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.

As you can probably guess from my lack of posts, this has been a busy week with little significant information to share. Work has been plodding along reasonably well which is a nice change. Waradwen got a new pet this morning (two actually, details below). Uncle Dave and aunt Martha were in Florida this past weekend to celebrate Dave’s birthday, so we got to have dinner with them on Monday. Emma had a day off on Wednesday and spent it with Susy at Epcot (pictures to come). Overall, I’d give the week a solid B.

As I mentioned above, work has been decent this week. My last two sets of mouse preps are looking good so far, so we might be able to actually generate some data in the next week, which would be terribly nice. These experiments are just confirmation of what a previous grad student saw (but never repeated and her probe was poorly located) and what a postdoc saw years and years ago (but was never followed up on). Assuming all goes well, we should be able to get a manuscript together pretty quickly, on which I may or may not be first author. Tom said I would months ago, but I haven’t been involved at all in the writing process. The former grad student has written a couple of drafts but Tom says they’re nowhere close to what we want, so he’s declining to share them with me. I don’t quite get it. The first author does the bulk of the experiments and the writing, right? We’ll see how it goes, but I’m expecting that I’ll be second on this paper. Not something to quit over, but yet another time where Tom has said one thing and then done something else.

Tiger is getting increasingly confident in her ball. She ran down the hallway last night, then came back to us. I don’t think that she’s just running blindly around, either, because she’ll go towards specific objects. Or cats. Heh. Last night we had the front door open because the weather was so nice and poor Rory was sitting, looking out through the screen, when Tiger charged at him. I’m actually a little happy about that…I’d prefer it if the cats had a healthy fear of Tiger, because I think they could eat her in about three bites if they decided to.

We also figured out a good way to give Tiger her baths. Chinchillas take sand baths, where they roll around in the dirt to get clean. Nifty, eh? We bought her a chinchilla-shaped ceramic…well…bathtub but she never seemed to really like it. This week we went lower tech. We bought a large tupperware container and found a place online selling large quantities of the sand. What we’re doing now is putting a nice layer of sand on the bottom, then putting her in with the lid on upside down (so she can, you know, breathe, but not run away). She freaking loves it. Yay! She digs down into the dirt then flops over and rolls around, then repeats herself. Very cute to watch. The container we bought has clear sides so we can watch her and one of these times I’ll remember to set up the video camera.

Much of my free time this week has been subsumed by Warcraft. For those of you sane enough to avoid the game, it’s Brewfest, which has been a heck of a lot of fun. There are racing games you can play for tickets and when you earn enough tickets, you can buy an epic mount that’s only available during the fest. The quests are repeatable, but only once or twice a day, so it’s taken a while to earn all of the tickets. I averaged about 70 a day, I think, so it took me ten days to earn the 600 tickets. I totally borked up the beer run last night and was six tickets short, so of course I had to get online early this morning and finish. I’ve been saving money from my arcanite transmutes (10g a pop, minus about 2.5 for the mats, so that’s not bad) and bought both the epic mount and the regular mount. I can’t use the epic mount until level 60 (and after I improve my riding skill which costs another bomb) and the regular mount was only 10g (compared to the 100g for the epic), so I went ahead and bought it. I realize it’ll live in my bank after about a month or so, but that’s okay. I’ll have fun with it until then. Plus, I had the money. Just barely, but I had it.

Now poor Wara’s flat broke. I sold some redundant junk in my bank to make a little money and I have the mats for more arcanite transmutes, but for the moment I’m basically penniless. Oh well. I can always bum money if I really need to, or I can just earn it again. Plus, as I understand it, money is easier to come by as you get higher up, which will be nice. At least I’m pretty set with gear and weapons for a while so not having money won’t be a huge inconvenience. Pretty soon I’ll be able to cross into Outland, whence the easy money, as far as I can tell. Well, easier. Until then I’ve got some reputation grinds to work on (Argent Dawn and the Cenarion Circle, to be specific, so I’ll be alternating between opposite corners of the world).

Enough nerding out. The sooner I get back to work, the sooner I’ll be done. The sooner I’m done, the sooner I can go home and get playing. Yay!

And my last posts were how short? Uff da!

Life has been pretty good here in Heggestad/Caplan-land. We’re enjoying the company of our newest resident, Tiger the chinchilla, who is un-fucking-believably cute. I put some pictures up on my Flickr page and will get some more up probably later tonight. She’s so so cute I just can’t stand it sometimes. The cats have been remarkably tolerant, too, which has been nice. Although…I am a little worried that they’ve been *too* accepting and am starting to question their observational powers. Maybe they don’t care because their lives are not too significantly disrupted. The only resource that Tiger competes for is our attention, and, well, they’re cats. As long as they have food and comfortable places to sleep, they’re pretty much okay.

I’ve been playing a little less WoW than previously, but I’m still progressing nicely. Waradwen’s up to 51, so woo-hoo! I ran Zul’Farrak this weekend with some guildies and the lovely and talented hunter Linada which was totally a blast. I sort-of screwed up the timing of the run, though, because I missed the season premieres of The Simpsons and Family Guy. Sigh. Family Guy sounds like it was great enough to go look for online. Hmm…anyway. No real progression in my tradeskills recently. I’m at 300 herbalism and 295 alchemy and can’t go higher until I get to Outland, which isn’t for a little while. I know I could buy a port there, or beg my guild friends, but I’m not in a hurry. Then again, it’d be nice to progress in the skills…I’ve been lax in my Monday Morning Screenshots of late because there hasn’t been a whole lot of change. I took a picture yesterday afternoon with my new hat and it’s at the bottom of this post. Do you like my hat?

Work has been okay the past few weeks. Nothing terribly exciting. No significant data or anything. I’ve got a committee meeting a week from Friday and am freaking out to a minor degree given my recent dearth of data. Maybe…maybe it’ll have to get rescheduled for some unknown reason. That’d just be tragic, wouldn’t it? Maybe we can push it back to…like…November? I should have some data by then. Oh, probably not.

Enough rambling for now. More work, less goofing off. Yeah, right.

I’m in a good mood this morning, and I can’t really explain it. I didn’t sleep well last night. Since Emma’s out of town, I’m eating fairly poorly. I’m certain I’m not getting enough exercise. The weather is pretty ugly, with it being overcast and drizzly all night. *shrug* Whatever it is, I guess it’s working for me. I actually feel moderately cruddy but am still in a good mood. Maybe I’m just happy it’s Friday.

I’m even feeling fairly charged up about work, which makes almost *no* sense whatsoever. We’re mired in some pretty nasty weeds right now, to mix a few metaphors, and it seems like we fix one problem to find two more new, worse ones on the other side. The current major problem is that our Southern blots aren’t working correctly. Sweet Jebus, Southern blots! How much more fundamental can you get? Our signal-to-noise ratios have plummeted in the past few weeks…I think that both sides are a problem. That is, we’re getting weaker signal for our bands *and* we’re getting more background noise. Both in- and out-of-lane background, for the two of you who know what that means.

At any rate, it’s frustrating. I think I’m going to spend the next week or so getting my hands dirty and really trying hard to solve the problems we’re having. We have an undergrad who has been doing most of the Southerns this summer so I can focus on some other experiments, but we’re having enough problems that I think I need to step in. She had lovely results while Jixiu was still around, but since then they’ve gone downhill. I don’t think it’s a buffer issue, because I’m using the same buffers for my LMPCR which is going reasonably well right now. I’m not as good as Jixiu yet, but I’m not bad, either, so I think our buffers and equipment are okay. That leaves technique, basically, as the problem. We spent all of lab meeting yesterday discussing the problems and I think we have some tweaks to the protocol that will help. I’m going to run a few Southerns myself this next week and we’ll see how they turn out. I’m optimistic.

Things are going well at home. Emma is out of town until Saturday, in Kansas City at a family medicine student and resident conference. She went a few years ago and had a really good time so I hope she’s having fun again this year. Her program didn’t get the best of residents in this recent class — it’s not that they’re bad, they’re just not quite as good as Emma and her group for whatever reason — so I think they’re going to try and recruit harder this year. I suspect that Emma will end up as one of the Chief Residents next year, which will be good and bad. I think it’ll be good for her because she really enjoys being in a teaching and supervisory role and I think she’s really good at it. It will also mean more responsibility and time which will be bad for both of us. Perhaps not “bad”, but harder. More time at work = less time at home.

I’m rambling, so I’m going to stop now and get back to work. My centrifuge must be almost done by now, so I should go attend to that. Happy Friday morning, my friends. I’ll type to you soon. I’m planning on eating Chinese take-out and playing Warcraft all night, so come find me on Arathor. I’m getting close to level 40 and that mount…

PS: Before I forget, I wanted to clarify something I wrote the other day. Emma didn’t really yell at me for playing Warcraft. She had just had an extremely frustrating experience at Walgreen’s and snapped a little. Not a big deal, not a fight. I just thought it’d be funny to write that we had our first fight over Warcraft, but I might have been mistaken. Okay. I’m off. Laters.