Les Miserables the Movie!

I'm writing this to take a break from job-searching, or PhD-searching, whatever it is. Should have posted it two weeks ago. Well, better late than never.

First of all, I prefer the pronouciation "le miz", it's short, neat and sounds beautiful compared to the "le meeser-a-bles". Anyway, I watched the movie last week and liked it. For musical movies, you really need to love musicals to appreciate them. I know when some people (e.g. my father) watch musicals, they only think about how silly it is to see people singing all the conversations instead of talking, even at moments of life and death. I agree that some musical movies overplay the drama and stuff in scenes where time freeze so the vocalists could express their momentary thoughts vocally (a.k.a. High School Musical). These instances are stupid indeed. Musical overall however, is an art form, and as art, it has the freedom to detach itself from reality. It's an acquired flavor, you need to appreciate it before you can enjoy it. Some people do, some never do.

Spoiler warning here!

The movie has quite a hype of itself, most notably Anne Hathaway's portrayal of the character Fantine. She cut off her long hair during filming, as demanded by the story of her character. Her painfully emotional version of the song "I dreamed a dream" is widely heard since it's featured in the movie trailer. Since I sometimes measure success by details, with my standard, Anne has proven to be an admirable actress/singer combined. Take this example. When she was singing a verse about how Fantine still wishes her past lover (the father of her illegitimate daughter Cossette) to come back and so they could "live the years together", in the extremely short-lived instant through the sad song, her face was suddenly full of spirit and optimism that her eyes literally glimmered. In the next moment, she lamented over how some dreams could never be fulfilled. By then her hope was completely replaced by despair, as she closed her eyes and let tears cover her face. The total screen time of Hathaway was shorter than I expected. Not even halfway into the movie, her character was dead. For her portrayal of Fantine, Hathaway has secured her numerous prizes as well as the nomination of Academy Award for best supporting actress. Although I'm still skeptical as to how short her role was in the movie, I agree that the recognition of her efforts in Les Miserables is completely understandable.

Hugh Jackman did a splendid job as Jean Valjean, you'd never expect anything less from this great actor. A little gossip about the guy: his wife is 13 years older than him (which makes her 57). He's not the typical womanizer-type of a famous actor, which makes him even more special. The problem with Jackman is, since he's known to be great, any great work from this guy doesn't come out as a surprise. Therefore, you'd be more amazed at how some previously unknown actor/actress rise up to the top. This brings me to my next topic, the character Eponine.

Eponine is played by Samantha Barks, an English actress who sang in theater, but never appeared in any movie before Les Miserables. Her portrayal of Eponine basically stole the show with her strong presence and touching performances. Eponine is the daughter of the Thenardier family, a bunch of thieves, burglars and fraudsters. Eponine however, turned out to be innocent and kind-hearted. She had an unrequited infatuation with Marius Pontmercy. Marius on the other hand, was in love with Cossette and even had Eponine running errands so he could meet Cossette. Dressed as a street girl in rags, Eponine was pretty for her crowd. She was good-looking, her voice stunning, and her story of a heart-breaker is something most people could relate with. All these factors contributed to the popularity of her character. Eponine later died at the hands of a Parisian soldier as she took a bullet for Marius. Her death-scene was a bit strange, from the camera angle, it looked like she was actively committing suicide by placing the soldier's musket on her chest. Then the weapon fired and she suffered a mortal wound. Couldn't she have just pushed it away, so she could save her loved one without sacrificing herself? Now think from the soldier's perspective. If you are the man on the firing end of the musket, you got your aim on your target, but suddenly another enemy combatant came and tried to grab your weapon. What would you do? A natural reaction would be fighting off the sudden assailant with your gun. So Eponine didn't try to get herself killed, she was just not powerful enough to wrestle with a well-trained soldier (or maybe she did want to die, but then the scene could have been played better). I think Eponine is a better supporting character than Fantine, partly because she leaves a stronger presence in the story.

Having Russell Crowe playing Inspector Javert was another good decision. From other works I've mostly seen Javert portrayed as a shrewd and cruel figure. Although I believe that Javert is not necessarily evil, it's his uncompromising devotion to the law in contrast to Valjean's kindness that made him spiteful. When the antagonist wears the face of the noble gladiator Maximus Decimus Meridius, it really blurs the "black and white" morality of the story. The struggle between Valjean and Javert is never about good and evil, they are just two men with different perspectives. It's another symbolization of the friction between the upper-class society and the commoners, which is basically what Les Miserables is about. The story is very sad at times, the narrative however, makes you focus on the unyielding, positive force of life and of love. Even if you don't like musical, this movie is still a must-see. The real musical-lovers should have watched it before reading my review.

Do you hear the people sing?
Singing the song of angry men?
It is the music of the people
who will not be slaves again!
When the beating of your heart
echoes the beating of the drums,
There is a life about to start
when tomorrow comes!
     - Enjolras, Do you hear the people sing?

Met a friend yesterday...

Lucky me. I got myself this friend in Zurich a year ago during the interview. We exchanged a few emails over the past year, but didn't do much more than that. This guy, he works at an institute that seems somewhat interesting for me at the moment. I asked for his advice, explained my situation to him. He suggested at once that we should meet and he would try to help me. How fortunate that the world still has good people around.

My friend, he totally recommended his institute as a good workplace. As our conversation went on, more and more was revealed. The epicenter of our talk was nevertheless about how you survive as a PhD student, an universal topic in academy. I realized, although with some initial shock, how trivial and commonplace it is for people to not complete one's first PhD. To be precise, how trivial it is to change group, if you are doing your PhD outside Sweden. Maybe the word "Sweden" can be swapped for "Scandinavia", but since I haven't involved myself with PhDs from Denmark, Norway and Finland, I cannot say the latter for sure.

So my friend got his master degree a couple of years before we ran into each other. During the time lapse between his master and the good PhD he enjoys so much nowadays, he tried a first PhD somewhere else. It was the first time he told me about this particular experience. I don't want to reveal his identity, so let's just say his first PhD was in an native English-speaking country. My friend doesn't wanna start talk about it, because once he starts he can't stop. The biggest problem of that place, as he told me, was corruption. The corruption came from the higher echelon of the institute. They tried to attract skillful people to their place, give them the resources to expand the area of expertise of the overall institute. Once the establishment phase is over, the institute kick you out, so they can take over your stuff. My friend's old boss from his first PhD got fired eventually, sometime after my friend left the group. For the professor it was not a big deal, he quickly secured another professorship in another country. Doing PhD in that English-speaking country required visa, even for EU-citizens. My friend had to wait for more than six months to get a visa. He left the group six months after entering the country. This practically means that he "lost" one year in the process.

Every scenario like this teaches you something valuable about life. My friend became much more careful after coming back to Europe. He walked carefully among the would-be employers, watching out for signs of misdeeds along the way. During one lab visit in Zurich, he was interested in the scientific methodology of the lab, but one hesitant answer from a seemingly traumatized PhD gave him second thoughts. As it later turned out, his suspicions were right. Nowadays he is enjoying his daily work in the lab that he carefully sifted out among the ones he applied. What about that lab in Zurich, did they find somebody? Yes, my friend said, a girl from his group got an offer, but from what my friend saw happening afterwards, she didn't stay there. He reminded me about some other guys we knew from the interview, let's call them Mr. K and Mr. M. They didn't stay in Zurich either. M was not heard from again. K started PhD somewhere in Germany, but he got into trouble with the guy shortly after he started and was forced to leave. He was on a short visa in Germany, before the visa expired he tried to apply to the same institute as my friend. It didn't work. After that, my friend has not heard from K. The last example he gave me was his postdoc supervisor, who sort of left the research field for good. She also went to two places for PhD, the first didn't work out and she graduated from her second. She was my friend's hands-on supervisor. Before she left the lab she taught him very well, a good supervisor.

The more stories like this I hear, the less I worry about myself, although you would say that my worry is completely unnecessary. The conclusion is, outside of Sweden, it happens that PhD candidates change places in pursuit of finding what they truly want. Turning the statement around, it also implies "in Sweden, it's rare that PhD candidates leave". Right now I don't want to explore further to explain why this disparity exists. To be frank I don't even know why I wrote this blog entry in the first place.

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. 

PhD and Aloe vera

Hello, I'm back.

I really shouldn't write long blog posts. For me I tend to put too many details in them, resulting in posts that never get finished, and thus, never get published. So this time, I'm gonna keep it short.

My last entry was about PhD interviews in Zurich. I passed the interview, and got a job offer. The lab of my employer is located in Basel, Switzerland. I started the PhD on July 1st this year. 5 months later, I'm leaving the group and have to find a new place. Lots of things happened in between. To keep my promise of keeping the text relatively short, I'll have to skip them for now. Basically, things didn't work out between me and my professor, that's why I'm leaving. In my life so far I have made a few good decisions, and some of them were based on walking away from things that didn't work. One example is the Math Olympics in high school. Despite the efforts I put in after more than 2 years of competing in mathematics on a national level, I knew I couldn't make it to the national team and be happy at the same time. Math competitions brought me nothing but misery. So I decided to go for Biology Olympics during the last year of high school, by then I had less than one year to prepare. With renewed effort driven by the genuine interest in this new-found direction, my result was ranked the highest among all Scandinavian countries in the International Biology Olympics that year. I also earned a silver medal. From then I learned that walking away could be equally important as seizing opportunities. Sometimes you really need to stand and fight, just like other times when you really need to run. Walking away is not a defeat, it's a tactical retreat that lets you fight another day. In fact, if you never walked away from what you dislike, you will not have the space and availability to discover true happiness and success. Leaving this lab, I think, will turn out to be one of those "walk away" victories. I have started applying to other labs already. Furthermore, in October I officially became a 2nd author of an article in SCIENCE. With this in my hand, there is nothing I fear. The story about how I managed to put my name in this prestigious journal of scientific community, will also be told another time. Not today.

I once got curious as to how difficult it would be to manufacture your own antibiotics, I mean home-made antibiotics. The things I read on the internet showed me how difficult it is. You need to have sterile equipment, sterile water, media and sterile air for ventilation. Besides, the handling procedure required makes it almost impossible to try at home. While penicillin cannot be made easily, other options of antimicrobial treatment were readily available. Silver for example, kills almost any known microorganism. I recalled stories from childhood, of how ancient people found treatment for diseases by drinking water from silver containers. Aloe vera on the other hand, is a true natural replacement for many antibiotics.

It's hard to remember when I first saw people using it. My grandma (mother's mother) seemed to have used the plant her whole life. She used to put leaves or branches of Aloe vera into hot water, making it an easy tea. Whenever kids like me hurt ourselves, she would come around to pick a leaf, tear it open, and apply the juicy interior of the thick, succulent branch on our wounds. She knew all the tricks long before Aloe vera made commercial successes, sold in supermarkets as gels, creams or drinkable juices. In places where state-of-art medicine is scarce, Aloe vera can make up for the lack of technical advancement. Since Aloe vera is essentially a desert plant (originating from northern Africa), it's very easy to grow it at home. My mom got some branches of the plant from her mother. They grew so fast in flower pots so she had to constantly buy new and bigger pots to split the plants and let them expand. I think next time I go home I will pick up some branches from my mother and try to grow them at my home in Switzerland.

And finally, a funny picture. If you don't understand Chinese, the captions say (from left to right, up and down): before becoming a grad student; dreaming of life as a grad student; in grad school; looks like this everyday; supervisor comes to check; being asked of recent work progress; thinking back to bachelor graduation; imagining life after grad school.



It's not that I see the life of PhD as something horrible. Although there is no doubt that every PhD student must have recognized themselves in these pictures at some point of their time.

Restarting, again.

I am in Zurich right now.

I have come here for an interview that will possibly set the course for my life the next few years.

I will write about it shortly, but just not right now.

Stayed tuned.

Goodbye, Yellow Brick Road!

The title is just a line I found from the back of my head. Don't get too serious about it. It's also the title of a song by Elton John, one of my favorites.

It suddenly occurred to me that I haven't updated my blog for ages. Recently a lot of things came to my mind. If you bother to read my blog, then you deserve to know what have happened to the blogger for the past few months. I hereby sincerely inform you.

I decided to stay in Sweden for a few more years. Not because of career choice, but relationship. I met a girl in November last year, after coming back from iGEM 2010. Initially, me and one of my friends are supposed to start some sort of A Capella choir, and that's how I met our soprano singer. However, to make the long story short, we formed bonds of love over exchanging our hearts' voices.

I still remember that night in late November. It was merely two weeks after knowing her name. I somehow sensed how she was interested in me. We could chat online for hours every day. The most notable sign she gave me, was even when the conversation had gone cold, she'd come back to me after the long silence, to tell me that she's going to bed and say good night. Maybe it's not that much of a big deal to you, but if you were in my shoes, you'd know how it felt. Between me and her, we had this running joke that she should punch me whenever we meet. That night, it was already past midnight. Suddenly she came online and told me she forgot to punch me. I joked about going over to her place right away to get punched. After exchanging a few more sentences, the joke became more and more serious. That's when I decided to run over to her place.

With my fastest pace I threw on me my jacket, and jumped into my giant winter shoes. I ran the whole 500 meter or so, with my heart thumping like pistons in a truck. I knew if I started running, I just had to at least kiss her that night. Or I would go home defeated, not feeling as a man as I was expected to be. Fortunately, I did it. I remember how electrifying it was when our lips first touched. Until this day, I remain thankful to whatever higher power in the universe, of not only granting me a woman I love, but also a woman who loves me back in return.

During my wildest moments in the states, with my thoughts crammed with pick-up techniques and carnal urges, I never thought this would happen this way. In the end, I have to say that the highest level of picking-up women is not about pick-up, but to love and respect women from your heart. Only then you will built a genuine connection with your would-be right one, only then, you can find your true soul mate without going through that much trial-and-error. Considering all the missed opportunities, times I tried but messed up, I'd say I have deserved it coming.

So, what do I mean by "Goodbye, Yellow Brick Road"? The Yellow Brick Road is an image taken from the 1939 movie "The Wizard of Oz". The road is to be followed, if you are looking for the magical Wizard of Oz. It leads to an Emerald City, often seen as a metaphor for "the road that leads to life's answers". Our heroes in the movie followed the road, only to find that they had what they were looking for all along. So tell me, do you see a connection there?

Safety questions from iGEM Uppsala 2010

Safety questions from iGEM 2010. Four of us stayed up til 3am in a hotel room in Hyatt Cambridge to finish them. As iGEM Headquarter informed us, we forgot to submit them. Luckily they still gave us a bronze for breaking one of the easiest iGEM rules.

1. Would any of your project ideas raise safety issues in terms of:
• researcher safety?

During the design process of this project, it was decided that the project idea involved only well-characterized, documented bio-bricks, and non-pathogenic, well-studied bacteria strain. No mutagenic experiments for making new bio-bricks and no pathogenic bacteria strain were ever involved. In the laboratory where the project was carried out, strict safety rules were employed for ensuring the well-being of the project participants. The rules include usage of lab coats, gloves, goggles and other necessary safety equipments. All the lab works were conducted under the supervisions of senior researchers. The project students were not allowed to work alone or without supervisions.

• public safety?

No pathogenic bacteria strains or virulent genes were involved either as precursor material, intermediate or final product. The laboratory where the project carried out is a closed environment. Safety rules were painstakingly followed to prevent the dispersion of, and to ensure the destruction of any lab waste. Autoclave was used to prevent any GMO from leaking out from the lab.

• environmental safety?

No mutations were designed in any of the constructs. The cells which incorporated the artificial plasmid do not secrete toxins as a result. They were destroyed to prevent any form of leakage into the environment. The bacteria strains used in the project possess no selection advantage over their wild type counterparts, other than antibiotics resistance. Although engineering bacteria metabolism through editing antibiotics resistance is a conventional feature.

2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,

There are no safety issues with our BioBricks. The constructed BioBricks consist of well-characterized parts without any intended mutations. They are only capable of expressing naturally occurring gene activators, repressors and harmless fluorescent proteins. All laboratory procedures were carried out under general microbiology and molecular biology lab regulations.

3. Is there a local biosafety group, committee, or review board at your institution?

In Uppsala University there is a bio-ethics group. One of the advisors, Daniel Camsund has taken a bioethics course taught by this group. Every stage of the project was closely monitored and approved by Daniel Camsund. Furthermore, under the guidance of Dr. Thorsten Heidorn, the project group complied with the established and applied biosafety regulations of Sweden.