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?