Thursday, October 26, 2006

Look, Ma, I'm a Citizen-Journalist

I drove to Baltimore after work today to attend the National Association of Science Writers' 2006 meeting, Science in Society. There will be seminars with writing tips, networking lunches, and a "science cabaret" featuring what promises to be Lehrer-esque entertainment.
This year, the 500 science writers attending this meeting are going to be driving right into a story. See, when I was driving into Baltimore I was following the directions on the hotel website. Unfortunately, police had cordoned off one of my turn streets, so I had to drive around in circles for a while until I could figure out how to get to where I needed to go. I happened to notice white smoke emanating from manholes in the vicinity of the roadblock.
It turns out that two manhole covers popped open near one of the busiest intersections in the city, possibly due to a leak in a natural gas main. I'm lucky I got here way past rush hour. Reports here and here say that the Maryland Dept. of the Environment found low levels of natural gas using handheld meters. For an 88 page pdf discussing U.S. Department of Energy-sponsored development of a state-of-the-art natural gas detector, click here.
I'm too tired right now to do any back of the napkin math to figure out how much gas pressure would have to have built up to pop a manhole cover. Any takers?
Anyway, no one in the hotel where I'm staying knows what's going on, but maybe by tomorrow something will be in the news. I guarantee someone at this meeting's going to make a story out of it.


Wednesday, October 25, 2006

My Sincerest Apologies

Devoted "She Blinded Me with Science" reader Ryan kindly pointed out that I didn't mention Mole Day, which happened on October 23rd. Shame on me. Ryan, did you play "Avogadro's Element Hunt"? It's on yesterday's link to the National Chemistry Week site. The mole is a fundamental unit of measurement in chemistry that lets us relate mass (something we can measure in the laboratory) to an amount of atoms or molecules (which we can't). When following chemical recipes, it's important to get the ratios of ingredients (molecules) correct. The "mole concept" is an extremely valuable tool that I use every day.
And now, for something completely different. One of the first things I learned about in Dr. Pearsall's Intermediate Inorganic Chemistry course was zinc phosphide, AKA "mole killer".

Here's how it works:
Zn3P2(s) + 6 HCl(aq) ---> 3 ZnCl2(aq) + 2 PH3(g)

Zinc phosphide reacts with the water and acid in the digestive system, where it breaks down to zinc chloride and phosphine gas. Nice favorable reaction, entropy increases due to gas formation, yadda yadda.

I had scribbled in the margin of my notebook that day and it reads: phosphine, spontaneously flammable in air or moles. I also imagine that a rapidly expanding gas wouldn't be good for the circulatory system, either.
See here for a little more zinc phosphide backstory and information about other rodenticides.

Tuesday, October 24, 2006

Gold is Hot

You might think, file that under "tell me something I don't know", but hear me out.
Yesterday, the American Chemical Society e-mailed me (and presumably all of its members with active e-mail accounts) a list of its "Hot Papers" to commemmorate National Chemistry Week. A quick glance at the hot papers in the journals clearly demonstrates gold's versatility as a catalyst and applications in materials science. If you're wondering why anyone would want to waste perfectly good gold on a chemical reaction, keep in mind that while gold is a rare element, it isn't as rare as a couple of other elements that organic chemists have put to good use, like rhodium. By the way, rhodium is often used to plate white gold jewelry.
a general ref: Org. Biomol. Chem. 2005, 3, 387-391.
See also this Tenderbutton commentary about a recent talk by F. Dean Toste, one of this field's more recognizable young researchers.
As a Jersey girl, I'm proud to note that my high school chemistry teacher helped us remember the symbol for the element gold by imitating a stereotypical mobster. I'll let you figure that one out.
The necklace, by the way, is sold in one of the more famous jewelry stores in St. Barts. The cutout is an accurate shape of the island.


Sunday, October 22, 2006

Taking the Easy Way Out

Yesterday, I presented my thesis research in a poster session that was open to the public. The organizers from Princeton's grad student government encouraged us to pitch our posters to a lay audience. Though we weren't really centrally located enough to attract the spillover crowds from the Princeton-Harvard football game, the locals who showed up were genuinely interested and asked questions. And therein lay the problem. Most of the questions I was asked were way beyond the scope of my research, because everyone was more interested in the potential applications of my work than in the work itself.
Maybe I'm being too hard on myself. It's possible that the crowd was already biased toward the biology end of things if they'd heard about the poster session from a relative or friend in the MolBio or EEB departments, who were vastly overrepresented. However, I copped out when I used 3/4 of my jargon-free abstract to describe a biological/medical problem that I thought more people would find familiar. The real challenge for me would have come up with a different way to explain what I do in the lab day in and day out. How do you explain the merits of synthesis to a lay audience? On the poster, I adapted the diagrams you can find on Phil Baran's or Scott Snyder's websites. Using color, I explained how organic chemists like to think backwards and why, if you need variety, it's good to build toward a couple of main components that you can snap together, as opposed to one long process. But it was too late. They'd read the abstract and wanted to know what I thought about the merits of Lysol sprays. I think I got a couple of sparks of interest when I said that many drugs are made using organic synthesis and I described what process chemistry is. It seemed like some people were under the impression that bioengineered bacteria did much of the grunt work.
This is something that'll probably gnaw at me for quite some time, as I struggle to find a voice as someone whose job it is to express why many different areas of science are important and relevant.


Monday, October 09, 2006

Knowing when to fold 'em

Science news reports that a team based at U.Penn. School of Medicine has found some common ground between Lou Gehrig's disease and a specific kind of dementia. Their results have pinpointed a known protein, TDP-43, as a culprit for the disease, and their work may instigate a reevaluation about how these diseases are studied, in addition to highlighting a potential drug target. TDP-43 is a major player in the signature "clumps" that develop in different locations of the brain during these neurodegenerative illnesses.
Background info: Clumps in brain tissue are generally not good. The place where clumps end up seems to determine which disease will affect a patient. Frontotemporal lobar degeneration is the #2 cause of dementia after Alzheimer's in people under 65. In that case, the clumps hang out in the part of the brain that controls good judgement and good behavior. With Lou Gehrig's disease (aka amyotrophic lateral sclerosis), the problem might be closer to the section controlling motions.
The ref:Science 2006, 314, 130-133.
I guess hindsight must be 20/20 for this research team, because in the past doctors have sometimes seen patients with Lou Gehrig's disease develop this type of dementia, and vice-versa.

Again: The important take-home message is that the final folded state of proteins in the brain is crucial. Proteins usually start out as a chain of amino acids and eventually fold up into an orderly structure. If a protein doesn't fold correctly, chances are it's not going to function correctly, either. This is a theme that happens over and over again, in Alzheimer's, mad cow disease, you name it. What comes to mind for me are all those origami fortune-tellers and paper footballs I folded as a kid. You needed to fold it just right to get a good game of cafeteria table football started. Scientists know very little about how to tell at-a-glance what a protein's folded-up shape will look like. That knowledge would be a major step forward in treating these diseases, and there are several different approaches out there researchers are taking to figure it out.
Off the top of my head:
-You've got the camp that designs proteins from scratch to study what specifically in the amino acid sequence calls out for a given folding pattern.
-You've also got the researchers using computers to attack the question.
-See this recent post at In the Pipeline about a very ambitious Japanese research project that seems to be relying on building a database of structures to search for pattern recognition in the future.
I'll leave you with a factoid that combines Lou Gehrig AND science from my brother, who knows far more about baseball than I ever will (and is probably the only kid who grew up in NJ that is happy the Yankees lost).
The Iron Horse was an engineering major at Columbia.


Wednesday, October 04, 2006

Nobel Roundup

The blogosphere lit up this week with rampant Nobel prize-related speculation and oddsmaking. So now that the big three science Nobels have been announced (sorry, economists), let me throw in my two cents.
It looks like RNA-related research projects are the leggings of the science community this fall. (I'll qualify that remark by saying that I have much more hope for the staying power of RNA research). The Nobels in Medicine and Chemistry both involve RNA in some way. You've almost certainly heard of DNA. I'll go out on a limb with an analogy here and liken RNA to DNA's free-spirited daughter. DNA usually is stably linked to another strand of its own kind, and it's always there when RNA is made. RNA is a more transient entity. It moves out of DNA's house in the cell's nucleus pretty quickly and promptly discloses all the family secrets. RNA has also been known to dabble in some funky activites, things like picking up habits from enzymes and dabbling in a little contortion.

The Chemistry prize was awarded for molecular-level snapshots of the "birth" of RNA, a process called transcription. The Medicine Prize was awarded for the discovery of RNA interference, an invaluable method for scientists trying to uncover a gene's function. Much of the media is framing both of the prizes as important for therapeutic applications, but we're still very far away from a real, live drug.

By the way, It seems like the Nobel committee is sweet on structural biology lately. The 2003 Nobel was awarded in part to another X-ray crystallographer. I blogged a little about X-ray crystallography here.

I was proud of myself this year, because I'm no physicist and it's the first time I can remember not having to read up on the science behind the prize. The Physics prize was awarded for work in cosmic microwave background radiation (CMB). Briefly, the CMB is a sort of residual signature of the Big Bang, and studying it has lent further support to the Big Bang theory and shed some more light (no pun intended) into the origins of the universe. I had read about CMB in a book, The Light at the Edge of the Universe, by my former science writing prof, Mike Lemonick. Looks like he has a little dirt on the Physics prize here.

In case you're wondering why I chose the title "Nobel Roundup", it's because I found this little gem while searching for a layperson-level RNA link. Giddyup!