BBA1, conducted from 1974 through 1979, was the first effort in North America to map the status of breeding birds systematically across an entire state. BBA2 is already showing how large-scale landscape changes over the past 30 years have affected wildlife. The results could help the state government and Mass Audubon formulate better environmental and conservation policies.

The atlas approach, in which volunteers survey 10-square-mile blocks across the state during breeding season for five consecutive years, is a way to measure the health of breeding bird populations on a large scale. “When you assess the condition of any population, you need to know how quickly members reproduce and die and the area over which they do it,” explains project coordinator Joan Walsh.

According to data collected in 2007, more than half of the Commonwealth’s breeding bird species are either stable or increasing. But others are declining at sharp rates, including meadowlarks and kestrels, both of which rely on shrub lands and open grasslands–habitats that have shrunk across Massachusetts due to residential and commercial development. National studies by the US Geological Survey have also recorded declines in these species.

The numbers of American kestrels (top), eastern meadowlarks (middle), and short-eared owls (bottom) appear to be declining in Massachusetts, according to the Mass Audubon’s Breeding Bird Atlas 2. (Credits: US Fish and Wildlife Service and Mass Audubon/David Larson)

Other species, including some that once were essentially extinct across the Northeast, are thriving now, including wild turkeys, red-bellied woodpeckers, and Cooper’s hawks. All three of these species are benefiting from the fact that forests, where they nest and hunt, have been growing back on abandoned Massachusetts farmlands over the past century. “The winners are birds that profit from human alteration of the landscape,” says Walsh. “Carnivores and fish-eaters are also doing much better since our pesticide and water-quality laws improved in the 1970s and 1980s, because they aren’t bioaccumulating as many toxics as they used to.”

Spot the bird

Birders use protocols adapted from British surveys, such as standardized classification strategies and codes. For example, “P” indicates a pair seen together in a suitable nesting habitat, while “S” stands for permanent territory, presumed through hearing a specific bird’s song at the same location seven or more days apart.

The atlas is designed mainly to inform conservation policy decisions. Mass Audubon is the second-largest private landowner in the state, so BBA2 may influence how it manages its own sanctuaries. The group will also use the bird data to advise state agencies that manage public lands and wildlife, says Walsh.

BBA2 will also help evolutionary biologists confirm long-term trends. “An atlas adds a geographic component to bird population databases,” says Trevor Lloyd-Evans, director of the bird-banding program at the Manomet Center for Conservation Sciences near Plymouth, MA. “Doing it a second time makes it really useful because that documents changes in populations and ranges, which either oppose or confirm what we’re seeing in our own work.”

BBA1 data is available on the state-run MassGIS website, assembled by the Executive Office of Energy and Environmental Affairs to support environmental planning and management, and will be updated with BBA2 counts. Correlating bird population trends with land-use changes helps regulators come up with policies to address major sprawl zones such as southeastern Massachusetts, which used to be mainly agricultural but is now one of the fastest-growing regions in the state.

Pooling data

Since the 1980s, most US states and Canadian provinces have completed their own breeding-bird atlases. When BBA2 is complete, Mass Audubon plans to integrate its numbers with those from Ontario, Vermont, New York, Ohio, Pennsylvania, Maryland, and Washington, DC, to create a contiguous data set for the Northeast. It will require a lot of coordination and management, but if done right, says Walsh, “I think it will be one of the best databases on bird changes in the world.”

Bird enthusiasts spotted this fork-tailed flycatcher last week in Brighton. It’s supposed to be in the Caribbean. (Credit: Wayne Petersen, Mass Audubon)

Like our robins and orioles, fork-tailed flycatchers migrate with the seasons. They fly north from South America to the tropics at this time of year—fall in the southern hemisphere. But their navigation systems don’t always get them to where they need to be.

There have been a few fork-tailed flycatcher sightings in the Boston area in the past hundred years, though never one this early in the spring, says Trevor Lloyd Evans, an avian conservation scientist at the Manomet Center for Conservation Sciences in Plymouth, MA.

It’s not unusual to find birds that have ended up in the wrong place during their migration. To make their journey easier, migrating birds try to take advantage of prevailing winds to help carry them to their destination, says Wayne Petersen, director of the Massachusetts Important Bird Areas program at Mass Audubon in Lincoln, MA. “It’s like jumping on an escalator,” he says. “They time it for getting a good tailwind. But that might have gotten this one into trouble–it got more of a ride than it had bargained for.”

This particular flycatcher in Brighton will either spend the summer here or re-orient itself and return south, says Peterson. It was lucky that it wound up here in the summer and not the fall. “If [vagrant flycatchers] come here in the fall, that’s bad news,” he says. Fork-tailed flycatchers feed primarily on insects, which all but disappear by winter.

Birds from the southern hemisphere that fly north in the fall likely have a genetic problem that disturbs their internal navigation system, Petersen says. “A leading hypothesis is that they undergo ‘mirror-image disorientation,’ where they migrate the wrong way,” he says.

Fall vagrants also tend to be young, first-season birds that haven’t yet completed a successful migration south, he adds. That lack of experience, coupled with their off-kilter compass, makes it unlikely those birds will make it home.

That’s probably not the case for the Brighton flycatcher, which is clearly an adult, Petersen says. And because it migrated in the right direction–it just went too far–it probably does not have mirror-image disorientation, he says.

“It may well be a veteran at migration, and it probably got caught up in a weather system where it wanted to go and it just kept on traveling.”

Only a small number of studies have looked into the health effects these flame-retardant chemicals have on the body, but their prevalence in consumer products and their increasing levels in humans led Boston University researchers to investigate how they are getting into our bodies.

Tom Webster and Mike McClean’s group at Boston University’s Center for Interdisciplinary Research in Environmental Exposures and Health has been testing Massachusetts residents and their homes for PBDEs for the past few years. “There’s quite a lot of concern that the exposure of people to things indoors might be much more substantial than outdoors,” says Webster. “We’re trying to figure how people are being exposed to prevent exposure in the future.”

Boston University graduate student Joseph Allen measures levels of bromine, a marker for a flame retardant commonly added to consumer products such as TVs. (Credit: Mary Kenda)

PBDEs are a type of persistent organic pollutant (POP)—they don’t easily degrade in the environment. They have been the major flame retardant used in furniture foam, small appliances, plastics for computers and TV cabinets, and other electronic devices since the 1980s. Unlike other persistent organic pollutants such as dioxin and PCBs, PBDE levels in humans have increased by a factor of almost 100 over the past 30 years, according to studies.

Dust carriers

Research from the last 10 years showing high concentrations of PBDEs in human breast milk intrigued Webster and McClean, so they began investigating how people could be exposed to PBDEs from household products. In 2004-2005, Webster, McClean, and graduate student Nerissa Wu gathered milk samples from 46 first-time mothers around Boston and vacuumed dust from their homes. They found that many women had high levels of PBDEs in their milk (30 ppb on average, and up to 263 ppb in some cases), and those levels were correlated with the amount of dust in their homes.

A few months later, Webster, McClean, and doctoral student Joseph Allen tested the air in the homes of 20 other Massachusetts residents and found that, compared with other rooms in the house, the air within a person’s immediate breathing space is most packed with PBDEs, probably due to the dust we kick up as we perform everyday activities.

Does exposure occur when we breathe PBDE-packed air or when we ingest dust via our hands? Webster’s group and collaborator Heather Stapleton at Duke University’s Nicholas School of the Environment and Earth Sciences wiped the hands of 33 people (including six children) with sterile gauze pads soaked in isoproyl alcohol to find out. Not only did every person have PBDEs on their hands—a median amount of 130 ppb—but some had extremely high levels—almost 2,000 ppb. “Finding it on the hands gives you an indication that it’s going from the dust to the hands and then probably incidental ingestion,” via oily finger foods such as French fries, activities such as nail-biting, or as a result of children putting their hands in their mouths, says McClean.

The team also wanted to know which products were the worst offenders. So Allen, Webster, McClean, and Stapleton developed a new technique whereby a handheld X-ray fluorescence scanner shoots X-rays at furniture, power strips, TVs, alarm clocks, DVD players, and other devices, and provides a spectrum showing the product’s levels of bromine. Bromine levels correlate with PBDE levels, and the team found that TVs had far more PBDEs than other products.

Questions unanswered

High PBDE levels in humans are worrisome, yet researchers still don’t know how much of a risk the chemicals actually pose to health. One of the few studies looking at the human health effects of PBDEs found that Scandinavian mothers with higher levels of the chemicals in their breast milk tended to have sons with undescended testicles. And animal studies have shown that large amounts of PBDEs (about 100 times the average human dose) are harmful to the endocrine system, reproduction, and neurodevelopment. But there are few other studies. “I’m not convinced yet that PBDEs are so harmful to humans that they need to be banned,” said McClean. “We don’t know enough about it.”

PBDEs are just one of many types of pollutants we encounter indoors, where we spend 69 percent of our time. “Still, I worry about PBDEs because they have turned out to be more toxic than first anticipated and they have disseminated widely,” says Philippe Grandjean, adjunct professor of environmental health at the Harvard School of Public Health.

Linda Birnbaum, senior toxicologist at the US Environmental Protection Agency (EPA), adds, “We’re beginning to find PBDE exposures in some people high enough to be similar to lab animals that have adverse effects.”

The EPA is currently compiling safe dosage levels for PBDEs. Eleven states have banned or phased out several types of PBDE, and many of the flame retardants have been voluntarily withdrawn from the market. The EU, which banned two types of PBDE in 2003, banned a third earlier this month. And some companies, such as IKEA, Sony, Apple, and Canon, have stopped using the chemical in their products. Yet PBDEs persist in older furniture and electronics.

“If we’re going to have flame retardants, they should stay in the product,” says Webster. “Either we redesign products so they don’t need the flame retardants or we design them so it doesn’t get into the home environment.”

Their vision is of a website open to the public, where people can post about the latest scientific results on climate change and debate how to cut carbon emissions, and where politicians can get a sense of public opinion. The website, which the researchers call the Climate Collaboratorium, would be something like the Wikipedia version of the authoritative reports from the Intergovernmental Panel on Climate Change (IPCC). Unlike Wikipedia though, the collaboratorium, now at the prototype stage, will have features to keep the debate more structured and organized.

The forum could not only help people get better information, but also help them work together to come up with and agree upon ways of tackling climate change, says Mark Klein of the Center for Collective Intelligence at the MIT.

“If there ever was a challenge that calls for the application of collective intelligence, climate change is it,” Klein and colleagues argue in a recent paper outlining the proposed forum.

Map that argument

Klein points to Wikipedia as an example of the reach—and also the pitfalls—of online collaboration. Although Wikipedia has gained a reputation for being comprehensive and fairly accurate on some topics, entries on controversial topics often suffer from tug-of-war battles, known as “edit wars,” over the content.

To try to avoid such problems, Klein and colleagues are giving the Climate Collaboratorium a structural backbone known as an argument tree. The structure requires people to present their comments in one of four categories: issues to be addressed, options for resolving those issues, the pros in favor of various options, and the cons against them.

In this way, the debate could become self-organized, making it easier for people to see what’s been said, and whether points have been supported or rebutted. When testing the prototype, users have not been able to edit others’ entries, but in the final version, the MIT team aims to make it more open, so that anyone can edit any entry. If the researchers get the structure right, they hope that the site could operate without much top-down moderation.

There’s evidence that such an argument tree structure helps groups make more-systematic and complete evaluations of issues, although they’ve only been used with small groups of around 10 people, Klein says.

“The idea behind the project was to take this argument-mapping idea and scale it up,” Klein says. He and his colleagues think mapping may actually be more beneficial to big groups than small ones by preventing repetition of ideas and by bringing structure to large amounts of information.

The MIT team also plans to incorporate other tools so that users can rate entries, vote on the accuracy of statements, or show support for certain options. These votes could be tied back to the people who posted the information or arguments, generating a sort of reputation score for each user.

Putting it to the test

In December, Klein worked with a team at the University of Naples in Italy to test a prototype of the collaboratorium, with 200 students debating whether biofuels should be used more and, if so, which kinds would be best. They’ve got another test planned with 300 students at the University of Zurich in Switzerland, where they’ll compare a more conventional online forum and a wiki with the collaboratorium to see which generates a more coherent, reasoned debate.

“Our hypothesis is that wiki models are going to have trouble when dealing with controversial and complex topics, where there’s substantial debate and a lot of options,” Klein says.

If the collaboratorium approach demonstrates advantages over wikis, Klein and colleagues aim to launch a public version of it.

How to moderate

Researchers engaged in the public discussion about climate change say the collaboratorium idea is promising, but they’re skeptical about whether it will work.

“Having some kind of system that is interactive and updatable instead of the static IPCC reports is a good idea,” says climate modeler Gavin Schmidt at NASA’s Goddard Institute for Space Studies in New York City, and a contributor to the blog, RealClimate.

“But it is extremely hard to generate respect for such endeavors, and that is by far the most challenging aspect of this proposal,” Schmidt adds.

Schmidt anticipates some kind of moderation will be necessary for the collaboratorium to work, but even with moderation, it will be hard to strike the right balance. “To be totally inclusive allows the contrarians to dominate the agenda, [while] being restrictive gives fodder for conspiracy theories,” he says.

Simon Buckingham Shum of the Open University in the UK agrees that moderation will be a major issue facing the collaboratorium. Shum, who works on tools for online collaboration, says one option could be to have “a cadre of experts who maintain a peer-reviewed layer that is the current ‘state of the debate’ view.”

If they can get the details right, Shum says, “then the tool could make a big impact.”

Steve Shoelson, a professor of medicine at Harvard Medical School and a researcher at Joslin Diabetes Center, is investigating the link between an overactive immune system and modern-day metabolic problems. He’s now working with clinical researchers at Joslin to move some of his findings in type II diabetes into a clinical trial to see if anti-inflammatory drugs can lower blood sugar levels.

Steve Shoelson of the Joslin Diabetes Center is studying the link between inflammation and diabetes. (Credit: Joslin)

If further trials confirm that these drugs benefit diabetics, anti-inflammtory drugs could be used to prevent disease in those at risk of metabolic disease, as well as help to treat it. “It’s very similar to hypertension and cholesterol,” Shoelson says, which are risk factors for heart disease that can be managed preventively. “You would decrease risk if you can suppress inflammation.”

Revisting an old idea

Inflammation itself has been well studied by immunologists: after an infection, a host of different types of immune cells are deployed to the infection site to control the infection.

But Shoelson says that the situation is different in patients with metabolic diseases: the same markers of an immune response are present, but they persist chronically at a low level instead of following the dramatic rise and fall in an infection. Patients destined to develop diabetes or suffer from heart attacks, for instance, have higher white blood cell counts. Although this chronic, low-grade inflammation has been observed in metabolic disease, it has been trickier to determine whether it’s a cause or an effect.

Several years ago, Shoelson’s team was studying mechanisms underlying insulin resistance—the failure of the body to respond to its own insulin, a condition that raises blood sugar and can lead to diabetes. They found reports from more than a century ago that high doses of anti-inflammatory medications called salicylates lowered the blood sugar levels of patients with diabetes.

Shoelson’s team has since shown that salicylates, which are related to aspirin, could reverse insulin resistance in mice by targeting a molecular pathway involved in inflammation. Further studies from Shoelson’s lab (including this one) and others have suggested that switching on this and other inflammatory pathways can cause insulin resistance.

Because salicylates are commonly used to treat inflammation and arthritis, Shoelson has been able to quickly translate his scientific findings into clinical trials. He and Allison Goldfine, director of clinical research at the Joslin, are leading a national, multicenter Phase II/III trial to investigate whether one of these drugs, called salsalate, can reduce blood sugar levels in people with diabetes. The trial began in January 2007 and is expected to yield results this summer.

Another smaller study headed by Goldfine recently reported that salsalate treatment lowered inflammation and blood sugar levels in 20 obese teens.

Other research has implicated inflammation in the development of heart disease, so a Boston-based study, also led by Goldfine, is being launched to investigate how well salsalate can slow the progression of cardiovascular disease.

Not just drugs

Meanwhile, Shoelson’s lab is working to understand the links between inflammation and metabolism. “What instigates the inflammation and how the inflammation works are areas of intense investigation,” he says. “We don’t know a lot of the details.”

Anthony Ferrante, assistant professor of medicine at Columbia University, says that Shoelson has helped to turn isolated observations about anti-inflammatory agents and diabetes and into a framework for thinking about how the two are connected, providing a rationale for pursuing anti-inflammatory treatments. “Going forward in the next 10 years, his observations will have a big effect on how diabetes will be treated,” Ferrante says.

Although his research has led to trials testing drugs for metabolic disease, Shoelson believes that we already know the ultimate prevention and cure: diet and exercise. “These are the cures for the entire epidemic,” he says. “We need to return ourselves to the exercise levels and diet that people had centuries ago.” But given the daunting task of changing society’s behavior, Shoelson says drugs can work in concert with lifestyle changes to help prevent disease.

In 2005, the European Union began its Greenhouse Gas Emission Trading Scheme to help companies and governments meet mandatory emissions limits. Established financial exchanges such as the New York Mercantile Exchange and the Montreal Exchange are launching new ventures to trade the carbon allowances that companies generate to fulfill EU or Kyoto Protocol reduction requirements. Global demand for carbon trading will likely expand as observers widely expect that the US government will place binding limits on greenhouse gas emissions in the next several years.

William Moomaw, professor of international environmental policy at Tufts and an advisor to the university’s climate initiative, recently spoke with Nature Network Boston about CCX and the growth of carbon trading.

William Moomaw, senior director of the Tufts Institute of the Environment (Courtesy: Tufts)

Why did Tufts decide to join CCX?
Tufts pledged in 1999 to meet or beat the Kyoto protocol targets [which required countries to cut greenhouse gas emissions 7 percent below 1990 levels by 2012], and we also signed onto regional targets that the New England states adopted in 2001. So far we’re meeting those targets even though we’ve added two energy-intensive buildings, and we’re approaching our 1990 emission levels. When we joined CCX, there was no emissions trading going on at the national or regional level, so there was nowhere to go except for this private initiative.

What are members required to do?
Each member organization signs a contract that obligates it to reduce emissions by specific amounts. If you cut below that level, you can sell emissions allowances. In Phase I, from 2003 through 2006, members had to cut emissions 1 percent each year below a baseline level (their average emissions from 1998 through 2001). Now they’re in Phase 2, which requires them to be at least 6 percent below their baseline by 2010.

Members can make sales at any time, but they are audited at the end of each year to see whether they have met their reduction targets. If they haven’t, they are required to buy allowances from other members, so they go into the marketplace and buy however many additional units they need to cover their commitments.

Does participating in CCX affect what Tufts is doing to shrink its carbon footprint?
CCX hasn’t been a major driver for us to reduce emissions because we had already made commitments before we joined. That’s also true of other members. There are more credit sellers than buyers in the system, which is one reason why the price for CCX’s allowances has been low so far. [CCX allowances have traded recently for about $5.50 per metric ton of carbon dioxide, compared to roughly $30 for European allowances.]

So what are the benefits of participating?
CCX evolved out of commodity markets, and all of the reductions are verified by a third-party auditor [the Financial Industry Regulatory Authority, formerly the National Association of Securities Dealers]. The audits are very detailed—they call up bills and check them to make sure we’re reporting things accurately. I’ve served on CCX’s compliance committee, which reviews reports from the auditors with identifying information removed. Some firms didn’t have a clue about measuring and tracking carbon emissions when they joined, but they’re clearly learning. We see members improving both in their accounting and in making emissions reductions.

Will all of the emerging carbon exchanges be harmonized at some point so they can sell to each other?
In the best of all worlds, yes. They’re all selling the same commodity, but they’re selling them under different rules. For example, since the U.S. isn’t a party to the Kyoto Protocol, there’s some question about what our reductions are worth and what they mean. That’s ironic, because a contractual cap on emissions like CCX’s can be more stringent than a legal cap like the EU’s. Governments may or may not enforce laws, but we know how to enforce contracts in this country.

How much can voluntary carbon trading systems like CCX do to slow climate change, compared to mandatory systems like the EU’s?
That depends on how strict government-mandated reductions are, compared to the cuts that are pledged under voluntary agreements. The fact that the US government is doing nothing while CCX members are legally committed to reducing their emissions means that those companies will have reduced emissions by at least 6 percent below their baselines before the US government mandates anything. CCX members’ total emissions are comparable to those of the United Kingdom, so that’s not an inconsequential amount.

Now clearly, we can’t rely on those contractual agreements to solve global warming, since they are not comprehensive enough. But it will be interesting to see how they are treated if the US ever requires greenhouse gas reductions. Would they be allowed to go on reducing within their own closed market, as long as they kept up with statutory requirements? I don’t know the answer.

What do you think is the future of carbon trading?
Giant corporations like Ford and IBM are making real reductions through CCX. They produce a significant share of US emissions, and they are receiving direct economic benefits for those reductions. It’s also a learning experience to see how different various members’ greenhouse gas emission concerns are–Chicago cares about electricity generation, Amtrak is focused on diesel fuel consumption, and Tufts looks at energy use for building operations and transportation. There’s a lot of educating going on.

Karl Iagnemma juggles a dual career as a MIT robotics researcher and published fiction writer. (Credit: Ann-Kristin Lund)

Iagnemma works full time as a research scientist in MIT’s mechanical engineering department, developing mobile robots, and squeezes in time for writing whenever he can. Last year he took a partial leave from MIT to spend one day a week working on his second book, The Expeditions, which came out in January. It’s about an amateur naturalist who joins a survey expedition to the unexplored northern parts of Michigan during the mid-1800s.

In his writing, Iagnemma delves into the human side of science and in doing so has struck a chord with some of his scientist-readers. “I was shocked after my first book when I was contacted by scientists who felt a connection to the stories,” he says. “They said they wanted to write and were thrilled to see people like themselves portrayed in fiction.”

While doing research and writing fiction may seem like polar opposite careers, Iagnemma says one can do both. There is a “universal human impulse to write,” he says. But some scientists may be deterred by perceived barriers to entering the writing field or sentiments from colleagues that fiction writing is a waste of time that detracts from their work as scientists. Iagnemma—who has been the subject of both praise and criticism from colleagues about his choice to write fiction—has shown it doesn’t have to be that way. “It seems to me there are a lot of scientists with an unrequited love for fiction writing.”

Dual careers

The son of an engineer and an aspiring writer of children’s books, Iagnemma, 35, began writing as an undergraduate at the University of Michigan. While studying mechanical engineering, he took a fiction-writing class taught by a writer he’d admired, Charles Baxter.

Iagnemma finds similarities between writing fiction and doing scientific research. For instance, both involve problem solving. In the case of fiction, Iagnemma must solve the problems of scientist characters facing the possible failure of their experiments.

“The creative moment feels very similar as a scientist and as a fiction writer,” says Alan Lightman, a physicist, writer, and adjunct professor of humanities at MIT who knows Iagnemma’s work.

For Iagnemma, most of the benefits of having a dual career flows from his research career to his writing, and less so in the other direction. Using an engineer’s approach, for example, helps his writing. “I tend to approach writing in a somewhat systematic way. I tend to break stories into components and figure out which parts need to work in order for the story to be satisfying.” And being immersed in research gives him insight on how scientists and researchers see the world.

Labcoat and pen

Still, Iagnemma and Lightman both encourage scientists to do some creative writing, even if they don’t get published, because it connects them to human concerns. “Even if you are doing science, writing forces you to give deep and considered thought to different aspects of life. You sit in a room with your thoughts and explore how you feel in the world,” says Iagnemma. “There’s an addictive quality about writing.”

Lightman advises scientists to start writing in stages, progressing from an essay to short stories and finally a book, if they’re so inclined. Reading good writers is a must. Iagnemma says aspiring writer-scientists can take a writing class, get involved in the writing community in Boston, and go to author readings at local bookstores.

It is estimated that 4 percent to 6 percent of those who gamble repeatedly will become pathological gamblers, according to the Massachusetts Council on Compulsive Gambling. (For comparison, 6 percent of those who drink develop alcoholism.) But until recently, there has been little research on the biological causes of compulsive gambling.

“It’s critical to understand the biological variables [of pathological gambling] so that policy makers can start to figure out what environmental controls—the only variables we have direct control over—would be appropriate,” says psychiatry researcher Hans Breiter of Massachusetts General Hospital.

Research on the biology of pathological gambling is so new that the American Psychological Association does not currently classify compulsive gambling as a biological addiction like alcohol or drug abuse, but instead considers it an “impulse control disorder.”

But brain-imaging studies from Breiter’s lab have recently shown that pathological gambling taps into the same neural circuits as cocaine addiction. If more studies from Breiter’s lab and others confirm that gambling can be biologically addictive like substance abuse, clinicians’ level of awareness will be greatly increased, allowing patients to take fuller advantage of existing infrastructure and services for substance-abuse treatment, says Breiter.

Functional magnetic resonance imaging of the brains of healthy subjects anticipating winning a game of roulette (top) and drug addicts anticipating receiving a small dose of cocaine (bottom) reveal similar activity in the nucleus accumbens, a key reward structure in the brain that has been implicated in addiction. (Credit: Hans Breiter, MGH)

Chasing the “rush”

Early in his career, Breiter began mapping the brain circuitry of motivation and reward in humans, which is hijacked by addiction. These circuits evolved to reward behaviors critical to survival, such as eating and sex, with feelings of euphoria and arousal. Addicts continually pursue this arousal feeling, or “rush,” which is triggered by the release of the neurotransmitter dopamine. All addictive drugs so far studied act by either directly or indirectly increasing levels of dopamine in a critical center of the brain’s reward pathway, the nucleus accumbens.

Breiter and his colleagues have found that gambling appears to act similarly on the brain. Using functional magnetic resonance imaging, Breiter scanned the brains of healthy people who were anticipating winning a game of chance, which resembled roulette. He found elevated activity in the nucleus accumbens similar to what he had seen in a previous study in which he had scanned the brains of addicts anticipating moderate doses of cocaine. He even mixed up the gambling and the cocaine study scans and, without knowing which study each scan came from, found they were so similar that he could not tell the difference.

Breiter’s brain-imaging work is “superb,” says Antoine Bechara, a professor of psychology at the University of Southern California who studies the neural basis of decision making in health and addiction. “It confirms at the neural level that money, at the end, activates the same neural processes that are engaged in reward in general, be it drugs or natural rewards.”

Bechara adds that money may represent a special kind of reward in our culture, capable of eliciting strong automatic visceral reactions, because it can buy “the best of natural rewards.”

With Breiter’s study, and those that have followed from other labs, there’s now plenty of evidence that gambling, like psychoactive substances such as cocaine or alcohol, can be addictive at a biological level, and that pathological gambling should be reclassified as an addiction, says Bob Breen, the director of the Rhode Island Gambling Treatment Program at the Rhode Island Hospital. In fact, Breen says he and other clinical psychologists are already successfully using addiction treatment models with pathological gamblers. Such a reclassification, he adds, may lead to an increase in funding for research and treatment for gambling addicts.

Beyond the brain

Both Breiter and Breen point out that the roots of pathological gambling aren’t all biological; environmental factors play a role as well. For instance, the quality of family life, the proximity to casinos or other gambling facilities, the types of gambling involved (fast-moving, repetitive slot machines tend to be more addictive than slower, more socially interactive table games), and the level of education in the mathematics of gambling odds may also influence if and how compulsive gambling comes about.

Altogether, Breiter says that policy makers should take into account both the biological and environmental factors involved in pathological gambling when making decisions about whether to allow casinos. Otherwise, says Breiter, “they’re playing with fire, because there’s a slippery slope between normal and addictive behavior.”

It might sound at first like some mad scientist’s scheme. But it’s actually a serious plan by Harvard researchers for pulling carbon dioxide, the primary greenhouse gas, out of the air. The chemical process would lock up CO₂ in the form of chalk that would be buried naturally at sea, so it could help lower carbon dioxide levels in the atmosphere and fight climate change.

Harvard researchers have an idea to exploit ocean chemistry to lower levels of greenhouse gases. (Source: Flickr)

The amount of carbon dissolved in the oceans depends on the acidity of the water; if the oceans were less acidic, they would be able to take up more CO₂. Kurt House, a Harvard graduate student in the earth and planetary sciences department, and colleagues have devised a way to remove acid from the ocean to drive and speed up this process.

“It’s a form of geoengineering, changing the chemistry of the oceans, in order to pull CO₂ out of the air,” says House.

Carbon to chalk

The first step is to draw water from the sea and run it through an electrochemical plant. It would use electricity to drive reactions that pull hydrochloric acid out of the ocean. This in turn would enhance the ocean’s natural ability to soak up carbon dioxide and store it in the form of bicarbonate.

Over hundreds or thousands of years, the bicarbonate would react further to form insoluble calcium carbonate—or chalk—that would become buried under the ocean floor.

To neutralize the acid from the ocean, the plant would run it over rock, producing sand and salt that can be safely disposed of. The procedure would resemble natural processes of rock weathering, but put into overdrive.

Energy sink

However, the process requires a lot of energy to drive the electrochemical reactions. Unless it’s powered by low-carbon electricity—from wind, geothermal, or natural gas—it would be counterproductive. So the Harvard team proposes putting the chemical plants in remote regions where they could harness wind or geothermal energy that would otherwise go untapped.

One major question is how much the process can be scaled up. Even under the most optimistic projections, at most it could reduce about 10 percent of current CO₂ emissions, says Michael Aziz, a Harvard materials scientist who worked with House on the idea. “So we can’t relax and all go out and buy SUVs,” he adds.

“Their process seems basically feasible,” says Ken Caldeira, a climate scientist with the Carnegie Institution for Science in Stanford, CA. “I think it’s relatively benign for the oceans.” He adds, however, “the main drawback is that it’s very energy intensive, so it’s likely to be very expensive.”

Peter Brewer, an ocean chemist with the Monterey Bay Aquarium Research Institute in California, is more circumspect about the idea. “It is a bit of a stretch—perhaps an A-plus for ingenuity and a C for practicality,” he says. One problem is that the process involves a number of complex steps that haven’t been shown to be manageable on large scales. “I doubt very much that this can be practical and cost effective,” Brewer says.

Pros and cons

Climate scientists have studied other ways of spurring the ocean to absorb more carbon dioxide, such as “fertilizing” it with iron to stimulate the growth of plankton, which take up CO₂. House’s proposal would certainly cost more and require more energy, Caldeira says. But, he points out, “fertilization of the ocean with iron seems to be limited to, at most, absorbing about 2 percent of current emissions.” House’s idea is, in principle, more scalable and won’t interfere as much with natural ecosystems, he says. And, he adds, since it would work by reducing the acidity of seawater, it could counteract ocean acidification, a side effect of rising atmospheric CO₂ levels that threatens marine life.

Despite the challenges, Aziz and House are pushing the idea forward. They say that a financial incentive to sequester carbon is first needed. “If and when a carbon tax or cap-and-trade system [for greenhouse gas emissions] creates a high enough price for carbon emissions, the story will be different,” Aziz says.

Neuroscientist Amir Lahav uses his musical talents to study how music can help with motor learning. (Credit: Heather Kraft)

In 2006, the same organization that hands out the Grammy Awards gave Lahav $40,000 to develop the machine, called an interactive auditory feedback device. It consists of cameras and a computer that “senses” a person’s movements and converts those movements into sound. Unpublished results from early tests on five stroke patients show that patients using the device appear to recover better motor control than those undergoing traditional physical therapy alone.

At the heart of the device is software that recognizes when a patient is doing a certain movement correctly. When a patient moves correctly (for example, fully extending the wrist), the device rewards him by playing parts of a familiar song, such as “Hey Jude” or “Hotel California.” If the movement isn’t done properly (only partly extending the wrist), the device plays a distorted version of the song. The patient is able to control how the song sounds based on how he moves.

If this sounds like music therapy, think again. Lahav’s approach is about “moving to make music,” says Lahav, not about “moving to music.” It’s an important distinction. Lahav says that using body movements to control music is the key to tapping into a subset of brain cells, called mirror neurons, which may be able to improve motor learning without the need for extra physical training.

Monkey hear, monkey do

The mirror neuron system is a set of brain cells that become active both when an animal performs an action and when the animal watches another animal perform the same action. The discovery of the system was groundbreaking, because it suggests a mechanism for how animals learn through imitation and for how animals understand the actions of others.

Lahav became interested in the mirror neuron system when a group of researchers from the University of Parma in Italy showed in 2002 that mirror neurons respond not only to the sight of actions, but also to their sounds. A subgroup of mirror neurons in monkeys, for instance, fire not just when monkeys see other monkeys breaking open a peanut, but also when they hear the sound of the peanut breaking.

Drawing on his musical background, Lahav hypothesized that mirror neurons in humans are at work when a person hears a piece of music that he or she knows how to perform.

“From my own experience, if there was a piece of music that I played, that I was really good at,” says Lahav, “every time I heard this piece I almost felt as if my fingers had their own will…. I felt as though I was rehearsing the music in my mind.”

Music and movement merge

To test whether music could become synonymous with action in the brain, Lahav orchestrated a study in which he taught several nonmusicians to play a piece of piano music, which Lahav composed. Then Lahav and his colleagues imaged the brains of the subjects while they lay still and listened to three pieces of music: the rehearsed one, one they had heard before but had not rehearsed, and a third one containing the same notes as the rehearsed piece, but in a jumbled order.

Lahav and his team found that the areas of the subjects’ brains involved in motor output (presumably including mirror neurons) became active when subjects listened to the rehearsed piece but not when they listened to the other familiar music. The jumbled version of the rehearsed piece also produced some motor-related activation but not to the same degree as the intact piece.

Lahav took this experiment a step further by demonstrating, in unpublished results, that merely listening to the rehearsed music improves the subjects’ ability to play it later on, even if they did not practice it again. He suspects that the sound of the music prompts the brain to “practice,” even if the fingers aren’t moving.

Music machine

This is where the auditory feedback device comes in. Since hearing the sounds associated with an action appears to improve the execution of that action, Lahav thought this mode of learning could be applied to people with motor deficits. Stroke survivors, however, often cannot perform even the most basic motor tasks; teaching them to do an activity as complex as playing an instrument was out of the question.

So Lahav designed his auditory feedback device to “musicalize” even the subtlest of movements. Early tests suggest that the musical reward helps patients using the device along with traditional physical therapy to outperform those doing physical therapy alone. The next step is to see whether hearing a song that a patient associates with a particular action—say, zipping up a jacket—improves the patient’s ability to perform that activity without practice. Even if such a device did work though, it wouldn’t replace physical therapy; it would just be another tool for physical therapists to use.

Mirror-neuron expert Marco Iacoboni, an associate professor of psychiatry and biobehavioral sciences at the University of California, Los Angeles, says Lahav’s experiments are very clever. But, he adds, “even if the treatment works, we can’t say for sure it works because of mirror neurons, although that would be a reasonable guess.”

Take Pedro Bordalo, for instance, who earned his PhD in physics from the University of Paris studying string theory. String theory describes fundamental particles as vibrating strings and offers a way to resolve the incompatibility between quantum mechanics and general relativity. It has been called “the theory of everything,” the theory that underlies all others. In short, it’s about as abstract and mathematical as science can get. “I was happy with my PhD, but for the rest of my life, I wanted to do something else,” Bordalo says.

A turning point came when he attended a biology conference for physicists, at Hebrew University in Jerusalem. He started to look around for labs and contacted biologist Marc Kirschner, the chair of the systems biology department at Harvard. Because systems biology looks at complex biological interactions from a more integrated point of view, Bordalo found that it fit his way of thinking as a physicist. “Conversely,” he says, “it is the place in biology where people are interested in having people [from other disciplines] come over, so it’s a win-win situation.”

Now, as a postdoc in Kirschner’s lab, Bordalo is studying how genetically identical cells exhibit different behaviors that might allow them to compete in or adapt to different environments. He spends about half his time in the lab doing simple experiments and the other half developing computer models to figure out how that behavioral variation comes about.

Hands-on learning

Morten Ernebjerg, another former string theorist in Harvard’s systems biology department, decided late in his graduate studies at Harvard that string theory was a little too specialized for him. “It was work on very small, very hard problems in a small corner of a technical field,” he says. “In the end, it didn’t really suit my personality, what I imagined science for me would be like.”

To explore other fields, Ernebjerg took a summer-school class in France, which had lectures on many topics, including biology. “Somehow that really triggered something in me,” he says. The lectures confirmed his feeling that biology had the same types of big, conceptual challenges and theoretical problems that first attracted him to physics. Now a postdoc with a PhD in physics, Ernebjerg is studying how complex microbial communities in soil work together and survive.

Bordalo and Ernebjerg knew very little biology when they started; they learned on the job and by talking to colleagues. Learning lab work wasn’t hard, says Bordalo, but doing it takes time and is important for theoreticians, especially in the beginning, to learn what is experimentally possible. “The biggest challenge when you change fields is to find out what are the important questions which are interesting and which you can solve,” he says. “It’s often not clear whether experiments you might want to do are possible–in general, they’re not. So you have to be close to people who are actually biologists.”

Flood of physicists

Neither Bordalo nor Ernebjerg applies string theory to his present work. But they both draw on their experiences dealing with abstract concepts and working with large amounts of data—skills that are needed in the field, says Timothy Galitski, a biologist with the Institute for Systems Biology in Seattle who has worked with three physicists in his lab. “We subscribe to the belief that biology is becoming an information science.”

Bordalo says a whole generation of scientists went into string theory because it was exciting and a lot of new work was taking place. Now, the same revolution is happening in biology. “Maybe many people who would have gone into string theory, in the next generation will now go into biology instead,” Bordalo says.

Allen Gontz, assistant professor of coastal geography and geophysics at UMass Boston, brings these two disciplines together. Gontz has worked with Boston’s preservation community for the past several years using geological tools to find, analyze, and conserve historic landmarks. “Traditional archaeology digs up remnants of society to see how people lived,” says Gontz. “Geology adds information about the landscape that they occupied, the climate, and how people interacted with the setting.”

For example, Gontz is working with the Paul Revere Memorial Association to locate old foundations at the Paul Revere House in Boston’s North End, using high-resolution ground-penetrating radar. Data are still coming in, but he expects to produce some findings later this spring that may show how the site has evolved over time.

Paul Revere’s house in Boston’s North End. (Source: Wikipedia)

“Curators have records of how the property changed hands and what existed around it, but they aren’t really sure exactly where those things were located,” Gontz says. “When the building burned down, did they salvage the foundation blocks for another house? Where are the privies and wells?”

If the team is able to locate the foundations, preservation groups can restore the property to the way it looked in the 1700s, when Revere began delivering messages for the American revolutionaries, Gontz says.

Geologist’s toolbox

Much of Gontz’s research looks at how coasts have changed due to forces such as erosion, glaciation, sea-level change, and human development since the peak of the last ice age, about 23,000 years ago. He and other UMass researchers contributed to a report published last year, which projected that rising sea levels due to global climate change could permanently flood parts of Cape Cod and Long Island, and most of New Jersey’s coastline.

Gontz measures coastal change using tools that include sidescan sonar (which emits fan-shaped pulses across wide swaths of the sea bottom), magnetometers, and sub-bottom profilers that map sediment layers using sound waves. He also uses some of these tools for his historic preservation projects.

Gontz directs UMass’s GeoSTRAT Lab, which brings together geological and archaeological methods to study how physical and sociological environments have evolved over time. The lab’s partners include the Massachusetts Board of Underwater Archaeological Resources (BUAR), which is part of the state’s coastal-zone management office, and Boston’s city archaeologist, who oversees the archaeological remains on Boston public land.

Underwater and underground

Among the lab’s recent projects are 2006 sonar surveys of the ocean floor in Boston Harbor for two proposed shipwreck sites: the French man-of-war Magnifique, which sank off Lovell’s Island in 1782, and the USS Niagara, a Civil War blockade-runner scuttled in the harbor in 1897.

“It’s a real collaboration,” says BUAR director Victor Mastone. “Archaeologists tend to do everything on a shoestring, but Allen collects data on a much bigger scale, so he’s always pushing us to do more.”

The team found promising targets but did not pinpoint either wreck. Still, Gontz says hunting for shipwrecks is useful for coastal studies. “If you know when and where a ship went down, you can look at erosion, deposition, and sediment transport in that tiny landscape,” he says.

Gontz is also working with Boston’s city archaeologist and the Dorchester Historical Society at Blake House, which dates back to about 1648 and is Boston’s oldest house. The building was moved from its original location to what was formerly known as Dorchester Commons in 1895. “We’re trying to determine what the commons may have looked like before they moved the house there,” he says. The team is excavating a filled-in pond and examining pollen and plant fossils to paint a picture of the landscape in the late 19th century. Geological excavation at the site will continue through this summer.

BU physicist Veronica Sanz gets set for the start-up of the world’s biggest particle accelerator. (Credit: Johannes Hirn)

Sanz recently spoke with Nature Network Boston about her upcoming European commute, the excitement surrounding the start-up of the behemoth collider, and the future of particle physics.

What does the start-up of the LHC mean for the field?
The LHC is the most exciting thing going on in particle physics. Do you know how many years we have been waiting for an experiment like this to come out? [Theoreticians and experimentalists] can’t sit around forever with pen and paper. The particle physics community needed a big push like this one to keep momentum going and to test theory. We are finally going to see real science and data.

The LHC could give us the ability to understand the origin of mass. One possible explanation is the Higgs boson [a particle that may give other particles mass], but there are other explanations as well. As a theoretical physicist, I come up with possible signals to look for.

What sorts of experiments will you be involved with at the LHC?
My work is relevant to the two general-purpose detectors at the LHC: ATLAS and CMS. ATLAS and CMS will record measurements on the particles created in the collisions. They will measure the particles’ identity, path, and energy. My work is to match these measurements with predictions from models of new physics [beyond the Standard Model].

How much trans-Atlantic traveling will you be doing and how much time will you spend at a time in Geneva?
Right now, I spend two or three months a year traveling. Thanks to the award I’ll be traveling twice a year to Geneva, instead of once. Probably, I will spend one month at CERN and another month at U.S. institutions.

Why did you choose to study particle physics?
There are many areas of physics that you can go into. But particle physics is the most beautiful. It’s the very end of the line, the last frontier in our understanding of nature. When you look through a microscope under higher power, you can see smaller and smaller components of life. Particle physics looks at the last and smallest components.

What does the future of U.S. particle physics look like?
Right now, the U.S. has a strong presence in particle physics and in the LHC. But the U.S. and the U.K. have recently cut funds for the next big project, the International Linear Collider (ILC). The LHC will give us a rough picture, but the ILC will give us a clearer image. For the next 10 to 15 years we will be busy with the LHC. But these types of machines are so huge and expensive that we are planning 20 years out. We need longstanding budgets to do this. We don’t know what will happen to the ILC and to the future of the field.

Throughout 2006, people from outside of Boston clamored for a website that included them as well. So we started drafting plans for a global networking website, Nature Network.

2007

February
• Nature Network launches with a new logo and look. Nature Network Boston relaunches as a local hub within Nature Network.

March
• The next local hub, Nature Network London, goes live. To celebrate, the NNL team hosts the first of many successful monthly pub nights for London scientists.

April
• The Nature Protocols Discussion Forum, one of the first groups to be formed on NN, begins to take off. It remains one of the biggest and most popular groups. Bench scientists use the group’s forum to ask each other questions about experimental procedures.

May
• The Nature Network Newcomers Forum is born, a place where newbies can introduce themselves and meet the editors and each other.

June
• Nature Network Boston hosts its first pub night for Boston scientists. It was a scorching day and the bar wasn’t very well air conditioned, so kudos to the 25 or so scientists who showed up and sweated it out.

July
• The Guardian, a major UK newspaper, highlights Nature Network in an article that features a rather sinister-looking photo of our very own NNL editor Matt Brown.

• A new and improved events calendar goes live on the Boston and London sites.

August
• The homepage of nature.com gets a complete makeover and Nature Network finds itself featured right in the center of the page. The number of new signups ramps up.

• We launch a new feature allowing NN members to send each other private messages.

September
• The Ask the Nature Editor forum is created and several editors of Nature and its sister journals pitch in to answer people’s questions about open access, peer review, careers in scientific editing, and other topics. It remains one of our most popular groups.

October
• We begin a series of page redesigns. The Blogs, Groups and Forums homepages are spruced up so that they show off more of the popular content on the site.

November
• We reach 500 groups formed.

December
• The Nature News team launches a group and in it starts off a discussion about the ethics of cognition-enhancing drugs, based on a commentary published in Nature. It becomes one of the hottest topics of discussion on Nature Network.

2008

January
• Four of our bloggers are chosen to be included in Open Laboratory 2007, an anthology of the best science blog posts.

• We partner with Euroscience Open Forum 2008 (ESOF) to create a group in which their 20,000 members will be invited to discuss the important issues affecting science today.

February
• The online journal club within the Neuroscience group gains momentum with more regular posts about the latest papers in the field (see the latest topic here.). Scientists join in to discuss the papers and membership breaks 100.

We at Nature Network look forward to another fun and exciting year and we thank you, our users, for your support and enthusiasm and for making our first year a success.

Best place to meet other scientists:
Seminars on the Harvard Medical School quad and Biotech Tuesday (a monthly gathering of biotech professionals in Boston)

Best place to celebrate getting published in your journal of choice (or defending your PhD thesis):
Eastern Standard in Kenmore Square. It serves fantastic French-inspired food and the bartenders are friendly and fun. It’s large enough that your personal celebration won’t detract from anyone else’s evening.

Best place to escape and decompress:
Anywhere on the water: Gloucester, MA, Newport, RI and Crane Beach near Ipswich, MA are good spots. On Georges Island in Boston’s outer harbor, you can picnic and explore the Civil War-era fort. Watch out for the packs of geese though; do not leave your lunch unattended. I speak from personal experience.

Best place in Boston to live:
I vote for Brighton. It offers a mix of people and cultures: Orthodox Jews, Russian retirees, and (often drunk) college kids.

Favorite restaurant:
Ten Tables in Jamaica Plain. Ask for the chef’s table and order the tasting menu. Watch the two chefs dance around the tiny kitchen as they prepare a five-course meal of seasonal and local ingredients.

Favorite pub/bar:
The B-Side Lounge near Inman Square in Cambridge and the Audubon Circle Restaurant and Bar near Kenmore Square. The B-Side is full of dark wood, heavily tattooed servers, and amazing food. The Audubon is always relaxed and reliably good.

Favorite café:
KooKoo Café in Brookline Village. You wouldn’t notice this small café if you weren’t looking for it, but it is absolutely charming. The dishes are handmade in the neighboring pottery studio while the Middle Eastern snacks and sandwiches are made onsite. And the owners happen to own and run the yoga studio next door.

For other recommendations, see the previous installment of “My Boston” here.

Post your favorite Boston spots as comments below. If you would like to be the next person interviewed for this series, please email c.lok at boston.nature.com.

One recent evening at the brightly lit store, Wallace alternated between filling special orders, chatting up customers, and tinkering with a machine that didn’t want to produce Oreo-flavored yogurt. Numerous customers lined up for the dessert, despite the late January chill.

“Working in a yogurt shop might not be as prestigious as working in science,” Wallace says, “but here, I get to talk to people all day long. When they come in the door, they already have a smile on their face. I can’t remember the last time I saw a face light up with a smile when I was in a research lab.”

BerryLine in Harvard Square, founded by a former postdoc, sells frozen yogurt and smoothies. (Credit: BerryLine)

The shop itself is also quite unlike any lab. The outside features a mural of bananas with smiling faces, pineapple slices, and yogurt cups, painted by Cambridge artist Bren Bataclan. BerryLine–named for the Red Line train that rumbles right below the shop—offers a rotating list of yogurt flavors, ranging from coconut to raspberry to chocolate cookies and cream, all made from scratch (using milk and other ingredients) in the shop.

Swapping lab coat for apron

Wallace, who has a PhD in molecular biology and biochemistry from the University of California, Los Angeles, came to the Boston area less than two years ago as a postdoctoral researcher.

But even as a graduate student, he thought about starting a business. He admits he was beginning to think about other career options by the time he moved to Boston.

“I was getting tired of the academic environment,” Wallace says. “Not necessarily science itself–but I was looking for a change and was excited about the opportunity to start a business.” He and his business partner, another LA transplant, missed southern California’s ubiquitous frozen-yogurt stands and saw a need for one in Boston.

So he and his cofounder walked into the office of the Harvard Square Business Association last February and asked what they had to do to open a frozen-yogurt shop. They spent several months making connections in the food service industry and learning the basic ingredients and processes for making frozen yogurt. “I’m still learning the food service business,” Wallace says.

Soon, they were scouting potential locations and enlisting friends to taste-test variations on their recipe. They pulled together their savings and took out loans to finance their business, which opened in September.

Yogurt experimentation

Perhaps the toughest part of starting his business was making the decision to–at least for now–leave academic life behind, Wallace says.

“It can be a bit of a letdown for all the people who supported you along the way,” he says. But so far, he adds, he hasn’t looked back.

Wallace doesn’t go so far to suggest his scientific background helped him make frozen yogurt. But he still speaks like a scientist when describing how he and his partner came up with their recipe.

“We did a lot of fine-tuning of our protocols so we could reproducibly make our yogurt every day and have it taste great.”

But at the end of December, Feldman, cospokesperson for the project, received some very bad news. Congress unexpectedly cut $94 million from the high-energy physics budget, slashing funds for NOvA and other projects at Fermilab and the Stanford Linear Accelerator Center. US research and design efforts for the International Linear Collider (ILC)—an international particle accelerator still in the planning stages that represents the next big step for the field—have also been suspended. Several countries are vying to host the ILC, and Boston-area physicists fear that the budget cutbacks will jeopardize any American bid to be the ILC’s home.

The shrunken budget has effectively cancelled or drastically cut back large-scale experiments—for example, construction of NOvA’s detector has been delayed indefinitely—and has put planning on hold, leaving many Boston physicists uncertain about the future of their field.

“Students worry about having to work on experiments in Asia and Europe after this,” says Mayly Sanchez, a visiting scholar at Harvard who works with graduate students on neutrino projects. “They don’t see an optimistic future for high-energy physics in the States.”

Out of America

Georgios Choudalakis is a graduate student at MIT working at Fermilab. He came to the United States from Greece because of America’s reputation for pioneering new scientific programs. “How does [the United States] manage to attract the best? A major factor is that it funds the best universities and laboratories,” he says. But after his PhD, Choudalakis plans to move to CERN, the high-energy physics laboratory in Geneva, Switzerland.

So far, only budgets for large-scale projects and facilities have been cut, but some Boston researchers are concerned that there may be less money available for smaller grants too, and that could affect the next generation of physicists. “If we don’t get funding, we can’t take on students,” says Ed Kearns, a professor of physics at Boston University. “Federal research dollars don’t go into rocket fuel that gets burned up; the money funds graduate students who we train in fundamental research. Those students go on to jobs not only in particle physics but also in the private sector here in Boston.”

Speaking up

Some Boston researchers are fighting back. Tufts physics professor Hugh Gallagher says that he’s been calling and faxing Senators John Kerry and Edward Kennedy, and Congressmen Ed Markey and Mike Capuano.

“One of the most concrete things that’s come out of this is the realization that the scientific community has to articulate to politicians and representatives why our research is so important and so vital to the training and education [of PhDs] in this country,” he says. “Nothing in Washington is safe unless there are people advocating for it.”

Feldman and his colleagues at NOvA have not yet given up hope. This spring, Congress could pass a supplemental appropriations bill to restore some funding. “We are doing everything we can to influence the political process and remain hopeful,” Feldman says.

Editor’s note: A correction has been made. Georgios Choudalakis is a graduate student, not a postdoc.

Massachusetts has long been a magnet for the biomedical industry. Despite high costs, the state has two big draws—a well-educated workforce and proximity to top-notch research institutions such as Harvard and MIT.

But supporters of Gov. Deval Patrick’s proposed $1 billion life sciences bill say those days are numbered. They argue that states such as Maryland and North Carolina–as well as countries such as Singapore–have become much more aggressive in recent years about marketing themselves to companies, including those in Massachusetts, citing their tax breaks and low cost of doing business. Preliminary results from an ongoing survey of Massachusetts life science companies indicate that 20 of 26 companies polled said they would consider moving out of state. More than half reported already receiving offers from other states.

However, as the bill picks up pace in the legislature, critics have begun questioning the premise that the state is about to lose its dominance in the life sciences. By most measures, they say, the state is an industry nexus and there is little evidence of an exodus of life science companies.

At issue is a section of the bill that would expand tax incentives—amounting to as much as $25 million a year for 10 years—and fund road and sewer improvements to lure new companies to Massachusetts.

“When we say we will pay you to locate in a thriving mecca of this industry, it is dangerous,” said Sen. Mark Montigny, a New Bedford Democrat, during a State House hearing earlier this month.

Supporters of the bill said the danger is in letting a valuable industry slip away.

“Leadership in life sciences is ours to lose,” said University of Massachusetts president Jack Wilson at the same hearing.

State competition

The bill aims to boost tax revenue and bring high-paying jobs to the state by setting up a range of programs to support biomedical research, product development, and manufacturing. As part of the effort, the state’s reinvigorated Massachusetts Life Sciences Center (MLSC) has already approved $12 million in matching research grants for scientists and $7.7 million for a new stem-cell bank and registry at the University of Massachusetts Medical School in Worcester.

But the MLSC—a group of state officials and appointees–needs the Patrick bill to pass in order to obtain additional funding that would sustain those programs, create an RNA interference research center at UMass, fund roads and utilities, and give tax breaks to life science companies.

Fueling the debate is a range of conflicting views on the state’s competitiveness. An April study by analysts at PriceWaterhouseCoopers called Massachusetts a growing “super cluster” for the life sciences but warned of rising competition from other states. Companies complain that the state’s economic development programs are poorly coordinated and local permitting is cumbersome, according to the Massachusetts Biotechnology Council.

At the same time, Massachusetts ranked second only to California in National Institutes of Health funding, drawing $2.2 billion in 2006, and is also one of the top ranked states in the amount of life science venture capital funding received. Suffolk University economists measuring state competitiveness ranked Massachusetts second in the nation for 2007, after Utah.

Massachusetts is a life sciences leader, so it is unclear what problem the Patrick bill is trying to address, says Greg LeRoy, the director of Good Jobs First, a nonprofit economic development research group in Washington, D.C. He says the plan needs to make a better case for the need for public subsidies.

“Without targeting the plan, you risk subsidizing investment that would have occurred anyway,” LeRoy said at the state hearing.

Stay or go?

For Josh Boger, the head of Vertex Pharmaceuticals, the need for incentives from the state is real. “I’m the one who regularly gets detailed reports about how much more favorable things would be if we moved Vertex to another state,” said Boger, who is also the current chair of BIO, the national association of biotechnology companies.

As Vertex looks to expand its headquarters, Boger has been listening to pitches from other states, as well as other countries. “Am I looking at Massachusetts? Yes,” he said. “That doesn’t mean that I’m not looking elsewhere.”

He said the tax incentives in the Patrick plan are “incredibly modest” and will put the state on par with competitors. As he decides where to expand, Boger says he will view incentive programs as a measure of the state’s commitment to the industry.

The members and staff of a joint House and Senate committee are now reviewing the testimony from the public hearings and will soon make recommendations that could include changes to the bill. Even critics of the industry incentives support other elements of the bill, such as the creation of a stem-cell bank and the RNAi research centers at UMass. While the bill has powerful supporters in the legislature, it may look a bit different from Gov. Patrick’s original plan.

Sarah Fortune of the Harvard School of Public Health says that the commonly held belief, that the tuberculosis bacteria are “in hiding,” is overly simplistic. She believes that, while in the human body, the bacteria undergo changes in the sequences and the expression of their genes and are able to divide and pass those changes down to the next generation. These changes, she says, keep the bacteria under the immune system’s radar indefinitely and enable them to resist drug treatment.

Harvard School of Public Health researcher Sarah Fortune is uncovering the mysteries of the TB bacteria.

Her lab is deciphering these alterations, which could lead to insight on how to improve treatment and prevent drug resistance, a growing problem among TB patients. “We want to understand what the genes look like and the patterns of mutability,” Fortune says.

Catch in the act

Fortune, assistant professor of immunology and infectious disease, has been running a lab for just about a year, but her approach to studying TB has already garnered a series of awards, including one of the newly launched New Innovator Awards from the National Institutes of Health.

To investigate how the TB bug changes during infection, Fortune’s lab is sequencing the genomes of different strains of TB isolated from patients and comparing them to identify patterns of mutation associated with persistent infection.

The Fortune lab is also opening up a new area of study by looking for possible epigenetic changes in the TB bacteria—modifications in the way the genes are expressed that don’t involve changes to the DNA sequence itself. “There are few examples of epigenetic inheritance in bacteria,” Fortune says. Bacterial DNA does not have the same elaborate structures usually associated with epigenetic control. But Fortune believes that bacteria “could have other ways of generating functional diversity,” such as simpler structural changes to the bacterial DNA that are akin to familiar epigenetic modifications in more-complex organisms.

TB mysteries

Genetic mutations associated with drug resistance are well known in other bacterial pathogens, but TB is less understood, in part because of logistical hurdles; the TB bacteria grow relatively slowly, and studying them requires strict security measures and expensive equipment. Fortune says that part of her approach is to look at mechanisms that other bacteria use to evade the immune system and see if they might also apply to TB.

A better understanding of the bacteria’s behavior during infection could shed light on mechanisms of drug resistance. Fortune, who trained as an infectious-disease doctor before switching to full-time research, says that the emergence of drug-resistant TB is often seen as a failure in treatment on the part of clinicians or a lack of drug compliance on the part of patients. “It’s not clear whether it’s all just institutional failure or whether it is similar to other bacterial infections, where there are subpopulations more likely to become drug resistant,” says Fortune. Some infectious bacteria, for instance, have subpopulations that mutate very rapidly and so are more likely to acquire resistance. M. tuberculosis could be one such bacterium, Fortune says.

William Jacobs, a TB researcher at the Albert Einstein College of Medicine in New York, says that Fortune’s work is especially important given the emergence of TB strains resistant to almost all current TB drugs. “It’s an unprecedented experiment in history,” he says. “We’re generating a larger number of mutated bacteria, there’s no doubt about it.” Yet no one knows whether these strains are gaining new characteristics that allow them to mutate more quickly, he says, and Fortune’s work may help answer that important question.

“There was more interest in burying the technology than in bringing it out. I felt obligated to do something,” says Leschine. “It took several months for me to decide to form a company.” She is a consultant for SunEthanol, the Amherst-based company she founded in 2006 to commercialize a processing technology designed to convert cellulose to ethanol more efficiently using natural, anaerobic microbes.

And so began Leschine’s journey into the world of business and finance, for which she had little training or experience. Working with colleagues at UMass’s management school, a group of successful local businesspeople, and the university’s technology transfer office, she learned everything from writing a business plan to raising money, essentially taking on another full-time job outside the university to get her company off the ground. “I was so naive,” says Leschine. “I was very frightened to do it.”

So far, it has paid off; SunEthanol has secured more than $2 million in funding in the last year from venture capitalists, a large biofuels company, and the U.S. Department of Energy. Leschine’s story shows how important it is for scientists to network with friends and colleagues who can introduce them to businesspeople with the skills to help move their science out of the lab and into the marketplace.

Using networks

In the late 1990s, Leschine and her research technician, Tom Warnick, identified a natural microbe that they later found efficiently ferments plant biomass, producing ethanol without the need to add the costly enzymes commonly used in conventional ethanol production. They filed a provisional patent in January 2006 and a full patent in January 2007 that is still pending. They licensed the technology from the university and formed the company with the help of local businesspeople who already had successful companies, mainly Internet firms, and were looking to help other entrepreneurs. Some of those businesspeople now are full time at SunEthanol, which has more than a dozen employees.

Leschine also had help from UMass management faculty, notably John Fabel, who heard about her work through the university’s technology transfer office. He is now the director of new technologies at SunEthanol.

She developed a level of trust with Fabel and the group of entrepreneurs, who took the lead in making the marketing and financial presentations to the venture capitalists. Leschine found the process of talking to venture capitalists, which involved a lot of probing and critical questions to assess the technology, somewhat intimidating: “They reminded me of the comprehensive exam committee for my PhD,” she says.

Dancing with investors

One of the most important lessons that academics learn when shifting into the business world is how to deal with venture capitalists. “Venture funding is a huge step,” says Leschine. “The obligation and pressure to perform is tremendous.”

So it’s important to scrutinize investors as potential partners, says Michael Naughton, chair of the physics department at Boston College who cofounded a nanotechnology company called Solasta in 2006 after coming in second in a Massachusetts business plan competition. “A personal connection is important,” he adds. “You have to trust them.”

Naughton speaks from experience. After an unfruitful summer of talking to venture capitalists, Naughton says he turned to his network of friends to find a venture capital firm that understood his company’s potential and needs.

He advises academics to not be afraid to ask venture capitalists questions about all aspects of the business relationship. “My advice is to be respectful but not awed by venture capitalists,” he says.

Leschine’s advice is to bring your technology as close as you can to the proof-of-concept or initial scale-up stage before going to a venture capitalist; this will increase your chances of meeting the milestones set for you and will also raise the value of your company, enabling you to potentially raise more money.

Start-up separation

Both Leschine and Naughton have decided to remain on faculty and consult for their respective start-ups, rather than work full time for them. There were differences between the academic and business worlds that gave them both pause. Naughton, for example, remains uncomfortable with the fact that venture capitalists do not sign the nondisclosure agreements (NDAs) that are commonly used among academics when discussing their research with outsiders. He and his cofounders decided to talk without an NDA, but for other academics, that’s a deal breaker, he says.

For Leschine, her heart remains in the lab where she can explore her own questions. “At the company we have objectives and goals. We can’t do basic research. It’s more focused on getting results.”

To remain as professors, Leschine and Naughton have had to carefully account for their time in order to abide by university policies that restrict the number of hours spent consulting for companies. To avoid any potential conflicts of interest, they’ve had to clearly separate research done for the company from their university work.

Leschine and Naughton had tenure when they decided to launch their companies. Leschine admits she wouldn’t have considered taking the plunge into the commercial world if she hadn’t been tenured. But Naughton says junior faculty members shouldn’t be automatically discouraged from starting a company, as long as they keep focused on their responsibilities to the university. “You just have to watch your time and benefit students and the university.”

Related careers articles on NNB:
Patent law
Working in the pharmaceutical/biotechnology industry
Teaching at undergraduate colleges
Participating in business plan competitions
The career path to venture capital
Writing about science rather than doing it

While still in the early stages of development, these microbial fuel cells could one day provide electricity to charge cell phones and other small electronics in off-grid locations around the world, according to the researchers.

Bucket power

When he began developing his fuel cell technology, Harvard University microbiologist Peter Girguis kept a lamp in a bucket of dirt in his basement. The lamp glowed as brightly as a 40-watt bulb for a few hours every night for a year, even though it wasn’t plugged into a wall socket. This prototype fuel cell was plugged into the dirt.

Girguis is founder and chief scientist of Living Power Systems, a new company created to commercialize his technology. Living Power recently received funding from the Charles A. and Anne Morrow Lindbergh Foundation to test its prototype in India and Mexico.

Girguis says the device is designed to attract naturally occurring, electron-producing microbes in the environment. The fuel cell consists of a pair of electrodes connected to a circuit board about the size of an iPod. One electrode is placed into any oxygen-deprived environment where bacteria thrive, such as soil, compost, or sediments. This electrode collects the electrons the bacteria kick out as they digest organic matter. These electrons flow through a wire to the circuit board and then to the second electrode, generating electricity.

The fuel cell offers a cleaner way to provide light in rural areas far removed from the grid, Girguis says. “In many parts of the world, organic matter, such as compost and animal dung, is burned for its light in open pits or open stoves in the home,” he says. “That animal dung or compost would be a perfectly good fuel for a microbial fuel cell.”

Team BioVolt

Last fall, a team of MIT students placed first in the MIT and Dow Materials Engineering Contest with a microbial fuel cell called BioVolt. Unlike the Living Powers System device, theirs relies on cultures of specific strains of bacteria to produce electricity from cellulosic biomass such as crop waste. The team also developed a membrane in the middle of the fuel cell that facilitates the movement of ions from one side of the fuel cell to the other, eliminating the need for costly platinum catalysts used in a traditional fuel cell.

Andrew Hoy, MIT sophomore and member of the BioVolt team, says the motivation for their project came from a market analysis of sub-Saharan African nations, where it’s common for people in rural areas to walk many miles to cell-phone charging stations in cities. “It’s expensive and time-consuming for people to do this,” Hoy says. “We’d like people to be able to charge their cell phones on the dinner table using food scraps,” he says.

Need more juice

A major challenge facing microbial fuel-cell projects is power output. The BioVolt prototype produces only a milliamp of current, Hoy says. At that level, it would take about six months for one of their devices to charge a cell phone.

This spring, members of the MIT team will work on ways to improve the efficiency of the device by redesigning the membrane to boost the rate of ion transfer and thus overall electricity production. They will also test other combinations of bacterial species to find the one that can pump out the most electrons. Coupling several devices together may also increase power input, says Hoy.

Girguis points out that with his system, power production is directly proportional to the surface area of the electrodes. While he wouldn’t give any precise numbers on the power output of his current prototype, he says that his soil-powered device could charge a cell phone at the same rate or faster than a conventional charger.

But Iwasa has a role unlike most of her peers: she is an illustrator and animator, bringing to life key concepts in molecular biology being studied by Jack Szostak’s research group at Harvard Medical School.

Iwasa is at the forefront of a trend in the life sciences, where biologists and biochemists are placing increased emphasis on the visual representation of their discoveries. They believe that sophisticated 3-D animations and graphics showing complex cellular processes will help in research, teaching, and public outreach. Indeed, Iwasa is developing bioscience displays for Boston’s Museum of Science. “We want to help people think in a molecular fashion,” she says.

Scientists believe protocells may have been an ancient ancestor of the cell. Single-strand RNA molecules are surrounded by a fatty acid membrane. (Credit: Illustration by Janet Iwasa for the Szostak Lab, Harvard.)

“It’s been incredibly useful,” says Szostak of Iwasa’s work, which depicts concepts such as the way RNA may have begun to replicate itself when life was just getting started on Earth billions of years ago. “I use her illustrations and animations in my own seminars to try to quickly get across ideas people aren’t familiar with, and I’ve had a very positive reaction from people. We hope over time her work will also find more of a public outlet.”

Iwasa’s graphics have also found their way onto the Szostak lab website and have been included in some of the group’s forthcoming papers, as well as others published by labs from the University of North Carolina, Chapel Hill and the University of California, San Francisco. Her work has even appeared on the covers of Cell and the Journal of Cell Biology.

At the moment, though, careers at the intersection of science and graphic design are both exciting and daunting. While the need for such work is expanding, there is no formal career path for it, so entering the field is a matter of personal initiative. Iwasa essentially created her Harvard post by securing a National Science Foundation grant for illustration and approaching Szostak’s lab to discuss how she could contribute.

Gear shift

Just a few years ago, Iwasa was on a conventional career track in academic science, but had a personal interest in Web and graphic design. “I’ve always been inclined that way and really enjoyed it,” she says. As a graduate student at the University of California, San Francisco, Iwasa was encouraged by a professor to explore animation to better study kinesins, a type of motor protein in the cell.

Before long, she was taking weekly animation classes at San Francisco State University while finishing her doctorate. Instead of looking for a conventional postdoc, she applied for NSF funding and even took an intensive nine-week course to learn how to use 3-D animation software called Maya at the Gnomon School of Visual Effects in Hollywood, a frequent stop for designers in the entertainment industry. After completing the course in September 2006, she moved to Boston to begin work at the Szostak lab.

For the Museum of Science, Iwasa is creating material in three formats: videos to accompany museum talks, touch-screen displays, and an online virtual exhibit on the origins of life.

Working for such a variety of clients means science illustrators must be able to tailor their work to different audiences, says Iwasa. In a museum, “somebody trying to understand what a protocell is probably doesn’t need to know how all these molecules move around.” Her MoS work is thus more abstract and symbolic. But at Harvard, Iwasa’s cell biology background allows her to collaborate with researchers to produce more-detailed visualizations based on scientific data. “I can show something to Jack, and he’ll say, ‘Maybe this way is better supported by the literature,’ and he’ll refer me to some papers.”

Skills in need

There is great pent-up demand for design skills in science, says Robert Lue, executive director of undergraduate education in the molecular and cellular biology department at Harvard. “I would be extremely surprised if this does not continue to grow as a major part of the doing, teaching, and communication of science,” says Lue, who also heads a Harvard project developing biological animations. “We’re in a world that is much more visually deep and powerful than anything we’ve seen before.”

Lue says many students now talk to him about acquiring illustration training, either as a standard science skill or as a career itself. Like Iwasa, Lue believes there is no template for science-design success. “If you want a well-established, safe, mature field, this may not be the thing for you. If you want to be an engine that pushes this field forward, there is an enormous opportunity.”

See Iwasa’s website for her other work.

Best place to meet other scientists: Starbucks on Longwood Ave.

Best place to celebrate getting published in your journal of choice: The Squealing Pig (a pub near the Longwood medical area)

Best place to escape and decompress: The basement of the Countway Library of Harvard Medical School. There is rarely anyone there and they have Internet jacks at every desk.

Best place in Boston to live: Wow, I have not found it.

Favorite thing to do in Boston outside of work: Visiting the Fogg, Sackler, Busch-Reisinger, Peabody, and Natural History museums. (A Harvard ID card means free entry!)

Favorite restaurant: Pomodoro in the North End

Favorite pub/bar: Cambridge Brewing Company in Kendall Square

Favorite café: 1369 in Inman Square

What are your favorites in Boston? Post them here.

Trying to trace out the complex wiring in the brain is enough to give you a headache. So Jeff Lichtman’s lab at Harvard developed a new tool for staining cells a veritable “brainbow” of nearly 100 colors, which could help researchers follow the connections between neurons.

Brain cells light up in a multitude of colors. (Credit: Jean Livet et al.)

Last month, Lichtman and colleagues reported how they engineered mice to carry genes coding for three different colors of fluorescent proteins—yellow, red, and cyan—as well as for an enzyme that blocks the activity of a random subset of these genes. The researchers fed the mice a specific compound to activate the enzyme in neurons; the result was that each neuron generated a different combination of fluorescent proteins, making each one light up with a different hue.

The technique could enable researchers to map out the connections between neurons and shed light on diseases such as autism and schizophrenia that may be caused in part by faulty wiring in the brain’s circuits.

Stem-like cells from skin

The announcement in November that human skin cells could be reprogrammed to act like embryonic stem cells made plenty of headlines. But Rudolf Jaenisch of the Whitehead Institute and Konrad Hochedlinger of Massachusetts General Hospital, along with Japanese researcher Shinya Yamanaka of Kyoto University, paved the way in June when they first showed the trick works in mice (see here and here).

The technique, developed by Yamanaka and colleagues, uses a virus to insert four genes—two of which are known to cause cancer—into skin cells. Once imported, the genes appear to repress activity of the cell’s own versions of these genes, reprogramming the cells so that they are indistinguishable from embryonic stem cells. This could be a strategy for generating large numbers of stem-like cells for research, although the utility of this approach as a therapy—by generating patient-specific cells to replace diseased tissue—remains controversial.

Planetary progress

David Charbonneau of the Harvard-Smithsonian Center for Astrophysics led several studies this year that advanced the field of exoplanet studies—the search for and study of planets outside our solar system.

In May, Charbonneau and colleagues made the first measurements of weather on an exoplanet. They found that the dark side of the planet HD 187733 is surprisingly hot, suggesting that it has supersonic winds ripping through its atmosphere.

In August, Charbonneau and colleagues reported the largest, puffiest planet yet, TrES-4, which has a density close to that of cork. Theorists hadn’t predicted that such planets were possible and they’re still trying to grasp how they hold themselves together. Such findings netted Charbonneau Discover Magazine’s “Scientist of the Year” award.

Cordless recharging for your cell phone

How many times have you rushed out the door in the morning, only to realize you forgot to plug in your cell phone and now it’s out of juice? MIT researchers aim to end this vexing problem with a scheme for sending power through the air—no wires necessary. Last year they theorized that this would work and in June they