Science Metropolis - Boston

One of several polls presented by Science Debate 2008

The advocacy group Science Debate 2008 will make an excellent documentary subject someday. In just 8 months, the growing group of concerned citizens, (although journalists, scientists and university presidents aren’t exactly your average American…), have built an aggressive campaign requesting a simple chat between the presidential candidates about science. However, with the date of that proposed debate having passed, and the presidential elections edging closer, the group is trying plan B, written responses from Barack Obama and John McCain.

What’s shocking about Science Debate 2008 is how much it has had to prove to the United States that science is important, not just to the country’s progress but to its citizens. It’s polls generally show a majority agreement that science-related issues like education, health care, energy needs and climate change need to be at the forefront of the next election. Yet, still the candidates have not responded.

In conjunction with Scientists and Engineers for America, Science Debate 2008 published today a list of 14 questions covering the biggest scientific issues of our day. After 8 years of a president who openly attacked science, (Read Chris Mooney’s “The Republican War on Science” for more information), knowing how each candidate plans to handle predicted water shortages and stem cell research would be change we can depend on.

As important as where the president stands on these issues, is how your local politicians support science. The SEA Website also tracks how congressmen vote on important scientific issues. Democratic Senator John Kerry and Democratic Congressman Michael Capuano are listed for the 8th district of Massachusetts.

Science Metropolis supports Science Debate 2008. If you’d also like to get involved, visit their Website.

Ask and Answer: Which of the 14 questions are most important to you?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Photo by Sven Hoppe/iStockPhoto.

Andrew Bouley wraps his right knee with an ace bandage and gently lays an ice pack on top. He hopes he won’t be in too much pain come Monday morning, when he and over 200 other participants will run the Boston Marathon to raise money for the American Liver Foundation.

The Boston Marathon is considered one of the most prestigious road races in America, and competitors must qualify in order to enter. But for amateur runners and marathon first timers like Bouley, a 23-year old Brighton resident who has been training for less than six months, there is another option: do it for charity.

This year, teams representing 24 Boston charities will take their marks on the starting line in Hopkinton, Mass. Ten of these teams, including the group from the American Liver Foundation, will compete in the name of science. “I knew I wanted to run for a science or research-related charity,” said Bouley. “The American Liver Foundation accepted my application, so I went with them.”

Twenty years ago, five male runners got their participant numbers from the mayor’s office and together raised $5000 for the American Liver Foundation. The team has grown each year, and today boasts 248 runners that have pledged to raise more than $1 million. To date, marathoners have raised more than $11 million for the charity. “The Boston Marathon is by far the largest fundraising program for the American Liver Foundation nationwide,” said Laura Dempsey, a spokesperson for the foundation.

Each runner must raise at least $3000 to compete in the marathon. Bouley quickly figured out that donations from family and friends, while generous, would not be enough. So he got creative. With the help from pastry-savvy friends and coworkers, Bouley stocked a conference room with baked goods and hoped his colleagues liked dessert enough to help him reach his goal. “Whatever I didn’t sell in the conference room, I put on a cart and walked around with for the rest of the afternoon,” Bouley explained. People bought the treats for the suggested prices, but often threw in a few extra dollars. In the end, the bake sale raked in over $600.

Bouley also set up an office pool, where bidders filled out squares based on when they think he will cross the finish line, right down to the minute. “I don’t think it will raise very much money,” said Bouley, but he is glad that everyone has gotten involved. “I update them with time stats and injury reports, and they bet accordingly,” he joked. “Some guy even made his own square that says ‘Does not finish.’”

But Bouley intends to finish, both because it has always been a personal goal of his, and because he has made physical and personal sacrifices to train for the event. He pushes aside other activities, like skiing and going out with friends, to focus on running. The American Liver Foundation offers its runners a free training program, and they get together on Saturday mornings to run together. They recently completed a 21-mile run along the marathon course, stopping just after Heartbreak Hill, the most notorious leg of the race.

The charity also gives its runners the option of meeting patients with liver disease, which Bouley says is a good source of motivation. “My knees might hurt, but some of these people are dying,” he said solemnly. Dempsey adds that it is a “terrific part of the program, because it gives the runners a face to put with the cause.”

The American Liver Foundation holds a reunion party a few weeks after the race, to congratulate the runners and give them a chance to exchange stories and experiences. But Bouley sums up his own post-marathon plans in one word: “Rest.”

To help Bouley reach his $3,500 goal, visit Andrew Bouley’s Fundraising Page.

Story by Lauren Rugani. Photo by Austin Cho.

Bad news for clean freaks: No matter how many floors swept, bathtubs scrubbed, countertops sprayed and windows washed, you will always miss a spot. No matter how sparkly the outside, there are trillions upon trillions of bacteria living comfortably inside your gut. It may sound like a germaphobe’s nightmare, but scientists say these intestinal tenants pay their rent by protecting us from disease.

Kidney stones, the sometimes-painful, crystal-like accumulations of waste in the kidney, were linked with great confidence last week to at least one gut bacterium. Researchers from Boston University’s Slone Epidemiology Center found that being colonized by Oxalobacter formigenes can reduce the risk of kidney stones by 70%. The link was first considered in 1986, when scientists learned the bacteria removes oxalate from the intestines. Oxalate is a key component of the most common type of kidney stone, so without it, the stones cannot form.

According to Dr. David Kaufman, lead author of the study published in this month’s Journal of the American Society of Nephrology, his group’s research is the most carefully conducted and largest-scale examination to date of the O. formigenes-kidney stone relationship. They analyzed the stool of participants with and without kidney stones for signs of the bacteria. The data revealed 17% of the 247 participants with kidney stones were colonized with O. formigenes compared to 38% of the 259 participants without stones.

If not having the bacteria increases your risk for kidney stones, then to prevent them, maybe you could just take a dose of O. formigenes? Enter the emerging field of probiotics, medicine that gives life to bacteria rather than taking it away. Scientists have already begun to experiment with bacteria-coated capsules, although the trials are still too small to be sure of their success. Years may pass before a probiotic kidney stone solution exists due to the pace of long-term clinical trials as well as unanswered questions as to how and when the bacteria colonize the gut, and whether its population remains constant or changes over time.

“That a bacterium can be potentially relevant for protection against a medical problem - that is not trivial,” says Dr. Kaufman. “Many other relationships need to be looked at between bacteria and disease, good and bad. The results will give further impetus to do these studies.”

Just something to think about next time you reach for the Purell.

The study: Kaufman, D.W., Kelly, J.P., Curhan, G.C., Anderson, T.E., Dretler, S.P., Preminger, G.M., and D.R. Vave. (2008). Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones. J. Am. Soc. Nephrol. (doi: 10.1681/ASN.200710101058)

Photo of kidney stone on X-ray from iStockPhoto.

If you’re lucky enough to see a comet whiz through the night sky, you’re likely to notice the trail of rock, dust and ice it leaves behind. But did you know bigger solar bodies, including Jupiter, the Earth’s moon and Mercury, also leave evidence of their movements through space?

To understand how these tails fit into the clockwork of our galaxy, scientists at Boston University’s Center for Space Physics have spent the past decade developing instruments and techniques to observe the planet closest to our sun.

Earlier this month the group published photographs of Mercury’s tail, already known to extend up to 25,000 miles off its surface, going as far as 1.5 million miles. According to the press release, that is 1,500 times the radius of the planet.

The figure above [credit: The Center for Space Physics, Boston University] shows Mercury’s tail captured by a wide-angle telescope. Since Mercury is close to the Sun, sodium atoms that escape the surface are pushed away from the planet by the pressure of light and form the tail. The bottom right corner of the figure is highlighting the regions of Mercury where the sodium comes from, mostly the high latitudes. Dr. Baumgardner, one of the paper’s co-authors, says there are probably other atoms in the tail, but because of their spectral lines they are not as easy to detect.

Because Mercury is never very far from the sun, getting a glimpse of the tail from Earth can be difficult. The 1.5 million mile tail has only been observed a few times since its initial discovery, raising the question of whether it is permanent or a snapshot of many possible lengths.

The answer lies in the mechanism behind what creates the sodium dust. It’s still unknown but competing theories say they are either the result of solar winds, micrometeorites or magnetic fields. Once Messenger, the NASA spacecraft sent to study Mercury, goes into orbit around the planet in 2011, there may be some definitive evidence.

Dr. Baumgardner and his colleagues are part of the International Mercury Watch, a collaboration of scientists in France, Italy, Japan and the United States who coordinate their efforts to cover as much of Mercury as possible. For more information on their work to reveal the mysteries of the night sky, check out Boston University’s Imaging Science Website.

Paper Source:Baumgardner, J., Wilson, J. and M. Mendillo. (2008) Imaging the sources and full extent of the sodium tail of the planet Mercury. Geophysical Research Letters. v. 35 (doi: 10.1029/2007GL032337)

– Photo by The Center for Space Physics, Boston University

Those in the artificial nose business dream of the day their products equal or surpass the olfactory repertoire of the real thing. For now, the human nose comes pre-packaged with a wider selection and faster detection of smells than any electronic device.

Neuroscientists at Tufts University School of Medicine who double as officers for the North Andover-based company CogniScent Inc may soon close this gap. Their research, published on PLOS Biology last week, found two new roles for single-stranded DNA: One as the latest in odor-sensing technology and the other as a possible small molecule receptor.

The detector works after attaching a florescent marker (Cy-3) to the end of a DNA strand and drying it onto a solid surface. From there it glows after exposures to various odor molecules. Some used in the experiments were methanol, DNT (previously undetectable by any other device) and propionic acid, all toxic in some way. In the long run this technology will benefit safety inspectors and law enforcement, the most likely customers for electronic noses.

The mechanism for making DNA glow is still not well understood. The researchers guess it is brought on by changes the three-dimension shape caused by binding to the correct odor molecule. It’s been known for a long time that DNA binds molecules in the nucleus, but this research raises the possibility for other receptor-roles in the cell.

From a business perspective DNA is cost-cutters dream. It is cheap and easy to replicate, once you have a DNA sequence that detects the odor you want, simply run it through an assay for more. This also has the potential for mass-production if they can make the detection devices small enough.

Just one cautionary note, while peer-reviewed this research has yet to be replicated and more reporting needs to be done on possible limitations before it is certain this is a true step forward for the field.

The paper:

White J, Truesdell K, Williams LB, AtKisson MS, Kauer JS (2008) Solid-state, dye-labeled DNA detects volatile compounds in the vapor phase. PLoS Biol 6(1): e9. doi:10.1371/journal.pbio.0060009

For more information, check out “DNA-based Artificial Nose” in Technology Review.

A paradigm shift in the way we think about autism has begun. Still considered by many as a one-size-fits all diagnosis, a recent explosion of news coverage over a small study linking autism and genetics could mean the media and scientists are predicting something big.Although some autistic cases have a known genetic cause, in coming years, many more points on the autism spectrum may be identified with specific genetic abnormalities. People displaying autistic symptoms now could learn those symptoms are the handiwork of genetic mutations, possibly ones affecting the development of synaptic communication in the brain. It would give many families a much-appreciated diagnosis as well as hope for potential treatments and individualized care.

A hint of what’s to come was revealed late December in a New York Times article by Amy Harmon titled ‘Hello 16p11.2. Are you just like me?‘ In her reporting, Harmon followed families of children with a genetic diagnosis looking for others in the same situation. After searching over the Internet, the parents were happy to meet others to share their concerns and experience of raising a child with special needs.

In the article, one family explained the difficulty of getting a diagnosis for their son without genetics:

“Desperate for a diagnosis, this February, the Dopps took Jackson to a psychiatrist. He told them Jackson was autistic.”

“‘Autism covers so much,’ Mr. Dopp, a manager at American Express, complained to his wife. ‘It doesn’t mean anything.’ And Jackson did not quite seem like the other autistic children they knew.”

It was a geneticist who ultimately helped the family find an answer, which means, many more families may be receiving a false diagnosis of autism and trusting their doctor or lacking the resources or funds, do not go further in their investigations.

Further evidence big news is coming is the coverage last week by The Boston Globe, New York Times, Chicago Tribune and Wall Street Journal of 16p11.2, the star of Harmon’s article, when genetic scanning of autistic patients revealed 1 percent of all autism cases are the result of the loss of 25 genes on chromosome 16. What is most startling about this finding is the loss seems to happen spontaneously, possibly from the rearranging of maternal and paternal genes to form their child’s genome.

Thousands of autistic patients were scanned by two groups of researchers, one sponsored by the Autism Consortium in Boston and the other in Chicago, but because of technological limits, they could only search for a few specific sections of the genome. As techniques improve researchers hope to find more hotspots like the one chromosome 16, so this is just the beginning. Scientists also want to understand why these deletions occur what these 25 genes do.

As always, this is an exciting time for science.

The studies:

Association between Microdeletion and Microduplication at 16p11.2 and AutismWeiss LA, Shen Y, Korn JM, Arking DE, Miller DT, Fossdal R, Saemundsen E, Stefansson H, FerreiraNew England Journal of Medicine. Jan. 9, 2008 (DOI: 10.1056/NEJMoa075974)

Recurrent 16p11.2 microdeletions in autism (pdf) Kumar, RA, Mohamed, SK, Sudi, J, Conrad, DF, Brune, C, Badner, JA, Gilliam, C, Nowak, NJ, Cook, EH, Dobyns, WB, Susan L. Christian Human Molecular Genetics. Dec. 21, 2007 (HMG advanced access)