Science Metropolis – Boston

The Boston Globe failed its readers last Tuesday. A new strain of the drug-resistant MRSA bacteria may be spreading through gay male populations in San Francisco and Boston, and the city’s leading newspaper prints a brief from the wire service Reuters. Days later, there has yet to be follow-up.

The Annals of Internal Medicine took extra care to release the finding a month ahead of print. Yes, it drew some media to the less-prominent journal, but it this case, it was more than a publicity stunt, it deserved the coverage. A short article in the New York Times on the second-to-last page of the Science section remained on the paper’s Web site most e-mailed for two days. I sent it to the friends I cared about who are at risk, because although this may not be a problem that will suddenly reverse its path, at least it will encourage people to seek help if they recognize symptoms.

In addition to the NYT, the new MRSA strain, similar to the previously recorded outbreaks in hospitals but potentially more virulent, was given a full coverage at the The Wall Street Journal, NPR, The Philadelphia Inquirer and even the BBC, but not the Globe. This is a shame since Fenway Community Health, Boston’s best known center for gay and lesbian health, was one of the institutions coming across infected patients.

The paper’s authors said they have been seeing MRSA in AIDS patients since 2004. According to the reports, it is now at the point where 1 out of 588 men in the Castro district of San Francisco, one of the largest gay communities may be carriers. Similar to herpes or HPV it spreads skin-to-skin and cannot be prevented by wearing condoms. The strain is resistant to all commonly-used antibiotics and can be deadly.

And here’s why The Boston Globe failed all it’s readers, not just gay men on Tuesday: Although drug-resistant MRSA may be gaining a reputation as a sexually-transmitted-disease in the gay community, because of the way it spreads, it will not stay in this niche. Unless treatments are developed, this has the potential to be a bigger health problem for the residents of Boston and the United States. We should all be disappointed.

The Study: Emergence of multidrug-resistant, community-associated, methicillin-resistant Staphlococcus aureus clone USA300 in men who have sex with men. Annals of Internal Medicine. v. 148, no. 4, 2/19/08

When attending a lecture titled: “Does spatial position in the nucleus influence transcription,” one doesn’t expect a crowd. But when such a topic is discussed at Massachusetts General Hospital’s Simches Research Building, the people will come.As med students and hospital employees finished poured in, Dr. Wendy Bickmore, a senior scientist at the Medical Research Council’s Human Genetics Unit in the UK opened her PowerPoint file and revealed the following:

All genes are not created equal, at least not according to the nucleus. There is a bit of favoritism going on in all our cells, and it concerns gene expression. Research in the past five years has found chromosomes containing the instructions for the most important or abundant proteins (11, 17, 18) are more likely to be found in the center of the nucleus. Chromosomes with less important, or genes with environmental-specific roles (4, 13, 16) are tethered to the nuclear periphery where enzymes keep them silent.

How chromosomes become positioned in the nucleus is not well understood. Although those closer to the center are thought to be pushed there by cell transport molecules, it does not seem to be the case for the silenced periphery chromosomes. Since all chromosomes go to the periphery during mitosis, it may be as daughter cells are forming, some just remain on the sidelines.

Those that make it to the center of the nucleus meet clusters of RNA polymerase, the enzyme responsible for making RNA from DNA. Contrary to what was originally thought, the proteins in charge of gene expression aren’t everywhere in the nucleus, they are localized in the center, explaining why the area is so gene rich.

Experiments by Dr. Bickmore have confirmed many of these relationships, but she is quick to point out this does not dictate expression of all genes for all chromosomes. These findings are most applicable for genes requiring high amounts of regulation such as the well-conserved HOX on chromosome 4, which plays a major role in development. Chromosome 4 also contains housekeeping genes, which despite their location on the periphery, are still active.

Although most of the data fits with Dr. Bickmore’s model, there are exceptions. Cell biologists recently found gene expression actually increases at the periphery around nuclear pores, holes in the nucleus allowing transport of key molecules. Why this happens is not yet understood. Also, even if a chromosome is in the center, surrounded by RNA-making machinery, it is trancription factors that determine gene production before anything else.

Can this research be useful in medicine? Dr. Brickmore says she has no idea how, but it is a thought. She is more interested in finding out if mislocated chromosomes can cause human disease.

She predicts this research may also add to our understanding of X-inactivation, the random silencing of either the maternal or paternal X chromosome in females, especially if it shares similar mechanisms with peripheral silencing.

With many unanswered questions and experiments to conduct, this work promises to at least provide the nucleus with a bit of personality.

After being hired as an after-school science teacher, I wasn’t sure what to expect as I traveled to different elementary and middle schools across Massachusetts. Today, I met my first group.The nine middle-schoolers looked bored as they wait in the cafeteria. They had been in classes since the early morning and it was now late afternoon and there they were, still in school. Heads finally come to rest on comfortable spots of fluffy jackets when I, with a big box and a suitcase on wheels, beckoned them into the cooking room. It was time for science.

Earlier in the day, I was pacing in my room, experiencing a bout of performance anxiety. For the first time, I would be alone. I would not be an assistant or an observer, I would be the teacher, responsible for keeping an entire class of Watertown 11-year-olds well-behaved, entertained and educated for an hour and a half. On top of that, my first lesson was the about cannons, which involved making small working mini-projectiles. Oh, and thanks to Monday’s storm a tree fell on my car the night before so I needed to hitch a ride, but that’s another story.

Before being able to explain cannons I first needed to make sure I understood fire. It’s a good quest to ask yourself, what is fire? If you’re Wikipedia, you’d respond “A rapid oxidation process that creates light, heat, and smoke, and varies in intensity.” If you’re The American Heritage Dictionary you’d say, “A rapid, persistent chemical change that releases heat and light and is accompanied by flame.” Luckily, neither are standing in front of the classroom. For a child, or an adult for that matter, phrases such as “rapid oxidation process” or “accompanied by flame” are nonsensical and don’t actually convey what fire is. The Straight Dope (My new favorite Web site) does an excellent job of reducing the jargon and coming up with a definition that comes close to perfect, but “body of incandescent gas” is still difficult to explain to an 11-year-old. Time was running out and I looked at the notes in my curriculum guide. Discuss oxidation and combustion it told me.

Rather than start with the circular definitions of fire I ended up asking the class what heat was. “It’s temperature,” replied one girl.

“That’s how we measure heat,” I replied. “But when we put our hand on this table or a light bulb, what makes one hot and one not?”

When the kids put on their ‘I don’t know’ faces, I explained how we sense the movement of molecules. The table molecules are not moving so fast, so we feel cold, while the light bulb molecules are moving fast so we feel heat and see light. I then asked them when they see fire. are they looking at a solid, liquid, gas, energy or something else? Three hands shot up and said energy. Wrong. We see fire because mostly gas molecules are moving just like in the light bulb, except they are very fast.

Thermodynamics is anything but easy, but I felt better about this discussion than simply throwing around empty words. By the time they were ready to build their cannons I was able to quiz them about what makes something hot and the three things necessary to build a fire (oxygen, heat and fuel) in front of the after-school supervisor. “We actually learned stuff,” said one student.

So for any teacher stuck with one day to learn how to explain climate change, photosynthesis or fire to an elementary or middle-school classroom I sympathize. There is not a lot of information easily accessible to students, and without a strong background it science, it can be nearly impossible not to get caught in the jargon. Science education would be easier for everyone if we taught even the basics conceptually rather than based on vocabulary.

It is everyone’s right to learn science, and it would be a shame for a student’s interest to end at oxidation process.

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) 

Sunday, January 13, 2008

Last Friday, I promised myself a one-day break from my news obsession. For my mental health I decreed a complete ban on newspapers, non-fiction books, magazines and especially the Internet. But after a craving for ice cream led me to a late-night trip to the local Shaw’s, I couldn’t resist the temptation of the last remaining copy of The Boston Globe.Oh the things I might have missed! The identification of all the proteins necessary for an HIV infection, a group of renegade stem-cell scientists with a challenge for President Bush, or most importantly, hidden in the Arts & Entertainment section, a short piece on Rebecca Watson, a local finalist of the Public Radio Talent Quest.

Ms. Watson, a Brookline resident (who loves her local bagel shop), is already known for co-hosting the podcast “The Skeptics’ Guide to the Universe” and as a blogger with a dedicated following at skepchick.org. In her posts she takes on everything from scientology and psychics to the separation of church and state. A self-identified skeptic, atheist and feminist, she is a champion against pseudoscience who is refreshingly direct about her beliefs.

Perhaps it is her humor and personality that earned her finalist status in the public radio competition. According to Clea Simon’s Boston Globe article, she was not one of the judge’s picks, but propelled through the competition American-Idol style, because voters like me and you liked her.

Without any supporting evidence, I would guess Ms. Watson’s success is part of a larger trend of people, specifically youth and people in higher education, disenchanted with beliefs they feel are irrational or illogical. After listening to a demo of her radio show (Round 4), she presents herself as someone who will question what she is told. When a Boston tour guide tells her blue spirit orbs sometimes appear in pictures taken of Capital Hill, she tries to find a legitimate explanation. Can’t get more anti-authority than that.

Is America ready for an openly-atheist host of a science-based National Public Radio show? We’ll have to wait a few more months before the final decision. Until then, it’s nice to learn of a person who is brave enough to stand by their non-beliefs and share their curiosity with others of the world as it is.

Just when you thought you had a handle on the Boston winter comes another seasonal perk. An unusual outbreak of potholes? Nope. A lack of government aid for people in need of heat? Closer. A 48-hour virus subjecting its host to hours of vomiting and diarrhea? Bingo!It turns out Boston may be a favorite vacation spot for an emergent form of Norovirus, a non-enveloped. single-stranded RNA virus with a history of making cruise passengers miserable. Between 2006 and 2007 the city saw 18 outbreaks, and staff members of two local hospitals have begun the count for 2008.

On a national scale, the bug is nothing new. The Centers for Disease Control reported 348 outbreaks between 1996 and 2000 with the majority of the sources being foodbourne. The concern over Boston’s outbreaks, as well as those seen in the UK, North Carolina, Wisconsin and New York is a nearly 800% increase people infected.

When the Boston Public Health Comission first reported an odd surge in holiday ER visits related to abdominal problems last January, (3,700 visits in six weeks), they knew it was norovirus but couldn’t explain the high numbers of patients.

Two months later, in March 2007, Stephen Smith at the Boston Globe reported on the link between the illnesses and two emerging strains of Norovirus. After analysis, more than 3/4 of those infected were found to have anitbodies to either of the new strains.

As we enter 2008, there is reason for hospitals, restaurants and universities to be concerned. (Boston University’s Director of Student Health Services has already sent an advisory). Not everyone infected by Norovirus shows symptoms, and those who do may be contangious for up to two weeks after aquiring the virus (but more likely a few days).

To avoid turning your apartment building or workplace into a public health hotspot, experts say to wash your hands. That’s it. Or more specifically before and after eating and always after using the bathroom.

So good luck surviving the season, with another snowstorm heading this way, it’s just begun.

How did eggs evolve? What would a hot or cold Earth look like? How do you take an artistic photograph of the hindparts of a rhinoceros?

The job sounded perfect. Great pay to share an interest in science with elementary school students eager for a lecture on DNA. With a few clicks, I rearranged my resumè and tried my luck.A few days later, I’m sitting in a Dunkin’ Donuts being interviewed by a young man holding an animal cell model as wide as a bathroom sink. This is what I would be making with the students he said between sips of coffee.

Fast forward to this week. I’m in training. My new boss spent two full days showing the new hires how to instruct a classroom of eight-year-olds to build everything from tornados, parallel circuits and cannons. This is my dream job, I thought, I can pay my bills and plaster my room with life-size replicas of genetic material.

The only downside is a few dozen Massachusetts second-graders will soon know me by the name of Mr. Caputo. It may not seem like a big deal, but for a 22-year-old with shaggy hair right out of college, it is an unexpected push into adulthood.

But don’t worry – this post won’t be a novella on my newly acquired quarter-life crisis, instead I’m going to explain why I’m gracefully accepting my new identity as Mr. Caputo, science teacher.

In mid-October, The Boston Globe published an editorial by Brandeis University professor Michael Rosbash, titled Why Teaching Science is Crucial. In his opinion, universities and high schools are not preparing a public able to understand science enough to see something like global warming as a threat because they are not providing enough science classes.

“The general point is that understanding science as well as our shrinking and increasingly interdependent planet often requires abandoning intuition, personal experience, and received wisdom. These can only be replaced by education.”

His opinion is nothing new, and neither is the debate he is contributing too. We have become an unscientific nation and there are many things to blame.

Scientists and educators are upset, but their demand for “Public Understanding of Science” is oddly vague. It seems to represent some undefined standardized knowledge base, as researchers often gauge it with surveys of basic science questions.

Rosbash doesn’t seem to be expressing himself or the problem clearly, but I think he is onto something by framing the solution as something able to change the way people interpret the world.

Increasing the number of science classes, however, doesn’t seem to be a way to do that. Science classes from elementary to undergraduate may teach science, but they don’t always teach scientific thinking.

Imagine a high school biology lab. The protocol is written up. There is a frog laying on its back in front of you, tools to your right as a teacher tells you to dig in. This isn’t scientific thinking. There is no problem you set out to solve. Everything is known and expected. There are even right answers.

The elementary school science fair, an annual pain for parents and children alike, works the same way. Most parents look online or buy a book laying out some nifty project, put one together, mount the procedure to some cardboard and the child gets a grade.

Scientific thinking requires problems and solutions, not arts and crafts. This is why we need Mr. Caputo. Although the program I work for produces things one may see at a science fair, the problems often begin as we construct or complete the projects.

“This tornado spun faster than my other one?” says one of the kids.

“Why?” I ask. “What did you do differently?”

This seems to be an important question since a group of kids are suddenty rattling their water and glitter filled soda bottles to make the fastest underwater cyclone. They learn a few things here: Answers aren’t always printed in a book, they take observation as well as trial and error. Science is full of different interpretations. And to get the answer (or the fastest tornado) may requires a stretch in imagination.

My job as Mr. Caputo is to help students explore the kinds of thinking possible with science, a skill they can take with them to use throughout their entire education and adult life. It’s something worth sacrificing my once youthful identify for.

In nine days I will be a blogger. To be honest with you, I’m a bit nervous. Like life, blogging doesn’t come with an instruction manual. Unlike life, you can always go back and revise.

The closest thing to an instruction manual I could find was The Open Laboratory: The Best Writing on Science Blogs 2006, edited by experienced blogger Bora Zivkovic. With the help of his readers, he chose 50 of the best posts of the year, and is currently working on the 2007 edition.Here are some of the science blogging ground rules I managed to pick up:

- A blog entry is more or less a stream of organized consciousness. It can take the form of a poem, an academic essay, a letter to the editor, news article or angry e-mail, but with a distinctive voice.

- Lengths vary, from a few paragraphs to a mini-thesis. Readers in a rush probably prefer shorter.

- Miniseries work well, as do weekly installments. If you take this route, make sure to remind readers what you last wrote about.

- Diagrams and pictures work well, and can be fun to look at, but not if they’re techinical.

- New content is key. Find another side to a story, do an investigation of your own, share your findings from a day at the museum, provide us with those middle-of-the-night-need-to-write-this-down-or-I’ll-forget thoughts.

- Personal essays or commentaries can be the best writing in any medium.

- Some bloggers aren’t necessarily the best writers, but their heart is there, which makes them readable.

- Pick up the phone or go on an adventure. Blogging is as much about personal enrichment as it is engaging an audience.
- Specialization helps give focus.

- It’s o.k., and encouraged, to make if funny or sexy, as long as it’s in good taste.

I will do my best to follow these rules over the next few months. I’ll definitely slip up. That’s a promise! But hopefully we can get some gems as well.

I look forward to spending more than a few sleepless nights writing for you.