Tuesday, February 24, 2009

Assistant to Robot, Promoted to Robot

I was telling my grad students this story last week, and they liked mocking me so much as "assistant to a robot" that I thought I should post the story on here so more people can mock me. My first job in a research lab was the summer before starting my undergraduate career at the University of Michigan as a physics major--1992. I was really lucky get a summer job in one of Francis Collins' labs at UM. Yes, I am name dropping. The name I just dropped was that of Francis Collins, who was leader of the NHGRI from 1994-ish to 2008. Prior to that he was at the University of Michigan, with primary roles of hiring me as a work-study student and also leading teams that found the genes for cystic fibrosis, Huntington's disease, neurofibromatosis, and other diseases.

I have been lucky so often in my life, and in particular in my career "planning." I'll tell you some other day how lucky I got in obtaining my current job at UNM. This is how I obtained my first job in a research lab: I was friends with Dr. Collins' daughter, and I liked science. I knew he had a research lab because he had visited our classroom in Junior High to tell us about cystic fibrosis and genetics. So, I asked my friend if I could work in her Dad's lab. A few days later, she told me, "he says yes," or something along those lines. I was 17 years old at the time. But when writing this story, it seems like I was younger, as I recognize this strategy as the same one I used for obtaining a rollerskating "skate" with a girl in the 6th grade. I think the song was "Manic Monday."

I actually worked in a lab led by Chandra Sekharappa, who I think now has this lab. He was such a great guy and I am eternally grateful to him, Dr. Collins, and the other people in that lab who welcomed the unusual physics undergraduate to their lab. As I am writing this blog entry, a flood of memories are coming back to me. I learned so many things from working in this lab, and now, 17 years later, they are still coming back to me and helping me in my research (which coincidentally, or probably not coincidentally is tending towards genomics applications). In this lab is where I learned to pipette. I learned what PCR was. I unfolded paper towels for Northern blots. I "stuffed tips" (FYI: I could use each hand independently on two different boxes). I helped with "rows and columns." I washed dishes. Wow, did I wash dishes. I became obsessed with: -80 freezers; dry ice; vacuum-bake ovens; centrifuges; liquinox; reverse-osmosis water; latex gloves; latex gloves filled with water and frozen in the -80C freezer; and latex gloves in the vacuum-bake oven.

I cannot even come close to expressing how important this experience was to my career. Being immersed in this environment was so valuable -- whether I knew it at the time or not. The lab was focused on cloning the gene for early-onset familial breast cancer. (I believe another lab ultimately beat them by identifying BRCA1, but I'm not sure.) There was such a palpable excitement about the race to find this gene and I loved watching it. I distinctly remember that Dr. Collins welcomed me into group meetings, where the postdocs or grad students (I'm not sure what they were) would pass around these developed images of gels with the faintest of bands that proved something about their PCR reaction. I distinctly remember that they'd let the ignorant physics undergraduate stare at the film and then tolerate it when I said, "I think you're crazy, there's no band there." Somehow they kept inviting me, and they kept trying to explain to me "gene jumping" or "chimerisms" or "FISH" or other topics. The collaborative atmosphere in Chandra and Francis's lab is something I'm striving to replicate in our lab at UNM.

OK, now onto the good part. Of course, being the undergraduate in the lab made me a target for the grunt work. More than that, I wasn't even a biologist! So, it happened that the lab (or someone on the floor) had gotten their hands on a robotic system that could essentially print microarrays on filter paper. Or perhaps the predecessor to microrrays. The "robot" could print media from sixteen 96-welled plates onto a single filter paper. Then, these 4x4 arrays could be used for some kind of hybridization assays. This was a big deal, and the robot cost something in the 100's of thousands of dollars. Basically, you'd put a stack of 16 microtiter plates in the holder next to the robot. You'd set up the filter paper, and then the robot would proceed to: grab a plate; take lid off plate; put plate down; stick pins in plate; stick pins on filter paper; clean pins; put lid on plate; put plate away; repeat with new plate.

The problem was, the robot was controlled by some kind of SGI machine that nobody knew how to program. It cost a whole bunch of money to have the tech rep come out and program the thing. Everything about the robotic system worked well. Except, after taking the lid off the plate, it accelerated too fast, and media would splash from one well to another. This was terrible. I know what you're thinking: ask the physics undergrad to reprogram the robot! This is what I was thinking too when the grad students (or postdocs) explained to me the problem. I'm pretty sure I could have figured this out, no matter how obscure and proprietary the programming language. But, this was not my fortune. Instead, what they had figured out was that my $5.50 / hour salary was a perfect solution. I could perform the first part of the robotic sequence (grab plate; take off lid) and then at the appropriate time, hand the plate to the robot. So, this is when I took on my esteemed position as "assistant to the robot." I don't know how many days this lasted ... probably not too many, I think maybe for a few hundred plates or so. I do remember how utterly boring it was. I actually tried to read a book in 20 second increments while I tag-teamed with the robot.

Perhaps during my time as Assistant to the Robot, I impressed people enough to get my first promotion in the lab: to actual robot. (I previously mentioned my prowess at stuffing tips and unfolding paper towels, which probably factored into this promotion.) This job took most of a summer (1993 maybe?) and actually I'm pretty proud of it. My task was to copy the Washington University YAC (yeast artificial chromosome) library. I think it was about 200 96-welled plates and it took me most of a summer to make two copies. I became the most efficient plate-pourer of all time (in my own mind), and discovered that you can actually pour them so thin that even yeast can't grow. I wonder if these YAC libraries are still around nowadays?

Well, that's the anti-climactic ending to my story. I don't have a coherent point, and I know this goes against all of the how-to-be-a-good-blogger advice. My points are: (1) I collaborated with a robot in the past because it was cheaper than fixing the robot and (2) I had an awesome undergraduate research experience that has profoundly impacted my career. In regards to (2), there are so many lessons I can learn to help me in my current position as a research mentor. The main thing I have been thinking is that undergraduate research can be valuable for the lab, and incredibly valuable for the undergraduate. I feel like we're not even coming close to achieving what we could at UNM in regards to undergraduate research, and I would like to change this over the next couple years. I routinely meet Junior-level physics majors who are interested in research, but haven't yet been in a lab. We are next door to Sandia National Labs, and only 2 hours away from Los Alamos National Lab...both of which have amazing resources and opportunities for undergraduate scientists. And of course, we have plenty of our own labs at UNM. One of my goals over the next few years is to help our students find research jobs earlier in their careers...perhaps even before they start at UNM. Whether their jobs can be as prestigious as my own assistant to robot jobs, I don't know, but I can definitely strive for that!

SJK Note 4/2/09: I found a picture in my garage of the completed robot project. That's me admiring my 400? or so microtiter plates, all nicely stacked and labeled.


  1. Nice post, Steve. So many of my students (undergrads) have had transformative experiences b/c of research, some of which was begun before college. For my part, I get to watch the evolution of research across campus b/c of my students -- I've been listening in as projects have moved from basic to clinical to various forms of application - and I get an earful of everything from enthusiasm to dismay. Based on my students' accounts, your experience is definitely among the better ones! Some of mine have been treated solely as grunts, without the opportunity to be part of the conversation. We agreed after vigorous class discussion that grunt work was an important part of developing as a scientist or science-user, but that doing so without the larger discourse was a depressing waste of time. We even joked about developing a lab leader's guide to making the best use of undergraduate energy:).

  2. Hi Mickey -- That would be a great lab leader guide! One distressing attitude I see so often is that undergrads are a net negative. It'd be interesting to see a poll of university professors on this issue. I would wholeheartedly disagree with this, but I think the majority would agree. Many of these people who have told me that undergraduates are a time sink continue to hire them. It's then a self-fulfilling prophecy, because they don't invest enough in helping the undergraduate succeed! Such a shame. I've had four undergraduate researchers in my short time here (2.5 years) and all have been net positives. Some have even been ridiculously productive. And that's just in terms of research productivity. When you factor in the satisfaction of seeing their careers take off, that just makes it even better.

    The grunt work issue will always bother me. I look back fondly on all the grunt work I had to do. But I really can't bring myself to assign it to anyone, including undergraduates. It's a non-talent of mine. I think the graduate students will take care of this for me, and I'll probably turn a blind eye to it :)

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  7. Thanks for taking the time to discuss this, I feel strongly about it and love learning more on this topic. boundlesstechno@gmail.com

  8. There are more children now more interested in robot technology. The like to help and make a robot. The latest technology is advanced for the science.


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