trip report: paradise to muir, mt. rainier

so last Saturday i did the hardest thing i have ever done, physically speaking: i climbed halfway up mt rainier, from paradise to muir. i suppose it's technically more of a hike, but it's all in the snow and all uphill. very uphill.

so we left seattle around 5:30, and drove to Eatonville where we met up with the rest of our party: 6 in all. We drove to the parking lot at Paradise and spent about an hour or so getting our gear together, using the restrooms, etc. We were all packed up and ready to hit the trail around 9:10.

The first thousand feet or so wasn't too hard at all. Walking through well-worn footprints in snow, through the trees. However, after some gentle uphills and one small downhill, we hit the first steep part of the climb. I had to use my hands to help myself up the slope (probably not the wisest idea, since it made my fingers really really cold without me noticing) and was the last one up that part. (actually, I was lagging behind everyone nearly the whole time... I was the pacesetter of the group, that's for sure.) After the first steep part, we were just about above the trees, and the mountain opened up in front of us. Our "guide" (my friend's dad, who has made 18 successful summits) told us that at that point, we had seen the steepest that we would see all the way to the summit - except that there would be about 6 hours of that on summit day. yikes.

So we kept pressing on, onwards and upwards... a couple of times the sun peeked out from behind the clouds, or the clouds would sweep off of the summit and let us see the mountain for a minute. Then it was back to climbing, just pressing upwards and onwards. It was really long and hard, honestly, and I am not in good shape right now so I have a bunch of training to do before the end of June.

Finally, around 4 or so, we reached Camp Muir. It's just a series of shelters... one occupied by the forest service, one or two for the commercial guide services, and one for the public. It's little more than a hut built into the side of the mountain, but inside you can get warm out of the wind, cook up a nice meal and maybe even catch some Z's. On a summit attempt, you generally try to sleep until about midnight, then get up and on the way up to the top by around 1AM.

We, however, weren't attempting the summit, we were just training. So after we got warm, we went back outside to practice self-arrests with an iceax. Definitely a valuable skill to have, especially when you're all roped in together going up to the top. One falling climber quickly becomes three or four if you don't act quickly and correctly. So we practiced for awhile before we went back inside and got ready to head down.

This is when the story gets interesting.

So in order to increase the load we were carrying for training purposes, as well as speed up our descent, everyone had decided to bring skis or snowboards to get down on. Only by the time I had climbed 4800 feet up with a 45+ lb pack, I was not able to get up on my board. (I'd be lying if I said I felt great at this point too... I was worn out, tired, and a bit anxious, especially after the self-arrest practice. That didn't help much at all. So I physically could not get up on my snowboard.. I tried multiple times, but I just couldn't get up. Too much weight, thighs WAY too tired. So I unstrapped from my board and started walking down.

Only everyone else was way ahead, because they were on skis or snowboards. So I tried running a little, and couldn't keep that up.

And then I got the bright idea to ride down on my snowboard on my butt.

Word to the wise: Don't. Ever. Do. That. It worked great for the first hundred feet or so, but soon I realized I was going way too fast, and tried to slow myself down with my feet (my iceax was strapped into my pack). That just made me spin out and fall off my board... so now my snowboard shoots way out in front of me, and I am tumbling down the mountain. Somehow I manage to stop myself, but my board shoots off into the white (oh yeah, forgot to mention we are at near-whiteout conditions since we started the descent; visibility is probably around 100 yards, and varying all the time.) I get up and realize I'm not badly hurt, but my right hand has become completely non-functional. (Well, I can move it, but if I try to grasp anything with it it hurts, or just won't go.) I hope it's not broken. And I just lost my snowboard.

We regroup (fortunately, everyone saw me fall, and was right there to help once I stopped myself). My iceax comes off my pack and into my (left) hand; the map is consulted, and it's determined that we are heading off course, and we need to bear to the right. But my snowboard is off to the left.

Just forget it, they tell me. It's not worth risking your life for a board. Plus, hikers are pretty honest people, and when the weather clears up someone will find it. Just report it missing as soon as you get home. I know they're right, but it still is a pretty big blow to my spirit - losing my snowboard AND hurting my right hand at the same time. We keep moving down the mountain, significantly slowed by me being on foot... but in the poor visibility, we do the right thing and stick close together as we head down.

I should elaborate on the conditions at this point. It had been a warm spring day, with tons of climbers heading up to Muir or partway. The snow had been very slushy, and lots of footholes had been punched into the snow. However, the sun went behind the mountain as we started down, and the temperature was certainly below freezing, especially up near the top. So the snow was not only icy, but full of footprints. Not optimal conditions, especially considering the weather. And soon I'm not the only one having trouble.

Anyway, I'm going to spare all the trials and tribulations of the hike down the mountain... it was a grueling trudge, believe me. However - one very good thing happened as we were coming back down the steep part I talked about on the way up - I slid down on my butt ("glissaded") and turned to see everyone else come down, when out of the grey mist at the top comes a snowboarder... carrying a snowboard. as he comes closer I can see... yep, it's mine! saved! It turned out to be a park ranger, just doing a sweep of the mountain before turning in for the night, and he'd seen the binding of the board... way out on the Cowlitz glacier. Damn board got quite an adventure. So I didn't lose my snowboard after all... success! (However, we were still probably an hour from the parking lot, and I had no choice but to hold the board in my right hand, since I needed my left for my iceax. Probably not the best for a fresh injury... but what else was I going to do? My friend Rian had insisted on taking my pack soon after I took my spill... some sort of macho i don't know, but I couldnt exactly ask anyone else to carry my board. I was already the wuss, the wimp... the girl. Eh... I made it.

So we made it back to the road (we took a wrong turn at some point and ended up at the visitor center, not at the Paradise lot) and waited while a few went and got the cars. We finally hit the road around 11 and weren't home until after 1... a long damn day. I spent the next day in bed and in the bathtub... I could hardly walk.

So it was an interesting adventure, that is for sure. Now I need to get my ass in gear and start training if I'm going to summit next month... I can't wuss out now, that would be bad.

it bears mentioning..

...that today marks the 30th anniversary, to the day, of the original theatrical release of Star Wars.

entirely coincidentally, I have the disc from Netflix and just watched it... I have to say, the DVD version just is not the same. I want to see the original version, with bad effects and obvious sets and no CG dinosaur-creatures. but i also have to say that it is a beautifully shot movie - some of the frames are just so awesome. I don't remember them having such attention to detail and simply beautiful frames in the newer films.

anyway... a childhood favorite revisited... it's never quite what it should be, but it's still one of my favorite movies ever.

aaaaugh.

so i've been waffling on whether or not to stay in my current place after graduation - it's not the perfect apartment, and i'm getting kind of lonely on my own, but moving is such a PITA... so I was leaning toward staying, until I got home just now and found a notice on my door...

they're jacking my rent.

not by just a little bit, either. it's going to go up to $850. that's a $100 increase. EIGHT FRACKING FIFTY. do I look like I can afford that?

$850 for a 600-sf, 1br, 1ba, tiny little 1-person apartment. $865 if you include Frida's rent.

no. fracking. way. guess i'll be giving them my notice and looking for somewhere else to live after graduation.

DAMMIT.

the mountain is out today... i keep staring at it. i think i'm fixated on it, and i won't be able to stop thinking about it until i summit. or at least attempt the summit.

my hand isn't broken, but it still complains if i try to type for more than a few minutes at a time. the doctor said to keep icing it and keep it wrapped, and try to stretch it out... man. not being able to use your right hand = the pits.

wow.

should he be impeached? go vote, then see the results... almost heartening.

glacier

check out that huge pile of ice crumbling off that mountain.

so's your face

climbed up to muir yesterday... it was certainly a trip. there will be a longer blog post forthcoming with more details and stories and pictures, but for now i'm nursing my sunburned face (ugh) and limiting my use of my right hand. (yes, there's a story. a stupid one. but you'll have to wait.)

yeah, rainier showed me which one of us is boss. i'm postponing my decision on whether to go for the summit until i recover from ths trip.

lolcats

icanhascheezburger is teh awesome.

i'm not an ambi-turner.

so i woke up this morning with an excruciating pain in my neck and the inability to move my head in certain directions. it's better now than when i first got up... the first hour that I was up was nearly unbearable. i wasn't even sure if i was going to be able to make it out the door. i'm not sure what's wrong... a pinched nerve or a muscle spasm or what - but it probably has something to do with the fact that i've been sleeping flat on my stomach, with my head at a 90 degree angle to the right, for the past few nights. something tells me my body doesn't like that so much. putting on my shirt this morning literally made me cry, and i couldn't lift my messenger bag up and over my head without causing severe pain. oh, and i can't look more than 45 degrees to the left unless I physically support my head with my hands. if this is what chronic pain is like, then anyone who suffers from it has my complete sympathies. i have no idea what i would do with myself if this doesn't go away. my apartment isn't exactly non-ambi-turner friendly, and I can't ride my bike like this, either, since there's no way for me to check over my left shoulder and see if there's a car there about to kill me.

all under the boughs unbound

The Decemberists' The Crane Wife is an album meant to be listened to on repeat. i'm not quite sure exactly why this is, but it has something to do with the seamless transition of the end of "After the Bombs" and the first sounds of "The Crane Wife 3"... like they meant to do it. HAHA we will trap listeners in an infinte loop of metaphor and legend!

so much shit to do this week - biochem midterm monday, symposium friday. mother's day tomorrow (complete with mom). 4 weeks until graduation - 3 weeks of classes left. homework due on wednesday and i have to find a windows machine to do it on. bleh.

and after graduation: 17 days until Rainier.

great.

so the puppy next door? yup, it's a pit bull. awesome.

it stared me down as i was locking up my bike a few minutes ago. and not in a "puppy wants to play" sort of way, but more like a "these are my masters and if you fuck with them I WILL KILL YOU" sort of way.

greeaaaaat.

all stocked up on gear

i managed to steal a good bit of backpacking gear from my aunt and uncle last night. i have a backpack, a 3-person, 4-season tent, a sleeping pad, a camping stove, and some other stuff too. hells yeah... i am ready for adventuring.

so i have at least 3 trips coming up in the next 6 weeks... next weekend we're climbing from Paradise to Muir, getting practice with all the ropes and stuff, walking across snow, etc. the weekend after that, i'm going backpacking, probably at the coast, but possibly in the desert, with the Mountaineers. and then on 24-27 june we are going to make a summit attempt on Rainier. hellz yeah!

i want to go backpacking in the Olympics, St. Helens, and maybe the North Cascades before the summer is over.

victory!

so the li'l scooting machine has awoken. i charged up the battery and hooked her back up, and after much labor managed to kick-start it to life. the electrical parts aren't so much working, but the motor, wheels, and brakes were working just fine. the throttle's a bit sticky too. but it's working! the groundskeeper at my apartment building came up to me while i was working on it and said he'd seen a few people kick it over on purpose. people are assholes. but it makes me glad i didn't spend more on it. it's a nice way to get from point a to point b, and will be great for those trips that are just too long/too uphill/with too much to carry for the bike.

my uncle was asking me the other day when i was going to take the test and get my motorcycle certification and get a real bike. it's worth considering... hella impractical in seattle, but then, if i end up in, say, SD for grad school, it could be worthwhile. (hi mom! yes your brother is a bad influence on me!)

ok, time to forage for dinner. me hungry.

augh.

crazy bitch fight in the apartment next door... details at 11. oh wait it IS 11 and i'm up past my bedtime because of the CRAZY BITCH FIGHT next door. I never knew you could slam the door so many times in one night... if I were a little older or more authoritative i would go out there and lecture them, but something tells me not to do that.

my new neighbors? they suck. when the puppy* isn't crying all night making it difficult to fall asleep, there is a CRAZY BITCH FIGHT! did i mention crazy bitches? good.

i need some earplugs.

* i say "puppy" to reassure myself that they don't have a huge pit bull in there... i have overcome my childhood fear of dogs, for the most part, but my neighbors owning pit bulls and having bitchfights on a regular basis... not what i signed up for.

go me.

i just rode up to lake forest park and back. if my math isn't horribly wrong, that's like... 20 miles. now i am enjoying a delicious slab of mahi mahi. and b33r. always need the b33r. mmm.

it's crunch time, it seems. less than 2 weeks until the symposium, i have to give lab meeting tomorrow, a practice talk at some point soon, and my real talk next friday. that's a lot of presentations. oh and i presented a figure from a paper today in calcium class. hi my name is sir presents-a-lot.

time to get to work. or maybe shower. (or bower. mmm, bower.)

science scouts!

merit badges!

asdf

don't talk to me about grades, man.

jesus and mo is the awesome.

also the awesome: i am now taking a class about nothing but calcium. we are going to learn about chromatin and transcription in biochemistry now. i have found a marker that is extremely close to my gene. i need to run more samples and confirm, but it looks solid. yay!

for the love of god

tell Bush to sign the bill.

We all know he's going to veto it anyway, but it's worth a shot to sign this petition (yes, it'll put you on the Edwards campaign mailing list, but there are worse fates) and urge Bush to end the war. More importantly, though, this petition urges Democratic leaders in Congress to not back down and give Bush the bill he wants (aka the bill they just passed, minus the timetable for leaving Iraq), but instead, demand accountability from the Decider in Chief for vetoing a bill which fully supported our troops.

Cheney is a War Profiteer, and Bush is his puppet. We must remove these thugs from office. They have already irreparably damaged our Constitution... it's time to stand firm and say NO to this administration.

So please, sign the petition, call your congressperson, email your senator, whatever it takes. It's time to END THIS WAR and the occupation of the White House by thugs and cronies.

go team!

Joe Biden is Dead Right on Iraq, according to Newsweek's Michael Hirsh. after reading this article, i think he's right.

crooksandliars is a great source of outrage material, if you're looking. i love it mostly for its downloadable daily show and colbert report clips. in a time when cnn will pick out the 5 seconds of 8 hours in which the attorney general sounded credible, and play it off as the Democrats attacking the Administration. there's something in its last throes, here, folks... and it's the Administration.

as someone who has officially been awake for the last 6 and a half years, let me say this: it's about damn time you all noticed this shit.

read. and be outraged.

Did the most powerful Republicans in America have the computer capacity, software skills and electronic infrastructure in place on Election Night 2004 to tamper with the Ohio results to ensure George W. Bush's re-election?
Are Rove's missing e-mails the smoking guns of the stolen 2004 election?

i'm a noid today

maybe it's the lack of sunshine, or maybe it's just random fluctuations, but i have to say that today was a high for me on the annoy-o-meter. it may have started in my biochem section, which is a complete waste of 50 minutes because my ta doesn't know what the hell he's talking about and doesn't really care, and because there's one Annoying Question Girl in my section (you know the type). it doesn't help that she speaks in this super-breathy, high-pitched voice that is Just. So. Subservient. it makes my skin crawl. AND! she raises her hand! who does that??? in a section of less than 10 people, don't you think you could just... say it? waaaaaagh.

it may have been the biochem section, or it could also have started earlier, when i was loading a gel and it just ripped in half. straight down the bottom row of wells. fortunately i noticed before i filled it with my DNA samples; but i wasn't able to load the bottom row of the gel, so i only got half the data i should have, and have to run another gel tomorrow to get the other half.

it also could have been earlier when i was setting up the PCR that i later loaded into a gel. i was going through the freezer finding all the DNA samples i needed, when a rack of tubes that had been just stuck onto a shelf came crashing down, spilling tubes everywhere. tubes go in boxes before they go in the freezer, or at least they should in order to prevent accidents like that one. the culprit was politely informed of the situation, but - of course, because this is seattle and we all do this - i was super-nice about it, though 30 minutes later i had been cursing and fuming. picking up 80 1.5-ml tubes that have scattered across the floor? not fun.

on the other hand, i did get data today, and the marker i got data from is very close to my mutation.... closer than any other i've tried so far. which is good. i need to run more samples to determine if it's on the other side of the mutation from my current closest marker, which would be good, or if it's on the same side but that much closer, which is actually also not bad. data is always good, especially when it doesn't make you go "WTF??"

what it boils down to is that i'm exhausted, mentally and emotionally. i have the urge go bury myself under the covers and let it all go away. but i have errands that aren't going to run themselves... sigh.

in which i digress from my own knowledge

... and speculate on fields in which i am no expert, nor a student, but merely an outside observer.

for some reason, it's not particularly common among scientists to believe in astrology, or to check one's horoscope each morning before leaving the house. but while it's doubtful that "personalized" daily predictions could ever be accurate - beyond what happens by coincidence and vague wording - there's one gaping hole in our understanding of the fundamentals of physics, and it might have something to do with astrology.

(caveat: speculative, moderately crazy-talk thinking follows.)

ok, i'm no physicist, but i do have a pretty good working understanding of mechanics and electromagnetism. i'm a bit shakier on the whole quantum thing, but i at least have a decent grasp on the basics, and can accept the fact that fundamentally, everything is stochastic and based entirely upon chance. (which is not to say that it is random.)

what's missing from our Theory of Everything is how gravity comes into play with the whole quantum theory thing... how it interacts with atoms and molecules, what forces gravity might exert on a chemical reaction. there have been numerous (purely theoretical) attempts to explain gravity's place in quantum theory: string theory and loop quantum gravity come to mind. frankly, i don't understand either one nearly enough to explain it. but it is true that gravity must *somehow* act at the molecular level, or else we wouldn't all be here. and there are other things at the large molecular level (protein folding is a big one) that have yet to be explained by anything but the most complex of computations (for the simplest proteins). and it's not just that. how does a protein find its binding partner, when the concentration of the ligand is infinitessimally small (in the case of biotin and streptavidin, the most extreme example, on the order of 10^-15 mols/liter, or the femtomolar scale*)? what determines whether one single (but critical) sodium channel opens or stays shut, triggering or preventing an action potential that could lead to many downstream consequences?

could gravity somehow be the answer? could the mass of the earth exert an influence on chemical interactions within cells? could the moon? the sun?

how the hell would you go about testing something like that?

* digression: i'm not sure you really get how tiny femtomolar concentrations are. Avogadro's number is 6.02x10^23... i'm going to round and call it 10^24. So there are 10^24 molecules in a mole, or 10^24 molecules per liter of solution at 1 molar (M). If the concentration is 10^-15 M, then that means there are 10^9 molecules, or about 10 billion, in a liter of solution. Now consider the fact that the volume of an average cell is around ***quick calculation*** 1.25x10^-16 (mm^3). a cubic millimiter is the same as a microliter of water - 10^-6 liters. so that makes our cell volume 1.25x10^-10 liters. 10^9 molecules per liter times 1.25x10^-10 liters = .125 molecules per cell volume. and yet this is how low the concentration of streptavidin must be before half of the bound biotin releases its SA! tell me there isn't something freaky going on there.

synapse assembly and plasticity!

so i went to a lecture this morning given by Ann Marie Craig, who is currently at UBC, talking about the work she's been doing there and previously at WashU on synapse assembly and plasticity. most of her work was focused on neurexins and neuroligins, which i incidentally did a project on last summer quarter for bio 401. i'm not going to go into detail about these molecules right here and now, but the short of it is that neurexins are expressed on presynaptic neurons and neuroligins on postsynaptic neurons, and the interaction between NXs and NLs is a key interaction in synapse assembly. what makes these guys so difficult to study is the fact that each one has several splice isoforms - especially the neurexins. the long (alpha) isoform of neurexins has 5 splice sites, and the short (beta) isoform has 2 (confusingly called S4 and S5, since they are homologous to the 4th and 5th splice site in alpha-neurexins). so the Craig lab (as i understand from her talk this morning) has shown among other things that the "insert" in splice site 4 (S4) of neurexin 1-beta makes it bind specifically to neuroligin-2, which is specific to GABAergic synapses (which are generally inhibitory), whereas the form without the insert is much more likely to bind to NLs 1, 3 or 4, which are more specific to excitatory/glutamatergic synapses. they also showed that fibroblasts (basic, non-neural cells) co-cultured with hippocampal neurons, and ectopically expressing NX, can induce dendrites to form what she termed "hemipostsynapses" onto the fibroblast, whereas fibroblasts expressing ectopic NL can induce axons to form "hemipresynapses". pretty cool work.

but by far the coolest thing (IMHO) in her talk was some time-lapse imaging they did on cultured neurons with a fluorescently tagged version of CaMKIIa, or calcium/calmodulin-dependent protein kinase II-alpha. (Protein kinases are proteins which add a phosphate group to other proteins, and they are crucial for many intracellular signal transduction events.) CaM kinases have a special domain or subunit, calmodulin, which binds to calcium ions and becomes active. this protein is important in transducing signals from Ca ion concentration into phosphorylation signals... which is key to promoting synapse assembly and potentiation. so the cool data that she showed in the talk was that if a cultured hippocampal neuron with this fluorescently tagged CaMKIIa is stimulated with a "puff" of glutamate/glycine solution, within seconds of application, the (previously uniformly located) CaMKIIa clusters at synapses, and this wave of CaM movement propagates (in some cases) across the neuron, from dendrite through soma to axon. so what is going on? Calcium binding to the CaMK is somehow triggering it to relocate. what exactly is going on, she couldn't offer any ideas... but it is a cool result and i'll be interested in seeing what else they find out.

question...

...for anyone who maintains their own blog-like site and uses a client other than blogger:

if i wanted to maintain two blogs, one similar to this one, and one where i only publish items tagged with "science", would that be easy to do? it seems like it should be easy to do, but blogger won't let me. it also won't let me hide posts "below the fold", or at least without a cheap hack which i was unable to figure out... the hosting and the software is free which i do love, but i would like to have better functionality, as well as having two blogs, one of which simply displayed posts from the other site with specific tags.

any suggestions on what i can do? what clients are best, what web hosting companies don't suck? i *suck* at HTML... or at least i don't have 5 hours to spend plodding through CSS and XML.

oh, kurt.

"No offense intended, but it would never occur to me to look for the best minds in any generation in an undergraduate English department anywhere. I would certainly try the physics department or the music department first -- and after that biochemistry. Everybody knows that the dumbest people in any American university are in the education department, and English after that."
- Kurt Vonnegut on Allen Ginsberg, quoted here, via Entertaining Research

more about pigment cells

note: i wrote this post and then Blogger crashed Safari. it was a good post, so i'm going to try to reconstruct it, but... aaargh! *curses blogger*

The close interaction in the cuttlefish between pigmentation and neural activity may seem like something out of a sci-fi movie. It may surprise you to learn that even in vertebrates, pigment cells have close developmental ties to the cells that go on to form the central nervous system. At the end of neurulation, the embryo's outer sheet of cells, known as the ectoderm, has rolled itself up and divided into two components, the neural tube, and the true ectoderm. However, a small population of cells that originally lay at the boundary between these two populations is destined for something else. These are the neural crest cells, and they go on to form a wide array of tissues, from sensory neurons and associated glia, to cartilage, muscles and bone, part of the heart and adrenal gland, and - you guessed it - pigment cells, including melanocytes.

Now, humans can't change their skin color - much less its texture or patterning - at will, so it may sound strange that these pigment cells share such an intimate past with much of our peripheral nervous system. However, many vertebrate species possess at least rudimentary control over their pigment cells*. Zebrafish can squeeze or spread their black pigment cells depending on environmental cues, and of course, the chameleon can change colors to blend in with its surroundings. Camouflage is a very useful adaptation - it's hardly a surprise that many species have evolved camoflage that changes.

(*Check out that link - there's a great descriptor of the cuttlefish pigmentation organ, which differs from - and is likely more accurate than - the quick explanation in my last post. Evidently each cell has every different color inside, and they just squish the cell around in different ways to express different colors. Awesome!)

There's a lot of really interesting research into the genetics and development of pigmentation patterns. The Parichy lab here at UW is using several different species of Danio - close relatives of D. rerio, the developmental biologist's favorite little fish, to determine the genetic factors responsible for different pigment patterns in adult fish. Pigmentation patterns are so crucial to the survival of any species, it is easy to imagine that the genes causing the patterns would be frequent targets of selection - both natural and sexual.

cuttlefish are awesome.

check out what it does around 3:30.

the cuttlefish (which is NOT a fish, or a vertebrate at all, in case you were wondering, but is closely related to squid and octopi) is interesting because it has such exquisite control over its pigmentation, such that it can change its patterning on the fly (as illustrated in the movie). each individual pigment cell has a cluster of muscle cells around it, controlling whether it is contracted (invisible) or extended (visible). pigment cells come in several colors, and by controlling each pixel at the cellular level, this amazing cephalopod is able to blend in with its environment, mimicking plants, other animals, and rocks as it chooses, or by parading around in threatening or seductive coloration it can warn off predators or attract a mate.

another interesting thing about cuttlefish is that although they can change colors, they cannot see colors, though they can detect the polarization of light. so somehow, though they do not have cone photoreceptors, they can match their own coloration to that of their environment.

read more about cuttlefish.

so totally wrong

on the biochem midterm today, there was a question in which it is insinuated that the exam taker's father not only takes viagra, but has admitted this to said exam-taker. sorry, dad, TOO MUCH FUCKING INFORMATION NEXT QUESTION.

it was also a flawed question because it said that the dentist was going to administer nitric oxide (NO) as an anaesthetic. dad, you need a new dentist. a dentist should know the difference between NO and NO2. one will make you goofy and dissociated, the other will GIVE YOU AN ERECTION. (actually, it wouldn't, because NO only makes it a short distance before it's oxidized to nitrites and nitrates, and would never make it from your lungs into your groin.) but it certainly won't do anything to make you feel less pain. bad dentist, back to basic chemistry.

can i forget this stuff yet? oh yeah, i have to take the biochem GRE.

Should they have locked down the campus?

(note: i wrote this as a letter to the editor on salon.com, but thought it was worth repeating here.)

We may be on the other side of the country, but students, faculty and staff at the University of Washington feel the echoes of the VT shooting perhaps more than those at other institutions - since we, too, had a campus shooting, just a few weeks ago. (For those who don't remember, Rebecca Griego, an alumna and staff member, was shot by a stalker ex-boyfriend against whom she had a restraining order. He then turned the gun on himself.) Should UW have locked down the campus after this tragedy? It's not an easy question, and it's easy to say in hindsight that yes, VT officials should have instituted a lockdown, but how was anyone supposed to know what the killer had in mind? Locking down a campus the size of VT's (or UW's) is no trivial matter - inconveniencing 30,000 people, canceling classes (and maybe exams), etc. What if Griego's killer had, instead of taking his own life immediately, gone across the street into busy lecture halls and opened fire? It could have just as easily happened here.

It's always easy to say in hindsight that more should have been done, but how is any of us to know what is going to happen? Both Griego's killer and the VT shooter were known to be dangerous - shouldn't something have been done on an individual level to either reach out to these people or to prevent these tragedies from happening? What should have been done? It's easy to say in hindsight that the campus should have been locked down immediately, but when you consider altering the daily activities of more than 30,000 people, a campus-wide lockdown is no trivial matter. And yes, what happened at VT is an atrocious tragedy, and measures should be taken to prevent such a thing from happening again. But we must remember that more than 30 people are killed in horrific acts of violence every single day in Iraq, in Sudan, in Afghanistan, and we barely look up from our paper long enough to take a sip of coffee when this happens. Yes, more should have been done to alert students at VT of the morning's events, but was it really forseeable that the shooter was planning on the biggest gun rampage in US history? Is a campus-wide lockdown an appropriate measure after an isolated act of violence? Or are we just trying to pin the blame on someone, since the real perpetrator is dead?

the light season

until about 20 seconds ago, when it went behind a cloud, the evening sun was reflected off the office building into my apartment, for the first time since august.

there should be a word for this half of the year... it's not technically summer, but it's getting there.

i love seattle in the summer.

i am a perl goddess.

first programming assignment for genome informatics: done, with almost 2 days to spare.

total time to run program, which has order of O(m*n), on large test file: 58 minutes.

number of biochem midterms to study for: 1.
days until said midterm: 1.5.

days until graduation: 54.

quickie

miles today: 8ish. total this week: >40. go me.

also this weekend: got both programming assignments for genome informatics working. one of the programs took over an hour to run on the sample file they gave us - damn file had somewhere around 500 entries, each more than 100 amino acids long. couple this with an algorithm of O(n^2) efficiency, and you keep a G4 busy for awhile.

kind of did my taxes. i made a mistake on one sheet and so i need to print out another copy, but they're virtually done. nothing paid, nothing owed, no refund... this is what happens when one makes less than $800 in a year and is claimed as a dependent. this is certainly the last year that'll be true, and next year i'll probably have real income, so it'll be a different story.

next: study biochem. i have a damn midterm on wednesday... how is it time for midterms already? on another, scary note: 55 days until graduation. less than 2 months left in my undergrad career. i really should start studying for the GREs. i figure, i'll take the biochemistry/cell/molecular biology one right after graduation, or even slightly before. then i'll cram for the generals and take it in july or august.

ok, time to study. g proteins and tyrosine kinases and signaling cascades, oh my!

obligatory bike post*

i went for a ride today, and i went further up the burke-gilman than i'd ever gone before... by far. (which isn't surprising considering i just got my bike, and i really hadn't explored it on foot beyond my usual stomping grounds.) i rode from the lab up to 112th street, when i turned around. it was a good ride, and i could have gone further if it hadn't been for the gel i was running at the lab (which turned out completely noninformative, boo). i don't know for sure, but i'm guessing it was around 7 miles each way, making today a 15-mile day. woohoo!

now i need to find more places to go. there used to be a map outside our old lab with bike routes in seattle, but since we moved i'm not sure where it went. so where are the best places to go without too many hills?

i took this picture on my ride, somewhere around 100th, where you can see the lake from the trail.


*or, "in which this starts to sound like my ex boyfriend's blog"

science diet!

so i had a pretty science-riffic day. this morning was lab meeting for the larger of the 2 labs i belong to, which was a presentation from (i think) the most senior grad student in the lab, who's been doing a ton of work on membrane biophysics in the nucleus magnacellularis (part of the cochlear nucleus) in chick. so evidently, neurons in this part of the brainstem fire with a stereotypical pattern that is different from many other types of neurons, and he's trying to figure out why. the short answer is that it has different potassium channels expressed, but the long answer sure was a lot more interesting than i'm going to be able to explain here. the data were pretty much a bunch of voltage traces, and associated graphs. interesting to me, not so interesting to other people... but very educational, and he presented it very clearly and succinctly.

after lab meeting, i had a meeting with the boss of that lab (the more senior of my two PIs) to "discuss my future." which was pretty cool... what i got from him was: 1 - yes, we'll pay you to stick around for a year before grad school, you're too valuable for us to let you go; 2 - a bunch of advice regarding which graduate schools to apply to and where he can get me in. so now i'm supposed to spend a day or so researching not just programs but also particular labs i'd be interested in doing my thesis work, which at this point i think will have something to do with determining the genetic mechanisms behind neuronal differentiation, development, circuit-formation, something like that. so his main point was that there are a lot of good neuroscience programs out there, but not a whole lot of people doing the kind of work that i'm interested in, so i should start narrowing it down. also, he said, fish for lab names not from nature, science, nature neuroscience, but go through issues of neuron, j neurosci, things like that, and try to find some names. so i'm supposed to meet with him again in a month to further discuss. hooray! someone on my side. oh, he also said he could get me into the sanger program "no sweat." so that's certainly something to think about! (sigh. just remembered that i have to take the GREs.)

so then after that, i went to a lecture by Gail Mandel, who did her doctoral and postdoc work on sodium channel expression, and in the process discovered a sort of "master switch" for neural cell fate. It's a transcription factor called REST - Repressor Element-binding Silencing Transcription Factor - and it's basically expressed everywhere but the nervous system. She had a ton of data and a really interesting model of how this particular switch is turned on and off and how that precisely determines whether a cell becomes neural or non-neural. Evidently there are binding sites for this protein beside nearly every gene involved in neural development - ion channels, synaptic proteins, and even other transcription factors known to direct neural cell fate, like NeuroD and neurogenin 1 (which a grad student in my (other, smaller) lab studies!)

After that seminar, I did some other stuff like work on homework, go to class, set up fish for next week, etc. And then at 5:30, when I was debating going home, I decided to go to the Neurology Grand Rounds (a seminar series I've never been to before) - Jeff Barker gave a talk summarizing 15+ years of work on neural stem cells. His group has pretty much amassed an ass-ton of gene expression data in different cell types, from flow cytometry/cell sorting to in situs with some really pretty fluorescent imaging data. I guess they have a 5-color confocal microscope up at the NIH (when you're government you get all the cool toys) - he had images showing expression of 5 different genes, all labeled with different colors, in different parts of the developing rat cortex. it was pretty amazing data, and i learned that what most people call "neural stem cells" are more accurately lineage-restricted progenitor cells which may or may not be multipotent. repeat after me: just because they're proliferating doesn't make them stem cells. There was also a lot of stuff about FGFs and FGF receptors... but I don't really have time to go into it all right now. (FGF stands for fibroblast growth factor, and it's pretty much one of many, many secreted peptides and molecules that guide development.)

so yeah, i'm completely geeked out right now. i felt super-special because Dr. Barker mentioned Elizabeth Grove in his talk, and I just heard her speak last month at the NW developmental biology meeting! they both work on FGFs. i had to flip through my talk notebook when he mentioned her name and try to remember her presentation... the key thing I remember is that she had showed that you can shift different brain structures forwards or backwards by increasing or decreasing FGF activity.

so anyway, now i have to write a program to mimic the way a BLAST search works, and then one to do a protein sequence alignment. why did i register for this genome informatics class again?

everything was beautiful

... and nothing hurt. it is a sad day. kurt vonnegut, one of my absolute favorite authors ever, is dead. so it goes.

(via pharyngula.)

order from chaos

i wonder what that is.

that thing. check it out!

i mean, wtf is that thing? it looks like some sort of alien molecule monster...

vaguely fulleresque, but is it designed or natural?

dude. its chlorine antennae are kind of cute, if improbable. and i KNOW nitrogen wouldn't bond like that... but it's still kinda nifty.



C14N4O2H12Cl4Br2

let's blame the victim!

they can't be serious: Seed is reporting that apparently Africa isn't doing enough to stem climate change. AFRICA. you know, that continent with all those gas-guzzling SUVs, that air-travel-addicted populace, their bustling industries, and their ample cash flow. jeez, really, they ought to be doing more, like turning off the lights when they leave the room or NOT BREATHING (which, for many Africans, might be the only way they possibly could decrease their carbon footprint). Of course. let's all point our fingers at africa, and say, until those guys in Ethiopia get their CO2 emissions down, we don't have to do SHIT.

Those assholes over in tuvalu should think about switching to Priuses, too. geez. can't these people do more to stop their own destruction? no? well, i guess we can't do anything either.

i'm a conformer

so i broke down yesterday and shelled out a little over a hundred bucks for what seems to be a fairly functional, decent ride.

of course, as i was rolling into the lab this morning, i upshifted too fast or something, and the rear derailleur went straight off the gear... fortunately, I was uphill from the bike rack, so I just cruised in and parked, and managed not to look like too big of an idiot. then later this afternoon i went out and fidgeted with it, and managed to get the chain back on. the other problem it has is that the front derailleur doesn't always upshift, but it always does after i move the lever back down and back up.

i'm already compiling a mental list of things i need for this baby:
1 - a name.
2 - a front reflector. (didn't notice that one when i bought it... could be important.)
3 - a new saddle (my ass is a bit sore... fortunately it's not my lady parts that are the bruised, like the last time i rode a bike. THAT was enough to put me off biking for like, a year and a half.)

we start getting wish-listy, and i think of many more ways i could throw money into it:
4 - new pedals (and maybe shoes)
5 - convert the shifters to being on the handlebars not the frame
6 - a new bike. this one is a wee bit big for me at 58cm... not TOO big, I can stand over it, but not flat-footed... but I might do better with a 54 or 56. but if i had, say, $500 to spend instead of $100 you bet i'd be a bit pickier.

we'll see how i feel after using it to commute for awhile. i tell you, it was nice not having to coordinate my departure this morning with the bus schedules... no more "shit! the 8:42 came already. i could wait until 8:57, or just walk..." fortunately, the weather cooperated today, for the most part. i'm sure it won't always be so nice, but it was a good first day of biking.

the next trick is to build mental bike-maps of my neighborhood. i think i found a good way to get to the lab, but there are so many ways. the key will be to find which has the fewest uphills. ;) also, i thought it would be scary biking on roosevelt in morning rush hour, but it wasn't too bad. maybe i just got lucky this morning. only time will tell. but it's also nice, because my lab is downhill from my house, so i can mostly just coast in in the morning, not have to worry about being sweaty, then get my real workout on the way home.

plus, i find when i get home and i've just worked out, i'm much more likely to have a healthy dinner, and not snack as much at night. this could be a very good thing for someone struggling to fit in her pants.

not your average online university

This ad: "Sanger PhD programme Fully funded 4 year studentships in genomics" has come up on my gmail with eery regularity... so one day i just randomly clicked on it. and again today, it came up and i followed it... and now i'm contemplating a Ph.D. abroad. i also spent some time perusing the page for cold spring harbor's phd program, at the Watson School. could i go to a school that carried jim watson's name, given his reputation as a sexist pig and my diehard, unshakable belief that women are people too? (is it wise to choose a program based on hearsay about the namesake's personality, regardless of his accomplishments?) Would I really be happy in such a small and secluded program, or would somewhere larger suit my lifestyle a bit better? it seems like there's a lot to be said about a 4 year phd program, as opposed to the usual 5 or 6 years... getting my degree faster would put me that much closer to tenure. and then there's a lot to be said about having a doctorate from cambridge, which i would if i did the sanger program. i mean, shit, people have been studying there for 800 years now. (cambridge. not the sanger institute. they instituted their phd program in like 1999.)

of course, there's a good chance that i'll just end up here at UW for my Ph.D.... I bet I could finish in 4 years, if i could keep working on something similar to my undergrad research...

theobromide saturation

last night i wrote a nice lengthy, thoughtful post, and just as i went to publish it safari crashed. i'm only using safari because firefox 2 doesn't work on my machine - it just randomly hangs and refuses to force quit, and crashes the finder, so i have to hard reset - not cool. what's the deal, is my g4 architecture really that outdated? i know i could just roll back to firefox 1.5.8 or whatever, but i'm lazy, and safari works okay... but it's just little things. sigh. hopefully firefox 2.0.0.4 will work.....

so it's easter, which means i'm stuffed full of food and family and chocolate. halfway through my last cadbury creme egg... but not even halfway through the chocolate. hell, even the bunny has everything but the ears. i am really going to have to get into the habit of running. and i am seriously thinking of buying a bike, and have actually tried a couple of times on craigslist, but craigslist users are flakes. i'll probably pop in to recycled cycles next time it's sunny, if i don't hear back about the 54cm vintage sekai in "good condition" in the u-district in the next day or two.

my productive streak has slowed this weekend... i've gotten nearly nothing done. i found a paper that i perceived to be scooping my research, from 2000, online on saturday and have been trying to absorb the results and conclusions they draw. upon further reflection, it's not what my data is showing, so my story is still new, but it's got some solid precedence in the literature. which is good... i guess.

i'm starting to get a small sense of dread for graduation. it's dawned on me that after i graduate, both the university and my parents are going to stop giving me free money. so i need to find someone else to give me money... ideally to do my own research (under someone's mentorship, of course)...

tgimffa

success! i have no sinus headache today. :)

it's also a gorgeous day, all warm and sunny-like. i'm coming to the conclusion that it's high time i bought a bike. but then i wonder, will i actually ride it, or will it end up like all the other things with wheels that i buy and then use for a period of time and then grow tired of? maybe i should just bust out my old longboard and hit the streets with that. but the problem with a skateboard is that it's only more efficient than walking if you're going downhill. bikes can be used either direction.

i also need to get my scooter up and running, now that it's scooting weather.

blag

one thing that always throws me for a loop is meeting someone that i realize is smarter than me.

i know it's uncouth to discuss such things as intelligence, but it's a fact that there is a wide range of human intellectual abilities, as there is a vast range of human abilities in nearly every aspect of life. and, well, i know all too well exactly where i fall on that range.

it's also not polite to discuss mental illness, but i think it's important to point out here the overlapping ground in both these categories. it's widely accepted that there's a "fine line between genius and insanity," but just how fine is that line, and how closely can one tread to the line without crossing over to the other side? story at 11 - don't go away!

for something that closely parallels my feelings at not infrequent times, mimi smartypants will do nicely.

also, awesome! this is a webcomic in a slightly different style, favoring the aesthetic of the comic book format* but addressing similar geeky issues as xkcd:


also awesome: the unicorns.

*shit! need to run down to comic store and buy buffy #2 before they run out!

looking back over that last post, i'm reminded of something my mom said once about a picture of me she found on the internet: "don't let anyone who doesn't know how pretty you are see that." so, just in case you weren't aware of the hotness that is me, i present my latest wall-art homage to narcissism:

in the background, that's a map of titan. fracking sweet.
in other, unrelated gripes: i hate that my cat drinks out of my water glasses which i leave sitting around. i just finished off a glass of water that had been sitting on my desk overnight, and now my tongue and esophagus are tingling (mild cat allergy). damn you and your antigens which cause my body to mount a histamine response!
in potty-training updates, we're moving along slowly but surely. she doesn't like the fact that there's now a big gaping hole in her litter box, especially since it's so dark in there. but she's getting used to it. my gripe is that now she can fling litter into the toilet, and i end up flushing quite a bit of litter. i guess it's some consolation that when we finish this i'll never have to buy litter again...

i thought weekends were for rest

good fracking gods i am tired.

i have been exceptionally productive this weekend - like, scary-productive maybe-shes-crazy bipolar-but-clearly-in-a-manic-phase type of productive.

i think i've finally cracked the story behind my hugenormous mapping project that i've been working on for the past year+. and what i'm cracking open appears to be a story that's never been told before... so i'm exhilirated, bewildered, and a bit dizzy.

but i have about 10 pages of notes, plus 6 text files of possible parts of papers (rough first verbal diarrhea, but words output to digital format nonetheless) and that's not even counting the hundreds of gels i was flipping through, or the two detailed chromosome maps i've been annotating in color-coded sharpie.

look! random desk shot! next thing i'll be posting pictures of my cat on the internet. (oh wait.)

unfortunately, i didn't do shit for either of my classes the whole weekend. i worked on my research project from 10 AM to 1 AM (with maybe 2 hours of breaks cumulative) yesterday, and today it's been less intense, but i've put in at least 11 hours of sometimes half-assed note-consolidation and cross-referencing. but i've convinced myself of what my data is telling me, and i'm almost ready to communicate my ideas to my postdoc mentor and my PI. not quite though...

i'm not ready to publish anything public on this, but i believe that i have my hands on something extraordinary. not earth-shaking or nobel-winning by any means... but significant. which makes me feel really, really good.

good, and tired.

sakura & sunshine

i hesitate to say it, but it seems like the weather in seattle has hit a turning point. it's supposed to hit 60 today, and the sun is shining. hooray!

and while the cherry blossoms in front of my apartment are now just a pile of pink petals (rapidly turning brown) on the sidewalk and the trees are leafing out, the trees down by the waterfront below the health sciences building are in full force. i stopped to snap a few shots yesterday on my way from one lab to another... data can always wait for sunshine and photography.

in other news... battlestar galactica! the season finale was a-fracking-mazing. i'm in the process of re-watching season 3 - just finished episode 4 last night - and in the interest of avoiding getting spoilerrific for my lovely readers who have not seen it yet, let's just say that information learned in that episode throws new light on many of the events earlier in the season. i'm not sure i'm super-stoked about the identities of the 4 cylons revealed at the end of the episode - but it's an interesting twist and i'm definitely holding my breath for season 4 (DAMN them for making us wait until Jan 2008!). i think i might get the miniseries and seasons 1 and 2 from netflix soon.... rewatch the whole thing to tide myself over.

and in other geeky news, i got my issue of Buffy Season 8 #1 yesterday and quickly devoured it. way too short. but hey, joss & co have figured out a way to get me to shell out $3.50 a month for the next couple of years, since you bet your ass i'l be reading the whole series.

in other, other news: t minus 72 days until graduation!! fracking finally.

solitude

i just realized that i haven't seen another person all day, at all. and i haven't uttered any words that weren't directed at my cat. reminds me of an everything but the girl song... "if no one calls and i don't speak all day, do i disappear?"

some days i thrive on solitude. i cleaned a good part of my apartment today, tidied up the kitchen and the dining area and the bathroom, just in case someone were to drop by. i got a good head start on the reading for this week (classes start monday) and watched a lot of buffy. i also blew my nose a lot - to the point where i ran out of kleenex - stupid sinus infection. i think my cough is getting better, though.

one more quarter. 77 more days. then i'll finally be done with my damn undergrad degree, only 2 years late.

what is wrong here
what is wrong here
where is your head?

do you ever get movies from netflix and then procrastinate on watching them? i do sometimes, especially if it's a movie that i've heard is really good, but depressing. i did it with hotel rwanda - i think i had that movie for a month before i watched it. i've had boys don't cry sitting on my coffee table for at least two weeks, but i just got around to watching it tonight. i'm glad i did, but damn! what a downer. though it's true, hilary swank really did deserve the oscar for that performance. she's so believable. anyway, if you haven't seen the movie, rent it, it's good. rent it and think about it, about what our society does to people who don't fit the gender binary. then think about all the ways in which you yourself don't fit the binary - things you do, or things about you, that are stereotypical for the opposite gender. no one fits perfectly into any binary - or at least, no one remotely interesting. and, well, i guess it's an understatement to say that brandon got hirself mixed up with the wrong crowd... especially if the movie portrayals of her "friends" are accurate... but still. no one deserves to die for being who they are. gender is nothing but a label society gives us. who are they to tell each of us who we are?

repeat after me: gender is a social construct. nothing more.

it's late; i should get to bed.

in which i refer to my cat's bathroom habits

So the Great Kitty Potty Training experiment is fully underway. I've had the citikitty doodad on my toilet for about a week and a half now, and I just took away her regular litter box on Wednesday, leaving her no option but to use the new litter box on the toilet. She's adapting pretty well... no accidents thus far (knock on wood). The only downside is that having litter at the height of the toilet means that she can throw it that much farther when she paws around in it. I think I've swept my bathroom every single day since Wednesday. But, she's using it consistently for both #1 and #2, so hurdle number 1 has been cleared. The next step, which I'm supposed to undertake on Wednesday, is to remove the innermost ring from the doodad so she has a hole to use. The hole gets gradually enlarged until there's just a ring of litter around the edge, and in the process, the cat is supposed to learn to stand on the seat, instead of in the litter, to use the potty. So, in about a month, we should be litter-free and fully toilet trained. I'll keep you posted on how it goes, because I know the internet is just dying to know what my cat's bathroom habits are.

afternoon delight

last night, the light from the sunset reflected off the safeco building in such a neat way. it's definitely spring. it'll be summer when the afternoon light bounces off the building and fills my apartment with warmth. but now, even though it's 50 and raining every day, it's definitely spring... and it's only going to get lighter.

work hard don't stop

so it's officially spring break, and i'm back from the Northwest Developmental Biology conference at Friday Harbor (hence the pictures earlier). It was fun, but I left right after my last final, and spent 3 days thinking about science. And now I'm home and ready for a day off before I get to work on my research over the break. I need to go buy food, but I'm running low on cash since I went out to dinner a few times this weekend, and I'm kind of stuck on the couch blowing my nose every 5 minutes. The cold is almost over, but it's left me with a lovely sinus infection. i don't want to have to get antibiotics, but I'm not sure what else can be done against a sinus infection. (And yes, I know it's an infection... I could share details here about the fluorescent color of my snot, but I don't think you want to hear about that...) Ugh! I feel fine except for the fact that my head is full of green gooey goodness.

So spring break means new quarter, and new quarter means new classes and new textbooks. I'm only taking 2 real classes, but they're not going to be easy, and I'm also trying to crank out some data for my project, mapping and characterization of my zebrafish mutant. That means that I'm going to need to get at least one pair of consistently breeding heterozygote pairs of fish, something I have had trouble with the last few months. Grragrh, the fish better start giving. My 2 real classes are 3rd quarter biochem and a genome informatics class, neither of which is going to be a walk in the park. Biochem is a ton of reading and memorization, plus 9 freaking quizzes this quarter (as opposed to only exams last quarter), and genome informatics is a programming assignment a week. Hopefully they won't be too difficult and I won't be too far behind in the programming aspect, since I haven't written even a snippet of code in probably 4 years. I think it's mostly Perl though, and from what I hear Perl is pretty easy to learn.

I think I'm going to give myself the afternoon to watch some Firefly and blow my nose some more. Cause I haven't done enough of that today.

half irish, full suburbs

Stanford is known for producing a lot of successful and talented people, in business, science, and engineering... hip-hop has not traditionally been one of their strongest fields. But graduating with the class of 2007 is K.Flay, a white girl from Illinois calling herself the Suburban Rap Queen. She's got a bunch of songs available for download from her website - you should check them out. My favorite is probably "Hey Ladies" - but I also like "Work". Definitely worth a listen.

friday harbor

more here, and more later.

ok, this is awesome

check this out: the moon's transit of the sun, as viewed from the STEREO-B spacecraft.
here's the explanation. I was completely unaware of the STEREO program, but it looks pretty cool. (found via this site)

more sakura

so it's sunday before finals week, which means it's apartment-cleaning weekend. (isn't it funny how it always works that way?) it's also laundry weekend... though at this point it's just all rounded up into the hamper and waiting by the door with the detergent; i'm considering putting it off until tomorrow in favor of... uh... studying.

the fun part of laundry day is always what you get away with wearing. i spent most of the morning in yoga pants (after doing hardly any yoga at all this morning), and when it was finally time to get myself to the grocery store, i rounded up the nearest pair of semi-clean jeans - ones i haven't worn in months. it wasn't until i had them on that i remembered just how flared these pants are. i've pretty much sworn off boot-cut/flare jeans, seeing as that's the word from On High, and in the last 8 months i've acquired about 4 new pairs of pants, all in the straight/skinny leg tradition. so it was weird to me to see my tennis shoes swallowed by gaping 14" maws when i'm finally getting used to seeing the skinny cuff all scrunched around the tops.

it must be finals week; i'm waxing prosaic on my wardrobe. god save me.

one more thing: go tell Starbucks that you don't like their decision to put Discovery Institute crap on their cups. for details, see pharyngula - he's got a good rundown of the situation.

meme time

ok, so you all know i don't do this stuff very often, but this one seemed cool: it's a list of the most significant scifi and fantasy of the last 50 years. in bold are all the ones i've read.

The Lord of the Rings, J.R.R. Tolkien
The Foundation Trilogy, Isaac Asimov
Dune, Frank Herbert
Stranger in a Strange Land, Robert A. Heinlein
A Wizard of Earthsea, Ursula K. Le Guin
Neuromancer, William Gibson
Childhood's End, Arthur C. Clarke
Do Androids Dream of Electric Sheep?, Philip K. Dick
The Mists of Avalon, Marion Zimmer Bradley
Fahrenheit 451, Ray Bradbury
The Book of the New Sun, Gene Wolfe
A Canticle for Leibowitz, Walter M. Miller, Jr.
The Caves of Steel, Isaac Asimov
Children of the Atom, Wilmar Shiras
Cities in Flight, James Blish
The Colour of Magic, Terry Pratchett
Dangerous Visions, edited by Harlan Ellison
Deathbird Stories, Harlan Ellison
The Demolished Man, Alfred Bester
Dhalgren, Samuel R. Delany
Dragonflight, Anne McCaffrey
Ender's Game, Orson Scott Card
The First Chronicles of Thomas Covenant the Unbeliever, Stephen R. Donaldson
The Forever War, Joe Haldeman
Gateway, Frederik Pohl
Harry Potter and the Philosopher's Stone, J.K. Rowling
The Hitchhiker's Guide to the Galaxy, Douglas Adams
I Am Legend, Richard Matheson
Interview with the Vampire, Anne Rice
The Left Hand of Darkness, Ursula K. Le Guin
Little, Big, John Crowley
Lord of Light, Roger Zelazny
The Man in the High Castle, Philip K. Dick
Mission of Gravity, Hal Clement
More Than Human, Theodore Sturgeon
The Rediscovery of Man, Cordwainer Smith
On the Beach, Nevil Shute
Rendezvous with Rama, Arthur C. Clarke
Ringworld, Larry Niven
Rogue Moon, Algis Budrys
The Silmarillion, J.R.R. Tolkien
Slaughterhouse-5, Kurt Vonnegut
Snow Crash, Neal Stephenson
Stand on Zanzibar, John Brunner
The Stars My Destination, Alfred Bester
Starship Troopers, Robert A. Heinlein
Stormbringer, Michael Moorcock
The Sword of Shannara, Terry Brooks
Timescape, Gregory Benford
To Your Scattered Bodies Go, Philip Jose Farmer

i would have guessed i'd done better than that... but i can't say there are any glaring omissions from my point of view. maybe a couple of gibson short stories, like the whole of burning chrome, but hey... i didn't make the list, i just posted the meme on my blog. (mad props to pz for his impressively-bolded list.)

saturday

listening: imogen heap, speak for yourself. the voice behind frou frou is equally strong on her own. i just love her voice, and her songs are perfect background music for studying time.

just finished watching: the season 7 - aka series - finale of buffy. it's a bit of a letdown to finish an epic, but since i know now that it's not really the end, just the end of the tv show, it's not as hard as it might have been if i'd been watching it on network tv in 2003. today also marks the 10th anniversary of the buffy tv show - it was picked up by the WB midseason in march of 1997. buffy was more than just another tuesday night drama - it was such a powerful story that has impact far beyond the realm of tv. joss whedon has said that he intended for buffy to live on in her fans, to become a part of every woman on the planet, and i think he succeeded at least a little bit. there were so few positive female role models on tv, especially tv geared at teenagers, before buffy came along. and it was a show that wasn't afraid to take chances. case in point: "once more with feeling" - the musical episode. "hush" - the episode where no one is able to speak. "the body" - the episode that chronicles the 24 hours after buffy discovers her mother dead on the couch. if ever there was a more influential tv show, i have yet to see it. so here's my advice for anyone who likes butt-kicking, funny quips, or hot girls, or for anyone who enjoys battlestar galactica, or serenity, or anyone who likes reading comic books or watching action-packed anime. start at the beginning - "welcome to the hellmouth" - and stick with it. those who are able to make it through the first season will surely not be able to quit after that - all 7 seasons come together as a fully fulfilling story, an epic tale of a postmodern hero, a female fighter we can all embrace.

and with that over, i am empowered and inspired to geek out on my textbooks for the next 4 and a half days. wednesday morning, it's all over. wednesday afternoon, i'll be in friday harbor, up in the san juans, surrounded by the beauty of puget sound and all the pacific northwest has to offer. and when i get back on sunday, i'll have an entire week off from school. woohoo!!!

a couple of awesome sites

first: brainmaps.org. Tons and tons of visual data from brains of various species, including our own. Zoom in to the cellular level on many of the images. Sweet stuff, plus it's all open access. (via cognitive daily)

second: the cochlea homepage. Lots of awesome images, plus a good primer on cochlear anatomy and function. (this one's via retrospectacle)

sakura

grr... arrgh

sigh. dark horse has pushed back the release date for Buffy Season 8 #1 until the 21st. this is the second time this has happened... it should have been out today. joss... what's the holdup?

home again, home again

trying to get back into the swing of things after a week off of classes is hard. trying to get back into the swing of things after a week in the most picturesque location in the world, with some of the most amazing people you've ever met surrounding you 24 hours a day, and coming back to the last week before finals, one or two lectures behind, and with a dose of apathy a million miles wide, is harder.

apathy's not the right word, either. it's not like i don't care about classes, it's just that i'm nearly completely caught up, and i'm sitting in a good place, if i just put in the work. i think i can 4.0 the quarter, but i'm having trouble focusing and buckling down due to other forces afoot.

focus. not on real ultimate britney, or plotting random acts of folly. especially don't focus on buffy. focus on biochemistry. your final is a week from today. focus for one more week, then for one more quarter.

and we're back...

so i'm back from my canadian sojourn, a bit behind in classes and with a stuffy, achy head and throat and general fatigue. if it's flu i don't want to know, i just want to keep plodding through this last week of classes without falling further behind.

this is the iconic mountain that is on all the postcards of Banff. it's not the one with the ski area (i was also surprised to learn that the Banff ski area is small and Lake Louise is far preferable to most locals), but right above the iconic Banff hotel. the name escapes me at the moment, but i have to post this picture of it because it is so amazing in person. the canadian rockies are incredible in general, but this particular mountain is especially cool because it is so easy to see how it formed. the whole area is formed of rocks that used to be seafloor in the Cambrian era, pushed up and broken into craggy mountains. see how one side is so smooth, and the other is a jagged series of layers? it's awe-inspiring to imagine what sort of a huge event caused this formation. so, so cool.

this is the view from the gondola from the base of the lake louise ski area. incredible view. amazing powder, good trails... a good day of snowboarding.

left to right: the weiglator (scott weigle, our mentor and professor, and all-around awesome dude), katie (testing her radio) and tim, not realizing i'm taking a picture and hiding behind his skis.

nels, ben and i on the gondola. good times.
as always, there are more photos on my flickr site.
in other news, insert vague reference to some sort of huge development afoot in my life. it turns out persistence, patients and guts pay off, occasionally. more later... maybe.

canadian rockies

mountains!

wikimapia is awesome. so will be lake louise, i predict. check out those craggy mountains! i can hardly wait. t minus 9 hours until departure...

hypoxia 2007

t minus 1 day, 9 hours, and counting until we leave for lake louise, for the 2007 international hypoxia symposia. i am really excited about this trip... it should be amazing. i'll only be gone for 5 nights, but it's going to be 2 *full* days of driving, 4 days of science, scenery, and skiing, and 5 nights of debauchery and fun with my white mountain buddies. woohoo!

check out our route. google maps makes it look like it's going to be hella pretty. i have never been to the canadian rockies before, but i was looking at pictures and satellite images online and it looks like i will not be disappointed. evidently they're some pretty impressive mountains.

so i'm sure i'll be taking lots of pictures, and there's wi-fi at the hostel, so i should be able to flickr stuff on the fly. the one thing that's going to be a bit harsh is the weather forecast - one day (tuesday?) the predicted high is -12 degrees C. that's like... 10 degrees Fahrenheit. BRRRR!!!

and now, for something completely random, my hand on a plate in negative color!

1,001!

i didn't even notice that my last post was the 1,000th to this blog.

oysters!

my friend kevin (whose couch i slept on in new york last summer) was in town for a microsoft interview, so he called me and we had dinner last night at elliot's oyster house. mmmm! oysters are tasty. we sat at the bar and chatted with the oyster guy (i'm sure he has a fancier name than that) about shellfish and seattle. he hooked us up with the last two of the ones on the bottom, the pretty round ones. they were super-tasty. but the icing on the cake was the champagne stuff in the middle. it's this icy, peppery really tasty frosty stuff made out of mumm's champagne and some other stuff. (sorry, i am so not a foodie... i should be able to describe that better.) anyway, it was yummy.

the picture was taken on my new camera phone. after the camera saltwater tragedy i figured it was as good a time as ever to upgrade my cellphone, especially since i was up for a contract renewal. so i signed my soul away to cingular for another 2 years, but i got a sweet sony ericsson w810i for just 75 bucks. it's got a 2 megapixel camera, which is the same as my old camera... slightly less zoom power, but definitely smaller. plus, it's two gadgets in one. plus, it's got video capabilities with a microphone, something my old camera was lacking, and it takes good pictures at high resolution. the downer is that it takes memory stick instead of SD (damn you and your proprietary formats sony!) so my 1gb SD card is no good, and i'm stuck with 128 mb unless i want to buy a memory stick. overall though, i have to say i am impressed. it's a great phone, and a pretty decent camera to boot. :D

sweaty basketball players

george takei is awesome. (tim hardaway is not, obviously.)

what good is half an eye? plenty!

From the Guardian's blog, an interesting tale about a bionic eye turns into an effective argument against Intelligent Design. (via Evolving Thoughts)

Part of the reason that ID is such a seductive argument is the way that adaptation is often referred to in popular culture. No natural history documentary script would be complete without a description of the polar bear as "perfectly adapted" to its habitat or a eulogy to the "exquisite camouflage" of the arctic fox.

But nature is much more interesting than the Discovery Channel would have us believe. Look closely and much of it wouldn't be winning any design awards. Rabbits, for example, have an inefficient and frankly gross way of digesting their food. Your furry pet has a side branch to its gut that is full of enzymes and bacteria. By munching on half-digested morsels from this side branch that have passed out of its backside the rabbit's stomach and intestines have a second go at extracting nutrients. It works, but from a design point of view it is crazy.

Despite looking pretty impressive, the human eye itself is put together in a way that a fairly unintelligent designer could improve on. The rod and cone cells that gather light and convert it into electrical impulses destined for the brain are wired up "back to front". So light hitting the retina has to pass through a maze of wiring before it reaches the light-gathering rods and cones. And anyone with a bad back could be forgiven for cursing our knuckle-dragging ancestors who gave us a spine that is not well designed for upright support. The point is, though, that all of these bad designs, with their echoes of ancestors long since gone, are good enough.

And as to the old creationist argument that half an eye (or half of any complex structure) would do no good, well, consider that one BUSTED. A rudimentary light-sensing patch with 4x4 resolution is far better than no light-sensing equipment whatsoever; a cochlear implant with 16 channels is better than no hearing at all. It's easy to see how just a single cell with the ability to sense where the light is conferred a huge advantage on the organism that posessed it. So too with the first animal to evolve a two-celled light sensing organ. Two becomes 4, 4 becomes 8. Add some protective extracellular material, wire up some neural networks, and add a couple hundred million years of hardcore selection for the ability to sense one's environment more and more acutely... poof! the vertebrate eye!

"Nothing in biology makes sense except in light of evolution." T. Dobzhansky

Molecular basis of neural activity

A primer on membrane potential, ion channels, and neurotransmitters.

Part I.

As you may have learned in your introductory biology classes in high school or college, the fundamental unit of the cell membrane is the lipid bilayer. A double leaflet of phospholipids, with their charged phosphate group pointing towards the aqueous inner and outer environments, and their nonpolar, hydrophobic tail groups clustered together, protected from water, the lipid bilayer is the perfect selectively permeable membrane - if a molecule is small enough, or nonpolar enough, it can simply float through the bilayer, but if it is too large, or highly polar or charged, it cannot pass without the aid of a specialized transmembrane protein. In this way the lipid bilayer forms a selectively permeable barrier - the cell can effectively choose what gets in and out and when. It's not hard to imagine that a cell needs many different types of transmembrane proteins specialized for the translocation of some species from one side of the membrane to the other. Some of the most basic, and most important of these are the ion channels and pumps. Together, these two types of proteins form the basis for many cellular processes, from blocking the entry of more than one sperm into an egg, to neurotransmission, muscle contraction, and exocytosis of vesicles containing hormonal signals. So, what are the basics?

1. Cells expend energy to establish and maintain a gradient of several ion species across the membrane. Your brain uses around 40% of your energy - and a large proportion of this energy is consumed by the Na/K ATPase, or sodium-potassium pump. This protein couples the breakdown of a molecule of ATP (the energy currency of the cell) to the transport of a few sodium ions out of the cell and a few potassium ions in. The result of this transporter's action is that sodium ions are present in higher concentration outside the cell, and potassium ions are present in higher concentration on the inside. Calcium is also higher out than in, though cells may also sequester calcium inside membrane-bound organelles such as endoplasmic reticulum, or sarcoplasmic reticulum in muscle cells.

2. Cell membranes hold an electrical gradient as well. The interior of the cell contains a number of negatively-charged species, such as phosphate groups and organic acids. In terms of classical E&M physics, the cell membrane acts as a capacitor, storing up charge without allowing it to pass. The extracellular sodium ions are strongly attracted to the negative inner membrane surface and build up along the membrane, making the extracellular face of the membrane highly positively charged. This adds up to a potential gradient across the membrane of around -70 mV in most cells. By convention, this number is negative when the intracellular environment is more negative than the extracellular.

3. By controlling the flux of ions across the membrane, a cell can harness the drive of cations to flow into the cell. Ligand-gated and voltage-gated ion channels are the two most important classes of transmembrane transporters that allow ions to flow down an electrochemical gradient and to be harnessed for intracellular signalling. Ligand-gated ion channels, those which are opened by the binding of a particular small molecule such as dopamine, open in the presence of neurotransmitters and allow sodium and (to a smaller extent) calcium ions to flow into the cell. Voltage-gated ion channels of many different types open and close at certain membrane potentials, forming the basis of the action potential, the fundamental unit of neural activity.

In summary, the ionic basis for neurotransmission can be thought of in terms of an equation straight out of high school physics: V=IR, or I=V/R. I, or current, is the flux or net movement of charged particles; in our case, it's the flow of ions across a membrane. V, or voltage, represents the gradient across the membrane. This gradient has two components: chemical and electrical. A higher concentration of sodium ions outside than in, combined with a negatively charged intracellular environment, in effect form two forms of "motivation" for a sodium ion to cross the membrane. R, or resistance, can be thought of as the path by which a species can cross the membrane. Ions are far too big and charged to cross the membrane without the assistance of a channel; without a channel present, R is very high (if not infinite), so no matter what V is, there is no I or current. The presence or opening of channels across the membrane lowers the resistance, thus increasing the current.

OK, that's enough for today. Next time I'll try to get into the mechanics of an action potential, and the roles of voltage-gated sodium and potassium ion channels. As always, wikipedia is a great place to learn more. Here's the article on lipid bilayers, in case you want to know more.

best weekend evar.

this morning i woke up, sat up, and saw the pacific ocean. that happened yesterday morning too. yesterday afternoon i spent in full rain gear, out on the tide flats, digging up razor clams with the entire citizenry of moclips, wa. i love the ocean.

after an entirely grey, rainy day, as i dug up my 15th clam (the limit) the sun broke through the clouds with an amazing deep pink-red sunset. the entire horizon, as well as the glistening sand on the beach and the waves as far as the eye could see, absolutely burned with this beautiful fiery red. it was amazing.

later last night, in between rain showers, i saw the milky way.

the only bummer of the weekend was my stupidity in not listening to brock's recommendation to leave cameras in the car when digging clams. i was patting down my pocket to reassure myself that the camera was still there when i felt something drop and saw a splash, then my camera about an inch underwater. FUCK. i took the batteries out and gave it to my friend who had a pocket that fastened better... but i still haven't tried to turn it on yet. salt water is not good for electronics. i'm holding out absolutely no hope for its resurrection; i figure that way i can only be pleasantly surprised if it still works.

so i need to buy a new camera now. i think what i might do is buy a new cellphone with a 2 or 3 mp camera (my old one was just 2 mps), and then when i graduate (or maybe before, depending on financial situations) buy myself a canon rebel xt. my aunt let me play with hers over christmas, and it was awesome. it's a perfect entry-level digital slr - and with the new version (the xti i think) out now, the older model is coming down in price. i found one online the other day for somewhere in the $200 range for the body... and i can get the lens that comes with the full camera package for like $150 off of ebay. like 400 bucks for a full-featured digital slr. fuck yeah.

delta(regime)

read this.

it's a very concise, well-written version of what we've all been thinking for the past 6 years. fuck the bush regime, fuck authoritarianism. mad props to the former republicans joining the ACLU. mad jeers to the man behind the curtain, dick "is a killer" cheney, and to several spineless senate democrats.

the 2006 elections didn't change anything about the president's willingness to ignore the rule of law. the fight has really just begun.

also: bring our damn troops home. yesterday.

so after i got all excited about my kenneth cole order, i log back onto the website and it doesn't show up in my account. i think the website lost the order. and of course none of the things i ordered are still in stock.

FUCK. if they fucked up my order, i am going to be SUPER FUCKING PISSED.

oh wait, i already am.

edit: i should have known it was too good to be true. i bet they messed up their pricing system and cancelled my order because of that. oh well... bleh.

um OMG

OMFGWTFWOOHOO!

WTF is with all these great bands from the past deciding to reform this year? first the police, now the fucking smashing pumpkins? 2007 is the best year EVAR.

(thx jrad, o btw cn i hv my mrtni glssz bck?)

aaaah

i just bought almost $500 worth of clothes from the kenneth cole website.
wide-leg slate grey high-waist pants (SO all over the runway this season). original price: $148. i paid: $17.98.

knee-length grey skirt with voluminous pleats. original price: $148. i paid: $19.79.

army green jacket. original price: $198. i paid: $16.19

HOLY SHIT.

total charged to my visa: $68.

i am the MASTER of bargain shopping.

nurdz.

Charles: IM IN UR MUNE ZYSTEM KILLIN UR LUKOCYTES

awesome video.

DNA wrapping and replication animation.

(via pharyngula, my favorite scienceblog)

a new adventure

so i've been thinking about this for awhile, and i've decided it's time... to toilet-train my cat.

citi kitty makes a toilet-trainer doohickey that is highly recommended across the internets, with plenty of photos and youtube videos of cats that have been trained with the citi kitty doing their business. hey, if i never have to scoop again, i would be a happy camper.

i'll let you know how well it works. and i will post pictures of my cat using the toilet, once she gets the hang of it.

ugh

i am NOT getting sick again.... i am NOT getting sick again. i am NOT GETTING SICK AGAIN.

maybe if i keep telling myself this, the tickle in my throat and the icky in my nose will go away.

because i can't be sick! i have too much to get done this week. especially before wednesday.

w00t!

after biochem lecture today, i found myself walking at the same pace and direction as the professor for the first half of my biochem class. we'd learned in class that the exam was graded, the mean was 52 and the median was 53. (out of 100.)

me: "hey dr. parson, i was wondering if you knew what the high score on the exam was."
dr. p: "oh, i think it was a 92 or a 93. very impressive."

fast-forward five minutes of walking toward health sciences, the brown spot on my nose growing by the second. i admit it, i was schmoozing. anyway, fast-forward to me, walking out of the biochem office and out of sight of my classmates picking up their graded exam. i unfold my exam and look at my score...

92.

that's right, bitches. hate me. :D

proenza schouler? must be thursday.

it's those pants again! (style.com.) must get me a pair like this! i could wait and hope they put something like that in their FW07 line for Target (if they're doing a FW line for Target) or i could buy vintage. must go thrifting this weekend! i hit jackpot at the buffalo exchange last weekend and found a pair of shiny black trousers AND a pair of faded black jeans, both in straight/skinny leg, for a grand whopping total of $27. i was proud.

so, am i officially a geek yet, or am i going to have to pre-order this? that's right, joss whedon is writing a new comic book series that takes place after season 7 left off. the slayer epic continues! issue #1 hits the shelves on march 7, and he says he's shooting for a 25 to 30 issue series, with monthly issues. sweet! and then, there's this: a compendium, a veritable series of tomes of the buffyverse comics. That doesn't come out until july... actually, just 3 days before Deathly Hallows*. Plus, it starts out with a *faithful* comic-book adaptation of joss's original screenplay, the one that was produced as the B horror movie starring kristy swanson. i'm anxious to find out what joss really intended the story to be like. eeee! it's going to be an awesome summer.

hoom de hoom, don't be hasty. i'm trying to savor Season 7 of Buffy, since i know it's all the great live-action Buffy we'll have, at least for a good long while. but it's so hard, when the show is just so awesome. and what with my midterms over for the moment and me thoroughly ahead of the curve in all my classes, i have time for a little s&s (staking and slayage).

*I've been reconsidering my position on the does-Harry-die issue. I saw a quote by JK Rowling the other day that said something to the effect of, "I knew Harry's story would come to an end after 7 books." hmmmmmmmmmmm. maybe he does die. but probably not really DIE-die... or does he? *squeal* can't wait!