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.



...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.



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.


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 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)...



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.



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.