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Authors Posts by Daniel Dunaief

Daniel Dunaief

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Halloween has always seemed like an opportunity to explore the creatively terrifying parts of our imagination. We put up ghosts, goblins, skeletons and spiderwebs around our houses; we dress our children as Dracula, Frankenstein’s monster and zombies; and we jump out from behind bushes, yelling “Boo” or “Happy Halloween.”

Maybe, instead of indulging the frightening side of life that seems present almost daily, we should take this opportunity to develop wouldn’t-it-be-nice costumes.

For starters, we could dress our kids, or ourselves if we’re in jobs that allow us to come to work in costume, as giant, dirty hands. When asked to explain ourselves, we could suggest that we’re helping hands, willing to get our hands dirty to help those in need anywhere. This includes Puerto Rico, where people are still without power and are seeking to meet basic needs such as food and water. It also could include a co-worker dealing with an illness or death in the family, or an injured neighbor who can’t get his recycling to the curb.

While we’re at it, we could dress as a door with a giant lever people could pull to knock. What are we? We could be opportunity. Every day presents an opportunity to become what we wish, whether that’s someone who can and will lose weight, or someone who sets an incredible example for our children and for other people’s children, or someone who no longer stays silent when he or she sees any type of injustice, whether that’s discrimination, harassment or bullying.

Maybe, we could send our kids out as giant ears. They could become the great listeners. We have so many aspiring great speakers who share every thought in their head, whether that’s online, in a tweet or on a TV show, scoffing, pontificating and second-guessing everyone and everything. What does a great listener do, besides absorbing the deluge of thoughts coming his or her way? That person imagines the ideas and motivation behind those words, considers the hurt or vulnerability that those ideas might convey, and thinks of ways to change negative thoughts and behavioral patterns into something positive and inspiring.

Extending the auditory idea, we could also send our kids out in togas with a bucket of fake ears. Why the togas? They could be Romans. Why the ears? Just ask Shakespeare, whose Mark Antony exhorts a crowd in Act III, scene ii of “Julius Caesar” with the opening line, “Friends, Romans, countrymen, lend me your ears.”

We could encourage children to listen and read one of the greatest and most often cited speeches from Shakespeare, helping them learn about the power of rhetoric and the passion of ideas. The older children might even suggest that they are a walking example of praeteritio, the literary technique Antony uses when he suggests he’s not going to discuss that which he shares in great detail, namely, the recently deceased Caesar’s contributions to Rome and its citizens.

For those who need something with a shriek component, we could create a costume in which someone dresses up in everyday clothing. An individual could hold a small cage or a tight box containing whatever horrifying image that person imagines in connection with a disease. He or she could suggest that the disease is contained and that this illness, which is locked in a box, is being taken for a walk. As a result, a horrifying disease is minimized and contained.

Finally, we could cover our kids in the kind of headlines we’d like to see, including “Peace breaks out all over the world,” “Children cure cancer,” “Bullying takes a day off,” “Endangered species recover from the brink of extinction” and “Leaders agree to work together.” What would we call such a costume? Fake news.

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Heather Lynch at Spigot Peak in the Antarctic. Photo by Catherine Foley

By Daniel Dunaief

Counting penguins is like riding the highs and lows of Yankees rookie Aaron Judge’s home run streaks, followed by his series of strike outs. He’s not as bad as his strike outs suggest, although he’s also not a sure thing at the plate either.

Similarly, in local populations, the Adélie penguin, which waddles to and fro squawking on land and gliding gracefully through the water, isn’t as clear a barometer of changes in the environment. Also, like Judge, when populations rise and fall, people are eager to offer their explanations for exactly what’s happening, even if the sensational explanations — he’s not that good, no, wait, he’s the greatest ever — may overstate the reality.

Heather Lynch visits Cape Lookout in Antarctica during recent trip that included an NBC TV crew that produced a feature for ‘Sunday Night with Megan Kelly.’ Photo by Jeff Topham

“We have to be careful not to be overreactive,” said Heather Lynch, an associate professor of ecology and evolution at Stony Brook University. “The concern is that, when we see increases or decreases, the implication is that there’s a miraculous recovery or a catastrophic crash.”

That, however, is inconsistent with Lynch’s recent results, which were published in the journal Nature Communications. Examining penguin data from 1982 to 2015, Lynch, Christian Che-Castaldo, who is a postdoctoral researcher in Lynch’s lab, and nine other researchers looked to see if there’s a way to connect the size of the population to changes in the environment. The study involved two teams of researchers, one supported by NASA and the other backed by the National Science Foundation.

“It’s a noisy system,” Lynch concluded. Managers of the populations of krill, small crustaceans that are the mainstay of the Adélie diet, try to use time series of key indicator species to understand what’s going on in the marine realm. In this article, Lynch said, local Adélie penguin populations may not be a clear signal of the health of the krill stocks because penguin abundance fluctuates for reasons she and her team couldn’t pinpoint.

These penguins, which Lynch has counted during her field work in the Antarctic, exhibit changes in population that can run contrary to the health, or stressed condition, of the environment.

“You can’t have your finger on the pulse” with the available data, Lynch said. “Part of our inability to model year-to-year changes is because we can’t measure the right things in the environment.”

The drivers of abundance fluctuations likely involve other animals or aspects of the krill fisheries they couldn’t model, she suggested.

“There’s a lot we don’t know about what penguins do under water, where they spend a large portion of their time and where they feed,” Grant Humphries, who was in Lynch’s lab for a year and now runs his own data science company in Scotland called Black Bawks Data Science Ltd, explained in an email. “The signals that drive year to year changes might actually lie there.”

Tom Hart, a researcher of the Department of Zoology at the University of Oxford who was not involved in this study, explores local scale variation in penguin populations. Locally, Hart said in an interview by Skype, “Things are incredibly noisy. When you aggregate, you get good signals, but with some error.” He suggested that this research drives him on further, showing that “local influences are important” because there’s so much variance left to explain. Lynch’s research is “a really good study and shows very well what’s happening on the regional scale, but leaves open what happens below that,” he said.

Indeed, Lynch suggested that by putting sites together, researchers can look at larger areas, which provide a clearer picture on shorter time scales.

Michael Polito, an assistant professor in the Department of Oceanography and Coastal Sciences at Louisiana State University who was not involved in the study, suggests that this extensive analysis indicates that “you can still look at the relationship between the abundance of penguins and the environment in a robust way. Even though any individual time series may not be the best way to understand these relationships, in the aggregate you can use them.”

Managers who set fishery policies in Antarctic waterways are often concerned about harvesting too much krill, leaving the penguins without enough food to survive and feed their chicks.

The challenge with this result, Lynch acknowledges, is that it makes setting krill boundaries more difficult.

A strategy that involves resetting conservation targets based on annual monitoring appears unrealistic given these results, Lynch said. “From a practical standpoint, we threw in everything we could and could explain only a tiny fraction of the variation,” she said.

Hart added that this is “not an argument to fish away,” he said. “We need to understand what’s going on at a local scale and we’re not there yet.”

To get people involved, Lynch and her team created a science competition, called Random Walk of the Penguins, to see who could predict the overall penguin populations for Adélie, gentoo and chinstrap penguins from the 2014 to 2017 seasons.

The competition, which was a collaborative effort with Oceanites, Black Bawks Data Science and Driven Data included $16,000 in prize money, which was donated by NASA. Entrants could use data from the 1982 through the 2013 seasons. The contest drew competitors from six continents. Of the five winners, all were from different countries.

Humphries, who was the lead on the data science computation, said the results were “somewhat humbling” because competitors were able to make “decent predictions” using only the time series. “With long-term predictions and for determining the tipping points, there is still a lot of work to be done.”

Lynch is relieved that her co-authors supported the direction the article took. “I’m a skeptic by nature and more than happy to throw orthodoxy (or even my own previous work) under the bus,” she wrote in an email. “I do hope that others will use our model as a starting point and we’ll never go back to the old days where everyone looked only at ‘their sites.’”

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I’m going to start with a headline relationship that would make Niccolò Machiavelli proud and work my way toward life on Main Street. You remember Machiavelli? That’s the author who wrote “The Prince,” which was first published way back in 1532, about how to manipulate people to survive and use any means available.

Wait, please don’t go. There won’t be a test and that’s the last date I’ll put in this column. Promise.

So, I’m thinking about relationships because of the new and improved dynamic between President Donald Trump and his Best Friend for Now — BFN, anyone? — Sen. Mitch McConnell. After a few tough losses, the Republican leaders seemed testy in their exchanges.

No, no, they said earlier this week, that wasn’t so. They are buddies and they agree on everything. Well, almost everything. According to sources, the senior senator also wants two scoops of ice cream when he visits the White House, but the commander in chief has no intention of changing his ice cream policies, even for his BFN.

Anyway, what brought these two older white men together? Did they talk about what it’s like to be misunderstood? Were they eager to find a friend in Washington, D.C., and did neither of them want to get a dog, as the expression goes?

No, they came together because they need to. It’s so much easier, they decided, to agree and to work together than to disagree. That sounds reasonable, but what would Machiavelli think? I suspect he’d be thrilled. After all, it’s about surviving, learning to fight another day and moving the chess pieces of life around on the board. Fortunately, and I won’t put the date in here because I don’t want to break my promise, chess was invented before “The Prince” was published. If you want to find it, you can look it up on the internet, which is the source of all information and misinformation in the universe. So, Machiavelli would have known about chess and the need to sacrifice the short-term humiliation of needing anyone and the mutually assured long-term gain of having allies in Washington.

OK, so let’s step away from the seat of our democracy and go out into the real world. Why do the rest of us need relationships and what can they do for us?

Are we like ants and bees, who need each other for specialized jobs?

Yes and no. Certainly, I would have a hard time building my own house. I feel as if I have an incompetence allergy to the words “some assembly required.” I am also visual-arts deficient. People offer all kinds of false modesty, saying things like, “I used to ski a little” or “I used to do a bit of singing,” when they almost made the Olympic team and were a few auditions short of starring next to Julie Andrews on Broadway. I, however, am not being modest. If I were responsible for building walls and decorating them, we’d be living in caves and would be staring at uninspiring chalk drawings of woolly mammoths.

So, yes, our individual deficiencies suggest we do need each other. But, maybe, we benefit not just what we get from others.

One of my good friends is in a new relationship. He has always been in decent physical shape. He’s not much of a reader and has shied away from even the shortest of reading assignments. Anyway, he’s dating a woman who is a regular runner and an avid reader. Lo and behold, he recently beamed after completing a half marathon and is happily building his own personal library.

Maybe the best and longest lasting relationships are those that push us to find the best in ourselves. It’s not exactly Machiavelli 101 and it doesn’t require a press conference, but maybe the right relationships are those that help us develop in unexpected ways.

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Adam Gonzalez. Photo from SBU

By Daniel Dunaief

More than four days after lift off, pioneering astronauts Neil Armstrong and Buzz Aldrin had landed in the Sea of Tranquility on the surface of the moon. The NASA schedule, which included preparing the vehicle for an emergency abort of the mission in the event of a problem, called for a nap of four hours. Once they were there, however, Armstrong and Aldrin couldn’t imagine taking a four-hour respite.

“Both Armstrong and Aldrin were, understandably, excited about where they were and decided to forgo the sleeping and changed history,” Thomas Williams, element scientist in Human Factors and Behavioral Performance at NASA, described in an email.

A future trip to Mars, however, would involve considerably longer delayed gratification, with the round trip estimated to take over 400 days. The stresses and strains, the anxiety about an uncertain future and the increasing distance from family and friends, not to mention the smell of cut grass and the appearance of holiday decorations, could weigh on even the most eager of astronauts.

Determined to prepare for contingencies, NASA is funding research to understand ways to combat the mental health strains that might affect future astronauts who dare to go further than anyone has ever gone.

‘Being in long-duration space missions with other people, we expect the mental health risk will be much more elevated’. — Adam Gonzalez

Gonzalez, an assistant professor of psychiatry at Stony Brook University, received over $1 million in funding from NASA to explore ways to help these future astronauts who might be anxious or depressed when they’re on the way to the red planet.

In a highly competitive process, Gonzalez received the financial support to provide guidance on what NASA considers a low-probability, high-consequence mental health event, according to Williams.

Gonzalez “was funded because of the soundness of his research proposal and the clinical and technological expertise of the research team he assembled to help NASA address this research gap,” Williams explained.

Gonzalez started providing three different types of psychological assistance to 135 people in the middle of September. He is testing ways to provide mental health assistance with a delay that could require over 40 minutes to travel back and forth.

One group of test subjects will use a system called myCompass, which is a mental health self-help program. Another group will use myCompass coupled with a delayed text messaging response from a therapist, and a third will have a myCompass system along with delayed video messaging from a therapist.

“Being in long-duration space missions with other people — in this case, months and potentially years — stuck in extremely close quarters with others, we expect the mental health risk will be much more elevated relative to what they are going to have on the International Space Station,” Gonzalez said.

Williams said astronauts to date have not had any diagnosable disorders, but NASA has seen fluctuations in their mood, which appears linked to workload demands and the phase of the mission, Williams said. For astronauts, NASA does not want a continuing negative trend that, over a longer term, could turn into a problem.

“Part of what we hope to achieve with [Gonzalez’s] research is a validated approach to address any of these concerns,” Williams said, adding that astronauts typically understand that their contributions involve work in “high-demand, extreme environments,” Williams said.

Still, like explorers in earlier centuries, astronauts on a trip to Mars will journey farther and for a longer period of time than anyone up to that point. MyCompass is a “good, efficacious program” that takes a “trans-diagnostic cognitive behavioral therapy approach,” Gonzalez said. He suggested that the program is broad enough to help individuals manage their emotions more generally, as opposed to targeting specific types of health disorders.

Gonzalez emphasized that the choice of using myCompass as a part of this experiment was his and might not be NASA’s. The purpose of this study is to investigate different methods for communicating for mental health purposes when real-time communication isn’t possible.

William suggested that Gonzalez’s work, among others, could lead to individualized procedures for each astronaut. In addition to his work with NASA, Gonzalez also assists people at the front lines after man-made or natural disasters. He has worked with Benjamin Luft, the director of Stony Brook University’s WTC Wellness Program, on a program that offers assistance to first responders after the 9/11 attacks.

Gonzalez’s father, Peter, was a police officer who worked on the World Trade Center cleanup and recovery efforts. The elder Gonzalez has since had 9/11-related health conditions.

Gonzalez and associate professor Anka Vujanovic, the co-director of the Trauma and Anxiety Clinic at the University of Houston, are putting together a research project for the Houston area. Vujanovic did a mental health survey on Houston area firefighters earlier this year. They are inviting these firefighters to complete an online survey and telephone assessment to determine their mental health after Hurricane Harvey.

They are also conducting a three- to four-hour resilience training workshop for Houston area firefighters engaged in Harvey disaster relief efforts. “This resilience program, developed by [Gonzalez] and his colleagues, has shown promising results in reducing various mental health symptoms when tested among first responders in the aftermath of Hurricane Sandy,” Vujanovic explained in an email.

Vujanovic has known Gonzalez for over 10 years and suggested his questions were focused on “how can we better serve others, how can we improve existing interventions and how can we develop culturally sensitive approaches for vulnerable, understudied populations.” Gonzalez, who grew up in Bensonhurst, Brooklyn, and came to Stony Brook in 2012, said he was always interested in helping others.

Williams suggested that this kind of research can help people outside the space program. “We openly share and encourage the sharing of any of our relevant research findings to help address societal needs,” he added. Gonzalez’s research is “a great example of how a NASA focus on delivering personalized interventions in support of long-duration spaceflight could potentially be generalized to more rural settings where mental health providers may be scarce.”

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What people don’t say can speak volumes.

Take the Harvey Weinstein allegations. Numerous women have come forward and described abhorrent behavior toward women by someone in power. That’s not a new phenomenon, but what’s new is the identity of the perpetrator and the time period involved — decades, it appears.

When asked about the allegations, President Donald Trump said he was “not at all surprised to see it.”

Hmm, not at all surprised? Didn’t the person whose every word and tweet gets splashed across headlines around the world have anything else to say, like, “If the allegations are true, it’s horrible and we should address this problem as a nation.” Or, “We as a country need to address this serious problem.”

No, he didn’t. In a follow-up question, a reporter asked if Weinstein’s behavior was inappropriate, and Trump responded that the movie executive said it was.

Again, not much there. I recognize this wasn’t a women’s rights forum and that he didn’t have prepared remarks or a flowing speech to cite, but he had an opportunity to address a real problem and he seemed more prepared to suggest he knew that Weinstein’s superstar public character had some tarnish.

The New York public transport system has run ads for years imploring, “If you see something, say something.”

That’s not always easy, especially when no one else might have been around to hear or see inappropriate comments or gestures.

This isn’t about political correctness: It’s about allowing people to do their best work without feeling threatened or uncomfortable. Locker room talk, or anything else that resembles a put-down for whatever reason, creates a hostile work environment.

Almost exactly a year ago, candidate Trump described several women who accused the Clintons of improper behavior towards women as “courageous” at a press conference before a debate with Hillary Clinton. While Trump hasn’t shared any such words of support for Weinstein’s victims, others have applauded them for coming forward. If Weinstein’s alleged victims had done so initially, taking on the equivalent of a movie icon could have put their careers at risk.

Gender politics are often a challenging and sore point at work. People can often dismiss inappropriate comments as being jokes or suggesting that their words weren’t what they intended.

Some jobs, like Wall Street trading, or, well, locker rooms, often involve a type of bawdy humor that is part of the culture.

But why should anyone have to tolerate it? With training and a heightened public awareness, the excuse “Well, that’s just the way it is” could turn into, “That’s not the way we do things around here.”

Pundits are suggesting that if eight women have come forward to accuse Weinstein, there are likely many more.

Then again, if he could and did engage in inappropriate conduct for decades, you have to imagine there are other men who did it, too.

Weinstein, in his own words, needs help. So, too, does the rest of society. He suggested he came from a different era. Others have taken him to task, indicating that somewhere along the line, he missed some major strides society made between whatever time period he imagined and today.

Who else is living in that era and how can we help them? Maybe, in addition to training the next set of up-and-coming managers, we should make sure the top executives — most of whom are men — understand what’s OK and what crosses a real line that is not only objectionable, but is also problematic for them and their careers.

We watch movies for many reasons: We want to be inspired, we want to understand other people and, sometimes, we want a perspective that helps us understand ourselves better. Maybe the inappropriate actions of a moviemaker can shed some more light on a problem that clearly isn’t unique to one person. A corollary to the transport ad, perhaps, should be, “If you hear something, say something.”

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From left, Zachary Lippman and Dave Jackson, professors at CSHL who are working on ways to alter promoter regions of genes to control traits in tomato and corn. Photo by Ullas Pedmale

By Daniel Dunaief

He works with tomatoes, but what he’s discovered could have applications to food and fuel crops, including corn, rice and wheat.

Using the latest gene editing technique called CRISPR, Zachary Lippman, a professor at Cold Spring Harbor Laboratory, developed ways to fine-tune traits for fruit size, branching architecture and plant shape. Called quantitative variation, these genetic changes act as a dimmer switch, potentially increasing or decreasing specific traits. This could help meet specific agricultural needs. Looking at the so-called promoter region of genes, Lippman was able to “use those genes as proof of principal” for a technique that may enable the fine-tuning of several traits.

For decades, plant breeders have been looking for naturally occurring mutations that allow them to breed those desirable traits, such as a larger fruit on a tomato or more branches on a plant. In some cases, genetic mutations have occurred naturally, altering the cell’s directions. At other times, breeders have sought ways to encourage mutations by treating their seeds with a specific mutagenic agent, like a chemical.

In an article in the journal Cell, Lippman said the results reflect a road map that other researchers or agricultural companies can use to create desirable traits. This article provides a way to “create a new, raw material for breeders to have access to tools they never had before,” he said. Lippman has taken a chunk of the DNA in the promoter region, typically on the order of 2,000 to 4,000 base pairs, and let the CRISPR scissors alter this part of the genetic code. Then, he and his scientific team chose which cuts from the scissors and subsequent repairs by the cell’s machinery gave the desired modifications to the traits they were studying.

Invented only five years ago, CRISPR is a genetic editing technique that uses tools bacteria have developed to fight off viral infections. Once a bacteria is attacked by a virus, it inserts a small piece of the viral gene into its own sequence. If a similar virus attacks again, the bacteria immediately recognizes the invader and cuts the sequence away.

Scientists sometimes use these molecular scissors to trim specific gene sequences in a process called a deletion. They are also working toward ways to take another genetic code and insert a replacement. “Replacement technology is only now starting to become efficient,” Lippman said. Clinical researchers are especially excited about the potential for this technique in treating genetic conditions, potentially removing and replacing an ineffective sequence.

In Lippman’s case, he used the scissors to cut in several places in the promoter regions of the tomato plant. Rather than targeting specific genes, he directed those scissors to change the genome at several places. When he planted the new seeds, he explored their phenotype, or the physical manifestation of their genetic instructions. These phenotypes varied along a continuum, depending on the changes in their genes.

By going backward and then comparing the genes of the altered plants to the original, he could then hone in on the precise changes in the genetic code that enabled that variation. This technique allows for a finer manipulation than turning on or off specific genes in which an organism, in this case a plant, would either follow specific instructions or would go on a transcriptional break, halting production until it was turned on again.

At this point, Lippman has worked with each trait individually but hasn’t done quantitative variation for more than one at a time. “The next question,” he said, “is to do this multitargeting.” He will also use the tool to study how genes are instructed to turn on and off during growth, including exploring the levels and location of expression.

Lippman is talking with agricultural and scientific collaborators and hopes to go beyond the tomato to exploring the application of this approach to other crops. He is working with Dave Jackson, who is also a professor at Cold Spring Harbor Laboratory, on applying this model to corn.

The scientific duo has known each other for 20 years. Jackson taught his collaborator when Lippman was a graduate student at Cold Spring Harbor Laboratory and Jackson was chair of his thesis committee.

They have worked together on and off since Lippman became a faculty member about nine years ago. Last year, the two received a National Science Foundation genome grant to work on using CRISPR to study the effect of changes in promoter regions in their respective plant specialties.

“Unfortunately for us, tomato has a faster life cycle than corn, but we hope to have some results in corn this fall,” Jackson explained in an email. Lippman hopes to continue on the path toward understanding how regulatory DNA is controlling complex traits. “We can use this tool to dissect critical regulatory regions,” he said. “When we create this variation, we can look at how that translates to a phenotypic variation.”

Lippman said he is especially excited about the fundamental biological questions related to plant growth and development. When other scientists or agricultural companies attempt to use this approach, they may run into some challenges, he said. Some plants are “not transformable [genetically] easily.” These plants can be recalcitrant to plant transformation, a step sometimes needed for CRISPR gene editing. Still, it is “likely that CRISPR will work in all organisms,” he said.

Lippman hopes others discuss this technique and see the potential for a system that could help to customize plants. “My hope and my anticipation is that people all over the world will look at this paper and say, ‘Let’s start to try this out in our own systems.’ Hopefully, there will be a grass roots effort to import this tool.”

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Thank you, mental health workers. If it weren’t for you, we might be living with even more unimaginable tragedies.

For reasons most of us, fortunately, can only imagine at a distance, people are tormented by destructive urges. When these moments arise, hopefully, a psychologist, psychiatrist, counselor or someone in a position to recognize the signs can step in and offer support, while redirecting that person toward a course of action that’s safer for them and for society.

Much of the time, we don’t see the people who soothe the minds. When they do their job well, the sun rises in the morning, we send our children to school, we clap at the end of their concerts and we feed them their meals before sending them to bed for the night.

When I was in junior high school, I read books such as “Lord of the Flies” and “The Crucible,” which my teacher Mrs. Wickle suggested were an important way to look at the “dark side” of the heart.

At the time, I found the subjects depressing and unnecessary. Why, I thought, did I have to read about such violence or mass hysteria.

In the modern world, we are in the crosshairs of everything from overseas terrorists to storms and earthquakes and, yes, to people without an apparent ideology whose final act before they take their own lives is to commit mass murder.

We look at the faces of the victims and feel the loss of those we never met. They look like our friends and neighbors, and we know their smiles, once filled with potential, will never again light up a room.

At the same time, hundreds of people lined up for hours to do what they could — give blood — to help save those in immediate need.

Clearly, a few people in our midst have headed toward the dark side of their hearts and minds, allowing the demons that plague their lives to release the unthinkable and unimaginable.

Maybe, in addition to the discussion about gun control, we ought to appreciate the legion of mental health professionals who dedicate themselves to helping those battling against destructive urges, whose thoughts wander into the wilderness of despair.

The toll their work often takes on some of these mental health helpers is enormous, as other people’s nightmares leap from the minds of their patients into their own subconscious. The flow of information travels both ways, putting psychologists, psychiatrists and social workers at risk.

These mental health workers often talk to others in their field to help them get through the difficulties of their jobs.

They listen, they encourage, they become involved and, ultimately, they can and so often do set people on better courses in their lives, helping them feel better and live better.

By the time you read this, perhaps we’ll have an idea of what triggered the madness from this latest gunman, and maybe it will have less to do with off-the-rails thinking than with an ideology that encourages mass violence.

If it wasn’t lone-wolf insanity, but, rather, someone following instructions, we ought to find the ones who encouraged these senseless and brutal murders.

Either way, we ought to dedicate more resources to battling with the burden of a broken brain. If, somehow, a mental health professional can redirect someone who might otherwise commit incomprehensible violence, that person not only has saved a life but may have turned a would-be murderer into another conscientious citizen lining up for hours to give blood instead of planning to spill it.

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Anne Churchland. Photo from CSHL

By Daniel Dunaief

Someone is hungry and is walking through a familiar town. She smells pizza coming from the hot brick oven on her left, she watches someone leaving her favorite Chinese restaurant with the familiar takeout boxes, and she thinks about the fish restaurant with special catches of the day that she usually enjoys around this time of year. How does she make her decision?

While this scenario is a simplified one, it’s a window into the decision-making process people go through when their neurons work together. A team of 21 neuroscientists in Europe and the United States recently created a new collaboration called the International Brain Laboratory to explore how networks of brain cells support learning and decision-making.

“We understand the simple motor reflex,” such as when a doctor taps a knee and a foot kicks out, said Anne Churchland, an associate professor at Cold Spring Harbor Laboratory and the American spokesperson for this new effort. Scientists, however, have only a limited understanding of the cognitive processes that weigh sensory details and a recollection of the outcomes from various courses of action that lead to decision-making, Churchland said.

Scientists likened the structure of the new multilaboratory effort to the circuitry involved in the brain itself. The brain is “massively parallel,” said Alexandre Pouget, a professor at the University of Geneva and the spokesperson for the IBL. “We know it’s working on consensus building across areas so, in that respect, the IBL is similar.”

A greater awareness of the decision-making process could provide a step into understanding the brain network problems involved in mental health disorders.

Churchland’s lab is one of three facilities that will house a new behavioral apparatus to study decision-making in mice. The other sites will be in the United Kingdom and in Portugal. Eventually, other labs will use this same technique and house the same apparatus.

An ongoing challenge in this field of research, Churchland said, is that scientists sometimes create their own models to test the neurological basis of behavior. While these approaches may work in their own labs, they have created a reproducibility problem, making it difficult for others who don’t have expertise in their methods to duplicate the results.

Creating this behavioral apparatus will help ensure that the collaborators are approaching the research with a reliable model that they can repeat, with similar results, in other facilities.

While the scientists will all be exploring the brain, they will each be responsible for studying the activity of circuits in different parts. The researchers will collect a wealth of information and will share it through a developing computer system that allows them to maneuver through the mountains of data.

To address this challenge, the IBL is creating a data architecture working group. Kenneth Harris, a professor of quantitative neuroscience at the University College London, is the chair of the effort. He is currently looking to hire additional outside staff to help develop this process.

Harris suggested that the process of sharing data in neurophysiology has been challenging because of the complex and diverse data these scientists share. “In neuroscience, we have lots of different types of measurements, made simultaneously with lots of different experimental methods, that all have to be integrated together,” he explained in an email.

The IBL collaboration will make his job slightly easier than the generic problem of neurophysiology data sharing because “all the labs will be studying how the brain solves the same decision-making task,” he continued.

Harris is looking to hire a data coordinator, a senior scientific programmer and a scientific MATLAB programmer. He has a data management system already running with his lab that he plans to extend to the IBL.

Pouget said there are two milestones built into the funding from the Wellcome Trust and the Simons Foundation for this new collaboration. After two years, the researchers have to have a data sharing platform in place, which will allow them to share data live as they collect it.

Second, they plan to develop standardized behaviors in all 11 of the experimental labs, where the behavior has to be as indistinguishable from one lab to another as possible.

In addition to the experimentalists involved in this initiative, several theoretical neurobiologists will also contribute and will be critical to unraveling the enormous amounts of data, Pouget suggested. “If you’re going to tackle really hard computational problems, you better have people trained in that area,” he said, adding that he estimates that only about 5 percent of neuroscientists are involved in the theoretical side, which is considerably lower than the percent in an area like physics.

Researchers involved in this project will have the opportunity to move from one lab to another, conducting experiments and gaining expertise and insights. The principal investigators are also in the process of hiring 21 postdoctoral students.

Churchland said each scientist will continue to conduct his or her own research while also contributing to this effort. The IBL is consuming between a quarter and a third of her time.

Pouget suggested that Churchland was “instrumental in representing the International Brain Laboratory to the Simons Foundation,” where she is the principal investigator on that grant. “Her role has been critical to the organization,” he said.

Churchland said the effort is progressing rapidly. “It’s moving way faster” than expected. “This is the right moment, with an incredible team of people, to be working together. Everyone is dedicated to the science.”

Harris indicated that he believes this effort could be transformative for the field. “Neuroscience has lagged behind many other scientific domains” in creating large-scale collaborations, he explained. “If we can show it works, we will change the entire field for good.”

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From left, Lisa Miller with her research team Andrew McGregor, Alvin Acerbo, Tiffany Victor, Randy Smith, Ruth Pietri, Ryan Tappero, Nadia Hameed, Tunisia Solomon, Paul Panica and Adam Lowery. Photo by Roger Stoutenburgh, BNL

By Daniel Dunaief

Most of the people at the building that cost near a billion dollars are pulled in different directions, often, seemingly, at the same time. They help others who, like them, have numerous questions about the world far smaller than the eye can see. They also have their own questions, partnering up with other researchers to divide the work.

Lisa Miller, a senior biophysical chemist at Brookhaven National Laboratory, lives just such a multidirectional and multidimensional life. The manager for user services, communications, education and outreach at the National Synchrotron Light Source II, Miller recently joined forces with other scientists to explore the potential impact of copper on a neurodegenerative disease called cerebral amyloid angiopathy (CAA).

Miller is collaborating with Steve Smith, the director of structural biology in the Department of Biochemistry and Cell Biology at Stony Brook University and William Van Nostrand, a professor in the Department of Neurosurgery at SBU who will be moving to the University of Rhode Island. The trio is in the second year of a five-year grant from the National Institutes of Health.

Miller’s role is to image the content, distribution and oxidation state of copper in the mouse brain and vessels. Van Nostrand, whom Smith described as the “glue” that holds the group together, does the cognitive studies and Smith explores the amyloid structure.

In an email, Smith explained that Van Nostrand’s primary area of research is in CAA, while he and Miller were originally focused elsewhere.

Potentially toxic on its own, copper is transported in the body attached to a protein. When copper is in a particular ionic state — when it has two extra protons and is looking for electrons with which to reduce its positive charge — it reacts with water and oxygen, producing hydrogen peroxide, which is toxic.

Miller and her colleagues are working on a technique that will enable them to freeze the tissue and image it. Seeing the oxidation state of the metal requires that it be hydrated, or wet. The X-rays, however, react with water, causing radiation damage to the tissue.

To minimize this damage, the researchers freeze the tissue. At NSLS-II, a team of scientists are working to develop X-ray-compatible cryostages that will allow them to freeze and image the tissue.

Miller is trying to figure out where and why the copper is binding to an amyloid beta protein. This is the same protein that’s involved in plaques prevalent in the brains of people with Alzheimer’s disease.

In Alzheimer’s patients, the plaques are found in the parenchyma, or the extracellular space around the brain cells. In CAA, the deposits are attached to the surface of the blood vessels on the brain side.

Lisa Miller and her dog Dora on a recent 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina Photo from Lisa Miller

The current hypothesis about how copper becomes reactive in the brain originates from work Van Nostrand and Smith published recently. They suggested that the amyloid fibrils in CAA adopt an anti-parallel orientation and the fibrils in the plaques in Alzheimer’s are in a parallel orientation. The anti-parallel structure predicts that there is a binding site for copper that, if occupied, would stabilize the structure.

“We are currently working to establish if this idea is correct,” Smith explained in an email, suggesting that the NSLS-II provides a “unique resource for addressing the role of copper in CAA. The data [Miller] is collecting are essential, key components of the puzzle.”

The NSLS-II will provide the kind of spatial resolution that allows Miller to measure how much copper is in the deposits. Ideally, she’d like to see the oxidation state of the copper to see if a reaction that’s producing hydrogen peroxide is occurring.

A challenge with peroxide is that it’s hard to find in a living tissue. It is highly reactive, which means it does its damage and then reverts to water and oxygen.

As someone with considerable responsibilities outside her own scientific pursuits, Miller said she spends about a quarter of her time on her own research. One of Miller’s jobs during the summer is to host the open house for NSLS-II, which allows members of the community to visit the facility. This year, at the end of July, she “was thrilled” to host about 1,600 members of the community.

“Most of them wanted to go on the floor and meet the scientists and walk” around the three quarters of a mile circle, she said. While they are interested in the research, the surprising mode of transportation strikes their fancy when they trek around the site.

“The thing that fascinates them when they walk in the door is the tricycles,” she said. The NSLS-II can’t take credit for being the first facility to use these adult-sized tricycles, which number over 100 at the facility. “It’s a synchrotron thing.”

The previous NSLS at BNL was too compact and had too many turns, which made the three-wheeled vehicles, which, like a truck, need a wider turning radius to maneuver on a road, impractical.

Miller, who is a part of the trike-share program, is an avid hiker. This summer, she completed a 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina. This section was located in the area of totality for the solar eclipse and Miller was able to witness the astronomical phenomenon at Siler Bald in North Carolina.

A resident of Wading River, Miller, who grew up in the similarly flat terrain of Cleveland, spends considerable time walking and running with her rescue mutt Dora, who accompanied her on her recent hike.

While Miller finds the research she does with copper rewarding, she said she also appreciates the opportunities NSLS-II affords her. “Every day is different and we never know what project will show up next,” she said.

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The next generation is afraid.

Can you blame them? They know about 9/11, as they should. When they’re not sending pictures of themselves and the food they’re eating to their group of best friends through social media, they read headlines and see pictures of people, just like them, who are living their lives one day and then becoming statistics the next.

This particular generation says it would pick security over freedom. Not all of them do, of course, but, in a recent discussion among some teenagers, I heard repeated arguments about how freedom is irrelevant if you’re dead.

That is a reflection of just how much the world has changed since I grew up. In my youth, I was aware of the Cold War. A nuclear war, although a possibility in the bilateral world that pitted the United States against the Soviet Union, seemed unlikely. After all, the biggest deterrent was the likelihood of mutually assured destruction. As Matthew Broderick experienced in the movie “War Games,” no one wins or, to quote the eerie computer from the movie, “the only winning move is not to play.”

In times of stress, Americans have historically pulled away from the ideals of freedom and democracy.

During the Civil War, President Abraham Lincoln suspended the writ of habeas corpus, which ensures that someone can challenge an unlawful detention or imprisonment. During World War II, after the attack on Pearl Harbor, President Franklin Delano Roosevelt established internment camps, where he held more than 100,000 people of Japanese decent, worried that they might be colluding with a government that had just attacked us.

At the start of the Cold War, Sen. Joseph McCarthy played into our worst fears, leading the House Un-American Activities Committee to question the beliefs and loyalties of its citizens. In the meantime, he ruined the lives of thousands of people and turned Americans against each other.

Many of these pursuits were designed to ease the minds of citizens about our friends and neighbors, some of whom might be working with an enemy and strike against us.

So, today, what are we willing to give up? And, perhaps more importantly, to whom are we surrendering these freedoms?

I recently watched a television reporter who was interviewing citizens in North Korea. He was asking them how they felt about their leader, Kim Jung-un, and the way he was rattling the saber against the United States and the rest of the world.

Not surprisingly, the North Koreans, or the translator with them, expressed unreserved support for the man who trades threats seemingly on a daily basis with President Donald Trump. Those interviewed were confident they were in good hands.

I doubt they felt comfortable expressing any other view. What consequences would they suffer if they publicly questioned their leader’s judgment? Their leader doesn’t seem receptive to opposing viewpoints.

On our shores, we can question our own leaders openly and frequently. We can gather in groups and protest.

Trump can bristle at the way the left-leaning press covers him, just as President Barack Obama shared his displeasure over the coverage from Fox News during his presidency, but presidents can’t shut down these organizations.

Early in our country’s history, our Founding Fathers, who had just emerged victorious in a costly battle with King George III of Great Britain and Ireland, didn’t want the leaders of the new nation to have unchecked power. The pioneering statesmen wanted to guarantee Americans protections from any government, domestic or international.

Every freedom we give up moves us further down a slippery slope.

For those of us who grew up before the fight against terrorism, freedom remains at the heart of the country we are protecting.

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