Tuesday, February 27, 2018

Saying "No" to Gnotobiotics

I have spoken on a number of occasions about my job, over the last two years, as the lab manager of a gnotobiotics lab. Gnotobiotics is the study of the microbiome. You are not an individual, but an ecology, something I find very exciting. Or rather, found exciting.

For those who are just joining us, gnotobiosis (from Greek roots gnostos "known" and bios "life") is a condition in which all the forms of life present within an organism can be accounted for. Typically gnotobiotic organisms are germ-free (axenic) or gnotophoric (having only one contaminant).

Your body's microbiome could be said to be an organ and your immune system could be said to be a regulatory system that keeps the microbiome in check.  Your microbiome is not as small as the name would imply; in terms of weight, your microbiome makes up 1-3% of you, or 2-6 pounds.  And here's another fun fact: 30% of the solid matters in every shit you take is dead bacteria from your gut.

For further reading I recommend this article or either of these books:

Also, honorable mention to "Life on Man" by Theodor Rosebury.  It was published in the 1970s

Anyway, the microbiome is awesome.  But despite the cutting-edge nature of my research, in November of last year, following my father’s death, I opted to quit my job.

The first year of my dream job was… well… a dream. I spent much of it establishing the lab: building isolators, stocking them with sterilized items, breeding mice. This was fun and it gave me a sense of accomplishment.

There was certainly a learning curve. I had not done very much benchwork prior to this and so I had to learn and tweak and perfect techniques like PCR to screen for contaminants and test for sterility. I was also woefully inadequate in my organizational skills; my style has always been one of last-minute, improvised bumbling that works out in the end. My boss engendered in me a newfound appreciation for the art of actual scheduling; she is a big fan of Google calendar and Google docs, and I got better at managing my time as well as my techniques.

My work environment was good. I liked my PI and I liked the labmates I worked beside; there was a vibe of casual camaraderie and I can honestly say anyone would be lucky to work in a lab like that.

So what happened?

The short answer is this: the techs.

You see, under federal law, lab animals need to checked on at least once every 24 hours. To meet this requirement, nearly all university labs have a separate, independent division from the research labs. At UCLA this is called DLAM (the Department of Lab Animal Medicine) and at USC it was called DAR (Department of Animal Resources). The idea is that having a third party to check on the animals at regular intervals (including weekends and holidays, when grad students may not be around) ensures the best possible care for the animals.

...boy, were they wrong.


See, the actual job requirements to be a lab animal technician are… not very high. You need, like, maybe a GED, probably. Since much of the job involves “unskilled” manual labor like changing cages or scooping food pellets out, the people hired for this job are paid little and valued even less. Worse, many of the employees have been around for years; with an annual raise and university benefits, the unskilled immigrant employees who were changing newspapers in cages 30 years ago are still around and couldn’t hope for a better job anywhere else, so they stay. Meanwhile, the job requirements have gotten more demanding and complex. We’re no longer keeping kittens in shoeboxes; lab animal care had gotten increasingly complex because of ever-increasing expectations to provide the animals with care that is not merely humane but exceptional. 

Here was the point of our contention.

If you're not involved in science or academia I might have lost you with all this talk of PIs and techs and such.  Please refer to this handy cheat-sheet for understanding the complex bureaucratic and political dynamics of a university research lab:

See, when I originally signed up for my job, I sort of expected to be doing half “lab manager” duties (like setting up breeding colonies or whatever) and half actual research. My title was Research Associate.

I fully expected to be spending 60% of my time defending myself from pushy vendors by my second year.

After two years I had only actually performed one major research project. I had a few ideas tucked into my pocket but I was way behind schedule on actually getting them done. I felt like I was losing steam and like my boss was getting frustrated with me. (My boss was remarkably patient in her tutelage.) But the problem was, I couldn’t just let go. In order to shift my job duties to labwork, I needed to be able to turn over the management of the vivarium to the techs. And at no point did I ever feel safe doing that.

The techs, unskilled and underpaid and overworked, did not have the energy or resources to care for my animals. And please remember, these weren’t merely regular mice. These were Boy-in-the-Bubble mice. Mice who were extremely sensitive and at constant risk of contamination. Keeping them sterile and healthy was an all-or-nothing endeavor. There was zero room for error.

It's an unforgiving business.

And as I told my boss, you can’t train the techs to care. If you’ve been working with lab rodents for 10 years and you can’t identify ulcerative dermatitis before the entire tail degloves, then I can’t help you. (If you didn’t understand the jargon in the last sentence, don’t worry: neither did my techs.)

In case you're wondering how bad it got, I reported 15 incidents in the facility between August and October.  Here is my favorite report of all time, though:

5 June 2017.  Issue: potential contamination vector.  Severity: 2.  Brought to DLAM's attention: 5 June 2017.  Incident report: Bottle was shattered inside of isolator. Techs informed lab that glass bottle was being used to break apart food during cage changes.  Resolution: Bottle was safely exited; no one was hurt and isolator was uncompromised. Lab ordered mallets for breaking apart food and advised techs not to use breakable glass instruments or fragile objects for concussive purposes.

That's right, ladies and gentleman.  I had to tell my techs not to use glass bottles as hammers.  That is the level of incompetence we are dealing with here.

I found myself hiding out from the techs and my boss, dreading the act of checking my e-mail and taking Ativan just to get through the day.

 Me, helping place orders like a pro.

I had no power to hire, fire, reprimand, or direct, beyond complaining frequently to my boss, because since DLAM is an independent department, the techs answered not to me but to their own boss. And in one month alone, at the end of my time there, we went through three department shifts and three different bosses. Telling, no?

So finally, shortly after my father’s funeral (during the time I was in Chicago there was, unsurprisingly, a contamination that brought down one of the isolators), I tendered my resignation.

My exact words were “I’m leaving this lab like a rat off of a burning ship.”


I’m being literal, by the way. I believe the lab in its current state is doomed.

It was a weight off of my shoulders.

I spent a tired yet frantic four weeks training my replacement, to whom I wish the best of luck.  But I can't say I envy her.  The problems the lab faced were systemic, a result of underfunded and outdated institutions.  It was hard for me to leave because I loved the research, and I couldn't have asked for a better or more supportive boss.  But the effects it was having on my mental health was not good.  And ultimately, I could not work for a place where animal neglect was a constant concern.   I stayed for as long as I did out of fear for the safety and well-being of the animals, but at the same time, I felt like I was only prolonging the inevitable.

 Artist's depiction of my time in the lab.

So now I'm out of STEM and working on, like, you know... life and stuff.


Specifically I'm focusing on my health and my writing.  I went for 32 days without drinking, have lost 10 pounds (so far!), am running another marathon in March, and have been able to resume many of my personal writing projects.

If you want to follow my Marvel endeavors you can visit me on Instagram.  Or you can simply check in on my blog every Tuesday, as my updates will now be more regular.

All in all, I think that leaving was the right move, even though I had nothing full-time lined up.  For now, I'm regaled to the shadows of the gig economy, the place of independent contractors and freelance writers.  And that's okay.  To quote Tony Stark in Iron Man 1 after losing 3 million dollars at craps, "Worse things have happened.  I think we're gonna be fine."

No comments:

Post a Comment