Science Metropolis – Boston

I’m turning pages in my French dictionary
when the elevator breathes open. An entire class
wedges out, amoebic around a tall man in fleece: le prof.

He looks around for affirmation but his flock
hunches, head-bent, impelling graphite
onto their forearms. He waits, stationed in front

of the elevator like Hades at Avernus
and tells himself: So the scale-clutching it-
is a function of time between floor one

and floor three. The elevator doors belch
into his side; he bucks them back into their
sockets with his hip and presses: Let’s go again;

acceleration versus time for the round trip, he says,
backstepping into the mobile classroom-
so your velocity going down will be negative.

His voice hits the back wall where the echo stops
and the doors close and all twelve are vaulted up
like the value of y when m, x, and b

are enough. I watch the metal plate
above the doors that make it impossible for anyone
to get lost: 1 2 3 2 1. And again

the steely labra divide, the professor
out first, holding the scale in front of him
like a cheese tray. He weaves between his students,

following their work with a finger
waving tildes down the page. Pencils flip
and shake the spines of notebooks and then

they’re corralled back into the elevator, but this time:
with their teacher on the scale, yes, he is
standing on top of it-my own neck lowers

as they double-over to the numbers. And suddenly
I’m in it with them, in a split-second I’ve decided
to race them to the second storey, le deuxième étage,

that is: to clobber up the stairs to the poem’s ending
and rewrite it. So I do-I race them like I raced
my brother in every hotel we ever stayed at,

and I beat them, just like I think I beat him,
and I can’t keep myself from doing it, not even
now, as I rewrite, because they won’t even know

who pushed it, this tiny lucent interruption, because it’s white
and then it’s orange, and it rises into my fingers
like the knuckles of infinity, and it feels soft, and warm, and

when I close my eyes I move inside and I hum.

by Melissa Barrett, Poetry Editor. Photo by Vladimir Vladimirov/iStockphoto.com

T. Aran Mooney monitors the squid as it is sedated by Magnesium Chloride before beginning the brainwave experiment. Credit: Joseph Caputo/MBL

The 2nd installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts.

The ocean is a noisy place. Although we don’t hear much when we stick our heads underwater, the right instruments can reveal a symphony of sound. The noisemakers range from the low frequency bass tones of a fish mating ritual to the roar of a motorboat. The study of how underwater animals hear is a growing topic in marine science, especially with regards to naval sonar and whales. This summer at the MBL, zoologist T. Aran Mooney will be the first scientist to look at cephalopod hearing, using the squid, Loligo pealeii, as a model. To learn how sensitive the translucent animals are to noise, he is monitoring squid brainwaves as they respond to various sounds, specifically the echolocation clicks of its main predators, the sperm whale, beaked whale and dolphin.

“Sound is one of the most important cues for marine animals. Light doesn’t travel well through the ocean. Sound does much better,” says Mooney, who is a Grass Fellow at the MBL and beginning postdoctoral research at the Woods Hole Oceanographic Institution this fall. He predicts that squid probably hear very low frequency sounds, which means they pick up on fish tones and boat traffic. A better understanding of what these animals hear could reveal how human-induced noise affect cephalopods and how their auditory system evolved separately from that of fish.

Reading a squid’s brainwaves will take days of preparation. Mooney has been testing his experimental protocol for the past few weeks. He begins his experiments with a trip to the Marine Resources Center, where dozens of squid swirl around in a tank the size of a small above-ground pool. They travel as a school, so catching one doesn’t look like much trouble. But squid with their big yellow eyes are visual animals, and can see a net coming as soon as it hits the water. He catches one that suits his experiment, transports it to a bounce-proof wagon and covers it with a black plastic bag so not to stress the squid out during its trip to the lab.

In the corner of of one of the wet labs in the MBL’s Loeb Laboratory is a sound proof booth designed with a squid in mind. Mooney places his catch, now sedated, on a netted hammock within a plastic basin filled with water. As carefully as a doctor tends to his patient, he hooks the squid up to an IV with the sedative, Magnesium Chloride, so it remains calm during the experiment. As soon as the squid stops jetting, pushing its body forward with a splash of water, he inserts two pin-sized electrodes near the squid’s brain.

The squid is submersed in a soundproof booth while Mooney measures its brainwaves. Credit: Joseph Caputo/MBL

With the squid in place, Mooney turns to his computer and watches the brainwaves. Another scientist, MIT/WHOI fellow Wu-Jung, keeps an eye on the squid. “Give it a squeeze,” Mooney says to her, “make sure it’s ok.”

“Yeah, he’s breathing,” Wu-Jung replies, referring to the squid.

While the squid is relaxed, Mooney transmits a sound chosen from a computer program he helped design while a Ph.D. student at the University of Hawai’i. The sound is just a tone, nothing the squid would recognized in nature. By playing a number of these tones across a frequency, Mooney can tell which the squid recognizes according to its brainwave activity, measured by the electrodes.

Mooney has many more weeks to go before he knows what squids can hear. If they happen to respond to one of the predator echolocation clicks, it would mean the two species might have an evolutionary relationship. His experiment teaches us that science doesn’t yet have all the answers, and finding them requires getting a little wet.

North Atlantic Squid swimming in a research tank at the Loeb Laboratory at the Marine Biological Laboratory. These squid have some of the largest nerve fibers in the animal kingdom. Scientists at the MBL dissect the squid to better understand how the brain works.

The 1st installment of “At MBL,” Joseph Caputo’s experience as a science writing intern at the Marine Biological Laboratory in Woods Hole, Massachusetts.

Dr. Joseph DeGiorgis came to Woods Hole at 21 as a diver. For an entire summer he spent his mornings underwater, searching for research specimens to be used by scientists at the Marine Biological Laboratory (MBL). Now a post-doc at the National Instiitutes of Health, DeGiorgis has and will continue to come to the MBL each summer. He and a number of people on the campus have described a magic about this place, where thousands of scientists pass through the laboratories each year and several chapters in the history of biology have been written.

After hearing Dr. DeGiorgis tell his story, and describe some new research about kinesins, a family of motor proteins he specializes in, we walked over to his lab to dissect a squid. This wasn’t a special request by me of course, he wanted to show the squid giant axon to a group of science journalists taking part in a week-long course in biomedicine. The axon, a nerve fiber that connects with multiple nerve cells to control the squid’s jet propulsion system, is one of the largest in the animal kingdom.

After entering Dr. DeGiorgis’s lab, passing tanks with the squid, he chose one of the backwards swimming creatures, cut off its head with a pair of scissors and began the dissection. He needed to remove the squid’s ink sac and multiple hearts before getting to the axon, which was an easy to spot ridge along the animal’s side.

Later that afternoon, the journalists and I prepared for an exclusive sea voyage aboard the RV Gemma, the MBL’s collecting boat since the 1980s. (Its named after the Amethyst gem clam, a small mollusk). The boat is equipped with large trawling nets, which scrape along the bottom of the sea as well as nets that pick up life in the water column. We waited as the boat sailed under the Water Street bridge and past Martha’s Vineyard to our trawling destination. Diamond, the ship’s seadog, circled the boat, occasionally poking her head over the water.

When the nets came back, all kinds of sea creatures were scattered over the boat’s floor. Many different species of whelks, sea stars, yellow sponges, crabs, and sea urchins were quickly sorted into buckets by the ship’s crew. Any organisms that wouldn’t be used for research were thrown back. The journalists and I passed the animals around. We felt the odd tickle of a sea star extending its legs to grab hold of your arm, the pinch of a small shore crab in an unfamiliar environment and the prickle of a purple sea urchin.

For the crew, some who have been aboard the Gemma for decades, others just weeks, this is just another day at work.

A lookout climbs high up on a ridge to search for a passageway through the ice choked waters during the reenactment of the 1881 Greely expedition to the Arctic for the film, Abandoned in the Arctic which will premiere at the Harvard Science Center on Thursday June 19, sponsored by the Harvard Museum of Natural History. Credit: James Shedd

In 1881, U.S. Army Lieutenant Adolphus W. Greely lead an expedition that traveled farther north than anyone in history–to within just a few hundred miles of the North Pole. This achievement was the high point in the worst arctic disaster in American history.

Greely and his men were ordered to travel far into the Canadian Arctic, set up a research base there and return after two years of data gathering. But it took three years and a 250-mile journey through the treacherous ice before the men could be rescued. Only six of the original 25 survived.

“This is an amazing story that almost nobody has heard of,” says documentary director Gino Del Guercio. In “Abandoned in the Arctic,” his first feature documentary, Del Guercio follows an expedition in which Greely’s great-great-grandson seeks to trace his ancestor’s incredible journey. The film will be screened in a free sneak preview at the Harvard Science Center, One Oxford St., Cambridge, on June 19th, 7 p.m.

Greely’s expedition was part of an international effort that set the baseline for modern Arctic research. As part of the First International Polar Year, Greely was appointed by the U.S. government to establish a research station in Ellesmere Island, the tenth largest island in the world. Greely and his men not only did so, they also beat the world record for reaching furthest north, which the British had held for 300 years. Two years later, an American ship was scheduled to arrive at the research station and take the men home. The ship never came.

Greely ordered his men to head south towards Cape Sabine, where a rescue ship was supposed to wait in case the first ship could not make it up to their base. Carrying a few months’ food, the men sailed through icebergs in small boats. When sailing was not possible they dragged their boats across the rough ice with temperatures of 50 below zero.

“At one point they were stranded on a piece of ice and about to die in a terrible storm,” says Del Guercio. When the men finally arrived at the rescue point there was no ship there. They spent eight months in an area with almost no food and shelter before they were rescued. The last six men were found lying together in a tent waiting to die. Greely’s first words to his rescuers were: “Did what I came to do. Beat the best record,” referring to the farthest north record.

The modern expedition also experienced the hardships in one of the world’s most dangerous areas. For six weeks in the summer of 2004, James Shedd and five other men rowed in their Kayaks or dragged them through the ice on their way to Cape Sabine. One of them was nearly killed when an ice floe crashed his boat against the frozen coastline. “This area has been called the horizontal Everest,” says Del Guercio, who will be at the preview with Shedd and other members of the expedition. “We discovered for ourselves how truly dangerous it can be.”

Story by Nuño Dominguez.

Those involved in building the Encyclopedia of Life (EOL), the largest biodiversity project in the world, have a lot of work ahead. In the next 9 years, they aim to add the rest of the 1.8 million known species. From birds to viruses, bacteria and dinosaurs, the Encyclopedia will be the place to go for vetted biological information on the Web.

Whether or not 1.8 million goal will be reached, however, is another question. “We need 1,000 new species going in everyday,” says Dr. David J. Patterson, a senior scientist at the Marine Biological Laboratory and the EOL project. “Over the past three months, not one species has gone in. If we don’t have a very aggressive trajectory, it’s quite possible people will get disappointed in it.”

The project is now repositioning its image. Rather than working towards a complete database of species in 10 years, those involved with the Website now say it will be a process. Just as Wikipedia must continuously update to stay accurate, so will the EOL.

“Not everything can be done at once, that’s info we want people to be aware of,” says Marie Studer, the EOL’s only Education and Outreach staff member. “We’re all in this for the long term. As content becomes available it will get up there.”

The project is now over a year old. Press began in May 2007 and the site launched last February with 30,000 species. Popular interest generated by stories like Carl Zimmer’s in the New York Times brought in so many visitors that in a matter of hours the site ’s server was overwhelmed and crashed.

The project is a collaboration of five core institutions, each working on a separate part. The Marine Biological Laboratory is headquarters for the database and Harvard University, specifically its Museum of Comparative Zoology, oversees education and outreach. According to Studer, this means finding out how the EOL can satisfy the needs of four target audiences: Formal educators, informal educators like nature centers and zoos, citizen scientists or hobbyists and professionals in developing countries.

“We’re working on some user surveys to understand who’s coming to the site right now and what they might want to be doing with it,” Studer says. “Over time I will form user groups so that I can create focused discussion with them. It’s really going to be a much better site with them in mind.” One way the EOL is communicating with users is by blogging.

Another of Boston’s contributions to the project is the scanning of thousands of books on biodiversity at the Boston Public Library (BPL). According to a press release, The Biodiversity Heritage Library, a consortium of ten major libraries, plans to scan 1 million volumes over the next five years to be accessible through the EOL. The BPL is the Northeast’s scanning center.

With so many institutions involved, tens of millions of dollars invested, and advances in technology, the EOL has the potential to be an important resource for the public. The questions now are how will it work and when will it be ready.

Valeria Alvarez and Angie Carmen cover the walnuts in the junk food mixture. Credit: Laura Mackin/BUGSDM

Meet the dental profession’s latest entrants.

Geared in white scrubs, masks and purple gloves, third-graders from Blackstone Elementary School in Boston spent part of their morning learning about the benefits of applying dental sealant, a thin, plastic film that dentists paint on teeth to prevent decay.

Students were handed two walnuts or “teeth” and a mixture of green goo to represent food and bacteria. Both of the walnuts, one with dental sealant and one without, were covered with the green mixture. The children then tried to brush off the mixture from the walnuts.

“This exercise lets the children see how a sealed “tooth” will repel junk food more easily, while the food gets caught in the grooves of the unsealed “tooth,” says Jackie Rubin, a spokesperson for the Boston University Goldman School of Dental Medicine.

All watching a computer monitor for the next instructions, the students performed their morning project in the School’s Simulation Learning Center, one of the most advanced spots for dental education in the city. Each year, the entire third-grade class from Blackstone Elementary come here to become “Dentists for a Day,” ridding walnuts of decay, working on dummy patients and participating in other oral health activities.

“Blackstone is a school that’s right in our area in the South End, we’ve had a relationship for several years,” Rubin says. The School also visits Blackstone annually as part of Smart Smiles, a school-based oral health initiative to provide free oral health education, screenings, and dental sealants to thousands of children in Boston Public Schools.

Aside from the public health aspect, Rubin says programs like “Dentists for a Day” and Smart Smiles could entice children into dentistry. According to the American Dental Association, the number of dentists entering the profession is diminishing. “Pipeline programs are one way we can interest young children who may not have considered a career in health sciences,” Rubin says.

Denis Herrera removes his examination gloves, turning them inside out so bacteria does not spread. Credit: Laura Mackin/BUGSDM

Scientists aren’t always known for thinking big. They can spend years answering a very specific question – like what kinds of molecules are binding to Protein X or which parts of the brain are being used when a nematode worm blinks.

Systems Biology is different because it takes these microquestions and uses them to understand how things are working on a whole. For example, researchers in this field are currently developing models for what cause cancer or heart disease.

A conference hosted by the Council of Systems Biology in Boston this Thursday and Friday will bring together the biggest names in the field to discuss how Systems Biology can be applied to human disease. Here’s a sneak preview of some of the topics on the agenda:

1) Integrating Systems Biology into Drug Design by Andrew Hopkins of the University of Dundee

Searching for drugs is hard and expensive work. For years it required trial and error by researchers to find the right chemical or molecule that could match with a specific target. But by combining what is known about genetics with biology it may be possible to create a new ‘network pharmacology’ approach to drug discovery, “to help rationally identify compounds that act on the level of the biological network rather than a single target.” This means affecting multiple targets at once or identifying better molecules for drugs.

2) Systems biology for the study of multiple sclerosis by Francisco J. Quintana, Mauricio F. Farez, Antonio H. Iglesias, Howard L. Weiner, Center for Neurological Diseases, Brigham and Women’s Hospital, and Harvard Medical School.

There are many mysteries surrounding Multiple sclerosis (MS), a disease in which immune cells attack the central nervous system. One unknown is the role of the innate immune system in its progression. But by using systems biology, researchers may be able to target potential therapies for the disease by identifying proteins that are allowing the renegade immune cells to do their damage.

3) Resistance in multi-drug treatments by Roy Kishony of Harvard Medical School

The emergence of resistance during multi-drug therapies is affecting the treatment of many human diseases, including malaria, TB, HIV, and cancer. “While multi-drug combinations have been studied extensively, very little is known about their impact on the long-term evolution of drug resistance,” writes Dr. Kishony in his speaker abstract. With a systems biology approach it is possible to design drugs that may could reverse the evolution of resistance.

Photo by Sven Hoppe/iStockPhoto.

KnowAtom teacher Sophia Kruszewski explains wind turbines. (Credit: Francis Vigeant.)

First-graders in one of Mr. V’s after-school science classes can tell you all about F-5 tornados. After a short lesson emphasizing vocabulary, students receive a couple of empty soda bottles, glitter and a liter of water. Using these materials, each child builds his own underwater tornado and soon terms such as vortex and debris are flying throughout the room.

Mr. V., known outside the classroom as Francis Vigeant, 24, is in the business of demystification. As co-founder and program director of KnowAtom North Shore, LLC, he oversees the development of curriculum and projects that explain scientific concepts such as thermodynamics, chemical reactions and cell biology to kids. Once a one-person show starring Vigeant, the company now sends teachers to 31 elementary and middle schools for after and in-school programs.

For a child to take part in a 10-week afterschool class with a dozen other student costs $225, but parents are willing to pay the money because of the substance of the product says Vigeant. Based on the topic of the class, each child leaves with their own hand-made projects, which range from soda-bottle tornados to balloon thermostats. The materials are gathered from recycled materials and housed in a 4,000 square foot space in Essex, MA, which accounts for half the cost of the class.

The fee also covers teacher rates. KnowAtom currently has seven teachers covering locations throughout Massachusetts and New Hampshire. All have backgrounds in science and education, and after being trained earn competitive wages, they are responsible for traveling to their assignments, studying the topic of the day and structuring project building time.

Parents also pay for the work done by Vigeant’s behind-the-scenes team: A four member work crew assembles classroom kits and preps materials. Artists illustrate posters to accompany the lessons. Others check with the state’s science education standards to ensure content both within and above what is expected of the average student. They also write the handouts students receive as further reading if they want to learn more about a topic at home.

Being a company that works with children using hot glue guns and hammers, a less obvious expense for KnowAtom is insurance. Many companies rejected Vigeant’s unusual concept before he found one that takes risks on unique businesses. Though there has never been an incident he pays nearly $40,000 a year, which is also accounted for in the fee.

While Vigeant does not see his company as replacing the science educators currently in schools, he does see it as a meaningful and efficient way for a school to spend money implementing a science curriculum. With future growth, KnowAtom hopes to offer extracurricular classes for lower-cost to students who wouldn’t normally be able to attend. “We aren’t benefiting unless we’re benefiting others,” says Vigeant. “If a parent is willing to give us their child for an hour and fifteen minutes that is not an investment we take likely. We reinvest that into the world.”

Even in rural areas, noise is a problem: residents in King City, Missouri, are complaining about the noise from wind turbines. Researchers are coining the phrase “wind turbine syndrome” to describe a collection of symptoms including headaches, anxiety attacks and high blood pressure. Researchers recommend that turbines be located at least a mile from homes, schools and hospitals. Credit: Jeff Meredith.

“America is the noisiest country that ever existed. One is waked up in the morning, not by the singing of the nightingale, but by the steam whistle. It is not surprising that the sound practical sense of the American does not reduce this intolerable noise.” – Oscar Wilde’s Impressions of America (1883)

America has evolved in noisier ways than Oscar Wilde could have ever imagined. In the place of the singing bird, one will hear car alarms, police sirens, motorcycles, jackhammers, and stereo systems as loud as jet planes. Urban settings, in particular, subject residents to potentially harmful levels of noise. Local governments are increasingly being pressured by city residents to either enforce existing noise ordinances or put new laws into effect that turn down the volume.

Normal conversations occur at 50-70 decibels, but many sounds in our environment are far above that level. Prolonged exposure to sound above 85 decibels may cause permanent hearing loss. Motorcycles commonly eclipse 85 decibels (at 65 miles per hour, they surpass 110 decibels), while small firecrackers can reach 100-110 decibels. Ambulance and police sirens fall in the 110-120 decibel range, and if you have poor enough judgment to attend a rock concert, you could experience 140 decibels. These sounds are staples of the urban experience. Out of the 28 million Americans who have some degree of hearing loss, one-third damaged their hearing through excessive exposure to sound.

Exposure to noise can do much more than make you deaf. There is a growing body of literature indicating that noise exposure can induce hypertension and ischemic heart disease, annoyance, sleep disturbance, and decreased school performance. Traffic noise has been shown to cause considerable disturbance and annoyance in exposed subjects. Evidence linking noise to changes in the immune system and birth defects is more limited, however.

The Washington, DC neighborhood of Capitol Hill is a hotbed for protesters and street preachers who not only like to shout their opinions, but amplify them – at a level often surpassing 90 decibels. “There are no regulations for amplified, noncommercial speech between 7 a.m. and 9 p.m.,” says resident turned noise activist David Klavitter, who notes that this loophole allows people to use amplifiers as a weapon. “They’re not content using speech to influence or persuade; they’re using the sheer brute force of noise to harass people into submission,” he says.

Klavitter and other DC residents bothered by the din have urged the city council to limit noncommercial public speech during the day to no greater than 70 decibels. Under their proposal, fines would be assessed for louder speech, as measured 50 feet from its source. And eventually, DC activists want to be even stricter than measuring sound from 50 feet away. “We’ve offered some amendments like a property line or occupied residence provision. If someone sets up (an amplifier) underneath the window of someone’s house, they could be at 90 decibels,” says Klavitter. “A property line or occupied residence decibel level would provide additional protection for residents in DC. In an open field, you can be as loud as you want. But once the sound hits a property line where it will impact someone else, there should be limits.”

It takes an organized effort among residents to demand and implement changes which will result in a less noise-saturated environment. It starts from the ground up; most politicians are not concerned about noise or educated about its health effects. So their constituents have to speak up and be heard; they have to educate their elected officials. If it takes a little kicking and screaming to get the job done, that noise is entirely forgivable.

Story by Jeff Meredith. Read the rest of his research on the Visitor Contributions page.