Science Metropolis – Boston

Eva Zadeh has the story:

It doesn’t take a philosopher to answer the question of “What is life?” According to science writer Carl Zimmer, the popular blogger behind the Loom, the answer can be found by studying Escherichia coli, a common bacterium living in your gut. “E. coli is an oracle,” he says, that tells about life and how life works.

Zimmer is a recent expert in the beauty and history of this bacterium, the topic of his new book “Microcosm: E. coli and the new science of life.” Wearing a tie covered in pictures of microbes, he told fans at the Harvard Book Store yesterday evening that he wanted to write about this “unjustly neglected” player in biology, because its scientific contributions are often unknown to the general public.

German pediatrician Theodor Escherich first discovered the bacterium in 1885 while investigating a string of childhood illnesses. As he looked at samples of sick children’s diapers under a microscope, he observed thousands of fast-growing rod-shaped bacteria. Since then, the bacterium has become a model organism for many scientific experiments. A French researcher once said, “What is true for E. coli is true for the elephant.”

The bacterium is popular because it is easy to grow, a crucial characteristic for bioengineering. The gene for insulin, a hormone produced by the pancreas and used in the treatment of diabetes, is routinely placed in E.coli. As the bacterium multiplies, scientists harvest the insulin and sell it in giant vats – much better than the previous method of stealing pancreases from butchers.

Zimmer, with the help of a fist-sized stuffed model, gave an enjoyable description of E.coli. He demonstrated the way it coils its hair-like flagellum to move forward, and then uncoils them to tumble around a Petri dish as well as the “nose” it uses to detect which tasty molecules to move towards. He even showed E. coli sex, which consists of a bacterium protruding a long tube to another bacterium, and exchanging genes.

Just as E. coli redefines the meaning of sex from the “exchanging of gametes” to the “exchanging of genes,” it also redefines other aspects of living organisms. Different strains of E. coli are found in nature, and even more are produced daily in labs. Despite their genetic differences, they are still considered the same “species,” making biologists question the definition of species. E. coli has been manipulated so much that some strains have fragments of DNA matching no other organism.

So, next time you hear mention of E. Coli, don’t think food poisoning – think knowledge.

Story and photograph of Carl Zimmer by guest blogger Mai Nitta.

Four-toed Salamanders have something to celebrate. Since 1983, these wetland creatures have been listed as a special concern on the Massachusetts List of Endangered, Threatened and Special Concern Species, but not for long.

A proposal to remove the salamander from the list is one of ten changes to be heard this Wednesday at a public meeting in Greenfield. Researchers are confident of the decision after surveys documented 240 salamander populations across 148 towns, a steady growth from previous years.

Over 700 plant and animal species are on the list, but not always because they are endangered. Sometimes there is just not enough information to declare their populations secure. For instance, the Coastal Plain Apamea Moth, will be taken off the list because it has not been seen in Massachusetts for over three decades.

“There are a lot of things we really don’t know,” says Henry Woolsey, Program Manager at the National Heritage & Endangered Species Program. “Certain taxonomic groups, like birds and mammals, are much better known than others. We just do not have enough knowledge as to what should/shouldn’t be on the list.”

According to Woolsey, one of the biggest challenges to tracking endangered species is money. The Endangered Species Program, part of the Massachusetts Division of Fisheries and Wildlife, does not receive any state assistance. Instead, it relies on private donors and conservation organizations.

Funding was proposed for the first time by Governor Deval Patrick last January, but was left out in the final budgets. “To document what we have right now, for future reference, is not very exciting to do,” Woolsey says. “They rather fund interesting planning or modeling studies.”

Baseline knowledge of local endangered species is increasingly important as climate change takes effect. Researchers around the world are noticing declines in plant and animal populations, but without knowing where Massachusetts is now, we can’t make comparisons later. “The purpose of the list is not to safeguard things that are rare,” Woolsey says, “It’s actually to make sure we don’t’ loose things.”

When a species is listed as endangered, and there is an active effort, numbers can be restored. Twenty years ago, it would have been impossible to see an American Bald Eagle in Massachusetts, now there are 25 breeding pairs. To restore the population, conservationists used hackery, in which baby chicks were removed from eagle nests in Nova Scotia and brought here.

“One chick doesn’t usually make it anyway,” Woolsey says. “After several years of doing this, the eagles came back to breed.” Because of these tactics, another edit to this year’s list is removing the bald eagle’s “federally threatened” label.

Piping Plover numbers are also on the rise. These small seabirds are considered threatened, but in just a few years, the Massachusetts population has multiplied from 130 to 500 pairs. Fencing off their breeding areas from predators is responsible. However, Woolsey is hesitant to declare victory just yet. The bird populations are fragile and can go quickly back to where they were. “It needs ongoing management,” he says.

The Endangered Species List public hearing will take place May 21, 2008 at 3:00 PM in the Downtown Campus of Greenfield Community College.

Photo of Four-toed Salamander (Hemidactylium scutatum) from The Nova Scotia Museum Website.

If MIT Physics Professor Max Tegmark had superpowers, he wouldn’t use them to fight villains, he’d go sightseeing.

“What if I had telescopic vision, like Power Girl or Hyperion?” Dr. Tegmark asked an audience attending a special screening of “Superman,” at the Coolidge Corner Theater in Brookline.

“I’d gaze up into the sky,” he answered. And with a click of his mouse, a three-dimensional map of the universe was projected on the movie screen.

Dr. Tegmark spoke about the science of superheroes as part of Coolidge Corner Theater’s bi-annual series, “Science on Screen,” which concluded its spring run last night. Each movie is paired with a local scientist, who goes into detail about some of the scientific accuracies the films may leave out.

For “Superman,” Dr. Tegmark tried to figure out the density of the planet Krypton based on how high Superman can jump on Earth, about 660 feet. If the average person can jump 3 feet, then the gravitational pull of the planet Krypton is approximately 100 times that of Earth. Applying this information to Newton’s law of gravity, finds that Krypton must be about a million times denser than the planet Earth, and three times denser than the sun. “It seems like a very interesting place,” Dr. Tegmark said.

He also mentioned that a similar calculation is made in James Kakalios’s book “The Physics of Superheroes,” but is incorrect due to a mathematical error.

Dr. Tegmark’s talk then went into his area of study, astronomy, with a superhero twist. Aside from telescopic vision, his powers would also include teleportation – “to go for a ride in space,” the power to travel through worm holes, and time travel – to see the Big Bang of course.

The irony of the evening was that all of the sightseeing Dr. Tegmark may do with these powers, has already been simulated by the computers he works with. Each of his superhero abilities was illustrated with a virtual voyage through space, from the first billions of years after the Big Bang, to the future of our galaxy, the Milky Way. According to a simulation, three-to-four-billion years from now, it will merge with neighboring galaxy Andromeda.

Astronomers’ understanding of galaxies and stars, a.k.a the super large, is based on mathematics. They look into the past by simply plugging in numbers. “We start with what we know now and calculate backwards in time,” said Dr. Tegmark.

Even compared to X-men’s Wolverine or Robert Downey Jr. in “Iron Man,” the work of scientists is still super cool.

“Science on Screen” at The Coolidge Corner Theater will resume with a new lineup in September.

Photo from iStockPhoto.com.

Guess who’s coming to dinner? If you live in Boston Public Housing – Probably roaches. These creepy crawlers aren’t just ugly, they can worsen symptoms of allergies and asthma. The quick fix are pesticide sprays, but experts now know, this solution may be just as unhealthy. Nuño Domínguez, Jeff Meredith and Joseph Caputo of the Boston University Center for Science and Medical Journalism have the story:

How much science has influenced my upbringing I don’t know. I’ve never asked what kinds of parenting books my mother read to prepare for her two children or what articles she found most interesting in the newspaper. I’ve never even understood what she does as a lab technician at Staten Island University Hospital. In fact, when a student reporter from the Staten Island Advance asked me what a day in my mother’s life is like, I couldn’t answer. What I do know, is that she taped my “I’m not sure what my mother does” response to the bulletin board at work.

As a science journalist, my job is to ask people about the role science plays in their lives. I question their motives, their choices and ask what is exciting and beautiful about their research. When I’m interviewing, I’m speaking to Dr. Carter the surgeon or Ms. Dunwoody the sociologist – not the mother, the wife, or the daughter.

Has science influenced my mother as a mother? Perhaps, but when she was microwaving dinner or driving my brother and I to school, she wasn’t thinking as a lab tech. Would it have been nice to see more than one part of her identity? Yes. I think I would have appreciated the kind of person she was when drawing blood or looking at malformed cells under the microscope, but she often kept that part of herself hidden.

There were times when it did show, however, especially science projects. My mother helped me put together an excellent exhibition of sink and float, barometers and p.h. during my elementary school years. Then there were the offers to analyze her children’s urine samples rather than doing it at the doctor’s office, which I would have none of.

Over the years, my mother has also expressed her regret for not going further with her education. She wished she could have been a doctor, but didn’t think she was smart enough. A career change as a high school biology teacher has also crossed her mind. Instead, she stayed loyal to the Hospital lab, a thankless and underpaid job, working night and double shifts.

Could this have been different? Science is still a paternal field, and history bears a lot of the blame. There are about a dozen fathers of science, but not one mother. Maybe it’s time for historians to take another look and find those women who did make a difference. Why isn’t Rosalind Franklin, Watson & Crick’s partner in the discovery of DNA, the mother of molecular biology? I’m sure, if we reframed our lenses, we could make their contributions more prominent.

Happy Mother’s Day. And thank you Mom.

On July 24, the first act to take the stage at the new Central Square Theater will be a science play.

“QED,” which stands for quantum electrodynamics, is a conversation with the late physicist Richard Feynman, best known for his work explaining the state of things at the super small scale.

Cambridge Science Festival participants were able to catch a sneak peek of the play at the Broad Institute, and judging from the audience’s reaction to the Saturday, May 3, performance, it was well received.

The play is set in Richard Feynman’s office at Caltech in 1986, about a year before he died of cancer. It is an imaginary day, but one that captures Feynman more as a man rather than a scientist. This is not a two-hour lecture on quantum physics. This is a series of anecdotes – about an obsession to see the country of Tuva, the pain of losing a wife, the excitement of building the atomic bomb, and what science does and does not know.

“Everything is interesting if you look deeply enough,” says the character Feynman. Part of what transcends QED from just a “science play” is its writing. The weaving of narratives, both funny and serious, and the conversational dialogue makes you see how human an endeavor like science is. When you leave the theater, you realize what made Feynman such a great scientist was his curiosity and playful personality.

Playing Feynman in the Underground Railway Theater production come July will be Keith Jochim. “This guy’s like channeling him,” said David Kaiser, an Associate Professor in Science, Technology and Society at MIT and author of a book on Feynman after the May 3 performance. A professional theater actor for 35 years, Jochim knows how to demand the audience’s attention and put just the right amount of emotion and dispassion into the performance. Part of his inspiration, he said, was coming from a family of scientists. “I’ve always been around people who have a curiosity of certain things,” said Jochim.

Because the play was focused on the human side of science, information about quantum physics was kept to a minimum. There were metaphors and graphics to help the audience, but to have gone too heavy into Feynman as a scientist wouldn’t have been as interesting. We do get a taste of Professor Feyman, however, in his interactions interacts throughout the play with imaginary student Miriam Field, played by Danielle Kellerman, a graduate of Boston University’s College of Fine Arts. While a nice job, Kellerman’s performance was a little too sexy at times, and it seemed like her character was trying to seduce Feynman more than inspire him.

As a celebration of science, “QED,” hits the spot. And it’s great to know a place like the Undground Railway Theater exists in Cambridge, that puts on science plays. On August 11 through 15 they will also show “Looking at The Life of Galileo: A History Play for Our Times,” also at the Central Square Theater. They are the troupe to go for interesting science theater.

See what Nature Network News Editor Corie Lok had to say about “QED” on her blog.

We were eating steamed dumplings from the Chinese place on Yonkers Avenue. The place where they know our friend Cole by name, by sight. “You moved?” the delivery guy asked when Cole once opened my apartment door.

“Are you serious?” I asked.

“Yeah”-and he laughed the laugh where his hair shook. Nervous laughter, but he wasn’t kidding. Joe’s eyes widened and he repeated: “I would not have any kids if I were you.”

“But that’s really . . . sad . . .” I said, stumbling. Not that there was anything in the oven, or that I was even sure I ever wanted kids.

“I’m just sparing my future generation the absolute disaster we’ve created.”

Joe wasn’t an apocalyptic guy. He didn’t even have the personality to exaggerate with a straight face. He was my one friend who was really into science, and I hung on to every word that came out of his mouth, knowing everything was rooted in tireless experimentation and research. He reached for the last dumpling.

“You’ll see. In ten years-you’ll see what I’m talking about.”

– by Melissa Barrett, Poetry Correspondent. Photo from istockphoto.com

The 7th installment of “Mr. Caputo Teaches…,” my experience as an extracurricular science teacher in elementary and middle schools across Massachusetts.

One of the most interesting things about overseeing a classroom of middle schoolers, is listening in on their conversations. Of course there is the occasional who likes who, but for the most part, kids talk about media. In my Thursday class of all boys, the topics of the day usually revolve around two things: YouTube and video games.

To no surprise, the types of entertainment the kids enjoy are far from virtual chess and Sesame Street, but that’s no reason to discount their value as teaching tools. Halo 3, for instance, a video game known for the violent killing of alien beasts, has taught countless players about physics and weaponry. Grand Theft Auto IV, perhaps a parent’s worst nightmare for its glorification of murder, theft, drug use and sex, is also an insightful look into urban sociology.

Thanks to these kinds of games, my students are experts on guns – past, present, and future. This came in handy when trying to explain the concept of plasma, the fourth state of matter. When first bridging the topic, the students quickly asked, “Are we going to make plasma guns?” They were disappointed to learn we were actually making electronic pens, but I saw a teaching moment.

I asked them to describe what comes out of the plasma guns they’ve seen in video games or movies. “Bright stuff,” one kid responded. “It melts everything,” said another. Exactly, stars are hot and shiny because they are mostly made of plasma. To call it by its official designation, ionized gas, didn’t seem the best tactic with a group of sixth graders.

Judging from my students’ interest in turning everything into a weapon, I would argue that a curriculum based on guns and explosions could have educational value. When I discussed light bulbs for instance, all this group wanted to do was break a bulb and attach it to a battery. (I did so and it caused a nice-sized flame to emerge.) When we built a crane, the kids used extra plastic rods and Popsicle sticks to make spears. When it came time for the cannons class, the students were so excited, they built two each.

Their task was to design the biggest explosion, using breath spray as a fuel and a pair of exposed wires, attached to a buzzer, to make a spark. The kids had to come up with the perfect fuel and heat combination to send their ammunition, in this case a film capsule, flying. By the end, everyone had a different style and we were even able to have a contest. Just think of the possibilities with catapults, bows and arrows, fireworks, shields, fortresses, etc… We could call it Explosive! science.

While shaping future Department of Defense employees could be interesting, realistically, it could be a stretch to find safe ways of covering this topic with kids. The point is, relevance is key. So next time a young person in your life is shooting an virtual alien, ask what kind of gun he or she is using.

In November 1987, Dr. Dave Ozonoff, an expert in public health, decided to return to the passion of his youth.

After reading a book about chaos theory, he pulled his old multivariable calculus text book off the shelf and solved every end-of-the-chapter problem set. That day Ozonoff, who hadn’t touched a math book since he was in college, determined he would get his skills back by doing one hour of math every day. “I said, ‘Wow, I gotta learn this stuff, this is going to be important in biology’,” he recalls.

Despite a busy schedule as Chair Emeritus of the Department of Environmental Health at Boston University (BU), and his intense involvement in research, he has not missed his math exercises for a single day. “Christmas, New Year’s, Thanksgivings, birthdays, anniversaries… I had kidney stones, I was operated on twice, and even then I managed to somehow do it,” says Ozonoff, 65.

A great part of Ozonoff’s work has focused on cancer in small communities of Upper Cape Cod, where cancer rates are 25% higher than the rest of Massachusetts. With 20 years of research, his team proved that a product known as perchloroethylene (PCE), once used to line the interior of the water pipes, raised the risk of breast cancer in the area. But exposure to PCE did not account for all cancers. There had to be something else.

Now, Ozonoff thinks his mathematical training could help him solve the problem. He is using a part of mathematics called lattice theory to scan his data for new connections between cancer and environmental exposures. Lattice theory had been used in marketing to figure out if people buying chips tend to also buy beer, for instance. Ozonoff thinks he can use these data mining techniques to figure out which health symptoms go together when people are exposed to a toxic substance.

“It is a very new way of thinking of a very old idea,” says 31-year-old Al Ozonoff, assistant professor of biostatistics at BU and Dave Ozonoffs’s son. While his dad works on his mathematical models in an office on Albany Street, Al is two blocks away working on how statistics can be used to forecast pandemic outbreaks. Also a mathematics major in college, part of his work involves studying small clusters of disease similar to the ones his father researches. “We need as many different ways of thinking about it as possible,” he says.

The elder Ozonoff’s work on water contaminated with PCE and other chemicals has sparked action from federal and state governments to reduce people’s exposure to chemicals. His work on PCE in Cape Cod “has been an important contribution,” says Perry Cohn, a research scientist at the New Jersey Department of Health and Senior Services. Cohn says the evidence that PCE was related with cancer in Cape Cod helped his Department set appropriate levels of PCE in drinking water in New Jersey.

But PCE is only one piece of the puzzle in Cape Cod and Ozonoff is now trying to find new connections between disease and the environment. To do that, he is going through his data all over again, this time using his new mathematical tools. “What these new methods allow you to do is find the hidden pattern in the data,” says Ozonoff, who has included lattice theory exercises in his daily mathematical training. “I don’t have the discipline to do what he does,” says his son, who was seven years old when his father started his math routine. But despite his admiration, he thinks it is going to be a long way until his dad’s math produces results. “The challenging part is translating theory into practice.”

- Story by Nuño Dominguez