onsdag 19 december 2012

How I made a successful master thesis

This story recounts how my name appeared in SCIENCE in October 2012. With the information I have disclosed in my blog, it should be extremely easy for you to find out my real name, unless you already know me. Hint number one is that you don't need to look up "Leo Kinmann" in PubMed. Nevertheless, if you really want to read it, I leave it to you to find that paper online. It should be obvious enough after reading this entry.

During iGEM 2011, I heard from a PhD supervisor of our team, Erik, that his boss (hence on refer to as Professor A) is a resourceful and agreeable professor. Indeed, one of the professors who organized the team claimed that Prof. A is so rich that he literally swims in money. Donald Duck's rich uncle anyone? By the way the rich uncle's name is Scrooge McDuck. Perhaps due to the difficulty of making the name sound native in other languages, it is often translated into something that completely lacks resemblance to the original. In Swedish for example, the name became "Joakim von Anka". 

Stop right there! We are off-topic. 

Anyway, initially I wanted to work for another guy whose field of interest was much closer to synthetic biology. This guy had problem of his own, since he moved to my university very recently, he had yet to mark his own turf. Funding was not his strong element at the moment. My past experiences has taught me to avoid under-funded research groups. Since Prof. A combined plentiful grants with benevolent leadership, I made my choice easily. It wasn't difficult to walk away from synthetic biology back then, because the entire university did not have any good lab in the field. I'd rather take a good deal in terms of research group than joining a group that works on something remotely closer to synthetic biology but lacks the necessary resources to do good research. Going for the group rather than the research direction proved to be crucial.

I contacted Prof. A during November, having Erik as my reference person. Thanks to the good words he put in for me, Prof. A picked me. I could choose from two small projects. One was in the field of evolutionary biology, the other involved antibiotic resistance. Since I had not prior experience in either field, I had no preference. I did have my thoughts though. First, antibiotic resistance was bread-and-butter to Prof. A. It seemed promising in the long term, the group just published a fairly groundbreaking paper. If I wanted to stay in the same group for PhD, it might be a wise choice. Erik warned me that working with antibiotic resistance could become very repetitive, and I wouldn't like it. The evolutionary biology project was more of a leap of faith, I knew next to nothing of the field. The work seemed more stimulating though, and the postdoc who would supervise me was extremely competent. With Erik's advice and some consideration, I picked the project in evolutionary biology. I wanted to try something new. In retrospect, I think I might have heard from Prof. A or my postdoc supervisor that they were going to publish the work of which my thesis is part of, but it was never a conscious choice from my side to jump onto an almost-finishing project. It was more of me trying to avoid something that Erik told me I wouldn't like, I trusted him and I still trust him today. I don't know if I can give any advice on how to choose master project, perhaps some of it was "avoid something you know you won't like", some of it being pure luck, and finally, "if you can, try to be as much of a freeloader as possible"? Be opportunistic, be lucky and think smart. But remember, none of them would matter if you don't work hard.

So I started, my postdoc supervisor Jocke helped me to write the thesis plan. He knew exactly what experiments needed to be done. Basically, my work was to characterize around 30 mutant variants of a gene by seeing how each genotype influenced the growth rate of the bacterial host. Having a detailed, realistic plan that you can actually follow always work. I ran the final phase of experiments so Jocke could focus on summarizing his data from the past 2 years and writing up the manuscript. I always tried to challenge my thesis plan by seeing how many days I could get ahead by working fast. Needless to say, not every experiment worked on the first try. In the middle, we lost more than one month on technicality issues and tried some side experiments that turned out to be fruitless. Luckily, Jocke was good enough to figure out what went wrong, so we could proceed as planned. I'm not lying here when I say that I worked my ass off for this project, especially when it became clear to me that my name could appear in the subsequent manuscript if I manage to have publishable data. For many weeks I tried to look ahead of what lies before me, to see if there is still enough time for me to finish with a good amount of data before my relocation to Switzerland for my PhD. I didn't take any breaks during Easter (although I did take some days off the week after to spend with my girlfriend in Paris), worked everyday of the week during the last two months, just to make sure I can get things done on time. My biggest fear was not managing to start the most relevant experiments that produced data, or not getting enough data to qualify for authorship. The more towards the end, the more I pushed for insane working hours. I remember one evening I dined with my girlfriend at a downtown restaurant. She left for choir rehearsal afterwards, and I headed back to lab. When the rehearsal was over around 10pm, she had to wait for me because I was barely finished. Another day, she had a gathering with her soprano friends. I had dinner myself after 11pm in a shabby downtown Subway, while people outside were roaring in the nightclubs. I got home about half an hour earlier than her, which was around midnight. Next to the final month I fought my way to the most relevant experiments: measuring bacterial growth rates using a machine called Bioscreen. Bioscreen is an extremely convenient tool. It upgraded the standard growth curve measurements with high-throughput, enabling the researcher to closely monitor the growth of 200 bacterial samples at a time. Since my bacteria grew slowly, each run in Bioscreen took two days. Furthermore, the preparation before loading into the machine could take up to three days. I scheduled my work so I could prepare for the next setup while one experiment was running. That machine? I occupied it for more than one month. It didn't get much rest, neither did I. I was glad that Prof. A actually purchased such an useful equipment. If he asked me to do the standard growth curve plotting, it may have taken me years to get the same amount of data that I obtained within less than two months. Advanced machinery exist for a reason, they are essential components of any arms race that turns the tide of war, academic as well as military. My master thesis presentation was held on June 5th. Prior to this date, I should have handed in the first draft of my thesis. The tricky thing was that I had no spare time to just sit down and write, away from experiments. I had experiments running during the daytime; evenings were dedicated to data processing; bulk of my thesis were written during late nights and weekends. Everyday I felt I was a fully stretched bowstring, pulled out to its absolute maximum. Any more force and I would've snapped. I pushed myself to achieve co-authorship; Dr. Jocke pushed me to perform scientifically strict experiments; Prof. A pushed for publication of the paper. Our synergy put together has pushed forth the ultimate result we wanted, I'd say that was the way of good science.

To summarize it all, I want to say the following:

1. people is more important than research topic. Join a lab where you can focus your mind on science and not money is crucial. Also one must choose supervisor wisely. Good people brings you success, as it has brought me. I have seen examples where the opposite worked out very bad. What the hell, I'm one shiny example of both theses! But don't go to the other extreme and replace competence with nicety!

2. if you can choose projects, be opportunistic if you can, but always be smart! The factor you cannot control is luck. The choice you make is the chance you seize, the other half is what you do with the chance firmly held in your hands. Hard work is a necessity or prerequisite to success.

3. design your experiments so you can plan ahead and follow the plan. If future experiments don't seem that obvious, you should make them that obvious.

4. advanced machinery can turn the tide of war, just think about how tanks ended WWI, and nukes WWII. I believe the same thing can be said for competitions in academia. With good equipment, experiments that takes years to finish can be done within months. The time-scale difference is rather exponential. Imagine how many competitors you can scoop by getting ahead years of time running the same experiments.

I finished my last piece of work on June 15th 2012. I left the lab that day, having compile all my data and given them to Dr. Jocke. I was saddened by the fact that I would hardly see the place again. Our manuscript was finished my Prof. A and Dr. Jocke. My data was presented in the paper in figures and tables. Out of four authors, my name was behind Jocke's. Prof. A submitted the manuscript to SCIENCE. It took almost four months from submission to publication. The reviews were excellent, so Jocke didn't have to do much extra work. For publishing in SCIENCE, it was as fast as it could get. I count all my blessings to thank the higher power of granting me such fortune. Two other guys who started their master theses at the same time as me, they weren't so lucky. Not until I was on my way out did I realize how good Prof. A's group was. I could've stayed, and I heard that Prof. A really wanted to keep me for PhD. But due to the circumstances, I chose another path. Another thing that saddened me a bit was that I spent too much time working so I barely got to know the people I worked with. Erik said I would've blended in very well. Right now, this lone wolf have yet to find another herd. 

2 kommentarer:

  1. Thank you for sharing this! Very interesting reading! I think the text had a lagom length!

    SvaraRadera
  2. Erika Christiansen30 juli 2013 23:39

    Your story was amazing! Well, at least you finished your MA thesis that way. Otherwise, you might regret it in the future. Anyway, I do hope you can post your MA thesis on site like http://thesishelpdesk.com/thesis-abstract/ that also features different thesis abstract from all around the world for the people to read, so that it can help them with their studies.

    SvaraRadera