Dear blog

I will update later, since I started typing my blog entry that covered the past few days and the entry turned into a (battery)power sucking monster. I am updating now just to say that SD weather is wonderful and ThinkGeek is freakin' awesome (I got the catalog in the mail today).

Holiday rush

I'm wondering whether or not to bother coming into lab at all tomorrow, since I've got most of the stuff planned so that all experiments can be wrapped up by the end of today. Transit by bus to and from campus will take me two hours. I need to arrive to the airport early, also by bus, which will take me at least one hours and thirty minutes. If I have a flight at two-ish that means I should probably leave house at around noon, which means I need to leave lab at eleven, which means even if I got to lab by eight in the morning I'll have a grand total of three hours which...is enough to run PCR and maybe a gel. Purify RNA maybe if already have samples prep'ed (which I don't, since I finished a fresh batch yesterday). Do some cell culture (also finished yesterday). More likely, I'll be doing comp bio stuff, and now that the initial downloading and compiling portion part is over, I'm collecting sequences, which I can do at home just well as in lab. Which leads me to ask why the heck would I come to lab tomorrow?

Therefore, unless I forget something important (such as an incubation) I probably won't even be in lab tomorrow.

...

I got the wheels changed on my car over the weekend, since they are pretty old and while a bit of dry-rot isn't too bad on the locals I didn't want to take the chances when Lucy and I drive long distance. I also had some time to make up my Christmas list for this year and spent some time staring at the calendar, trying to figure out when I need to mail what to whom so that it arrives on time, given that the speed of delivery by USPS seems to asymptotically approach zero the closer we get to Christmas. (Well no, it isn't that bad. I'm exaggerating by a lot. The point is the speed will be slower and the margin of error greater and if I were to plot it it would probably look a little like something from the half-life decay graph.) I have not yet heard from Malvina (does anyone have her current email address? Does anyone mind checking the emails I've sent out to make sure that I am using her current email address?) but I think we're good to go for everyone else.

...

My mice had two litters last week. One of which got eaten over the weekend. Lab mice are very inbred and strange. (Read: disgusting.)

...

I went out to dinner with some of my labmates (and whichever of their spouses that could make it) last night. It was fun. The atmosphere was a lot more relaxed since the PI (who is, when all's said and done, our "boss") wasn't there. Wendy and her husband were nice enough to give me a ride so I won't have to navigate the two highways that's between where I am and where the place is. There was a lot of ribbing involved for everyone regarding lab and life. Considering the fact that it was a Monday night, it was very relaxing.

Radioactivity: day 3

Did you know that ethanol is now considered to be a toxic controlled substance? As in a) we're no longer allowed to dispose of it down the drain (even though I'm sure people are allowed to pour liquor down the drain without having to fill out a gazillion forms) and b) we can't order more ethanol without going through paperwork. Lots of paperwork. Like hospitals and many other labs around, we use 70% ethanol to disinfect working surfaces, add to that the fact that we are a genetics lab and need ethanol to precipitate DNA and such, we go through a lot of ethanol. Supposedly they changed b) because they were worried people would just order ethanol from lab and then drink. To which I say: you know, given where we are, there are easier ways to obtain better drinking-quality alcohol illegally than navigating the forms for lab reagent orders.

Silly EH&S people.

I've successfully labelled my probes and my blot is now hybridizing. The washing and the exposure starts today which means that today is the last day I have to deal directly with high beta emission before Thanksgiving. I used about 15 mCi yesterday and all went well. The sweep for radioactivity gave all clear down to the 0.1mCi level. No one will have to die from radiation poisoning. Life is good.

In between I've also figured out how to compile all the programs on Daemon for my comp bio stuff. (Had to download a bunch more packages for xorg to support the cladogram-drawing functions, and Fedora 11 put the X11 files in weird locations, but otherwise wasn't too bad.) Now off to class!

I drink from the keg of glory

Or at least the keg of geekdom. I've finished configuring Fedora and this time around with Linux I've managed to add in the configurations for my tablet including pressure sensitivity. Everything works! I have wireless! Also, Fedora continues to be super shiny and very much faster than my xp system.

That just makes my day.

My PI quoted Tolstoy at me to illustrate the process of antibody synthesis (which I will be making for my protein at some point). It is awesome, horrifying, and hilarious at the same time. I mean, Anna Karenina? Really? Was that necessary?

Sometimes I think I like my thesis advisor because of his strangeness. Other times I just wonder.

On Daemon again. Now running on Fedora (the Ubuntu CD had an error in it and didn't check out with the system). I have internet. And also a very shiny GUI that has 4 separate desktop spaces. Huh.

Hee

Daemon says its "respawning". Which isn't good, but I'm too busy being amused.

Respawning. Really.

This week's been a lot more productive, lab-wise, than I have been in a while (read: before qual took over). I finally got an in situ to work, got some qPCR data, and some E14.5 mouse embryos (the dissection of which is truly nasty). My radioactive reagents have also arrived later in the week, which means that I'll probably be shifting my focus to that the next two week while the material's still fresh (beta particle radiation, in case anyone's wondering). I've also had to collect material from adult mouse brains and got bitten many times in the process, since my strain is, unfortunately, one of the most aggressive (I call them bloodthirsty) strains. Mostly I feel bad though, because Wendy got bitten too while she was helping me scruff the mouse (she's been working with mice for years and years, after all) and she bled a whole lot more than I did with my multiple bite marks. Eventually Dorothy had to rescue us and I learned one more thing to add to the Unexpected Uses for Tweezers list.

We also had to defrost a freezer. The ice build up in it was preventing the door from closing properly and so things weren't freezing like they were supposed to.

At the home front...well when I last posted it was already this week, and not much generally happens during the week. Plane tickets have been ordered. I will be flying out Wednesday afternoon and returning Sunday morning. Christmas plans are in the making. For those of you who haven't heard yet, Lucy and I will be driving up for Christmas. I wonder how well cookies travel. (All of my baking material are here.)

Okay, time to head into lab briefly, and then do the grocery run.

Knock on wood

I've called ATT and things seem to have sorted out on that end. I've also called my mom and found out that my grandpa's officially stabilized. It seems like I've reached a resolution of sorts with life.

At least, for the first time since August, I'll be able to go through the mental run-down of recent events in my life without the knot of dread in the bottom of my stomach. I will not miss it.

I feel very cheery now. The sun's out today, without the foggy haze, and the sky's so blue that looking at it gives me an afterimage that tinges everything yellow. It's warm enough that I'm sitting around in my shirtsleeves with my sleeves rolled up. I should get tea. Then it'd be perfect (though I probably will not have the motivation to finish the experiments I'm currently running) (am boiling an enzyme while waiting for the reagents for my next two reactions to thaw).

Also: holiday emails. "If I'm an emoticon right now my symbols would be colon capital 'd'."

Someone should be enjoying this

I went and got the tire changed yesterday (it had been sitting too long with a flat + it was old = tire was beyond repair) and then ran my chores. Afterwards I felt so cheery and productive that I went and cleaned my apartment, made lasagna, and put in the new extension cord so that the lamp in the corner of the apartment will be actually usable. Unfortunately that meant unplugging and then re-plugging my wireless, which then promptly stopped working.

By which I mean the DSL was on, my computer was connected, by neither the ethernet or the wireless were connecting me reliably.

After some phone calls I was told that this was because I didn't register my new internet connection when I moved (leaving me to ask, indignant and more than a little confused, why on earth did my internet work for three month without registration and probably would have kept on working had I not unplugged it?) (the agent didn't have an answer). (Also she was just...unhelpful. Somewhat less than competent. I like the other guy I had to call in the summer better.) Then it came on that for whatever reason, I could register, because the connection was intermittent even with ethernet and so the agent unhelpfully told me to keep my computer open and see if the page ever loads and scheduled me for a technician on Monday, from 12 to 4pm, without telling me that she'd scheduled me for a technician. (I discovered this from another phone call, four hours later to try to figure out why the hell she had't called back like she said she would, and had to reschedule the appointment for Wednesday because they need a date and time when I'll actually be home.)

(Meanwhile I finished two books, made food, backed up my files and finished season 2 of Due South.)

But yeah, this morning, for whatever random reason, I've managed to register, without downloading that hideous help program that the other times the att page keep insisting I need (which would then take forever to load and my connection would always cut at sometime around 76% done). I appear to have internet now. I have no idea what happened. But I'll go and see if this lasts and if it does, then I'll call on Tuesday and cancer my appointment.

That was my little adventure (read: frustration) this weekend. I've a peach pie baking in the oven. When it's done I think I'll go and walk to the beach. Too bad my mp3 player is still broken and no amount of troubleshooting on my end seems to fix it. (I need to get a set of those small tools. You know, like the one you use on watches?)

Well, cheers. Fingers crossed on the internet!

[edit 10:21]
Verified: both ethernet and wireless now works. What the hell, 2wire? What the hell?

Passed. (Then went home directly afterward and slept.)

Well, onwards and upwards.

I...just...

Got a flat tire today. In addition to not knowing how to change a tire (someone really should teach me that, one day, before I try to navigate it on my own based on some print out from Google) (which will not end well) I know for a fact that I don't have the tools I need to change a tire.

Annie used to say, when these sort of things happen, that this just proves that there is a God and that He hates me. Although I, for the most part, remain agnostic, sometimes I have to wonder at fate's sense of humor.

[edit 11:09]
AND I just found out that the ATT account I thought I'd closed when I moved is still open and they are, apparently, still billing me. In addition to my current address's billing I mean. The phone system at ATT claims my number doesn't exist (no doubt due to the fact that I closed it) and the actual people who are in charge of this sort of thing work normal M-F hours.

[edit 12:13]
AND I think I have termites in the walls of my apartment. What the hell, life?

This is apparently how it works

Wendy told me the other day that "if you haven't gone insane yet, you haven't been in grad school long enough". After the general up-spike in panic the past few days (how is it that the PIs managed to do that, long after I'm convinced that I just don't have the energy to panic anymore, I'll never know) I'm beginning to gain a new appreciation of that sentiment.

On that cheering note, my defense's next Tuesday. It was scheduled for next Tuesday (confirmation of rooms and everything) by Wednesday, because due to the schedule of the professors and the rooms (which we do need to schedule ahead of time) the only weeks that are available are either next week or, it seems, the last week before Thanksgiving (which is also my deadline for this). Then of course it's juggling the times until the PIs said, okay, this time will work. (In between all this I've gone through my slides twice already and found a photo where people are monitoring the circadian rhythm of lobsters, of all things, by putting a wheel in their aquarium that's hooked up to the computer and seeing when they'd run. On wheels. The photo was titled "Lobster In Wheel". ) Then yesterday one of my PIs emailed me and said that she had an eye appointment at the time of my defense, and could I reschedule, please. Of course, the person who is in charge of scheduling the meeting room for my building was gone for the day, so I ended up frantically looking up room schedules for other school of med buildings and discovering that, within the next few weeks, there is apparently only one hour when all the PIs will have time for me. (The qual is designed to be 90 minutes long, with 40 minutes for my presentation and 50 minutes for questioning afterwards.)

At which point I might have said, "Oh my God" and banged my head against my desk a few times. My labmates seemed concerned.

But the problem (sort of) resolved itself. One of the PIs is still going to leave early, but the other two will make it. (Or at least, after I scheduled the new room I sent out an email which said "IF YOU CAN'T MAKE IT, LET ME KNOW ASAP!" and no one has replied yet.) It is still on Tuesday. I still need to figure out what food to get for the PIs. ("Cookies," suggested Wendy, "And bottled water. Because even if they don't like water, if they're thirsty enough, they'll still drink it!") In between all this I need to figure out how to explain the math model behind my comp bio stuff (yep, I ended up doing that for my third aim, after all) without confusing the people even more. My PI is of the opinion that I should put in the math equation so at least even if the other PIs are still confused, they can at least see that I know what I'm talking about. I'm of the opinion that as soon as I say "For the function, rho, of X and Y at residue position i" their eyes will glaze over. But that may be my inherent cynicism speaking. (Or possibly what I know from my time explaining my written qual to my committee, but I'm trying hard not to think about that right now. A healthy dose of denial seems to be how most of my upperclassmen handled it, after all.)

(I seem to spend a lot of time lately thinking "this, too, shall pass". Did you know that in order to schedule a meeting with the thesis committee, which contains more people than the qual committee, my upperclassmen have to start the scheduling process two months ahead of time?)

Thank you, everyone, for your comments. I will probably take up the offers (practice is good; practice is always good), though it'll be a little sad since the movie of my mice will only play in the slides if it's .odt. (The original movie file is .mov and it converted weird, but since it's a mac thing I guess Kate, at least, should still be able to see my twitchy mice if I mail it as a separate file.)

Christ, it's Saturday. I need to find the time to wash my car sometime this weekend. The amount of dirt on it is approaching critical mass. Or at least, approaching the level where I might consider starting a roof-top garden.

Cheers guys. Happy Halloween. Eat some candy for me. Or something.

Volunteers needed

Anyone interested in going over my qual presentation with me, over the phone, this weekend? I need as much practice as possible. Please email if you've 40 minutes free this weekend. Thanks!

Dear Diary,

Today I discovered that my laser pointer is, in fact, a ball point pen as well as an old fashioned pointer (the pen end pulls out). As I was extending the pen-cum-pointer link by link and marveling at it, the PI happened to wander by. He asked if I was planning to thwack someone with it.

Sincerely,

S

[edit 17:08]
Fedora or ubuntu?

Am mostly better by now, just feeling a bit wrung-out and exhausted. Still on schedule for qual though. (Did end up having to drag myself home Tuesday afternoon because I got too sick.) Practice talk next Tuesday. I've taken to carrying a bottle of acetaminophen in my backpack and I am all out of cough drops. Also, my transcript hasn't been received by the right place yet despite of the fact that it was sent on the 14th and my mp3 player broke this week.

All this all this has been a very crappy week and I look forward to having it end, soon.

Bad timing to the power of x

Caught a cold. Or a flu. Augh this is so stupid.

This is a little appalling, but

I think I've had too much tea today, as that I am currently exhausted, unable to sleep and harboring a strong urge to scrub out the kitchen and the bathroom. Unfortunately I do not have bleach, which, in my current state of mind, seems like a minor tragedy. (No, you do not understand. Detergents contain bleach won't do it. I'm at the mindset where I need to pour liquid bleach into a large container and soak things in it so they'll be nice and disinfected.) Clearly what I need to do tomorrow morning, in addition to going to the lab to put away my in situ stuff and stow my slides at -20C, is to buy bleach. And tea, since I'm running low.

I'm on the 6th draft of my qual now. Not counting all the v3.2, 4.5 and so on that I've taken to doing (because the comments between the PIs on what I should change are almost always different).

Oh God. I've wanted to sleep since 8 this morning. What is wrong with me?

Yes that's rhetorical.

On the bright side, my current bout of insanity should end before Thanksgiving?

(Admittedly it's not just qual right now so much as qual + four different experiments of mine that keep on failing + Stuff In Beijing. It's a lethal combination that managed to do what GRE + grad school app + scholarship app + senior thesis + classes failed to do two years ago.)

(And you know what? I still think grad school is most likely the best thing to have ever happened to me. Clearly I am insane.)

D:

My qual has a vestibular dysfunction.

It's going around in circles.

Prognosis, anyone?

This is sort of a wtf_nature type post

I found out what a tenrec is, while going through the cladogram again for my protein of interest.

Have I ever mentioned that my lab has a rubber duckie in the 37C waterbath?

Hm, a new phase

I'm experiencing a sudden and inexplicable urge to eat hotpockets and do system maintenance sort of stuff to all three of my laptops. I think it's a sudden spike in geekiness level, which is more fun than spike in hormone level, but less predictable. However, this spike did not in anyway increase my desire to work on my qual right now. It's a shame, since I think my enthusiasm for the qual has reached an all time low around this point. The fact that the people on my committee are giving contradictory advise could have something to do with it, though more likely it's just that I've reached the inevitable low point all large long-term project-type things must reach and I will spent a couple of evening on the floor with my laptop, surrounded by far too many piles of papers and abandoned mugs of tea.

(I've incidentally discovered that black tea that's been left to steep for too long, without the addition of any kind of sweetener, is actually quite vile. They remind me of those meds I used to take when I was four that usually resulted in me throwing up.) (Mom claims that the smell of those those will even make her nauseus. Then again, of the two of us, I'm the less squeamish one. Got nothing on Annie of course.)

The seminars and talks have started again for this quarter. I am still trying to average at least one seminar/talk per week. Yesterday there was a talk by a student who reprogrammed skin fibroblasts (cell type) from Alzheimer's patients back to being stem cells so he can differentiate them into neurons to study patient specific phenotype & genotype changes for Alzheimer's. It was pretty cool. Afterwards I had lunch with my labmates and Wendy and I (via a long, somewhat convoluted line of conversation starting around lost wallets) ended up reminiscing about Davis. The post-doc in the lab looked at us askance when we said that yes, Davis weather is nowhere near as nice as SD, its water can be toxic to plants and fish (and humans), and the allergen level has a way of giving people who never had allergies before allergies, but we still miss Davis.

What's in a place?

Dry ice in ethanol looks just like Sprite with ice.