Better yet, picture 100 drinking vessels, all of different sizes, lined up next to each across a long table.
Now, on a cold day, when you’re not that thirsty but could use something to warm your hands, you might choose a mug that allows heat to bring comfort against a cold wind and frigid temperatures.
On a hot day, when you’re running, gardening or watching your child play yet another sporting event, you might choose an insulated cup that has plenty of ice cold water. That container also might have condensation on the outside, which could give your palms a respite from the pools of sweat clinging to them.
When you’re handing your two-year-old a cup filled with milk, soy milk, water or juice, the container likely has a lid and a drinking attachment.
These cups can all be different sizes and shapes, can serve various purposes and can hold different amounts of liquid.
Even before you touch one of them or take a sip, no matter how eager you are for the liquid inside, you can imagine the feel of the cup in your hand, and you can gauge just how much your mouth and body can expect. You’re likely to take small sips of a scalding cup of hot chocolate, while you might down eight ounces of iced cold water in a matter of seconds.
What would you do if you had a cup mismatch?
Let’s say you were incredibly thirsty after a long run on a mid-July day when you pushed yourself to go further or faster than you had in months. Instead of a tall glass filled with water or a water bottle, you take out a shot glass. The water might be just as cold, but the amount could leave you wanting more and disappointed, even before you lift that small glass to your lips.
At various points in life, the size of the glass (OK, now I’m speaking figuratively) from which we drink doesn’t align with our expectations or hopes.
We want a day, an interaction, or an outing that fills a large cup, and, yet, the lived experience falls short of our hopes.
As a barometer of our expectations, the cup, like the small shot glass filled with barely enough water to wet our parched lips, can feel like it’s too small, leaving us disappointed and thirsty.
As we go through life, we, our friends, and our family members experience times – after a storm, amid a physical or mental health crisis, after leaving a satisfying job, to name a few – when the size of the cup, as a measure of the expected dose of happiness, coherence, joy, or meaning, falls short.
Those tough times become disheartening. We might lose faith or feel slighted or cheated. We need more to fill our cup.
While we can seek to fill the largest cup around with successes, accomplishments, support, and affection, we can also rethink the container.
A small child pouring water into a Dixie cup, for example, might be incredibly successful if a few drops make it.
As adults, the juxtaposition of our daily expectations against our experiences can dictate our mood and reflect our evaluation of the quality of the day. When something happens that reduces the likelihood of our achieving or enjoying our lives, we can feel like we’re holding a frustratingly empty cup that we have little prospect of filling.
Instead of being disappointed, we might consider reaching for a different container. I’m not suggesting that we aim low or that we stop striving for personal achievement and growth.
A smaller cup, however, breaks the iconic model of the optimistic half-full cup or the pessimistic half-empty container. Instead, we can choose to fill a smaller cup.
Over time, we can increase the size of the cup, filling it each time until it runs over.
This process might restore our sense of accomplishment and help us appreciate what we have and not lament what’s missing.
As life changes, we can redefine what we need to feel fulfilled.
From left, Sam Kleeman, Assistant Professor Tobias Janowitz, Miriam Ferrer Gonzalez and Emma Davidson. Photo by Caryn Koza/CSHL
Sam Kleeman at Lake Tahoe
Sam Kleeman in front of a sequoia grove at Yosemite.
By Daniel Dunaief
This is part 2 of a two-part series.
Cancers not only compromise human health, but they can also suppress the body’s immune response. A little studied small protein called cystatin C, which is secreted by numerous cells, may render the immune system less effective in its response to tumors.
Sam Kleeman, a PhD student in Cold Spring Harbor Laboratory Assistant Professor Tobias Janowitz’s lab, recently published results in the journal Cell Genomics that demonstrate a link between elevated levels of this protease inhibitor, the suppression of the immune system, and the development of cancer.
Kleeman was able to demonstrate a potential role “Cystatin C might play in damping down the immune response to tumors,” he said.
Cystatin C is a known cysteine protease inhibitor, but the biological and organ-level relevance of this has not been characterized in detail. This protein could be one of many mechanisms by which glucocorticoids can reduce the effectiveness of the immune system.
Cystatin C could drive the progression of the disease, which could explain why Kleeman has found evidence that higher levels coordinate with worse outcomes.
Starting with the data
Pursuing an interest in data- driven research, Kleeman, who has a Bachelor of Medicine and Surgery from New College at the University of Oxford, searched the UK Biobank, which provides health data for numerous people in the United Kingdom.
In this Biobank, Kleeman, who joined Cold Spring Harbor Laboratory in August of 2020, found that cystatin C was the best prognostic indicator of cancer deaths.
“I was a little surprised by this,” Kleeman said as he had heard of cystatin C as a marker of kidney function, but was not aware of any association with cancer mortality. Some studies had found evidence for this previously, but those were in small cohorts and were poorly understood, he explained.
A healthy kidney clears most proteins quickly, pumping it out into urine. A kidney that’s not functioning optimally, however, allows it to accumulate.
In his research, Kleeman removed cystatin C selectively in cancer cells, causing the tumors to grow more slowly. The main changes in the architecture of the tumor was that it reduced the frequency of macrophages with expression of a protein called Trem2. While the exact mechanism is not known, it’s likely that immune control of the tumor increases without cystatin C.
Kleeman also demonstrated a similar effect on the connection between levels of Covid-19 and mortality in a paper published in iScience.
The biological mechanism explaining the correlation is nuanced. Patients with higher levels of glucocorticoids can be associated with poor outcomes. It is not a simple relationship, he said, which makes causality difficult to assess.
Kleeman believes cystatin C secretion in response to glucocorticoids has context dependency. Not all cells posses inducible cystatin C secretion.
The research primarily found that only macrophages and cancer cells can secrete cystatin C in response to glucocorticoids.
He describes a “two hit” model, by which glucocorticoids plus an inflammatory stimulus recruit macrophages. The model applies to all inflammatory stores, but is co-opted in the case of cancer.
At this point, drugs aren’t available to inhibit or reduce cystatin C. Instead, Kleeman suggested that a viable research target route might involve creating a specific antibody.
Some researchers have created so-called knockout mice, which don’t have this protein. These mice can survive without it, although eliminating all cystatin C creates other problems.
Kleeman speculated that the protein could play a role in preventing significant immune reaction against sperm.
Indeed, this protein is secreted at high levels in the testes. Males without it have lower sperm function and production.
Kleeman hopes this work acts as a starting point to understand the mechanism better by which glucocorticoids modify immune response to cancer, and to investigate cystatin C as a possible therapeutic target.
Long standing partnership
As an undergraduate, Kleeman took a class with Janowitz, which kicked off a mentorship that now spans two continents.
Kleeman appreciates the comfort level Janowitz has in working on higher-risk, higher-reward topics or on ideas that haven’t already attracted considerable attention from other scientists.
“There’s a tendency in science towards group think,” Kleeman said. In the history of medicine and science, many widely accepted theories turn out to be wrong. “Patients undoubtedly benefit from a diversity of thought in science and medicine,” he explained.
When he completes his PhD, Kleeman said it would be a “dream to have a dual appointment” in which he could conduct research and work in the clinic with patients. To get there, he knows he needs to establish his research profile that includes a genuine track record of achievement while demonstrating that he can function as a reliable and effective clinician.
Kleeman’s thesis research lies outside the field of cystatin C, which started out as a curiosity and developed into the recent publication. He wanted to “understand what UK Biobank could teach us about cancer patients.” With Janowitz and Cold Spring Harbor Laboratory Professor Hiro Furukawa, Kleeman is working to understand how a specific type of cancer could cause an auto-immune disease.
A resident of Forest Hills, Kleeman lives about 45 minutes from the lab. Outside of work, he enjoys visiting national parks. He has visited 10 so far, including Yosemite National Park, Zion and Rocky Mountain National Park.
Professionally, Kleeman feels it is a privilege to be a PhD student. He appreciates that he can explore his interests without too many restrictions and is eager to make the most of the opportunity.
Yes, sometimes, I’m an annoying morning person, ready to poke my wife in the arm, kiss her cheek, or play peek-a-boo with a son who can barely open his heavy lids to notice me.
No, my son is not two, and yet, I still have the urge to smile at him and play games in the morning.
I’m the lone morning wolf in my family. Even my dog, who is as far from a wolf as a dog could be, sometimes closes his eyes tightly when I get up too early for him, hoping I’ll go away or, maybe, I won’t see him. No matter how much his fur blends in with the carpet, it’s impossible not to notice a 95-pound dog.
On the other end of the circadian spectrum, I start to fade early each day. Surrounded by family and friends, much of the time, who enjoy late-night snacks, conversations, giggle fests, and games, I can barely keep my head up and my eyes open.
“You look so tired,” someone will say at about 10 p.m.
“Huh?” I’ll respond, trying to figure out if they’re talking to me. “Oh, yeah, well, I got up early today.”
I get up early almost every day. Getting up late for me means climbing out of bed after 8 am.
I’d like to alter my circadian clock sometimes, but I can’t.
Sensing my imminent departure into dreamland, my wife sometimes asks me a question or two at the utterly reasonable hour of 10:30 pm. I do my best to pick up my head and offer a coherent answer, knowing that the top few floors of my cognitive team have packed up, turned off the lights and tucked themselves in for the night.
The balance between the morning and night person in our marriage means that one of us can handle whatever time-sensitive needs or responsibilities might arise throughout the day. We have shifts.
When we go out on dates, which we can do on any given night as empty nesters, we typically lean towards the earlier side for our outings. The other diners at the early bird special are often decades older than we, although we also sometimes eat with families who have young children.
Our circadian differences extend to the seasons as well. I love the winter, when the sun isn’t too bright, and the air is cooler. Skiing is one of my favorite sports.
My wife, naturally, revels in the summer sun, basking in the extra sunlight each day and soaking up the warmth of the midday sun.
These seasonal differences also mean that one of us often feels energized and inspired by the season. With my wife dressed in numerous layers, we can take a stroll in cooler weather.
During those days when the sun bakes the sidewalk, and the humid air weighs on my shoulders, I can carry ice water or my wife can obligingly dump a welcome ice cube down my back.
Apart from the bookends of each day, we find times when we can give each other our best, reveling in the accomplishments of our children, observing the absurdities of life, and laughing at the differences in approaches to play between our dog and cats.
Even as we are in the middle of my wife’s favorite season, I enjoy the summer more than I otherwise would, knowing that she’s fulfilled and, when I need it, ready to search for a comforting ice cube sometime around mid-afternoon, when I prepare to pass the baton towards her favorite time of day.
From left, Sam Kleeman, Assistant Professor Tobias Janowitz, Miriam Ferrer Gonzalez and Emma Davidson. Photo by Caryn Koza/CSHL
By Daniel Dunaief
This part one of a two part series.
It’s a bit like shaking corn kernels over an open flame. At first, the kernels rustle around in the bag, making noise as they heat up, preparing for the metamorphosis.
That’s what can happen in any of the many laboratories scattered throughout Long Island, as researchers pursue their projects with support, funding and guidance from lab leaders or, in the science vernacular, principal investigators.
Sometimes, as happened recently at the benches of Cold Spring Harbor Laboratory Assistant Professor Tobias Janowitz, several projects can pop at around the same time, producing compelling results, helping advance the careers of developing scientists and leading to published papers.
PhD graduate Miriam Ferrer Gonzalez and MD/ PhD student Sam Kleeman recently published separate studies.
In an email, Janowitz suggested the work for these papers is “time consuming and requires a lot of energy.” He called the acceptance of the papers “rewarding.”
In a two-part series, Times Beacon Record News Media will describe the research from each student. This week, the focus is on Ferrer Gonzalez. Check back next week for a profile of the work of Kleeman.
Miriam Ferrer Gonzalez
Miriam Ferrer Gonzalez. Photo by Caryn Koza/CSHL
Miriam Ferrer Gonzalez was stuck. She had two results, but couldn’t seem to figure out how to connect them. First, in a mouse model of the ketogenic diet — heavy on fats, without including carbohydrates —cancer tumors shrunk. That was the good news.
The bad news, which was even more pronounced than the good, was that this diet was not only starving the tumors, but was triggering an earlier onset of cachexia, in which bodies weaken and waste away. The cachexia overpowered the mice, causing them to die sooner than if they had a normal diet.
Ferrer, a student in residence from Spain who was conducting her research at Cold Spring Harbor Laboratory while earning her PhD at the University of Cambridge in the UK, thought the two discoveries were paradoxically uncoupled. A lower tumor burden, she reasoned, should have been beneficial.
In presenting and discussing her findings internally to the lab group, Ferrer received the kind of feedback that helped her hone in on the potential explanation.
“Finding out the mechanism by which a ketogenic diet was detrimental for both the body and the cancer was the key to explaining this uncoupling,” Ferrer explained.
The adrenal glands of mice fed a ketogenic diet were not producing the necessary amount of the hormone corticosterone to sustain survival. She validated this broken pathway when she discovered higher levels of corticosterone precursors that didn’t become functional hormones.
To test this hypothesis, she gave mice dexamethasone, which boosted their corticosterone levels. These mice had slower growing tumors and longer lives.
Ferrer recently published her paper in the journal Cell Metabolism.
To date, the literature on the ketogenic diet and cancer has been “confusing,” she said, with studies that show positive and negative effects.
“In our study, we go deeper to explain the mechanism rather than only talking about glucose-dependency of cancer cells and the use of nutritional interventions that deprive the tumor of glucose,” said Ferrer. She believed those factors are contributing to slower tumor growth, but are not solely responsible.
Thus far, there have been case studies with the ketogenic diet shrinking tumors in patients with cancer and, in particular, with glioblastoma, but no one has conducted a conclusive clinical trial on the ketogenic diet.
Researchers have reported on the beneficial effects of this diet on epilepsy and other neurological diseases, but cancer results have been inconclusive.For the experiments in Janowitz’s lab, Ferrer and technician Emma Davidson conducted research on mouse models.
Ferrer, who is the first author on the paper, has been working with this system for about four years. Davidson, who graduated from the College of Wooster in Ohio last year and is applying to MD and MD/PhD programs, contributed to this effort for about a year.
Next steps
From left, Emma Davidson, Assistant Professor Tobias Janowitz, Sam Kleeman and Miriam Ferrer Gonzalez. Photo by Caryn Koza/CSHL
Now that she earned her PhD, Ferrer is thinking about the next steps in her career and is considering different institutions across the country. Specifically, she’s interested in eating behavior, energy homeostasis, food intake and other metabolic parameters in conditions of stress. She would also like to focus on how hormonal cycles in women affect their eating behavior.
Originally from a small city in Spain called Lleida, which is in the western part of Catalonia, Ferrer appreciated the opportunity to learn through courses and conferences at Cold Spring Harbor Laboratory.
Until she leaves the lab in the next few months, Ferrer plans to work with Davidson to prepare her to take over the project for the next year.
The follow up experiments will include pharmacologically inducing ferroptosis of cancer cells in mice fed a ketogenic diet. They hope to demonstrate that early induction of ferroptosis, or a type of programmed cell death, prevents tumor growth and prevents the tumor-induced reprogramming of the rest of the body that causes cachexia.
These experiments will involve working with mice that have smaller and earlier tumors than the ones in the published paper. In addition, they will combine a ketogenic diet, dexamethasone and a ferroptosis inducing drug, which they didn’t use in the earlier experiments.
Janowitz has partnered with Ferrer since 2018, when she conducted her master’s research at the University of Cambridge. As the most senior person in Janowitz’s lab, Ferrer has helped train many of the people who have worked in his lab. She has found mentoring rewarding and appreciates the opportunity to invest in people like Davidson.
Ferrer, who is planning a wedding in Spain in September, is a fitness and wellness fan and has taken nutrition courses. She does weight lifting and running.
Ferrer’s parents don’t have advanced educational degrees and they supported their three children in their efforts to earn their degrees.
“I wanted to be the best student for my parents,” said Ferrer, who is the middle child. She “wanted to make my parents proud.
The hand off
Emma Davidson and Miriam Gonzalez Ferrer examine an adrenal gland sample section from a cachectic mouse. Photo by Caryn Koza/CSHL
For her part, Davidson is looking forward to addressing ways to implement further treatment methods with a ketogenic diet and supplemental glucocorticoids to shrink tumors and prevent cachexia.
Davidson appreciated how dependable Ferrer was during her time in the lab. Just as importantly, she admired how Ferrer provided a “safe area to fail.”
At one point, Davidson had taken all the cells she was planning to use to inject in mice. Ferrer reminded her to keep some in stock.
“Open lines of communication have been very beneficial to avoid more consequential failures,” Davidson said, ”as this mistake would have been.”
Davidson developed an interest in science when she took a high school class called Principles in Biological Science and Human Body Systems. When she was learning about the cardiovascular system, her grandfather had a heart attack. In speaking with doctors, Davidson acted as a family translator, using the language she had studied to understand what doctors were describing.
Like Ferrer, Davidson lives an active life. Davidson is preparing for the Jones Beach Ironman Triathlon in September, in which she’ll swim 1.2 miles, bike 56 miles and run a half marathon. She plans to train a few hours during weekdays and even more on weekends for a competition she expects could take about six hours to complete.
Davidson started training for these events with her father Mark, an independent technology and operations consultant and owner of Exoro Consulting Group.
Longer term, Davidson is interested in medicine and research. After she completes her education, she will try to balance between research and clinical work.
Donald Triplett. Photo from Wikimedia Commons/
Ylevental, CC BY-SA 4.0 , via Wikimedia Commons
By Daniel Dunaief
Daniel Dunaief
At a recent national meeting of experts in his field, Matthew Lerner said the gathering paused to toast the remarkable life of Donald Triplett.
Born and raised in Forest, Mississippi, Triplett died on Thursday, June 15 at the age of 89, after a full life in which his family, his community and a medical and research field around him learned about a condition he helped various communities understand.
Triplett was different from other children growing up, and in 1943, after his parents brought him to psychiatrist Dr. Leo Kanner, he became “Case 1” for a new diagnosis called autism.
“Everything we know about autism started with what was learned from Donald,” said Lerner, associate professor in Clinical Psychology at the Stony Brook Neurosciences Institute. “I’m still confident the field would have found its way to autism,” but the interaction between Triplett and Kanner helped establish some of the parameters that define a condition that researchers estimate affects about one in 36 children today.
As with people who have other diagnoses, the reaction people have to those with autism varies.
“There are two broad threads in the history of how we’ve understood, studied and treated autism since the 1940s,” said Lerner.
In one, people consider it a lifetime disability, in which the diagnosis is limiting and stigmatizing.
In the second, people see autism as a different way of being, in which individuals have an opportunity to develop a meaningful and happy life, as was the case with Triplett.
“The idea of autism as being so different and so impairing was the prototype,” Lerner said. Triplett’s life “didn’t follow that trajectory at all. He had a life filled with community in which he felt supported and accepted.”
This second model of autism, Lerner added, is achievable in “far more cases than we may have historically assumed.”
Triplett, who worked at the Bank of Forest for 65 years and traveled the world, had unusual cognitive abilities that set him apart from neurotypical people. He could multiply two three-digit numbers rapidly without a calculator. He also could look at the side of a building and could indicate the number of bricks without counting them one by one. He had perfect pitch.
As he was growing up, he didn’t interact socially in typical ways for children his age. His parents institutionalized him for a year, where he became withdrawn and disinterested. When they brought him back to their home, he became more engaged, earning a high school and bachelor’s degree in French from Millsaps College.
“He may have been the first, but he was far, far, far from the only autistic person who ended up exceeding the horizons set for him when he was young,” Lerner said.
Lerner believed people in the autistic community, like Triplett, have something to teach others about challenging circumstances.
“Kids are going to get where they are going at their own pace,” Lerner said. Being patient and kind and taking time to meet people where they are as individuals can help people grow. Lerner suggested that “we need to be okay with the idea that what that person is going to be is themselves and the best thing we can do is create a space” for that development to occur.
People will develop when they don’t feel like they are failing because people around them are setting expectations that don’t match them or are underestimating what they can do, he added.
“It’s important to feel validated and valued” through life, Lerner said.
Parents of children from a wide range of abilities sometimes hear what their offspring will never do.
People are frequently “proven wrong” by that child in that family, he added.
As for Triplett, Lerner encouraged people to watch the movie ’In a Different Key” about the person later known as Case 1.”
Above, a photo of Turkana taken from a single engine plane shows the Koobi Fora spit and Lake Turkana alongside a time map. Photo from Bob Raynolds
By Daniel Dunaief
In a wide-ranging interview, Louise Leakey, Director of Public Education and Outreach for the Turkana Basin Institute and a Research Professor in the Department of Anthropology at Stony Brook University shared her thoughts on numerous topics in the field of paleontology.
Louise Leakey at the Richard Leakey Memorial Conference on June 5. Photo by John Griffin/SBU
Leakey, who earned her PhD at the University College London, suggested that the process of finding fossils hasn’t changed that much, although other options beyond scouring a landscape for fragments of the world’s former occupants may be forthcoming.
“It may very well change if we can implement machine learning with high resolution imagery, using drones,” she said. “That’s one of the things we’re looking at the moment.”
What’s really changed, however, is the accuracy field scientists have in marking where, and, importantly, when new discoveries originated, she said.
Geologists like Bob Raynolds, Research Associate at the Denver Museum of Nature & Science, have created time maps that indicate the approximate age of sediments around a fossil in some select areas of the Turkana Basin.
These maps “can be uploaded onto an iPad app for use in the field that shows you in real time where you are on the geological map,” Leakey explained. “This is a game changer for field work in the basin.”
A time map created by Bob Raynolds in collaboration with Geologic Data Systems, a Littleton, Colorado company.
The maps represent the work of many people, Raynolds explained.Originally, teams of Master’s students used air photographs, tracing paper and ink to make a map. These students spent many weeks walking systematically on the ground and tracing the patterns on the photos.
The rugged and isolated nature of the ground in Northern Kenya makes the work done on foot difficult, Raynolds explained.
The original maps, which were made in the 1970’s, took months to make and were presented as paper copies in unpublished Master’s theses. After numerous enhancements, Raynolds, working with companies including Geologic Data Systems in Littleton, Colorado, created time maps.
The internal GPS on an iPhone enables a blue dot to indicate a person’s location on the map.
“I have worked on the maps to make a new set of derived products that are maps of the age of the rocks,” said Raynolds who created these time maps earlier this year. “The resolution of the time maps is 100,000 years” which is an “astonishingly detailed resolution for us who are accustomed to million year packages of time.”
The maps cover the entire Turkana Basin at various scales, Raynolds added.
More broadly, Bernard Wood, University Professor of Human Origins in the Center for the Advanced Study of Human Paleontology at George Washington University and the first speaker at a recent Stony Brook University conference to honor Richard Leakey, explained that dating fossils has become increasingly accurate.
The first dates of fossils in the KBS Tuff, which is an ash layer in the Koobi Fora Formation east of Lake Turkana, was estimated within 260,000 years of a specific date. Using improved methods, a study published this year has reduced that range to 600 years.
Publishing pace
In the meantime, the pace of publishing has slowed considerably.
“There’s so much more material” that can serve as a frame of reference for new discoveries, Leakey said. “The rate of publication is frustratingly slow for some of these specimens.” This contrasts dramatically with the experience of Leakey’s father Richard.
When the elder Leakey submitted his letters or paper to the prestigious journal Nature, the late editor John Maddox never sent them out for review. “[Maddox] explained that he couldn’t see the point, because they concerned fossils so recently discovered” that few had seen them, Wood explained in his presentation.
Louise Leakey also differed from Richard in earning her bachelor’s degree and PhD, while her father dropped out of high school and never received any additional formal education.
Wood suggested that, next to marrying Meave, the elder Leakey described leaving school as one of the best decisions he’d ever made.
For his daughter, though, Leakey “encouraged me to go and do that,” Louise Leakey said. The education helped “in terms of being able to be [principal investigator] on grant applications,” she said.
Leakey suggested it was a “real privilege to be able to spend time” earning her PhD. She also found that the educational experience gave her the opportunity to “stand on my own two feet” in her research.
Like her father, Louise Leakey is concerned about conservation and declining biodiversity. When she was younger, she saw areas that were teeming with wildlife. On a recent three-hour drive, she only saw a golden jackal and a dik-dik, which is a type of small antelope, compared with the much wider variety of creatures she would have seen decades ago, such as Grévy’s zebra, Burchell zebra, lesser kudu, ostriches, warthogs, topi, gerenuk, oryx and, possibly lions and cheetah.
She attributes this decline to hunting as some have exterminated these species as result of competition for grazing areas and hunting the animals for meat. Record droughts are also threatening their survival.
Leakey is working with the next generation to get “kids to care about nature” so they can “think about what they’re doing and the real impact it has.”
In addition to preserving biodiversity, Leakey remains passionate about studying the past, which could help the current and future generations tackle climate change. “We might be able to learn lessons” from those who survived during such challenging conditions, she said.
Leakey is able to maintain her involvement and commitment to numerous efforts by working with talented collaborators.
“If you don’t have teams to really hold it together, you can’t do any of it,” she said.
I don’t intend to describe it, compare notes, or ponder the meaning of bending over after our dogs relieve themselves to take their excrement and dump it in our garbage cans or, perhaps, to ship it to Mars so Matt Damon will have fertilizer for a crop of potatoes.
It’s the whole picking up of the steaming logs that I’d like to address.
You see, the other day, my son and I took our 95-pound dog for a walk. Yes, bigger dogs make larger and, often, smellier poops. I know because I’ve walked smaller dogs recently and am amazed at the delicate little pebbles they gingerly push out of their smaller digestive systems.
So, there we were, the three of us, on our happy stroll, with my dog smelling everything and nothing and my son and I talking about, shocker, sports!
My dog did his thing. At that point, I reflexively leaped into action, opening a small plastic bag that I turned inside out so I didn’t have to come into contact with, you know, it.
I bagged it up, the way I always do, tied the bag twice, as is also a part of the routine, and gently lay the bag near a tree, preparing, as I have for the last five years, to retrieve the bag on my return trip.
That’s when a bald, angry, younger man honked at me from his car and threw out his hands in a frustrated “are-you-kidding-me-right-now” pose.
I shrugged and kept walking because other people’s anger, particularly when I don’t feel responsible for it, isn’t about me.
But the gentleman didn’t leave well enough alone. He circled around and found my son, my dog and me, rolled down his angry window and demanded to know if I was planning to pick up the poop.
“Yes, of course,” I said. “I’ve been walking him for five years, and I pick it up every time.”
My son seemed more than a bit amused.
“Are you the dog poop police?” he asked.
“Yes,” the man in the pickup truck replied without a touch of irony.
“Can I see your badge?” my son asked.
This was heading in the wrong direction.
“I hate it when people leave their dog’s poop all over the neighborhood,” the gentleman, who was coming across as anything but gentle, said. “Are you sure you’re going to pick it up?”
“Yes,” I said. “I always do.”
“Do people leave poop everywhere?” my son asked.
“Yes, they do,” the man said.
The stare down lasted another few minutes. Why, I thought later, would I bother to bag up his poop as if it were a holiday present if I intended to leave it? Wouldn’t I continue walking, ignoring the doggy remains of his dinner?
The man drove off. No, he didn’t spin his tires. When I picked up the bag, I looked around to see if he was hiding, waiting to catch me in a dog-faced lie.
Alas, despite the numerous pickup trucks that sped by, none looked like his truck or had his scowl leaning out of the window.
We sure are an angry and confrontational society these days, aren’t we? This man took time out of his day to confront me about a bag of poop.
I guess the good news is that he’s protecting us from dog poop scofflaws. The sad part, however, is that he figured I was prepared to bag it up and leave it behind. He didn’t know me and quickly assumed the worst.
I wonder if he feels the same level of concern for, say, the wrappers people toss out of their car windows. Does he knock on car doors to ask people sitting with their engines on to turn them off so they don’t pollute the air?
Now, that’s an idea that makes sense to me. Then again, the dog poop patrol probably made sense to him. If my dog had any idea what was happening, he’d have quite a tale to share with his canine companions.
Ali Khosronejad in front of the Santa Maria Cathedral, which is considered the first modern cathedral in Madrid.
By Daniel Dunaief
An approaching weather front brings heavy rains and a storm surge, threatening to inundate homes and businesses with dangerous water and potentially undermining critical infrastructure like bridges.
Once officials figure out the amount of water that will affect an area, they can either send out inspectors to survey the exact damage or they can use models that take time to process and analyze the likely damage.
Ali Khosronejad
Ali Khosronejad, Associate Professor in the Department of Civil Engineering at Stony Brook University, hopes to use artificial intelligence to change that.
Khosronejad recently received $550,000 from the National Science Foundation (NSF) for four years to create a high-fidelity model using artificial intelligence that will predict the flood impact on infrastructure.
The funds, which will be available starting on June 20, will support two PhD students who will work to provide an artificial intelligence-based program that can work on a single laptop at a “fraction of the cost of more advanced modeling approaches,” Khosronejad said during an interview in Madrid, Spain, where he is on sabbatical leave under a Fulbright U.S Senior Scholar Award. He is doing his Fulbright research at Universidad Carlos III de Madrid.
Stony Brook University will also provide some funding for these students, which will help defray the cost of expenses related to traveling and attending conferences and publishing papers.
In the past, Stony Brook has been “quite generous when it comes to supporting graduate students working on federally funded projects,” Khosronejad explained and he hopes that continues with this research.
Khosronejad and his students will work with about 50 different flooding and terrain scenarios, which will cover about 95 percent of extreme flooding. These 50 possibilities will cover a range of waterways, infrastructure, topography, and coastal areas. The researchers will feed data into their high fidelity supercomputing cluster simulations to train artificial intelligence to assess the likely damage from a flood.
As they build the model, Khosronejad explained that they will collect data from floods, feed them into the computer and test how well the computer predicts the kind of flooding that has can cause damage or threaten the stability of structures like bridges. Over the next four years, the team will collect data from the Departments of Transportation in California, Minnesota and New York.
Nearly six years ago, his team attempted to use algorithms available in ChatGPT for some of his AI development. Those algorithms, however, didn’t predict flood flow prediction. He tried to develop new algorithms based on convolutional neural networks. Working with CNN, he attempted to improve its capabilities by including some physics-based constraints.
“We are very enthusiastic about this,” Khosronejad said. “We do think that this opportunity can help us to open up the use of AI for other applications in fluid mechanics” in fields such as renewable energy, contaminant transport predictions in urban areas and biological flow predictions, among others.
Planners working with groups such as the California Department of Transportation could use such a program to emphasize which infrastructure might be endangered.
This analysis could highlight effective mitigation strategies. Artificial intelligence can “provide [planners and strategists] with a tool that is not that expensive, can run on a single laptop, can reproduce lots of scenarios with flooding, to figure out which infrastructure is really in danger,” Khosronejad said.
Specifically, this tool could evaluate the impact of extreme floods on bridge foundations. Floods can remove soil from around the foundation of a bridge, which can cause it to collapse. Civil engineers can strengthen bridge foundations and mitigate the effect of future floods by using riprap, which is a layer of large stones.
This kind of program can reduce the reliance on surveying after a flood, which is expensive and sometimes “logistically impossible and unsafe” to monitor areas like the foundations of bridges, Khosronejad said. He plans to build into the AI program an awareness of the changing climate, so that predictions using it in three or five years can provide an accurate reflection of future conditions.
“Floods are getting more and more extreme” he said. “We realize that floods we feed into the program during training will be different” from the ones that will cause damage in subsequent years.
Floods that had a return period of every 100 years are now happening much more frequently. In one or two decades, such a flood might occur every 10 years.
Adding updated data can allow practitioners to make adjustments to the AI program a decade down the road, he suggested. He and his team will add data every year, which will create a more versatile model.
What it can’t do
While the AI programs will predict the damage to infrastructure from floods, they will not address storm or flood predictions.
“Those are different models, based on the movement of clouds” and other variables, Khosronejad said. “This doesn’t do that: if you give the program a range of flood magnitudes, it will tell you what will happen.”
High fidelity models currently exist that can do what Khosronejad is proposing, although those models require hundreds of CPUs to run for five months. Khosronejad has developed his own in house high fidelity model that is capable of making similar predictions. He has tested it to examine various infrastructures and used it to study various flooding events. These models are expensive, which is why he’s trying to replace them with AI to reduce the cost while maintaining fidelity.
AI, on the other hand, can run on a single CPU and may be able to provide the same result, which will allow people to plan ahead before it happens. The NSF approved the single principal investigator concept two months ago.
Khosronejad has worked with Fotis Sotiropoulos, former Dean of the College of Engineering and Applied Sciences at Stony Brook and current Provost at Virginia Commonwealth University, on this and other projects.
The two have bi-weekly discussions over the weekend to discuss various projects.
Sotiropoulos was “very happy” when Khosronejad told him he received the funds. Although he’s not a part of the project, Sotiropoulos will “provide inputs.”
Sotiropoulos has “deep insights” into fluid mechanics. “When you have him on your side, it always pays off,” Khosronejad said.
Allison McComiskey, chair of the Environmental & Climate Sciences Department at Brookhaven National Laboratory
By Daniel Dunaief
Daniel Dunaief
The wildfires last week in Quebec, Canada, that brought an orange haze, smoke and record pollution to New York were not only disconcerting, but also were something of a reality check.
These raging fires occurred earlier than normal and, with a so-called cut-off low in Maine acting like a bumper in a pinball game driving the smoke down along the eastern seaboard, created hazardous air quality conditions from New York through Virginia.
“There’s a real concern about this intensity, the size of the fire, happening this early in the season,” said Allison McComiskey, chair of the Environmental & Climate Sciences Department at Brookhaven National Laboratory. “Typically, wildfire season starts later in the summer and extends through the fall. If we’re going to be having wildfires of this size this early in the season and it continues, [there will be] much more of an impact on people in terms of air quality, health, and well being.”
Dry conditions caused by climate change intensified the severity of these fires, making them more difficult to extinguish and increasing the amount of particulates that can cause lung and other health problems thrown into the air.
“Wildfire season is getting longer,” said Dr. Mahdieh Danesh Yazdi, an air pollution expert and environmental epidemiologist from Stony Brook’s University’s program in Public Health. These fires are “spread because we have drier conditions, the vegetation is dry, we have droughts. Those require long-term solutions of trying to tackle climate change on a fundamental level.”
The intensity of the smoke and the cancelation of events like the Yankees and Phillies games has raised awareness of the downwind dangers from wildfires.
“This is like our Hurricane Sandy from an air quality perspective,” said Brian Colle, division head in Atmospheric Sciences at the School of Marine and Atmospheric Sciences at Stony Brook University.
Scientists urged a multi-level approach to tackle a wildfire problem that they believe will become increasingly dangerous for human health.
Forest management, including controlled burns, would reduce the available fuel for fires started by natural causes such as lightning.
“Forest management may be one approach,” said Dr. Danesh Yazdi. That alone, however, won’t solve the threat from wildfires amid higher temperatures and more frequent droughts, she added.
McComiskey added that researchers are “certain” that wildfires are going to increase in the future due to climate change and suggested that these events ratchet up the need for getting better predictive models about what these fires will mean for human health and the climate.
The heavy smoke that descended on New York, which some health officials described as creating conditions for those who spent hours outdoors that are akin to smoking several cigarettes, is “a wake up call that we need policies” to deal with the conditions that create these fires, McComiskey said.
The increase by a “fraction of a degree in temperature is really not the point,” McComiskey added. “We need to decarbonize our economy and we need to move toward addressing the bigger causes of climate change.”
A wildfire occurring earlier in the year with smoke filled with particulates could raise awareness and attention to the dangers from such events.
“Having this kind of thing happen in the East Coast through New York and [Washington] DC, as opposed to where we typically think of bad wildfire happening out west, in Washington State and the Rocky Mountains, might help in terms of the awareness and urgency to take some action,” McComiskey added.
Speakers at the “Africa: The Human Cradle" International Conference paying Tribute to Richard E. Leakey” on June 5. Photo by John Griffin/Stony Brook University
By Daniel Dunaief
Combative, loyal, determined, consequential, energetic and courageous. These are just a few of the many traits paleoanthropologists and others shared to describe the late Richard Leakey at the “Africa: The Human Cradle” memorial conference at Stony Brook University this week.
The founder of the Turkana Basin Institute in Kenya, Leakey, who partnered with SBU and received 34 grants from National Geographic over the course of his decades in science, was a part of nearly every presentation and discussion on the first day of the week-long event which closes tomorrow, June 9.
From left, Stony Brook University President Maurie McInnis with Louise Leakey on June 5. Photo by John Griffin/Stony Brook University
Held at the Charles B. Wang Center on the main campus, the conference brought together luminaries in the field who interlaced stories about their science in Africa with anecdotes — many of them humorous — about Leakey. Marilyn and Jim Simons, whose Simons Foundation announced last week that it was donating $500 million to the university, attended the entire slate of speakers on the first day.
Leakey was “one of the most important paleoanthropologists of our time,” Maurie McInnis, President of Stony Brook, said in opening remarks. His impact “can be felt across our campus and across the world.”
In an interview, former Stony Brook President Shirley Kenney, who helped bring Leakey to the university, suggested that he “put us into the elite of that whole research field.”
Leakey stubbornly entered his parents Mary and Louis’s chosen fields when he dropped out of high school, eager to make discoveries on his own and to contribute to his native Kenya.
In 1968, during a meeting at the National Geographic headquarters, Leakey “lobbied the committee to divert funding from his father’s money” to his own research, Jill Tiefenthaler, National Geographic CEO, said during her presentation.
‘Sitting on a knife edge’
Like Leakey, however, these scientists looked deep into the past to understand the lives of early humans, our distant ancestors and other organisms while looking for lessons that might help with the present and the future.
Dino Martins, Chief Executive Officer of the Turkana Basin Institute and Lecturer in the Department of Ecology & Evolutionary Biology, suggested that Leakey was driven by a sense of “childlike wonder” and a need to know “where we are, where we’re coming from and where we’re going.”
Leakey suggested that the extremely hot climate in Kenya was a potential model to understand how ancestral humans survived in hotter conditions, which are becoming increasingly prevalent amid global warming.
“There are many parallels in the past” in terms of extreme environments, Louise Leakey, director of public education and outreach for the Turkana Basin Institute and Richard and Meave Leakey’s daughter, said in an interview. “We’re sitting on this knife edge of really dramatic change now.”
In addition to encouraging science in Africa, Leakey also believed in engaging with students and researchers from a range of backgrounds and experiences. He wanted to ensure that people from every continent had an opportunity to join the ranks of scientists.
When presenting his research on Homo naledi, an extinct human with a brain a third the size of modern humans from South Africa who created burial sites and left behind etchings on a cave wall, Lee Berger, National Geographic Explorer in Residence, explained that he wished Leakey “had seen this and I think he would have been really angry with me.”
Words from a devoted daughter
In the final presentation of the first day, Louise Leakey shared memories of her upbringing and her father.
Among many pictures of her father and his discoveries over the years, Louise shared one in which she highlighted a pipe in the corner of the photo.She believed her father “rarely smoked it” but liked to pose with it in photos.
Louise Leakey speaks at the memorial conference for her father on June 5. Photo by John Griffin/Stony Brook University
Louise Leakey recalled how one of her father’s partners, Kamoya Kimeu, proved a valuable partner in the search for fossils. When Kimeu died soon after Richard Leakey, Kimeu’s daughter Jennifer reached out to Louise to raise money for his funeral.
Louise Leakey has since learned that Jennifer never saw her father searching for fossils in the field. Rather, she learned all about his exploits when her mother read his letters each night to her before she went to bed.
A second generation of the two families is working together, as Jennifer has joined Louise in some of her fossil hunting work. The two daughters are also creating a comic strip, in many languages, that depicts the two of them hunting for fossils.
Leakey believes Jennifer Kimeu will serve as an inspiration to other Kenyans.
On the east side of Lake Turkana, Leakey and her team recently discovered the new head of a fossil. Before his death, her father said it was “time you found new skull.” Richard Leakey was right.
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