the hardest part

We had a lab meeting earlier this week, and I was the presenter, so I spent a good amount of time putting slides together last week. If the old rule of "a minute a slide" applies, my presentation should have been a little less than 20 minutes long.

It was an hour and a half.

I got interrupted at practically every slide.

And I didn't know the answers to a lot of the questions.

So to fill in some of the gaps, I spent a good chunk of time this past week adding, deleting, and rearranging some stuff so it addressed the comments made in the meeting, and I ran it by my advisor today. The verdict: read some more.

The slides I got the most interruptions at were the slides that described questions I wanted to address via experiments. I kept getting called on for clarifying what the question really was, what my hypothesis was, and the reason why I formed that hypothesis. It turns out that the vast majority of my background information came from studies done in mice, and while it's generally assumed that the results would be the same for frogs, that's obviously not a good enough reason to base a series of experiments off of. There were a lot of preliminary questions that needed to be addressed first, using the FROG as a model before moving on, and I didn't realize that, since I had automatically assumed that an important molecule would be evolutionarily conserved between frogs and mammals.

That being said, there's a surprising amount of information we DON'T know (or I don't know) about frogs. This information had been well-documented in mice, but I had taken this info from mice, extended it to frogs, and proceeded to the next step, without bothering to test to see if the information also held true for frogs.

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Last term in that grant-writing/prelim-giving/paper-reading class, we had a professor come in and talk to us about what makes a good grant. Three basic parts:
1. whats the question?
2. how do you test it?
3. so what? (why should we give you money?)

He said that the reason why a lot of grants are tossed out is because they don't have a good question in mind, and that the "what's the question?" part of the grants is the most difficult to answer. Originally I had disagreed; I thought "so what" was the hardest, since not everyone is going to be utterly fascinated in learning about social behavior in purple carnivorous snails (just an example). However, after the past two weeks of working on these slides, looking over at the comments made, and going back to revise things, "so what" is actually a pretty easy question to answer... once I figure out the question I want to test in my experiments.

So I'll be writing up a list of things that need to be answered, and try to weed out which question is the most fundamental...which will be the starting point for subsequent months.

faith in science

I was laboring on Labor Day; apparently my cloning experiment didn't work again. The concept is simple enough: cut plasmid/inserted gene, purify, and then glue together. So why has it taken me over two months to do this? (aside from losing the DNA, breaking machines, fighting the Incredible Shrinking Insert...)

Molecular biology (or science in general) at its best (read: textbook figures) is a great concept. We have machines we didn't have a decade ago, protocols that have been refined multiple times, and reagents that can be mass-produced so that they aren't nearly as expensive (although $150 for a tiny bottle of Taq is still way too expensive, for my taste), but even with the technology we have now, everything is far from foolproof. PCRs will just fail for no apparent reason, and the only "logical" explanation was that whatever day the experiment was done on was just a "bad lab day." Likewise, the first sentence in our lab protocol for ligations (where two pieces of DNA are glued together) is "sometimes it works, sometimes it doesn't," making it seem like you should mix the necessary ingredients together, follow the guidelines, and *hope* that it works.

Science is like a religion in itself; sometimes things just happen and nobody knows why. I've been restriction digesting and purifying "my favorite gene," which is supposed to be 500 basepairs long. Somehow after purification, the gene "shrinks" to 300 basepairs. I've ruled out every possiblity I can think of, and there's nothing that can really be done except start over (and maybe whine about it for a while). Yes, cloning sucks, but I suppose I just have to *believe* that whatever I'm doing is the right thing, and that one day after tapping my foot 55 times while wearing a red tshirt and singing along to some given song on my iPod, I'll get my ONE much-needed clone.

Seriously though, howcome superstition isn't more blatant in the research field?

Information Overload

It's generally a good idea to read up on papers related to your research topic as preparation for prelims, and a rule of thumb is to read about two papers a week. My advisor told me about two weeks ago that I could probably be more ambitious than that and read a paper a day.

He has a good point, since my undergrad career consisted of a wide smattering of classes with no particular emphasis on one subfield in bio. But a paper a day? I'm not sure I can absorb all that info at once; I have to read a paper at least twice to get the most out of it. The first time I read it, I skip the methods section and all the figures. Second time around I'll actually look at the pictures, and (maybe) come up with more questions.

Hopefully I get better at info absorption over the next month; once school starts, my schedule is gonna be insane.

Year 1 in retrospect

I've been meaning to write this post for about two weeks now... first off, I finally decided to stay in this current lab (working with frogs). That doesn't mean I'm not intimidated by my PI; I've gotten a bit used to it, and plus, being a little more intimidated by this PI than the other one would push me to work a little harder and really know what I'm doing.
That being said, I don't think I'll ever get over this "being terrified of my boss" phase. Hopefully by prelim time? If not, it better be by defense time...
***
Several weeks ago, one of the professors down the hall was talking about the learning curve in grad school. He said it's pretty amazing how much of a difference one year of grad school makes on a student's reasoning, presenting, and writing skills. It's hard to say where the learning curve is the steepest, but I would guess somewhere in the first two years. I was archiving my rotation presentations and written summaries the other day and before putting them away, I was reading through them. Frankly, my first written summary in grad school sounds like an 8th grader wrote it. :-/
It's gotten easier for me to see the connections between theory and experiment design (something that took me literally forever to do in my undergrad lab), but I still have a ton of stuff to learn. I thought of a possible thesis project about three weeks ago, and talked to my PI about it. There doesn't seem to be too many people working on that particular topic as far as my PubMed searches tell me, but I suppose I could go off on a tangent and search for somewhat related topics...

doing science properly

Last term I took a grant-writing/prelim-giving/paper-reading class, and one of the sessions was dedicated to writing a good grant. The guest speaker was a professor in the department who has never had to resubmit an NIH grant in his 30+ years of tenure as professor. He brought in his experiences as a grad student at MIT and how there were two professors there who did science very differently, but both ways were ideal, depending on your personal style.

The first way is to go off on crazy tangents from one root project. It's like saying, "mutant A has an obvious eye defect as heterozygotes, but homozygous mutants for A die." You could have someone in your lab working on what this eye defect is and how it relates to the mutated A, and another person working on the timing of death. Why do the homozygotes die? What stage? What went wrong?

The second way is to keep working on one central question, discovering things that relate to it along the way, but never fully answering the question. Going back to mutant A, you could ask "why do homozygotes die?" Then you could find out that they have defects in gene A, which is part of pathway B. But that doesn't mean pathway B is the ONLY one in the system that is making mutant A unhealthy. In other words, is there anything working with pathway B? Does it act alone? Is there a mutant A that doesn't have problems in pathway B, but has problems with receptor C instead?

The unfortunate part about getting grants is that the government expects neatly-laid out experiments, with not much wiggle room for failure (one of the main laments of one of the professors I talked to). But since NIH grants are stretched over a five year period, how is anyone supposed to have the insight to know that some project that looks promising now won't be a dead end? How do you account for pop-ups that are related to your project, but are completely unanticipated?

Science is already a competition for funds, but the restrictions on what you can write in your proposal and what you can't possibly foresee makes it more and more difficult. We can't possibly outsource research, but will the sheer difficulty of getting money drive down the population of scientists?

panic

Recently I got an email from the PI of the zebrafish lab I worked in last summer, saying she heard from the grant review panel, and now she has sufficient funds to support another grad student. I'm also finishing up the rotation project in this current (frog) lab, so now the question is where do I want to go for the next 4+ years?

Both PIs are tenured professors in developmental biology, working with different model organisms. They give good mentoring advice, are both stationed on the third floor of NatSci, and are well-known in their fields. When it comes to the important parts of grad school (like what kind of guidance you're gonna get), they're pretty much identical.

So now I think the question becomes "who am I a little less intimidated by?"

Here goes...

on being old and boring, part 2

The fear of being boring seems pretty common; I was talking to one of my friends who is in grad school for chemistry in Japan, and we were discussing the difficulty of meeting people outside our given departments. Not just for fun, but for the sake of diversity in conversation topics.

Since lab is such a large component of the doctoral program, it's impossible not to think about it even when I'm not there. And since a large part of research seems to be troubleshooting, conversations with other students center around what could be done to fix things, or getting advice with dealing with advisor expectations, etc. I think for the past two weeks that I've been out of classes, most of my in-lab conversations circle around "where do we keep the pipette tips?" or "my Western Blot flunked. What now?"

Last term I took a seminar-based class called "Teaching in the Sciences," and as a so-called "midterm project" we were supposed to put together a powerpoint presentation on something not science-related. (gasp)

The instant the professor gave us that stipulation, we all panicked a little, as if saying "but I don't know anything outside of science! I don't even remember what hobbies I have besides from PCRing and pipetting!"

I guess my non-lab related work is cut out for me this summer.