Science Metropolis – Boston

The weather broke,
and it reached 50.
This month’s science,
was pretty nifty.

We learned happiness
comes with age,
and beekeeping is
all the rage.

Gene therapy helped
a blind man see.
And we lost the brain
behind chaos theory.

Bush released his
climate change plans,
and scientists found poop
from a prehistoric man.

Archeologists battled over
Egyptian history,
while activists tried to save
the last marsh tacky.

A science festival
made Cambridge a happening place,
and artists used computer models
to visualize space.

There’s toxins in plastics,
and infection in wheat,
and nanotechnology
could have cancer beat.

E. Coli are all unique,
said Carl Zimmer,
and the narwhal is becoming
one endangered swimmer.

So as the spring colors
begins to show,
Science Metropolis
will continue to grow.

- by Lauren “FZX” Rugani and “Blogger Joe” Caputo

Photograph of the Yamato. Credit: The National Archives

Tonight’s science-programming on WGBH, Boston’s public broadcasting station, reminded me of that classic conversation generator: If you could have dinner with anyone alive or dead, who would you choose?

Your first choice is John Kane, a former schoolteacher who campaigns for tissue engineering research. Kane became an advocate after skin, grown from infant foreskins, treated a diabetic ulcer on his left leg. Since the treatment was prepared by Canton-based company Organogenesis, the local news show, Greater Boston, featured Kane’s story to emphasis the importance of tax cuts for life science companies in Massachusetts.

Your second choice is Mercedes Doretti, a leading authority in the use of forensic anthropology for the investigation of human rights violations. She got her start 20 years ago, investigating mass graves in Argentina after democracy was restored to the country. When asked about her choice of career, Doretti told One-On-One host, Maria Hinojosa, “I discovered, to my surprise, that I was able to do it, and that was o.k. It doesn’t mean you don’t feel,” she said. “Your defense mechanisms must kick in and you are able to work.”

Your third and final choice is Naoyoshi Ishida, one of 269 survivors out of a crew of 3,000 aboard the Japanese battleship Yamato, which was sunk by American warplanes in April 1945. As bombs fell and his comrades drowned, Naoyoshi jumped into the water and swam, thinking all the while about his newborn son. Eventually rescued by a Japanese boat, he and the other survivors were hidden for a month before returning to their families. This was done to hide the news of losing the Yamato, the largest battleship ever built, from the Japanese people.

NOVA: Sinking the Supership, investigates why the Japanese chose to deploy the Yamato if they knew a battleship could not compete with air attacks. According to interviews with Naoyoshi and others, the men in the Yamato were told to celebrate and tie up any lose ends in the days before the mission. It is hypothesized that the ship was heading towards the American fleet near Okinawa, a major Japanese stronghold, to complete a grand kamikaze or suicide mission.

The programs mentioned in this post were aired as part of the week-long Cambridge Science Festival. For more ideas for people to have dinner with, as well as science-related shows, visit the WGBH Website.

Your genes are mostly nonsense, says molecular biologist Philip Sharp.

“When I look at your DNA, only 2% codes for genes, 98% of your DNA is considered almost junk,” Sharp told a crowd lunching at the MIT Museum.

Human genetics was the topic of the hour at the first “Lunch with a Laureate,” an informal sit down, (or in Sharp’s case – stand up), with a Nobel Prize winner. Sharp shared the Prize for medicine in 1993 for discovering the genome is more complex than previously thought.

“There are many cases of the same gene making different functions in different tissues,” explained Sharp.

Despite his status, Sharp made a good effort to make the research he does understandable for a general public.

“The fruit fly that lands on your banana has the same number of genes as you. The worm that crawls around in the dirt has more,” he said in a particularly colorful example.

Although, when it came down to where research genetics is headed, Sharp began to slip into scientific jargon. The work being done with RNA interference and nanotechnology is fascinating stuff, but it is a little difficult to explain what it is to an unfamiliar audience with a 20-minute talk, especially without visuals.

One anecdote that did catch the crowd’s interest is the construction of the Koch Institute of Integrated Cancer Research at MIT. Integrated because within the building’s walls will work 12 engineers and 12 biologists. Although they will work on separate floors, they will be forced washroom and dining hall interactions, Sharp joked. The possibility of bringing different fields together, allows for the possibility of new “mental models,” as one audience member put it.

Another great question, and one relevant to the Boston area, since so many research institutions are located withing 10 miles from one another, is how competition and collaboration affect science. Sharp, who sees both sides as an MIT Professor and co-founder of companies like Biogen and Alnylam Pharmaceuticals, responded, “A balance is important to move things along.”

“Lunch with a Laureate” will continue all this week as part of the Cambridge Science Festival. Come by the MIT Museum between 12:00 and 1:00 p.m. Tuesday to meet Wolfgang Ketterle, Physics, 200. Wednesday – Dudley Herschbach, Chemistry, 1986. Thursday – Jerome I. Friedman, Physics. 1990. And Friday – Susumu Tonegawa, Medicine, 1987

Don’t forget to bring a sandwich.

Above: School of Groove Guitarist Ivan Sifrim and Drummer Trevor Doherty Demonstrate the Science of Rock. Below: Christopher Vuk

Not many science events begin with a guitar and drum overture, but “The Science of Rock” by the School of Groove, isn’t your ordinary lecture.

Live musical performances, on-stage demonstrations and audience participation are major (not minor) elements of the show, which premiered this afternoon at The Museum of Science.

For instance, to teach how sound waves travel, bassist and physics PhD candidate Dan Bissex extends a long cord across the stage. Holding one end, as drummer Trevor Doherty holds the other, they demonstrate the difference between a loud and soft sound. The large wave produced by a loud sound causes Doherty, in a Tony-worthy performance, to fall to the ground in pain. The smaller wave generated by a soft sound, produces a gentle “ping.”

Christopher Vuk, the event’s host and Director of the School of Groove, a performance-based music school located in Cambridge, spent three months preparing a show that would teach the physics of music in an engaging way. He auditioned over 30 people, looking for performers who could play as well as connect with audiences.

As a large portion of the audience are elementary-school aged, the musicians are careful to use simple but effective language to explain the science. Instead of going too deep into wavelengths and frequency, they say sound is vibrating air and leave it at that. The performers do the same with musical terminology. During the segment on making music, the take-away message is major chords have a brighter tone as opposed to the sadder minor chords.

Another feature of the show is the use of multimedia, in particular, a computer program that visualizes sound waves produced by the band and audience. “Music is undeniably part art and part science. Let me teach you about this complex relationship,” said guitarist and vocalist Ivan Sifrim, during an explanation of intervals.

“The Science of Rock” band will play four more times next weekend (May 3rd and May 4th at 1 & 3 p.m) as part of the The Cambridge Science Festival. Check them out and bing the kids.

.
 – by Joseph Caputo

Researchers at The Southern University of Chile are watching the mailbox. Since a fire swept through four of the University’s science departments last December, they have been in need of equipment for their teaching and research laboratories.

“The situation is now critical,” wrote Maite Castro, a Chilean researcher. “There is no equipment and we’re being relocated to different places in and out of campus. But even when that happens, I don’t have any equipment to work with. All my things are gone, I really need help.”

It was a small group of Harvard Medical school students, alums and postdocs that came to the rescue. Wearing purple latex gloves and noting inventory on the back of thesis proposals, they volunteered two Saturdays in April to pack over 3,000 lbs. worth of used lab equipment, all destined for Chile. The shipment is valued at tens of thousands of dollars.

It was the largest packing event in the history of Seeding Labs, a volunteer-run non-profit that puts unused lab equipment from the fix-it shops and basements of research facilities into the hands of foreign scientists facing a lack of resources as basic as gloves and test tubes. Similar organizations exist to equip hospitals in need, but this is the first to aid research scientists.

“These are our colleagues,” says Executive Director Nina Dudnik, who co-founded Seeding Labs five years ago as a Harvard Medical School student. “What we throw away without a second thought can make a real difference.”

This may seem like the obvious thing to do, but as Dudnik explains, the process is a bit like recycling. Although scientists may support and be aware of the cause, without a little blue bin to remind them and reduce the effort, it won’t happen. Seeding Labs, which is based in Cambridge Massachusetts, provides the boxes and transportation for equipment so researchers can do the right thing without breaking a sweat.

“The equipment is a little bit older, but we try to fix and clean it up,” says Dudnik. “It’s still usable.”

Donors from all over Massachusetts, including Harvard Medical School and Biogen Idec, a pharmaceutical company, supplied the test tubes, pipette tips and occasional mystery machine for the Chile shipment. When the day started, the volunteers carefully organized the hundreds of pieces of lab equipment on the warehouse floor. Hours later, after rolled-up sleeves and some sweat, boxes the size of dryers filled the space.

“Sometimes it’s overwhelming, but it gives you a nice feeling of accomplishment and a good work out,” said Melissa Wu, the event’s coordinator and a member of the Seeding Labs board. “Your research can go for years before you see anything tangible. With Seeding Labs, it’s easier to see your results.”

Now 5 years in operation, Seeding Labs has equipped 14 labs with nearly all of their equipment needs. One success story is a donation to Partners in Health, an organization that improves access to health care in developing countries. “In 2003, our five facilities in Haiti experienced approximately 655,000 patient visits. The laboratories work full time, so the donation, especially the microcentrifuge and the water bath, help us save countless lives,” wrote Dr. Paul Farmer, Partners in Health co-founder.

Currently running on volunteers and a shoestring budge, Seeding Labs is ready to grow. When asked about the organization’s needs, Wu verbalized an instant list: Warehouse space, tax lawyers, customs experts, boxes, vehicles, storage space, money, shipping donations, packing materials, lab equipment, volunteers, a parking space, and a moving company were just a few mentioned.

Dudnik, who became Seeding Labs’ first full-time staff member in January, is now dedicated to finding funding. The non-profit was recently selected as a finalist to receive $10,000 from ideablob.com, but they need votes to win the money. If you’d like to get involved, e-mail Nina Dudnik or visit the Seeding Labs Website.

What better way to kick off The 2nd annual Cambridge Science Festival than a Science Carnival at Cambridge City Hall.

Instead of riding ferris wheels or downing cotton candy, families, students and volunteers had the opportunity to pet chickens, learn about Madagascar hissing cockroaches and discuss how to be eco-friendly. Meanwhile, the MIT Marching Band provided musical entertainment as attendees took pictures by a giant inflatable duck sponsored by Think Blue Massachusetts, a water conservation effort.

Hundreds of people were present by the time MIT President Susan Hockfield gave the opening address. “Last year’s Festival was an experiment,” she said, “And no surprise, it worked.” This year’s festival is bigger thanks to a collaboration of Boston area science organizations, including MIT, Harvard, the Museum of Science and WGBH.

Over 200 science-related events for kids, teens and adults will take place in the next 9 days. It began this afternoon with a countdown from 10, (so even the kids could could participate), led by Hockfield. When zero was reached, streamers of green, blue and silver fell from the sky.

For the rest of the afternoon, science-related demonstrations took place throughout the Cambridge City Hall building. On the third floor, kids learned how a tornado works with water and soda bottles. Downstairs a chemist from a local biotech company struggled to explain what she did using molecular modeling. Nearby, a Draper Laboratory representative told children to be gentle with the robot prototype.

Science Metropolis will provide day-to-day coverage of this exciting Festival, because as Hockfield said, it is just an example of how Cambridge (just like Boston) truly is a center of science, engineering and innovation.

Photos by Kristina Grifantini.

It’s finals time at Boston University, and student science journalists here are hard at work calling researchers and reading journal articles. As a way to pay my classmates tribute, here is a special post showcasing some of their work this semester. Below are excerpts from controversy features about nanotechnology, pharmacrops and biometrics. If you’re a student and have a science story that you’re proud of, e-mail me, and we can post it here or on the visitor contributions page.

“The Promise (and Potential Perils) of Nanotechnology” by Lauren Rugani

Asbestos was once heralded as a miracle material, only to cause hundreds of thousands of deaths. Genetically modified foods were supposed to cure world hunger, but ended up creating the first artificial cancer. Now, as nanotechnology promises improved consumer products, potential cancer therapies and a cleaner global environment, should we take a hint from the past and abandon all efforts, or should we give this emerging technology the benefit of the doubt as it grows into a trillion dollar industry?

Nanotechnology has grown steadily over the past few decades, but has also faced questions about its unforeseen and unintended health and environmental consequences. Because nanoparticles are so small – on the scale of one billionth of a meter – most of the atoms sit at the surface and are able to interact with other materials better than their bulk counterparts. However, the unique physical and chemical properties that make them so useful are also cause for concern, since relatively little is known about their long-term effects. continue reading…

“Farming Drugs: Playing with Pharmacrops” by Nuño Dominguez

Paul Christou’s corn may look ordinary, but inside each kernel is an ingredient found in no other corn crop in the world.

Christou, an expert in plant biochemistry working at Lleida University in Spain, has tweaked the genes of his corn so it produces 2G12, an antibody that blocks HIV infection. The research is part of a European project to use genetically modified plants to generate inexpensive drugs that could help developing countries fight infectious diseases on their own. In the United States, other researchers are also using plants to develop easy-to-use vaccines with an eye on poor countries. The philosophy of the transgenic plant researchers is clear: why manufacture a drug, when you can grow it? continue reading….

“The New Lunch Money: The Business of Biometrics in Schools” by Jeff Meredith

It’s becoming much tougher for the class bully to steal your lunch money these days. Thousand of schools in the US now allow students to pay for their meals by simply placing their index finger on a fingerprint scanner: a cashless system. But the growing use of biometrics in cafeterias has many parents and civil libertarians worried about identity theft and violation of children’s privacy. And their voices are being heard as many states are either banning fingerprint scanning in schools or requiring parental consent.

Biometrics, physical or behavioral characteristics of a person that can be measured and used for identification, were once relegated to spy thriller movies and classified government installations. Now they’re being used in schools for a variety of purposes: recording attendance, preventing unauthorized building access, and managing the checkout of library books. But most schools focus upon speeding up lunch lines; the rationale is that students may lose their ID cards or forget PIN numbers and slow down a transaction, but they can’t forget their index finger. continue reading…

Happy Earth Day from Science Metropolis. The holiday has taken on a new significance with growing awareness about global warming. Boston Mayor Menino is talking big about turning Beantown into Greentown, but is the city taking the right steps? Science journalist Lauren Rugani shares her thoughts:

In an effort to reduce carbon emissions, 28 cities around the world turned off their lights between 8:00 and 9:00 p.m. on March 29, 2008. Although many Bostonians participated in this event, known as Earth Hour, the city of Boston did not publicly support the event.

Kudos, Boston.

Earth Hour organizers argue that the goal of the campaign is to raise awareness about the connection between energy use and climate change, not to boycott electricity. Unfortunately, many Boston residents interpreted the movement literally and are angry that Boston did not participate. One Boston.com discussion board displays numerous Earth Hour posts: “Boston should have invented it,” says one user; “Why make it one hour? Make it a week, then a month,” says another.

The problem with such organized, grand-scale events is that they receive too much media attention, while doing relatively little to actually help the environment. It’s time to stop “raising awareness” and time to start taking action that will make a difference – which is exactly what Boston is doing.

Popular Science magazine ranks Boston as the third greenest city in America, out of cities with populations over 100,000. The criteria for this ranking includes renewable electricity sources, public transportation, green spaces, and recycling programs. Boston and Cambridge (number six on the list) are the only places on the East Coast to make the top 15.

Mayor Thomas M. Menino and James W. Hunt, the Chief of Environmental and Energy Services, recently released a Climate Action Agenda and Executive Order that outlines goals for a greener Boston. Menino hopes to reduce greenhouse gas emissions to 7 percent below 1990 levels by 2012. Since many emissions come from city buildings, all new developments must be certified by the Leadership in Energy and Environmental Design (LEED) Green Building Rating System.

Menino also plans to purchase over 11% of the city’s electricity from renewable sources such as wind or solar power. City diesel vehicles run on low-sulfur fuel, school buses are retrofitted with technology to control pollution, and Boston sponsors the Clean Air CABS program, which offers rebates and tax credits to companies who drive electric, hybrid, or low-emission alternative fuel vehicles. Finally, the mayor aims to plant 100,000 new trees in Boston by 2030.

But the impact from these initiatives will take time. Unlike Earth Hour, the success of these programs cannot happen at the flick of a switch or be measured by a meter reading.

In the age of instant coffee, instant messages, and instant approvals, it’s no wonder that the instant gratification from Earth Hour was evident around the globe. But it’s not about the big things you can do once a year; it’s about the small things you can do every day. Buy more efficient lighting, shut off your computer overnight, and take the T to work. Be patient, Bostonians, and your efforts will be appreciated by generations to come.

Photo from iStockPhoto.

Despite her status as a best-selling author of books about cadavers and the afterlife, a signing event with science writer Mary Roach is great fun. Over a hundred people abandoned this evening’s cool spring air to listen to Roach speak about her newest work, “Bonk: The Curious Coupling of Science and Sex,” at the Brookline Booksmith, an independent bookstore near the Coolidge Corner T stop. Luckily, sex research is anything but sober, and the audience laughed out loud as Roach candidly discussed some of the more surprising findings.

One of her favorites was the list of items emergency room employees regularly remove from patients’ rectums. From light bulbs to spectacles and a magazine, the list goes on and on. Another surprise, learned from her interviews with scientists. is the number of recipes for synthetic semen used for experiments. Each recipe, said Roach, yields one ejaculate, to which she joked about doing a “Bonk” cookbook. Another notable interview, Roach mentioned, was with a woman who could think herself to orgasm within a minute. Roach asked the woman if she did this constantly. ”I’m usually too tired by the time I get home,” the woman responded.

“Doing a book on sex, there’s a lot of room for embarrassment,” Roach said. This couldn’t have been more true when she and her husband “performed coitus“ as Dr. Jing Deng, a senior lecturer in medical physics at University College London Medical School, took a 4-D ultrasound. She compared the experience to getting a colonoscopy because of its medicalization. Plus, said Roach, ”I was taking notes the entire time.”

Roach also shed light on the rate at which sex researchers historically experimented on themselves and their staff. ”Everyone in the Kinsey Institute was performing on film,” said Roach, referring to Alfred Kinsey, the biologist famous for his research into human sexuality throughout the mid-1900s. The current practice today, says Roach, is to entice undergraduate students with course credit.

For more on these stories and answers to questions like – Can a woman find happiness with a machine? –  and - Is the clitoris a tiny penis? – be sure to pick up a copy of “Bonk” today.

Sad news from MIT. Edward Norton Lorenz, an MIT professor and meteorologist best known for developing what became known as the butterfly effect, died last Wednesday of cancer in his home in Cambridge. He was 90.

With every loss of a prominent scientist or doctor, the obituaries that follow are often exquisite examples of science writing. In the case of Lorenz, The Boston Globe delivers with a clear explanation of the effect chaos theory had on predictability and pop culture.

Ironically, Lorenz happened upon his observation of the butterfly effect by accident. (The term grew out of an academic paper he presented to the American Association for the Advancement of Science in 1972. After consulting a friend, he entitled the talk: “Predictability: Does the Flap of a Butterfly’s Wings in Brazil Set Off a Tornado in Texas?“)

According to the Globe obituary, the butterfly effect refers to tiny changes that could have catastrophic, and often unpredictable consequences. “Exact measurement of all the conditions could be upset by one small event, such as the flap of a gossamer wing.”

Losing a member of the Boston science community not only gives us a moment to reflect on the scientist, but also on how their science affected us. Lorenz’s existence is indirectly responsible for television episodes, (e.g. The Simpsons, Family Guy, Scrubs) and movies, (e.g. The Butterfly Effect, Back to the Future, Run Lola Run ) that use time travel to explore how a small change in the past could affect the future.

He is also responsible for inciting quasi-philosophical inquiry. An anonymous writer from the It’s Over Nine Thousand blog, calls Lorenz a hero. The writer became interested in the butterfly effect and chaos theory as a kid, which had some interesting consequences.

“My science projects were all based off of Chaos Theory (resulting in quite a few failing grades I might add), and I remember getting into many arguments about the theory, not only with my science teachers, but my school principle when I was called down asking why I kept failing my assignments.”

One element of chaos theory holds true, while consequences may be random, there is a pattern. In the case of Lorenz, definable clusters of curiosity.

A memorial service for Edward Lorenz will be held today, April 20, 2008 at 3:00 p.m. at Swedenborg Chapel, 50 Quincy St., Cambridge.

Photo of Professor Lorenz provided by MIT.