i just want back in your head

tegan and sara at the triple door, seattle, tonight

1,111

eleven hundred and eleven posts to this blog. holy crap.

it's been a good week. i found out today that i for sure have a job, with a high likelihood of it turning into a full year-long appointment with benefits and a salary and all that good stuff. :D

and then today i got a text from a friend i haven't heard from since january, saying she had a sick friend and an extra ticket to tegan and sara at the triple door tonight! woohoo! it is my lucky dayweek.

other really good things have been happening to me recently, but i'm not going to go into much detail here. suffice it to say i have met a number of amazing individuals over the past few weeks and have been having a blast. it's almost like a summer vacation should be.

on monday, it's back to work, back to science, but with a completely refreshed perspective. these past few weeks have done wonders for my mental health.

and now, have some pretty pictures:

slow sunday

too true

change "mario kart" to "mario party", and "segfaults" to "pcr" (because i'm a different kind of nerd)

it's sunday.

it's weird, days of the week have so little meaning to me these days... i love it. but it's sunday, which means another weekend is over, and perhaps another shot at full-time employment this week. cross your fingers.

oh man. approaching full-on geekitude with the harry potter book release this friday. i will be there, and i will have a book at midnight. i should probably pre-order, huh. i'm more than a little stoked that the parselmouths will be there... i'm a little blown away by the sheer volume of wizard rock. really, some of it is quite good. and fun.

let's see... other things. i've really been enjoying this summer vacation i'm having here, for the first time in awhile. i feel like i'm finally hitting my stride with this city, after only 3 years here... today, i think i might have to stay at UW for grad school. we'll see, of course. the beaches of san diego sound mighty nice during the winter months here... eh. it'll figure itself out.

blog entry

so i still haven't gotten the ultimate thumbs-up from the Powers that Be on the job situation, so i've been basking in the glow of unemployment for the last few weeks. OK, more accurately, part-time employment. but today was an Unemployed day, and also the hottest day so far of the year (it hit 95!) so I hit the beach. Madison park was (predictably) packed, but lying in the shade of a huge tree near the water and occasionally dipping in the lake made the day much more bearable than sitting in my sweltering apartment. (I need to get a fan.)

kitty is stretched out to her fullest length (she can actually be quite long when she tries) and is so lethargic she barely bats an eye at things that would usually cause her to jump up and run off.


the mountain was out at the beach.


and so were the butterflies.

When I grow up...

So PZ has posted in reply to a question posed by David Ng - Do Biologists have Physics Envy? I'm going to have to disagree with PZ's reply with a resounding YES, I do wish I had a better grasp on physics. That said, I also think that all (ok, not all, but most) physicists should stop chasing elusive particles and seductive mathematical models and start working on problems posed by biology.

So, here are my replies to the 3 questions:

1. What's your current scientific specialty?
I just finished my undergraduate degree in Cellular, Molecular, and Developmental Biology, so if that's a specialty, then it's mine. However, that's a bit vague, so I'll narrow it down by saying that I'm most interested in developmental neurobiology, and that I'm also well-versed in the niche field of hair cell death by ototoxic drug exposure. I could go on here (for days, probably) about everything I find interesting, but really, I'll spare you. You get enough of that if you read my blog. :)

2. Were you originally pursuing a different academic course? If so, what was it? Yes. I started my undergraduate career at Stanford studying mechanical engineering. I burned out, dropped out, went through an "I'm going to be an art major!" phase, and then rediscovered my love of science prior to enrolling and finishing my BS at UW.

3. Do you happen to wish you were involved in another scientific field? If so, which one? Well, not exactly, but I do want to expand my knowledge base into other fields. I am probably going to apply mostly to neuroscience programs, instead of traditional cell biology or genetics programs, because I want to gain exposure to some more of the computational and physics side of things. I think it's important to start formulating our biological questions in ways that people more trained in computational sciences can understand and contribute to, and in order to do that, I need more exposure to math, especially network theory and statistical modeling, and to physics, including quantum physics and physical chemistry.

i ride my bike

44 miles today. not bad. also: i got a spoke card which i did not promptly lose. woohoo!

now it is bedtime.

things i am worried about

1) the cut on my big toe. i sliced it open on a razor-sharp tree stump at the park on Wednesday. it's a doozy, not quite stitches material, but I'm not quite sure how deep it is because of the angle of the cut. i have been keeping it clean and have my eyes peeled for oozing, because the last thing I need is a superbug infection in my foot. I need that like I need a lobotomy.

2) my knees. the surly is great, it really is, but the gearing ratio is not optimal for the amount of hill climbing i do. i need to start taking it easier, keeping my cadence up, and standing up when i get tired. i raised my seat by about a half-cm and moved it back a bit, which should help.

3) whether or not this job is going to come through. OTOH, i have been doing some phat networking over the last week or so, and am reasonably sure i'll be able to find another job in a reasonable amount of time, and i have guaranteed hourly work until then, so i'm not *too* worried. that's why it's #3.

hells yes.

check out my ride today. oh plus the 11+ i did earlier today when I rode around lake union for the first time ever. i almost hit 40 today.

:D

add in beer, about 20 people, a fire, and the beach at Lincoln Park, and you have yourself a nice time. the .83 kids? they're alright.


and the highlight of the evening, the grand central bread dumpster:

How do you map a gene?

One of the questions that's most frequently asked about my research, and one that I'm never able to answer concisely and satisfactorily, is this one: How do you map a gene? And although the answer is a bit long and involved, it's not too difficult conceptually, once you get a few basics out of the way.

The first thing you need in order to map a gene is some sort of variation in that gene, be it mutants vs. wild-type, or a polymorphism in the population (say, red hair vs. brown hair). You need to be able to sort out, based on phenotype, which individuals have the wild-type version and which ones have the mutation or polymorphism. Usually, this means you need an assay, whether it's based on morphology, drug treatment, behavior... however you do it, you need to sort your animals into two categories. One other important thing to keep in mind is that the mutants and the wild-types, in most cases, come from the same families: they are siblings, so they're genetically nearly identical except for the gene you're looking for, which is causing the phenotype you're sorting by.

The next thing you need is a library of markers of known genomic location. For zebrafish and many other animals, this has been published - and new markers are added constantly. zfin.org is one place to find these published markers. Here is a link to a map of these markers. Click on a chromosome button (referred to as LG, or linkage group, on that site) to see the map of the chromosome and all the markers. Click on an individual marker to see all the published information about it - location, sequence, who discovered it, etc.

Most of the markers in this particular map, which is one that I use extensively in my work, are known as Z markers, and are identified with a Z and then a number, such as z1234. These "markers" are also known as SSLPs, or simple sequence-length polymorphisms. This means that they are sites which vary in length between different strains and even individuals within a strain. This makes them very handy for our purposes.

SSLPs are usually found around sequences of di- or tri-nucleotide repeats, such as a stretch of AGAGAGAGAGAG base pairs. The reason they have length polymorphisms is that when the DNA replication machinery is copying these short repeated sequences, the enzyme is likely to "slip" and copy a few bases twice. These events happen fairly often (evolutionarily speaking), and randomly, and the end result is that there are many different length alleles in the population. Length differences are easily detected by PCR and gel electrophoresis. This gives us an easy way to determine a fish's genotype at a particular site. By comparing individuals to their parents, we can determine which chromosome is from Mom and which one is from Dad.

There's one more important point to make before I get into the nitty-gritty of actually mapping the gene. Mutations are made on a lab "wild-type" strain - in our case, we use the *AB line for mutagenesis. ABs are useful because they are fairly genetically uniform, and have very few lethal mutations hiding out in their genome. But they are bad for mapping, because the SSLPs tend to be the same length in all the fish. Once a family has been identified with a mutation, one of the carrier parents is outcrossed to another strain - WIK, in our lab - which has different SSLP sizes at most of the sites, and is actually known as a "polymorphic mapping strain" in many labs.* So once the outcross is done and another carrier pair identified - these fish are *AB/WIK genotype - the offspring of this cross are sorted by phenotype and then their DNA is extracted. We also get the DNA from Mom and Dad, as well as the founder grandparent fish, and the wild-type WIK animals used for outcrossing.

The first step in mapping the gene is to determine gross linkage, or to answer the question: What chromosome is the mutation on? In order to figure this out, we make pools of DNA samples from the mutant and the wild-type sibling fish. We then test SSLP markers on pooled mutant DNA, pooled sibling DNA, and Mom, Dad, and grandparent DNA samples. Here, we're looking for a particular pattern: Mom, Dad, and the wild-type siblings should each have two bands, or two length alleles for the marker (since they have both an AB and a WIK chromosome); the grandparent and mutant samples should each only have one, and it should be the same one (since the mutation was made on the AB background).

Here are some simulated ASCII gels. The lanes, from left to right are: mutant pool, sibling pool, Mom, Dad, Founder Grandparent. (Note: on all these gels, the single line should line up with the bottom of the double lines. It doesn't really work right in this font, but pretend.)
The first gel is a non-informative marker:
----- All the samples have a single band of the same size. We can't learn anything from this.
The second gel is an informative, but unlinked, marker:
====- Mutants, siblings, Mom and Dad all have alleles from both the AB and the WIK chromosomes. These are recessive mutations, and the mutation is carried on the AB chromosome, so it can't be here, since the mutants have AB/WIK genotypes.
The third gel is an informative, linked marker:
-===- Mutants have just the AB band, meaning they are homozygous at this location. This is good evidence that the marker is near the mutation.

So you test markers on each chromosome (zebrafish have 25) and look for the linkage pattern. Once you find a chromosome that shows linkage to the mutation, it's time to switch tactics and go for fine mapping.

For fine mapping, or determining where on the chromosome the mutation is, we abandon our pooled DNA and work with individual DNA samples. We need as many of these as we can get, so we keep breeding our mapping pair (Mom and Dad) and sorting out the offspring based on mutant phenotype. (Remember that recessive traits are found in 1/4 of a carrier pair's offspring... do a Punnett square if you can't remember how that works.) So 1/4 of the offspring are identified as mutants, and the other 3/4 are siblings. Of these siblings, 2/3 (or 1/2 of the total) are heterozygous, or carriers, and 1/3 (1/4 of the total) are homozygous wild-type, or don't carry the mutation. Most importantly, though, every individual identified as a mutant must be homozygous at the site of the mutation.

So what we do here is we test markers all up and down the chromosome we've identified on all of our DNA samples - mutant, sibling, and parents and grandparents. Due to recombination, not all the mutants will be homozygous at all of the locations we test - and the proportion of those who are homozygous (show up with just one band - instead of two =) is directly proportional to how close the marker is to the mutation. Recall that during meiosis, when germ cells (sperm and egg) are being formed, crossing over occurs between homologous chromosomes (i.e. your copy of 5 from mom and your copy of 5 from dad), creating new chromosomes with bits of each. BUT - we know that all the mutants must have the AB chromosome only at the location where the mutation is, so we use this information to narrow down where the mutation is.

Here's another sample gel. This time, individuals are listed vertically, and each column is that fish's genotype at each of 5 different markers.

mutant A - - - = =
mutant B = - - - -
mutant C = = - - -
mutant D - - - - =
mutant E = = - - -
wt sib A = = = = =
wt sib B - = = = =
wt sib C - - = = =
wt sib D = = = - -
wt sib E = = = = -

Based on these results, we can conclude that the mutation is closest to the third marker - since all the mutants are homozygous and all the sibs are heterozygous here. (In reality, some siblings would also have just one line corresponding to the upper band, but I can't really do that with the ASCII at my disposal.) By testing hundreds, if not a thousand, mutant and wild-type fish, you can find a pair of markers between which the mutation must lie. By testing markers that are closer and closer together, you can narrow down the region to a few hundred thousand base-pairs, after which the mutation is mapped, and now needs to be cloned. But that's another post for another day.

This all sounds pretty easy and straightforward, and while it's conceptually simple, it's a lot harder in practice. One challenge that has hampered my progress is finding polymorphic markers - markers with different lengths between AB and WIK fish. There are also challenges with breeding and identifying mutant fish - sometimes the fish don't "give" (spawn) well, and after about a year an old pair will just stop giving. It can take a long time to map and clone a gene, as I've proven by taking more than a year and a half to find this one... or you can also get lucky and find it relatively quickly. Like anything in science, it's probably 50% luck, 50% hard work.

So that's my post on how to map a gene. The details vary by organism, but it's pretty much the same in principle - whether you're mapping the cystic fibrosis gene in humans or a novel mutation in zebrafish, fruit flies, or yeast. This whole process is known as "positional cloning" - finding the gene by its position in the genome. It's labor-intensive and slow at times, but it's a powerful method for finding a mutation that could be anywhere.

(* I have my own theories as to why this line is so polymorphic, but they're all unfounded at this point, just based on observation and hearsay. There's a chance that I'll end up exploring this as a part of my Ph.D. work... but until then, I'm going to leave those theories out.)

1100

this is my eleven hundredth post to this blog.

nothing more for right now; just that. i'm working on a science post, but it'll take awhile.* so right now, just an 1100 celebration.

*edit: i guess not so much.

nerd convention

yeah, so i met pz myers last night at drinking liberally... he's every bit as scary as the rumors suggest. fortunately i managed to escape unscathed. we even got to talk science for a bit, after the throng of worshippers died down. there were also several candidates there, stumping for the primaries, so I had a chance to talk to bill sherman, who is running for county prosecutor... who says he will do "everything that's good, and nothing that's bad" if elected. well gee, you've got my vote...

flora

surreal life

every single night, the same arrangement

just got home from seeing the Buffy Musical - Once More With Feeling... the singalong. it was AWESOME. we sat in the front row which meant that i got a drycleaning shirt and got to dance to the mustard song! amazing!

yeah. i'm a huge nerd... but so was everyone at the egyptian tonight. well, everyone except for my date, who was actually my ride home from the cabiri show, and whom i bamboozled into coming even though he'd never watched much buffy. i think he had fun. i certainly did.

quickie

1) still not done moving. aaaargh. i'm almost done, i promise... just a goodwill/salvation army/dumpster run and maybe 2 things to come to my new place. then i give them the keys and say goodbye to that old place in the u district. and then they give me my deposit back, which i am very much looking forward to.

2) i have found myself involved with a rather elaborate stage production, going on this weekend. my friend john, whom i met in genome informatics this past quarter, is evidently the director of an aerial dance troupe that does "performative mythology". and i have to say, the show is fucking rad. sorry guys, it's sold out (has been for like a month, in fact)... so you'll have to take my word for it. but seriously cool. i'm not contributing in any meaningful way, because i just showed up yesterday, but i am actually able to help occasionally (rather than just get in the way) and i've met a bunch of new cool people. which is always good. they have me working the dressing room during quick changes - handing out costumes, hanging things up, pinning, zipping... cake. plus it gets me into the shows for free (though i had actually already bought a ticket)...

master of all he surveys

i love capitol hill

one more thing:

09-F9-11-02-9D-74-E3-5B-D8-41-56-C5-63-56-88-C0

upon walking home from the bar, largely sober and happy

as i am walking home from the bar tonight, i feel almost like i am in another city, somewhere more cosmopolitan, more european. i've been transported to somewhere more urban and complex, more storefronts and apartments and more people. it's a strange dissociative feeling, like i have teleported to another time or place, somewhere in another life. i feel strangely like i'm in prague, or berlin, but at the same time, i know where i am and where i am going. and as i walk home over streets i've never walked, i know precisely where to go. unfamiliar, yet strangely perfect, like this really is home.

stupid design

:D

(via pharyngula)

i forget that there's a bike beneath me

it feels a little like flying. cruising down the trail, becoming one with the outdoors. i can't figure out how i survived this long without a bike.

the only problem i have with the new bike (predictably) is the saddle: it sucks. it takes about 10 minutes of riding before my seat is hurting. it's ironic that the saddle on the old bike is more comfortable than the one on the new bike, even though the old saddle is, as far as i know, stock on that 1970's bike. how funny would that be, to switch out the saddle on my brand new surly for the one on a 30-year-old sekai... heheheh.

mmmm. yes. do like riding. do want more please.

SURLY!!!

*grin*

i discovered the real reason cyclists wear gloves. it's so when you completely bite it (usually in front of at least 5 people) you don't scuff up your hands.

of course i had to fall at least once, since it's the first day i've had the bike. i almost fell on broadway, but i caught myself on some dude's car. then i got to the corner of boylston and olive and realized i couldn't start going uphill from a dead stop in the gear i was in, and didn't want to go downhill away from home, and the street turned into an alley if i went straight, so i decided to turn around. and i didn't get my left foot out of the pedal soon enough and i just sprawled out on the street. yes, in front of several people. sigh. but i just bounced back up and went on my way... unscuffed even! hard to believe. but it was from a dead stop. so i'm just not quite coordinated enough with the clipless pedals yet. i'll get better i'm sure...

food is expensive

i've been so spoiled living right by a trader joe's... everything at the QFC by my new place is about 25% more expensive (at least)! i rarely spent more than $30 on my weekly TJ's run, and that was when i really stocked up and bought beer or wine and maybe fish or meat. today, i spent $28, and i got none of the above... just produce and yogurt and a few other things... yow.

then again, i'm saving $190 a month on rent by not staying in that old place... something tells me i won't spend *that* much more on food.

first night

so i have maybe 1/3 to 1/2 of my stuff up here in the new place, and i'm in for the night. i don't have a bed, so it'll be all camping stylee, but i just kinda wanted to get a feel for the place at night. i left my kitty at the old place, since i haven't moved the bed or the couch yet, and i figured it'd be better to let her be surrounded by familiar things rather than running around all freaked out while i try to move a bed and a couch in here.

things i like about the new place:
1) location, location, location.
2) efficient stylings of a studio.
3) rad 1960's architecture.
4) POOL! heated swimming pool in the basement!
5) tons and tons of closet space.

downsides:
1) small. tiny-ass kitchen - it's just like SINK STOVE FRIDGE. not much counter space; even less cabinet space.
2) single-paned windows.*
3) ...

*fortunately, the building is heated by boiler, not by electricity, so heating costs won't be sky high in the winter... it might be a bit drafty though.

anyway, back to assembling furniture, and then probably swimming. woohoo!

yay!

the place is mine! i get to sign the lease tomorrow!

one more.

7. dude. cake. who's up for it?

more (or less) quick

5. i put $300 down on a shiny new surly today. it should be mine next wednesday... being the picky customer that i am, i'm having them swap out the frame on the complete bike they had on the floor for the slightly smaller frame they had hanging from the ceiling. it turns out i have weird proportions (very long torso/arms, shorter legs) and a bianchi wouldn't really work for me. it's cool though, the cross-check is a very solid bike for a decent price. here's hoping it'll last me years... i need to invest in some serious locks and chains now.

6. tessa... ask me sometime about the job i am applying for. i don't want to post it on the blog, but you'd be totally excited about it.

quick things.

1. why did i step over horse shit on my way to bartell's this afternoon? really, there was horse crap on the sidewalk on 45th. what gives?

2. moving. i just filled 2 boxes in the span of 10 minutes. that was the easy stuff though... need to go through/get rid of lots of stuff.

3. moving... to capital hill! i'll be just a few blocks off Broadway. sweetness! and for less than i'm paying now! double sweetness!

4. in case you hadn't noticed, tons of new flickr pictures. i ordered a pro account, so expect photographic diarrhea. except awesome, not gross.

shutterbug

my new camera got here last night, but i haven't quite figured out how to use it or taken any pictures worth posting yet*. i'll try to snap some shots at graduation, but it's raining*, so the camera might stay in my bag. but it's the sweetness... manual aperture, shutter speed, ISO, even manual focus. 15x optical zoom with image stabilization. 8.1 megapixels.

*okay, here's one.

a portrait of frida, with macro mode on, and relatively long shutter. hopefully i'll get good at using this thing... i'm excited :)

**it's like raaaaiiaaaiin, on your graduation day... or something.

food for thought

watch this video. now.

watch some of the other ones on that site, too. then go to worldchanging.com and learn more.

kicking it hipster style

i looked at the most awesome apartment today... i have my fingers totally crossed. trying not to get my hopes up, since there were tons of people looking at it, but i think i might have gotten my application in first.... so i might have a shot. it was this funky, cute little loft studio in old town ballard, in a building from 1902. it's a bit farther out, but by bike it is 20 minutes to the lab, on the trail or flat streets the whole way.

it's a tiny apartment, maybe 400 square feet, but it has super-high ceilings and a loft above more than half the apartment, meaning it has plenty of storage space. exposed brick walls... non-square floorplan (it's a triangular building)... climbing a ladder to get in bed at night... it just felt like home somehow. so i'm hoping he calls in the next day or so. that would make my life so much less stressful right now. and i'd have an awesome apartment. something tells me the kitty would like a loft to prowl.

cross your fingers for me... i have to have this apartment.

i'm done.

well, i'm not done done, I have a paper due on Friday, but it's for a 500 level class and thus doesn't count; i'm done with my undergrad. FINALLY.

though the paper is definitely proving to be a pain in the ass. i've got everything i need conceptually, i think, but the words just aren't coming together. it's annoying.

so close, and yet so far.

wow... commenters!

ok, this post about bikes has created by far the biggest discussion ever on my blog. thanks for all the advice guys... i think i am just going to go into freerange and see what they can do for me. (after graduation.) (and after john recovers from whooping cough(!).

ps jared and tessa, i saw you on the trail at the 25th crossing last night, brian was driving me home with my new shiny.

FAUX News

I guess all black people look the same to FOX... check out this clip of them announcing the indictment of Congressman Bill Jefferson on corruption charges... the video in the background is of John Conyers, not Bill Jefferson. One black congressman, another black congressman... what's the diff?



They aired a weaksauce apology the next day, but didn't mention anything about who it really was in the video, or what the video was of... FAUXkers. (I guess they couldn't actually mention that it was footage of the AG* testimony, since that would be, like, fair or balanced or something.)

* Has anyone else noticed that Alberto Gonzales' initials also stand for Attorney General? And Bush's secretary of education is Margaret Spellings. I think he picks these people based solely on their names, or nicknames, and not at all on their qualifications.

whew

biochem final: exactly like the practice finals. good thing i spent last night poring over the practice finals and their solutions. I think I ended up doing ok (by my standards, which = very well by anyone else's standards)

thinking about buying this bike. it was recommended to me by a friend... never heard of the brand, but he knows his bikes, so i trust him. or maybe this one. according to another friend, "you can't go wrong with bianchi." but the jamis comes in a female-specific frame, which is an advantage. plus it looks like it's got the horizontal brakes, which i kind of like... i think after graduation i'll go into a dealer and get fit. see what they have to say.

tuesday

biochem final this morning... boy will it feel good to be done with it. i fear that i blew off classes this quarter due to senioritis and lab work. so hopefully the biochem final won't kick my ass *too* much.

t minus 4 days... huh?

i think i might go to the apple store and buy myself an imac this afternoon. it'd certainly make writing my paper more fun/easier. i'm going to get the 20" one.

another weekend come and gone...

t minus 6 days until i'm a college graduate, a bachelor of science. weird.

i signed up to take the GRE in august. i need to get my ass in gear and start studying for that. bleh standardized tests.

two finals and one paper, and then i am officially done. paper's due on friday, but with a little luck i'll have it done before that. (not that i've gotten *anything* done this weekend, i've been kind of a waste. i blame the heat and the senioritis. i'm ready to be done.

OMG

I CAN HAV PLAY NOW PLS?

(via

severus, please.

Phoenix Rising, the convention of All Things Hogwarts, gets a great writeup at Salon. makes me kind of wish i could have been there.

it also makes me want to get a costume and dress up for the 5th movie/7th book this July... also, to go to a Parselmouths show sometime this summer. because what could be more fun than watching a couple of 19-year-old girls dressed up like Slytherins sing about how great it is to be wicked?

also, just in case there was any doubt:

I'm a Ravenclaw!

mawwiage.

this is about the cutest damn thing i've read in a while. we should all be so lucky.

toosday

i decided to ride my bike in to class this morning. bad idea. my hand is not really recovered at all, even though it's been a week, and it ended up hurting quite a bit. super-lame. this injury has seriously impacted my contribution to my Bike to Work team; i was already the slouch, even though I was commuting every day, since my commute is so short, but now I am contributing absolutely nothing. i feel so useless.

my handwriting has regressed considerably as well.

in other news: graduation is just 11 days away. insert slight panic. oh... you mean i have to get a job now?

noo shoos

and new socks. hooray for target.

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.)