The Saga of Snowpocalypse 2010

One of the advantages of being on vacation is getting away from the internet and what is "going on in the world". Luckily, family members read the paper. So while Tom and I were peacefully enjoying our holiday break in Ohio, we were informed that a blizzard was going to hit the East Coast. Just about the time we were to fly to Newark to depart for Israel.

The Interdisciplinary Side of APS

I like going to conferences. I like having results and being an expert on something enough to stand up in front of my peers and tell them about it. I think it is a big, important part of science.

But now the question is, what conference would I go to? As a particle physicist the answer was either APS April Meeting (their big particle/astro/cosmo meeting) or a division meeting - the division of nuclear physics or particles and fields. These conferences are fairly big and have lots of students. There is often support from APS for students to go. Sure, there were other conferences (usually in more exciting places) that had a specific topic, like a specific type of detector technology or type of particle interaction. But those conferences had fewer students and usually only one (or a few) people from a single experiment. The APS meetings had plenty of overlap - a session of double beta decay people each giving the same overview of double beta decay, for instance.

Now March meeting is slightly more appropriate - the HUGE condensed matter meeting has biophysics as well. Am I a biophysicist? Well, sortof. I'd like to present the Cerenkov Light Imaging simulations I am working on. It involves simulations of particle interactions (physics) and it is used for biological measurements. So it sounds like biophysics to me.

Transparent Mice

I'm currently taking a course on "Multi-Modality Molecular Imaging in Living Subjects" which covers MRI, CT, Optical, and PET imaging. The first topic was optical (fluorescence and bioluminescence) imaging which, in a way, is easiest. Certain molecules give off light, either when exposed to specific other molecules or when excited with light. You then look for this light to see where the molecule of interest is. The problem is, tissue isn't transparent to light. Red light gets through the easiest, which can be seen by shining a flashlight through your hand.

Sequelae: Word of the day

The common advice for encountering unknown words is to "look at the context"... well, that doesn't really work in academia, let alone biomedicine:

Among any groups of patients given the same radiation treatment, some show more sever normal-tissue reactions than others, and a small proportion suffer unacceptable late sequelae.

What is sequelae? Well it is apparently bad and can potentially result from radiation treatment. I decided to try my handy new Dorland's Illustrated Medical Dictionary, Twenty-fifth Edition and looked up the word:

sequelae plural of sequela

Had I taken Latin I suppose I could have seen that coming.

sequela any lesion or affection following or caused by an attack of disease.

Only slightly more helpful, I suppose - "any affection"? I went to wikipedia to understand better and got

a pathological condition resulting from a disease, injury, or other trauma.

Ah! Much better! Just in case it isn't clear yet, let me translate. A sequelae is something (usually known as a symptom or bad shit) that occurs because of something medical happening. If I was writing the textbook, (maybe I can volunteer for the 7th edition) the original paragraph could have read:

Among any groups of patients given the same radiation treatment, some show more sever normal-tissue reactions than others, and a small proportion suffer from some bad shit so they refuse treatment .

Back to what I know

So it has been a week. A week of reading papers and textbooks and trying to learn what the different cell lines and genes and tissues are. I've had some success - yesterday I attended the MIPS (Molecular Imaging Program at Stanford) seminar, and I actually understood a few of the things the speaker said. Not much of what he said, but it was a comfort to see I had made some progress.

Enough is enough. My brain is melting and I can't read any more papers and textbooks. At least, I can't occupy 8 hours a day with it. While I feel like I've fought to have my new "research life" look very different from my old one, I can feel myself going back into the same pattern. I need to go back to what is comforting, what I know. Unfortunately, this also is what will piss me off: computers.

Now, the slide already began a few days ago. The Stanford MedWiki (my group has their internal site on it) is done in Confluence. So I set up a personal space to take notes on all of the stuff trying to force its way into my brain (and complained about the lack of plugins). Now I'm spiraling further down. First, I'm upgrading my laptop. Sure, I used to be one of the first to upgrade. Then I realized how much time I was 'wasting' configuring my laptop. It is time for some upgrades, file clean up, and configuration! This will kill what, 2 weeks?

Truly, what I am after is simulation software. I found a medical suite using GEANT4 that I wanted to start playing with. I wanted to try to radiate some stuff and see what happens. My initial plan was to run everything locally, so the simulations would take some time - I could still do some reading while all of this is going on. GAMOS has a binary for Ubuntu 10.04, which is why I'm upgrading.

So I go back to the land of computers. Since I have to wait 1.5 weeks to get my animal training and over a month to get my radiation training, this was more-or-less inevitable. Hopefully bricking my laptop isn't...

Zombie Cancer!

Theory: The original zombie myth came from an old "disease" caused by immortal cancer cells.
Plan: Write a screenplay based on this.

Well, sortof. The HeLa cell line has gotten a lot of publicity lately due to the book that is still on the best-seller shelves. In brief: cervical cancer cells from a biopsy half a century ago are still alive and replicating and are one of the standard human cell lines in biomedical research. "Normal" cells stop replicating after about 50 times since there is always a little bit of DNA lost in the process. There is a bunch of "junk" DNA at the end that is lost so good stuff isn't lost. "Immortal" cells like the HeLa line actually repairs the end of the DNA so it can keep replicating (so do stem cells).

Some people (ok, maybe just one) believe the HeLa cells should be considered its own species, Helacyton gartleri. Whether or not they are, they have contaminated a variety of other cell lines and caused problems in biomedical research. They spread. They are hard to kill. They sound a bit scary... like some sort of disease... but it gets worse.

Drove to work today (Day 2)

Yesterday was my first day "at work". It was quite exciting - I fought with Ubuntu to add a printer (without searching the entire Stanford network first), I did some online training, and then I searched for the women's restroom. That last part was far more traumatizing than you might imagine.

Now I'm on Day 2. I've brought my coffee mug, some posters, and the PDG. While the PDG is far less applicable to my new field, it still is the single most useful book I've ever had. Also, it weighs a ton. So I drove to work today! I more or less filled the back with stuff I wanted to bring in, so it didn't feel like cheating... too much.

Goodbye Carlsbad, NM

I only have a few minutes left of my last shift at WIPP. Did I manage to do everything I ever wanted to do here in Carlsbad?

• Eco Location The last thing I did was stop in a small store in Carlsbad with cute hand-made gifts and very friendly people working there! I'm glad I stopped by.
  
• Swimming in the Pecos I always figured it would just happen one night if I drank too much, but last night was my last chance. I got to chase some geese. The water was warmer than I imagined, and my skin didn't melt off. Overall, a success.
  
• Hobbs, NM Yesterday I drove to Hobbs after my shift to go shopping. I only had about an hour before I thought stores would close, so I had to work fast and didn't end up making it to all of them. But Il Cicerone was awesome - much cheaper than the stores in Italy, but very similar stuff. Also a great Western Wear shop that had some great Ariat shirts on sale.
  
• The Living Desert This small 'zoo' showcases the different ecosystems of the local desert, including some exciting wildlife. Unfortunately it is so small that most of the animals are by themselves, and a bit depressed. I really wanted to rescue the badger - who knew they were so cute? Also: mountain lion. The sign said not to try to pet it, no matter how cute it looked.
  
• Bat Flight I've gone once a summer to see the bats fly. I absolutely love it - not only do you get to see ~300,000 bats leaving the cave, but you can actually hear their wings flapping. And smell them. How often does one get to smell bats?
  
• Roswell I went... I wasn't abducted. Unfortunately we got there after most everything was closed. And my camera battery was completely dead. But I can at least say I've been there!
  
• The Wellhead my favorite New Mexican microbrewery makes delicious beer and a delicious prime rib.
  

I can't really think of anything I missed. While I could have gone shopping in Artesia one last time, hitting up Hobbs was better. I had hoped to go salsa dancing around here... but it seems to not exist. No dancing for me.

So, goodbye, Carlsbad.

Small Spaces hate me

I shouldn't be cramped up in tight spaces. I'm far too clumsy. Now while I can sit still for long periods - say, on airplanes - working in such an environment is a different story. I slam my arms and hands into walls and doors. I find every corner of every shelf (or mounting structure or table or..) by hitting my legs on them. And I am the perfect height: too short to have hazards at eye level, but too tall to miss them completely.

Working in the cleanrooms this week has occasionally felt like a gladiatorial gauntlet. At one point I was maneuvering around the xenon system by our detector. I caught my right side on the unistrut, struggling to duck under a refrigerant line I hit my left side on our pumpout cart, and then as I was angrily leaving I hit my head on a large portable lamp hanging down.

The 'joys' of shared housing

I'm in New Mexico for my final shift on my old experiment. While it is a little awkward, I now get to say "goodbye" to the apparatus itself, and do some of the local things that I always meant to do. I'm sure this will be a more positive experience in the past since I know this is my last trip here.

But there is one thing that a positive attitude can't change: sharing a house with my collaborators. This is much more a problem of the house than the people. People come and go on a weekly basis, so everyone loses track of how old the bread on the counter is. And we collect a large number of cans of shaving cream on the counter.

I find the maintenance and cleanliness standards the worst. While most people are very good about taking care of their dishes, no one bothers to sweep the floor. When there are now small piles of dead cockroaches in the corner, this is a problem. No one has the tools or motivation to fix things around the house, so they just go unfixed. Theoretically the land-owner should deal with these things, but there is no one to continually call them and get them to take care of it.

The room I am sleeping in has no door latch. You know, that thing that keeps the door from randomly opening without a doorknob being turned. This is a new development and actually has a good reason: the latch has been very sticky for a long time. Someone got stuck in the room and had to climb out the window. I don't blame him for taking the latch off. It's much more proactive than the solution some others would have come up with - always going in/out the window.

The microwave is broken. This actually occurred the last time I was here (in June). The power went off and when it came back on the microwave was dead - I searched the internet and couldn't come up with a good way to fix it. I e-mailed the faculty member who pays our rent (I don't have the land-owners' contact info) and some of the post-docs who are here most. I guess the land-owner never did anything. Now, I like microwaved eggs in the morning, so this is a major tragedy for me.

If you are a somewhat reasonable person, you are probably wondering why I don't take care of these things instead of just complain about them. Yeah... you're right. That's what I'll do.

Kid's day talk

Tomorrow is Kid's Day at SLAC.  I have been given the honor - perhaps responsibility is a better term - of giving the opening talk to the 12-16 group.  I wasn't given a lot of guidelines, but I have about 5 minutes to talk about how I became interested in my field of research.  I suppose I'm supposed to excite and inspire these young people and then they get to ask me questions.

What is an AMU?

I've been reading "Radiobiology for the Radiologist" by Eric Hall for the past week or two.  I'm learning a lot from it, but a lot of the cancer terminology is unfamiliar to me.  I'd stop to look everything up, except this book is from the Lane Medical library and I'll need to return it before I leave for WIPP on August 24th.  Since I'm on page 106 of 518, I figure I don't have too much time for backreading.

I decided to simply read the glossary - only a few pages, but should give me almost all of the terminology I need.  Not only are there lots of medical terms, but there is also a lot of physics terms.  I was very confused to see the atomic mass unit (amu) defined as "one sixteenth the mass of a neutral  atom of the most abundant isotope of oxygen, 16O." Oxygen?  The amu I know and love is defined by Carbon!

It's Official!

Today was officially the day the torch was passed.  I talked to Marty and said I found a new lab, Marty talked to Ted, then I talked to Ted.  As of September 7th, I will no longer be part of EXO and will be 100% of the Graves group.