Authors Posts by Daniel Dunaief

Daniel Dunaief

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didn’t see a horrifying and preventable accident this morning. I didn’t see a little girl, let’s call her Erica, on her way to her first week of school.

Erica, who, in our story, is 10 years old, wants to be a veterinarian, and has pictures of animals all over her room. She begged her parents so long for a kitten that they relented. They saw how well she took care of the kitten, putting drops in her eyes when she needed them, making sure she got the correct shots and even holding her kitten in the office when they had to draw blood to test for feline leukemia, which, fortunately, her kitten didn’t have.

Two years after she got her kitten, Erica continued to ask for additional animals, adding a fish, a rabbit and a hamster to her collection. Each morning, Erica wakes up and checks on all the animals in her little zoo, well, that’s what her father calls it, to see how they’re doing.

Her mother is convinced that the animals respond to her voice, moving closer to the edge of the cage or to the door when they hear her coming. When mother leaves to pick up Erica from school, the animals become restless.

I didn’t see Erica walking with her best friend Jenna. Like Erica, Jenna has a dream. She wants to pitch for the United States in softball in the Olympics. Jenna is much taller than her best friend and has an incredible arm. Jenna hopes the Olympics decides to have softball when she’s old enough and strong enough to play. Jenna thinks bringing a gold medal to her father, who is in the Marines and has traveled the world protecting other people, would be the greatest accomplishment she could ever achieve.

I didn’t see a man, whom I’ll call Bob and who lives only four blocks from Erica and Jenna, put on his carefully pressed light-blue shirt with the matching tie that morning. I didn’t witness him kissing his wife Alicia, the way he does every morning before he rushes off to his important job. I didn’t see him climb into his sleek SUV and back quickly out of his driveway on the dead-end block he and Alicia chose more than a dozen years earlier.

I didn’t see Bob get the first indication from his iPhone 7 that he had several messages. I didn’t witness Bob rolling his eyes at the first few messages. I didn’t see him drive quickly toward the crosswalk where Erica and Jenna were walking. The girls had slowed down in the crosswalk because Jenna pointed out a deer she could see across the street in a backyard. Jenna knew Erica kept an animal diary and she was always on the lookout for anything her friend could include in her cherished book.

I didn’t see Bob — his attention diverted by a phone he had to extend to see clearly — roll too quickly into the crosswalk, sending both girls flying. I didn’t see the ambulances racing to the scene, the parents with heavy hearts getting the unimaginable phone calls, and the doctors doing everything they could to fix Jenna’s battered right arm — her pitching arm.

I didn’t see it because it didn’t happen. What I did see, however, was a man in an SUV, driving way too quickly through a crosswalk, staring at his phone instead of looking out for Erica, Jenna and everyone else’s children on his way to work.

It’s an old message that we should repeat every year: “School is open, drive carefully.”

Richard Moffitt, who joined Stony Brook University’s Biomedical Informatics and Pathology departments at the end of July, recently contributed to an extensive study of pancreatic cancer. Photo by Valerie Peterson

By Daniel Dunaief

It may take a village and then some to conquer pancreatic cancer, which is pretty close to what The Cancer Genome Atlas project assembled.

Pulling together over 200 researchers from facilities across the United States, the TCGA recently published an article in the journal Cancer Cell in which the scientists explored genetic, proteomic and clinical information from 150 pancreatic cancer patients.

Richard Moffitt, an assistant professor in the Departments of Biomedical Informatics and Pathology at Stony Brook University who joined the institution at the end of July, was the analysis coordinator for this extensive effort.

The results of this research, which worked with pancreatic ductal adenocarcinoma, the most common form of this cancer, offered a look at specific genetic changes involved in pancreatic cancer, which is the third leading cause of death from cancer.

“The study has several immediate clinical implications for patients facing the diagnosis of pancreatic cancer,” Ralph Hruban, one of the corresponding authors on the article and the director of the Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins University School of Medicine, wrote in an email.

The work “provides hope for future clinical trials in that 42 percent of patients within this cohort had cancers with at least one genetic alteration that could potentially be therapeutically targetable, and 25 percent of the patients had cancers with two or more such events.”

These genetic findings suggest a potential basis for genetic change-driven therapy trials down the road, Hruban suggested. As the analysis coordinator, Moffitt “played a critical role” Hruban continued. “He brought hard work, amazing creativity and great scientific knowledge to the project.”

Moffitt joined this effort about four years ago, after the collaboration began. The assistant professor said he pulled together the various data sets and analysis results from different teams and helped turn that into a “coherent overall story.”

Moffitt was also in charge of the messenger RNA analysis. He had been at the University of North Carolina as a postdoctoral researcher in Vice Chair of Research Jen Jen Yeh’s lab for the last five years until his recent move to Stony Brook.

Benjamin Raphael, another corresponding author on the article and a professor in the Department of Computer Science at Princeton University, suggested Moffitt played a critical part in the recent work. “In any large-scale collaboration such as this one, there tend to be a smaller number of researchers who play an outsized role in the project,” Raphael explained in an email. Moffitt “played such an outsized role. Without his dedication to the project over the past few years, it is doubtful that our analysis” would have been as comprehensive.

Members of TCGA contacted Moffitt and Yeh because the tandem were working on a new approach to studying gene expression that would eventually be published in a 2015 Nature Genetics article.

Working with Yeh, Moffitt helped tease apart the genetic signature of pancreatic cancer cells from the different types of cells around it, which also includes healthy cells and a cluster of dense cells around the tumor called the stroma.

“The proportion of cancer cells in pancreatic cancer is low so if you imagine a mix of marbles of the same color on the outside but different on the inside and only having 10 in a bag of 100, figuring out what 10 [are] ‘tumor’ colors on the inside was very challenging,” Yeh explained in an email.

The TCGA study explains subtypes of cancer Moffitt didn’t know existed just a few years ago, while exploring the possible role that micro RNA and DNA methylation — the process of adding or taking away a methyl group from a genetic sequence to turn on and off genes — has in describing those subtypes.

Researchers “need projects like TCGA that are a really well-controlled way to study almost every molecule you want to study systematically for 150 cases to reveal these networks,” Moffitt said.

Moffitt has coupled his appreciation for algorithms and math with an interest in biology and engineering. His Ph.D. was done in a dry lab, which didn’t even have a sink. When he moved to UNC to conduct his postdoctoral work, he took a different approach and worked with surgical oncologists on tissue samples.

Moffitt plans to continue working with TCGA data and also to see how the subtypes can be used to predict responses to therapies. Some time in the future, researchers hope patients can get a diagnostic biopsy that will direct them to the specific therapy they receive, he said.

Moffitt grew up in Florida and earned his bachelor’s and doctoral degrees at Georgia Tech before completing his postdoctoral research at UNC. He has been gradually drifting north. Moffitt and his wife Andrea, who just started her postdoctoral work with Michael Wigler and Dan Levy at Cold Spring Harbor Laboratory, live in Stony Brook.

A competitive water skier during his youth in Florida, Richard Moffitt, dons two skis when he’s out with friends on Lake Oconee, Georgia in 2013. Photo by Andrea Moffitt

The water on Long Island is colder than it is in Florida, where Moffitt spent considerable time on a show skiing team. This was his version of a varsity sport, where he spent about six hours a day on Saturday and Sunday during the spring and about three hours a night before tournaments performing moving pyramids, among other tricks. When he was in high school, Moffitt wrote a computer program that automates the show skiing scoring process.

Moffitt processes the world through probabilities, which figured into the way he chose stocks in high school as a part of a stock picking competition and the way he approached his picks for March Madness. His basketball bracket won a competition for bragging rights among about a dozen entrants in 2016 and he was one game away from repeating in 2017 until UNC beat Gonzaga.

As for his Stony Brook effort, Moffitt plans to collaborate with members of the Cancer Center as well. “Being in demand is a good thing.”

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How difficult must it be to become someone else? Somehow, Abby Mueller, an actress who probably isn’t a household name, transforms into the legendary singer Carole King in the Broadway musical “Beautiful.”

It’s a risky proposition. Many of us already know songs like “So Far Away” and “Will You Love Me Tomorrow,” which means we know what the song should sound like, even if we can’t sing it in tune.

And yet, Mueller, who is clearly the star of a show about another star, pulls it off incredibly well, giving us the energy, the soul, the innocence and the ambition of a remarkable talent.

Watching and, more importantly, listening to the show is a transformative experience. Music has that remarkable power, bringing us back to a car when we might have often heard “Up on the Roof” or sending us back in our minds to a dance party where we threw ourselves across the floor of a friend’s house as we invented our own steps to “The Loco-Motion,” where “everybody’s doing a brand new dance, now.”

Even though the dance isn’t so brand new anymore, it feels revived when we watch the high energy action on stage.

My wife and I snuck away before the end of the summer to see the musical, which left us humming and singing the songs through the next day.

The musical itself, like many other Broadway stories, is a collection of dialogue, a loose story and a compilation of rollicking music. The story line follows the musical career of King and her writing partner and husband Gerry Goffin, whom she married when she was 17 and pregnant. The audience feels as if it’s witnessing the birth of these songs, as Goffin pairs his familiar lyrics to the music King wrote.

The first half of the show, which is considerably longer than the second, is like a collection of musical candy tossed to a hungry audience.

I snuck glances around the room at some of the other people fortunate enough to take a musical joyride and I saw that, like me, several of the guests, who were mostly in their late 40s and older, had smiles plastered on their faces.

The second act doesn’t contain as many songs and delves into the more challenging and sadder parts of King’s life, where she endures the hardship of her husband’s infidelities and the creative tension that sometimes won the battle over his creative talent.

King, as we know, lands on her feet, becoming the legendary composer, singer and songwriter who was inducted with Goffin into the Songwriters Hall of Fame in 1987 and the Rock and Roll Hall of Fame in 1990 for their songwriting.

The energy on stage throughout the show, with performances by a talented team reviving the style and moves of the Shirelles and the Drifters, rival the thrill of watching the cast of “Mamma Mia!” who belted out the familiar Abba songs.

The difference here, however, is that the script is not a plot written to tie together songs, but evolves as the backstory behind the early days of music that long ago circled the United States and the world.

“Beautiful: The Carole King Musical” definitely lives up to the awards it has won, including the 2015 Grammy for best musical theater album and its two Tony Awards in 2014, which include a well-deserved honor for Mueller.

The only speed bump during this otherwise wonderful ride is the dramatic downshifting in the second act, where the drama, while no doubt true to life, slows the musical momentum. Still, the conclusion and the experience are rewarding, allowing us to reconnect with the legendary singer’s past, and our own.

Above, Ken Dill shows how molecules fold and bind together. Photo from SBU

By Daniel Dunaief

The raw materials were here. Somehow, billions of years ago, these materials followed patterns and repeated and revised the process, turning the parts into something more than a primordial soup.

Ken Dill, who is a distinguished professor and the director of the Laufer Center for Physical and Quantitative Biology at Stony Brook University, took a methodical approach to this fundamental development. He wanted to understand the early statistical mechanics that would allow molecules to form long chains, called polymers, which contained information worthy of being passed along. The process of forming these chains had to be self-sustaining.

After all, Dill said, many activities reach an end point. Putting salt in water, for example, creates a mixture, until it stops. Dill, however, was looking for a way to understand auto-catalytic or runaway events. Lighting a forest fire, for example, is much more self sustaining, although even it eventually stops. Life has continued for over four billion years.

On Aug. 22, Dill, Elizaveta Guseva and Ronald Zuckermann, the facility director in biological nanostructures at the Lawrence Berkeley National Laboratory, published a paper in the journal Proceedings of the National Academy of Sciences (PNAS).

The researchers developed a fold and catalyze computational model that would explain how these long chains developed in a self-sustaining way, in which hydrophilic and hydrophobic polymers fold and bind together.

Random sequence chains of each type can collapse and fold into structures that expose their hydrophobic parts. Like a conga line at a wedding reception, the parts can then couple together to form longer chains.

These random chemical processes could lead to pre-proteins. Today’s proteins, Dill said, mostly fold into a very particular shape. Pre-proteins would have been looser, with more shape shifting.

The workhorses of the body, proteins perform thousands of biochemical reactions. Dill suggested that this model “rates high on the list” in terms of the findings he’s made over the course of his career.

Zuckermann described this work as significant because it lays out predictions that can be tested. It highlights the importance of chemical sequence information in polymer chains and “how certain sequences are more likely to fold into enzyme-like shapes and act as catalysts than others,” he explained in an email.

Zuckermann works with substances he figured out how to make in a lab that are called peptoids, which are non-natural polymers. These peptoids are a “good system to test the universality of [Dill’s] predictions,” he said.

The “beauty” of Dill’s work, Zuckermann suggested, is that “it should apply to most any kind of polymer system” where researchers control the monomer sequence and include hydrophobic and hydrophilic monomers in a particular order, putting Dill’s predictions to the test.

For her part, Guseva worked in Dill’s lab for her PhD thesis. She had started her research on something that was “more standard physical biology” Dill said, but it “was not turning out to be particularly interesting.”

The scientists had a discussion about trying to develop a chemical model related to the origins of life. While exciting for the scope of the question, the research could have come up empty.

“There was so much potential to fail,” Dill said. “I feel pretty uncomfortable in general about asking a graduate student to go in that direction, but she was fearless.”

Dill and Zuckermann, who have collaborated for over 25 years, are trying to move forward to the next set of questions.

Zuckermann’s efforts will focus on finding catalytic peptoid sequences, which are nonbiological polymers. He will synthesize tens of thousands of peptoid sequences and rank them on how enzyme-like they are. This, he explained, will lead to a better understanding of which monomer sequences encode for protein-like structure and function.

Zuckermann suggested that the process in this research could have the effect of transforming a soup of monomers into a soup of functional polymers. This, he said, might set the stage for the evolution of DNA and RNA.

Proteins could have been a first step towards a genetic code, although life, as currently defined, would not have blossomed until a genetic code occurred, too, Dill suggested.

The origins of DNA, however, remains an unanswered question. “We’re trying to think about where the genetic code comes from,” Dill said. “It’s not built into our model per se. Why would biology want to do a two polymer solution, which is messy and complicated and why are proteins the functional molecules? This paper doesn’t answer that question.”

Dill and Zuckermann are in the early stage of exploring that question and Dill is hopeful he can get to a new model, although he doesn’t have it yet.

Dill moved from the University of California at San Francisco to join the Laufer Center about seven years ago. He appreciates the freedom to ask “blue sky questions” that he couldn’t address as much in his previous work.

Wearing a hat from his native Oklahoma, Dill, in a photo from around 1997, tinkers with a toy boat he made with sons Tyler and Ryan. Photo by Jolanda Schreurs

A resident of Port Jefferson, Dill lives with his wife Jolanda Schreurs, who has a PhD in pharmacology. The couple has two sons, Tyler and Ryan.

Tyler graduated with a PhD from the University of California at San Diego and now works for Illumina, a company which which makes DNA sequencers. Ryan, meanwhile, is earning his PhD in chemistry from the University of Colorado and is working on lasers.

“We didn’t try to drag our sons into science,” Dill said. “With both kids, however, we had a workshop in the basement” where they often took anything that was within arm’s reach and nailed it to a board. One of the finished products was a remote-controlled and motorized boat.

As for his lab work, Dill is thrilled to have this model that he, Guseva and Zuckermann provided, while he recognizes the questions ahead. Scientists “see something puzzling and, rather than saying, ‘I need to avoid this, I don’t have an answer,’ we find it intriguing and these things lead from one step to the next. There tends to remain a huge number of super fascinating problems.”

Im not a scientist and I don’t play one on TV. Nonetheless, I think science is undervalued in America. I believe the typical American takes science for granted, thinks science owes them something and figures they’ll never understand what scientists are saying.

Wrong, wrong and wrong.

For starters, science isn’t just about trying to create the best iPhone, the highest quality and thinnest televisions, or medicines that act like magic bullets, destroying evil in our cells or our DNA without damaging the healthy ones.

Science often starts with a question. Why or how does something work? And, perhaps, if we change something about the way it works, does it get better or worse? The conclusions scientists draw when they solve one puzzle leads to the next set of questions.

It’s as if a child asks his parent if he can go west and the parent says, “No, don’t go west, but here are the keys to the car.”

The answer may seem like a non sequitur, but it’s also a way to navigate somewhere new, even if, for whatever reason, the car isn’t supposed to go west. Maybe, by learning more about the car and where it can go, the child also learns what’s so forbidding about going west, too.

We want science to succeed and we’re annoyed when science doesn’t solve our problems. We can’t get something to work or we can’t get ourselves to work and we blame scientists. After all, if we can send a man to the moon, why can’t we conquer the morning rush hour or the common cold?

Then again, how does the study of dark matter — neutrinos or sphingolipids — affect our morning commute? We may not understand these areas, but that doesn’t mean basic knowledge can’t or won’t lead to advances we can’t anticipate.

Knowledge, as we know, is power. If we know, for example, that an enemy is planning an attack and we know where and how that attack will occur, we can defend ourselves, even if that enemy exists at a subcellular level.

Learning the playbook of the enemy takes time, which technological innovation, dedicated researchers and people battling against a disease often don’t have.

Worst of all, though, science is somehow too hard to understand. That is a defeatist conclusion. Yes, scientists use technical terms as shorthand and, yes, they may not be selling ideas or themselves in the kind of carefully crafted tones often reserved for CEOs or politicians.

That, however, doesn’t mean they are planting a keep-out sign in front of them or their ideas. While scientists reduce a question to an attainable goal, they also often keep a larger goal in mind.

A few years ago, my daughter had to draw a picture of what she thought a scientist looked like. Rather than imagine a person in a white lab coat with one pocket full of pens and the other holding a radiation badge, she drew a baby.

Science may be frustrating because scientists often come across as uncertain. For example, they might say, “We believe that the shadow in our telescope may be caused by an exoplanet orbiting a star that’s outside the solar system, and which is the same distance from its nearest star as Earth is from the sun.”

Scientists can be wrong, just as anyone can be wrong in their job, in their opinions or in their conclusions. That, however, doesn’t make science wrong. Scientists are often most excited when a discovery they make defies their expectations or bucks conventional wisdom.

Just because conventional scientific wisdom changes doesn’t mean every part of it is wrong.

Science doesn’t have all the answers and it never will. The most likely person to tell you that, though, should be a scientist, not a journalist.

Alex Orlov on the campus of the University of Cambridge. Photo by Nathan Pitt, University of Cambridge

By Daniel Dunaief

The Ukranian-born Alex Orlov, who is an associate professor of materials science and chemical engineering at Stony Brook University, helps officials in a delicate balancing act.

Orlov, who is a member of the US-EU working group on Risk Assessment of Nanomaterials, helps measure, monitor and understand the hazards associated with nanoparticles, which regulatory bodies then compare to the benefit these particles have in consumer products.

“My research, which is highlighted by the European Union Commission, demonstrated that under certain conditions, [specific] nanoparticles might not be safe,” Orlov said via Skype from Cambridge, England, where he has been a visiting professor for the past four summers. For carbon nanotubes, which are used in products ranging from sports equipment to vehicles and batteries, those conditions include exposure to humidity and sunlight.

“Instead of banning and restricting their production” they can be reformulated to make them safer, he said.

Orlov described how chemical companies are conducting research to enhance the safety of their products. Globally, nanotechnology has become a growing industry, as electronics and drug companies search for ways to benefit from different physical properties that exist on a small scale. Long Island has become a focal point for research in this arena, particularly at the Center for Functional Nanomaterials and the National Synchrotron Light Source II at Brookhaven National Laboratory.

Alex Orlov on the campus of the University of Cambridge. Photo by Nathan Pitt, University of Cambridge

Indeed, Orlov is working at the University of Cambridge to facilitate partnerships between researchers in the chemistry departments of the two universities, while benefiting from the facilities at BNL. “We exchange some new materials between Cambridge and Stony Brook,” he said. “We use BNL to test those materials.”

BNL is an “essential facility,” Orlov said, and is where the postdoctoral student in his lab and the five graduate students spend 30 to 60 percent of their time. The data he and his team collect can help reduce risks related to the release of nanomaterials and create safer products, he suggested.

“Most hazardous materials on Earth can be handled in a safe way,” Orlov said. “Most scientific progress and environmental protection can be merged together. Understanding the environmental impact of new technologies and reducing their risks to the environment should be at the core of scientific and technological progress.”

According to Orlov, the European Union spends more money on technological safety than the United States. European regulations, however, affect American companies, especially those that export products to companies in the European Union.

Orlov has studied how quickly toxic materials might be released in the environment under different conditions.

“What we do in our lab is put numbers” on the amount of a substance released, he said, which informs a more quantitative understanding of the risks posed by a product. Regulators seek a balance between scientific progress and industrial development in the face of uncertainty related to new technologies.

As policy makers consider the economics of regulations, they weigh the estimated cost against that value. For example, if the cost of implementing a water treatment measure is $3 million and the cost of a human life is $7 million, it’s more economical to create a water treatment plan.

Orlov teaches a course in environmental engineering. “These are the types of things I discuss with students,” he said. “For them, it’s eye opening. They are engineers. They don’t deal with economics.”

In his own research, Orlov recently published an article in which he analyzed the potential use of concrete to remove pollutants like sulfur dioxide from the air. While concrete is the biggest material people produce by weight and volume, most of it is wasted when a building gets demolished. “What we discovered,” said Orlov, who published his work in the Journal of Chemical Engineering, “is that if you take this concrete and expose new surfaces, it takes in pollutants again.”

Fotis Sotiropoulos, the dean of the College of Engineering and Applied Sciences at SBU, said Orlov has added to the understanding of the potential benefits of using concrete to remove pollutants.

Other researchers have worked only with carbon dioxide, and there is “incomplete and/or even nonexistent data for other pollutants,” Sotiropoulos explained in an email. Orlov’s research could be helpful for city planners especially for end-of-life building demolition, Sotiropoulous continued. Manufacturers could take concrete from an old, crushed building and pass waste through this concrete in smokestacks.

To be sure, the production of concrete itself is energy intensive and generates pollutants like carbon dioxide and nitrogen dioxide. “It’s not the case that concrete would take as much [pollutants] out of the air as was emitted during production,” Orlov said. On balance, however, recycled concrete could prove useful not only in reducing waste but also in removing pollutants from the air.

Orlov urged an increase in the recycling of concrete, which varies in the amount that’s recycled. He has collaborated on other projects, such as using small amounts of gold to separate water, producing hydrogen that could be used in fuel cells.

“The research showed a promising way to produce clean hydrogen from water,” Sotiropoulos said.

As for his work at Cambridge, Orlov appreciates the value the scientists in the United Kingdom place on their collaboration with their Long Island partners.

“Cambridge faculty from disciplines ranging from archeology to chemistry are aware of the SBU/BNL faculty members and their research,” Orlov said. A resident of Smithtown, Orlov has been on Long Island for eight years. In his spare time, he enjoys hiking and exploring new areas. As for his work, Orlov hopes his work helps regulators make informed decisions that protect consumers while making scientific and technological advances possible.

Ever walk into a room and wonder why you’re there? As I say to my wife when she looks up expectantly if I appear and then stop in my tracks, I get distracted by air.

We are flooded by stimuli from the bird soaring overhead, to the vibrating cellphone alerting us to an incoming message, to the lists that run in our heads. We have numerous opportunities to lose track of the principle task we assigned ourselves.

I’ve decided on a mantra to deal with these moments and others through the day: “While I’m here.” Yes, I know that’s not exactly a new turn of phrase and I know it’s a type of mindfulness, but my suggestion is about hearing and responding to the phrase.

For example, I might walk into a drugstore to buy shampoo and conditioner. I might realize, before I head to the checkout line, that “while I’m here,” I might also get some dental floss. After all, it’s not like dental floss spoils and, if you’ve seen the movie “Prelude to a Kiss,” you know the old man, once he returns to his own body, advises the young couple at the beginning of their marriage to floss. After several painful episodes with gums that had previously been a breeding ground for painful bacteria, I can attest to the value of that advice.

If you’re a suburban parent and you’re sitting at another baseball game, at a concert or at a dance recital, let’s imagine you’re waiting for the action to begin. “While you’re here” you might want to talk to the parent sitting near you and ask about his or her life or job.

“Hey, wait,” you say. “You’re in the same industry as I am? I had no idea. Of course, I’d love to write an elaborate freelance article that you’ll feature on the cover of your glossy magazine and that will lead to a long and fruitful business collaboration.”

That might not happen, but it certainly won’t if you dive deep into your cellphone to tell someone in another state that you’re not sure whether you’re going to eat the leftover salad from lunch or order chicken with broccoli from the Chinese restaurant down the street.

Maybe you’re at a job interview and you’ve hit all the talking points. You said your only serious flaw is that you take work so seriously that you won’t rest until you’ve secured whatever victories the company needs to beat its closest rivals.

“While you’re here,” however, you might also want to make sure you ask enough questions about the interviewers, so you know their career paths and so you have a better idea of the people with whom you’ll interact if they offer you the job.

Not all the “while you’re here” moments have to be of immediate benefit to you. You might, for example, be on a beach on one of the final days of summer and a strong wind might blow someone’s hat toward you. “While you’re here” you might want to help that person retrieve it. Or maybe you see a plastic wrapper heading into the water. “While you’re here” you also might want to grab this offensive litter and bring it to a garbage can so that it doesn’t damage a fish or a turtle.

If we consider a few times a day what we can do “while we’re here,” we might not only become more efficient, but we also might make that unexpected trip into the room worthwhile. The moment when we’re trying to recall what drove us into the room can transform into an opportunity … “while we’re here.”

From left, scientist Lin Yang at the LiX beamline demonstrates how the beam hits the sample to high school teachers James Ripka, Mary Kroll, Fred Feraco, Janet Kaczmarek and Jocelyn Handley-Pendleton. Photo from BNL

By Daniel Dunaief

He helped build it and now a range of researchers are coming.

Lin Yang helped create the LiX beamline at the National Synchrotron Light Source II at Brookhaven National Laboratory, which is attracting researchers eager to study the fine structure and function of everything from proteins to steel.

The lead scientist for the LiX beamline at the NSLS-II at BNL, Yang was the control account manager for the construction of the beamline and was the spokesperson for a team that wrote the original beamline development proposal.

“In our case, the scattering from the sample is sensitive to the underlying structure” of materials, Yang said. “That’s why people want to use scattering to study their samples.”

Like the other beamlines at the NSLS-II, the LiX enables scientists to use sophisticated equipment to search for links between structures and function. Each beamline has a three-letter acronym. In the case of LiX, the “Li” stands for life sciences, while the “X” represents X-ray scattering.

When they designed the beamline, LiX researchers were seeking optics that were capable of producing a beam to conform to the specifications required for different types of measurements. They then designed an experimental station that is suitable for handling biological samples. Specifically, that involved developing an automated sample handler for measurements on protein molecules in solution.

“With atomic resolution structures and functional assays, we do get new insights [about] important ions such as calcium,” which are involved in signaling and physiology, Qun Liu, a principal investigator in the Biology Department at BNL, described in an email. “LiX will be essential to allow us [to see] the transport process in real time and space.” Liu wrote that Yang is an “outstanding X-ray beamline scientist” who is also well known for his pioneering work on membrane diffraction.

The ability to perform measurements using a beam of a few microns is “pretty unique right now,” which also attracted researchers working with steel samples, Yang said. “When we designed the instrument, our focus [was] on the biological structure” but the beamline is “versatile enough” that it has found other uses, Yang said.

Researchers working with steel realized that the same diffraction-based approach to finding underlying structures in living tissue could also shed light on the structures of their samples.

In everyday life, diffraction is visible from the wavelengths of light that form the hologram on a credit card. Scientists working with steel have been applying for time on the LiX beamline, too, creating a competitive environment for researchers working in both fields.

Lynne Ecker, the deputy department chair in the Nuclear Science and Technology Department at Brookhaven National Laboratory, has used the beamline to study the effect of neutrons and ions on steel.

“Ions will only damage steel so far,” Ecker said. The LiX is “perfect” to study the degree of the damage. Ecker said she’s tried this kind of analysis in other places, but the LiX provides better spatial resolution. The LiX scientists are working on improving the degree of automation for sample handling and data processing.

“We are about to install a six-axis robot, which is typically seen in industrial automation, to help realize unattended overnight measurements on protein solution samples,” Yang said. The robot is already at the facility and Yang and his team will be installing the support structure to mount the robot in the experimental station this month. “The more challenging task is to put the software in place so that the beamline can control the robot,” he explained in an email.

The LiX beamline uses lenses made from beryllium, which are transparent to X-rays. For X-rays at the wavelength of about one angstrom, about 93 percent can pass through about a millimeter of beryllium. That compares favorably to aluminum, which allows about 2 percent to pass through at the same thickness.

The LiX beamline can run at 500 frames per second, which produces a wealth of data. In practice, it may take up to a second for the detector to accumulate enough signal from the sample. Still, the beamline can generate enough data that the experimenter may not be able to examine it frame by frame, which makes automated data processing more important.

Scientists have used the beamline to explore the structure of plants. These researchers mainly want to understand how materials like cellulose are organized within different parts of the plant and in different plants.

In bones, researchers can differentiate between organic matter like collagen and inorganic matter. Not only can they determine where they are, but they can also explore their orientation in a sample. Bones are easy samples since collagen and minerals in bone have distinctive scattering and diffraction patterns, Yang said. Researchers “like to look at how biological molecules change their shape as they interact with their functional partners,” Yang said.

A resident of East Setauket, Yang lives with his wife Mian Wang, who is an architect in Farmingdale, and their two daughters. A fan of tennis, Yang plays as often as he can during the summer at the Three Village Tennis Club.

Yang grew up in Yunnan province in the southwest of China. Trained as a physicist, Yang picked up knowledge of molecular biology from his years of working with other scientists. In his work, he gets to combine his talents in engineering, programming and molecular biology.

“We learn new things when we interact with our users/guest researchers since we first need to learn about their problems before we can help solve them,” he described in an email. Yang hopes the research he and the team at the LiX support will result in high-impact publications. “As more researchers know about us and our capabilities, I expect more people will want to perform experiments at our beamline,” he said.

Journalists need to embrace Detective Sgt. Joe Friday’s line from “Dragnet,” “Just the facts, ma’am.”

Caught up in intense public passions, journalists can either throw their opinions at the inflamed cacophony or they can seize an opportunity to do something that has escaped most politicians: Represent broader interests.

We live in a world of spin, where claims and counterclaims come out so rapidly that reality has become a blur. The challenges in sifting through fact and fiction have increased as officials of all stripes shout their truths from the rooftops, even if they have an obstructed view of the world down below.

When I was in journalism school more than two decades ago, a good friend from Bulgaria, who was one of the few people who could pronounce my name correctly when she read it in my mailbox, shared her writing with me.

I noticed a flaw in the way she recorded dialogue. The quotes in her story often lacked the syntax and vocabulary that native English speakers possess. When I asked if she only spoke with other Bulgarians, she playfully punched my shoulder and said she needed to hear better.

That was an unintentional consequence of the way someone who spoke three languages translated the world.

The chasm today between what people say and what others hear, even those who speak the same language, has gotten wider. Editors and reporters return to their desks or take out their laptops, ready to share quotes, events and facts.

These fellow members of the media may find themselves seeing what they want to see, much like the parent of an athlete on a field or a coach who has become an advocate or cheerleader. In editorials, where we’re clearly sharing an opinion, that works, but in news reports we should share the facts, offer context — and increase the value of fact-based reporting.

With facts under regular assault, the search for them, and the ability to verify them, becomes even more important.

A divided nation needs balanced, fair, accurate and defensible reporting. In their publications, scientists share materials and methods sections, which should allow other researchers to conduct the same experiments and, presumably, find the same results. Far too often, opinions disguised as news urge people to trust the writer. Why? Readers should be able to pull together the same raw materials and decide for themselves.

I know government officials don’t always deal in facts. I also know numbers can be repackaged to suit an agenda, turning any conclusion into a specious mix of farce and mental acrobatics. To wit, he’s the best left-handed hitter every Tuesday there’s a full moon below the Mason-Dixon line. Just because it’s presented as a fact doesn’t mean we have to report it or even mock it. If it’s meaningless, then leave it alone. The argument that other journalists are doing it doesn’t make it acceptable.

Several years ago, someone called to berate me for what he considered errors in my story. Rather than shout him down, I gave him the chance to offer his perspective. Eventually he calmed down and we had a measured, detailed discussion. This became the first of numerous conversations and interactions in which he provided important perspectives and shared details I might not otherwise have known.

Reporters face a public acutely aware of its own anger. Almost by definition in a country where the two major political parties struggle to find common ground, some group of readers disagrees with our coverage. We shouldn’t try to please everyone. In fact, we should try to please no one — we should merely work harder. It’s time to allow facts to speak for themselves.

It’s become an Abbott and Costello comedy routine, except in the nation’s capital. Let’s take a look:

Trump: “Strange as it may seen, they give ball players nowadays very peculiar names.”

Costello: “Funny names?”

Trump: “Nicknames, nicknames. Now, on the Washington team, we have who’s on first, what’s on second, I don’t know is on third.”

Costello: “That’s what I want to find out. I want you to tell me the names of the fellows on the Washington team.”

Trump: “I’m telling you. Who’s on first, what’s on second, I don’t know is on third.”

Costello: “You know the fellows’ names?”

Trump: “Yes.”

Costello: “Well, who’s playing first?”

Trump: “Who was playing first, but I fired him.”

Costello: “You fired him? Who did you fire?”

Trump: “Yes. I most certainly did. It was time for a new first baseman. We’ve got a better one coming in to play first.”

Costello: “Oh yeah? Who is that?”

Trump: “No, who was on first.”

Costello: “What are you asking me for?”

Trump: “I’m not asking you, I’m telling you. Who was on first.”

Costello: “I’m asking you, who’s on first?”

Trump: “I already told you, not anymore.”

Costello: “Not anymore is on first?”

Trump: “Yes.”

Costello: “You won’t tell me the name of the fellow on first base?”

Trump: “Yes, not anymore.”

Costello: “OK, so not anymore is playing first?”

Trump: “He was, but he just left, too, so now I have no one.”

Costello: “You don’t have a first baseman?”

Trump: “Yes, I do, no one.”

Costello: “How can no one play first?”

Trump: “He’s very talented. He’s one of the best players I’ve ever seen at the position. He’ll win games for us.”

Costello: “When you pay the first baseman every month, who gets the money?”

Trump: “He did, but no one gets it now.”

Costello: “So, you’re not paying anyone?”

Trump: “No, we’re paying no one. Sometimes his wife comes down and collects his paycheck.”

Costello: “No one’s wife?”

Trump: “Yes. After all, the man earns it.”

Costello: “No one does?”

Trump: “Absolutely.”

Costello: “Washington has a good outfield?”

Trump: “Oh, it’s great again.”

Costello: “The left fielder’s name?”

Trump: “Why.”

Costello: “I don’t know, I just thought I’d ask.”

Trump: “I just thought I’d tell you.”

Costello: “Then tell me who’s playing left field?”

Trump: “No, who was playing first, but he was fired.”

Costello: “Stay out of the infield! The left fielder’s name?”

Trump: “Why.”

Costello: “Why?”

Trump: “I’m thinking of moving why to center field after he did such a great job in left.”

Costello: “Who did a great job in left field?”

Trump: “No, who only plays first and he’s not on the team anymore, so I don’t want to talk about him.”

Costello: “You got a pitcher.”

Trump: “Wouldn’t this be a fine team without a pitcher?”

Costello: “Tell me the pitcher’s name.”

Trump: “Tomorrow.”

Costello: “Why not now?”

Trump: “No, why is in left field. He never pitches, but he might play center field.”

Costello: “Now when the guy at bat bunts the ball against tomorrow — me being a good catcher — I want to throw the guy out at first base, so I pick up the ball and throw it to no one.”

Trump: “Now, that’s the first thing you’ve said right.”

Costello: “I don’t even know what I’m talking about.”

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