Science Monkey

This has been a fairly long week, but an overall decent one, I think. I’ve managed to get some decent work done — well, not good work so much as good troubleshooting — and have managed to have some nice time with my wife. My bike wipeout wounds are even healing decently, although the bruise on my leg extends from about my hip to my knee at this point. It’s part of the healing process, I suppose, but it’s still fairly impressive.

The past few months — actually, the past three years — of work have been moderately to excruciatingly frustrating. I’ve been able to generate some data, but have had an absolutely nightmarish time trying to reproduce any of it. I’ve become increasingly concerned of late that it’s me, that the problem is my hands. Well, perhaps not my hands exactly, but you understand what I mean. I mean, what’s the common factor in all of these experiments? Me. My hands on the pipettes, my eyes looking through the microscope. Me.

I think that my problems are related to my poor focus. The mistakes I make are little stupid things: using the wrong buffer and not noticing until it’s too late; skipping a step in a protocol I think I have memorized; missing some teeny, tiny, infinitesimal aspect that completely borks up my work. And I’m not sure what do to about it in the short term. Long term, my psychiatrist and I are working on some things, but what do I do for Monday? Is it an attitude change? Do I need to get obsessive about making (and then following) lists? Checklists? Work when noone else is around to distract me?

I can do this job. I honestly believe that I can be a good scientist and professor at a major research university. I think I have the brain power, the interest, the drive, and the communication skills. Unfortunately, the path to that chair leads straight through the lab. And if my skills are at least good enough, I’m not going to be able to get through that obstacle.

Maybe I’ll try to blog my progress. I’ll post my to-do lists every morning, then in the evening I’ll write a summary of my day. I realize that this is not terribly exciting for you, dear reader, but I think there are only about three of you so I hope you’ll forgive me. If you can entice me out of the house some weekend, I’ll buy you a beer or seven.

Anyway. Speaking of post-graduate-school life, I had a nice little chat with one of the new professors on campus about spending a year with him after I graduate. My hope and my plan are to be done at this time next year. The problem with that, however, is that Emma will still have one year remaining on her residency, so it’d really be convenient to be able to stay in town. So what I’m thinking is this: I spend that year in a more hardcore biochemistry lab and learn how to do protein and protein complex purifications, that take that with all of my molecular biology techniques on to a more long-term postdoc. I think I’d be hellacompetitive with those skills. ChIP, expression studies, some FISH, 3C, LMPCR, DNase hypersensitivity, RNAi, *and* protein complex purification? That’s not bad. That’s not bad at all.

So anyway, as I was saying. I had made a joke in one of the joint lab meetings early in the term about coming to him for a postdoc and apparently he remembered it and was at least a little interested. It really was like 90% joke, but there was that 10% reality in the back of my mind. The joke was pretty good too…one of his students was presenting and she had forgotten a pointer. I don’t remember if she couldn’t find the stick or just didn’t want to use it, but I offered her my pointer. As I sat down I called across the room, “Just remember who helped your student out when I’m coming to you for a job in a year.” Everyone laughed…then they laughed more when the batteries died about three-quarters of the way through her talk! So he came by the lab on some day this week…Thursday, maybe, and wanted to know if I was at all serious. So we talked about it for a bit. I explained to him my situation and what I wanted out of that year, what I hoped to accomplish, and said that his lab actually was one of the three that I was thinking about. He said that by this time next year he expects to have protein purifications up and running in the lab, so it’s definitely a possibility. It’s still a long way away, of course, and there’s a lot that can happen between now and then, but it was encouraging. I think I’d learn a lot from him and his lab, too. He’s at least as full of energy as Tom is, but he seems to put more of it into his work. From what I hear he’s something of a hardass, but that’s not necessarily a bad thing. He seems to be really rigorous about his science (and his trainees science) and seems to really ‘get’ being a mentor in a way that jives with me. He has a shitton of data, too, and actually publishes papers, which can’t be a bad environment to be in either.

Enough about work. The homefront has been pretty nice this week. For some reason I was motivated to make a meal plan this week that we stuck to reasonably well. Well, three nights out of four isn’t bad. Emma went out last night to the CMC’s SpringBoard (I, being an introverted recluse, declined) and she’s working tonight, so those nights don’t really count. Thursday night she really, really wanted something fried, so we went out to Las Margaritas, our favorite Mexican joint in town.

The pets are all doing well. The chickens have all stayed inside the coop since the incident I blogged about a few days ago, so that’s good. The cats are very cute, of course. The weather has been beautifully cool much of this week, so we’ve had doors open and haven’t needed the AC much. The cats love this weather, because then they can curl up on the old futon on the breezeway and feel like they’re almost outside. In fact, I’m sure that’s where they are now. We have a new friend in the neighborhood, too, which is exciting. For two nights in a row there has been a rabbit in our front yard when I’ve come home from work! I took a bad picture of him (her?) the other day that I’ll get online sometime tomorrow or Monday. He’s really very cute. I’m not sure what he’s found to eat, though, in the front yard…hopefully he won’t destroy the garden on the other side of the house. There’s lots of stuff there that I think he’d enjoy.

And the squirrels. The squirrels are shameless. They have knocked down the birdfeeder at least four times this week. On Thursday, they knocked it down twice! They knocked it down early in the morning, but it had just fallen to the base of the pole that it hangs on, so I saw it and put it back up before I left for work. When I came home that night, the birdfeeder was down again, and this time it was under the hammock. They had taken it and pulled it away so they could eat all the tasty goodness inside. Stupid squirrels. Well, smart squirrels, actually, but slightly annoying nonetheless.

There was something else I was going to write about, but I’ve forgotten what it was (see? the lack of focus?). Oh well. If I remember, maybe I’ll write again later tonight. For now, though, I bid you good evening and share with you this picture I took the other day in our front yard. I’m rather pleased with how it turned out. It’s almost artistic or something.

It’s the end of March and as good a time as any for a little navel-gazing. I thought I’d take a few minutes and review my resolutions and see how I’m doing and how I might be able to improve over the next three months.

1. Lose 40 pounds.

This is the one I’ve been struggling with the most. Since January I’ve been on a 10-pound yo-yo. Very frustrating. I tend to eat and exercise well on Monday through Wednesday or Thursday, then slack off the rest of the week.

I’m going to try and take up running. Well, jogging for the near future and walking for the immediate future. I figured out a nice two mile walk around the neighborhood earlier this week, but haven’t walked since Wednesday. I’ve been pretty good about riding my bike or walking to work, though, which makes me at least a little proud. I’ve only driven in or gotten a ride about five times this year so far.

2. Spend more time with my family.

If by family, I mean wife, I’m doing pretty well with this one. I’m trying to work hard in the lab when Emma is on a more time-intensive rotation and then spending more time at home when she’s not. Er, not on a time-intensive rotation, not not at home. You understand. I haven’t spent much time with my immediate (or extended) family but…so be it.

3. Make new friends and spend more time with old ones.

Yeah, this one is trying. I’m reasonably good at being social and amiable at work (I think), but I’m a total loner afterwards. Let’s work harder on this one, eh? Maybe I’ll get my happy ass to a Florida Free Culture or Alacloud meeting, given my desire of being that sort of geek. I should go flogging, too…that’s almost like exercise.

4. Drink good beer.

Check. I’ve been enjoying Leinenkugel’s Sunset Wheat and Sam Adams White Ale this season very much. I’ve been on a wheat beer kick for this last year or so but think these are really nice. I could always go check out the homebrew shop and learn to make my own. That might be social, too, but will probably work contrary to goal #1.

5. FINISH MY GODDAMNED DEGREE.

Getting there. I had a committee member tell me that I’m essentially ready to move on, other than having a coherent story that I can turn into a manuscript, a thesis, and a job talk. I’ve got a decent plan to get that story right now, so we’ll see what I can bang out in the next three months. I suspect I can get a lot of data if I can maintain my focus.

6. Take piano lessons.

Check.

7. Ride 1000 miles on my bike.

So far, I’m at approximately 178 miles for the year, so I’m a little off the thousand-mile pace. I can pick that up this next quarter.

8. Write something every day.

Meh. Not so good. I’m blogging more regularly, which is almost like writing, but I’m not doing the productive, work-related writing that I’d like to have done. Now that I have a good idea of my final project, I should start working on my thesis. I can do the Introduction, Relevance, and Materials and Methods sections now, and work on the rest as I get the data.

9. Get my happy ass organized (GTD).

Nope. Haven’t even read the book yet. I’m trying to write lists of what I need to do at the beginning of each day which helps, but I’m nowhere near organized yet.

10. Learn to use my camera well.

This one has been fun. I’m having a great time taking pictures with my new camera, as you’ve probably noticed. I should try and learn some of the features of the camera and see if I can’t take some more artistic pictures. That’d be nice. There are lots of great birds around the house right now, including a great blue heron in the pond up the hill, so I’ve got some good subject matter.

Okay…that’s enough navel-gazing for now. New petite protopodcast coming soon, I promise. I know you’re all on tenterhooks waiting for the next one. Go Gators!

One last question. What do you think: Haircut? Or no?

My month of presentations is over! Woo! This afternoon I gave my last Biochemistry Journal Club presentation and I think it went pretty well. Well, I think the first three-quarters went pretty well, then I started to feel the effects of my lack of sleep. Plus, the last few figures were extremely repetitive and it felt like there were a dozen slides of the same thing again and again. Anyway.

Oh, and I get to be a guinea pig for a new evaluation procedure. I think it’s a good idea…we don’t usually get a whole lot of feedback on our presentations, so providing everyone a form to fill out will give at least some minimal feedback. I’ll let you know how it goes.

On Friday and Monday I got to teach the little med students a little about molecular biochemistry. The med school thinks that all of their future doctors should have some lab experience, so there’s a two-day lab course for anyone who hasn’t worked in a lab before. They do a little Southern blot and a couple of PCRs and then never have to worry about running a gel ever again. It’s not a bad gig, actually — $600 for two days worth of work (and availability to answer questions afterwards) — and it’s actually a little fun. I mean, I got paid to hang out with Val, Amanda, and Vijay and didn’t even have to go to the lab. How nice is that?

On the homefront, Emma and I have built one new garden bed and are working on a second. The seeds I planted a month ago are growing well and…well…I didn’t exactly think this thing through completely. You see, it’s time to move the seedlings to the garden bed and we’re a wee bit short of space. Oh well. It’s a great excuse to borrow the rototiller and build the new beds in the back.

Have a happy evening. Type to you tomorrow!

This weekend was far too short. I could totally use another week or so of vacation. Still, I survived the first day back from Spring Break (not that I went anywhere, but…) and kept busy all day.

I presented at the Epigenetics Supergroup meeting this afternoon and it was pretty crappy. Tom and I were supposed to go over my slides on Friday, but he had a doctor’s appointment that kept him away from the lab from the end of my committee meeting until after I left for home. I assumed he was going to be in today — he hadn’t told us otherwise — but was wrong. That’s what I get for assuming. Apparently he has out-of-town company here this week, so he couldn’t come in until 4 this afternoon. Supergroup starts at 4, so there wasn’t really time to prepare before I had to present. Oh, and he was late. His company is going to be around for the next few days, so we’re not expecting him to be at work until Thursday. Nice, eh?

Despite being busy, I didn’t get a lot accomplished today. I was asked to go to a seminar early this afternoon (there was a lack of warm bodies, I think) and then spent the rest of the afternoon preparing for my talk. The agenda for tomorrow includes 54 minipreps (plus digestions), running gels for the total of 72 minipreps I’ve done over the past few days, labeling two LMPCR probes, starting a gel to make some Southern test strips, and mucking about in the tissue culture hood. I also have a meeting for the med school lab course I’m TAing for tomorrow afternoon over at the new building, so that’ll burn up a decent chunk of my midafternoon. I’m also going to try and do some RNA preps and RTs tomorrow, so that those are out of the way. And I need to check on that RACE kit…

Anyway, enough mindless babble for this evening. I’m going to go practice the piano for a little bit and then hit the sack early. Happy Monday, friends and neighbors.

So today is March 15th, one of my favorite days for no discernible reason other than that I can call it the ides of March. I know there are ides for all months, not just March, but if I said to you, “Beware the ides of September!” would you care? I’m guessing not.

Of course, you might not care if I said to beware the ides of any month…I know how you are.

It’s been a busy past few days, so I’ve been a slacker on my blogging. I’ve put in a goodly number of hours the past three days and have gotten a lot of low-level stuff accomplished. Lots of PCR and cloning, which correlates to lots of minipreps, digestions, and gels. Man, I love minipreps…there’s something so relaxing about them to me. I get into a nice zone of mindlessness. It’s almost but not completely unlike meditation.

The rest of my time has been spent preparing for my committee meeting tomorrow, which should be short. Hopefully. I just had a meeting in December, so I don’t have a lot of new data to present to them. I have decided, though, that rather than spend the next eighteen years doing an analysis of the long-range interactions in the entire domain in multiple tissues, I’m going to focus on one gene in particular. It’s not a terribly interesting gene in and of itself — there’s no phenotype to the knockout — and it’s not conserved between humans and rodents (it appears to have retrotransposed into the domain sometime after our ancestors split), but it is imprinted and I’ve found varying levels of expression in a few different tissues, nicely paralleling what other genes in the domain do. High expression in brain, low expression in fibroblasts, etc.

My plan is to do a complete epigenetic profile of the gene’s promoter in a few different tissues. As of right now, we’re thinking newborn brain (high expression), adult spleen (no expression of the other genes…I haven’t checked this one yet), newborn or adult liver (moderate expression) and fibroblasts (low expression). I’ll do a DNase I hypersensitivity analysis in the tissues at the promoter and ChIP for a variety of histone modifications. H3K4 and H3K27 methlyation, for instance. We also have a model for the involvement of a few specific transcription factors, so I think I’m going to ChIP blindly for those factors. I have to wait on an antibody for one of them, but for the rest we have good antibodies. I’m also going to do an in vivo footprinting analysis of the promoter (and probably the early body of the gene, based on predicted transcription factor binding sites). I think we’re going to start with the fibroblasts and cross our fingers. Expression is relatively low in the fibroblasts which may correlate to weak footprints, but Jixiu has found absolutely blazing footprints at another gene which is expressed in a similar fashion.

Nothing else terribly exciting to report at the moment. I’ve recently (as in yesterday) been in touch with a Heggestad in Norway and we’re exploring to see if we have any common ancestors. Emma and I are going to go to the beach this weekend and relax. This is her first weekend completely off in months (and the last for at least many weeks), so we’re going to seize the opportunity to catch a few rays.

The chickencam is today facing the woods around our hammock (visible in the lower right corner of the picture). I think the cats mess with it during the day, because I’m convinced that the picture shifts between the time I set it up in the morning and the time I get home. I could try to figure out how to keep an archive of each picture, but that’d just be clever. Better to guess, right? Okay…back to work. Those 30 minipreps aren’t going to prep themselves!

Tom let our postdoc go today, because we’re broke. This really sucks. He’s a great guy and a really good scientist, but I’m concerned about him. Because he’s been in Tom’s lab, he doesn’t have any publications yet. He’ll have one soon (assuming it goes out, etc.), but it hasn’t been published yet. There’s one professor in the department who has already expressed an interest in talking with him, so I’m hopeful that he’ll be able to find a new job soon.

What is the point of scheduling a standing data review appointment if you’re not going to be there? I assume it’s not malice but what does that leave?

According to Tom, our fiscal person, “jumped the gun” yesterday. We’re not completely broke. I do wonder, however, by how much he jumped the gun. Six months? One month? A week?

In happier news, I saw footprints today! You may recall my spazzing out over seeing bands on a film last week. That night, I put the film between two intensifying screens and threw it in the -80 freezer. I meant to pull it out over the weekend but…well…I forgot. I remembered it this morning and ran downstairs to develop it. The autorad was overexposed, of course, but there were some very clear, obvious footprints. My loading wasn’t even horrible! Sadly, the region that was the most important to duplicate was too fuzzed out to read clearly, so I have to repeat it, but I’m certainly encouraged.

I also found out today that Tom took my name off of a poster for the Mkrn3 footprinting. Jixiu wrote an abstract for some upcoming local jollification…er…poster session and put my name in the middle of the list of authors, as I’m repeating his footprinting work. Apparently one of Tom’s revisions was to take my name off. I wonder if he’ll put it back now.

Courtesy of the incalculably awesome Merlin Mann, GTD for Scientists (written by Drew McCormack at MacResearch). One of these days I’m going to actually read that book.

I think the lab is in trouble. Jason went to get a PO number today so we could get some sequences run through ICBR (Jingda, who usually does our sequencing, is out of town for the next three weeks). He was denied, because we’re apparently broke. One of the senior fiscal people in the department was reported to have said that the department’s support of Tom is over.

Yikes!

I asked Tom about our funding situation after joint lab meeting (or, as the presenter called it, “supergroup meeting,” which I really liked). He said that we weren’t completely broke just yet, but that things were going to get tight. He claims that it’s the Dean’s Office money that is over and that there is still departmental money for our experiments. I’m not so sure. Tom is going to talk with the department’s fiscal person tomorrow. I’ll report whatever I hear.

Fuck a hairy duck.