Science Monkey

Dear Self,

Don’t forget that you’re trying to post an entry every day for a month. I know you were busy yesterday, so I’ll let it slide, but let’s not let that happen again, okay? Cool.

Love you, man.

You/me/us.

As I’ve mentioned to some of you, yesterday was the second Big Meeting between me, my boss, the department chair, and the associate dept chair/member of my committee. And like the first meeting, yours truly got beaten around pretty badly. This time they were all upset with me because I hadn’t finished writing up a list of specific aims to finish my studies in this lab. This was something that I knew I had to work on, but somehow I missed that this past meeting was the deadline to have it done. I wrote a draft which I sent to the associate chair/committee member but hadn’t heard back from him, so I figured that this was an ongoing project. Had I realized that I was going to get yelled at for half an hour, I would have pressed him harder for his revisions, especially after I saw him last week and he said something like, “I got your draft and need to get my comments back to you.”

Now I have another Big Meeting next Wednesday. I wrote a draft of the specific aims in precisely the format that they asked for last night (another one of my problems…I didn’t realize that they wanted it formatted as in a grant proposal, which is apparently the way a list of specific experiments is supposed to be organized) and sent it out. I’m supposed to meet with Tom today to go over it but have yet to hear anything. Of course, it’s only 10.

Here’s the thing that’s really bothering me, and I can’t decide whether I’m being overly whiny or not. I feel like Tom is the person who has screwed up and I’m the one being punished for it. I’m at the end of my fifth year of grad school. Our departmental graduation average is 5 and a half years, so even if I finish this summer I’d be ahead of average. In this lab, nobody finishes in five years. As far as I know, every former student has taken at least six years to finish his or her degree, and some have taken longer. So how is it fair or reasonable to threaten to cut off my funding because Tom has failed at his job?

I haven’t actually said any of this to Tom or the other people at the Big Meeting and I can’t decide whether I should or not. I understand the realities of the fiscal situation. It’s a difficult time to get funded right now and I realize that it costs money to support me, both in terms of my salary and the reagents I need to actually do the experiments. However, my job as a graduate student is to learn how to do the experiments and to perform the research while the job of my mentor (and I use that term loosely) is to advise, teach, and find the funding to support his lab.

Enough ranting. Time to do some bench work, although that apparently doesn’t matter until I have a “road map” in place. It apparently doesn’t matter if I can actually do the experiments, so long as I have a plan to do them, or at least that’s the lesson I’ve learned in the last 24 hours. Grumble, grumble…

Dear Brain,

Why are you so easily distracted? I intentionally left Lappy at home so we couldn’t play internet and get some work done. But you, you devious lump of gray matter between my ears, you figured out that there was *another* computer here in the lab which can internet. And facebook. And blog.

I even brought you our current knitting project, so we could pretend to be productive, while waiting for the Southern probe to label. And yes, you did humor me for a while and let me knit for half an hour, but then we were back on internet before I even knew what was happening. But know I know your trick, Brain. I’m wise to you. “Let’s just check our email,” indeed.

A.

PS: Dear Focus, as I know you’re reading this with Brain, let’s get it in gear, eh? You know we’ve got that meeting with Dr. Flanegan Wednesday, and I think that all three of us (you, me, and Brain) can agree that we’d like to have something useful to present to him then. So chop chop! And hop to! And some other obscure, unused motivational phrase from thirty years ago!

Gosh, how has it been a week since I’ve written? The time, she does fly by. Current mood: pretty good; could certainly be worse. Current music: the hum of my box fan (stupid A/C).

Life has been pretty hectic this past couple of weeks. I finally got over that nasty virus on Tuesday, so I’ve been trying to put a bunch of hours in at the lab since then. I’m moving a little more slowly than I might like but I feel like I’m making deliberate, forward progress.

I can’t remember if I blogged it or not, but I finally got some radioactivity in at the end of the previous week, so I got to do some Southern experiments this past week. At this point it looks like either my probes or my membranes are shitty. I labeled a probe of mine and a probe from our former postdoc (who graciously took time away from his work to supervise me and make sure I wasn’t doing anything obviously stupid), then hybed my probe to a test strip that I made and the postdoc’s probe to a membrane he provided. Mine came back all black and nasty and smeared, but his was lovely, a single, clear line well above the background noise. After seeing that, I decided to throw out all of my probes and re-create them from the original PCR. I could spend a month trying to reisolate a single clone from each of the probes (and be sure that it’s right), or I can take a week and generate them fresh. Progress.

Ah, work. Enough work typing. I’ve been doing a few things to keep my sane outside of work. Sleeping, mostly, but not exclusively. While looking for some old test scores in my office closet, I came across a bunch of pictures of me that came from my Grandma Henderson. I was at work late one night and borrowed the scanner between experiments, then posted a bunch of them on Facebook. That link should work, even if you’re not a member. There are a couple of particularly cute ones, including one of me all bundled up in a snowsuit from about 1978, and one of me in front of the Golden Gate Bridge from about 1983. Hee! I plan to keep expanding the album as I find more pictures and get them scanned.

I’m still knitting, too. I’ve moved on to the Next Project, which I think I’ve written about before. At least I think I’ve written about the concept behind the Next Project. I’ve ordered a “stitch dictionary” and am going to make a bunch of little dishtowels (or whatever, but about that size) and learn as many stitch patterns as I can. Well, maybe not learn, but practice and get used to manipulating the yarn and the needles with the clubs that I call hands.

The colors are pretty good, right? And I think they’ll all work together with each other. The yarn is thin enough that the cool ladies at our favorite yarn store — who must think I’m nuts…I made this quick, quick stop earlier to look at a couple of the 4″ square pieces that they have hanging on the walls and are very similar to the dishcloth project, and must have spent all of 90 seconds in the store because I had to get the groceries home — suggested using two at a time so I tried to pick colors that would look nice paired. Clearly the two blues look decent together and the two pinks, but I think that either of the pinks will be decent with either of the blues. We’ll see. Worst case I hate it, and I don’t do that one any more.

I’m also still playing WoW, of course. The weekly adventures are over on Wara’s blog, but in summary I’m still having a lot of fun. I left my old guild which had become too raid-focused for my tastes, and have found another guild that is pretty fun so far. A friend of mine is an officer and I’m looking forward to getting to play with her a little bit (if she ever come back online…hint, hint). They’re pretty cool and casual and mature, which is basically all I want. I don’t need to be (or have time for) doing the real hard-core endgame raids right now, and that’s not their focus at the moment. Maybe eventually, but not right now, and that works well for me.

Enough for now. Time to go wake up the wife so she can take a shower and get to work, the poor kid. My hero. Seriously.

The day we’ve been dreading here in the lab has finally come. We’re broke.

Actually, in the interests of full disclosure, we’ve been officially broke for about three weeks. It’s taken me that long to get around to finishing this entry.

This day has been clearly on the horizon for the past year or so, as grant after grant went unfunded. We had good scores and good comments, but at the end of the day it wasn’t enough. I’m not too surprised that our grants aren’t getting funded, either, as we haven’t had a publication since 2005. Over two years without a publication! I know if I were on a study section and had two equal-quality grants in front of me, one from a lab who publishes regularly and one from a lab who doesn’t, the choice of which grant to fund first would be easy.

So what does this mean for your favorite monkey’s graduation? Stress, mostly. Stress and uncertainty. I had a meeting last Wednesday with our chair, the associate chair (who is also on my committee and a family friend), and Tom. It was part venture capitalist, part swift-kick-in-the-ass meeting. For the VC part, there is some emergency funding available from the department but not an infinite amount and the chair wanted to make sure that it wasn’t going to be wasted, that there was a reasonable chance of a return on their investment, if you will. It was hypothetically an open and honest conversation, but I felt too much stress and threat at the time to be very effective at presenting my side, I fear.

The chair said that he saw three paths that I could take to resolve this problem. 1) Continue with my current project and finish soon, ideally by August but by December at the latest. 2) Leave now with a Masters. 3) Find a new lab who will support me and start a new, safe project that I can finish within two years. Option 2 is completely unacceptable to me. I’ve spent too long and worked too hard on this degree to leave now with a Masters. If I wanted a Masters, I would have gone into that program and been done three years ago. Option 3 is acceptable, but suboptimal. While I would probably enjoy being in a lab other than this one, I don’t really want to start a new project at this point. Also, I don’t know where I would look for funding. I have a half dozen professors that I would ask, but I don’t know what any of their funding situations are like, if they would be able to take me on. So that leaves us with option 1, which I think is the best choice for me and my career (and sanity).

The hurdle between me and finishing right now is largely technical. Since Tom fired our postdoc because we couldn’t afford him last May, we haven’t been able to do Southern blots. Not just me, the lab. We can’t figure out what’s wrong, either. We’ve had an undergrad working on the problem for much of this past year, while I focused on another technique, but it has gotten to the point where I need to put that down and figure out what’s going wrong. At the meeting with the chair, in fact, we agreed that I needed to solve this problem, and I effectively have a month to get it working. Despite Tom repeatedly claiming that he could come down to the lab and make it work, he hasn’t, so I’ve talked with our former postdoc and he is willing to take time away from his current work (he works down the hall) to help, so we’re going to go through the whole procedure as soon as we get fresh radioactivity. But that brings up problem #2 (or 200, whatever): we can’t get radioactivity right now. Because we’re broke, Tom’s purchasing accounts were temporarily frozen. The department has been using a credit card to order most of our supplies since then, but apparently 32P can’t be ordered on a credit card. We need a purchase order, which requires getting a new account number from Purchasing, which will take an unknown amount of time. The order left the department on Monday, but it’s unclear how long it will take to actually be placed. Meanwhile the clock is ticking. I’m down to less than three weeks now until my next meeting and am trying to figure out what to do. I discussed this with Tom yesterday and he didn’t have any suggestions or advice.

This brings me to a minor rant about this whole situation. At our meeting last week, the chair expressed concern about my working relationship with Tom and Tom said that I don’t communicate with him enough. One of Tom’s biggest complaints last week was that I don’t bring him negative data. I probably don’t, honestly, but feel that it’s a waste of my time. He impassively takes it in and doesn’t provide any advice. I don’t need him to say, “Oh,” or “Do it again.” I can figure out that myself. If he were to say, “Oh, do it again but try crammulating the freezelberg,” I’d bring him all of my negative data. Especially when I don’t have an idea of what’s going wrong. That might be useful. But when I get, “Go read the Red Book,” what’s the point?

I’m not even going to start complaining about the schedule he works and how little he’s available during the day.

Okay, I’ve spent far too long on this and need to get back to work. My plan for the moment is to work as hard as I can until the next meeting with the chair. I’ve put in 10 hour days every day since the meeting, which I think will help demonstrate how serious I am about wanting to get this degree. I also think that I’ll go try and beg some radioactivity from other labs, at least until we can order our own. And cross my fingers that I can make this work.

850A0053, originally uploaded by arne h.

I’m not sure why The Powers That Be decided that this would make a good time for a fire drill. It’s raining, so nobody wanted to go out from underneath the building. Had this been a real fire, we all probably would have been killed. Good times.

Or perhaps not, but I’ve been listening to too much JoCo lately and really love that line.

Dear Blog,

I know it’s been like eight and a half years since I last wrote. I’m sorry. I’ve been staring at a blank New Post screen for the past several days, unsure how to compose my thoughts and then translate them into typing. I should worry about that less, I suppose, but I don’t want people who read this to thing I’m a complete idiot. I know in my head that I write this blog mostly for me but I also recognize that some friends and family (and a few random strangers) read it.

Let’s start this much-belated entry with my committee meeting on Monday. My hellaciously-frustrating and soul-sapping committee meeting. For those of you not familiar with the process, I have an advisory committee composed of my PI and four other professors who are supposed to help guide my progress towards my PhD. I’m supposed to meet with them twice a year. This meeting was a little late — my last meeting was in March — but the one before that was in December, so I’m on track on average. One of the professors couldn’t make the meeting time but that was not really a problem…the other three (not including my PI) are who I look towards for the most guidance and approval.

I prepared about 35 slides detailing what I wanted to do to finish my degree and the rationale behind the experiments. A lot of them were “structural” slides and I figured going through them all would take about 30 minutes, which is a just a hair long but not horrible. We were there for just over two hours. The first hour actually went pretty well. I talked about the background and previous work from the lab and think I answered all of the committee’s questions well. I probably *should* have know the answer to one or two more of them than I did, but I think I acquitted myself reasonably well. The second hour was another story, especially the last half hour.

I knew going in to the meeting that I didn’t have a ton of data to share and that they’d be upset with my lack of forward movement. I knew that and was ready for that. What I didn’t fully expect — and perhaps I should have — was my boss playing spin doctor as much as he did. Maybe that’s not quite what he did, but I’m not sure how to describe it any better.

About two months ago we had a lab meeting where I stood up in front of a blackboard and we came up with every possible experiment I could be doing to finish my project. Feasible, unfeasible, realistic, unrealistic, everything. Afterwards my PI said to pick three to do to finish my degree. I’m not as foolish as I may come across, so I picked the three that would allow me to finish as quickly as possible. The story might not be fantastic but it would be enough to build a thesis and get at least one first-author publication. When I presented this to the boss he noted that I had picked the easiest and least time-consuming experiments and said that I needed to think about “pizazz” and “career management.” I might have a thesis at the end of that work, but who would want to hear the job talk? If I wanted to get a good postdoc position I would need to do something a little more flashy. I went back to the list and picked up a set of experiments involving immunofluorescence and FISH which would address some of the more speculative parts of our working model. Not experiments I particularly wanted to do but they would be showy and give me some really great pictures to use at the end of my job talk. I was told to present these as experiments to do “as time permits.”

My committee was less than thrilled about this idea. They said that what I needed to do was to focus on getting enough data to write a thesis and get at least one first-author paper, not start a new, speculative series of experiments that feel — to me, at least — like a fishing expedition. Tom’s response? “That’s what I’ve been telling him for the last two months!” When I brought up his denigration of my plan to just do the experiments I needed to graduate and his insistence of adding pizazz he claimed that he had told me all along that my original plan was fine with him. I…I just don’t know what to say at this point.

Crap. I need to go proctor an exam and I know if I don’t post this now I won’t go back and finish it. More later, I promise.

I can’t believe it’s been almost two weeks since I last wrote. I know there’s only a half dozen of you who read this at least semi-regularly, but that’s no reason for me to slack off on writing. I write for me, not for you. Well, for you a little, my lovelies.

At the time I’m writing, it’s mid-Friday morning and I’ve gotten almost no work done yet. I was up a bit too late last night procotoring a biochem exam and woke up several times during the night, so I’m a bit sleep-deprived. There were about 60 kids in my room last night and all of them were done except for one after about an hour and a half. That last one? He took the entire two hours. I’m not really complaining that much — I realize I get paid to be there — but it was a little odd. Then I had to come back to the lab and start a bunch of cultures for today, go home and close up the chickens, run to the movie store and return the movies, then come home to eat dinner. And maybe play a little WoW.

Speaking of the chickens, they seem to be doing well. I’ve been diligent about closing them up at night each night so we haven’t had any problems with that damned raccoon opossum [thanks, Shermi!]. Between reinforcing the lower half and closing them upstairs at night, I think they’re pretty well secured.

Work is going reasonably well right now, which is a pleasant change from the previous few months. I’m starting to get some data back, so perhaps there’s hope for me yet. I have a couple of pup litters due in the next week and am hopeful about getting a bunch of good data out over the next month. Maybe, just maybe, enough to start writing. Maybe.

Speaking of work, I should probably get back to it. Or to it, at any rate. I’ll try to write more soon, including our adventures at the Downtown Arts Festival (we has some arts!) and some book reviews I’ve been meaning to write. Type to you soon.

I was at work late last night, proctoring the first biochemistry exam. It wasn’t too bad, although I apparently had the best room. One of the four TAs didn’t show up (and has apparently quit the TA-ship, if not grad school in general, but neglected to tell the professor in charge of the class) so one TA had to run between two rooms. Meanwhile, in the big auditorium room we were about 50 exams short! Poor Dr. Allison had to keep running to the copier to make more exams. There were 506 people scheduled to take the exam last night and he ordered 540 copies of the exam, so we should have had plenty, but somehow we ended up *way* short. I’m wondering if the 5 and 4 didn’t get transposed, so we actually got 450 copies instead.

Otherwise, it really wasn’t too bad. There were a few typos that people caught along the way and there were a few silly questions — “What does he mean by ’size’? Weight?” “Um…I think he means size.” — but nothing truly ridiculous. The first person done in my room finished after about a half hour (the exam was scheduled for 2 hours) and I suspect that she did well. She was the first one in the room when I opened it up, sat down front, was well-organized with her pencils and calculators…she had the facade of a diligent student, at the very least.

And now that this exam is done, my TA responsibilities are essentially over. This exam had a lot of acid/base questions — yay, math! — so traditionally people come to the office hours for help with those. The next few exams are glycolysis and the TCA cycle and things that you just have to memorize, essentially. As a TA, there’s not much I can do to help you learn those pathways, so I suspect my office hours will be held in the lab, with a sign on the library door saying where to find me if needed. Not bad for $600, eh? Plus, I get to say the word “proctor” a lot, which always makes me giggle inside. Proctor.

Well, perhaps not my soul, but certainly the vast majority of my free time the past few weeks. Damn you, World of Warcraft, how I love you so. I’m hoping that my insatiable (note: I mistyped that as unstable twice which amuses me) desire to play will calm down over the next few weeks, ’cause it’s a little ridiculous. However, I’m still having a hell of a lot of fun playing, with the exception of yesterday morning. I was in a pick-up group playing healer for a run through Blackfathom Deeps. Frustrating as hell. BFD is the last of the lower-level instances from what I can tell, and rather than pull one mob at a time, these guys would aggro an entire room and whine for healing. We’d survive for a while, then I’d get attacked (as I was healing so often) and call for help which would arrive only about half of the time. I’d then have to spend my manna healing myself…they’d die, I’d die (or vice versa) and we’d get rezed by the one guy who’d survive. Frustrating. I managed to make enough money off of the little loot I got to pay for my repairs, but that was about it. Nothing fancy. Saturday I ran through Shadowfang Keep with a guildie and his friend and it went much better. They did a much cleaner job of pulling one (or at most two) mobs at a time, so I had an easier time keeping them alive, and we all had a really fun morning. No true phat lootz, I don’t think, but I got some decent junk. And had a fun time, which is why I’m playing.

Sorry about that. I got a little tangential there. For those of you who skimmed that last paragraph, let me summarize: “Nerd nerd nerd, nerdnerd, nerd nerd nerdnerd.” Heh.

To help tame the WoW beast a little, I’ve decided to make two deals with myself (and we’ll see how long I stick to them) and how much time I spend in game. First, for every half hour I play I’m going to spend five minutes cleaning my office until it’s done. Second, for every evening I play I’m going to spend a minimum of 20 minutes on the exercise bike. Those shouldn’t be too tough to follow and I’ll end up much happier at the end.

So what else has been going on? Work, I suppose. Work has been hella-frustrating, which is part of why I’ve just been playing WoW when I get home at night. We had a manuscript rejected last week which was annoying. It wasn’t my manuscript but the job of getting it resubmitted and published is going to fall on me. Why? Because I’m the only person left in the lab listed on the paper. Well, other than Tom, and I’m having a hard time seeing him do benchwork anytime soon.

I’m not really okay with this. Our deal was that I would repeat some of the data analysis, as we had some beautiful footprints but had only done the footprinting one time. They were clear and reproducible within that one time, but we still wanted confirmation, just to be sure. For doing this (and it ended up being a couple months’ of work) I’d learn how to do footprinting and would get my name on the manuscript, somewhere in the middle. Done and done. However…Now that the manuscript is back, Tom wants me to plan what to do next to address the reviewers’ concerns and I don’t see what I’m going to get out of it. I’ll work on the plan as an intellectual exercise and as practice for my future manuscripts, that makes some sense, but as for doing the experiments we’ll need to do? Not so much. I’m not going to become first author on this paper, and who cares if my name is third instead of fifth? You know what that’s not going to do? Get me graduated. We’ll see.

Okay. Time to stop whining for a bit and go do some work. Type to you guys later. Sooner than a week, I promise.

Today is my last day of work before I head off on vacation, and I have absolutely *no* desire to do anything productive. I was hella-lazy this morning and didn’t leave home until just after 9 (usually I’m at work by 8:30, tops), but it actually turned out well for me. There was a fire drill in my building today, so when I rolled down the big hill on my bike I was greeted by a large crowd milling around outside and the faint sound of a klaxon. I still had to wait outside while they cleared the building (although I think they just make people wait outside for a random amount of time, then let them back in) and then got my daily stair climb in. Good times.

Item number two: my friends are bums. Or, perhaps I have fewer friends than I thought I did. I invited about 25 or 30 people from school over to the house tonight for dinner and early-summer festivities. Know how many responses I’ve received? About 6. Actually, that’s not true. I’ve received exactly one response to my email. The rest are from people I had already invited in person (namely, the people I actually see on a daily basis). *sigh* I’m trying not to let it get to me, but I’m failing. I just feel so fucking isolated much of the time and thought this would be a fun way to spend time with people I like in an non-work or non-class setting. Feh.

Okay, enough navel-gazing. Item number three: trip preparations. As I mentioned above, this is my last day before a week and a half of road tripping with my wife. Woo!

You know (back to the party stuff), I don’t think I would be nearly as bothered if everybody wrote back saying they already had plans. I know it’s Memorial Day weekend so some people are going home and others are going on a grad school camping trip (that I completely spaced about when picking this weekend to have people over). But nothing? Grrr. Anyway.

Sorry about that. Back to the trip. Woo! Vacation! I’m trying to get things cleaned up and organized at work today so I don’t come back to a huge pile of disorganized crap after the trip. It’ll just be a moderately large pile of disorganized crap. I need to do some cleaning and equipment maintenance before I go and make a backup of my lab data in case something horrific happens to my computer on the trip.

Oh, so yeah, I’m going to have my laptop on the trip, but mostly I plan to use it for picture storage. I don’t know how much of a chance I’ll have to check my email or blog while we’re going. I’d like to post pictures as we go, but we’ll have to see how realistic that is. Probably not terribly.

The other things I need to do before I leave today involve making lists. I need to make a list of things I’d like “my” undergrad to work on while I’m gone so we can hit the ground running when I get back. Mostly probe testing, that sort of thing. The other list I want to make is one of my current projects and the next few experiments and things to do for each one. I feel like I’ve got about a million things I’m doing right now and am afraid that projects are slipping through the cracks. I think I’m on the verge of gathering a lot of useful data and don’t want to miss any opportunities.

I’ve got a bunch of “fun” reading to take with me on the trip. I had been planning on taking my pile of papers to read, which is about three inches thick at the moment, but have recently changed my mind. Instead, I’m printing out all of the recent PWS/AS papers and am going to re-read them. Most of these papers I haven’t looked at in a few years, so I’m sure there’s a lot of information I’ve missed. I’m going to try to take notes on each one and may be able to start writing my thesis introduction, which would be awesome to have out of the way. I’ve got a bunch of recent review articles as well, but most of it is primary literature…mouse models (with or without phenotypes), case reports, that sort of thing.

Otherwise, I think we’re mostly prepared. We still need to pack, of course, but we’re not leaving until Tuesday. We’ve got our maps and junk from AAA and have heard from everybody we’re planning on visiting. One of these years we’ll get to northern Michigan, Julie, I promise. Some summer, I think…I don’t think I could handle a northern Michigan winter.

I’m about done burning a set of mixed CDs for the trip. I don’t think that Emma will hate *all* of the music. I’m going to try to introduce her to a little nerdcore, so we’ll see how that goes. Just a little of tha Front. Nothing major. Oh, I should probably quickly type up the contents, because I’m never going to remember.

Okay, time to do a little work. I’m planning to knock off a little early so I can take a shower and straighten up a little before people come over. Happy Friday! Don’t forget: dinner at my house tonight at about 6:30 or 7. I’m planning on grilling — we bought hamburgers and hot dogs (as well as their vegetarian equivalents) and some great-looking corn. The weather should be good, too, so hopefully people can hang out both inside and outside of the house. Email me if you’re planning on coming, so I’ll know if I need to make an emergency Publix run.