Grad Student’s Worst Nightmare

Grad student’s worst nightmare:

Source.

Apparently this happened to a Rutgers student.  You can read the full story here.

When I read it, my stomach got a knot in it.  I remember as a grad student and post-doc having nightmares about losing data.  I backed stuff up often- on Zip discs, later CDs or DVDs, external hard drives, servers, lab computers, email attachments, etc.  It’s kind of odd how academic labs vary dramatically in their data back-up approaches.  Some are totally DIY and up to the student.  Others are standardized- with university back up servers and such.

Now that I’m in industry and data is literally the work-product I’m responsible for producing, there are rigid and advanced protocols for backing EVERYTHING up.  From computer files to actual lab notebooks.  My entire hard drive is backed up in almost real time.  On days I’ve forgotten my laptop at home, I get a loaner from IT, log in, and I have access to my exact hard drive on a server- I don’t even miss a beat.  Old-school lab notebooks (for which there is no replacement and are still used despite existence of computers) are routinely collected and scanned so there are digital backups.  The company has onsite servers and backup servers.  They also have two different offsite servers for backing up the back ups.

When I posted the above image and story on Facebook, I was regaled with stories of lost/destroyed/damaged computers.  Unzipped backpacks seem to be common.  As are spills (root beer and nail polish remover amongst them).  I also got comments like, “I’m backing up right now…”

I feel horribly for that student.  However, I’m really hoping his raw data is backed up elsewhere and he’s just hoping to not have to reanalyze it or remake/rewrite figures/chapters of his thesis.  I know when I was working on my thesis I saved it on my hard drive and on a flash drive every single day- so I had every change each day.  There were also less frequent back ups to an external hard drive and the various chapters I emailed to myself or my advisor.

Another grad student (or any researcher) nightmare:

Imagine going to your animal facility and finding this? Source.

NYU Langone Medical Center was heavily damaged by SuperStorm Sandy- you can read about it here, here, and here.  While the news was filled with images and stories of medical staff evacuating patients, researchers everywhere were also wondering about the research labs.  Precious samples, genetically engineered mouse colonies, years of work, all in peril.

NYU’s entire animal facility, located in the basement, was flooded by the storm.  Almost all of their colonies were destroyed.  Years and years of work were destroyed along with them.  In addition to the lost colonies, without power, everything else in the labs that were not flooded was also in jeopardy- since the back up generators were swamped.

A friend and researcher on the Upper East side made room in the lab freezers for trash bags full of materials from colleagues at NYU.  Students, techs, and post-docs had basically run into the damaged buildings to dump armloads of samples (cell lines, cloning vectors, strains of bacteria and yeast, etc) from thawing freezers, clearing their bench tops with a sweep of the arm into garbage bags in the hopes of salvaging years of their lives spent constructing all of them.

Another friend who is a sales rep reported that a client (an industrial lab) busted out the walls of their building to load -80 freezers onto flat beds and move them out of lower Manhattan when it became clear how bad the flooding would be.  Holes in the building would do less damage than losing those samples.

I cannot imagine the sense of loss these researchers must have felt (or still be feeling), having years of their life’s work destroyed.  I cannot image being a 4th year grad student and being instantly back to square one- 4 years of work undone.

These are the things my nightmares are made of.  My heart breaks for colleagues living those nightmares.

A new low

Have you ever watched a nature show on The Discovery Channel or Animal Planet and thought to yourself, “Who in the hell spent their time figuring that out?!”

The one that comes to my mind is an innocuous show I was watching about some lake in Africa and the hippos that lived there.  Seemed like standard nature show fair.  Imagine my utter shock and surprise when the focus switched to one aspect of hippo biology that I could have lived my life without ever knowing.  You could live without it too, so skip the next paragraph if you wish.

Apparently there is a species of leech, Placobdelloides jaegerskioeldi, that breeds in the rectum of a hippo.  Yeah.  The show was replete with close up VIDEOS of the leeches and the hippo hiney hole. It opens a whole can of worms (or leeches?):  Who cares?  How did somebody figure that out?  Why is the name of all that is holy did someone pursue it?  What poor scientist spent his/her field work literally up the butt of hippo?!  Who thought there was something even more gross that leeches mating?  How about leeches mating in a hippo rectum?

I’ve wondered these same things with other research I’ve read about.  Like the impact of sleep deprivation on fruit flies- where some poor grad student had to be similarly sleep deprived to stay awake and shake the container of flies every time they started to nod off before the Sleep Nullifying Apparatus was invented to do it for him/her.

Source: xkcd.com

I’ve also wondered these same things with my own research.  As an undergraduate I studied the role of DNA Polymerase Beta in mismatch repair during meiosis in rats. [See here for an irreverent and hilarious take on Pol Beta and its function.]  Now, in case you forgot from high school biology, meiosis is the special version of cell division that creates gametes (ie sperm and eggs).  To study meiosis, we needed cells in which meiosis was taking place.  Where are gametes made?  Well, eggs are mostly made in fetal ovaries of female rats.  Sperm are made 24/7 in the testes of male rats.  So, if we were given the option of trying to track down meiotic cells it’s much easier to get your hands on rat testicles than fetal/embryonic rat ovaries- trust me.

Thusly, I spent a good portion of my undergrad research time dissecting out rat testicles, mincing them up with scissors, putting them in a very (ironically) phallic looking Waring blender, then further crushing the cells in another (ironically) phallic looking dounce- all in the name of making cell lysates so we could look for proteins that interacted with Pol Beta during mismatch repair.

I certainly raised a lot of eye brows and elicited many disgusted reactions from people when I discussed my research- particularly when on a grad school prospective student weekend a prof who studied spermatogenesis shouted to me loudly at a social function, “Ah yes!  So exciting!  You’re the student working with testicles!”

Things didn’t exactly improve from there.  The summer after college I got a job working at the county health department in their West Nile Virus Monitoring Program.  This means trapping mosquitoes, sorting them with a dissecting microscope, and sending them off to the state lab for testing for West Nile.  This part wasn’t that bad- other than the nasty water we used to attract the mosquitoes (we were only interested in the females, since they’re the ones that bite, and they like to lay their eggs in nasty fetid water- see here) and all the mosquito bites.

The grossest part of the job involved the ‘monitoring’ of the bird population.  The community was encouraged to call the health department to report any dead birds they found, then we’d go and get those dead birds, pack them on ice, and ship them off to the state lab for testing.  I responded to calls from helpful citizens who swiftly bagged the bird they found and conveniently refrigerated it until we could pick it up.  I also responded to calls from people who reported a pile of rotting flesh and maggots that was once a bird as a dead bird.  I also responded to calls from people who were so irrationally terrified of West Nile that they left the dead bird to rot and bake in the sun rather than go near it.  There was also the concerned citizen who hit a Canada goose with his car and reported it to us (Note to caller:  you hit it with your car, it didn’t die from West Nile Virus!).  It was pretty gross.  Some were pretty far gone and so decayed and stinky that we just disposed of them because they couldn’t be tested.

I should mention that I was the only woman on this team with four other men.  When I interviewed for the position the man who would be my manager said, “Are you sure you’ll be OK picking up dead birds?” (which I’m guessing was a concern because I am female and thus averse to ‘yucky stuff’) to which I replied, with a totally straight face, “My last job involved grinding up rat testicles.  I don’t think this will be a problem.”  He was appropriately and humorously silenced by my reply and offered me the job.

As a grad student I did pretty well.  My breast cancer research was relatively innocuous.  No in vivo work.  No dissection.  Standard blood and guts-free in vitro benchwork.

As a post-doc I had to help out with the harvesting rat hepatocytes (liver cells) that involved some surgery, but I was just assisting and didn’t have to get my hands dirty.

I mistakenly thought I’d moved on from the realm of research that makes people ask “Why in the hell would you do that?!  Gross!”

The operative word here being mistakenly.

I think my research is going to take me to a new low this year.  How low?

Hmm…. how should I convey the lowliness of this?  I think two words will sum it up.

Mouse enemas.

Yeah.

Part of my research this year will involve engrafting cells into mouse colons.  How does one get cells into the colon of a mouse?  Basically by giving the mouse an enema of cells.

Yay.

Seriously not looking forward to this new low.

What about you?  Any ‘lowly’ research projects under your belt?  Any bizarre nature shows that made you feel bad for the researchers?