harry potter

ok, you've had a week, so i'm going to write now about how i felt about the harry potter book.

my initial reaction to finishing was anger and disappointment. i felt cheated by some cheap plot tricks that were just too convenient, and i hated the epilogue.

that said, overall, i guess it's exactly what we should have expected from the end of harry potter. and i did like it, i really did. i ate that book up like candy, finishing it probably 28 hours after i bought it. it was satisfying, since who doesn't love an epic that ends well, but... and I guess I have had these feelings throughout the series... but I thought the end was a little too traditional-values. be a hero, grow up, marry a nice girl and have a flock of children. meh.




dreaming in stereo

i had a dream about bikes last night.

it's not particularly surprising, since i spent all last night riding bikes.

i dreamed about the fixie conversion i am going to embark on with my old sekai frame. i dreamed that it had been turned into a singlespeed (not a fixie) and i remember being highly annoyed at the ability to coast.

critical mass/greenlake madness

there were a lot of people at critical mass tonight.
it was my first time, and it was definitely interesting... it's the one night a month when we just really fuck up traffic.
and then there was... shenaniganery.
and imagery.
and this was how i ended the night: up the fucking stairs. with my bike. cyclocross boot camp, hell yeah!


great new music

(not even a harry potter related post here. enjoy, those of you who haven't finished the book, and read faster, dammit!)

in our bedroom after the war, stars

i bought this album last night off of itunes on a kind of an impulse. i'd logged onto itunes with the intent of buying the new polyphonic spree, but after listening to a few clips and reading a few reviews, i decided that i was not, in fact, in the mood for that exact album (though i will probably grab it eventually), and clicked, based solely on the name of the album, on this one. i'd heard of the band stars before, maybe even heard a track, enough to know that i liked their stuff, but i'd never really listened.

and now i've had 24 hours straight of listening, and i am in love. it's the best album i've heard since the crane wife, and though it's not quite as literary as the decemberists, or quite as amazingly catchy as the postal service, it comes close on both. and it stands up to repeated (at least up to 5) listenings in close succession, a definite sign of a good album (in my opinion).

best. impulse. album. purchase. EVER.

and now, more long-exposure madness:


plant photo geek

and, one that should only be experienced in the largest size possible: the new frond unfurls

a sunday post

I'm posting again this morning because I want to put a post between my last one and the top. It's not really a spoiler, but it's just my initial emotional reaction to the end of the book, and so if you don't want to know ANYTHING AT ALL don't read it.

OK. now that's done, and I need to think of something other than HPatDH to write about.

Today is the end of my un(der)employment streak... I start at the lab full-time tomorrow. Getting paid pretty decently too, evidently. Pretty stoked about that. I have enjoyed having a break from science, but I'm really looking forward to getting back in the lab and cranking out data. Butt? Time to get in gear. OK.

My job for today is to get my apartment clean. Or at least semi-clean. Or at least fight the tide of entropy. Damn that law of thermodynamics, stating that things always have to get messier unless you expend energy to tidy them. Why can't it be the opposite? Oh wait, because that would indicate a contracting universe, and no one wants to head back towards the singularity that preceded the big bang just yet...

One more thing. Check out the world sunlight map, complete with real-time (updated every 3 hours) cloud cover data, for the entire planet. WAY cool. While you're there, note the huge low-pressure system hanging out in the northeast Pacific, right off the coast of WA/BC/AK. It's been raining here for days, and that system doesn't look like it's going anywhere. Dammit.

deathly hallows

just finished.

will repress commentary for a few days, but it's going up by tuesday. be warned & read fast.

in a word:



long-exposure madness



i just want back in your head

tegan and sara at the triple door, seattle, tonight


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.


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.)


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...







surreal life