Authors Posts by Daniel Dunaief

Daniel Dunaief


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Horizontal gene transfer has the Rafflesia potentially using the host’s information against it

They’re a member of a group that includes some of the world’s best thieves. They’re so good at stealing that they don’t make or produce food for themselves.

And, to top it off, like the high school students who rule the school because they are the tallest, most attractive or most athletic, they are physically stunning. Known in the scientific community as Rafflesia cantleyi, they have some of the world’s largest flowers, spanning as much as two feet across.

Found in Malaysia and named after a 19th century curator of the Singapore Botanic Gardens, the Rafflesia doesn’t have chlorophyll, the critical green molecule that allows plants to turn light, carbon dioxide and water into food. Instead, it lives deep inside the host vine, Tetrastigma rafflesia, a member of the grape family.

But that, it turns out, is not the only thing the parasitic plant pilfers. Recent research from Stony Brook assistant professor Joshua Rest, in collaboration with Harvard Professor Charles Davis, suggests Rafflesia has somehow taken something surprising: 49 genes from the Tetrastigma.

While bacteria and viruses take genes wherever they find them and attach them to their own set of life blueprints, it is much more unusual for plants to take genetic material, much less a region this large, from another plant. That means the Rafflesia is not only invading the space and food of the Tetrastigma plant, but it is also grabbing some of the plant’s hard-earned genetic identity.

When he first examined the genetic sequence of the Rafflesia, Rest was so stunned, he wondered whether he might have “just contaminated something,” by mixing the genes of the two plants.

Careful analysis, however, confirmed it was not the researchers who mixed the genes, but rather the plant that had gone through a process called horizontal gene transfer. Unlike vertical gene transfer, where individuals get their genes from their parents, in horizontal gene transfer, an individual can acquire its code from something outside its genetic tree.

“It definitely turns the way we think about things a bit on its head,” acknowledged Rest.

This discovery is new enough that scientists like Rest and Davis can only begin to guess at what advantage the Rafflesia gets from copying the genes of its host. One plausible explanation is that the parasite weakens the grape plant’s ability to defend itself against its unwelcome guest. The copied genes might send a signal to the host plant that disguises the parasite, allowing it to live like a disguised but sated wolf among sheep.
Rest cautioned that scientists don’t understand how the gene transfer affects the ongoing battle.

“We don’t know that there’s any cost” to the grape plant, Rest offered. “To whatever extent the transfer makes the parasites better at what they do, it could make the [grape] vines worse off.”

While the copied genes may protect the parasite against an immune response, they are also a part of other activities, including metabolism and respiration.

“They are involved in different cellular functions,” he explained. “We were expecting maybe we would find genes that were just involved in the immune response.”

To be sure, the notion of combining different genes to form a new organism isn’t unique, even in the world of eukaryotes. In fact, because the DNA from mitochondria and chloroplasts are different, scientists believe that, at one point, these organelles existed separate from each other, and proto-eukaryotic cells enveloped them. The parasitic gene copying is “on a much smaller scale,” Rest assured.

Given the range of parasites, it’s likely that others besides the Rafflesia have taken more than just food, sunlight or structural support at the expense of their hosts.

“Nature is a big place, so it’s unlikely that this mechanism is unique,” Rest suggested.

When he’s not looking closely at the genes of plant parasites, Rest, a native of the Chicago area, enjoys the chance to explore nature on Long Island, where he likes to run and hike in parks along the North and South Shore.

Rest lives in Bellmore with his husband Scott Stuart, a music therapist who works in a nursing home.

As for his work, Rest is fascinated by the implications of the range of what Rafflesia takes from its grape vine.

“The parasite,” he explained, “is potentially using the host information against it.”

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Glotch studies how water altered Mars’ surface; wife Deanne Rogers studies how Mars’ crust formed

Tim Glotch has his head high above the clouds, but his wife, Deanne Rogers doesn’t mind — she does too. An associate professor in the Geosciences Department at Stony Brook, Glotch met Rogers, an assistant professor in the same department, when they were graduate students at Arizona State University.

After forming a match made in the heavens, the two scientists moved to Selden and started raising a family that includes two preschool children.

Glotch studies rocks and minerals on Mars by examining data from orbiting satellites. He’s interested in how water altered the surface of Mars. Rogers, meanwhile, is trying to understand how the crust of Mars formed.

Recently, Glotch shared good news with his planetary partner. The National Science Foundation awarded him the Faculty Early Career Development Award. The recognition includes a five-year grant for $494,000 that supports his research, allowing him to add a post-doctoral researcher and a graduate student to his lab.

“It’s a fantastically exciting opportunity,” Glotch said. It allows him to delve deeper into the spectroscopy that he has used to study the makeup of minerals on Mars and the moon.

By looking at the surfaces, Glotch tries to piece together how Mars and the moon became what they are. He studies the minerals in inactive volcanoes and at impact craters to come up with models for how these orbiting bodies might have changed over time.

“I’m trying to understand how Mars evolved,” he explained. “How did basaltic rocks (like some of the ones in Hawaii) get there and how did liquid water change their minerals.”

Glotch recently took a trip to Hawaii, where he looked at rocks that have Martian cousins millions of miles away. He expects the interest in Mars to build from now through August, when the rover Curiosity is scheduled to land.

Glotch hopes to submit a paper for publication soon about a Martian volcano called Syrtis Major. It’s called a shield volcano, which means it’s a broad, flat volcano made from basaltic lava.

When he looked at the “squiggly lines” from the spectral data of the volcano, he noticed basaltic rocks and carbonate decomposition products. The carbonates might help explain where the atmosphere Mars might have had billions of years ago has gone.

“The carbonates could sequester a lot of an ancient atmosphere,” he offered. While this is indirect evidence, it’s an exciting step in understanding the history of the Red Planet.
At the same time, Glotch is also studying the moon. As talk of returning to the moon in the next decade builds, Glotch had an unusual companion on his recent trip to Hawaii: astronaut Jeanette Epps. She wanted to see how geologists work in the field and gain an understanding of the kinds of problems planetary geologists and volcanologists address by working in a volcanic terrain.

In recent years, Glotch’s approach to the moon has yielded interesting data.

“When we first looked at the data, we saw these squiggly lines that were fundamentally different than anything else we’d seen on the moon before,” he said. “That was very exciting.”

Those lines were examples of silica rich volcanoes, which are evident in places like Mt. St. Helens. On Earth, they form as a result of plate tectonics. The moon has no such underlying shifting land masses.

Glotch believes basaltic underplating could explain the presence of the silicon dioxide on the moon. In that case, basaltic magma didn’t rise to the surface, but rather melted the crust around it. Because the silicon dioxide was buoyant, it rose to the surface.

The Stony Brook associate professor is developing a workshop for high school science teachers that will allow them to work with lunar data. He recommended a step-wise approach to generate interest in the moon.

“The easiest way to start is to show a picture of a volcano on the moon,” he offered. Teachers can compare those images to volcanoes on Earth. Students who want to know more can look at remote sensing and study images the eye can’t see to understand the composition of rocks and minerals.

As for life in the Glotch home, he said it’s been incredibly valuable to share his passion for his work with his wife, and to lean on her for support. She can commiserate on one of the least glamorous parts of being a scientist: writing and submitting proposals on deadline.

Even with some overlap in their work, looking up into the skies leaves the two scientists with plenty of space to define their own interests.

“There’s so much to do, there’s plenty of room for everybody,” offered Rogers.

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Physicists from SBU and BNL comment on finding the ‘missing link’ between theory and reality

A quest over 40 years in the making finally ended recently, as physicists announced they had found a subatomic (read: extremely tiny) particle that had become the missing link between the theory and reality of the origins of mass in the universe.

Billions of years ago, the universe was filled with energy, but not mass. That meant there were plenty of particles racing around, through and past each other, but none of them had the kind of mass that would allow them to become planets, beds or hot fudge sundaes.

In 1964, a group of physicists, led by Peter Higgs, suggested there was an energy field that gave some particles mass, albeit for the briefest of time. Physicists have been slamming highly charged particles into each other, hoping to find this elusive Higgs boson particle.

With the words, “I think we have it,” Rolf-Dieter Heuer, the director-general for the European Organization for Nuclear Research, suggested they’d found what was like looking for the dissolving pieces of a needle in a hay field.

While it’s not exactly as poetic as Neil Armstrong’s “one small step for a man, one giant leap for mankind,” the words heralding the discovery of the so-called “God particle” have generated considerable excitement in the world of science in general and physicists in particular.

Stony Brook physics professor John Hobbs and Brookhaven National Laboratory senior physicist Howard Gordon were watching from their home computers in the early morning hours of July 4 when the official announcement arrived.

When the audience at the CERN Particle Physics Centre near Geneva erupted in applause as scientists described the result as five sigma (a threshold for statistical significance — the equivalent of a mathematical reality test), “I got a tear in my eye,” recalled Gordon.
“I was very satisfied,” explained Hobbs. “This has been the pursuit of many people for a long time.”

The Higgs boson theory, which five other physicists proposed along with Higgs, suggested energy passed through a Higgs field, attracting other particles along the way. Some scientists describe this field as being like molasses that sticks to the particle or like a snowball rolling down a hill, attracting other pieces of snow.

After that particle obtained mass, it quickly reverted to a state of energy, giving it mass for only a short time. To find the so-called Higgs boson particle, scientists needed to look for decaying pieces of it and then put those back together.

“Any time you have a massive particle of any sort, unless there are things which prevent its decaying, it will naturally do so,” explained Hobbs. “In the case of Higgs boson, there are many ways it can decay.”

One of the challenges of finding the Higgs boson particle was that its mass could be in a broad range.

“Previous experiments had ruled out Higgs below 114 GeV (gigaelectronvolts),” explained Gordon, but it could still be anywhere higher than that, up to 600 GeV or more.

Results from CERN found that the elusive particle was at a mass close to 125 GeV.

So, after all these years of searching for something scientists had predicted would be there, does this change the world?
Scientists suggest the answer is: no and yes. It doesn’t affect the cost of gas, speed up a slow Internet connection or lower the unemployment rate — at least, not yet.

Like other basic research, however, it does provide an answer to questions about the universe.

“We have now validated what we think about how the basic building blocks of matter got their mass,” said Barbara Jacak, a distinguished professor of physics at Stony Brook and member of the National Academy of Sciences. “I don’t know how that’s going to affect our daily life, but I suspect it will. If you think about earlier discoveries in physics that seemed basic, people figured out how to build smaller [electronic] devices. I’d be willing to bet this will end up driving new technology somewhere.”

Even before it does, however, it is likely to lead to a whole new set of fundamental questions, including about such things as dark matter, which comprises over three-quarters of the universe.

“We’ll use this to address another set of questions,” explained Hobbs. As such, it’s both “an end and a beginning at the same time. It is not the end of the questions by any means. It is a very significant waypoint along the route.”

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Amid the moving chaos of New York City, Thomas Watson has stopped and watched the steam that rises out of manholes. On one side of the street, the steam drifted one way.

On the other, it headed in the opposite direction.

While the complexity of the wind might seem fitting for a city where people blow in from all over the world, the shifting air currents are much more than a metaphor to the chemist from Brookhaven National Lab. They have become a part of research he — and emergency management personnel in the city — use to understand how gases, particularly toxic or dangerous ones, might move through the street canyons created by buildings of all shapes and sizes.

In 2005, Watson conducted an extensive study of air currents in and around the city. He released perfluorocarbons at different points throughout the area, tracked where the gases went and put together how they might have gotten from one place to another.

This year, he’s starting another similar study. His work, which in 2005 was funded in part by the Department of Homeland Security, is designed to help emergency management crews in the city deal with an accidental release of gases that might pose a threat to public safety. The city also uses his research in the event of the intentional release of harmful substances.

“The research we do supports emergency response decision making,” said Watson.

Watson leads a unit at BNL called the Tracer Technology Group. They release harmless gases to see how different elements travel under a broad range of meteorological conditions.

The gases, called perfluorocarbons, are “totally nonreactive” and can be detected at incredibly low levels: parts per quadrillion.
Tracer gases are sometimes used across much larger areas than a metropolitan region as well.

“We can get an idea of how air is moving across the continent,” he suggested.
In the Across North America Tracer Experiment (Anatex) in the late 1980s, for example, gases released from Glasgow, Montana and St. Cloud, Minn., could be seen on the East Coast.

The science of tracking air movements using tracer compounds as they move across different terrains started about 30 years ago, Watson recalled, as part of a comprehensive safety plan amid the development of nuclear power plants. While a release from a plant is unlikely, “prudence dictates we should be able to predict where a release would go,” Watson offered.

Watson also studies indoor air quality, looking at infiltration rates into buildings. The ventilation systems of large buildings, he explained, often bring outside air into the system at a measured rate.

This work not only has implications for safety and public health, but also for energy efficiency, as buildings can use the data he collects to figure out whether more outside air than anticipated is entering the building. On a particularly hot or cold day, the introduction of outside air could raise heating or cooling costs.

Watson has also been involved in finding leaks in underground systems for utility companies. In some of the subterranean systems, power companies have underground wires that are surrounded by oil, which helps insulate and provide some cooling. When the oil leaks, it’s difficult to find. Enter perfluorocarbons.

“We ride around in a van and can find [the perfluorocarbons],” he described. By tracking the gases, “we can come within a couple of feet of the leak.”

The alternative to using the tracer chemicals is to freeze the line and see where the pressure drops. The freeze method sometimes requires digging several holes before finding the leak.

Tracer gases are also “important for climate work,” Watson offered. He looks at the exchange between the biosphere and the atmosphere. He validates transport models used to help interpret carbon dioxide exchange measurements.
When Watson, who lives in Ridge with his wife Phyllis, isn’t tracking gases through the air or underground, he enjoys spin casting for striped bass. He said he usually keeps one a season.

Although he grew up in Delaware and was a Phillies fan, he has seen the error of his ways and, after seven years on Long Island, has seen his allegiance drift to the Mets.

As for his work, Watson is convinced he’s doing something important and that he needs to provide the best possible information to emergency personnel.

“No scientific data is ever exact to an infinite number of decimal places,” he concedes. “We strive to get the best possible information to all our sponsors and always provide uncertainty limits.”

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Professor’s study of lemurs helps them, conservation and medicine

Patricia Wright loves Madagascar and its lemurs — and the country returns the favor. On July 2, Wright will inaugurate a state-of-the-art, four-story research center adjacent to a rainforest — complete with a high-speed Internet connection. At the same time, the Stony Brook anthropology professor will receive her third Legion of Honor medal, becoming the first foreigner to receive three of the island nation’s highest awards.

The star-studded opening of the facility — called Namanabe (for Friendship) Hall — will have over 600 guests. The attendees span the world, from Stony Brook President Samuel Stanley, to Madagascar’s minister of the environment, to the vice rector of the University of Helsinki, Finland, to the ambassador for the U.S. to Madagascar, Eric Wong, to local kings from 33 villages, and 21 traditional healers.

The building, which overlooks a waterfall, river and rainforest and has a garden and solar panels on the roof, will provide a home for the study of biodiversity and infectious disease.

Wright, who has been studying lemurs since 1985, will soon announce that there are three kinds of dwarf lemurs in nearby Ranomafana National Park. Previously, scientists believed the park only contained one species of dwarf lemur. Ranomafana has 14 species of lemurs, one of the highest counts for a single park in the world.

Wright has a long list of notable achievements in her studies of the Madagascar primates, whose name comes from the lemures of Roman mythology because of the animal’s ghostly calls and reflective eyes.
In the 1980s, Wright was searching for the greater bamboo lemur, which some scientists believed had become extinct. She not only found the endangered animal, but also discovered the golden bamboo lemur, a species scientists didn’t even know existed.

For the second year in a row, she was a finalist in the $100,000 Indianapolis Prize, the top award for animal conservation. While she didn’t win this year, she was one of only six finalists from a competitive field of conservation biologists.

“It’s a great honor,” said Wright. “Many fantastic people are on that list that have done amazing things. I’m proud to be a part of that.”

Stuart Pimm, the Doris Duke professor of conservation at Duke University, called Wright “Madagascar’s savior” for working to conserve an environment scientists describe as the “eighth continent” for its remarkable diversity of species, some of which are threatened or going extinct.

“Nobody does conservation work in Madagascar without coming under her influence,” Pimm declared. The new research facility Wright helped build is “an amazing meeting house for people who want to protect the Malagasy environment. That contribution will last for decades. It’s a very tangible achievement.”

Wright explained that her current research, which she conducts in Ranomafana, addresses three questions. First, she is studying lemur behavioral ecology and demography and aging in the wild.

Second, she is looking closely at the mouse lemur, the world’s smallest primate. Some mouse lemurs in captivity, who were as young as four years old, developed Alzheimer’s. She is tracking 500 mouse lemurs in the wild. So far, she has examined wild mouse lemurs as old as 10 and hasn’t found any similar cases. That could be because lemurs that suffer from age-related cognitive problems could become easier targets for predators. It also could be related to the mouse lemur’s diet or to its more active lifestyle in the rain forest.

And, finally, she is examining seed dispersal in trees by lemurs. She’s planning to study how far away seeds get from the parent tree. She also wants to see if seeds from a wide range of canopy trees with large, sweet fleshy fruits that pass through the digestive system of a lemur sprout faster and live longer.

“We’re really interested in ecosystem dynamics,” she explained. “To really understand how to restore a habitat, we have to know how it works to begin with. That’s not easy in a rainforest.”

Although she applies science to just about everything she does professionally, Wright knows she needs much more than good intentions and a clipboard to wander through the rainforest to study lemurs.

“Whenever you are exploring in new places, when you meet people, you have to be a little cautious: they don’t know who you are and you don’t know who they are. You have to obey the rules of the local culture,” she explains.

She visits with the village elders first, to describe what she’s doing. She travels with permits signed by authorities. She has put considerable effort into sharing information about the rainforest and about health with the Malagasy (the name for people from Madagascar).

“When we’re dealing with health, we like to have it science-based,” she said. “We’re not just dispensing pills. We like to do health and hygiene education to prevent health problems before they happen.”
In addition to her scientific contribution, Wright has helped build and shape communities around the rainforest, Pimm said.

“She has done an extraordinary job in ensuring that people in the local community benefit from having a national park right next to them,” observed Pimm, who has known Wright for more than 15 years. “There is now a community of small businesses that have learned through [her] leadership.”

In addition to respecting the people in the remote areas where she treks — often on foot and while carrying her own food and cooking utensils — Wright remains aware of other threats.

“I’m quite a careful person for someone who does all these crazy things,” she offered.

Indeed, she has encountered the deadly fer-de-lance snake — a reptile whose venom can be fatal to humans. Always on the lookout for the deadly snakes, she has seen them several times. She was on a trail following monkeys one night when she encountered another dangerous creature. She explained that the path was wet, so neither one could hear the other coming. She rounded a bend and stopped inches from a jaguar.

“There we were, eye to eye,” she recounted. “I thought to myself: that animal is bigger than me. I’m getting off the trail.”

The predatory cat jumped away, perhaps because a headlight Wright wore to navigate through the soggy jungle confused him.

While assiduously avoiding jungle cats, Wright has tried to attract sponsors for her research.

In April, she held a rock concert at Centre Valbio, where the U.S. Embassy invited some of the wealthiest people in the country to enjoy music by popular Malagasy bands while learning about research in the rainforest.

“What I actually do is very complex,” she explained. “It’s very important that the science is not done in a vacuum. It has to be incorporated into public awareness.”

As for the future, Namanabe Hall, Wright hopes, is just another step in research and conservation in Madagascar.

“There are so many things we need to make the research dream come true,” she offered. “I would love to put sensors out into the forest that could stream back to our network and databases information on microclimate and animals. The Namanabe Hall is just the beginning of what I hope will be a fountain of inspiration to study this tropical rainforest in innovative ways and to study and assist the people, too.”

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SBU professor R. Lawrence Swanson uses hair conditioners as chemical markers to study sewage

Hair conditioners aren’t just helpful for the heads of Hempstead residents. They also serve as chemical markers for what happens to sewage released through the Bay Park outfall in Reynolds Channel.

That’s just one of a host of findings in an ongoing study of Hempstead sewage that Stony Brook University professor R. Lawrence Swanson is managing. Swanson is leading a group of 10 scientists and three graduate students who are examining the Western Bays in Hempstead to determine what’s happening in the area and to recommend what actions, if any, policy-makers might need to take to protect the region.

While the hair care chemicals, which Stony Brook associate professor Bruce Brownawell is studying, aren’t necessarily damaging to the environment, they do act as markers for the bay.

“Looking at the results of hydrodynamic modeling in conjunction with some of the work that’s been done looking at hair care [products] in sediments has indicated to virtually all of us that the removal of material from the vicinity of the Bay Park outfall is not very good,” Swanson stated. “There’s a lot of sloshing back and forth in the Reynolds Channel.”

Swanson suggested that the choice of the channel in the 1950s probably seemed like a logical one because tidal currents are “quite rapid” twice a day. However, the problem is that “much of that water seems to slosh back and forth, as opposed to exiting.”

Just as the sewage begins to drift east and north away from the bays, the tidal current reverses and pushes it back. Swanson explained. The residence time in Reynolds Channel is between 50 and 240 hours. That means a particle released in the channel would take that long to leave the general area, Swanson said, citing the work of Stony Brook associate professor Robert Wilson.

Additionally, Reynolds Channel and areas to the north are struggling with a “tremendous biomass of sea lettuce,” Swanson observed.

While sea lettuce is common around Long Island, it is so dense in those areas that residents are referring to it as “green bergs.” It accumulates at Point Lookout near the entrance to Jones Inlet to such an extent that the hydrogen sulfide smell is noticeable.

The Hempstead Bays project, which started in September of 2010, runs through March 2013. At the end of it, Swanson and the rest of his team will summarize the results and make recommendations to policy-makers.
As he enters his fourth decade in the environmental sciences at Stony Brook, Swanson indicated he has become increasingly outspoken about the dangers of poor waste management.

“We’re in trouble,” Swanson declared. “We have reached our limit in terms of population growth. In Suffolk County, we are still relying on septic systems that are not the best technology. Many of them are probably not functioning particularly well.”

Swanson said the nitrogen concentration in the Magothy aquifer is about 200 times greater than it was in the 1980s, citing data from the Suffolk County Health Department. The Magothy aquifer is the largest bed of permeable rock that provides water to Long Island.

Still, Swanson isn’t ready to give up on Long Island or on the possibility of improving an environment he said he has thoroughly enjoyed since moving here in 1973.

Swanson lives in Head of the Harbor with his wife, Dana, who is an artist. One son, Michael, lives in St. James, while Larry lives in Seattle, where Dana grew up and where her extended family has lived for four generations.

The Swansons live in a 170-year-old house that was the site of a water bottling business known as the Soper Bottling Works in the late 1800s.

“Every day, the house wakes up and says, ‘What are you going to do for me today?’” laughed Swanson.

Swanson is optimistic that the right programs and approach can improve the environment. He points to the New York Bight, a region between Cape May and Montauk where ocean dumping occurred until around 1990.
Since the cessation of dumping, “You would see a remarkable resilience of the marine environment and its ability to recover, once we stop abusing it.”

Swanson cautions against continued environmental abuse. “An ounce of conservation is worth many pounds of restoration,” he offered.

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SBU professor Scott McLennan part of team studying ancient Martian rocks to understand its geology

Terrestrial trucks with tough names and gritty commercials have nothing on a six-wheeled golf cart-sized vehicle. Operating millions of miles away on the unforgiving surface of Mars, the rover, Opportunity, landed in 2004 and was only expected to last for three months.

Eight years later, Opportunity is going strong, sending back useful information about the red planet. Using solar power, Opportunity outlasted its twin, Spirit, which stopped responding to Earth-bound signals about two years ago. The scientific vehicle recently provided even more evidence that Mars once not only had water, but that the water may have contained life.

Venturing near the Endeavour crater (named after the British ship that explorer James Cook led to New Zealand and Australia at around the same time as the American Revolution), Opportunity found rocks and minerals that provided more clues about the evolution and history of the surface of Mars.

“When we came onto the rim of the Endeavour crater, the fundamental geology completely changed,” explained Stony Brook University geochemistry professor Scott McLennan, who recently teamed up with scientists at several institutions to publish a paper in Science on their findings.

Looking at rocks that are likely older than 3.8 billion years old, McLennan and other scientists found extremely high zinc contents. Usually, zinc is at a level of 30 to 300 parts per million, but in these rocks, zinc was closer to 6,300 parts per million.

Zinc combines with sulfur and phosphorous. Scientists would expect to find these minerals, such as zinc sulfide or zinc phosphate, in rocks that had hydrothermal fluids that ran through them.

“People have known there was water on Mars for a long time,” McLennan explained. “The real issue was whether the water was in a liquid form at a time when you could have had environments in which life could have survived. We’re finding more geological environments in which water was active and conditions could have been habitable.”

Scientists also discovered gypsum near the crater. The chemical name for this mineral is calcium sulfate dihydrate. The last part of that name means the mineral has two water ions per molecule embedded in it.

“This was completely unexpected,” said McLennan.

Finding water tied up in the structure of minerals and rocks means they could become a resource for future exploration of Mars. For astronauts to make a round trip, they would need to make use of whatever water and fuel they could extract from Mars.

McLennan cautioned, however, that the volumes of water in the minerals on Mars are “not great.” Indeed, for every kilogram of gypsum, scientists could likely remove just over 200 grams (or 20 percent of the mineral’s weight) in water.

Much of McLennan’s research comes from analyzing the information sent back from Mars and simulating what he sees in his Stony Brook lab.

“What we were able to do,” said Joel Hurowitz, a research scientist at Jet Propulsion Laboratory who worked in McLennan’s lab to earn his doctorate, “was go into one lab and make rocks in a furnace and then take them to another lab and alter them in the presence of fluids that might have existed in the past on Mars. We could analyze the products of those water-rock reactions.”

Hurowitz described Stony Brook as a “spectacular place to grow up in as a student” and called McLennan a “leader” and “pioneer” in his area of research.

So, after all this extra time and information from Opportunity, where does Mars research go from here?

“Mars exploration is at a crossroads,” McLennan suggested. The first scientific priority over the coming decade is to begin the process of bringing samples back from Mars, so geologists like McLennan can study them.

President Obama, however, “cut planetary science and Mars exploration dramatically.”

The House and Congress have tried to reinstate some of the funding in those programs, but “who knows how it’ll end up,” McLennan added. He predicts the next year or so will determine whether scientists and politicians can make progress toward a return to Mars.

In the meantime, McLennan, who lives in Centerport with his wife Fiona, an assistant vice president of Human Resources at Columbia University, will continue to analyze information from the durable Opportunity rover.

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Scientist studies wild ancestors of domestic fruit to increase productivity

Going into his tomato project, Zachary Lippman expected something different. After all, over thousands of years, breeders had been growing the juiciest tomatoes they could.

A team of scientists from 14 countries had already put together a genetic blueprint of the 35,000 genes spread across 12 chromosomes for the “Heinz” tomato.

Lippman, meanwhile, led a group of scientists at Cold Spring Harbor, including Richard McCombie and Doreen Ware, to put together a similar genetic blueprint for the naturally occurring wild type. The tomato Lippman studied, which is an edible South American currant tomato, was much more like the original fruit our agricultural ancestors stumbled upon thousands of years ago.

Even before he finished the two-year effort to create his own genetic blueprint, Lippman suspected there would be plenty of genetic differences. After all, corn and rice, among others, had changed a great deal since its domestication.

“The expectation was that we’d see a lot of changes in the DNA,” offered Lippman. “What we found was the opposite. We see a remarkable similarity between the wild and domesticated tomato.”

Indeed, that scientific finding — and the years of work preparing and comparing the genetic libraries of the different tomato types — was flavorful enough for the scientific journal Nature to include it in its most recent issue.

Calling the genetic sequence of the two tomato types a “major first step,” David Spector, Cold Spring Harbor’s research director, explained that this type of research could help identify critical genes that scientists could manipulate to help improve the tomato, in terms of number of flowers that might give more fruit, or its ability to withstand drought conditions or insect infestations.

Longer term, identifying specific genes that could improve the quality and durability of the tomato could have implications for the world’s food supply, suggested Spector.

“Any developments that can be made to help increase yield and resistance to various conditions such as drought or insects will have a huge impact worldwide. What he’s doing is going to have huge global significance. He’s starting with the basics of the sequence of the plant and is working his way up from there.”

Lippman plans to use the information from the genetic sequences of the two tomato types   in several ways.

Using classical and modern genetics and breeding technologies, he studies tomato mutants that affect how many flowers are produced by a tomato plant on a branching structure called “inflorescence.” These mutants can cause tomato plants to produce either fewer than normal or more than normal flowers, by changing how many branches are produced on the inflorescence.

He then identifies the genes that are “not working properly” in the mutants and studies how these are turned on and off during growth of the tomato plant. He specifically looks at how these genes change in their activity as the tomato plant transitions from making leaves to making flowers.

He is also crossing wild species that produce a lot of branches and flowers with those that producer fewer flowers. He then “genetically maps” the location of the responsible genes. He studies how these genes change during the reproductive transition and what DNA changes occurred to cause the evolution of the different species that produced different numbers of flowers.

Lippman lives in North Bellmore with his wife Shira, a dentist, and their four children, who range in age from three to nine years old.

Lippman isn’t just a leading expert in the field of tomatoes: he’s also a consummate consumer, carting containers of V8 juice back from trips to Costco.

“It’s not a joke,” he insists. When he’s not working on tomatoes, he likes to eat, or drink, them.
Indeed, his favorite way to eat tomatoes is in a cold tomato salad, with basil and fresh mozzarella, and a pinch of salt and pepper.

Lippman, who was raised in Milford, Conn., first became interested in plants and agriculture, particularly pumpkins and tomatoes, when he took a summer job at Robert Treat Farm, a family-owned farm within a mile of his house.

Lippman hopes large-scale farmers, farm stands and backyard gardeners from around the world will benefit from his research on the genetic sequences and the genes of wild and domesticated tomatoes.

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Working on three stopping points, scientist tries to anticipate terrorists’ next move

One day, Joseph Brady hopes he’s unemployed. He doesn’t hate his job, but he wishes it weren’t necessary. Brady teams up with law enforcement — the Suffolk County Police Department and the Federal Bureau of Investigation — to prevent those bent on blowing things up from succeeding.

Brady, who joined the Nonproliferation and National Security Department staff at Brookhaven National Laboratory last summer, is a chemist who specializes in explosives. He explained that there are three potential points when law enforcement can stop the “bad guys” (a term he uses to describe would-be bombers).

First, law enforcement can prevent them from making explosives. They can interfere with one of the key ingredients — even a household product — in making deadly weapons. He calls this process denaturing explosive precursors.

Brady has put additives in hydrogen peroxide — yes, the same liquid parents apply to skinned knees after their kids fall off a bicycle — that make it less reactive with other chemicals. Those additives don’t interfere with the disinfectant’s intended use.

The second stopping point is in detection. Once an explosive is made, law enforcement may be able to detect it at airports, bridges, tunnels and other areas he calls “choke points.” Brady mimics the way bad guys manufacture explosives and studies the results. He looks at the properties, searching for byproducts that might be indicative of illicit activities. He examines how current detection technologies respond to these materials.

The third stopping point is to figure out how to get rid of a device once it’s detected — without allowing it to explode. Scientists can accomplish this by stabilizing the materials in the device or by introducing some new element that could “chemically digest the explosives.”

Brady has worked with triacetone triperoxide, the common homemade explosive that was part of the shoe bomber’s device. Attempting to move TATP could result in an unintended detonation because it’s so unstable. As part of Brady’s dissertation, he showed that chemists can destroy TATP on the 100-gram scale without detonation by using combinations of commonly available chemicals.

Brady, whose research is funded in part by the Department of Homeland Security, explained that “Bad guys are always finding new materials to use against us. A lot of times, they find old materials that have no value to military or commerce.”

He pointed to nitrate esters as one explosive he expects to see “on the scene.” Brady is working on ways to detect the presence of these homemade explosives.

Brady feels he’s playing a type of cat and mouse game with would-be terrorists, trying to anticipate what they’ll do next. Fortunately, he said, he’s working with a team of skilled law enforcement officials who offer suggestions.

“It’s a feedback loop,” he explained. Law enforcement “comes with a question, he provides an answer, then they have a new question.”

While Brady plans to conduct lab experiments with chemicals that can create explosives, the amount of materials he uses is on the order of milligrams — the equivalent of a few grains of salt. He’s unlikely to see explosive reactions that could cause any of the destruction he’s trying to prevent.

Brady, who worked on chemotherapeutic agents in college at the University of Rhode Island, studied explosives when he realized he could play a role in protecting people.

“You see that the bad guys are trying to do something and you can do something about it,” he said. “They are always working hard, so you try to work harder.”

Brady earned his Ph.D. from the University of Rhode Island. He’s been writing for grants to build his lab. The proximity of BNL to New York City and Washington, D.C. makes it an ideal resource for national law enforcement, he said.

Brady was involved with the FBI and the Suffolk County Police Department in presenting a class for Transportation Security Administration screeners on explosiveness awareness. Because BNL is on a former Army installation, the Suffolk County police could use an old grenade range to show TSA officials how the homemade, commercial and military explosives work.

Brady, who is not married, said when he’s not working to build his lab, he enjoys visiting beaches on the North and the South Shore.

Brady said his father, John, a counselor for troubled children, and his mother, Judi, a psychologist, are supportive of his work.

“They are proud,” he offered. “They say, ‘Good for you. Go get ’em.’”

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Post-doctoral student Attreyee Ghosh and Professor William Holt study plate tectonics

They only travel about four inches per year. That makes a sloth, which can achieve a top speed of 6.5 feet per minute, seem like a furry blur by comparison. And yet, when they move, they can change the face of the planet.

The slow shifting of the enormous tectonic plates — like puzzle pieces pressing against and pulling away from each other over the surface of the planet — can not only cause devastation through earthquakes, but can also build mountains and form deep-water ocean trenches.

Ever since the 1960s, when scientists accepted the theory of continental drift, they have been trying to understand and predict where those plates move. There has been a rift in the scientific community itself over what forces (and where those forces are located) that determine plate movement.

“Some people have been saying the deep Earth is everything and is the most important role and force in making the plates move,” said Attreyee Ghosh, a post-doctoral student at Stony Brook University’s Geosciences Department. “Another group has been saying that the deep Earth doesn’t have to play that much of a role and they can explain [the movements] looking at the top 100 kilometers of the Earth.”

As it turns out, both groups are right, depending on where you are on the planet, Ghosh explained.

The viscosity (or thickness) of the middle layer in between the top Earth and the deeper parts of the planet determines which contribution can be more important in driving the movement of the plates.

“A higher viscosity increases the contribution from the deeper mantle,” Ghosh suggested. “When the viscosity is weaker, there is a decoupling from the deeper mantle, so the [deeper Earth] doesn’t play as dominant a role” as the lithosphere, or the upper layer.

Working with professor William Holt, Ghosh created a mathematical model to predict movements of the plates. The scientists input readings from “literally hundreds if not thousands” of other researchers using data points from seismic records and earthquakes as they built and tested their computer model, Holt recalled.

The results were so much more effective than most of the models that one of the most prestigious journals in the country, Science, published their findings earlier this year.
Despite its effectiveness, the model, which was created on a relatively simple computer, can do better, Holt said.

“We are not very far away from having models that can predict surface observations at a level of accuracy that approaches the uncertainty in the measurements themselves,” Holt suggested.

What that means is that the models may become as accurate as the data they receive.

So, what does this increased accuracy mean for anticipating earthquakes?

While the science of predicting earthquakes is still years away, this is an important step toward building a better foundation for long-term earthquake forecast models. Holt explained. “We’re getting more accurate forecasts for the probabilities of earthquakes in particular regions,” he explained. “That enables one to prepare through proper retrofitting of buildings and construction for long-term mitigation of potential hazards from earthquakes.”
Holt, who has been working in this field for 20 years, said scientists have boosted dramatically the amount of information they gather about the Earth.

When he started, “we didn’t have observations to understand how the interior of Tibet was moving or how the interior of Nevada was moving, so there was this big revolution through the 1990s, with the advent of space geodesy,” he said. “I can see incredible progress over the last 20 years.”

When he’s not collecting and interpreting data about the planet, Holt is a busy father of two primary school daughters and the husband of Troy Rasbury, a geochemist at Stony Brook.
Holt enjoys sea kayaking and, more recently, fly fishing, although he said most of the time, he “catches nothing.”

As for Ghosh, she is a resident of Manhattan and commutes to Long Island. She expects to finish her post-doctoral work at Stony Brook in the next few months.

Inspired by her progress thus far, Ghosh expects to continue to look deep into the Earth to understand the movement of some of its larger pieces.

“I’m intrigued by how much of our Earth we still don’t know,” she offered.