New Blog Location

I've decided to move my blog and give it a new look. The design isn't yet complete, but it's about time I just jump ship and redirect readers. My blog can now be seen at:

www.chrisbrow.net

Little victories in the snow

What you see below is a picture of a TimTam. For those who don't know, a TimTam is a little treat from Australia. It's a chocolate covered wafer-like cookie, and there's a traditional way you're supposed to eat one. First, you nibble off the chocolate on opposite corners. Then, you dunk it in your coffee and use it like a straw sucking coffee up into the wafer. Once the coffee hits the wafer, the entire TimTam begins to dissolve from the inside-out. You have to stuff the whole thing in your mouth immediately. It's melt-in-your-mouth goodness! (Yes, I know, the living room in the background is an absolute mess. Please ignore that.)


These things are not easy to come by. Aussie members of our department bring them as treats for lab meetings, and more often than not, the TimTams arrived in care packages from the land down under. Well, last month I found them at a fabric store in town. Random, I know, but what a find! I had one left over, and today was its day. So why am I talking about TimTams in terms of a "little victory in the snow"? Here's why:


Yup, Portland has just been hit by what the weather men are calling the worst storm in 5 to 10 years. We normally don't get much snow here, but the past week or so has been a weather event for the record books. There was an ice storm that shut schools and businesses down for several days last week. Half a block from our house we did a 180 in my car just trying to get off our little street on Tuesday. My PhD qualifier exams were even postponed a few days. Yesterday morning I was supposed to play a disc golf tournament in Estacada. I made it half a block up the street (in the other, flatter direction this time) before my car got stuck on the ice. There was just no safe way to make it to the tournament. Turns out that was a good thing because throughout the day yesterday, Mother Nature dumped anywhere from 6 inches, to over a foot of snow in town. That's on top of ice already up to 3 inches thick on the roads. We live in the hills, and got the worst of it.

In leiu of disc golf, Ryan and I walked to a neighborhood cafe for breakfast. I think I was wearing 5 layers of clothing because the wind chill was so cold. On the walk home, we were crossing a street. It was icy, and I went down about 5 feet from the curb. Ryan was a few steps ahead of me and didn't notice that I had fallen until he turned around a few steps later and saw me sitting on my butt in the road. I landed hard on my hip and my knee. My knee is pretty sore today, so in keeping score, that's Mother Nature: 1, Chris: 0.

But today, I evened the score. My knee hurts, it's bitter cold and windy, and there's a half inch of ice covering every surface out there (that's a picture of me holding a sheet of ice above). But I managed to get up, layer up, walk to the village, buy a nice hot coffee, bring it back to the house, and enjoy it with a Tim Tam, all without taking another digger. Mother nature nature: 1, Chris: 1. It may look like a tie, but I call that a victory.

Random mismoshed updates

Economic crisis hits home

Got a letter in the mail yesterday today from Citibank regarding my credit card. It was a "notice of change in terms and right to opt out." Basically put, they were informing me that as of October 1, 2008 (and yes, I did just get this notice yesterday, go figure) they were increasing my APR on purchases to 16.99% for my current 8.99%. I got worried. Had I missed a payment? Had my identity been stolen? I called to ask the reason for the change. The lady on the phone assured me that my account was in perfect standing, and I had done nothing to incur the change. It was simply do to "business reasons" (a.k.a. they're running out of loot due to bad investments and are trying to recoup losses by screwing their customers). I've been a cardholder since 2003, and have never missed a payment and this is how they show their appreciation for my business? No thank you. I chose to "opt out" which basically means that I'll hum along at my 8.99% APR until my card expires in 2011, at which point my card will effectively be canceled. I won't be able to use the card to make any purchases, but my original APR will be locked in and I can continue to make payments at that rate. Obnoxious. Didn't Citigroup just get $20 billion in bailout money? What the heck are they doing with that money that the still need to jack my rates for absolutely no reason? Grr!

I sold a photograph!

Ryan has 7 of his photographs on display at the Laurelthirst. He surprised my by putting two of my pinhole photos in the show. I found out last week that one of them sold! I've never had my work on display, and certainly didn't expect to have anything sell. It was a pretty good feeling. Here's the pic that sold. It's a 20 min pinhole exposure at Ecola State Park in Oregon.

Politics

It's been quite a while since I've left any political post here. That's partially because I'm busier than ever and I usually give these posts a lot of thought and include references to back up facts, etc. I do have a little list going of topics I've been meaning to write about. But for now I'll simply say this. I'm 29 years old, and have only been around to vote in 3 presidential elections. For the first time, and with much hope and optimism, I can say that I voted for the winning ticket. Now when I travel overseas, I won't have to automatically either a) be an an apologist for American foreign policy, or b) straight out pretend I'm from Canada. Living in Switzerland in 2003 in the the beginning stages of a unilateral "-ism" war was a very interesting experience. Everywhere I went there was anti-Bush graffiti and signs and protests. Most Europeans I encountered were sophisticated enough to distinguish the anti-Bush stance from an anti-American one, but it still gave me an unsettling feeling traveling around as an American. I finally have hope that the next time I'm abroad, that feeling won't be there.

Would you like a bag for your tampons?

Ok, now that I've made all male readers squeamish, I'm going to tell a story. I was at the grocery store this morning buying, yes, tampons. There was only one cashier, a middle-aged rough-looking guy. I got in line, and immediately behind me two firemen got in line with their cart full of groceries for the firehouse. Embarrassing enough already, sure. I put the box on the belt, no other purchases, and the cashier scanned it. "Wow," he exclaimed, "did you see the price on those?"...he motioned to the LED screen. It read, "$1.20." Now, the sign on the shelf did say "$4.49" but it's not like I care. This isn't exactly the type of item you shop around for the best price on. "Um, that's um, pretty good," I say. "They must be on final clearance or something, you lucked out!" he exclaims. "Um, yea, I guess so," I reply. Now really, do we have to stand here having this conversation on what a great deal I'm getting on my tampons?...the whole time with these two firemen unloading their cart on the belt right next to me? After I handed him some cash and he handed me a receipt, he finished by asking, "would you like a bag for those?" No mister cashier, just duct tape the box of tampons to my forehead with the receipt attached so I can run into the parking lot and let everyone else know what a great bargain I just got on tampons!

Elevator Master

I just joined a gym for the winter. This is one of the luxuries that the ARCS scholarship affords me, quite literally. I went there for the first time after work yesterday. All of the cardio equipment is on the 2nd floor in a loft-ish area overlooking the rest of the gym. As I jogged along on the treadmill I watched as 4 girls came up the elevator...and got immediately on stair climbers. ?!?!

Spoke too soon

Yup, I spoke too soon. Got too excited. I must always remember...PCR-SSCP is cursed in the hands of researchers in lab number 7309. Cursed. The image looked great. The overstaining problem appeared to have been solved. I changed the resolution setting, and clicked go for the high resolution image of my gel to be scanned. This is what I got:



Waaay too dark! Not enough contrast to run and decent image analysis and develop electroferrograms. And this happened repeatedly for the next 4 hours. Garbage. As a last ditch effort, I turned the scanner off and repositioned the gel in a different corner of the scanner:

Much lighter background....but my bands were lighter too...disappearing. It had been 5 hours since I unhooked the voltage on the gel, and now the DNA was starting to diffuse through the gel. These faint fuzzy bands are worthless to analyze. I tried restaining to see if I could get the bands any darker. No good. The stain wasn't faded, the bands were just diffusing and fuzzing out. Boo. PCR-SSCP strike 3. This is the closest I've come to getting actual results. The bands I see confirm my hypothesis, so I know I'll be happy with the result and that it fits in nicely with the rest of my data. But this is the one last crowning experiment that I'm trying to finish so that I can include it in a paper. And I really want to get the paper submitted before I start taking my prequalifying exams this fall. To top it off, I'm just about out of the DNA I was using in these experiments. That means I have to go back to square one in order to repeat the SSCP. It'll take at least a week. Grr. That's the last time I celebrate until the data is actually in hand.

Success!

Finally!!! This image looks better to me right now than da Vinci's Mona Lisa, or Van Gogh's Starry Night. It's a picture of a PCR-SSCP polyacrylamide gel that I ran this week. This is my third attempt at PCR-SSCP, and if this didn't work out, I was going to have an aneurysm. It takes days to prepare everything needed for this experiment, extracting the DNA, running the PCR, converting to single-stranded DNA, pouring the gel, running the DNA on the gel, and staining the gel. It's the last part that has been hindering me for a few weeks now. It should be the easy part, but it hasn't been. My entire gel was turning black, not just the bands of DNA. No one in the department could figure it out. I stumped tech support from the stain's maker. My advisor said to me, "Chris, I encourage you to come up with creative solutions, not creative problems." Sooooo frustrating. Turns out it's alot of little things....like that the stain that is designed to bind "exclusively" to DNA happens to also bind to the type of plastic we put the gels on in order to scan them. Once bound, it fluoresces...and appears black in the image. If the gel isn't completely washed of the stain before going on the plastic, poof! A big black mess. Keeping the stain off the plastic just about takes more effort than the entire PCR-SSCP process before that. Lots of other little things factor in too. The staining process is definitely much more art than science. None of the manufacturer's suggested staining times or concentrations came even close to working. This here is just the prelim, 2 minute scan image. A much more detailed and resolved 30 minute scan is going on right now. This has been such a headache. I think I deserve a beer! Maybe two.

And we're off!

First thing this morning I awoke to this picture mail from Jerry. I think it's going to be a good day, through and through. The last week or so has been really busy because I've been trying to get some things sorted out in the lab before my birthday trip to Snowater resort in Glacier, WA with Jerry, Brian, Ryan and Bob. Nothing is currently working in the lab the way its supposed to. The Archaeal qPCR primers aren't working with the bioreactor DNA. The new DAPI isn't staining the neucleic acid for some reason. And the primer design software is so primative that I'd be better off just pulling an amoA gene sequence out of my butt than using it to design primers. That, and I'm pretty sure that when I finally check on the PCR-SSCP that I've been running for two days, it will have failed too. I just think the DNA is too degraded. But not even that will put a damper on today. Nope, today is my birthday, and Jerry and Brian will be flying in tonight from San Diego. I could ask for no better present! And tommorrow, we're all off to Glacier! The resort accomodations include no TV, no phone, and no internet. No outside-world distractions, just good friends, good food, and good fun!