One upper, one downer.

I'll start with the upper. When I got home last night, Ryan had a surprise waiting for me. He dyed a disc for me with a picture of Albert Einstein. How much does that rock?!?! I actually worked in the very same physics department that he worked in at the University of Bern in Switzerland a few years ago. I walked by his statue every day to get to my lab, and by his apartment every day to get to and from my own apartment. I'm so excited about this disc. I had been having a rough few days, and the disc really put a smile on my face.

So as for the downer....I was getting my things together to go to school this morning. I have a class at 10am. I realized that I locked my keys in my car the night before. Ryan has a set, and we had been using his, so I left mine in the glove box. Well, shoot. Ryan was already at work, so I went to the Tri-Met website to figure out the public transportation system. Their system is easy, you enter your starting and ending addresses, and it gives you all you need to know to get from point A to point B. Still, by the time I figured out my travels, it was 9:43 am. Hmm....the next bus leaving from 2 blocks away comes at 9:44 am. Eeek! Grab coat, wallet, directions, and the container with all our laundry quarters (I carry no cash, and the bus won't take a credit card). Run! I barely catch the bus, huffing and puffing.

I took the buss to downtown Portland, walk a few blocks, and catch the Max train into Beaverton. About a third of the way there, and conveniently inside a really long tunnel, the train starts experiencing "technical difficulties." It can't get itself up to full speed. So there we are, crawling at a snail's pace through a tunnel under the zoo. We all have to get off at the underground station, and wait for the next train to come through. Of course, even when it gets there, we immediately catch up to our crippled old train, and have to crawl along behind it until we reach a service turn out for it to pull off the main line.

When I finally reached my stop, I still had to walk a half mile to get to campus. Oh, did I mention it had started to rain? In my mad rush to catch the bus, I hadn't even considered rain, and neglected to bring an umbrella. So I finally arrived in my lab at 11:32 am. Class ends at 11:40, so I missed the whole thing. Oh, ya, and I'm soaking wet too. Yippy!

Oh, and 48 hours and still no response from my advisor about the email I sent her. Perhaps I should have just stayed in bed.

Arghhhh....there be no more rooms!

One of my best friends from college is getting married this August in Cape Vincent, NY. The wedding is in a castle on some small Island in Lake Ontario, just a stone's throw from Canada. The town is tiny. Quaint. Quintessential upstate NY. Ryan and I are flying in for the festivities. Here's the kicker: The tiny little town doesn't exactly have hotels...more like bed and breakfasts. And as far as I can tell from my search so far today, they're all booked. Turns out that Christy and Todd scheduled their wedding for the same weekend that a huge pirate festival descends on little Cape Vincent. It seems the room have all been rented by salty dogs already. I don't know if Christy and Todd knew about the pirates before planning their wedding. It wouldn't entirely surprise me if they picked that weekend for that express purpose. I say they may as well make it a pirate themed wedding. I can SO picture them doing that.

Boat captain: "Todd, do you take Christy to be your wife? Through smooth and rough seas? With scurvy and without?

Todd: Ayeee! Me do!

All the funny aside...I seriously can't find a hotel for under $200 a night within 50 miles. We just might end up camping it. Arghhh..!!!!

Standing up for myself

I've been a pretty disgruntled employee for the past several weeks. There have been caddy, sarcastic, demeaning notes left around the lab by our PI that have really brought lab morale down. In addition, I've been frustrated by something else. Last weekend was one of the first sunny weekends in months. In addition, with Ryan working Sundays, we haven't gotten to do fun outdoors weekend stuff together in quite sometime.

Well, our lab PI has been avoiding people, including students, ever since she started teaching a class this quarter...been too busy. I couldn't find her last Thursday, so I sent her an email:

Hi (PI),
I tried stopping by your office, but must have missed you. Since Ryan works weekends, we haven't had a nice day off together in quite a while. I was thinking that I'd swap tomorrow, Friday, with Sunday so we can spend tomorrow together since he has Fridays off. I hope this is OK. See you Monday.
Cheers, Chris

Well, we had a great day on Friday, and I don't regret swapping it for Sunday. But that night when I got home, this email awaited my in my box:

Chris, graduate school is not a five day a week job, you should be doing whatever it takes to get your research and classwork done, including working on nights and weekends. So, swapping a weekday for a weekend day makes very little sense from my frame of reference, since they are essentially all the same. It always surprises me when I don't see students around on the weekends, because I know what it takes to make it in science.

I don't know what part angered me more. The insinuation that I wasn't in the lab enough, or that she really thinks she knows what it takes to make it in science. Sure, she may have her PhD, but she has a horrible reputation among students. Since starting to work here, she's apparently lost several post-docs and a lab manager, all on not-so-nice terms. In addition, she hasn't graduated a single student yet. And the one graduating with a MS this summer was supposed to be here for a PhD, but decided he couldn't stand to work under this PI anymore. Until this email, I though I had a fairly decent relationship with the PI. I had been extremely disheartened by the nasty notes in the lab, but the complaints in them never really applied to me...they had been more of a downer than personal attacks.

But the email was personal and it struck a nerve. I cried my eyes out. I work my ass off and really don't appreciate the insinuation that I'm not working hard enough. I do work plenty of weekends and I know I'm the best student to come through this lab. I really want my PhD. But at the same time I'm simply not willing to tolerate such a hostile work environment. And hostile is putting it nicely. I've wanted to talk to the PI about the lab work environment for several weeks, but like I said, the PI has been too busy for students and has canceled all our meeting so far this month.

Today I cracked. I'm here in the lab...yes, on a Sunday...and I reread the email. Then I looked through my lab notebook to account for all my weekend time in the lab. Then I wrote and email to the PI laying out my case and defending myself. I'm not good at that. I've very rarely had to do it before. I'm a hard worker and none of my advisers or bosses have ever questioned how much time I put in before. Additionally, I've been blessed with amazing advisers and bosses until now. They were professional, were amazing mentors, and showed appreciation for work well done. Anyway, I wrote an email, and after an hour of hesitation, I finally sent it:

Hi (PI), just so we're on the same page here, I thought I'd try clarify somethings.

When I said that I would swap Friday for Sunday, it was not to say that I'd "still" be working a 5-day-week...it was to emphasize that i wasn't going to be working a 4-day one. Going back through my own lab notebook shows me that I've actually been in the lab running experiments 10 of the last 16 weekends. And that doesn't count the times when I've come in to just to analyze data, do homework, or do other work. I reserve weekends for doing chores like the dishes, for example. And I even came in one recent Sunday for the sole purpose of assembling the shelves in the new deli case, a chore I doubt any one else would set to unless asked.

I do realize that it takes a lot of time and effort to be a successful doctorate student. I'm not a slacker, and all of my old advisers and bosses will attest to that. But that being said, there are things I will not do, and will not sacrifice for graduate school, or anything else for that matter. Those things include my physical, and emotional well-being, and meaningful relationships with family and friends. Experience has taught me, sometimes in harsh ways, that life is too short and too precious to squander. The time we have with loved ones today cannot be banked until tomorrow. There are few people in this world upon whose death beds would claim their biggest regret to be not having spent enough time at work. I work to live, and not the other way around. And I do not believe that mentality, in any way, diminishes the quality of my work, or my enthusiasm regarding the science. I am a committed student, and put 100% into my work. But I am also an adult, and owe it to myself to live as I know is reasonable and right.

I hope that this sounds reasonable to you as well, and that you can understand where I'm coming from.

Cheers,Chris

So there it is. That's what I said. I now have that sinking feeling in the pit of my stomach, and I sort of want to throw up...but I know it needed to be done. I wanted to address the nasty notes too, but this was about as much as I could set to for the moment. Besides, I'm sure we haven't seen the end of the nasty notes, so there will, no doubt, be other opportunities for that.

Stupid Stimulus Check

Ever since filing my taxes, I had thought I was getting a stimulus payment from the good 'ole IRS. I knew I didn't qualify for the full $600, but I thought I was getting the $300 check. I went online today to see when I should be expecting my deposit to appear. Woo hoo! I'm in the first batch and would see a deposit on May 2nd! But then I went and actually entered my tax info into the stimulus calculator. What?!?! As you can see above, I don't qualify. You needed to earn $3000 in 2007 to qualify. I "earned" $2460 from my job at UCSD before I moved to Oregon. Of course, I've been taking home $1886 a month as payment for working in the lab at school...but since my check doesn't come from the payroll department, none of that money counts in the eyes of the Fed. Very, very boo.

Proving the sky is blue

Sure, it may not look like much, but this little graph here is what I spend just about every day producing. It's the optical fluorescence readout from a real-time polymerase chain reaction. This little graph contains information on 96 samples that I've painstakingly prepared. 30 of sample A, 30 of sample B, 24 standards, and 12 blanks. With a little mathematical witchery, I can convert this graph into information about the relative concentrations of my samples, the amplification efficiency of each sample, and the linear range of amplification for the particular gene I've extracted from my bugs.

This one isn't finished yet, but it's looking good so far. You can see 5, almost 6, distinct groups of curves. These correspond to my 6 dilutions. And you can see that the second group of curves has a whole lot of lines, 60 to be exact. Those are my two samples. It's good to see them pretty closely packed like this. It tells me their standard deviation is low, and that sample A isn't a whole lot different from sample B.

That's a pretty big deal. The whole point of this research is essentially to quantitatively demonstrate that samples A and B are the same. In reality, it's the same sample, but half was treated one way, and the other half was treated another way. Scientists have assumed A and B would be the same for years, but it had never been shown quantitatively because there had been no real-world application in which it would be neccessary. Engineers have now come up with a real-world application that requires quantitative data, so now us quazi-scientist/engineers have to proove A = B. So this is it. This is what I do, day in and day out. With different bacteria. Different genes. Different primers. It's my job to proove A = B...the mathematical equivalent of proving the sky is blue or that acceleration due to gravity is 9.8 meters per second squared.

OK, maybe it isn't that obvious, but alot of the pure-science types around here can't fathom why it's necessary to proove something that's been assumed for so long. They kind of see my research as the equivalent of... well... proving the sky is blue. "It just is," they say. Well, that's all fine and good when your research never extends outside the doors of a lab. But to engineer real-world solutions to address real-world problems, I need real world numbers...otherwise any design is based on a whole lot of arm waving and no substance. When addressing public and environmental health concerns, that's just not good enough. That's why this little graph here is so great.

Disc Dye Party

Now that we've refined the method, we've been really excited to dye some discs. On Thursday we had our friends Russ and Amanda over to dye some discs. They were really excited about it, and it was a lot of fun to get together and do this as a group. Here's a pic of the discs we dyed that night. Russ did the pig, Amanda did the bride of Frankenstein, and I did windmill one.

Bowl-a-rama!

Yup, it's true. Ryan and I have joined a bowling league. It starts in a few weeks and we're pretty excited about it. A fellow PhD student (and Shamrock Run runner) in my department got 6 people together and we formed a team. We've called ourselves "The Pin Pals" (yes, like Homer Simpson's bowling team.) We'll be drinking beer and bowling on Thursday nights through mid June. Beats the usual Thursday night routine of staying late at the lab and watching TV. None of us are experienced bowlers. I played on Sunday night and shot a 96, a 114, and a 128. In the 114 round I alternated between shooting strikes and shooting zeros. But regardless it will be fun, and it's another excuse to make team shirts.

Oh, and it's 10-pin bowling, aka "big ball bowling." That's what we used to call it back in New Hampshire. We called it "big ball bowling" to differentiate it from "candlepin bowling." And for the last time, NO, I'm NOT making this up! Candlepin bowling exists! Apparently it's primarily a New England thing. The pins are skinny like candles, not fat like the "duckpins" in 10-pin. The balls are smaller with no finger holes, and you get three shots, not two. I've been asking EVERYONE around here if they've heard of it. They all think I'm crazy and that I'm making it up. No one from the Western or Central U.S. has heard of it. I even asked someone from New Jersey thinking an East coaster would know of it, but no. Anyway, read all about good 'ole New England style candlepin bowling at Wiki:

http://en.wikipedia.org/wiki/Candlepin_bowling

Dye Job

And no, I'm not talking about my hair. I'm talking about my new fly dyed disc! Last weekend we went out and bought sign-making vinyl to make stencils with. We've dyed discs before, but using contact paper stencils. The contact paper just doesn't adhere to the disc well enough, and the dye bleeds out so you can't get clean lines. The vinyl works much better. Here's a pic of my first two-color dye job.

The Research Dance

"If we knew what it was we were doing, it would not be called research, would it?"- Albert Einstein

Well, that about says it all. The pace and tempo of research is so painfully slow. It is marked by moments of extreme excitement, followed immediately by moments of utter exasperation. For every step forward, there seems to be a step or two back. Last Thursday after a short presentation of my work, I was beginning to see what I like to call, "the paper at the end of the tunnel." Publications are the currency of my industry. Before last Thursday, neither myself, nor my advisors could envision a stand-alone paper coming out of the work I'm currently doing. That's not to say it isn't necessary or important work, it's just that it didn't have a stand-alone spin to to, and so would end up sandwhiched in a paper with some other related work some time pretty far in the future. But Thursday I was able to find the spin that would make the research stand on its own. In fact, it could actually end up being a fairly substantial methods paper addressing some technical and mathematical aspects of a very common reaction that have been largely overlooked by members of my field. So Thursday...Thursday was one of those exciting days.

But Thursday is where the excitement stopped. Nothing came up that threatens my paper, but work has come to a stand still. I spent 8 hours in the lab Saturday ramping up for phase two of the work I'm doing....and I'm having technical problems with some of the reagents I need, and the solution isn't readily available. I simply need 2 more duplicates to finish up the first block of experiments in phase 1 of my work...but the DNA I'm working with has started to degrade and that forces me back to square one....such a waste when I just need to squeeze two more runs out of the DNA I already have. It's not a problem, just a bummer, because the ramp up is time-consuming, and expensive. I really want this to work out, and soon. It would be AMAZING if I could get a paper submitted for publishing before my first year here is up. That is my goal. I'm crossing my fingers that by August I'll have two solid blocks of experimental data ready and in manuscript form. The dance continues...

Ecola State Park

I just got another roll of film developed from my Zero Image pinhole camera. Here's a shot from Ecola State Park on the Oregon coast (where part of The Goonies were filmed). I think it's the best one yet. With the weather getting nicer and nicer, I'm looking forward to getting out to shoot more this spring and summer.