Thursday, January 8, 2015

Lots to Cover: Leaving Grad School

Part I of V : Introduction and Back-Story

One of my primary reasons for starting this blog is so that I can keep distant friends aware of what I'm up to. I've had an eventful year, so before I can get on with describing the present, I should dispense with the necessary back-story. Chiefly, I should explain to everyone who last heard that I was in graduate school why I no longer am. Fortunately for both of us, it works out pretty well. Nobody needs other people's problems, so I wouldn't have started a blog if I was going to discomfit friends by waving failure in their faces. You are now free to read on with the knowledge that this won't get awkward.

At this time last year, I was a graduate student at the University of Southern California, pursuing my PhD in marine biology. I was studying carbon fixation in the ocean's crust. My PhD, however, was not to be. Midway through a PhD study, each student is required to present their work so far to a panel of expert scientists. This demanding ritual is a qualifying exam. While defending one's thesis is the final rite of receiving a PhD, a qualifying exam is the stage at which a student is either allowed to proceed to their eventual defense or concluded as unfit to continue any further. I originally took my qualifying exam in June of 2013 -- 18 months ago. I was told that my proposed research relied on antiquated techniques and that my pace so far did not inspire confidence. I was given a chance at redemption in 6 to 12 months, though, and allowed to continue provided that I could address the committee's concerns.

Next : Andy learns new things and Julie illustrates why the pioneers died of colds so much.

Part II : The Lead-Up to Leaving Grad School

Despite first impressions, my first qualifying exam wasn't a terrible experience. For years, I'd feared meetings with my adviser, Katrina. I was aware that I was constantly trying to catch up from a weak first year. Katrina never proffered assessments on my performance, but I still feared with each meeting that she might express my shortcomings out loud. Following my exam, Katrina had finally broken the silence with words of direct encouragement. Her approval was like cool water after a long, long hike.

We discussed the necessary steps to retaking the exam successfully and she agreed to send me to a week-long course on metagenomics in September.

Metagenomics is the process of analyzing sequenced DNA using very powerful computers. Neither sequencing nor modern computing power really existed 20 years ago, so it's a very new science. I'd never been sent to a specialized workshop before. It was a step in a very new, far more productive direction.

Jack had a cold when he picked me up from the airport. A day later, Julie was exhibiting similar symptoms. Jack warned her that it was a doozy, but she insisted that she had the constitution of an Ox. Unfortunately, this particular ox has asthma. Julie bullies her way through most colds, but this one triggered a mucus production feedback loop that sent Julie home from work gasping wetly, then to the emergency room an hour later, then to the front of the line when the orderlies concluded that she was about to literally drown.

The timing was unfortunate. My sister was getting married in less than a week. The doctor allowed Julie to leave the hospital on the condition that we rented an in-home air compressor to supply her with pure oxygen at all times. Instead of a lovely resort vacation to meet my family, Julie got to spend the rest of the month at home, tethered to a constantly humming robot in the center of our dining room.

During October, November, and December I put what I'd learned at the workshop into practice with gusto. I began coding simple programs in Python. It was a good time for Katrina, too. She had been suffering very physical health complications as a result of stress over the last two years. A skiing injury that put her on painkillers complicated her condition. It had been affecting her personal life badly. The day following my failed qualifying exam, Katrina had not shown up to our meeting. Without any notice, she hadn't showed up to work at all, which had become a sadly common occurrence. In the last quarter of 2013, though, it looked like she was finally recovering. She became a regular presence. In fact, she become more present than I'd seen her in all time time I'd been in the lab.

I discovered that I really enjoyed bioinformatics, and that I seemed capable at it. I scheduled to retake my qualifying exam. By the time it arrived, I was quite adept at methods I'd been completely unaware of 8 months earlier and I had a manuscript nearly ready to submit for publication. The first time I took my exam, I was humbly confident. This time I was boldly confident. I could think of nothing I could have done better in the intervening months, and I'd left nothing up to chance. For 16 months, my life had been directed by my goal of attaining PhD candidacy. Finally, it was certainly at hand


Part III : The Qualifying Exam

When I left my second qualifying exam, I still had the confidence I'd had when I went in. My confidence persisted for over 20 minutes, but as the wait while my committee deliberated approached 30 minutes I began to reflect on the familiarity between the present moment and my previous shock 8 months before.

My committee called me in, and with glum faces informed me that I had not passed. I know I said at the beginning that this story wouldn't get awkward, so I apologize if this paragraph is the exception. If it's a little uncomfortable to read, that is only because it was a pretty big disappointment, and I was totally unprepared for it.

Why? Well, the simplest answer is that I wasn't quite good enough. I was strong on the technical side but did not effect a comprehensive understanding of the state of the field and it's direction in the coming 10 years. If this sounds demanding it was my own doing. Students select their committee members, and mine included the most exacting professors in the department. These were scientists who'd made names for themselves, and then done so a second, third, or even fourth time. I believe that my general intelligence and effort were on par with the other students in my department. I chose a committee that was looking for students who would follow in their gigantic footsteps, though, and I didn't cut the mustard.

The failure wasn't so bad, though. Firstly, I wasn't thrown straight out on my ass. I had until August to wrap up my research, at which point I'd leave with a masters. Very few jobs give you five months notice of severence, and I can't complain about getting a free masters degree. I also learned quite a few lessons about my strengths and weaknesses.  Lessons which I really needed to learn.

Immediately after the exam, I met with Katrina. She'd expressed her support after my last exam, but this time she was even more explicit. She declared it one of the most exhaustive and demanding exams she'd ever witnessed. If she'd had her say, she proclaimed, she would've passed me without hesitation. She urged me to continue my research over the summer, publish what I could and pass the rest along to others in the lab. And she informed me that she was proud of me and of the work I'd accomplished over four years. This meant a great deal.

The summer was productive. My work moved ahead very well, and in May Julie competed in a dog show held by a local club for pet owners and took home Best in Show. Most notably, I began looking for a job. It was during this experience that I learned how truely, undeservedly lucky I was.

Next : Andy enters the real world.

Part IV : Get a Job!

In parts I, II, and III of my story I described the conditions leading up to my qualifying exam and the immediate aftermath. In the final parts -- IV and V -- I will recount the months of August and September. If March was the month when I learned that I wasn't as special as I thought I was, August and September were the months in which I learned how much worse my situation could've been.

After reading an explanation of why I failed, one might still wonder: “But why not just let you pass? Did these grey-beards really have to put their ideologies in front of your career?” As I began searching for jobs, I learned the truth of what my committee and many others had told me: the job market for biologists is terrible, and if you don't have a post-doctoral position waiting for you, your fancy PhD can become a lead weight around your neck.

I could go on at length about the characteristics of the biology job market, but the gist is that the field is over-saturated even within a larger job market that still stinks. Furthermore, a PhD is a SPECIALTY. A PhD doesn't allow someone to compete better for the same job as a biologist without one, it disqualifies them from that job completely (and qualifies them instead for a different, smaller set of jobs with even greater competition from other PhDs). I can't say to what degree my committee's decision was based on my career interests. All I can say is that when they told me that my skills would make me a competitive applicant with a masters degree and a generic and over-educated one with a doctorate, they were completely right.

Looking for jobs, I discovered that I'd completely neglected essential career planning steps. I was just as surprised to find that despite this, I'd become a very marketable biologist out of pure dumb luck. I managed to find a great job promptly during a time when others I knew were enduring years of rejections or moving back in with parents. I looked exclusively in Los Angeles, as Julie had been promoted at work and we were putting down roots together in a nice neighborhood. I found a job close enough to home that I could continue biking to work.  It was at Cedars-Sinai medical center in Beverly Hills. There, I would be a lab manager. Part of my time would be spent carrying out business such as ordering supplies, while the rest of it would be spent culturing and experimenting on stem cells. My new PI, Dhruv, even encouraged me to continue developing my skills as a bioinformaticist.

There was two full months to pass, though, between when the job was offered and when it was available for me to start. During this time, I had the surreal adventure of presenting at an international conference in sub-surface microbiology.

Next : An unemployed scientist addresses an audience of his betters

Part V : Conclusion comes in the form of a Conference

Overall, this is a story about me gaining perspective. The months after my exam showed me my strengths and weaknesses. My job search required me to consider the best ways to pursue my ambitions. Presenting at a scientific conference -- as the final act of my graduate studies -- gave me a chance to examine the value of the prior four years and how my colleagues viewed me.

Months before I left USC I'd been offered the chance to deliver an oral presentation at the 9th International Symposium of Subsurface Microbiology (ISSM) just south of San Francisco. Katrina had offered to pay for my registration, since it was her lab's research on which I was presenting. As the conference approached, though, it became clear that she'd be unable to provide any financial support. By the end of the summer, all of Katrina's progress had been undone. She was no longer showing up to teach her classes. Our lab manager explained at a lab meeting at which Katrina was absent that we were running out of money. I made plans to cover the costs out of pocket and go anyway. I got registration covered by agreeing to volunteer with setup and organization.

Under these circumstances, I asked myself why I was attending. Normally the point of these meetings was to allow researchers to update one another on the direction of their projects. I wasn't going to be using any of the information provided by others, and it was unlikely that any information I had would greatly affect the course of anyone elses' work. I concluded that I was there because first and foremost I wanted to enjoy the experience. It was a small achievement, but I was proud to get to present. I wanted to hear the latest findings even if I had no use for them just because it would be entertaining. Secondarily, I wanted to see my colleagues and I wanted them to see me. I'd been relatively isolated during my studies, by the standards of scientists. Most travel a great deal and exchange ideas widely. Attending the conference would be scientists I knew personally, scientists I knew through emails, and scientists who I knew by reputation only. I wasn't sure if they knew about my change of direction, but I wanted to chat. To thank some, and to prove to others (at least in my head) that I was not washed up.

Above all, I was curious what sensations it might stir in me. What if the upper-level talks revealed to me how truly unqualified I was? What if they reminded me of all that I was losing? Would it be painful to wander among the researchers I admired, unknown and invisible to them? Or to feel that I'd let down the few who'd reassured me years earlier that they had confidence in me?

As it turned out, I understood much of the talks. I enjoyed them but did not become depressed by them. Though I was a new face to most, I was recognized by some and greeted warmly by many. Several expressed their condolences regarding the state of Katrina's career and my graduate studies. One -- a man I admired greatly -- insisted that a change of field need not be permanent and an unsuccessful PhD attempt didn't preclude a successful one later. He encouraged me to stay in touch when I might be looking for a job in several years. My talk was well received. And the evening conversations were effortless and pleasant.

When added to the self-reflection of the exam and the job hunt, the perspective provided by the conference brought me more or less full circle. I learned I was better than I thought in some ways and worse than I thought in others, but it all pretty much evened out. Nearly a year of intense consideration has revealed to me that I have pretty much the same amount of self worth that I originally thought I did, though in slightly different ways and with a bit more detail than I had before.

Anyway, I rather like the way it's worked out so far. My career pivot is certainly not a delicate topic. If anyone has any questions or comments, I love to talk about all of this as much as I love to talk in general, so feel free to ask or opine. With the back-story dispensed of I will now move on to regular, more mundane matters. Matters such as sandwiches recently enjoyed or whatever it is bloggers blog ablog.

Next time : Hannukah recap? Sure, let's got with that.


  1. "Matters such as sandwiches recently enjoyed "

    Club sandwiches. Are they really as exclusive as they sound? Stay tuned...

  2. Hey Andy, finally got around to reading your first post - it's great! I'm very happy to hear that you're excited about your new job. I would be too - it sounds interesting, challenging, engaging, AND in your field! (This is an accomplishment I dare not dream of for the day if/when I too am forced out of academia). Just one question: how do you deal with the moral dilemma that your work with stem cells (i.e. dead baby-bits abhorred by The Lord) must torture you with during those long sleepless nights.

    But seriously, is there still a big stink about those little baby-bits?