August News and Press from SoMAS

Welcome back everyone, and greetings to our new students! Here’s the latest news and press from SoMAS for the month of August!

Seven members of the Chen Lab here at SoMAS co-ran the Lenfest Ocean Program’s International Crustacean Fisheries Task Force workshop the week of August 1^st in Honolulu, Hawaii. This task force was designed with the purpose to leverage its collective international expertise in crustacean fisheries stock assessment and management to develop technical guidance on the most effective scientific and management approaches to sustainably manage crustacean fisheries across the globe. Crustaceans represent the fastest-growing component of global fisheries catch.  The growth of these fisheries has been fueled not only by their high values but also by the ecological space left behind by overfishing finfish and other species. Many global communities, particularly in Asia, are becoming increasingly dependent on crustacean fisheries. This creates important socio-economic implications for fisheries that are exacerbated by data limitations and other capacity constraints, including monitoring programs, enforcement resources, management experience, and others. Therefore, it was the goal of this task force to build technical guidance on the development and evolution of integrated scientific and management systems for crustacean fisheries, with rapidly rising ecological and socio-economic importance across Asia, USA and elsewhere in the world. In Honolulu, over the course of four days, Nathan Willse, Claire Ober, Ming Sun, Yunzhou Li, Noah Khalsa, Cameron Hodgdon, and their advisor, Yong Chen, worked as project leads and/or subject experts on myriad projects with members of the scientific and fisheries management communities of the U.S., China, Indonesia, and the Philippines to achieve these goals. The group photo is above.

Dr. Daniel Knopf has received a new award from NSF (CHE Division), in support of the project entitled “Collaborative Research: Experimental and Computational Examination of Biomimetic Peptides Acting as Anti-freeze Molecules“, in the amount $463,315, for the period 9/1/22 – 8/31/2025.

Abstract:
This award from the Environmental Chemical Sciences Program in the NSF Division of Chemistry supports this collaborative project of Profs. Daniel Knopf and Robert Grubbs at Stony Brook University and Prof. Amir Haji-Akbari at Yale University to examine and generate organic molecules that can control the freezing of water. The ability to inhibit ice formation is crucial in critical technological applications such as preservation of biological materials, food processing and storage, and preventing ice growth on exposed surfaces such as those on aircraft and offshore platforms. In nature some organisms can produce so-called antifreeze proteins (AFPs) to control ice formation allowing their survival at freezing temperatures. This collaborative project aims to understand and mimic those AFPs to allow for generation of designed synthetic antifreeze molecules that can be used in various research areas and industries. This project will train three graduate and two undergraduate students and provide a course module for a summer outreach program for high school students.

The team will design AFP mimetics (AFPMs) with less complex structures than natural AFPs that can lead to practical and cost-efficient ice inhibitors and anti-icing coatings. A mechanistic understanding of the antifreezing capability will be sought by translating arrangements of hydrophilic and hydrophobic amino acid side chains found in ice-binding faces of β-helical AFPs to peptide-polymer conjugates covering various length scales from single molecules to arrays of substrate-anchored AFPMs. Ice nucleation and ice recrystallization inhibition experiments will determine the antifreezing efficacy of synthesized biomolecules. Theoretical studies using path-sampling will resolve the water-AFP mimetic interactions on length scales similar to those in the experiments. This comprehensive approach will determine the importance of the location and strength of the hydrophobic and hydrophilic groups and the flexibility of the AFPMs for antifreezing efficacy, thereby advancing the design of biomimetics that influence ice nucleation and growth.

Dr. Joyce Novak has received a new award from the Town of East Hampton in support of the Peconic Estuary Partnership for the project entitled “Peconic National Estuary Program Local Government Support“, in the amount $148,575, for the period 8/1/22-12/31/22.

These funds support operational costs of the Peconic Estuary Partnership and a groundwater investigation in Three Mile Harbor in East Hampton.

One of the most significant pollutants to the Peconic Estuary is nitrogen derived from groundwater. Septic inputs represent the greatest contributor to groundwater nitrogen pollution in many areas throughout the Peconic Estuary, although fertilizers and the atmospheric deposition are also major sources. Excess nutrients in groundwater are due in part to the region’s sandy soils which are susceptible to leaching nutrients and other pollutants, making the underlying aquifer vulnerable to contamination. Groundwater then enters coastal ponds and estuaries through a process called submarine groundwater discharge (SGD). SGD is the process by which porewater, which originated as inland groundwater, percolates up through the surficial sediment and enters the surface water.

Three Mile Harbor has been identified as a priority embayment by the Peconic Estuary Partnership Management Conference and is one of several priority embayments PEP has identified for moving forward our 2020 Water Quality Monitoring Strategy. In Three Mile Harbor, poorly flushed areas experience nocturnal hypoxia and high levels of nitrogen that exceed health conditions for eelgrass. Eel grass beds, although historically present in Three-Mile Harbor have disappeared. This project aims to understand where points of SGD occur, the nutrient contents at these sites, and allow the Peconic Estuary Partnership to move forward actions for remediation.

Abstract:
Weather phenomena come in all spatial scales, from the turbulent up-and-down motions within clouds to frontal systems that span a time zone to the jet streams that circle the globe. Naturally different models are used to capture phenomena at different scales, including Large Eddy Simulation (LES) models with grid spacings of perhaps 10m used to simulate individual clouds or small cloud clusters. LES models are typically applied on a limited domain, perhaps 10km to 100km wide, and the influence of larger scales of motion on the clouds is represented by imposing domain-wide conditions, for instance a single vertical profile of temperature and moisture for the whole domain. The drawback of such simulations is that they fail to capture two-way interactions between small and large scales, for instance the effect of small clouds on the large-scale temperature and moisture profiles. Models that can capture a larger range of scales would thus be quite valuable.

One model which has proved quite useful for this purpose is the System for Atmospheric Modeling (SAM), developed by the Principal Investigator (PI) in the early 2000s. SAM has been used as an LES model, for instance in simulations of flow around a building at 1m resolution, but has also been used with grid spacings around 5km to simulate wave motions in a channel domain spanning the tropics. SAM has been a workhorse model for studies of cloud behaviors including the aggregation of convective clouds and the response of clouds to greenhouse gas-induced warming, in particular the extent to which the cloud response intensifies or counteracts the warming.

Recently the PI developed a global version of SAM called gSAM, which extends the Cartesian coordinates to spherical coordinates and makes other modifications to represent flow on a global domain. The model inherits all of the features of SAM and also adds an immersed step topography, an advance over previous versions which were more idealized and assumed a flat surface. Another way in which gSAM adds realism is the ability to run simulations starting from observational initial conditions, allowing short-term “forecasts”, also called hindcasts, of real-world weather system evolution. A recent study used this feature, along with “nudging” to reanalysis data, to simulate conditions observed during the SOCRATES field campaign (see AGS-16628674). The study concluded that the formation of cloud ice particles from the shattering of earlier ice particles plays a role in determining the width of clouds, thus regulating the amount of sunlight that reaches the surface of the Southern Ocean.

The goal of this award is to further develop gSAM and make it available to the worldwide research community as a resource for weather and climate research. The work includes tasks devoted to improving model behavior near the poles, improving the accuracy and efficiency of radiative transfer calculations using machine learning techniques, improving input/ouput performance, and validating simulations against satellite data. Additional resources are developed to facilitate use and adoption of the model, including a full suite of documentation and tutorials, initial and boundary condition datasets for multiple configurations and resolutions, and model output for several six-month simulations. The model is maintained on GitHub and users can contribute to code development using GitHub repositories. The PI also maintains a model website that tracks publications using the model and provides additional information and resources. Since gSAM is an extension of SAM it is easily configured to run as a limited-domain LES model, thereby continuing to serve the SAM user community.

The work has broader impacts due to the power of gSAM as a tool for conducting basic science research on a wide range of topics. One area of particular interest is the interaction between clouds and climate change, as the sensitivities of clouds to a warming climate could affect the amount of warming that occurs. gSAM can also contribute to our understanding of how the intensity of extreme precipitation events is likely to change in a warming world. In both cases gSAM serves to lower the barriers between the research communities studying climate processes on the global scale and cloud properties on the local scale. The project also supports a graduate student, thereby building the next generation scientific workforce.

Congratulations to Donovan Finn who has been appointed as a new Associate Editor of the journal Urban Climate.

Dr. Roy Price’s recent expedition to Iceland is featured in this great write up in Polar Journal. It explains very nicely about the project objectives, as well as describing what it’s like to work in Iceland and collect samples during such an expedition. It’s written by renowned author and photographer Jacopo Pasotti, who joined the trip as well.

Congratulations to Graduate Student Sarah Weisberg has received a NMFS-Sea Grant fellowship in Population & Ecosystem Dynamics.

Stony Brook News Highlights

• Two SBU Students Selected for Competitive Knauss Marine Policy Fellowship
• SoMAS Summer Program Gets Students on the Water for Immersive Experience
• Scientists Recover Collapsed Clam Population and Water Quality in Shinnecock Bay

Press Highlights

CNN: Two ultra-rare floods in a single week; a wildfire generating its own weather. Here’s how it’s connected

• Expect more of these extremes as the planet warms, said Kevin Reed, a climate scientist at Stony Brook University, and prepare for them. Also ran on KMIZ-TV, WSEE-TV, Local 3 News, Albany Herald, KEYT-TV, Jackson Progress-Argus, Electric City Magazine, KESQ-TV, Local 3 News, Henry Daily Herald, KRDO-TV and many other outlets.

Newsday: Water conservation urged amid LI drought after region’s unusually hot, dry July

• Long Island “started to trend into the abnormally dry category” about two weeks ago, said Kevin Reed, an associate professor at Stony Brook University’s School of Marine and Atmospheric Sciences, citing an official metric, published by the U.S. Drought Monitor, based on data including rainfall, soil moisture and streamflow.

Reporter Wings: No state is losing land like Louisiana—but no other state has a bolder plan

• “It’s been nine years since Sandy destroyed much of the coastal area of New York and New Jersey,” William Golden, a coastal ecologist at Stony Brook University, said last year. “And in those nine years since Sandy, there has been no regional plan to protect the people of New York and New Jersey from the next Sandy.” Also ran in Honest Columnist

New York Times: 3 Downpours in 8 Days: How Extreme Rain Soaked the Midwest

• “We anticipate that these type of events might become even more frequent in the future or even more extreme in the future as the earth continues to warm, which means that this is kind of a call to action that climate change is here,” said Kevin Reed, an associate professor at the School of Marine and Atmospheric Sciences at Stony Brook University in New York. “It’s not a problem for 50 years from now. It’s a problem now.” Also ran in DNYUZ, Singapore Time  and Canada Express News.

CNN.com: Kentucky Flood Survivors Brace for More Rain

• Professor Kevin Reed discusses why weather events like the Kentucky flood and California wildfires are signals of global warming.

Daily Mail: NOAA warns US could be hit by DOUBLE the usual number of hurricanes this fall and predicts up to 20 named Atlantic storms during ‘above-normal season’

• ‘I think we often have this feeling in early August that it’s been relatively quiet even though hurricane season started on June 1, but a majority of the storms really come in the next two month period,’ Kevin Reed, an associate dean at Stony Brook University’s School of Marine and Atmospheric Sciences told DailyMail.com. Also ran on Mail on Sunday,

Yahoo/New York Times: 3 Downpours in 8 Days: How Extreme Rain Soaked the Midwest

• “We anticipate that these type of events might become even more frequent in the future or even more extreme in the future as the Earth continues to warm, which means that this is kind of a call to action that climate change is here,” said Kevin Reed, an associate professor at the School of Marine and Atmospheric Sciences at Stony Brook University in New York. “It’s not a problem for 50 years from now. It’s a problem now. Also ran in News Net Daily.

Wall Street Journal (India): Are Shark Attacks a Sign of Conservation Success?

• A similar network being developed for Long Island should be ready by next summer, said Michael Frisk, professor of Marine and Atmospheric Sciences at Stony Brook University.

Outsider: Massive Amount of Great White Shark Sightings Reported Off the Coast of Cape Cod

• A naturalist and professor at Stony Brook University’s Marine Sciences Center put it pretty simply. The high number of sharks shows that waterways are likely more clean than previously. The way Christopher Paparo puts it, the sightings “shows a clean environment.”

Times Beacon Record: BNL’s Katia Lamer studies urban heat in Houston and New York

• Indeed, Katia Lamer and her team launched 32 small, helium-filled party balloons. She and Stony Brook University student Zachary Mages each released 16 balloons every 100 meters while walking a one mile transect from the suburbs to downtown Houston.

Newsday: Stony Brook scientist warns oxygen loss in warming Sound may aid in fish kills

• The hottest water temperatures in years have depleted oxygen levels in Long Island’s North Shore harbors and may have contributed to a recent spate of fish kills, a Stony Brook University marine scientist said.

Newsday: Fish kills spotted off Long Island’s North Shore

• Fish kills have recently been spotted off Long Island’s North Shore. A Stony Brook professor attributes the deaths to warmer water and an overload of nitrogen. Newsday TV’s Cecilia Dowd reports. Credit: Kendall Rodriguez.

Iloilo Blogger: Getting to Know NIMBB’s New Director Dr. Carmelo del Castillo

• Dr. Castillo gained experience including as a PostDoc Associate at the Marine Animal Diseases Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, New York, USA (2012-2014).

All Things Supply Chain: Six Industries That Can Merge Circular Economic Practices With Supply Chain Management

• Prior to taking on the role of Social Media Manager, article author Nicolle Portilla served on the Sustainability team for nearly three years, assisting clients in achieving their sustainability goals through external communications and event organizing. Preceding Nicolle’s time on the RTS team is her work with Clean Water Action, where she promoted clean water initiatives. Nicolle graduated from Stony Brook University in 2018 with a B.A. in Sustainability.

Fox 5 News: Polio has been circulating in NYC area for months: CDC

• “It’s the idea that when people are infected, they’re passing these viruses through their waste,” said Prof. Chris Gobler, who runs the New York State Center for Clean Water Technology at Stony Brook University.

CBS News: Boy’s Leg Partially Amputated After Shark Attack Off Florida Keys

• In an interview with CBS News’ Michael George, Christopher Paparo, manager of the Marine Science Center at Stony Brook-Southampton, pointed to conservation efforts as one reason behind the uptick. Also ran on KWTV-TV,  KOTV, MSN, Times News Express and Yahoo News.

Livingston County News: Editorial — Out of control: The problem of plastic pollution has become a worldwide crisis

• The New York Sea Grant began in 1971. It is “a cooperative program of the State of New York and Cornell University, with administrative offices at Stony Brook University, extension administration at Cornell University in Ithaca and extension specialists located in Stony Brook, Kingston, Brooklyn, Elmsford, Buffalo, Newark and Oswego” information on its website reports. Also ran in the Daily News.

Fire Island Patch:  Blue Crabs Spotted On Fire Island’s Robert Moses Beach

• Chris “the Fish Guy” Paparo, a marine and atmospheric science expert, who manages the 5,000 square foot seawater lab at the Southampton Marine Science Center at Stony Brook University, said the blue crabs are typical for the area, but people just don’t notice them.

WNYC-AM/NPR: Thursday Morning Nat’l Politics; NY-10 & NY-12 Ahead of Primary Election Day; Are We in a Drought?; Generational Politics: 70s and 80s

• Much of New York is experiencing “abnormally dry” conditions, according to the US drought monitor. And some parts of NYC even hit “severe” levels. Kevin Reed, associate professor at Stony Brook University’s School of Marine and Atmospheric Sciences, describes these conditions and explains what they actually mean.

Newsday: East Hampton affordable rental project starts construction

• Building more affordable housing on the East End is critical for the region’s economy, said Richard Murdocco, an adjunct professor in economic development and planning at Stony Brook University.

Long Island Advance: What’s that smell?

• According to Save the Great South Bay, they have called on their colleagues at Stony Brook University School of Marine and Atmospheric Sciences, who are looking into the issue.

WNYC-AM: Drought Conditions… in the Tri-State Area?

• Much of New York is experiencing “abnormally dry” conditions, according to the US Drought Monitor. Kevin Reed, associate professor at Stony Brook University’s School of Marine and Atmospheric Sciences, describes these conditions and explains what they actually mean. Also on Player FM.

Washington Times: Experts blame spate of shark attacks on combination of successful conservation efforts, bad luck

• Christopher Paparo, manager of the Marine Science Center at Long Island’s Stony Brook University in Southampton, said in a backgrounder video that conservation and environmental efforts in the New York City area are in large part responsible for the rise in shark incidents.

Eco Magazine: Sea Grant, NOAA Fisheries Announce 2022 Joint Fellowship Program Awardees

• New York Sea Grant: Sarah Weisberg, Stony Brook University, Faculty Advisory: Janet A. Nye. Project: Advancing climate-informed, ecosystem-based fisheries management through food web modeling, indicator development and risk analysis in the rapidly warming Gulf of Maine.

Fox Weather: Much of New York experiencing ‘abnormally dry’ conditions

• Much of New York is experiencing “abnormally dry” conditions, according to the US Drought Monitor. Kevin Reed, associate professor at Stony Brook University’s School of Marine and Atmospheric Sciences, describes these conditions and explains what they actually mean.

Broadway World: Staller Center’s Paul W. Zuccaire Gallery Announces Fall Programs

• The Staller Center’s Zuccaire Gallery at Stony Brook University announces fall programs organized in conjunction with CONNECTING THE DROPS: THE POWER OF WATER, an art exhibition featuring seven environmental artists.

WOFL-TV: Video: Shark spotted swimming just feet from shore at Florida beach

• Bradley Peterson, a professor of marine science at Stony Brook University, suggests avoiding getting in the ocean during the early morning or late evening and staying clear of schools of fish.

WCBS-TV: Shinnecock Bay’s environmental recovery lauded worldwide (also picked up on Times News Express)

• More than a decade after CBS2 first covered the pollution, die-offs, suffocating algae, red and brown tide, considered more intense than any other waterway worldwide, Stony Brook scientists are getting global recognition for the restoration of Shinnecock Bay.

Fox 5 News: Hard clam population rebounds in Long Island’s Shinnecock Bay

• The 10-year effort led by Dr. Christopher Gobler, the endowed chair of Coastal Ecology and Conservation at Stony Brook University, identified ideal conditions inside a lab and then replicated them in parts of the bay where harvests were essentially unheard of.

News12: Stony Brook University scientists see improvements for marine life in Shinnecock Bay

• Stony Brook University scientists released the findings Tuesday of a 10-year restoration effort for the Shinnecock Bay.

WSHU-FM/NPR: Once on the verge of collapse, Shinnecock Bay clams recover

• A Stony Brook University study shows hard shell clam restoration efforts in Shinnecock Bay have reached a new milestone.

Newsday: Stony Brook project helped restore Shinnecock Bay clam population, report says

• A 10-year effort led by Stony Brook University marine scientists to create special “spawner sanctuaries” of hard-shelled clams in Shinnecock Bay restored clam populations in a wider area while vastly improving water quality, a new scientific paper reports.

Newsday: Clam restoration of Shinnecock Bay shows success (video)

• Christopher Gobler, from Stony Brook University’s School of Marine and Atmospheric Sciences and his team, on Friday said they were pleased to announce that after years of planting more than three million clams in the Shinnecock Bay, the water quality has improved significantly. Newsday TV’s Steve Langford reports. Credit: Kendall Rodriguez.

Innovate LI: SoMAS enjoys victory lap after Shinnecock Bay revival

• Scientists from Stony Brook University’s School of Marine and Atmospheric Sciences are trumpeting their efforts to revive a “collapsed” hard clam population – the devastating loss of a keystone organism that significantly weakened the ecological health of the entire Shinnecock Bay estuary.

Innovate LI: No. 719: On Breathalyzers, hydrogen hubs and trail mix, at the virtual end of a never-ending summer

• To shell and back: After a decade of hard science, Stony Brook University’s School of Marine and Atmospheric Sciences is celebrating the Shinnecock Bay estuary’s remarkable revival.

Southampton Patch: Scientists Save Clams, End Brown Tide In Shinnecock Bay: Study 

• On Tuesday, scientists from Stony Brook University’s School of Marine and Atmospheric Sciences gathered to announce the culmination of a decade of science in a paper published in Frontiers in Marine Science, an international peer-reviewed journal

Sag Harbor Express: Clam Restoration Has Spearheaded Ecological Reversal In Shinnecock Bay, Study Shows

• Shinnecock Bay has seen a sweeping reversal of once chronic misfortunes in the last 10 years, spurred seemingly simply by the depositing of millions of clams in just two well-chosen corners of its sandy bottoms, scientists from Stony Brook University attest in a new peer-reviewed paper released on Tuesday, August 30.

Phys.org: Scientists recover collapsed clam population and water quality in Shinnecock Bay (press release)

• Scientists from Stony Brook University’s School of Marine and Atmospheric Sciences (SoMAS) announced the culmination of a decade of science in a paper published in Frontiers in Marine Science, which describes a novel restoration approach used in Shinnecock Bay that has led to a 1,700% increase in the landings and densities of hard clams in that estuary, along with the expansion of seagrass meadows and the end of harmful brown tides. Also ran in Honest Columnist, Swift Telecast, My Droll, Verve Times, WhatsNew2day,  Samachar Central and News Explorer Net.

Southampton Press: Stony Brook Student Testing Scallop Die-Off Theories

• A young Stony Brook University graduate student is hoping to definitively show whether a voracious species of stingray that arrived in local waters the same year the scallops suffered the first summer die-off could be playing a larger role in the disappearance of the scallops than previously believed.

WKBW-TV: Plastic Pollution and You: NY Sea Grant Ways to Reduce Impact

• The curriculum is co-authored by Nate Drag, New York Sea Grant Great Lakes Literacy Specialist and Great Lakes Program Associate Director at the University at Buffalo, Buffalo, New York, and Kathleen Fallon, Ph.D., a Coastal Processes and Hazards Specialist with New York Sea Grant, Stony Brook, New York.