Archive for the ‘Science PhD’ Category

Have read a few interesting articles lately that were passed on by my science buddies.

First is how to be a productive procrastinator, via Lisa. I think i have a lot of potential for using this technique, as i find myself being incredibly productive while i avoid working on my thesis.

Second, via Melanie, is about surviving the rat race that is tenure track… by not racing. Some very good advice in there. I have been pretty good in grad school about not subscribing to the whole “good graduate students work 80 hours a week” insanity or the list of things i must accomplish to succeed, like networking (i hate networking) or attending as many conferences as possible, or publishing x number of papers. It may all come back to bite me in the butt later if i ever try to get a tenure track position, but whatevs, i’m having fun now.

And a third linked to by the above article about life-work balance in academia. Now, this one is interesting too, and brings up good points about how weird it is to expect ourselves and our colleagues to work so goddamn hard that we have to give up most other aspects of our lives. The emphasis here, as it is in many articles written about life-work balance, is on splitting oneself between career and family and how we women can’t have it all if these crazy career expectations continue.

All fine and good, but i am bothered that in the discussion of life-work balance, life = children. Life does not equal children. It’s unfair that, in our consciousness, life = children for women and thus women have to choose between a career or raising children (or be mediocre at both), yet not many people feel that men have a similar choice to make. For men, life = life apparently, and more work means fewer adventures with friends, wooden canoe building, and brewing beer. In fact, life = life for everyone, and anyone can choose to make their life revolve around kids. Parents bemoan that they can’t possibly work the same hours that their childless colleagues work if they are to be good parents. Why the hell aren’t people without kids complaining that they have to work insane hours and they don’t have time to play city league softball or volunteer at the animal shelter or write a novel? It’s all crazy- the hours and hours of work for shit-tastic pay (shouldn’t forget here that science grad students get paid to go to school; not all disciplines are so fortunate), the stress of trying to be known by lead scientists in your field, the race to publish papers to beef up your CV… Forget the damn kids, our whole lives are suffering because we’re trying so hard! My dog is bored, my garden is neglected, I barely see my friends, and I’m getting skinny-fat for chrissake!

Ahem. So. Life-work balance. What i aim for is to do what i want. Maybe what you want is to spend time with your kids. What i want is to spend time with my husband (yeah, we got married, whut!), make sure my dog is happy, grow beautiful veggies, pickle and jam everything in sight, get off my ass, chat with my buddies, see my family, go on adventures. That’s what i’m going to try my best to do.

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I passed my general exam yesterday, in no small part due to the all natural gift basket that Danny sent. It was full of delicious goodies like potato sticks and whole grain chips and pistachios and fancy mustard and salsa. It all came in a customized tote bag, pictured below, with all of our pictures on it. I don’t know what I like more- that I’m wearing a blonde wig and lipstick, that David is wearing only a tie, or that Tilly is purple. Inks looks pretty normal. Also, the all natural packaging is perfect bedding for the worm bin!

Well done, Daniel!



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While it may be hard for science PhDs to find jobs, apparently we still need more scientists, engineers, and mathematicians in this country!

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Science careers

My grad school buddies and I often send each other humorous articles about how we’ll never find jobs in science, or global health policy, or whatever, in some sort of sick attempt to cheer ourselves up about being stuck in grad school.  Melanie just sent this one, which actually does cheer me up a bit.

These are my favorite two career paths that the article mentions:

Science advocacy
Let’s face it: Scientists aren’t great at expressing themselves. We end up saying things like, “Hepatitis kills over 1 million people every year. THEREFORE GIVE ME MONEY TO BUILD A MECHANIZED KANGAROO WITH LASERS.” That’s why there are science advocates, people who explain to nonscientists why we matter. And if I have to explain why that’s important, I guess that makes me a science advocate advocate.
Science policy
Unlike a consulting firm, which overpays you to advise wealthy companies to rely too heavily on your minimally informed advice, a job in science policy will pay you to advise lawmakers who’ll ignore you. “We value your advice!” they’ll tell you, then go vote against the laws of thermodynamics.

Hee hee hee hee!


Also, I take my general exam next Wednesday- after which point i will un-neglect my garden (the neglect of which is actually causing me more stress than the exam, even though the winter garden will only produce kale, broccoli, rutabaga, and chard and passing the general exam is arguably the most important thing in our PhD program), and begin eating real food and exercising again.  Studying so hard makes me skinny-fat.



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Stealing this from Tony:

“If you’re going to be a scientist, there are three things you have to believe. Number one, the universe really exists — I’m not just a butterfly dreaming I’m a scientist. Two, you have to believe that the universe makes sense. It’s not chaotic; there really are underlying laws and we’re able to find them. And the third and hardest thing, the most religious of the beliefs, is you have to believe it’s worth doing.” – Brother Guy Consolmagno, astronomer to the Vatican

Adding to it the cute but still inspirational quote that’s printed on a plaque above my desk, given to me by my grandpa:

“If we knew what we were doing, it wouldn’t be called Research”  – Albert Einstein

So essentially- believe that science can be done, that it’s important to do, and be ok with not knowing what the heck you are doing.

And one of my favorite xkcd comics:

The laws of nature are discoverable, sure, but the more we find out, the more aware we become of what we don't know, and (at least in my case and perhaps in all things immunology) the more we are guessing wildy at how to conduct our experiments.




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Talking to my Ma on the phone the other day, she said that she and Pa decided not to build an outdoor fireplace on their new patio after all- both of them being space cadets, overhanging trees may catch on fire if they forget to put it out and the whole house and yard could burn down.  And the whole neighborhood and bone dry foothills of Boise- that’d be no good.  I said, “Oh, that’s too bad.  Wait, you guys are both space cadets?!” (This whole time i thought that my dad was the only one with a horrible memory.)  She laughed, “Yep- you’re doomed!”

So that partially explains my increasingly gawd-awful short-term memory of the past… oh… 10 years.  Add to that the medical finding that stress can cause short-term memory malfunction, and you have a good explanation for why, when i decide to go backpacking post-giant experiment or post-fellowship application deadline, i forget to pack a crap-ton of fairly important gear.

First example- following my latest giant experiment (of previous blog post fame), i slept for 4 hours, booked it back to lab to finish some stuff before Lauren arrived in Seattle, ran home to literally throw handfuls of gear into my backpack and get in the car for a 2 night trip with Lauren and Natalie.  Upon arrival at our first campsite, realized that i had forgotten my sleeping bag.  My SLEEPING BAG!  Who forgets their damn sleeping bag on a backpacking trip?!   Fortunately, Natalie happened to have a lightweight summer bag in the trunk of her car for emergencies.  So with long underwear and Nat’s emergency preparedness, i was saved from the emergency of me being a dumbass.  I also forgot my trekking poles, but luckily Nat doesn’t use hers going downhill, so that saved my dumbass knees as well.  And my sunglasses, but hopefully my hat saved my dumbass eyes from too much UV light.

Second example- after i spent the last 2 weeks working waaaaay more than i usually do in attempt to have awesome data and write an awesome research update for the training grant that i’m on- it’s up for competitive renewal, and if i don’t get it there will be some serious scrambling in my lab as we do not yet have grant funding for my project- aaah!!!- i got home, chose a trail with David while again throwing handfuls of gear into my pack and then left for another 2 night trip.  I did remember my sleeping bag this time, and upon settling down into said sleeping bag, realized that i had forgotten my hiking boots.  GAH!!   Hilariously, i did remember to take my Superfeet insoles out of my shoes and bring them along to put in my forgotten boots, so i managed to make some surprisingly comfortable footwear by putting the Superfeet in my Crocs.

Sidenote- i only condone Crocs as slippers for getting the paper, putzing around the yard, walking the dog, and as camp shoes.  Chacos and Tevas are of course better than Crocs in almost every way, but for backpacking Crocs have become my camp shoe of choice because they weigh negative 3 ounces (I think they’re made of marshmallows), and Chacos weigh a ton.  You can’t cross treacherous streams in them like you can in Chacos, but for knee-deep lazy streams they work just fine.  And you can waterproof them by putting plastic bags on your feet inside them, in case you are camping in rain or snow.

And apparently, you can hike in them.  Granted,  we hiked four miles to a campsite on a very easy trail, then day hiked sans-packs up a crazily steep trail to a sweet lake (Tuck lake)- so i was not carrying any weight on any sort of difficult trail…  good, because i also forgot my trekking poles. Again.  In any case, my feet did not die and the trip was pretty great despite my dumbassitude, perhaps because i walk the dog every morning for half an hour in my Crocs, and have built up some strength in the arches of my feet.  I did wipe out and scrape up my hands a couple times on the trail because Crocs have negative 3 traction, but there were no broken ankles or tweaked knees.  David even hiked the whole way in his Chacos to show solidarity.

Our feet were horridly, horridly dirty when we got home, which added to the shame of having forgotten that Jodie and Lisa were coming into town to stay with us that evening.  (David is experiencing job search stress, so he’s almost as bad as i am these days.)  Luckily we made it back into cell phone range just in time to prevent them from renting a hotel room.  I’m hoping that fresh eggs for breakfast partially made up for some of our dumbass (lack of) planning.


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It’s not often that i work long hours in lab.  I usually come in to do what i need to get done, then go do something like walk the dog or tend the garden or go hiking.  Sometimes i read articles in the backyard.  It is apparent to me and to most people i work that i do not do as much work as i could.  But, i am happy not working at break-neck speed so that i may enjoy other realms of life a bit more.  My PI may not be too happy with this, but he’s exactly the same way and knows it.  Brags about it, even.  But then, he probably worked pretty hard in grad school… still, i’m secretly hoping that one day he will tell me he was a slow poke too.

So, 8 straight hours of work in lab will tire me out.  I’ll wonder how people in real life can do it 5 days a week.  But then, seemingly out of nowhere, i will muster a stupendous amount of energy and stamina and complete a  16 to 18 hour experiment that requires almost constant work-  every time i stop to pee or stuff food in my face i feel like i’m letting the quality of my data decline.  Luckily i am able to recruit people to help me- the experiments would be impossible without their help (ie, all the cells would croak and i’d get shit for data and there aren’t enough hours in a day), and i just wouldn’t survive mentally or physically without their support.  I learned this craziness from Jess- i used to think her 20 hour experiments (into which i put my share of grunt work) were pure insanity.  How could she possibly stay up into the wee hours of the morn running the flow cytometer?  But i get it now.  Especially the part about supplying snacks for your helpers.

Anyway, i”ll start with yesterday’s preparation for today.  It involved mixing up several liters of buffer and media; making 8-color fluorochrome-tagged antibody cocktails; mixing cell separation gradients to the correct percentage and aliquoting to tubes; prepping solutions – formadehyde, sugar water- and tubes in which to collect bits of liver to section and stain for beautious fixed and fresh-frozen immuno-histochemistry pictures; wrapping and autoclaving several dissection kits- scissors, blunt forceps, pointy forceps; collecting all the crap that i needed to bring down to the vivarium- like pipetmen, pipets, slides, tube racks, petri dishes, etc- and putting it on a big cart (the sight of which always makes the vivarium staffs’ eyeballs pop out because they know it’s going to be a bloody, stinky, sweaty mess down there for 4-5 hours); labeling no fewer than 263 tubes; then biking up Capital Hill at 8pm to have a Molly Moon’s sundae for dinner in celebration of Goo’s birthday.

I am slowly, slowly learning to prepare for experiments (especially big ones) before the day of.  Now, by the end of my third year in school, i seem to be doing ok.  I am at least less of a pain in the ass to the people helping me with the experiment and to my own self.   So, as i sit here at the flow cytometer at 9:30pm on the day of the experiment, it is not because i was under prepared and had to scramble around making buffer and labeling tubes this morning, it’s because this is a big fucking experiment.  I mean, i stopped at PCC to buy bagels for my helpers on my way in and was still here, showered,  in lab by 8am.  Granted, i could always prepare more.  More reading and research into the best techniques, or looking at past notes wouldn’t hurt.  I just realized that i forgot to stain my cells for an activation marker that’s fairly common in these types of experiments.  Whoops.

I should mention at some point that this experiment is aimed at measuring/evaluating/figuring out what the heck is going on during T cell priming against immunization with genetically attenuated malaria parasites. In mice.  Who get injected with transgenic T cells.  That are green.

This morning i biked in and before i showered, got the collagenase buffer out of the fridge to start warming up in the water bath so that the soon-to-be-added collagenase would dissolve.  Then i went downstairs to shower.  I did not wash my hair, because it always gets nasty and matted down by 5 hours in a vivarium hair net anyway…  but now, at the end of the day it’s especially gross-tastic.  I finished my day-of preparations which included weighing out and adding collagenase to the buffer, grabbing a tube of  mouse anesthesia,  filling two ice buckets with ice, and getting all of my collection tubes out of the fridge/off the bench and onto the cart.

8:45 I headed downstairs to the vivarium, where i was met by my new malaria buddy, Jess #2, and we transferred all the stuff from the lab cart onto a clean vivarium cart.  We went through the vivarium barrier (read “super clean area for immunologically messed-up mice”), which involves putting on a second layer of booties, gloves, a humongous gown (hence why we get all sweaty),  a face mask (which i just wear under my chin because it drives me crazy) and a hair net.  We set up the work side of one mouse room with a liver-perfusion station, a liver smushing station, and a lymph node and spleen smushing station.   Each gets a dissection kit, pipets and tubes and filters, slides, petri dishes, etc.  I brought four cages of mice (18 total) around on a cart just outside the door because we had occupied every other flat surface in the room.

9:20 Isaac joined us (he has a new baby so he doesn’t have to be on time anymore) and we gave Jess the run down on what was about to happen… for the next 4.5 hours.  I anesthetized the first mouse, perfused the liver (a technique that requires straining your eyes to find and insert a needle into the portal vein, all the while hunching over an open mouse with an amazing crick in your neck and upper back, and cramping up your needle-holding hand while trying to remain very still), handed off the liver to Jess and the spleen and lymph nodes to Isaac.  All of these are smushed up into single-cell suspensions via being pushed through a mesh strainer or rubbed between two frosted (rough) glass slides.   The liver cells are spun down to get rid of the hepatocytes, and the lymphocytes in the supernatant are taken off into a new tube.  All of the cell suspensions get filtered and go into a huge tray of ice.  Isaac and i switched off between perfusing livers and processing the spleens and lymph nodes.  When Isaac perfuses, he can collect blood after he snips the portal vein, then cut and remove a lobe of the liver with one hand while he holds the perfusion catheter with the other.  So for all the mice Isaac perfused, i have blood and tissue samples as well as spleen, lymph node, and liver cells.  I have not yet learned how to perform such acrobatics.

This disassembly line (heh heh) went on until about 2pm accompanied by discussions of running, frisbee, babies  and the birthing process and how much pampers suck, Jess’s upcoming wedding, and how much PIs gossip.  And occasionally the experiment or techniques at hand.  When we had finished the 18th mouse, we cleaned up the aftermath, peeled off our now nasty gowns, gloves, and hairnets, wheeled the cart of cells to the elevator, and booked it to the lunch room for bagels and cream cheese.  It’s gross to get hungry while perfusing mouse livers, but it can’t be helped.  Isaac swears he’s found the perfect timing and dose of coffee in the morning to suppress his appetite but allow him to hold his hands still while dissecting mice.  I am always starving about 2 hours before we finish.

2:15ish   After bagels (very little conversation, mostly just furious chewing), i put more media in the spleen and lymph node tubes to keep my cells healthy  (apparently swimming in fetal bovine serum- blood without the cells- makes cells happy), and spun down my liver cells.  I got Katie to help me resuspend the pellets and layer cell separation gradients (kind of like making a black and tan, but with cells and buffer)- these get the crud out and leave me with lymphocytes that i can stain.  While those were spinning for half an hour, i began spinning down the lymph node and spleen cells and resuspending them in preparation for staining.  This takes a while because our two centrifuges only have enough buckets to hold 24 50mL tubes.   The liver gradients were done half way through, and i paused with the spleens and lymph nodes to carefully remove the lymphocyte layers from each gradient  (more eye strain and crick in the neck)  into other tubes to be washed.  Eventually everything got spun down, concentrated, resuspended in staining buffer.

4ish   Next i pipetted cells from each tube into a set of flow cytometer tubes, including a full second set of liver samples for a second staining panel.  Out came the antibodies and the antibody cocktails that i had so cleverly mixed up yesterday.  Each tube got a miniscule volume of antibody mix, which is a brilliant purple color from all of the different fluorophores in there.  Each single stained control got its tiny drop of antibody.  The CFSE (bright green dye that dilutes out as T cells become activated and proliferate) -stained control T cells that i had been culturing since last week came out of the incubator and went into a tube.  (The CFSE stain currently looks fantastic on the flow cytometer, i might add- a first for me.)  Once mixed, I put all of the flow tubes into the fridge for 20 minutes, ran into Isaac who made sure i was doing everything right- i wasn’t- corrected a few of the single stain controls, and then cleaned up my bench and the cart a bit.  And called the program manager back around 5 to tell her that i am unable to TA this fall quarter, no matter how behind on my grad school progress checkpoint list i may be… being a late bloomer  doesn’t bother me (here’s hoping i bloom!).  Also got a phone call from Nicky saying she and her teammates would not be staying at our house tonight… too bad, but now i don’t have to worry about the unsettling number of flies that have migrated from the chicken poop farm outside into the spare bedroom in the basement.

11ish Gah… my eyeballs hurt.  So close to being half way done with flow….!

7ish  Post-incubation in the fridge, i added more buffer to the cells and spun them down to wash excess antibody away,  pipetted off the extra liquid, forgot to resuspend the pellets in fixing buffer, and found Isaac to help me set up his amazing new 8 color T cell staining panel and 4 color B cell, liver antigen presenting cell panel on the flow cytometer.  Awesome.  Awesome possum, you might even say.

9ish  Phone call from David saying that Joakim and the visiting Swede Stefan are leaving the car parked near lab so that i can drive home.  Those boys are just so, so sweet.

11:30ish  Running samples.  After these next two i will stop to fill up the buffer tank and empty the waste tank, and eat some chocolate and go to the bathroom.

I may have just passed from the silly late night lab work mood into angry late night lab work mood.

rrrrrrrRRRRROOOOAAAAARRRRRRR!!!!  Need. Snack. Now.

12am Feeling better after hot chocolate and half bagel.  Contact lenses very blurry.

D’oh!  Failed to collect and stain enough cells from the lymph nodes to get good data.  Pause flow cytometer, stain all of the remaining cells at bottom of lymph node tubes.  Ah- this is how these experiments get so long…

1:45am  Alright!  Running the last 18 samples- new and improved lymph node lymphocytes!  Watch flow tubes carefully to catch when they get sucked dry by the machine.  Put next sample on. So close!

This is dumb.  Next time i will collect cells and stain them, then fix them in one long day, then run them on the flow cytometer the next day- still after hours so i don’t hog the machine, but after a night’s rest.

2:45am  hay-zoos christie.  I’m about to bash this machine in with a baseball bat.  It’s being so finicky and i only have 5 samples left!  5 samples!!!!!

3am   YESSSSS!  Last one!  VEEKTORY!

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Often when we go on vacation for more than a couple days, the basement of the house is relatively quiet and the rats that live in the neighborhood feel they can infiltrate through the cat door and explore.  Then we come back, and Tilly immediately catches one, carrying it around the house like a prize, fighting off the dog for it.  This most recent rat was only half dead- still breathing and aware, but unable to move except for the occasional outburst of squeaking in pain.  While we do like Tilly to catch rats to keep them from living in our walls, we like when she kills them quickly.  This was not one of those instances, and animals in pain cause both David and i much distress.  So i decided that since i have learned through my lab work how to kill mice, i would employ those skills to help this rat pass quickly.  What an odd feeling it was to have decided that.

In lab, when a mouse experiment is done or when it comes time to collect immune cells or blood or the liver from a mouse to gather data, we generally euthanize the mice by CO2 inhalation in a small chamber.  Though it’s apparently the nicest, least painful way for the mice to die- they essentially pass out and then die in their sleep- it’s not enjoyable to watch as they first scrabble around the cage to find air and then lay heaving as they take their last few breaths.   Then, the international animal care committee has a rule that we must kill them a second way to make sure they are dead and do not come back to life only to find themselves in a plastic bag in the freezer- a fate surely more terrifying than dying in one’s sleep.  The second method is cervical dislocation, in which you hold the mouse’s head/neck down between pinched thumb and forefinger, then yank the base of the tail away with the other hand until you feel the skull pop away from the spine. This is painless for the mouse, because it’s already dead.

So, i wrastled the rat away from Tilly and told David to stay inside while i took the rat out back.  David is even more sensitive than me about animals dying, and since i already have my issues and hundreds of dead mice under my belt, i wanted to spare him the experience.  I grabbed the rat with a plastic bag, held the neck, and pulled on the tail.  I’m not sure why it surprised me that a live rat would struggle, unlike the dead mice.  It took me a couple tries to pull hard enough against the rat’s contracting muscles, but once i got it, the body went limp instantly.

I did feel like i had accomplished something, for the rat’s sake and for my, uh, gutsy-ness, but i’m not sure i would do the same thing again.  There’s a sharp difference between seeing an animal die and doing it with your own hands, and i don’t know that most people (including me) are strong enough to have the benefits of putting an animal out of its misery outweigh the toll that killing the animal takes on one’s heart.

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Decided, after a long while of thinking, that it would be at very least, incredibly bold, and at most, a terrible idea, to start an internship of a farm in the months before i’m slated to take my general exam. David has advised me time and again that if i stick with my PhD, i need to do it well. And though it’s difficult to put in long hours of lab work during the Seattle paradise season, i agree with him- if i’m not going to quit, i should buck up and git ‘er done.

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I’ve gotten so many responses to my first post telling me i’m not alone in my scrabbling search for what the heck to do with my life. Some “I feel exactly the same way every summer,” some “it’s the curse of the liberal arts education,” and my favorite, from a recent grad school dropout, “I am guaranteeing greener grass on the other side.”

I don’t know if y’all feel similarly, but for me part of it is a fear of failure- like i have to keep educating myself so that i know what i’m doing. I have to understand my subject so deeply, and understand all related subjects, so that i don’t get out there and screw up whatever project i’m attempting to implement. But, while i’m doing all this studying, i’m not helping anyone or anything!

It’s the age old question of giving a man a fish or teaching him to fish, except that most of the world’s problems will take much longer to fix (months, years) than teaching someone how to fish. Kids are out there dying and suffering from brain damage, missing school, dropping out of school to work while i’m here working (slowly) on a malaria vaccine to save them all. The planet is falling apart while we’re studying the best way to scrub carbon out of the air or the most sustainable source of energy. Perhaps a rough balance of immediate aid and long-term research exists throughout organizations and institutes working to ameliorate these problems, but it’s frustrating not to have that balance in my own life.

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