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Interns Nylette Lopez (rear) and Stephanie Taboada characterize catalysts as they attempt to convert carbon dioxide and methane into synthesis gas this past summer at Brookhaven National Laboratory. Photo from BNL.

By Daniel Dunaief

This article is part two in a two-part series.

Local medical and research institutions are aware of the challenges women face in science and are taking steps to ensure that women receive equal opportunities for success in science, technology, engineering and mathematics (or STEM). Times Beacon Record News Media reached out to members of each institution and received an overview of some initiatives.

Brookhaven National Laboratory 

The Department of Energy-funded research facility has created a number of opportunities for women, including Brookhaven Women in Science. This effort has been active for over four decades and its mission, according to Peter Genzer, a BNL spokesman, is to support the development of models, policies and practices that enhance the quality of life for BNL employees and emphasize the recruitment, hiring, promotion and retention of women.

BWIS offers annual awards, outreach events and various networking opportunities in the lab and community, while the lab’s Talent Management Group partners with BWIS to bring classes and speakers to discuss issues specific to women.

In October, the group hosted Kimberly Jackson, a vice chair and associate professor of chemistry and biochemistry at Spelman College, who gave a talk titled “Realigning the Crooked Room in STEM.”

The Leona Woods Distinguished Postdoctoral Lectureship Award at BNL, meanwhile, celebrates the scientific accomplishments of female physicists, physicists from under-represented minority groups and LGBTQ physicists and to promote diversity and inclusion. BNL awarded the lectureship this year to Kirsty Duffy, a fellow at Fermi National Accelerator Laboratory.

For the past five years, BNL has also partnered with a local chapter of Girls Inc., which helps to “encourage young women towards careers” in STEM, Genzer explained in an email.

BNL has also collaborated with the Girl Scouts of Suffolk County to organize a new patch program that encourages Girl Scouts to work in scientific fields. As of September, county Girl Scouts can earn three new Brookhaven Lab patches, and the lab hopes to extend the program nationwide across the Department of Energy complex.

BNL also provides six weeks of paid time off at 100 percent of base pay for a primary caregiver after birth or adoption and one week of full pay for a secondary caregiver. BNL is exploring plans to enhance support for primary and secondary caregivers, Genzer said.

Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory has taken several recent steps as part of an ongoing effort to encourage gender diversity.

In October, a group of four CSHL administrators traveled to the University of Wisconsin in Madison to discuss mentoring. The goal was to train them on how to design and deliver mentoring training regularly to the faculty, postdocs and graduate students on campus, said Charla Lambert, the diversity, equity and inclusion officer for research at CSHL. The first version of the training will occur next spring. The ultimate goal is to ensure the research environment at CSHL emphasizes good mentoring practices and is more inclusive for all mentees.

CSHL has also hosted a three-day workshop in leadership practices for postdoctoral researchers and junior faculty since 2011. The workshop, which is run through the Meetings & Courses Program, trains about 25 postdoctoral researchers and junior faculty each year and has about one per year from CSHL, addresses how to hire and motivate people, while providing constructive feedback.

Lambert said family-friendly policies were already a part of CSHL policies, which include a child care facility. Members of the faculty receive extra funding when they travel to conferences to provide additional child care.

Lambert, who is a program manager for extramural Meetings & Courses overseeing diversity initiatives, has worked to get the demographic data for participants centralized, analyzed and used in developing policies. She believes this kind of data centralization is an area for potential improvement in the research division, where she is working to ensure an equitable distribution of resources among CSHL scientists.

Throughout her nine-year career at CSHL, Lambert said she has worked with the meetings and courses division to make sure the 9,000 scientists who visit the facility each year include women as invited speakers. She also works to reach course applicants from a wide range of institutions, including outside of prestigious research schools.

Ultimately, Lambert is hoping to help change the culture of science among the researchers with whom she interacts from a wide range of institutions. She feels that those people who leave the STEM fields because something about the culture of science didn’t work for them represent a “huge loss” to the field and creates a “survivorship bias.”

Stony Brook University 

For Stony Brook, gender diversity is “very important,” said Latha Chandran, the vice dean for Academic and Faculty Affairs at the Stony Brook University Renaissance School of Medicine. 

Chandran said more men entered the field of medicine 14 years ago. That has completely changed, as women have outnumbered their male counterparts in medicine for the last three or four years.

Chandran cited a number of statistics to indicate changes at the medical school. For starters, women faculty constituted 38 percent of the total in 2011. This April, that number climbed to 48.1 percent. That puts Stony Brook in the top 79th percentile of medical schools in terms of female representation.

While the overall numbers are higher, women are still underrepresented in the top tiers of the medical school, as 18 percent of the department chairs are women. She hopes more women can lead departments and that they can serve as role models that others can aspire to follow.

As for harassment, Chandran said Stony Brook was above the national mean in 2011. For almost all categories, Stony Brook is now below the national mean.

In 2011, Stony Brook created We Smile, which stands for We can Eradicate Student Mistreatment in the Learning Environment. The goal of this program is to educate people about harassment and to ensure that any mistreatment is reported. Through this effort, Stony Brook medical students are aware of the policies and procedures surrounding reporting.

Stony Brook is also addressing any bias in admission procedures by prospective applicants, who receive a standardized scenario to address with an admissions officer. In 2025, admissions officers will not have any information about the qualifications of the individual and will evaluate his or her response during interviews only based on response to scenarios.

Stony Brook University has almost finalized its search for a chief diversity candidate. Chandran expects that the medical school will “continue to make progress.”

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By Daniel Dunaief

Daniel Dunaief

The Democratic hopefuls for the presidency sure seem angry these days, as the election clock counts down to less than a year. Last week, a man in Iowa had the audacity, the temerity, the unmitigated gall to ask Joe Biden, the front runner, about his son Hunter, who is at the center of this Ukrainian maelstrom.

Biden reacted with anger and righteous indignation, calling the man a “damn liar.”

Good one. Or was it? Is that really the best way to react? Biden then nicknamed him “fat.” Yikes! That seemed cruel and disrespectful.

The man was throwing salt in either self-inflicted or Republican-directed wounds. But, hey, Biden’s son did sit on the board of an energy company in the Ukraine, which creates bad optics. It doesn’t mean he or his son did anything wrong.

What’s weird now, though, is that Biden seemed to feel the need — or perhaps the test-marketed driven necessity — to attack the man who dared ask the question. That seems to be taking a page out of the book of the incumbent, who uses anger as a regular tool to define his enemies and keep them off balance, while rallying his troops.

So, what happened to Mike Bloomberg? The billionaire was recently asked whether he was trying to buy the election. Out came the righteous indignation, along with a story about how he made his money, all the great work he did as mayor and how he won’t be beholden to any special interests. Grrr!

What about Bernie Sanders? He’s a cult figure among many Democrats, but his demeanor seems to be one of the angry, older white man. He reminds me of the Howard Beale character, played by Peter Finch, in the 1976 movie “Network.” Beale urges people to get up out of their chairs, go to the window and shout, “I’m as mad as hell, and I’m not going to take this anymore!” 

Sanders, or the Larry David version of him, could easily be uttering the same line in response to (a) health care costs, (b) the cost of college tuition for people who could otherwise use education to change their lives, (c) climate change or (d) all of the above.

And then there’s the Speaker of the House Nancy Pelosi. I know she’s not running for president, but she finally lashed out at a reporter — does that also sound familiar — and suggested that her religion kept her from hating people. Her tone, method and message had more than a hint of anger, if not toward the president whom she and the Democrats were impeaching than to the reporter.

The words she spoke, as she pointed her finger, were, “Don’t mess with me.” I was reminded of the line Geraldine Fitzgerald, as Martha Bach, said in the 1981 movie “Arthur,” starring Dudley Moore, “Don’t screw with me, Burt.”

If this past week is a preview of the upcoming primary and general elections, we’ve got about 11 months of Beale slogans and Bachs slaps to the faces.

The wrestling match may once again change its tune for “the Ds” and “the Rs” when we know which D will be facing off against the most likely R.

Maybe the Ds host a party for themselves where they describe the hopes, opportunities and promise of the American Dream for one and all.

Maybe the Rs decide counterpunching has been overplayed, and they start hosting their own party, where they celebrate low taxes, low unemployment, a strong economy and their plans for an even better future.

Primal anger, however, seems more likely as we prepare for a testy election. Wouldn’t it be a welcome relief if at least one of the candidates offered civil, calm, graceful and pleasant replies, even to questions he or she found challenging?

Photo by ©Constance Brukin, 2018/ CSHL

By Daniel Dunaief

This article is part one in a two-part series.

Women have made great strides in science, but they haven’t yet found equal opportunity or a harassment-free work environment.

After the National Academy of Sciences published a study in 2018 that highlighted sexual harassment and unconscious bias, a team of scientists came together at Cold Spring Harbor Laboratory last December to discuss ways to improve the work environment.

Led by Carol Greider, an alumni of CSHL and the director of molecular biology and genetics at Johns Hopkins and a Nobel Laureate, and Jason Sheltzer, a fellow at CSHL, the group recently released its recommendations in the journal Science.

While the atmosphere and opportunities have changed, “It’s not a clear-cut enlightenment and everybody is on board,” said Leemor Joshua-Tor, a professor at CSHL and a member of the group that discussed the challenges women face in science at the Banbury Center last year.

The Science article highlights earlier work that estimates that 58 percent of women experienced unwanted sexual attention or advances at some point in their careers. The authors write that this harassment is often ignored or excused, which can cause talented and capable women to leave the field of scientific research.

A member of the group that came together to discuss how to continue to build on the progress women have made in the STEM fields, Nancy Hopkins, an Amgen Inc. professor of biology emerita at the Massachusetts Institute of Technology, helped bring attention to the disparity between opportunities for men and women in science in the 1990s.

“My generation pushed [opportunities for women] forward and got through the door,” Hopkins said. “We found out that when you get through the door, the playing field wasn’t level.”

Hopkins said the progress is “still not enough” and that leaders like Greider and Sheltzer, whom she praised for tackling this nettlesome issue, “are now identifying problems that we accepted.”

For starters, the group agrees with the National Academy of Sciences, Engineering and Medicine, which believes treating sexual harassment in the same way as scientific misconduct would help. 

The scientists, which include CSHL’s CEO Bruce Stillman, recommend creating institutional and government offices to address substantiated claims of sexual misconduct and to educate institutions on harassment policy, using the same structures for research misconduct as models. 

An office that verified these claims could offer reporting chains, consistent standards of evidence and defined protocols.

Additionally, the scientists believe researchers should have to answer questions from funding agencies about whether they have been found responsible for gender-based harassment at any point in the prior 10 years, as well as whether they have been a part of a settlement regarding a claim of professional misconduct, research misconduct or gender-based harassment in the same time period. 

This policy, they urge, could prevent institutions from tolerating serial offenders who have generated a high level of research funding over the years.

“People that go through a complete investigation and have been found to have committed egregious harassment [can] get a job somewhere else, where nobody knows and everything happens again,” Joshua-Tor said. This policy of needing to answer questions about harassment in the previous decade would prevent that scenario.

The dependence scientists have on lab leaders creates professional risk for students who report harassment. The fortunes of the trainees are “very much dependent on the principal investigator in an extreme way,” explained Joshua-Tor. Senior faculty members affect the future of their staff through letters of recommendation.

“There’s a lot at stake,” said Joshua-Tor, especially if these lab leaders lose their jobs. Indeed, their students may suffer from a loss of funding. The authors recommend finding another researcher with a proven track record of mentorship to manage the lab.

Even though many senior scientists have considerable responsibilities, Joshua-Tor said principal investigators have assumed mentorship duties for others in unusual circumstances. 

“There were cases where people died,” so other scientists in neighboring labs took over their staff, she explained.

If, however, the institution can’t find another researcher who is available to take on these additional responsibilities, the authors recommend that the funding agency make bridge funding available to these researchers.

In addition to claims of harassment, the scientists discussed the difficulty women face from conscious and unconscious bias.

Joshua-Tor recalls an experience in a physics lab when she was an undergraduate. She was a lab partner with a man who was a “fantastic theoretician,” but couldn’t put together an experiment, so she connected the circuits. “The professor would come and talk” to her lab partner about the experimental set up while ignoring her and treating her as if she were “air.”

The scientists cited how male postdoctoral researchers tend to receive higher salaries than their female counterparts, while male faculty also receive larger salaries and start-up offers. Men may also get a larger share of internal funding, as was alleged with a $42 million donation to the Salk Institute.

To provide fair salaries, institutions could create anonymized salary data to an internal committee or to an external advisory committee for regular review, the scientists suggested.

Additionally, the researchers urged work-life balance through family-friendly policies, which include encouraging funding agencies to consider classifying child care as an acceptable expense on federal grants. Conferences, they suggest, could also attempt to provide on-site childcare and spaces for lactation.

While these extra efforts would likely cost more money, some groups have already addressed these needs.

“The American Society for Cell Biology has a fantastic child care program, where, if you are traveling, they have funds to alleviate extra child care services at home,” Joshua-Tor said. “If this is something we need and it’s in everybody’s psyche that it has to be taken care of for a meeting, it will be commonplace.”

Finally, the group addressed the challenge of advancing the careers of women in science. Female authors are often underrepresented in high-impact journals. Women also tend to dedicate more time to teaching and mentorship. The group encouraged holistic evaluations, which focus on an analysis of a candidate’s scientific and institutional impact.

Hopkins suggested that the solutions to these challenges at different institutions will vary. “You have to pick solutions that work in your culture” and that involve the administration. Ultimately, leveling the playing field doesn’t happen just once. “You’ve got to solve it and stay on it,” she urged.

Next week’s article explores some of the efforts of Stony Brook University, Brookhaven National Lab and Cold Spring Harbor Laboratory to provide an inclusive environment that ensures women have an equal opportunity to succeed in the STEM fields.

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File photo from Stony Brook University

An award-winning scientist, grandmother, aunt, mother and wife, Dr. Lina Obeid, died Nov. 29 at the age of 64 after a recurrence of lung cancer.

Lina Obeid spending time with her granddaughter Evelyn. Photo by Marya Hannun

Born in New York and raised in Lebanon, Obeid was a State University of New York distinguished professor of medicine and the dean of research at Renaissance School of Medicine at Stony Brook University, where she conducted research on cancer and aging. In 2015, she was named as one of The Village Times Herald’s People of the Year along with her husband Dr. Yusuf Hannun.

A Celebration of Life memorial service for Obeid will take place Dec. 7 at Flowerfield in St. James from 11 a.m. until 2:30 p.m. and will include remarks and a reception. Attendees are encouraged to wear bright colors.

SBU faculty appreciated Obeid’s scientific, administrative and mentoring contributions, as well as her engaging style.

Michael Bernstein, interim president of SBU, said Obeid was “very well liked and respected” and that her loss leaves a “big hole” at the university.

Obeid “oversaw our research programs, specifically the core facilities on which all our laboratory scientists depend, for sample analysis, for microscopy of cells” among other areas, Dr. Kenneth Kaushansky, dean of Renaissance School of Medicine wrote in an email.

He lauded Obeid’s personable approach, which he said, “rubbed off on many people,” creating a “renewed sense of optimism in our ability to impact all three missions: research, teaching and clinical care.”

Obeid and Hannun, who is the director of the Stony Brook Cancer Center, knew each other in high school, started dating in medical school and were married for 36 years. The couple recently shared a Lifetime Achievement Award at the 16th International Conference on Bioactive Lipids in Cancer, Inflammation and Related Diseases in October. The award represents the first time a woman received this honor.

Supriya Jayadev, who was a graduate student in Hannun’s lab at Duke University and is the executive director of Clallam Mosaic in Port Angeles, Washington, called Obeid a “role model” for women in science. “Not only was she a strong leader with the ability to compete in a male-dominated field, but she retained her femininity and grace.”

Daniel Raben, a professor of biological chemistry at Johns Hopkins Medicine, has known Obeid and Hannun for more than two decades.

“She had a huge impact on the sphingolipid field because of the contribution she made,” Raben said. “It’s a huge loss. She was a giant.”

Dr. Maurizio Del Poeta, a professor in the Department of Microbiology and Immunology at SBU, knew Obeid since 1995.

“I once asked her if she had any advice for my grants to get funded,” he recalled in an email. Obeid suggested she didn’t know how to get funded, but that his work wouldn’t get funded if he didn’t submit proposals.

She “never took ‘no’ for an answer. She would insist and insist and insist again until she [would] persuade you and get a ‘yes,’” he added.

Del Poeta said Obeid did a “marvelous” job enhancing research facilities, while she was a “caring physician” for veterans at the Northport VA Medical Center.

Obeid and Hannun were co-directors of a National Institutes of Health program in Cancer Biology and Therapeutics, which this year received a grant renewal for another five years.

Obeid’s daughter Marya Hannun recalled her mother as “warm, honest, and funny” without being cynical. Marya said her mother cared about everyone around her and was rooting for them to succeed.

“During my childhood, she taught me that nothing was impossible if you are determined and gutsy.”

— Mayra Hannun

“During my childhood, she taught me that nothing was impossible if you are determined and gutsy,” Marya Hannun wrote in an email.

She suggested her mother was passionate about food, which shaped how they lived and traveled. When the family visited Greece, Obeid swam out for sea urchins, cracked them on rocks and ate them on the beach. She was a passionate cook who learned from her mother, Rosette, who wrote a Palestinian cookbook.

The Hannun family laughs “about how we plan out holidays around food and spend
our meals talking about the next meals,” Marya wrote.

Obeid was part of one of the first class of women admitted into the International College High School. She earned her bachelor of arts at Rutgers University, but was also creative as a child and interested in fashion and design.

“Anyone who [saw] her wouldn’t be surprised,” Marya said.

Obeid is survived by her husband, her parents, Rosette and Sami, her nieces and nephews, her triplet children and her two grandchildren.

Obeid and Hannun’s daughter Reem is married to Dr. Khaled Moussawi and lives in Baltimore. Awni and his wife Kathy Hannun have two children, Evelyn and Yusuf, and live in New York City.

Binks Wattenberg, a professor in the Department of Biochemistry and Molecular Biology at Virginia Commonwealth University, believes that “people like [Obeid] only come along a few times in one’s lifetime.”

In an email, he recalled how she had a
“way of looking into your eyes and persuading you to do an experiment that she thought absolutely had to be done.” He appreciated her enthusiasm, which made Wattenberg feel as if he was doing “absolutely
essential work.”

Obeid regularly invited her researchers for meals at her house, where they felt as if they also joined the family, said Dr. Gerard Blobe, a professor of medicine at Duke University School of Medicine who earned his doctorate in Yusuf Hannun’s lab over 20 years ago.

In lieu of flowers, the family has asked for donations in Obeid’s name to the Stony Brook University Cancer Center. Potential donors can access the site at cancer.stonybrookmedicine.edu/giving.

Daniel Dunaief

By Daniel Dunaief

What is it about “The Play That Goes Wrong” that is just so right for so many people, including me?

My wife and I recently went to this farcical show, where my wife informed me that she, the couple attending the performance with us, and just about everyone around us could tell how much I enjoyed the experience. 

In case you haven’t heard about it and can’t figure it out from the title, “The Play That Goes Wrong” is an absurd show where everything goes so wrong — the props, the actors, the staging, the lighting and the music. Indeed, it’s almost challenging to follow the simple murder mystery plot amid gales of laughter, much of it coming from me.

My family has numerous qualities that we have shared from one generation to the next. My late father laughed so hard at the pratfalls and theater-of-the-absurd dialogue of Danny Kaye movies like “The Court Jester” (1955) that I can still picture him gasping for air as he wiped away the tears slaloming down his face, where they joined the muddy sneaker stains, the dirty paw prints and the soda spills on a white carpet that chronicled our active lives.

The current play follows in the footsteps of Kaye, Benny Hill, the Three Stooges and a host of other characters who do anything for a laugh, stepping on rakes that slam into their heads or interacting in nonsensical ways with other actors as a part of a skit. The show makes the sketch comedy of many of today’s late night shows appear pedestrian by comparison. Granted, the plot follows a singular theme and, once completed, can and does create a full length and ridiculous drama.

Now, some people may find the pedestrian antics of the cast too absurd. I agree that the show isn’t for everyone and doesn’t provide life lessons, memorable songs, gritty entertainment or an insightful view of existence.

And yet, it does offer much needed self-parody and perspective on a country thoroughly divided by events in Washington, D.C. The people who run our country seem intent on making their supporters cheer, while their detractors roll their eyes, shake their heads and seek solace from people who share their beliefs.

Fine, but, the actors in a show written by Henry Lewis, Jonathan Sayer and Henry Shields of the Mischief Theatre Company, seem intent on roping as much of the audience as possible into their shenanigans. 

One of the actors, who plays Cecil Haversham, seems delighted by the presence of the audience. He plays to the crowd so often that he shares in their enthusiasm when he does something well or when the crowd appreciates an ongoing joke.

This intentionally imperfect play isn’t perfectly imperfect, either. Some moments fall flat. The second half of the show, which is shorter than the first, isn’t quite as engaging, entertaining and uproarious.

Knowing the general plot of the story before I attended, I tried to anticipate the wide range of possible intentional stumbles and humorous moments that actors struggling to maneuver through a story might endure. The range of mistakes and blunders exceeded my expectations among numerous welcome and delightful surprises.

A play that delves in the world of funny gaffes takes real work on the part of the writers and the actors. To anyone sick of the political headlines, the conspiracy theories, the name calling, the accusations and counter accusations, this play is a welcome comedic retreat. It’s no wonder it won Best New Comedy at the 2015 Laurence Olivier Awards in London and is now on Broadway.

Mirna Kheir Gouda

By Daniel Dunaief

Mirna Kheir Gouda arrived in Commack from Cairo, Egypt, in 2012, when she was entering her junior year of high school. She dealt with many of the challenges of her junior year, including taking the Scholastic Aptitude Test, preparing for college and adjusting to life in the United States.

Her high school counselor at Commack High School, Christine Natali, suggested she apply to Stony Brook University. Once she gained admission, she commuted by train to classes, where she planned to major in biology on the road to becoming a doctor.

She did not know much about research and wanted to be involved in it to learn, especially because Stony Brook is so active in many fields.

“After some time conducting research, I came to be passionate about it and it was no longer just another piece of my resume, but rather, part of my career,” she explained in an email.

She reached out to Gábor Balázsi, a relatively new faculty member at the time, who suggested she consider joining a lab.

Balázsi uses synthetic gene circuits to develop a quantitative knowledge of biological processes such as cellular decision making and the survival and evolution of cell populations.

Balázsi knew Kheir Gouda from the 2015 international Genetically Engineered Machine team, which consisted of 14 members selected from 55 undergraduate students.

“Having this iGEM experience,” which included deciding on a project, raising funds, carrying out the project and preparing a report in nine months, was a “very promising indication” that Kheir Gouda would be an “excellent student,” Balázsi explained in an email.

Kheir Gouda chose Balázsi’s laboratory, where she worked with him and his former postdoctoral fellow Harold Bien, who offered her guidance, direction and encouragement.

As a part of the honors program, Kheir Gouda had to conduct an independent research project.

She wanted to “work on a project that involved adaptations and I always thought, ‘What happens when the environment changes? How do cells adapt?’”

She started her project by working with a mutant gene circuit that was not functioning at various levels, depending on the mutation. She wanted to know how cells adapt after beneficial but costly function loss.

An extension of this research, as she and Balázsi discussed, could involve a better understanding of the way bacterial infections become resistant to drugs, which threaten their survival.

“The idea for the research was hers,” Balázsi explained in an email. Under Bien’s mentorship skills, Kheir Gouda’s knowledge “developed quickly,” Balázsi said.

Balázsi said he and Kheir Gouda jointly designed every detail of this project.

Kheir Gouda set up experiments to test whether a yeast cell could overcome various mutations to an inducer, which regains the function of the genetic gene circuit.

Seven different mutations caused some type of loss of function of the inducible promoter of the gene circuit function. Some caused severe but not complete function loss, while others led to total function loss. Some were more able to “reactivate the circuit” rescuing its function, while others used an alternative pathway to acquire a resistance.

The presence of the resistance gene was necessary for cell survival, while the circuit induction was not necessary. At the end of the experiment, cells were resistant to the drug even in the absence of an inducer.

“This synthetic gene circuit in yeast cells can provide a model for the role of positive feedback regulation in drug resistance in yeast and other cell types,” Balázsi explained.

Kheir Gouda said she and Balázsi worked on the mathematical modeling toward the end of her research.

“What our work suggests is that slow growth can turn on quiescent genes if they are under positive feedback regulation within a gene network,” Balázsi wrote.

This mathematical model of limited cellular energy could also apply to cancer, which might slow its own growth to gain access to a mechanism that would aid its survival, Balázsi suggested. 

Recently, Kheir Gouda, who graduated from Stony Brook in 2018, published a paper about her findings in the journal Proceedings of the National Academy of Sciences, which is a prestigious and high-profile journal for any scientist.

“Because PNAS has a lot of interdisciplinary research, we thought it would be a good fit,” Kheir Gouda said. The work she did combines evolutionary biology with applied math and synthetic biology.

The next steps in this research could be verifying how evolution restores the function of other synthetic gene circuits or the function of natural network modules in various cell types, Balázsi suggested.

Kheir Gouda’s experience proved positive for her and for Balázsi, who now has eight undergraduates working in his lab. “The experience of mentoring a successful undergraduate might help make me a better mentor for other undergraduates and for other graduate students or postdoctoral researchers, because it helps set goals based on a prior example,” Balázsi said.

He praised Kheir Gouda’s work, appreciating how she learned new techniques and methods while also collaborating with a postdoctoral fellow in Switzerland, Michael Mahart, who is an author on the paper.

“It is unusual for an undergraduate to see a research project all the way through to completion, including a publication in PNAS,” marveled Balázsi in an email. He said he was excited to have mentored a student of Kheir Gouda’s character.

Kheir Gouda has continued on a research path. After she graduated from Stony Brook, she worked for a year on cancer research in David Tuveson’s lab at Cold Spring Harbor Laboratory. She then transitioned to working at the Massachusetts Institute of Technology for Assistant Professor of Chemical Engineering Kate Galloway. Kheir Gouda, who started working at MIT in October, plans to continue contributing to Galloway’s effort until she starts a doctoral program next fall.

Kheir Gouda said her parents have been supportive throughout her education.

“I want to take this opportunity to thank them for all the sacrifices they made for me,” Kheir Gouda said.

She is also grateful for Balázsi’s help.

He has “always been a very supportive mentor,” she explained. She would like to build on a career in which she “hopes to answer basic biology questions but also build on research and clinical tools.”

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Daniel Dunaief

By Daniel Dunaief

Last year at this time, I wrote a column celebrating words. I feel compelled to share another homage this year. This may start a new annual tradition. I hope you enjoy.

Words dart away, just out of reach, like a fish in the ocean, a butterfly in a meadow or a Frisbee lifted overhead by a sudden breeze.

Words emanate from nearby, startling us while we lay in bed, coaxing us to search the house, the closet, the garage for the source of elusive sounds.

Words give strength to our arguments, power to our convictions, and a method to share our hopes, desperation, dreams, fears, needs, wants and cravings.

Individually and collectively, words enable us to invite others to share experiences.

Words form the backbone of a democracy always challenged by new words, concepts, people and ideas.

When we hold an infant, listen to the sound from the air leaving the lungs of a whale surfacing nearby or gaze from the top of a volcano at the rising sun over the horizon, we hope the words we choose to describe what we see, feel and experience bring us back to these magic moments.

Words grow into unmanageable bundles as jargon triggers a metamorphosis that confounds and clutters their meaning, turning them into a sesquipedalian mess — that is the practice of using long-winded, obscure words.

Words tell tales, show emotions and reach out across time from generations long since past, urging us to pay attention and learn lessons from those who came before.

We select rhyming words that sing like chirping birds. 

Words make us laugh, offering a salve to suffering and transportation out of intransigence.

When we can’t understand something, we name it, giving a word to the unknown that allows us to refer to something in the cosmos, in our minds or buried under our fingernails. Ancient Romans used words to construct fantastic stories about the stars, the heavens and the gods, who exhibited a wide range of emotions that seemed remarkably human.

We remember the words from our favorite movies: “May the force be with you” (“Star Wars”) and “Louis, I think this is the beginning of a beautiful friendship” (“Casablanca”). And from our favorite presidents, such as John F. Kennedy’s “Ask not what your country can do for you, but what you can do for your country” (1961) or Franklin D. Roosevelt’s “The only thing we have to fear is fear itself” (1933).

We carry with us the words that mean the most from our own lives. We don’t need to check them at the airport when we are in group 9, stuff them in an overstuffed backpack when we go to school or keep them from getting waterlogged when the evapotranspiration cycle decides to dump rain, sleet, hail or snow upon us. We remember the person so critical to our existence that he or she “ruined us for all other” men or women.

The words that elevate, inspire and encourage us to do and be our best allow us to stand straighter and taller, enabling us to wear a cryptic smile that those who know us best perceive immediately.

Words give us hope, help us believe in ourselves and allow us to feel connected to someone halfway across the world.

We pause from uttering words during moments of silence, as we pay respect with the unspoken words in our minds.

We are surrounded by paper thin walls of meaningless, angry, spiteful, hateful words. We can combat those messages with words that reflect the best of us and our country. Words fill the toolbox with the parts to build the world as we choose.

As you ponder words that matter at this time of year, I’d like to wish you and your family a Happy Thanksgiving.

Ellen Pikitch, left, with Christine Sanora, taken in 2015 while the two scientists were researching Shinnecock Bay. Photo by Peter Thompson

By Daniel Dunaief

It’s one thing to make a commitment to a good idea; it’s another to follow through. Ellen Pikitch, endowed professor of ocean conservation science in the School of Marine and Atmospheric Sciences at Stony Brook University, is making sure countries around the world know where and how they can honor their commitment to protect the ocean.

In 2015, the United Nations had agreed to designate at least 10 percent of the oceans as Marine Protected Areas, which would restrict fishing and foster conservation. The goal of the proposal is to reach that figure by next year. 

Three years ago, with the support of the Italian Ministry of Environment and private donations, Pikitch started the labor-intensive process of finding ocean regions that countries could protect. 

Ellen Pikitch, right, with Natasha Gownaris at the United Nations Ocean Conference in June of 2017. Photo Courtesy of IOCS

She published the results of her analysis in the journal Frontiers in Marine Science. Her research could help countries move from the current 7.8 percent of oceans protected to the 10 percent target, and beyond that figure in the ensuing years.

The United States has met its target, although most of its marine protected ares are far from human population centers, so the coverage is uneven, Pikitch explained. The rest of the world has some gaps in high priority areas.

“I’m hoping that the study will light a fire under the policymakers so that they do meet their commitment,” said Pikitch. “It’s quite feasible for them to meet the goal. We’ve given [policymakers] advice in this paper about how exactly it could be done.”

The maps in the paper show areas that are within the current jurisdiction that are priority areas and are unprotected.

“There is quite a bit of area that meets this description — more than 9 percent — so there is flexibility in how countries can use the results and reach or exceed” the 10 percent target by next year, Pikitch explained in an email.

To determine where nations can enhance their ocean protection, Pikitch, Assistant Professor Christina Santora at the Institute for Ocean Conservation Science at Stony Brook University and Stony Brook graduate Natasha Gownaris, who is now an assistant professor in environmental studies at Gettysburg College, pulled together information from 10 internationally recognized maps indicating the location of global marine priority areas.

“We are standing on the shoulders of giants, capitalizing or leveraging all the hard work that has gone into other maps,” said Gownaris. 

One of the most unexpected findings from the study for Pikitch is that 14 percent of the ocean was considered important by two to seven maps, but over 90 percent of those areas remained unprotected. A relatively small part of this area is on the high seas, while most is within exclusive economic zones, which nations can control.

To preserve this resource that continues to remove carbon dioxide from the atmosphere while serving a critical role in the world’s food chain, conservationists have focused on marine protected areas because they provide the “one thing we felt was going to be the most effective single step,” said Mark Newhouse, the executive vice president for newspapers at Advance Publications and president of the Ocean Sanctuary Alliance. “It could happen overnight. A country could say, ‘This area is off limits to fishing,’ and it is.”

Countries can protect areas within their exclusive economic zones “more quickly than figuring out a way to solve global warming,” Newhouse added.

Santora explained the urgency to take action. “The situation in the ocean is worsening and we can’t wait to have perfect information to act,” Santora wrote in an email. “What we can do is put strong, effectively managed MPAs in the right places, with a high level of protection, that are well managed and enforced.”

Members of the Ocean Sanctuary Alliance, which counts Pikitch as its scientific officer, recognize that the 7.8 percent figure includes areas where countries have announced their intention to protect a region, but that doesn’t necessarily include any enforcement or protection.

“Intentions don’t protect the environment,” Newhouse said.

Ambassadors from several nations have reached out to OSA to discuss the findings. 

These diplomats are “exactly the people we want paying attention” to the research Pikitch and her team put together, Newhouse said.

Pikitch also plans to reach out proactively.

According to Pikitch’s recent analysis, the largest gaps in policy coverage occurred in the Caribbean Sea, Madagascar and the southern tip of Africa, the Mediterranean Sea and the Coral Triangle area, although they found additional widespread opportunities as well.

Pikitch calculated that an additional 9.34 percent of areas within exclusive economic zones would join the global marine protected area network if all the unprotected area identified as important by two or more initiatives joined the MPA network. 

“When effectively managed, when strong protections are put in place, they work,” Pikitch said.

Indeed, one such example is in Cabo Pulmo, Mexico, where establishing a marine protected area resulted in an 11-fold increase in the biomass of top predators within a decade. Many MPAs become sites for ecotourism, which can bring in hefty sums as people are eager to see the endemic beauty in their travels.

Pikitch hopes this kind of study spreads the word about the benefit of protecting the ocean and that policymakers and private citizens recognize that protecting sensitive regions also benefits fisheries, refuting the notion that environmentally driven policy conflicts with the goal of economic growth.

The groups involved in this study are already discussing the new goal for the ocean. Several diplomats and scientists would like to see the bar raised to 30 percent by 2030, although the United Nations hasn’t committed to this new target yet.

“Studies show that 10 percent is insufficient — it is a starting point,” Santora wrote. “I do think that targets beyond 2020 will increase.”

Pikitch said the ocean has always been one of her passions. Her goal is to “leave the world in better shape than I found it” for her children and six grandchildren.

Stock photo

By Daniel Dunaief

Daniel Dunaief

I have been working out at a gym, where my routine consists mostly of pushing my body as long as I can on a treadmill, bike or elliptical machine until my sweat has soaked through my T-shirt. I play mind games while I’m running, telling myself that I can take a break once I get to 3 miles, or maybe 4 or closer to 5.

Each time I hit a milestone, I think about how much better I’ll feel if I can go just a bit farther, even as I’m taking an inventory of all the barking body parts, which typically includes my knees and back.

What helps get me over the hump lately, though, is the music I listen to as I work out.

I started with a collection of ’80s songs, hoping, perhaps, that the combination of familiar tunes from my youth would make my body remember the energy that defined this younger period.

As I was running, the songs reminded me of the times I danced with friends at Ward Melville High School, played Uno in a friend’s living room or decorated a Christmas tree with another friend who patiently showed a group of us how to thread popcorn and cranberries through a line.

As I was running, a montage of these images played through my head, making me feel as if my legs were turning back the clock. Fortunately, no one at my gym looks closely at me or my facial expressions, so I could indulge in musical — and life — nostalgia without interruption or without questions from people wondering what I was thinking as I reacted to people who have long since gone their separate ways.

For a few days, I switched to my favorite singer, Billy Joel. Hearing the words from “Only The Good Die Young,” “Piano Man,” and “Movin’ Out,” brought me back to the study breaks I took in high school when I stared out the window between my house and the neighbor’s colorful Santa sleigh down the street, hoping that the snow forecast for that evening was sufficient to close school the next day.

I’m planning to see Billy Joel in concert before too long, so I switched to another genre, playing the soundtrack from the original 1975 version of the musical, “A Chorus Line.” While others rarely cite it as one of their favorite musicals, I know it was the song “Nothing,” in which Diana Morales receives nonstop criticism from her teacher Mr. Karp, that brought to life the magic of Broadway for me. 

I always measured every other performance, including of musicals like “West Side Story” that I supported by playing clarinet in the pit orchestra, against the desperate hopes of each of the cast members in a chorus line to “make it” into the show.

Eventually, I needed a pulsating beat, so I shifted to exercise music, which, of course, included songs from “Rocky the Musical,” as well as other inspirational films. Each time the beat got faster, I found another pocket of energy that helped me conquer the next mile, using the beat as a metronome for my legs.

Music, in all its forms, serves many functions, allowing us to connect with the artist, to travel on an acoustic journey, to remember friends, and to exercise feelings and emotions even as we exercise the rest of our bodies.

I coached many sports when my children were younger. If I could do it over again, I would have added contemporary music to mundane practices to spice up the experience in real time and to inspire me on the nostalgia treadmill.

By Daniel Dunaief

It’s a big leap from an encouraging start to a human, especially when it comes to deadly diseases like amyotrophic lateral sclerosis, or Lou Gehrig’s disease. Cold Spring Harbor Laboratory Associate Professor Molly Hammell knows that all too well.

Hammell has been studying a linkage between a mutated form of a protein called TDP-43 and ALS for eight years. About a year and a half ago, she worked with 178 human samples from the New York Genome Center’s ALS Consortium and found a connection between a subset of people with the disease and the presence of abnormal aggregate forms of the protein.

“It’s really rewarding to see evidence in clinical samples from the processes that we predicted from cell culture and animal models,” she explained in an email.

Molly Hammell. Photo from CSHL

About 30 percent of the people with ALS Hammell examined had pathology of this protein in the upper motor neurons of the upper cortex. In this area, the mutated form of TDP allowed more so-called jumping genes to transcribe themselves. A normal TDP protein silences these jumping genes, keeping order amid potential gene chaos. The change in the protein, however, can reduce the ability of the protein to serve this important molecular biology maintenance function.

By using complementary studies of cell culture, the associate professor tried to determine whether knocking out or reducing the concentration of normal TDP caused an increase in these retrotransposons.

When she knocked out the TDP, she found a de-silencing of these jumping genes “was rapid,” she said. “We could see that in the samples we collected.”

Before she got the larger sample, Hammell worked with a smaller pilot data set of 20 patients. She found that three of the patients had this abnormal protein and an active set of these jumping genes.

“It’s hard to make an argument for something you’d only seen in three patients,” she said. “Getting that second, independent much larger cohort convinced us this is real and it’s repeatable, no matter whose patient cohort we’re looking at.”

Several diseases show similar TDP pathology, including Alzheimer’s and fronto-temporal dementia. She started with ALS because she believed “if we’re ever going to see” the link between the mutated protein and a disorder, she would “see it here” because a larger fraction of patients with ALS have TDP-43 pathology than any other disease.

The findings with ALS are a compelling start and offer a potential explanation for the role of the defective protein in these other conditions.

“We think it’s possible in a subset of patients with other neurodegenerative diseases that there might be overlapping” causes, Hammell said “We’re trying to get more data to branch out and better understand overlapping alterations.”

With these other diseases, she and her colleagues would like to explore whether TDP pathology is a necessary precondition in conjunction with some other molecular biological problems or whether these conditions can proceed without the disrupted protein.

The reaction among researchers working on ALS to Hammell’s finding has been encouraging.

Hemali Phatnani, the director of the Center for Genomics of Neurodegenerative Disease at the New York Genome Center, suggested Hammell’s work “opens up really interesting lines of investigation” into a potential disease mechanism for ALS. The research suggests a “testable hypothesis.”

Phatnani, who has been in her role for about five years, said she and Hammell speak frequently and that they serve as sounding boards for each other, adding that Hammell is “definitely a well-regarded member of the community.” 

Hammell has also been working through the Neurodegeneration Challenge Network in the Chan Zuckerberg Initiative, or CZI. This work brings together scientists who study Alzheimer’s, Parkinson’s, ALS and Huntington’s diseases. The group works to develop new approaches to the treatment and prevention of these diseases. These scientists, which includes researchers from Harvard University, Stanford University, Vanderbilt and Mount Sinai, among others, have webinars once a month and attend a conference each year.

Hammell was one of 17 researchers awarded the Ben Barres Early Career Acceleration Award from the CZI in 2018, which helped fund the research. She thinks the scientists from the CZI are excited about the general possibility that there’s overlapping disease mechanisms, which her work or research from other scientists in the effort might reveal. The CZI is “trying to get researchers working on different diseases to share their results to see if that’s the case,” she explained in an email.

She recognizes that numerous molecular and cellular changes also occur during the course of a disease.“There are always skeptics,” Hammell concedes. In her experiments, she sees what has happened in patient samples, but not what caused it to happen. She also has evidence that the retrotransposon silencing happens because of TDP-43 pathology.

“What we still need to confirm is whether or not the retrotransposons are themsleves contributing to killing the neurons,” she said.

If Hammell confirms a mechanistic link, other studies may lead to a treatment akin to the approach researchers have taken with viruses that alter the genetic code.

Future therapies for a subset of patients could include antiviral treatments that select specific genes.

Over time, she said her lab has cautiously added more resources to this work. As she has gotten increasingly encouraging results, she has hired more scientists who dedicate their work to this effort, which now includes two postdoctoral fellows, two graduate students and three staff scientists.

Some scientists in her lab still explore technology development and are devoted to fixing the experimental methods and data analysis strategies she uses to look for transposon activity.

Hammell is inspired by the recent results and recalled how she found what she expected in human samples about 18 months ago. She said she was “giddy” and she ran into someone else’s lab to “make sure I hadn’t done it incorrectly. It’s really exciting to see that your research might have an impact.”