificial intelligence, computer scientists typically plug enormous amounts of data into a model that searches through individual or combined factors and comes up with a prediction through a deep learning process.
The factors, which may be in the hundreds or even more, that contributed to the conclusion about a risk level aren’t always clear, which makes them difficult for doctors to explain and for patients to understand. Many of the factors may not be clinically intuitive.
Deep learning models can provide certain types of information about the prediction, such as a ranking of top factors. These factors, however, may not necessarily be clinically relevant, Wang explained.
To balance the need for data-driven analysis with the desire to create a product that people feel confident using, the scientists plan to become a part of the process.
“We are all going to educate each other,” said Rosenthal. “Patients will tell you what it means to be a patient, to be at the receiving end of some doctors telling them something they don’t know” while each group will share their lived experience.
Each participant will be a student and a teacher. Rosenthal believes this stakeholder in the loop approach will create a tool that is clinically relevant.
“There’s an opportunity to produce a highly accurate predictive mechanism that is highly acceptable based on transparency,” he said.
To be sure, people involved in this process could deemphasize a factor that doesn’t make sense to them, but that might otherwise increase the predictive accuracy of the developing model.
“This might come at the expense of the performance metric,” Rosenthal said.
Still, he doesn’t think any human correction or rebalancing of various factors will reduce the value of the program. At the same time, he believes the process will likely increase the chances that doctors and patients will react to its prognosis.
A program with a personal touch
Wang created the model the scientists are using and enhancing. He reached out to several physicians, including Director of the Primary Care Track in Internal Medicine Rachel Wong and later, Rosenthal, for his addiction research expertise.
Dr. Richard Rosenthal
Rosenthal started collaborating on grant proposals focused on big data and the opioid epidemic and attending Wang’s graduate student workgroup in 2018.
Wang recognized the value of the clinician’s experience when communicating about these tools.
“Studies show that patients have lots of skepticism about AI,” he explained. Designing a tool that will generate enough information and evidence that a patient can easily use is critical.
The kind of predictions and risk profiles these models forecast could help doctors as they seek the best way to prevent the development of an addiction that could destroy the quality and quantity of their patients’ lives.
“If we can identify early risk before the patient begins to get addicted, that will be extremely helpful,” Wang added.
If opioid use disorder has already started for a patient, the tool also could predict whether a patient has a high chance of ending treatment, which could create worse outcomes.
Refinements to the model will likely include local factors that residents might experience in one area that would be different for populations living in other regions.
Depending on what they learn, this could allow “us to frame our machine learning questions in a more context-dependent population, population-dependent domain,” Rosenthal said.
Opioid-related health problems in the northeast, in places like Long Island, is often tied to the use of cocaine. In the Southwest, the threat from opioids comes from mixing it with stimulants such as methamphetamines, Rosenthal added.
“Localization increases the accuracy and precision” in these models, he said.
Eventually, the model could include a risk dashboard that indicates what kind of preventive measures someone might need to take to protect themselves.
The scientists envision doctors and patients examining the dashboard together. A doctor can explain, using the model and the variable that it includes, how he or she is concerned about a patient, without declaring that the person will have a problem.
“Given these factors, that puts you at greater risk,” said Rosenthal. “We are not saying you’re going to have a problem” but that the potential for an opioid-related health crisis has increased.
Unless someone already has a certain diagnosis, doctors can only discuss probabilities and give sensible recommendations, Rosenthal explained.
They hope the tool they are developing will offer guidance through an understandable process.
“At the end of the day, the machine is never going to make the decision,” said Rosenthal. With the help of the patient, the clinician can and should develop a plan that protects the health of the patient.
“We’re aiming to improve the quality of care for patients,” he said.
It’s back, bigger than ever, with an added Peter-and-the-Wolf style musical debut.
This year’s version of Science on Stage at Stony Brook University, which brings together the research and life experiences of three scientists with the artistic interpretation and creative talents of three playwrights, focuses on the theme of climate change.
Before the reading of the plays at the free October 28th event at the Staller Center’s Recital Hall, a group of eight high school students and two graduate students will perform an original piece of music composed by Professor Margaret Schedel called “Carnival of the Endangered Animals” (see accompanying story below).
Christine Gilbert with graduate student Emily Gelardi. Photo by Conor Harrigan
The event, which has a seating capacity of 379, which is almost triple the potential audience size from last year, and requires advance registration, is sponsored by the Collaborative for the Earth (C4E).
The organizers of Science on Stage “want people to be thinking about [climate change] from new ways or with new perspectives,” said Heather Lynch, inaugural director of the C4E and Endowed Chair for Ecology and Evolution at Stony Brook’s Institute for Advanced Computational Science and Professor in the Department of Ecology and Evolution.
In these performances, professional actors, directed by Logan Vaughn, share a dramatic reading of the scripts, titled “Ghost Forest,” “Counterfactual,” and “Resplendence.” After the performance, the scientists and playwrights will participate in a question and answer session led by Lecturer J.D. Allen, who is managing editor of NPR affiliate WSHU.
Provost Carl Lejuez, whose office provides funding for the C4E, celebrated the ongoing collaboration between the humanities and the sciences.
“Science on Stage is one of our true interdisciplinary gems,” Lejuez explained. “In a time of such misinformation, the arts provide such a powerful vehicle to communicate science in accessible and inspiring ways.”
Indeed, in addition to hearing an original piece of music and listening to a reading of the plays, audience members will have the opportunity to share their perspectives on climate science before and after the performance.
Christine Gilbert, who holds a joint appointment at the School of Communication and Journalism and the School of Marine and Atmospheric Sciences and is one of the participating scientists, is conducting a study of the effect of the experience with audience members.
Attendees can participate in a short mobile-based survey before the plays and immediately afterwards. A social scientist, Gilbert will follow up with those members who are willing to engage in individual interviews in the weeks after the performance.
Event organizers wanted to know “what is it that’s so magical in the intersection between science, humanity and art” that drew a crowd so large last year that the fire marshal had to turn people away, said Gilbert.
By polling the audience, Gilbert, who was one of the people who couldn’t watch the show last year, hopes to explore the effect of teaching complex science in this forum.
She also hopes to assess how audience members feel after hearing more about climate change and plans to share what she learns with Stony Brook and with the broader scientific community through a published paper.
Heavy and humorous
The scientists and the playwrights appreciated the opportunity to learn from each other and to engage in a creative effort designed to use science, or the life of scientists, to appeal to audiences.
Lynch, who participated in the Science on Stage effort last year, suggested that this year’s plays are powerful and evocative.
“These are deep, adult serious issues,” she said, cautioning that the language includes some cursing and that the themes include loss, parenthood and grief. “This is not Disney.”
To be sure, the plays blend a wide range of emotions.
“With short plays that deal with heavier topics, playwrights will gravitate towards humor,” said Ken Weitzman, Founder and Associate Professor of Theater at Stony Brook, who started Science on Stage virtually in 2020. “It’s how we engage” and commune with an audience.
Counterfactual
Playwright Mat Smart
Author of the play “The Agitators,” about a true narrative describing the 45-year friendship between suffragist Susan B. Anthony and abolitionist Frederick Douglass, Smart said he has taken long Uber rides with people whose views differ from his, leading to spirited conversations.
When Smart described his experiences to Reed, they discovered they had similar interactions.
While much of the script involves a combination of conversations and ideas, Smart explained that part of the dialogue in the play came from a discussion he and Reed had about food choices and climate change.
The interaction about cheeseburgers is “based on something [Reed] said to me,” Smart said. Reed explained the high carbon footprint of a cheeseburger, although he urged Smart to cut back rather than eliminate them from his diet.
“The play is about two people who see things very differently who choose to have a dialogue and to have a tough conversation,” said Smart. “They’re both affected by it.”
Ghost forest
Playwright Gab Reisman
Elizabeth Watson, Associate Professor in the Department of Ecology & Evolution, teamed up with Gab Reisman, who wrote “Ghost Forest.”
In this play, a climate researcher’s subjects spring to life as she writes an important grant proposal.
While it doesn’t reflect how field research or grant writing typically goes, it does capture “some things that have happened to me,” Watson said.
Her field work has involved considerable challenges, including getting stuck in the mud, being covered in ticks, crawling across mudflats, and being abandoned on a raft in a lagoon.
Watson appreciates how the artistic effort allows her to connect with people who probably aren’t the same ones who would read a publication she wrote or come to a presentation.
She also added that the world has what it needs to deal with climate change and that people need to understand the kinds of partnerships and actions that make a difference.
Resplendence
Playwright Kareem Fahmy
After speaking with Gilbert, playwright Kareem Fahmy wrote “Resplendence,” which follows three generations of a family who try to save their island off the coast of Maine.
The New England State is an important setting for playwright and scientist.
“Maine has such a special place in my heart,” said Gilbert, who has family in the state and attended college at the University of Maine. The pull of the “wild, eastern coast of Maine is so ubiquitous.”
Gilbert appreciated how Fahmy did a “great job of personalizing the context” of the state.
The challenge of preserving destinations, particularly those close to sea level, will likely persist.
“When you do any research about climate change, you have to be aware that this is not just a problem for people living today, but for people 200 years from now,” Gilbert said.
Weitzman said the play was an epic despite its short running time and thought it was “quite touching.”
Beyond the performance
Weitzman suggested that the plays can provide an educational component beyond the confines of the Staller Recital Hall.
While people can’t produce the plays as part of paid entertainment, teachers can read and use them in the classroom. Actors Bill Heck, April Matthis, Tina Benko, Mandi Masden and Taylor Crousore will provide dramatic reading of the plays.
In a short time, the actors are “practically off the book,” as they embrace the opportunity to bring the words to life, Weitzman said.
He suggested the plays offer a glimpse into researchers’ lives. “Here is this person on the front lines. I’m surprised at the angles that are taken” in these plays.
Stony Brook University’s Staller Center for the Arts, 100 Nicolls Road, Stony Brook will present this year’s Science on Stage: Climate Edition on Monday, Oct. 28 at 4 p.m. Doors open at 3:30 p.m. The event is free and open to the public but reservations are strongly recommended.
To register, go to: https://bit.ly/4dcDtsi or click here.
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SBU’s Margaret Schedel brings endangered species to life through musi
Margaret Schedel discusses the ‘Carnival of the Endangered Animals’ with the band and conductor Justin Stolarik during rehearsal. Photo by Heather Lynch
Science on Stage at Stony Brook University added a new dimension to the performance this year, as Margaret Schedel, Associate Professor of Music, composed “Carnival of the Endangered Animals.” The original music, which will debut on Oct. 28 at 4 p.m. at the Staller Center’s Recital Hall, is a recreation of the sounds of a wide range of animals who are in danger of becoming extinct.
“It’s melodic, interrupted by moments of trying to translate” the calls from these animals, Schedel said.
Ken Weitzman, Founder and Associate Professor at Stony Brook, appreciates how quickly music can resonate for audiences.
“Music appeals to the emotions,” said Weitzman. “I’m jealous of how quickly music can do in 10 seconds what it takes me hours to do.”
The animals featured in the piece, along with the instrument that captures their sounds, are: the Atlantic Right Whale (Marimba); the A’kikiki bird, which is a Hawaiian honeycreeper (flute); Sumatran Tiger (trumpet); sage grouse (clarinet); Bajii, which is a Yangtze river dolphin; and the Jiangtun, which is a Yangtze finless porpoise (four-hand piano); gorilla (french horn); African bush elephant (trombone); Koala (bassoon); and the penguin (oboe).
Schedel plans to share information about each piece, which eight area high school students and two graduate students will perform, with the audience through a QR code, so they can connect the sounds with the message or visuals she was conveying.
Schedel tried to use a logical progression of the instruments, mixing up the woodwinds, percussion and brass.
Threatened by land development, the sage grouse includes high and low notes from the clarinet that gets covered up by the sounds of a flute and trumpet, imitating the sounds excavators make when they back up and develop McMansions.
Endangered by the spread of avian malaria carried by mosquitoes, the Hawaiian A’kikiki bird had been able to evade these insects by traveling higher up the mountain, where the colder temperatures kills the mosquitoes. That is not happening as much because global warming is enabling the blood sucking creatures to survive at higher elevation.
The sage grouse music starts with a melodic theme on the flute and as it goes higher, the theme becomes compressed. The buzzing brass, meanwhile, gets louder and louder as the mosquito pursues its meal, infecting the bird with a lethal parasite.
Reflecting the struggle for survival these creatures face, the Yangtze river dolphin, which had about 20 members when Schedel first started composing the music, may have become extinct by the time of the performance. That is, in part, why she combined the dolphin and the finless porpoise on the four hand piano.
As for the sounds of the elephant, Schedel recalled a safari she had experienced when she had been in South Africa. Elephants charged at Schedel and her group, who had come too close to the younger ones in the herd.
The elephants growled at Schedel and her companions.
“You can feel it in your chest, the sound waves moving,” she said. “Little by little, the younger ones put up their trunks and eventually a big momma elephant with a broken tusk put up her trunk, which is a symbol of, “we are calm,’” she said. With the trombone representing the elephant, the bass drum connotes its growling sounds.
When she was growing up, Schedel listened to the Leonard Bernstein version of “Peter and the Wolf” so many times that the recording is “nearly dead,” she laughed. She hopes people enjoy her piece with the same energy and excitement, connecting the sounds and the stories with the endangered animals.
Schedel described the experience of creating the music as a “labor of love.”
Shushan Toneyan and Peter Koo at Cold Spring Harbor Laboratory. Photo by Gina Motisi/CSHL
By Daniel Dunaief
The real and virtual world are filled with so-called “black boxes,” which are often impenetrable to light and contain mysteries, secrets, and information that is not available to the outside world.
Sometimes, people design these black boxes to keep concepts, ideas or tools outside the public realm. Other times, they are a part of a process, such as the thinking behind why we do certain things even when they cause us harm, that would benefit from an opening or a better understanding.
In the world of artificial intelligence, programs learn from a collection of information, often compiling and comparing enormous collections of data, to make a host of predictions.
Companies and programmers have written numerous types of code to analyze genetic data, trying to determine which specific mutations or genetic alterations might lead to conditions or diseases.
Left on their own, these programs develop associations and correlations in the data, without providing any insights into what they may have learned.
That’s where Peter Koo, Assistant Professor at Cold Spring Harbor Laboratory, and his former graduate student Shushan Toneyan come in.
The duo recently published a paper in Nature Genetics in which they explain a new AI-powered tool they designed called CREME, which explored the genetic analysis tool Enformer.
A collaboration between Deep Mind and Calico, which is a unit of Google owner Alphabet, Enformer takes DNA sequences and predicts gene expression, without explaining what and how it’s learning.
CREME is “a tool that performs like large-scale experiments in silico [through computer modeling] on a neural network model that’s already been trained,” said Koo.
“There are a lot of these models already in existence, but it’s a mystery why they are making their predictions. CREME is bridging that gap.”
Award winning research
Indeed, for her work in Koo’s lab, including developing CREME, Toneyan recently was named a recipient of the International Birnstiel Award for Doctoral Research in Molecular Life Sciences.
“I was genuinely surprised and happy that they selected my thesis and I would get to represent CSHL and the Koo lab at the ceremony in Vienna,” Toneyan, who graduated from the School of Biological Sciences, explained.
Toneyan, who grew up in Yerevan, Armenia, is currently a researcher in The Roche Postdoctoral Fellowship Programme in Zurich, Switzerland.
She said that the most challenging parts of designing this tool was to focus on the “interesting and impactful experiments and not getting sidetracked by more minor points more likely to lead to a dead end.”
She credits Koo with providing insights into the bigger picture.
New knowledge
Without taking DNA, running samples in a wet lab, or looking at the combination of base pairs that make up a genetic code from a live sample, CREME can serve as a way to uncover new biological knowledge.
CREME interrogates AI models that predict gene expression levels from DNA sequences.
“It essentially replicates biological or genetic experiments in silico through the lens of the model to answer targeted questions about genetic mechanisms,” Toneyan explained. “We mainly focused on analyzing the changes in models outputs depending on various perturbations to the input.”
By using computers, scientists can save considerable time and effort in the lab, enabling those who conduct these experiments to focus on the areas of the genome that are involved in various processes and, when corrupted, diseases.
If scientists conducted these experiments one mutation at a time, even a smaller length sequence would require many experiments to analyze.
The tool Koo and Toneyan created can deduce precise claims of what the model has learned.
CREME perturbs large chunks of input sequence to see how model predictions change. It interrogates the model by measuring how changes in the input affect model outputs.
“We need to interpret AI models to trust their deployment,” Toneyan said. “In the context of biological applications, we are also very interested in why they make a certain prediction so that we learn about the underlying biology.”
Using ineffective and untested predictive models will cause “more harm than good,” added Koo.“You need to interpret [the AI model’s] programs to trust them for their reliable deployment” in the context of genetic studies
Enhancers
Named for Cis Regulatory Element Model Explanations, CREME can find on and off switches near genetic codes called enhancers or silencers, respectively.
It is not clear where these switches are, how many there are per gene and how they interact. CREME can help explore these questions, Toneyan suggested.
Cis regulatory elements are parts of non-coding DNA that regulate the transcription of nearby genes, altering whether these genes manufacture or stop producing proteins.
By combining an AI powered model such as Enformer with CREME, researchers can narrow down the possible list of enhancers that might play an important genetic role.
Additionally, a series of enhancers can sometimes contribute to transcription. A wet lab experiment that only knocked one out might not reveal the potential role of this genetic code if other nearby areas can rescue the genetic behavior.
Ideally, these models would mimic the processes in a cell. At this point, they are still going through improvements and are not in perfect agreement with each other or with live cells, Toneyan added.
Scientists can use the AI model to aid in the search for enhancers, but they can’t blindly trust them because of their black box nature.
Still, tools like CREME help design genetic perturbation experiments for more efficient discovery.
At this point, the program doesn’t have a graphical user interface. Researchers could use python scripts released as packages for different models.
In the longer term, Koo is hoping to build on the work he and Toneyan did to develop CREME.
“This is just opening the initial doors,” he said. “One could do it more efficiently in the future. We’re working on those methods.”
Koo is pleased with the contribution Toneyan made to his lab. The first graduate student who worked with him after he came to Cold Spring Harbor Laboratory, Koo suggested that Toneyan “shaped my lab into what it is.”
Prateek Prasanna and Chao Chen at the NCI Informatics Technology for Cancer Research meeting in St. Louis in 2022.
By Daniel Dunaief
Cancer often involves numerous small changes before it become a full blown disease. Some of these alterations are structural, as otherwise healthy cells make subtle shifts that favor out of control growth that often defies the immune system and threatens the health of tissues, organs and the entire body.
Associate Professor Chao Chen and Assistant Professor Prateek Prasanna, both in the Department of Biomedical Informatics at Stony Brook University, recently received a four-year, $1.2 million grant from the National Cancer Institute to continue to develop an enhanced breast cancer imaging tool that could detect some of those changes.
Using advanced mathematical modeling and machine learning and working with clinical collaborators in radiology, radiation oncology, surgery and pathology, the researchers are developing a tool called TopoQuant. They hope they can provide a way to look at the changes in tissue architecture that occur during the growth and development of cancer and during radiation treatment.
Receiving the grant means “other researchers also think highly about the subject,” Chen explained. “This further boosts our confidence and is an approval for our effort so far.”
By combining two-dimensional and three-dimensional data, the Stony Brook researchers, including radiation oncologist Dr. Alexander Stessin, hope to provide an analytical tool that helps doctors and patients confronting cancer all the way from the early steps the disease takes to the ways it resists various treatments.
The researchers are using tomosynthesis and MRIs, both of which are three dimensional, and conventional mammographs, which are two dimensional.
Stessin will work closely to evaluate the efficacy of the TopoQuant framework to provide a predictive and useful interpretation of breast images.
The diagnostic and prognostic tool these scientists are developing has potential applications outside the world of breast cancer. The deep learning technique could help analyze images and information for other types of cancer as well as for various neurological challenges.
“In the tools we develop, a lot of the algorithms are domain agnostic,” said Prasanna.
The approach should work as long as the researchers can get structure-rich imaging data. To be sure, while this approach has had some promising early results, it has to proceed through numerous steps to help in the clinic.
In the meantime, the researchers plan to use the funds, which will support salaries and travel budgets for researchers, to continue to develop TopoQuant.
Chen and Prasanna envision providing physicians with an explanation of why artificial intelligence is guiding them towards a particular decision.
Doctors could “place more trust in a system like this,” Prasanna said. “It lends interpretability to an analysis that is typically more opaque.”
Healthy cells
When health care technicians gather information about breast cells, they often focus on developments in and around the cancer cells.
“The premise of the work” Chen and Prasanna are doing is to look at signals “even in the normal [healthy] areas of the breast, Prasanna said. “It’s important for physicians to look at these normal areas before they begin any treatment. What our tool lets them do is extract these signals.”
The process of developing this tool started about five years ago, as the scientists shared ideas and did preliminary studies. The work became more involved and detailed around 2020.
“The challenge is to have a harmonic combination between mathematical modeling and deep learning,” Chen explained. “Incorporating principled math modeling into deep learning is important yet not trivial.”
In their work, the researchers used phantom data called VICTRE from the Food and Drug Administration. They used simulated magnetic resonance images and validated that the method can extract the tissue structure faithfully across different breast density types. They are also using data from The Cancer Imaging Archive for initial model development.
At this point, the researchers have some evidence that the alpha version of the tool has been “promising” in the context of neoadjuvant chemotherapy, which they demonstrated in a paper they published in 2021.
The results from that study indicated different topological behavior of breast tissue characterized by patients who had different responses to therapy.
The researchers plan to continue to establish that the tools are properly characterizing what is happening. After that, they will validate the effort with a Stony Brook University Hospital cohort.
Clinicians from Rutgers are working with Chen and Prasanna and will do additional testing through external data sets.
Complementary skills
Chen and Prasanna, who have joint lab meetings and discuss their research every week, work in different parts of the campus. Chen’s lab is on the west campus, while Prasanna is in the east campus.
The researchers have combined their interests and skill sets to apply a computer science driven approach to medicine and the field of bioimaging analysis.
Chen does considerable work with topological information and machine learning. Prasanna, meanwhile, is also involved in the clinical world, combining his passions for engineering and medicine.
A native of Gansu Province in China, Chen lives near New York City and commutes to the university two or three times per week, working the other days from home and meeting with students and collaborators by Zoom.
When he first joined Stony Brook in 2018, Chen was concerned about jumping into a different department.
After visiting the department and speaking with Chair Joel Saltz and other faculty, he developed greater confidence when he learned of their passion for research, their research philosophy and the chemistry within the department.
Six years later, he thinks it was “the best career decision” he made.
A native of Cuttack, India, Prasanna and his wife Shubham Jain, who is in the faculty of Computer Science at Stony Brook, have worked together professionally.
The couple enjoys hiking and has been to 47 of the 63 national parks. One of their favorite parks is Katmai National Park and Preserve in Alaska.
Prasanna’s father’s family includes many physicians and his mother’s is involved in engineering. In his career, he has combined the professional focus from both sides of his family.
Early in his career, Prasanna worked on a project that used a smart phone to obtain fundus images of the eye to predict diabetic retinopathy.
At the time, he thought “this is where I want to be,” he recalled.
Ellen Pikitch at the United Nations when she spoke at the 9th International Day of Women and Girls in Science back in February. Photo from E. Pikitch
By Daniel Dunaief
Even as Covid threatened the health of people around the world, a group of 30 leading researchers from a wide range of fields and countries were exchanging ideas and actions to ensure the sustainability of ocean fisheries.
Starting in 2020, the researchers, including Stony Brook University’s Endowed Professor of Ocean Conservation Science Ellen Pikitch, spent considerable time developing operating principles to protect the oceans and specific actions that could do more than ensure the survival of any one particular species.
Earlier this week, the researchers, who come from fields ranging from biology and oceanography to social sciences and economics, published a paper titled “Rethinking sustainability of marine fisheries for a fast-changing planet” in the Nature Journal npj Ocean Sustainability, as well as a companion 11 golden rules for social-ecological fisheries.
The researchers, who were led by first author Callum Roberts, Professor of Marine Conservation at the University of Exeter, plan to share their framework with policy makers and government officials at a range of gatherings, starting with Brussel’s Ocean Week and including the United Nations Ocean Conference in Nice.
“We felt something like this was needed in order to reach these audiences effectively,” said Pikitch.
The extensive work, which included two series of workshops, outlines ways to regenerate the ocean’s health and to put people before profits.
The authors suggest that fisheries need to address their contributions to the climate crisis through activities that are polluting, such as dumping fishing gear or plastics in the ocean, carbon intensive or destructive, through the disturbance of sediment carbon stores.
The paper suggests that lost or discarded fishing gear often make up the largest category of plastic waste in the open sea. This gear is not only polluting, but leads to ghost fishing, in which fish die in abandoned or discarded nets.
The authors suggest that labelling fishing gear could encourage better stewardship of the ocean. They also argued that fisheries management has historically focused on economic output, without considering social value and effects.
“We take the view that marine life is a public asset, and its exploitation and management should work for the benefit of local communities and the public,” the authors wrote in their paper.
Pikitch described the work as an “urgent” call to action and added that the researchers will be “meeting with policy makers, retailers, fishery managers and others to discuss these results and how they can be implemented.”
The researchers engaged in this effort to find a way to compile a collection of best practices that could replace a hodgepodge of approaches that overlook important elements of sustainability and that threaten fish species as well as ocean habitats.
“Fisheries are in bad shape worldwide and are degrading rapidly with overexploitation and climate change,” Philippe Cury, Senior Emeritus Researcher at the Institute of Research for Development in Marseille, France, said in a statement. “Efficient and renewed fisheries management can really help to restore marine ecosystems and to reconcile exploitation and biodiversity.”
Pikitch anticipated that some might offer pushback to the suggestions. “If you don’t get pushback, you’re probably not saying something that is important enough,’ she said.
Ecosystem focus
Using research Pikitch led in 2004 from a paper in Science, the group constructed one of the 11 actions around developing a holistic approach to the ocean habitat.
Pikitch’s expertise is in ecosystem based fishery management.
“Fish interact with one another, feed on one another, compete with one another and share the same habitats,” Pikitch said. “For those reasons alone and more, we need to stop managing species one at a time.”
Some policies currently protect ecosystems, including the spatial and temporal management of the Canadian lobster fishery to protect whales and the no-take marine reserves to protect artisanal reef fisheries in the Caribbean.
Still, these approaches need to be applied in other contexts as well.
While some people believed that researchers didn’t know enough to create and implement holistic guidelines, Pikitch and her colleagues suggested that it’s not “necessary to know everything if we use the precautionary principle.”
Pikitch suggested that the Food and Drug Administration takes a similar approach to approving new medicines.
The FDA requires that researchers and pharmaceutical companies demonstrate that a drug is safe and effective before putting it on the market.
Fisheries are making some headway in this regard, but “much more is needed,” she said.
Subsidy problem
The authors highlighted how government subsidies are problematic.
“Many fisheries are highly carbon intensive, burning large quantities of fossil fuels often made cheaper by capacity-enhancing government subsidies,” the authors noted in the paper. “Among the worst performers in terms of fuel burned per tonne of landing gears are crustacean fisheries, fisheries that operate in distant waters, deploy heavy mobile gears like trawls, or target high value, low yield species like swordfish; most of them propped up by subsidies.”
When overfishing occurs, companies switch to catching less exploited species, even when they don’t have any data about new catches. The new species, however, soon become overfished, the authors argued.
In urging fisheries management to support and enhance the health, well-being and resilience of people and communities, the scientists add that abundant evidence of widespread human rights abuses occurs in fishing, including coercive practice, bonded, slave and child labor and unsafe, indecent and unsanitary living and working conditions.
“Abuses at sea continue and more needs to be done to stop this,” Pikitch explained.
Additionally, the authors hope to give a voice to the global south, which is “often ignored in many of these discussions about how to appropriately manage these fisheries,” she suggested.
A beginning
While the paper was published, Pikitch explained that she sees this as the beginning of change and improvement in creating sustainable fisheries policies. She anticipates that the collection of talented scientists will continue the work of protecting a critical resource for human and planetary survival.
“This group will continue to work together to try get this work implemented,” she said. “I’m enormously proud of the result.”
From left, Oscar Rivera-Cruz from the University of Puerto Rico, BNL materials scientist Anibal Boscoboinik, Alexander Bailey from West Virginia State University, and Jeremy Lopez from the University of Puerto Rico. Photo courtesy of BNL
By Daniel Dunaief
It’s been a banner year for ideas and potential products that trap noble gases at Brookhaven National Laboratory. So-named for their full complement of electrons, noble gases tend to be less reactive than other atoms that can add electrons to their outer shells.
While their name sounds grandiose, these gases are anything but, particularly when people inhale the radioactive and prevalent gas radon, which can cause lung cancer or when the decay of uranium into xenon makes a nuclear reactor less efficient.
When he was studying how hydrocarbons react at the active site of zeolite models, Brookhaven National Laboratory’s material scientist Anibal Boscoboinik made an accidental discovery about a decade ago that some nanomaterials, which are incredibly small, trap these gases.
Among several other projects he’s working on, Boscoboinik has since studied these nanocages, learning about the trapping mechanism and making variations of these materials and trapping methods that can be useful for a wide range of applications.
The Battelle Memorial Institute, which partners with Stony Brook University to form Brookhaven Science Associates and manages nine national labs across the country, named Boscoboinik an “inventor of the year” for his work developing these materials.
Battelle awards an inventor of the year to a researcher from each institution under its management, recognizing efforts that contribute to science or engineering and that can have a positive impact on society.
“It feels really good to be recognized for the work,” said Boscoboinik, who is proud of the many people who made this progress possible directly and indirectly. “It would be amazing if we get to see something that stemmed from an accidental discovery doing very basic fundamental research becoming a real-life application that can benefit society.”
At the same time, three students from minority serving institutions were selected to receive seed grants as a part of MSI (for Minority Serving Institutions) Connect at BNL, in which they seek to commercialize a way to remove radon from the air.
They may work in a business to business model to supply other companies that can incorporate their materials into products.
The students, Jeremy Lopez Flores and Oscar Rivera-Cruz from the University of Puerto Rico and Alexander Bailey from West Virginia State University, will enter phase 2 in the process. The next phase of funding comes from other sources, such as FedTech. Boscoboinik will advise the students as they develop the company and any potential products.
These undergraduate students are looking to remove radon from the air at a concentration of four picocuries per liter, which is equivalent to smoking eight cigarettes a day.
“I am certainly pleased that the value of our collective output was recognized,” said Bailey, who is from St. Albans, West Virginia, in an email. Bailey, a sophomore double majoring in chemistry and math, plans to attend graduate school after completing his undergraduate studies.
Rivera-Cruz, who is a senior majoring in Cellular and Molecular Biology, appreciated the guidance from Boscoboinik, whom he described in an email as an “incredible resource for the team” and suggested that the team was “extremely grateful and lucky” to have Boscoboinik’s support.
In other research
As a staff member at the Center for Functional Nanomaterials, Boscoboinik spends half his time working with scientists from around the world who come to the CFN to conduct experiments and half his time working on his own research.
The process of granting time to use the facilities at BNL is extremely competitive, which means the projects he works on with other scientists are compelling. “While I help them with their research, I get to learn from them,” he said.
Boscoboinik regularly works with the group of Professor Guangwen Zhou from Binghamton University. In recent work, they explored the dynamics of peroxide formation on a copper surface in different environments.
In his own work, Boscoboinik is also interested in trying to help the nuclear energy community.
During the breakdown of radioactive uranium, the process heats up water in a tank, moving a turbine that produces energy.
The breakdown of uranium, however, produces the noble gas xenon, which is a neutron absorber, making reactors less efficient.
Boscoboinik anticipates that any new product that could help the field of nuclear energy by removing xenon could be a decade or more away. “This is a highly regulated industry and changes in design take a very long time,” he explained.
Boscoboinik is also collaborating with researchers from Johns Hopkins University on metal organic frameworks. Some molecules pass through these frameworks more rapidly than others, which could enable researchers to use these frameworks to separate out a heterogeneous collection of molecules.
Additionally, he is developing processes to understand dynamic conditions that affect different types of reactions. At this point, he has been looking at the oxidation of carbon monoxide, which he called the “drosophila” of surface science for its widespread use and versatility, to develop the methodology. In oxidation, carbon monoxide mixes with oxygen to make carbon dioxide.
In his work, Boscoboinik has collaborated with Qin Wu, who deploys artificial intelligence to interpret the data he generates in his experiments.
The long-term plan is to develop complex-enough algorithms that suggest experiments based on the analysis and interpretation of data.
Outside the lab
Boscoboinik is a part of a collaborative effort to combine science and music. “We use music as a way to enable conversations between scientists and the general public” to help make the sometimes complex and jargon-laden world of science more accessible, he said.
In Argentina, research groups have taken famous musicians to the lab to perform concerts while encouraging conversations about science. During the course of their visits, the musicians speak with scientists for the benefit of the public. In prior seasons, the musicians used popular songs to relate to the research the scientists they interview do. Part of the plan is to make new songs related to the research.
Boscoboinik is part of a collaboration between Music for Science, the network of Argentinian scientists abroad, and the Argentinian diplomatic missions, including the embassies and the consulates. At some point in the future he may create a show that relates noble gases and music.
As with his some of his scientific work, the connection between music and research is a developing proof of concept that he hopes has broader appeal over time.
Minghao Qiu presenting at the American Geophysical Union Conference in San Francisco last year.
Photo courtesy of M. Qiu
By Daniel Dunaief
When Minghao Qiu woke up in Beijing on Jan. 12, 2013during his freshman year in college, he couldn’t believe what he was seeing or, more appropriately, not seeing. The worst air pollution day in the history of the city mostly blocked out the sun, making it appear to be closer to 8 p.m. than a typical morning.
Minghao Qiu
While Qiu’s life path includes numerous contributing factors, that unusual day altered by air pollution had a significant influence on his career.
An Assistant Professor at Stony Brook University, Qiu straddles two departments that encapsulate his scientific and public policy interests. A recent hire who started this fall, Qiu will divide his time equally between the School of Marine and Atmospheric Sciences and the Renaissance School of Medicine’s Program in Public Health.
Qiu studies fundamental questions in atmospheric sciences as they influence human health.
He is part of several new hires who could contribute to the climate solutions center that Stony Brook is building on Governors Island and who could provide research that informs future policy decisions.
Noelle Eckley Selin, who was Qiu’s PhD advisor at the Massachusetts Institute of Technology and is Professor in the Institute for Data, Systems and Society and the Department of Earth, Atmospheric and Planetary Sciences, suggested Qiu is a valuable scientific, policy and educational asset.
“Stony Brook is doing a lot to address climate in a serious way with great research,” Selin said. Qiu joining the institution “could really help out the university’s broader climate efforts and make them more impactful.”
Selin appreciated how Qiu was eager to dive deeper into questions, wanting to ensure that conclusions were valid and asking how to use data to test various ideas.
As a mentor, Qiu has proven inspirational.
“A lot of my current students will go and talk to him and come back to me and say, ‘[Qiu] had five excellent ideas on my project,’” Selin said. “That’s characteristic of how he works. He’s really generous with his time and is always thinking about how to look at problems.”
Policy focus
Using causal inference, machine learning, atmospheric chemistry modeling, and remote sensing, Qiu focuses on environmental and energy policies with a global focus on issues involving air pollution, climate change and energy transitions.
Qiu would like to address how climate change is influencing the air people breathe. Increasing heat waves and droughts cause people to use more energy, often through air conditioning. The energy for the electricity to power temperature controls comes from natural gas, coal, or fossil fuels, which creates a feedback loop that further increases pollution and greenhouse gases.
“Our work tries to quantify this,” Qiu said.
He also analyzes the impact of climate change on wildfires, which affects air quality.
In a research paper published last year, Qiu joined several other scientists to analyze the impact of wildfires on air quality.
The study, published in the journal Nature, found that since at least 2016, wildfire smoke eroded about a quarter of previous decades-long efforts to reduce the concentration of particulates above 2.5 microgram in several states.
Wildfire-driven increases in ambient particulates are unregulated under air pollution laws.
The authors showed that the contribution of wildfires to regional and national air quality trends is likely to grow amid a warming climate.
In his research, Qiu seeks to understand how to use energy and climate policy to address air pollution and greenhouse gases.
“Renewable energy and climate policy in general provides potential benefits,” Qiu said.
He uses publicly available data in his models.
New York pivot
While wildfires have been, and likely will continue to be, an area of focus for his work, Qiu plans to shift his focus to the kind of pollution that is typically more prevalent in New York.
In large urban cities, pollution often comes from a concentration of traffic, as people commute to and from work and drive to the city for entertainment and cultural events.
“We are going to pivot a little bit, especially to factors that are more relevant” to the Empire State, he said.
While climate change is a broad category that affects patterns across the world, air pollution and its impacts are more regional.
“The biggest impact of air pollution happens locally” particularly in terms of health effects, Qiu said.
From Beijing to MIT
Born and raised in Beijing, Qiu began connecting how climate or energy policy influences air pollution at MIT.
“When I started my PhD, there was not much real world data analysis” that linked how much renewable energy helps air quality, Qiu said. “We have historical data to do that, but it’s a lot more complex.”
After he graduated from MIT, Qiu moved to Stanford, where he shifted his focus to climate change.
“There, I got to collaborate more directly with people in the public health domain,” he said, as he focused on wildfires.
Personal choices
Despite studying air pollution and climate change, Qiu does not have HEPA filters in every room and, by his own admission, does not live a particularly green life. He does not have an electric car, although he plans to get one when he needs a new vehicle. He urges people not to sacrifice the living standards to which they are accustomed, which can include eating their preferred foods and traveling to distant points in the world.
Qiu believes there are choices individuals can make to help, but that the kind of decisions necessary to improve the outlook for climate change come from centralized government policy or large enterprises.
“I have great respect for people who change their personal behavior” but he recognizes that “this is not for everyone.”
A resident of Hicksville, Qiu lives with his wife Mingyu Song, who is a software engineer. The couple met when they were in high school.
When he’s not working on climate models, he enjoys playing basketball and, at just under six feet tall, typically plays shooting guard.
As for his research, Qiu does “rigorous scientific research” that draws from historical data.
“I feel a sense of urgency that we would like to get the answers to many of the scientific evidence as quickly as possible to communicate to policy makers,” he said.
He wants his research to be impactful and to help policy makers take “appropriate measures.”
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