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Daniel Dunaief

Bruce Stillman. Photo courtesy of CSHL

By Daniel Dunaief

Bruce Stillman, the president and CEO of Cold Spring Harbor Laboratory, was recently awarded the prestigious Canada Gairdner International Award for his contributions to research about the way DNA copies itself. The 60-year-old prize, which Stillman will receive in a ceremony in October and that he shares with his former postdoctoral fellow John Diffley, includes a financial award of $100,000 Canadian dollars that he can spend however he’d like.

A native Australian, Stillman, who has been at Cold Spring Harbor Laboratory since 1979, recently shared his thoughts about the award, research at the lab and his concerns about science in society with Times Beacon Record News Media. 

How does it feel winning the Gairdner Award?

It’s one of the most prestigious awards in the life sciences in the world and it’s certainly a great honor to win it and to join the list of spectacular scientists in the history of the award. There are some really fantastic scientists who I very much admire who have received this award.

How does it relate to the research you’ve conducted?

The field of DNA replication and chromosome inheritance was recognized. It is something I’ve devoted my entire career to. There are a lot of people that have made important contributions to this field. I’m pleased to be recognized with [Diffley] who was my former postdoc. [It’s validating] that the field was recognized.

Has CSH Laboratory been at the cutting edge of discoveries using the gene-editing tool CRISPR?

Cold Spring Harbor didn’t discover CRISPR. Like many institutions, we’ve been at the forefront of applying CRISPR and gene editing. The most spectacular application of that has been in the plant field. Zachary Lippman, Dave Jackson and Rob Martienssen are using genetic engineering to understand plant morphogenesis and development, thereby increasing the yield of fruit. Hopefully, this will be expanded into grains and have another green revolution.

CSHL has also been making strides in cancer research, particularly in Dave Tuveson’s lab, with organoids.

Organoids came out of people studying development. Hans Clevers [developed organoids] in the Netherlands … Tuveson is at the forefront of that. The full promise hasn’t been realized yet. From what I’ve seen, we are quite excited about the possibility of using organoids as a tool to get real feedback to patients. It is rapidly moving forward with the Lustgarten Foundation and with Northwell Health.

What are some of the other major initiatives at CSHL?

The laboratory’s investment about 10 or 15 years ago in understanding cognition in the brain has paid off enormously. Neuroscientists here are at the forefront of understanding cognition and how the brain does computation in complicated decisions. [Scientists are also] mapping circuits in the brain. It took a lot of investment and kind of the belief that studying rodent cognition could have an impact on human cognition, which was controversial when we started it here, but has paid out quite well. At the same time, we are studying cognitive dysfunction particularly in autism. 

Any other technological advances?

There’s been a real revolution in the field of structural biology… [Researchers] have the ability to look at single biological molecules in the electron microscope. It shoots electrons through a grid that has individual biological molecules. The revolution, which was done elsewhere by many people actually, led to the ability to get atomic resolution structures of macro molecular complexes. 

Cold Spring Harbor invested a lot of money, well over $10 million to build a facility and staff a facility to operate this new technology. I’ve been working on this area for about 12, 13 years now … Our structural biologists here in neuroscience, including neuroscientists Hiro Furukawa and Leemor Joshua-Tor have really helped introduce a lot of new biology into CSHL.

What are some of the newer efforts at the lab?

One of the big new initiatives we started is in the field of cancer. As you know by looking around, there’s an obesity epidemic in the Western world. We started a fairly large initiative, understanding the relationship between obesity and cancer and nutrition, and we’re not unique in this. We’re going to have some significant contributions in this area. 

Cancer cells and the tumor affect the whole body physiology. The most severe [consequence] is that advanced cancer patients lose weight through a process called cachexia. We hired [new staff] in this new initiative, renovated a historic building, the Demerec building at a fairly substantial expense, which was supported by New York State. 

What will CSHL researchers study related to obesity?

We’re absolutely going to be focusing on understanding mostly how obesity impacts cancer and the immune system, then how cancer impacts the whole body physiology. Hopefully, once we start to understand the circuits, [we] will be able to intervene. If we can control obesity, we will by logic reduce cancer impact.

What worries you about society?

What worries me is that there is a tendency in this country to ignore science in policy decisions … The number of people not getting vaccinated for measles is ridiculous. There is this kind of pervasive anti-science, anti-technology view that a lot of Americans have. They want the benefits of science and everything that can profit for them. 

There are certain groups of people who misuse data, deliberately abuse misinformation on science to promote agendas that are completely irrational. One of the worst is anti-vaccination. … We should as a society have severe penalties for those who choose to go that route. They shouldn’t send their children to schools, participate in public areas where they could spread a disease that effectively was controlled. Imagine if polio or tuberculosis came back?

How is the lab contributing to education?

People need to act like scientists. It’s one of the reasons we have the DNA Learning Center, to teach people to think like scientists. If 99.99 percent of the evidence suggests [something specific] and 0.01 percent suggest something [else], you have to wonder whether those very small and vocal minority are correct.

By Daniel Dunaief

Daniel Dunaief

As I write, we are 530 days away from the 2020 election. It’s nice that so many people want to lead this nation. Notwithstanding William Weld, the former Massachusetts governor who is a GOP challenger, it seems clear that the Republican nominee will be President Donald Trump, while the Democratic nominee could come from any of at least 23 candidates — and counting.

I’d like to ask these candidates a few questions to get the ball rolling.

1. How will you try to unify the nation? Clearly, we are a divided country. We can’t agree on anything from abortion to gay marriage to the job Trump is currently doing. We have become the Divided States of America. That doesn’t sit well with those of us who have enjoyed the benefits of a country pulling together through so many crises and conflicts, and who have appreciated the opportunity to travel from state to state, feeling like a part of something that spreads from sea to shining sea — and to Hawaii, Puerto Rico, the U.S. Virgin Islands and Guam. What will you do in the interest of unity?

2. Is there any way to bring the world closer together? If an extraterrestrial force landed today and threatened society, we would set aside our geographic and historic squabbles, and work together to understand this new species and protect ourselves. Why would it take such a threat to unify humans? Is there any way to spread peace, while allowing for differences? If you believe peace is possible, in what turbulent area would you start and how would you bring any two sides together?

3. Can we establish any political rules? It seems that the old days of agreeing to disagree or civil discourse are gone. Were those measured words and polite disagreements a matter of political correctness and do some candidates benefit from attacking each other? Would all of the candidates agree to a level of respect for each other, for the process and for the American populace?

4. What kind of role model will you be as president? Can you lay out any rules you would follow as president, in terms of what you would do and what you wouldn’t, as our leader? What should the penalty be for you if you don’t follow your own rules?

5. How will you measure your own success? It’s so easy to declare yourself a winner and to tell the country and the world what a great success you are. So many of you will run under the banner of bringing change or steering the nation toward a better or, some might say, great future. Don’t just tell us you’re wonderful, give us an idea of how to recognize it. What metrics will you use to know that you’re successful? Are the polls more important, or is the economy, the stock market or anything else a good barometer of your success?

6. What will you offer children that they don’t get now? Parents often care more about their children than they do about themselves. What will you do to make schools, food choices, activities or other options better for children than they are today?

7. How will you protect our elections? It’s clear that other nations feel like they can influence our elections. What can you do to ensure that the process proceeds as it should?

8. What’s wonderful or great about your spouse or partner? What do you admire about this person and what is one of your favorite memories with him or her?

9. Do the ends justify the means? Is it as important to ensure that the journey obeys certain rules and that the country follows a specific compass, or is it acceptable to get to the final destination by any means necessary?

Gordon Taylor with technician, Tatiana Zaliznyak. A Raman microspectrometer is pictured in the background. Photo by J. Griffin

By Daniel Dunaief

Something is happening in the Twilight Zone of the ocean, but it’s unclear exactly who is involved and how fast the process is occurring. 

Plants and animals are eating, living, defecating and dying above the so-called Twilight Zone and their bodies and waste are falling toward the bottom of the ocean. But most of that matter isn’t making it all the way to the ocean floor.

That’s where Gordon Taylor, a professor and director of the NAno-RAMAN Molecular Imaging Laboratory at the School of Marine & Atmospheric Sciences at Stony Brook University, comes in. 

Taylor and Professor Alexander Bochdansky of Old Dominion University recently received a $434,000 three-year grant to study the way microorganisms eat, process and convert organic carbon — i.e., carbon that’s a part of living organisms like plants, sea birds and whales — into inorganic carbon, which includes carbon dioxide, carbonate, bicarbonate and carbonic acid.

“The inorganic carbon moves back and forth among these four chemical species,” Taylor explained in an email. Understanding the rate at which carbonic acid builds up can and will help lead to a greater awareness of ways the ocean, which used to have a pH around 8.2 — which is slightly basic, as opposed to levels below the neutral 7— is becoming more acidic.

Above, incubators that Alexander Bochdansky has used in Bermuda. The ones Taylor and Bochdansky will analyze will be smaller than these, which won’t require such a large A-frame to deploy. Images courtesy of A. Bochdansky

They will start by deploying the traps at a single depth, about 985 feet, along the ocean off the coast of Virginia. “We are going to look at who the players are,” Bochdansky said. “There might be only a few key players that degrade this organic carbon. With [Taylor’s] great methods, we can measure the uptake rate in single microbes. This is really exciting.”

The Twilight Zone received its name because it is 650 to 3,300 feet below the surface of the water. Some faint light reaches the top of that zone, but most of that region, which includes creatures that use bioluminescence to attract or find prey, is pitch black.

“The directory of which inventories and fluxes decrease [is] still poorly understood,” Taylor said. “Animals eating the material is one mechanism and we don’t know how important that is compared to microbial decomposition or remineralization,” adding that the goal of this project is to “better define the role of microorganisms in returning carbon to the inorganic pool.”

Taylor is exploring this area with new tools that will allow a greater depth of understanding than previously possible. His group has developed new experimental approaches to apply Raman microspectrometry to this problem. The organisms they examine will include bacteria, fungi and protozoans.

Their experiment will explore which organisms are recycling organic carbon, how fast they are doing it and what factors control their activities. Through this approach, Taylor will be able to see these processes down to the level of a single cell as the instrument can identify organisms that have consumed the heavy isotope tracer.

The Raman microspectrometer uses an optical microscope with a laser and a Raman spectrometer. This tool will measure samples that are micrometers thick, which is smaller than the width of a human hair. The microspectrometer can obtain data from a 0.3-micrometer spot in a cell and he has even produced spectra from single viruses.

The scientists will place phytoplankton common to the region in incubators that Bochdansky developed. They will use a heavy carbon isotope, called carbon 13, that is easy to find through these experiments and see how rapidly microorganisms that colonize are incorporating the isotopically labeled carbon.

Taylor and Bochdansky received funding for the project through the Biological Oceanography Program at the National Science Foundation in the Directorate of Geosciences. Twice a year, the division makes open calls for proposals on any topic of interest to researchers. The scientists submit 15 pages of text that the NSF sends to peer reviewers. A panel meets to evaluate the reviews and ratings and decides which projects to fund.

Bochdansky and Taylor have been “acquainted for a long time and have shared similar interests,” Taylor said.

The carbon experiments in the Twilight Zone account for about a quarter of the work Taylor is doing in his lab. The other research also employs Raman microspectrometry. The United States only has one or two other facilities that do environmental research comparable to the one in Taylor’s lab at Stony Brook. Europe also has three such tools, which can look into single cells using lasers.

One of the other projects Taylor hopes to get funded involves studying the distribution of microplastics in the ocean. “The instrument I have is one of the best tools to look at microscopic plastic particles,” because it identifies the plastic polymer and its source, said Taylor, who is awaiting word on funding from the National Oceanic and Atmospheric Administration.

The other work involves exploring viruses that attack plankton.

“We are exploring Raman methods for early detection of viruses that attack plankton,” Taylor explained. Every organism in the ocean has at least one virus that has evolved to attack it.

As for his work on the Twilight Zone, Taylor said the area acts as a filter of sorts because less than 20 percent of the organic material entering at the top exits at the bottom.

Bochdansky added that these microbes are critical to processes that affect oceans and the planet.

“That’s something people often overlook,” Bochdansky said. “We can’t understand the ocean if we don’t understand it at the level or the scale that’s relevant to microbes.”

Bochdansky is thrilled to work with Taylor, who he’s known for years but will collaborate with for the first time on this project.

“In my lab, we have measured the turnover and release of carbon dioxide,” Bochdansky said. In Taylor’s lab, he measures “the actual feeding of microbial cells.”

Seth Rogen and Charlize Theron in a scene from the film. Photo courtesy of Lionsgate

By Daniel Dunaief

An improbable relationship between a hot-headed and schlumpy reporter Fred Flarsky, played by Seth Rogen, and a driven and successful Secretary of State Charlotte Field (Charlize Theron) forms the basis of Jonathan Levine’s rom-com “Long Shot.”

Set in contemporary Washington, D.C., and New York, the Lionsgate film addresses some current political issues, even as it centers around the pairing of the brilliant and successful Field with the less polished but talented writer Flarsky.

Charlize Theron and Seth Rogen and a scene from the film. Photo courtesy of Lionsgate

For starters, the movie earns its R rating with numerous bawdy humor, phallic references and strong, unrestrained language. It is not a cute parable about modern times that forces people to reconcile their differences and clean themselves up because of some broad theme like love conquers all — it is a feather duster heading for the audience’s funny bone. If you liked other Rogen films like “Knocked Up,” you’ll likely enjoy this one as well, even without his customary collection of collaborators.

The film offers few true surprises, even as it hits its humorous target several times, evoking laughter from an audience that appreciates the hijinks that spring from the combustible and rule-breaking Flarsky and the controlled Field, who entered the political fray because she wanted to change the world.

Flarsky isn’t exactly a trophy partner for Field, who is putting together an international environmental policy as a triumphant final act as secretary of state before she announces her candidacy to succeed her vacuous boss, President Chambers, played by Bob Odenkirk. A former TV star — hmm, I wonder where they came up with his character — Chambers is leaving the highest office in the land as he attempts to become a crossover film star.

Once she decides to run for office, Field learns from an image team that she needs to add humor to her speeches. Enter Flarsky, a former neighbor whom she used to babysit, who is also a talented and shoot-from-the-hip writer.

Every movie, even an odd-couple rom-com needs some kind of villain. Parker Wembley, played by Andy Serkis, fills that bill. Wembley owns an expansive and conservative media empire — uh, yeah, the challenge to figure out the inspiration for this character isn’t terribly taxing, either.

Wembley meanders in and out of the film, offering a menacing and overblown presence who will force the couple not only to confront their differences but also to maneuver through the kind of tension those who live public lives desperately try to avoid.

“Long Shot” has a few sidekicks who add necessary spice to the film, including Maggie Millikin (June Diane Raphael), who says what many in the audience are thinking as Field allows her developing attraction to Flarsky — say what? — to threaten her promising political career.

Creating Flarsky’s one-person entourage, Lance, played by O’Shea Jackson Jr. who bears a striking resemblance to his father Ice Cube, offers support, encouragement and a few surprises for the strong-willed Flarsky.

As with some of the other supporting actors, Agent M, played by Tristan D. Lalla, has a memorable and solid deadpan line when Flarsky asks him not to tell anyone about his relationship with Field.

While Rogen and Theron genuinely try to bridge the differences between the characters, it is unclear, other than through Flarsky’s compelling writing, why Field is so enthralled with him. Sure, Rogen has been successful in other movies and has built an effective career as an underachieving underdog, but her character doesn’t know that.

Even if the movie doesn’t break much new ground, deliver any huge surprises or provide grist for intense postmovie discussions, it does offer an easygoing and humorous break from our own reality.

Stock photo

By Daniel Dunaief

Daniel Dunaief

As I ponder the next step before my pint-sized daughter leaves the proverbial nest, I recall the incongruities between what we expected, what happened and what we remember. Please find below a list of some magical and not-so-magical moments.

The birth of our daughter

What we thought would happen: We had 40, no, make it 42, weeks to get ready for the birth of our daughter who waited well past her due date to appear. We took Lamaze classes — “breathe honey, breathe, there you go” — we read baby books and we had a birth plan. I figured my wife would let me know “it’s time” when her water broke or when the squint-through-them-and-then-smile-radiantly contractions arrived. We’d jump in a taxi and a wonderfully cheerful nurse would welcome us to the hospital.

What actually happened: Our daughter really didn’t want to come out, so the doctor scheduled an induced delivery. We casually packed our small bags, drove slowly to the hospital and walked up to the entrance. Numerous drugs, two days, almost no sleep and considerable anxiety later, our daughter still hadn’t made her appearance.

What we remember: This is tough, because we recall some of the hours of confusion and anxiety, but the end result was so life altering that one of our recurring memories was of a nurse coming in, to ask how many times we changed her diaper after she spent hours in the room with us. Wait, were we supposed to change her diaper?

Early trips to the doctor

What I thought would happen: He’d examine her and tell us what a wonderful job we were doing, and would offer us timely and helpful advice about surviving without sleep.

What actually happened: She weighed less than she did at birth. Is that good? Is that bad? No, it’s normal, he assured us. Why are you giving her shots already? Can’t she get shots later? She looks so peaceful. Why are you making her cry?

What I remember: That shot seemed so painful. We don’t remember our first shots, but we both felt as if the doctor were stabbing us with a sword when he gently inserted the needle in her arm.

First steps

What we thought would happen: She’d take some steps, we’d clap, and she’d be on her way.

What actually happened: We didn’t take away her walking toy until someone told us it was keeping her from learning to walk.

What we remember: Silly us, we delayed her walking because we let her keep using the toy, but, hey, she did just fine.

First athletic event

What I thought would happen: She’d try to throw or catch and ball and I’d be thrilled with her effort.

What actually happened: She played with dandelions and chatted with her friends.

What I remember: She looked great in that red T-shirt with her mitt turned backward toward her knee.

Going to high school

What we thought would happen: She’d share her daily experiences with us and we’d laugh and offer sage advice.

What actually happened: She grunted, we growled, and now she’s graduating

What we remember: She smiled and waved at us from the volleyball court and she laughed with us while we made cookies for her friends.

Driving 

What we thought would happen: She’d drive slowly and carefully and listen to us.

What actually happened: She told us all the advice we gave her wasn’t how we drove.

What we remember: She passed her driver’s test and can do errands and drive herself around. Thank goodness.

A rendering of Suskityrannus hazelae by Andrey Atuchin

By Daniel Dunaief

Even the name Tyrannosaurus rex seems capable of causing ripples across a glass of water, much the way the fictional and reincarnated version of the predator did in the movie “Jurassic Park.”

Long before the predatory dinosaur roamed North America with its powerful jaws and short forelimbs, some of its ancestral precursors, whom scientists believed were considerably smaller, remained a mystery.

A team of scientists led by Sterling Nesbitt, an assistant professor at Virginia Tech, shed some light on a period in which researchers have found relatively few fossils when they shared details about bones from two members of T. rex’s extended ancestral family in New Mexico. 

These fossils, which they named Suskityrannus hazelae, help fill in the record of tyrannosauroid dinosaurs that lived between the Early Cretaceous and latest Cretaceous species, which includes T. rex.

Sterling Nesbitt, assistant professor of geosciences at Virginia Tech, with a partial fossil of Suskityrannus hazelae found in New Mexico. Photo courtesy of Virginia Tech

The researchers, which included Alan Turner, an associate professor of anatomical sciences at Stony Brook University, chronicled the history of these fossils from the Late Cretaceous period, or about 92 million years ago.

“Getting a chance to understand the origin of something is compelling,” said Turner. “Having a discovery like Suskityrannus, which helps us understand how the body plan of tyrannosauroids evolved, is super interesting.” The fossils reveal the “humble beginnings” of a group that would “later dominate North American terrestrial ecosystems.”

Indeed, the new dinosaur was considerably more modest in size than future predators. The Suskityrannus, which included one individual that wasn’t fully grown when it died after living at least three years, measured about three feet at the hip, weighed about 100 pounds, and was about nine feet long, which made it more like a full grown male wolf, albeit longer because of its extended tail.

Scientists had found earlier tyrannosaur relatives from the Early Cretaceous as well as T. rex and its closest relatives near the end of the Late Cretaceous. They were missing data about tyrannosaurs from the middle of the group’s history because fossils from this time period are so rare.

The researchers cautioned that this paper, which was published in the journal Nature, Ecology & Evolution, does not suggest that Suskityrannus was a direct ancestor of T. rex. It does, however, fill a fossil gap in the extended T. rex family.

Suskityrannus hazelae,

The Suskityrannus species has a broad mouth and a muscular skull. Additionally, the bones in its foot were built in a way that made it good at absorbing shocks.

As far as fossil specimens, the bones from this finding are “well represented” across various parts of this creature’s anatomy, including a “lot of limb anatomy and a good portion of the skull and vertebral column,” Turner said. 

This collection of bones help define where on the evolutionary map this new species belong. Some of the anatomical characteristics in this new species appear to be well-suited for future predators, even as they likely also provided an adaptive advantage for the Suskityrannus. 

“These are features that were already in place much earlier” than this new species needed them, Turner said. They may have been adaptations that helped with their agility or with the environment in which they lived. Eventually, evolution turned them into the kinds of anatomical features that made them useful when T. rex eventually grew to as large as 16 tons.

“That’s something you see often in evolution: the way a species is using [its anatomy] isn’t always necessarily what the features evolved for,” Turner said. “Evolution can only work with what it has. What we see with Suskityrannus is that it had these things that became important later on.”

Turner’s role was to help compile and analyze the enormous amount of data that came out of this discovery. He explored how the number of species changed along the boundary between the first half of the Late Cretaceous and the second half of the Late Cretaceous periods, adding that the process of exploring and analyzing such a discovery can take years. 

Indeed, Turner first saw the fossil in 2007. “The studies take a long time and you can get lost in the details,” he said. “You do try and keep the big picture in your head. That’s the thing that makes [the work] interesting.”

Alan Turner while conducting fieldwork in Kenya last summer. Photo by Eric Gorscak

Turner became a part of this work through his connection to Nesbitt. The two scientists attended graduate school together at Columbia University. They have been doing field work together since 2005.

Nesbitt explained in an email that he thought of including Turner immediately “because he is an expert on aspects of paleobiology and theropods, plus he is an excellent colleague to work on papers with.”

In the research paper, the scientists have created an artistic rendering of what this new species might have looked like. While Turner acknowledges that the image involves a “bit of an artistic license,” the image is also “bound by what we know.” 

Nesbitt said this finding provides information about the theropods as a whole. “We really don’t know why T. rex and its closest relatives got so big,” he said, but researchers do know this happened at the end of the Cretaceous period, after 80 million years of being relatively small.

Turner lives in Port Jefferson with his wife, Melissa Cohen, who is the graduate program coordinator in the Department of Ecology & Evolution at Stony Brook University. The couple has two children.

Turner, who grew up in a suburb of Cleveland, recalls a field trip when he was 17 that encouraged him to pursue a career in paleontology. He was conducting research in Montana and he was exploring dinosaurs and sharing a sense of camaraderie with others on the expedition.

“I remember feeling like that was an affirming experience,” Turner said.

As for the discovery of Suskityrannus, Turner shared the wonder at finding a new species, something he’s been a part of eight times with dinosaurs in a career that now includes 11 years at Stony Brook.

“It’s always pretty exciting when you get to work on something that’s new,” he said.

West Meadow Beach at low tide. Photo by Beverly C. Tyler

By Daniel Dunaief

Daniel Dunaief

If you ever move away from Long Island, you may find relief and a longing.

The relief could take many forms. For starters, you may find a place with magnificent sidewalks that allows you to walk for miles without needing to step out into the road. Yes, there are such places, although they are mostly in urban environments, where you can watch people, find restaurants and not just bars that are open at all hours, and where you can shift from one ethnic neighborhood to another within a few blocks.

You may also find road relief, as people in other places may allow you to merge readily, may move at a different pace, and may smile and wave at you as you pass them while they are on their lawns, walking their dogs, throwing a ball with their daughters or sitting on a rocking chair on their front porches, appreciating the flow of human and avian traffic that passes by their houses.

You also may not miss the delays at the airports or the train stations, as you wonder if you’ll make it to the job interview, the meeting, the wedding or the date on time when construction, lane closures, accidents, sun glare or road flooding slow everything around you to a stop or a crawl.

You might also find yourself relieved that the delis — if you can find ones you like outside of Long Island — are much quieter, as people in other regions may not be as compelled to raise the decibel level in public to outcompete each other for stories or to place their turkey club orders.

But, then, you might also find yourself missing some key ingredient of Long Island life. There are plenty of landlocked places you can visit that have wonderful lakes, rivers and streams, but how many of them truly have Long Island’s magnificent and varied beaches?

You might miss sitting on a bluff in Port Jefferson and staring out at the harbor or looking through the channel into Long Island Sound. You might miss the chance to visit your favorite rocky beach on the North Shore, where you can walk slowly along, looking for the perfect skimming rocks, recalling the days decades ago when your grandfather taught you how to use surface tension to make a rock bounce its way far from shore.

You might miss the toughness of feet so accustomed to the uneven rocks that you pause momentarily when you see someone struggling to navigate them, remembering that you once found these rocks hard to cross as well.

You might miss the wonderful intertidal zone, which at low tide allows you to wander across rippled and water-cooled sand far from shore.

You might also miss winter beaches, where winds whip along the abandoned dunes and where, if a cold snap lasts long enough, you can see the top layer of water frozen as it heads toward shore.

If you ever took advantage of the myriad cultural and scientific opportunities on Long Island, you might also miss spectacular performances at the Staller Center, lectures and symposia at Stony Brook University, Cold Spring Harbor Laboratory or Brookhaven National Laboratory.

You might also miss the farms or vineyards on the East End, where you can admire the way rows of vines, trees or grass expand out from the road.

You might also miss the secrets hidden beneath the surface of the water. If you’ve ever had the opportunity to snorkel at Flax Pond or at a beach, you know that magnificent creatures — arthropods that live on yellow sponges and look like ancient creatures under a microscope — populate a completely different world that is within surprisingly easy reach.

Members of the quantum materials team, from left, Gregory Doerk, Jerzy Sadowski, Kevin Yager, Young Jae Shin and Aaron Stein. Photo from BNL

By Daniel Dunaief

Henry Ford revolutionized the way people manufactured cars through automation, speeding up the process, reducing waste and cutting costs.

Similarly, at Brookhaven National Laboratory, researchers like the newly hired Young Jae Shin, who is a staff scientist at the Center for Functional Nanomaterials, hopes to improve the process of automating the handling of thin flakes of material used in a next generation technology called quantum information science, or QIS.

Working with scientists at Harvard University and the Massachusetts Institute of Technology, Shin is looking for ways to handle these flakes, which are one atom thick, of two-dimensional layers from different materials. Stacked together, these flakes can help create structures with specific electronic, magnetic or optical properties that can be used as sensors, in communication, or encryption.

Young Jae Shin at Harvard University, where he was a post doctoral researcher. Photo from Y. Shin

“Researchers are building these kinds of customized structures manually now,” explained Kevin Yager, leader of the CFN Electronic Nanomaterials Group, in an email. “QPress [Quantum Material Press] will allow us to automate this.” At this point, QPress is just starting, but, if it works, it will “absolutely allow us to accelerate the study of these materials, allowing researchers to find optimal materials quickly,” Yager continued.

Theoretically, quantum computers overcome the limitations of other systems, Shin explained.

The flakes come from the exfoliation of thin structures taken from a bulk material. This is akin to a collection of leaves that fall around trees. According to Yager, the structures scientists hope to make would be akin to a collection of leaves from different trees, put together to make a new structure or material with specific properties. “The idea is for the robot to sift through the flakes, and identify the ‘best’ ones and to stack these together into the right structure. The ‘stacking’ will involve combining flakes of different materials,” he said.

The less desirable flakes typically are the wrong size, have tears, ripples or other defects and have contaminants. Groups of scientists are predicting the kinds of layered designs that will have desired properties.

Shin suggested that the CFN supports the needs of the end user community, as CFN is a “user-based facility.”

Physicists at Harvard and MIT plan to use the QPress to study unusual forms of superconductivity. By tapping into materials that conduct electricity without losing energy at lower temperatures, researchers may make progress in quantum computing, which could exceed the ability of the current state-of-the-art supercomputers.

Stacking the flakes can create new materials whose properties not only depend on the individual layers, but also on the angle between the stacks. Scientists can change one of these new structures from having metallic to having insulating properties, just by altering the relative angle of the atoms. The challenge, however, is that putting these fine layers together by hand takes time and generates errors which, BNL hopes, an automated approach can help reduce.

“Ultimately, we would like to develop a robot that delivers a stacked structure based on the 2-D flake sequences and crystal orientations that scientists select through a web interface” to a machine, Charles Black, the head of the Center for Functional Nanomaterials at BNL, explained in a recent BNL feature. “If successful, the QPress would enable scientists to spend their time and energy studying materials, rather than making them.”

Barring unforeseen delays, scientists anticipate that they will be able to build a machine that creates these flakes, catalogs them, stacks them and characterizes their properties within three years. These functions will be available online in stages, to allow the use of the QPress prior to its completion.

Each stage in the QPress process uses computer software to reduce the effort involved in generating and interpreting usable structures.

Minh Hoai Nguyen, an assistant professor in the Department of Computer Science at Stony Brook University and doctoral student Boyu Wang from the Computer Vision Lab at SBU are creating a flake cataloger, which will use image analysis software to scan and record the location of flakes and their properties.

“The flakes that scientists are interested in are thin and thus faint, so manual and visual inspection is a laborious and error-prone process,” Nguyen said in the BNL feature.

At BNL, Shin is one of three scientists the Upton-based facility is hiring as a part of this effort. They are also seeking robot or imaging process experts. Shin has “been in the CFN just a short while, but is already having an impact- — for instance, allowing us to handle classes of two-dimensional materials that we were not working with before,” Yager said.

The field of quantum information science is extremely competitive, with researchers from all over the world seeking ways to benefit from the properties of materials on such a small scale. The United States has been investing in this field to develop leadership science in this area.

The University of Tokyo has developed an automation system, but Shin explained that it is still not perfect.

Yager said that numerous unknown applications are “waiting to be discovered. Researchers are working hard on real quantum computers. Prototypes already exist but creating viable large-scale quantum computers is a major challenge.”

A resident of on-site housing at BNL, Shin was born in the United States and grew up in Korea. He is married to Hyo Jung Kim, who is studying violin at Boston University. 

As for the work Shin and others are doing, Yager suggested that the effort has generated considerable interest at the CFN.

“There is huge excitement at BNL about quantum research broadly and QPress in particular,” said Yager. Shin is “a big part of this — bringing new technical knowledge and new enthusiasm to this ambitious project.”

From left, Megan Crow, Associate Professor Jesse Gillis and postdoctoral researcher Sara Ballouz Photo by Gina Motisi/CSHL

By Daniel Dunaief

Diversity has become a buzz word in the workplace, as companies look to bring different perspectives that might represent customers, constituents or business partners. The same holds true for the human brain, which contains a wide assortment of interneurons that have numerous shapes and functions.

Interneurons act like a negative signal or a brake, slowing or stopping the transmission. Like a negative sign in math, though, some interneurons put the brakes on other neurons, performing a double negative role of disinhibiting. These cells of the nervous system, which are in places including the brain, spinal chord and retina, allow for the orderly and coordinated flow of signals.

One of the challenges in the study of these important cells is that scientists can’t agree on the number of types of interneurons.

“In classifying interneurons, everyone argues about them,” said Megan Crow, a postdoctoral researcher in Jesse Gillis’ lab at Cold Spring Harbor Laboratory. “People come to this question with many different techniques, whether they are looking at the shape or the connectivity or the electrophysiological properties.”

Megan Crow. Photo by Constance Brukin

Crow recently received a two-year grant from the National Institutes of Health to try to measure and explain the diversity of interneurons that, down the road, could have implications for neurological diseases or disorders in which an excitatory stimulus lasts too long.

“Understanding interneuron diversity is one of the holy grails of neuroscience,” explained Gillis in an email. “It is central to the broader mission of understanding the neural circuits which underlie all behavior.”

Crow plans to use molecular classifications to understand these subtypes of neurons. Her “specific vision” involves exploiting “expected relationships between genes and across data modalities in a biologically thoughtful way,” said Gillis.

Crow’s earlier research suggests there are 11 subtypes in the mouse brain, but the exact number is a “work in progress,” she said.

Her work studying the interneurons of the neocortex has been “some of the most influential work in our field in the last two to three years,” said Shreejoy Tripathy, an assistant professor in the Department of Psychiatry at the University of Toronto. Tripathy hasn’t collaborated with Crow but has been aware of her work for several years.

The interactivity of a neuron is akin to personalities people demonstrate when they are in a social setting. The goal of a neuronal circuit is to take an input and turn it into an output. Interneurons are at the center of this circuit, and their “personalities” affect the way they influence information flow, Crow suggested.

“If you think of a neuron as a person, there are main personality characteristics,” she explained. Some neurons are the equivalent of extraverted, which suggests that they have a lot of adhesion proteins that will make connections with other cells.

“The way neurons speak to one another is important in determining” their classes or types, she said.

A major advance that enabled this analysis springs from new technology, including single-cell RNA sequencing, which allows scientists to make thousands of measurements from thousands of cells, all at the same time.

“What I specialize in and what gives us a big leg up is that we can compare all of the outputs from all of the labs,” Crow said. She is no longer conducting her own research to produce data and, instead, is putting together the enormous volume of information that comes out of labs around the world.

Megan Crow. Photo by Daniel Katt

Using data from other scientists does introduce an element of variability, but Crow believes she is more of a “lumper than a splitter,” although she would like to try to understand variation where it is statistically possible.

She believes in using data for which she has rigorous quality control, adding, “If we know some research has been validated externally more rigorously than others, we might tend to trust those classifications with more confidence.”

Additionally she plans to collaborate with Josh Huang, the Charles Robertson professor of neuroscience at Cold Spring Harbor Laboratory, who she described as an interneuron expert and suggested she would use his expertise as a “sniff test” on certain experiments.

At this point, Crow is in the process of collecting baseline data. Eventually, she recognizes that some interneurons might change in their role from one group to another, depending on the stimuli.,

Crow hasn’t always pursued a computational approach to research. 

In her graduate work at King’s College London, she produced data and analyzed her own experiments, studying the sensory experience of pain.

One of the challenges scientists are addressing is how pain becomes chronic, like an injury that never heals. The opioid crisis is a problem for numerous reasons, including that people are in chronic pain. Crow was interested in understanding the neurons involved in pain, and to figure out a way to treat it. “The sensory neurons in pain sparked my general interest in how neurons work and what makes them into what they are,” she said.

Crow indicated that two things brought her to the pain field. For starters, she had a fantastic undergraduate mentor at McGill University, Professor of Psychology Jeff Mogil, who “brought the field to life for me by explaining its socio-economic importance, its evolutionary ancient origins, and showed me how mouse behavioral genetic approaches could make inroads into a largely intractable problem.”

Crow also said she had a feeling that there might be room to make an impact on the field by focusing on molecular genetic techniques rather than the more traditional electrophysiological and pharmacological approaches.

As for computational biology, she said she focuses on interpreting data, rather than in other areas of the field, which include building models and simulations or developing algorithms and software.

In the bigger picture, Crow said she’s still very interested in disease and would like to understand the role that interneurons and other cells play. “If we can get the tools to be able to target” some of the cells involved in diseases, “we might find away to treat those conditions.”

The kind of research she is conducting could start to provide an understanding of how cells interact and what can go wrong in their neurodevelopment.

Gillis praises his postdoctoral researcher for the impact of her research.

“Just about any time [Crow] has presented her work — and she has done it a lot — she has ended up convincing members of the audience so strongly that they either want to collaborate, adapt her ideas, or recruit her,” Gillis wrote in an email. 

Crow grew up in Toronto, Canada. She said she loved school, including science and math, but she also enjoyed reading and performing in school plays. She directed a play and was in “The Merchant of Venice.” In high school, she also used to teach skiing.

A resident of Park Slope in Brooklyn, Crow commutes about an hour each way on the train, during which she can do some work and catch up on her reading.

She appreciates the opportunity to work with other researchers at Cold Spring Harbor, which has been “an incredible learning experience.”

By Daniel Dunaief

Daniel Dunaief

Advice is wonderful, unless it isn’t. The giving and receiving of advice is nothing like the process of exchanging gifts around the December holidays.

Often, there is a not-so-subtle subtext to advice that sitcoms have used to relatable comedic effect. 

A comment like, “You’re wearing that to your date?” isn’t advice, per se, although the underlying message is clear: “You could do so much better.” Extending this even further, the speaker seems to suggest that the listener returns to his or her dorm room, finds something that’s not wrinkled and doesn’t smell like the gym, and then go out on the date.

With high school and college graduations on the horizon, it’s inevitable that people will share their thoughts, opinions and ideas with the person they are celebrating. Here are a few pieces of advice and the translation for them:

Advice: “You might want to study a little harder in college than you did in high school. It’s much harder.”

Translation: “You’re probably lucky to graduate from high school and you won’t be so lucky in college, so take this time to start over and get your act together. Maybe you should consider studying more than 12 hours before a test on material you read all night the day before.”

Advice: “The time goes so fast. Take the time to appreciate and seize every opportunity.”

Translation: “I missed out on a lot of things in college and I’d like to go back and take better classes, find different friends and start over again. How about if you invent a time machine while you’re in college and send me back, so I can do it right this time?”

Advice: “Not everything your professors tell you is true, accurate or in your best interests.”

Translation: “Someone told me to major in chemistry. I hated it. I did something else for a living and it would have helped to take courses that made more sense. I could really use that time machine about now. How about if you make that your senior thesis?”

Advice: “Pick your friends carefully.”

Translation: “I didn’t really like your high school friends and I wish social media didn’t exist, so you wouldn’t stay in touch with all those people who steered you the wrong way. How about if you pick the nerdy woman who’s going to start her own company some day or the intellectual guy who plans to open a new school? Maybe, instead of asking me what classes I think you should take, you should send me a list of your prospective friends. That way I can be like a Roman emperor, putting a thumbs up or thumbs down on the relationship.”

Advice: “Pizza and soda are killers for the waistline.”

Translation: “I had the “freshman 20” and it took months to lose it. I blame pizza and soda which, at college, is pretty much 90 percent of your diet. Good luck avoiding the easy sugars and carbs when you’re up late at night, having the conversation of your life and you need energy so you don’t nod off when your friend from New Zealand with the cool accent shares some story you know you’ll want to recall the next day.”

Advice: “Floss your teeth.”

Translation: “This comes from hard-earned experience. Flossing is the best way to prevent root canals and those are among the most painful procedures many of us endure as we age. That is probably the best advice for graduates leaving the nest. If you floss, the older version of yourself will be eternally grateful.”