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."

Friday, February 23, 2018

2017: In Memoriam

If you asked most Americans about 2017 they’d probably agree it was a rough year. I mean, there was the whole Trump thing and that idiotic Szechaun sauce deal and the release of Captain America: Steve Rogers #1, which was about as well received as the news that McDonald’s was out of Szechaun sauce.

It was basically sweet and sour mixed with BBQ sauce okay?

But 2017 was also a difficult year for me personally which is one of the reasons why I didn’t update this blog much (#sorrynotsorry). The next three posts are going to highlight three of my big experiences, and I’m starting with the biggest, which is actually three experiences in and of itself.

In 2017 I lost my three biggest paternal figures: one in the first week of the year, one in the middle, and one in the last week of year, in what really felt like the universe giving me a big “FUCK YOU” for no discernible reason. My father, my grandfather, and my godfather all passed in 2017 and they will be missed, and going to funeral after funeral was emotionally and financially draining, much like trying to acquire Szechaun sauce.

If you don’t like serious posts then I recommend not reading any further since I think, from here on out, it would be difficult for me to inject any tasteful humor into the subject matter.

And this blog is all about tasteful humor. Wubba lubba dub dub.

Here is my overview of three great men I lost in 2017.

December/January: Lionel “Julian Ernest” Roy

In December of 2016 I was informed that my godfather and namesake, Brother Julian, was in hospice. I always knew him as “Brother Julian” because he was a Marist Brothers monk. He was my namesake (“Julianne” ring any bells?) and my father’s best friend. He was very present in most of my childhood as a sort of uncle figure. I had been discussing a trip to Chicago to visit him; hearing he was in a care facility was a rude wake-up call that, if I wanted to visit him, I’d better be quick about it.

Sadly, I could not be quick enough. He passed away on Christmas morning. Thanks to the messiness of the holidays, his funeral was delayed until the third of January. This gave those closest to him, including my family, the opportunity to travel to New York, where he had passed.

My father had met him at Mount St. Michael’s academy in the Bronx, where Brother Julian was a teacher. Theirs was a lifelong friendship/mentorship.

Andrew and I boarded a plane on New Year’s Eve, literally during the countdown. There was no countdown. 2017 came silently and uncelebrated while we were struggling to cram our carry-ons into the overhead storage bins.

New York was bitterly cold as one would expect. We stayed in a motel in the Bronx. The funeral was a small affair held in the Chapel at the Marist Brothers’ monastery. My family is Catholic (as you might have guessed by now). My father gave the eulogy, which was titled “Saying Good-Bye to My Best Friend.”

After the ceremony, we followed the casket outside, down an ice-packed drive toward the brothers’ cemetery, where identical gravestones stood in severe, precise rows. I needed m cane as the cold stiffened my knee. We stumbled back to the luncheon, where there were hundreds of pictures of Brother Julian set out. Many of them featured him with me and my brother. It was looking through those pictures that I saw evidence of the family-bond we had, the thing Brother Julian has (supposedly) disavowed in his decision to become a monk. And there was something sad about that, to me, seeing evidence of such a rich life that had ended after eight decades with an identical, unadorned gravestone that would soon be lost to the rows of other gravestones.

As a young man.

As I knew him.

It did not capture the man he had been, the guy who climbed onto the roof to fix TV antennas after another another one of the brothers had already broken his leg doing so, the guy who one used sanctified BBQ ashes for Ash Wednesday because of a locked sacristy, the guy who has a small sign in his garden identifying it as the “Garden of Weedin’.” Brother Julian was a grounded man with a good sense of humor and a fiercely practical sense of stewardship. He spent his life teaching, mentoring, and caring for the other aging brothers. He was generous with his time and his wisdom. The Catholic church was lucky to have had him.

August: Vincent Paul McGinn

My father was both a complex and a simple man. His tastes were easily summarized but his person was not. He liked helicopters and cats. He was a devout Catholic. He sounded like Donald Trump and, according to Andrew, looked a little like Tom Clancy.

My dad was Tom Clancy's inspiration.

He worked a job he loathed to provide for me and my brother. He wore a yarmulke to my wedding. He did not understand my (gay) brother’s relationship nor my lifestyle, but our relationship with him in adulthood was good.

Circa 1986.

Complex man, simple tastes. He liked cats and engines.

In early August I got a call from my mother that Dad had had a heart attack. He was admitted to the ER in the wee hours of the morning with chest pains and was in the hospital. I was assured he was getting taken good care of and that I should not be worried about buying a plane ticket or anything like that.

The heart attack had, seemingly, come out of nowhere. My father was in his seventies, overweight, and suffered heart problems. This was his second heart attack. However, he had been cleared by a flight surgeon recently and was actually one week away from moving out to Torrance to work on his commercial pilot’s license. He also had a deal with Robinson helicopters. Having flown since the sixties, it was a dream come true for him.

My dad in the '50s. Farthest kid on the right.

My dad in the '70s.

Within a week I got another phone call. My father would need a triple bypass. The doctors had attempted to remove the blockages in his heart using a stint but were unsuccessful. He’d been airlifted to a long-term hospital to await surgery.  (Note on this: he was airlifted by helicopter.  We all joked that, come hell or high water, he'd found his way into a helicopter even after having a heart attack.)

Then another call. His kidneys, in response to the medication he was on while awaiting the bypass, were failing. He was on dialysis. My brother and I were summoned. We went.

We spent four or five days in the family room of the hospital. In the ICU, only three people were permitted at a time. My father had a slew of visitors. He seemed in good spirits. When my aunt came to see him, the first thing he declared was, “You got fat.”

He laughed uproariously when Andrew said, “Dr. McGinn, I’m a Jew who works in a Beverly Hills hospital and even I’m impressed by this place!” He repeated the joke to his fellow professors and grad students who came to visit him. They brought us take-out.

After a week, seeing he was stable and cheerful, we were sent home.

My dad in 1978 at St. Brigid's chapel. The smokin' hot lady on his left is my mom.

My father spent his time learning about LVADs, which you might recall is what Dick Cheney had instead of an actual heart. There was talk of putting him on a transplant list.  My father, not Dick Cheney, although if you'd like to feel justifiably outraged right now, you should know that Dick Cheney got a heart transplant in 2012 at the age of 71 after suffering 5 heart attacks.  Also, you've been pronouncing his last name wrong all along.  It's pronounced "Chee-nee," not "Chey-nee."  Go ahead and Google it.  I'll wait.

So.  A week after we’d returned, he took a turn for the worst. Systemic organ failure. I was told, over the weekend, to plan accordingly. I went into work on Monday morning and during lab meeting explained to everyone I would be leaving to see my father again. I had a plane ticket for that afternoon.

As I was leaving that morning, I got a call. My father had passed away. I returned home to add one item to my already-packed bags: a dress for the funeral.

The next week is a bit of a blur. It was spent mostly sleeping and drinking in a motel, two rooms down from my brother. Scattered throughout the rest of the hotel were my aunts and uncles who had come to support my mom. We went out drinking together at the Texas Roadhouse across the street from the Motel 6; late at night, my brother and I watched Mystery Science Theatre and shared memories.

Circa 1998.

During the day, Nate, my brother, helped my mom with much of the planning for the funeral. A funeral is like a wedding in that, because it is very emotional, everything costs extra. Unlike a wedding, it is planned in a week; it is a rushed affair of trying to get flowers and select a coffin and speak to a priest and buy a burial plot. And, of course, to inform everyone.

My brother and I went through the house. My brother got a safe-cracker to open my father’s safe and remove the handguns from the house. There were 8, along with a bunch of Peruvian and Nicaraguan money. (?) I found his uniforms in the basement but they had molded. He would be buried in the same tuxedo he wore to my wedding, instead.

This was less than 1 year before his passing.

Thankfully I found his undisturbed officer’s hat in the room I’d had in high school, which was set up during the wake as well as at the reception afterwards, along with other personal items that represented the life he’d lived: a ham radio speaker, a bottle of Drambuie, his childhood teddy bear named Theodore, et cetera.

The funeral was traditional, and Catholic. My mother did the first reading, and I the second. The priest delivered the homily which did not quite capture my father’s relationship with God, who Dad always maintained “loves everyone but loves me a little more.”

Andrew helped serve as a pall-bearer; one of his grad students did, as well, with red, wet eyes.

The funeral was religious and the burial military. Here’s a link to the video taken by my Uncle Tony of the seven-gun salute my father received:


Afterwards, the reception was in the town’s local Irish pub.

Left to right: Andrew, me, Aunt Theresa, Cousin Stephen, Aunt Cece, Aunt Kim, my mom (in blue), Uncle Jon (Cece's husband), Uncle Michael, my brother Nate, and Aunt Katie (Michael's wife.)

I went home with my father’s hat.

I’ll probably have more to say on this subject later, but at present, I am still digesting it. My father was a larger-than-life figure with many contradictions and his mortality seems almost offensive to me.

He was buried on August 21st, 2017, during which Andrew and I had had plans to be in Oregon to see the total solar eclipse. My father was buried under a blacked out sun, a fitting symbol and one he would have appreciated greatly.

End of a legacy.

December: Herman Joseph Richarmé

Herman Richarm√© was known only to be as “Grandpa.” We were penpals when I was a kid. Born in Louisiana and occasionally called the Ragin’ Cajun, Grandpa was a product of the Depression through and through. He was remembered for his frugality, practicality, and innovation.

He dropped out of school in third grade to help feed his family. He worked in a bread factory, bringing home the squished loaves. When was about 15 or 16, he lied about his age and went to fight in World War II. Later, he would go on to fight in Vietnam. On this point, there is disagreement in the family about whether he won one or two Purple Hearts.

This is Grandpa getting one of his many military distinctions while stationed in Shu Linko, Taiwan.

Without a formal education, Grandpa was a jack of all trades. He drove a taxi, and he kept bees. He decorated cakes and he tried his hand at plumbing (which resulted in blowing up the family’s living room). Every house he had expanded under his own patient hand. He had eight children and he kept a roof over their heads and food on their plates, even if that food came from his own garden.

Grandpa with my mom.

I had been pen-pals with Grandpa as a kid. He called me Miss Julie and sent me stories from his childhood along with tiny trinkets: bits of Spanish moss ("Just put that in water and it'll grow."), mummified frogs in tiny jars, pressed flowers, piggy banks homemade from V8 jars and filled with foreign coins. Grandpa, like Brother Julian, was someone Andrew and I had been planning to visit. We knew he had Alzheimer’s and may not recognize us, but that didn’t matter. I still wanted to see him. He passed the same way Brother Julian had: hospice and, before we could hurry down, passing.

Like my father, Grandpa was a military man and so he was entitled to a similarly decorated send-off. He was not an officer so the funeral was different but nonetheless moving. The flag was folded by two young men while a third played “Taps” on the trumpet, and presented to the eldest child, my Aunt Cece, who had been the one most present in taking care of him in his later years.

Grandpa having a chuckle, in a Penn State shirt from my Mom. 
She was was the second person in the family to get a Ph.D, if I recall correctly.

If there was any positive to this third death in an already difficult year, it was that it brought the family together. All eight of his children were together for the first time in twenty or thirty years. My brother and I got to spend Christmas with my mom; previously, the three of us were planning on spending it separately, divided by state lines. I don’t know that I believe in fate, but many of my (very religious/superstitious) family agreed that this was Grandpa’s final gift to his child: my mother’s first Christmas without her husband of thirty years was spent surrounded by family.

In conclusion, 2017 took from me three of my most influential patriarchal figures. And I wish it hadn't.

I really wish it hadn't.

Brother Julian, Dad, and Grandpa: I miss you.