'08 in retrospect

I know... I know... it's Christmas Eve and instead of going to another one of those family-friendly holiday parties (read: the one where people my parents' age tell me how much I've grown), I'm sitting here listening to whatever music I have stored on my computer and updating this blog I created. Anyway, the cell bio final (which I was panicking about) turned out to be pretty easy, and I don't have to think about class for another week, so now I intend to forget all about RTKs and G proteins. Oh wait... what about next term's rotations? oh well...

Quite a year in retrospect...originally I thought that graduation would change a lot of things. So many people moving out of AA, getting jobs, off to med school, grad school, or whatever plans they have... clear across the country. I had thought that this past summer would be pretty mellow, since my friends were leaving and grad school, along with a complete shift in priorities, was starting. But in reality, this summer was pretty much one big hurrah interrupted with labwork, locking myself out, and accidentally flooding the zebrafish room. That and drama... not the minor kind that keeps life interesting, but the kind that I haven't seen since middle school. Best song to describe it would prolly be that Maroon 5 song "Tangled."

Grad school in itself is relatively enjoyable; it makes me a little sad that people in PIBS aren't as close knit as the physics grad students I know. The first year physics students have their offices all in this one hallway, and even tho there are assigned desks and rooms, nobody really pays attention, so books, like their owners, are all over the place. It's not just studying either; Michelle says that the boys in the department have already broken a grand total of three ceiling tiles, got reprimanded by both the building manager and older grad students for playing soccer/kickball/football in the hallway, and I guess for just being obnoxious in general. And maybe for also throwing full Nalgene bottles at each other. Gotta love 'em...and their whiteboard of inappropriate quotes.

I think it's nice that even though we're all in grad school and have definitely matured since freshman year of undergrad, we're in no way transcending insane or boring.

Looking forward to next term, since I'm taking development (finally!) and a seminar on teaching in science. Should be fun. Plus my lab rotations will be back in Nat Sci, so maybe a little more time to visit the physics department and promote, er, PREVENT, future ceiling tile destruction. That, and Michelle and I decided that we need to go sledding in the Arb. But since nobody has a sled or toboggan or sorts, we'll use Ben as the human sled. He won't mind.

Hopefully.

obligations...

The postdoc who's training me during rotations was out at a conference the past few days, so I slacked a little in lab. I know that grad students make their own schedule, so they go to lab whenever it's necessary and leave whenever experiments are done. Although a lot of the times I feel like I "need" to be there for the entire 8-hour block, or however long it takes, even if there's nothing to do except sit and wait for something to finish (thank god for the thermocycler).

I'm not entirely used to this med school lab yet... it's been two months! There's two more to go before the end of the rotation, and I'm moving back to Nat Sci in January, but I'm relatively sure now that I want to do a thesis with MCDB...

some natural light would be nice too, I suppose. :-)

Month 1

Cell bio is driving me insane. We're covering stuff on protein transport and we're supposed to read these three papers for discussion, along with answering questions. The problem I'm having is that I understand the gist of the papers, but the questions that we're supposed to answer ask for basically "what were the authors thinking when they did this?" And being papers from Nature, data was usually "not shown," or "in the supplementary material"

I guess another problem is that I write down what I think is the right answer to the question, that nagging "what if this happened" scenario pops up, and then I have to change it.

Or maybe I'm just having an "off" day.

...and I'm gonna go study genetics now.

Week 1

New project: get to be working with embryonic stem cells isolated from mice. There's a paper out there that plated ESCs in media and pretty much "forced" the cells to differentiate into hormone producing cells of the pituitary. So I'll be repeating their experiment; growing cells in a dish, extracting RNA, and doing RT-PCR to find out what kind of markers are expressed in the different stages of development.

Classes just started last week, so the workload hasn't gotten into full swing yet; on the flip side, there's a lot more papers to read. First years take two classes, an ethics seminar, and do lab rotations. Which translates to four papers to read a week, at least.

We'll see how things go once the ethics seminars begin.

Another note.. the new rotation student in my previous lab (zebrafish one) tracked me down in class earlier this week to ask me a question about my lab notebook. He's working on the extension of my rotation project this summer: still trying to map the mi40 gene. But he gets to jump right into the mapping part; I spent my entire summer looking for mi40 hets. Anyways, there's another gene in that lab, mi215, which, when mutated, gives the same phenotype as mi40. The fish don't complement, which means two things are possible:

a. mi40 and mi215 are the same gene
b. they are different genes, but in the same pathway to get a functional eye. So if one of them is faulty, the entire pathway collapses

The new rotation student told me that mapping mi40 was essentially a "waste of time" because he's done linkage mapping before, and when two genes don't complement, they are always the same gene. He wasn't even willing to consider the other option, even though the professor was unsure of the first possibility.

So seriously.. how does he know already? He hasn't even tried.
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Finally, I've noticed since grad school started I've became much more impatient about a lot of things outside of school. The program here (along with every other program I've interviewed at) expects grad school to be everyone's #1 priority. I think I'm a little scared of losing interest in what I'm doing if I lost focus, so I've channeled a lot of energy into learning what has been done in the past, what's going on now, and what new things might pop up in the future. Unfortunately that doesn't leave much room in my attention span, so everything else gets treated as a black and white issue.

I should probably take up yoga as a new pastime...

Defaulting

I ran into one of my former GSIs today who told me that he was leaving UM in December, three and a half years into his doctorate program. He'll be teaching his last class this upcoming fall term, then leaving for a science-related job in New York. He told me that his labwork hasn't been making much progress, and that he'll be defaulting with a Masters.

A sad story.

He was a great GSI and I'm sure he would have been a excellent scientist; but with the roadblocks in his labwork, it might have taken him longer than his expected two years to finish the thesis. I'm glad he found a job he likes in New York; he'll be doing some science outreach stuff for another university.

The particular department I'm currently rotating in accepts about five or six Masters students each year, but a lot more students graduate with this degree because they default out of their PhD program. Research is a game, but it's also a test of how much you can take.

As Einstein once said "If we knew what we were doing, it wouldn't be called Research."

"Nobody does biology JUST to do biology."

Next lab rotation is set in place; I'll be working on mouse pituitary development in the med school. In the meantime, I'm still trying to find more zebrafish carriers before the end of the summer.

I'm somewhat surprised at the sheer amount of reagents that this lab uses as compared to my former lab downstairs. It seems like we did much more PCR downstairs, so it could account for why we needed use smaller amounts of everything, especially enzymes, which cost about $100 a tube (not even half a mL). One of the grad students was running through how to set up a PCR involving animal DNA, and I didn't realize that the total reaction volume was 2.5 times larger than those used in my old lab. I'm wondering if it's really necessary to use that large of a reaction; I remember two summers ago when Susana (lab manager #1 downstairs) showed us this booklet sent by one of the supply companies. It called for a reaction volume of 100 microL: 10 times larger than what we used, which means 10 times more than what was necessary.

And then there's Hope (aka lab manager #2 downstairs), who had all sorts of ways to "cut corners" (or "be efficient," as she says). She used three times less then what we were accustomed to when Susana was in lab, and somehow the experiment still worked.

Obviously, everything is about saving money. Which brings me to the next point.

So much modern science research is human-centric. The more relevant it is to human health and prolonging the human lifespan, the more grant money set aside for it (even though there is also greater competition). How long ago did we transform our thinking from "I want to understand how nature works" or "I want to know where this came from" to "I want to study this because it helps people"?

And how many scientists out there are really trying to get a better understanding of something....simply because it's interesting and not because it can be applied to people one day?

The title is a reply from a person I met freshman year. They found out that I was a bio major and NOT pre-med.

Adjustments

Definitely making some progress on the zebrafish project; first two weeks of the lab rotation were all about learning how to take care of fish, and I've spent the rest of this time identifying carriers for the mi40 mutation.

I'm definitely not ready for classes to start; at least in lab I don't have to study...unless analyzing my own data counts.

In the end, I think I might come back to this lab to do my thesis...but first we'll see how the other few rotations work out.

Day 2

I spent all of yesterday reading the zebrafish manual and learning (or trying to learn) how to care for them, their embryology, and necessary staining techniques. Oh, and digging up long-forgotten genetics and molecular biology topics. I'm going to be helping out a second year grad student on mapping a gene called mi40. When mutated, it screws up the placement of UV photoreceptors in the zebrafish retina.

At least I think all the above information is correct... searching "mi40 UV photoreceptor mutation in zebrafish" on PubMed yields a listing of papers on UV photoreceptor development, but nothing on the mi40 gene, even though there is a poster about it outside the lab.

Other than that, today I got to prep the fish for map crosses; in other words, I separated the fish according to sex and put each fish in their own tank. Then we feed them for a week, or until they get big enough for us to determine their sex with certainty. Apparently males are supposed to have slimmer yellow bellies, while females are more silver and look pregnant all the time. The problem here is that males that eat a lot of food also look pregnant.

So I still feel completely lost as to what I'm doing; there's so much stuff to learn in too short of a time period...

17th Grade Orientation

Today was the last day in the plant lab, and thus the last day as "not yet a grad student." Moving upstairs for the rest of the summer isn't much of a physical change, although it means getting used to the techniques used by a different set of people, a new lab manager with a new style, and the biggest one, being much more proactive about my own work. Not like I don't suggest things to try when screening primers in the plant lab; there wasn't as much pressure to understand exactly how a particular experiment fit into the larger picture. And definitely no pressure to read as much primary literature as possible and do critiques.

I'll miss a lot of the things that come with working in Chris's lab, like...

• the lab candy
• coming into lab and realizing that Hope just bought a gazillion pairs of primers...that all need to be diluted...
• ...and tested
• the "toxic room" (aka electrophoresis room)
• swapping dumb stories with Hope, or with anyone who has a story to share
• the centrifuge story (which is partially my fault)
• Sandra's singing
• Shalene and Susana singing along to Sandra's ringtone (yeah...)

So we'll see how tomorrow (technically today, in a few hours) goes. It almost feels like the first day of school...back in kindergarten.

half a month

...before the start of lab rotations. I've been so lazy; in mid-May I made this half-assed promise to myself that I'd read several papers a week to get background information, jot down questions, and get possible inspiration for thesis projects. And the reality? I think I read quite a few, but only enough to make up for the month of May, at the rate of "several" per week.

As a lame attempt to justify my laziness, I've been trying to squeeze in as much time as possible to see people who are going to be leaving AA before they actually do. It seems like most people are leaving at the end of June, if not, then the end of July... and scattered all over the place too. One of my friends is seriously considering taking up a teaching job in DC; another is moving to Ohio, taking a trip to Spain, then starting her grad degree in psych in September. A few more will be in med school, others are traveling the world, coming back, then scrambling to get their first "real" job.

Makes me realize how much I need a road trip of some sort...just as a last hurrah. :-)

At this point I have mixed feelings about starting grad school. In a way, I'm looking forward to it, since it's in something I've loved for the past 5 years, but I'm also a bit nervous. There's that worry about "what if someone else gets to my thesis idea first" or "I can't narrow down a project because everything sounds cool." But more than anything is... am I ready to let science consume my life?

zebrafish summer + letting go

A little less than a month and a half before grad school starts...and the first project will be on zebrafish. Either cell fate determination or stem cells/regeneration, both in the eye. The prof says zebrafish can regain their sight (when blinded with hot copper wire) within a week.

On a totally different note, I had this dream last night, and all the elements in the dream were pointing to a need to purge my old way of thinking and to make a change in my life. I distinctly remember that during the dream I was concerned with an issue outside of grad school, something I've been trying to figure out for the past month.

I guess I'll just have to stop stalling then...

on learning

So I have to make a decision in 11 days as to where I'll be doing lab rotations this summer: it's down to zebrafish v. mice. For background info, both labs gave me a bunch of papers to read. Set 1 is on mouse development, specifically of the pituitary, and set 2 is on the zebrafish eye.

In any case, I've been trying to read these papers (plus a few more I found on fruit fly development), and I understand the gist of them, but unfortunately there are parts that go completely over my head. Basically, I don't know anything. Which makes me wonder... what were the last four years for?

Reading these papers makes me feel so incompetent. :-(

entering the Transition Summer

So... Saturday was graduation and marked the official end of undergrad.

I took my parents and my sister to a departmental reception hosted by the biology department, and made my dad meet several of the people I was /I will be working with. Let's just say he was surprised that I wasn't shy. But you'd think four years of college would change people so they wouldn't be, right? Doesn't college force you out of the shell, if you had one to start with?

There's two months before of start of grad school lab rotations. Two months of freedom. Well, sorta. I'll be in the mol ecol lab until June 30, and leading physics study groups for spring half-term. Then I switch labs on July 1 and start working on fish. Or mice. Need to make a decision in half a month...

Summer is gonna be interesting. Congratulations, class of 2008!

five more years

Here's to five more years of school beyond college. It's 1:13am, and there's so much running through my mind now that graduation is so close. Even though the past four years in itself was a transition, I've named this "The Transition Years" because it marks the brink between getting a college degree and finding a "real" job, which will probably happen... when I'm 30?

Oh, and I chose spots as the background because it reminds me of a microarray. ;-)