My Labonews

My boss Mike Hall received this year a very important scientific prize (actually you get more money than for the Nobel prize, but that's not the important part) from the Louis-Jeantet foundation, and they decided to film our lab for a whole day. This is what came out... Don't worry, I hid well.

Well you may be interested that I just co-authored my first scientific publication. It's nothing like a first author, I know, still it is a decent journal (Human Molecular Genetics) and a nice reward for my internship in Harvard last year.
A hypomorphic allele of Tsc2 highlights the role of TSC1/TSC2 in signaling to AKT and models mild human TSC2 alleles.[Pubmed]

Somehow I never find time to write anymore... During the regular week, I'm quite exhausted after coming home and enjoy our regular movie Mondays and my Japanese course and so... I'm even happy if I find time to read a book. Not that I have too much stress, I just want to enjoy what's left after a long day of work. This week, it's been especially bad. I have to take the LTK (lab animal course) in order to be allowed to actually manipulate animals. It's every day till half past 6, and half of it is theory and half is practical work. The Swiss animal legislation is probably the most rigorous in the world, and so we started off by learning a lot about that. Yesterday I learned all about i.p. and s.c. and p.o. injections in mice and I absolutely hated the per os. Today was rats, and I was a bit freaked out because they are about 7 times the size of my mice and they are quite strong. But I learned that they are very nice and learn quite fast. Then we tried anasthasia and then gave the antagonists to weak the animal up again. Let's see what's still to come.
Oh by the way don't forget to come on Aaron, Julie and my Fasnacht parties on Saturday and Sunday respectively, in case you're around Basel!

Sounds like a nice initiative to me. Maybe I can make it.

... a countdown worth mentioning: The Large Hadron Collider is about to fire up!

Upper: David Kwiatkowski, Charles Betz, Jian Ma, Wei Qin, lower: Kristen Pollizzi, Cheryl Doughty, Izabella Malinowska, June Goto. We are celebrating (better commiserating Kristen's departure. She's been a highly skilled technician in this lab for quite some years, and we all wish her a very good start at Johns Hopkins.

I have a couple of interesting experiments with uninteresting results running, the amount of whichis inversely correlating with the time I dedicate to the writing of blog posts. Anyhow, this morning, as I was walking my daily 30 min walk to work, I suddenly noticed a difference between me and the many people that I see on that trail every day, also on their ways to work. I wouldn't say I'm a overly excessive morning person, cheering up as soon as I get out of bed. Neither to I walk to work with a smile on my face. But what I see on the faces of so many people in the morning is something different: It's hard to describe, although you probably all know what I'm talking about. A mixture of resignation, disgust, boredom... the knowledge that you have to spend the next 8 hours waiting to get home again, doing a dull job that is slowly degrading your moral in a stressfull environment. Then I think how lucky I am to have found a job for myself that is so different from all these points.

You see, research can also (sometimes) produce valuable information. Thanks Don!

Link: http://scienceblogs.com/drugmonkey/2008/04/science_20_open_access_lab_not.php

Here's a very interesting article on the DrugMonkey blog. Quoting:

The basic concept is that "THE WEB TOTALLY CHANGES EVERYTHING!11!!!!!1!ELEVENTY!11!!!!!1!" and scientists are and/or should be going to completely alter their way of communicating their findings to one another. One aspect of this is the notion of "Open Access Lab Notebooks", pursuant to which scientists will keep their lab notebooks on publicly accessible Web sites where other scientists can view them and update the information they contain on a daily basis.

This is completely nuts. Reading other people's lab notebooks will decidely not provide a "leap forward in clarity". You can barely understand your own lab notebook entries weeks or months after they occur. Lab notebooks contain a huge amount of totally irrelevant obscure information, the vast majority of which relate to failed experiments.Half of the pages of my post-doctoral lab notebooks contain stuff like "God fucking damnit!!! Ran desired fragment off end of gel while drinking in bar!!!! Fuckit!!" Who has the time or inclination to wade through all of that irrelevant boring shit, just to find some nugget of useful information? 

Elevators are great. Especially if you work in a big building and are kind of lazy. Our building has 12 floors and 5 elevators. Don't get me wrong, it's not that I'm going to die if I have to wait a minute in front of the elevator. But somehow I have the feeling that these elevators are running on a strange software. Not considering the fact that they sometimes run amok (I start at floor 6 and want to go down to 1 (which is the ground floor). I press 1, it goes up to 7 where somebody gets in, I press 1 again, he presses 12, and it goes up to 12. He gets out, 2 more get in, they go down to 8, I continue to 6, where I have to press 1 again, now he's getting it), I think the positioning of the 5 elevators could be greatly optimized.
So I thought what I'd do when programming one. Not that it makes any sense, but still. First I would think about statistics. How many people work on the different floors, at which hours, which of them have to get down more quickly than others (like the doctors who get beeped). What are the dynamics? Does floor 12 have a lot of exchange with 5? In which case it was stupid to keep them far apart, but hey, what can you do? This can easily be done by keeping logs and analyzing them for a time. Then the elevator would have to know about working hours, rush hours and holidays. E.g. at 8:00 in the morning, chances are there are a lot of people going up etc. Then several other rules apply. There should always be one empty elevator on floor 1, and with a smaller priority one at floor 12 and 6. The remaining 2 should mainly circulate in between, with the rules changing a bit according to the above rules. Am I making any sense? Nevermind.
Oh, btw, only now do I realize why you shouldn't take an elevator if a fire breaks out. Sounds silly, but would you know it?

In fact, we already went there by last week but I didn't have any pictures back then, so thanks June and Iza for providing them... I didn't feel to comfortable bringing my heavy camera to the tracks... It was fun though, I had been crosscountry skiing when I was a child a couple of years ago, but didn't remember too much, so lucky us David is a great ski instructer. Snow was not too bad afer the Friday night snow storm, although you coul feel it getting warmer by lunchtime. We went around, exploring the treks of what is essentially a golf course in summer and spring, did some racing and finally got home all wet, cold, tired and hungry... Had sore muscles for a week, no wonder...

I wanted to discuss with you the dilemma I'm facing right now. I have two possibilities to do my PhD this autumn. On one had, and this is what I always had taken for granted, is the possibility of going to London. Ever since my early Bachelor study years, I thought of going to the UK someday. I'm not really sure anymore why that is. On one hand, it's certainly the fact that the UK are really pushing their science and their research funding if probably one of the highest in the EU. Objectively taken, the UK's universities are ranked best among Europe in biology and biomedecine. But what does this tell me? Does this imply that although maybe being more prestigious, my PhD project will automatically be better? And what does better mean? In Science, it would mean something like being able to say that you did your PhD in a prestigious lab, in a famous university, and produced a powerful thesis that leads to the publication in a major journal. Personally, I'd say it's also very important to do your project in a sympathetic environment, to have a good relationship an team spirit in your group, and most of all, have an interesting project. At the beginning, I used only to take the first group of arguments into consideration. It was more or less settled that I'd go to the UK, and that's it. UK:10, Basel:0.
During my masters thesis, Prof. Hall was my coevaluator. He's one of Basel's more prominent researchers, with a high profile record of publications, and some major discoveries in the field. In fact, the protein around which most of my work revolves, namely TOR (target of rapamycin, not related to soccer), was identified in his lab in 1991. Nowadays, the TOR pathway is a major target in almost any biological processes from ageing to cancer and diabetes. He apparently was impressed by my work and asked me if I wanted to do a PhD in his lab. I of course was extremely honoured, but did not really take it seriously into consideration, I always thought of coming back to Basel or Switzerland in general after my PhD. UK:10, Basel:1. So I did not really put many thoughts into it, because anyway at that moment I was finishing my lab work and had to think about everything related to my trip to the US.
What happened? Prof. Hall talked to my boss, Prof. Moroni, and he wanted to discuss the matter with me. It was of course his personal thoughts about it, but now I realise that I was overly happy that we had this talk. Because sometimes, there are opportunities that are right in front of your eyes, but you're not really looking. So I reconsidered and thought a lot about it. Talking about a sleepless night! I had a talk with Prof. Hall, and as I was just leaving, and he wanted some further information about me and my work, he invited me over to the Biozentrum, and I had to put together a talk for his research group in a day or so, which was not really a problem. I talked to everybody in his group, and apparently, their impression of me was just as positive as mine of them. UK:5, Basel:5.
The project would be sort of a continuation of my previous work, as Prof. Moroni will be retiring, and shows a lot of potential in my opinion. The most striking difference to doing the work in the UK would be that in Prof. Hall's group, I would have to be very independent, be able to pursue my own ideas, while getting help from the others in the groups. Comparing to the UK, from which I already received a schedule of what my work would consist of the next 3-4 years. Don't get me wrong, that techniques I would be using in London would be extremely interesting, especially the work with 3D and 4D microscopy etc. But I have to admit, the project itself was not so interesting than mTOR is. Maybe I say that only because I know a lot about mTOR, I'm not sure, but others agreed with that observation. I always considered this schedule to be of a help, knowing more or less what you're going to have to do at which point. But Mike Hall convinced me otherwise. In fact, doing your PhD, you should be able to make decisions of your own. I'm not saying that won't be possible in the UK. But certainly the degree of input from you principal investigator (PI) will be much more dramatic. Again, this may well be a big favour for some, but I always had the feeling that I am able to act independently while of course listening to the advices from others. Maybe that's what everybody says, but there's a certain degree of frustration in every project, regardless of the fact that you took that direction yourself or whether your PI told you so. UK:3, Basel:7.
What changed since then? Well I thought a lot, mainly. I also got some inputs from my present boss, who of course is biased as he's also working on mTOR. But there's more to it. Besides of course being 5000km from my girl-friend, my family and my friends, I'm also 5000km from Basel. I always suspected I'd miss it after having spent 5 wonderful years there. But still I can't ignore the fact that this is biasing my decision more and more. I miss Basel. I miss my friends from Basel. I felt enormously conformable there, regardless of the fact that I was happy to leave the Borromäum, my dormitory, as I felt it was time for me to get an apartment of my own. Basel is a wonderful city. I'm sure London is too (never been there before, it's a shame). Paris is too. I'm always happy to visit Paris, but I wouldn't look forward to living there, too big, too complex, too noisy. Maybe I'd change my mind after some years, I can't tell for sure. But I can't ignore that feeling either.
So where am I standing now? I'd say a wobbly UK:1, Basel:9. I'm not excluding London. I'm really looking forward to meeting their researchers, making up my own mind. I give them a (more or less) fair chance. I changed my mind before, why not once again. That's the main reason why I'm travelling 10'000km and killing the rainforest while at it. It may be selfish? It will certainly be a superb experience. We'll see, who knows what I'll be telling you in 4 days or so.

--

So today actually was the first day, and I had the opportunity to meet the Prof. from the position I've applied for. She seemed very sympathetic and even seemed to remember my CV (there's the Luxembourg bonus for you). I think her project is highly interesting, both from the technical and theoretical backgrounds. I think she would be a nice group leader to work for, if I can judge that from the couple of discussions I had so far, and from listening to my guts. Furthermore, I seemed to get along quite well with a couple of the other potential students, and that's different from what it would be like in Switzerland, because there would certainly be fewer other students starting at the same moment, having the same classes etc. So from what I can guess, London wins from a social point of view. The institute itself looks not that different from the Biocenter, if you consider the structure and working conditions. So far, that leaves me with an UK:6, Basel:9. We'll see more tomorrow, and as there'll be another round of selection, maybe I even already know the final answer...

--

The interviews went well I guess, but I made an important realisation: Choosing between London and Basel would come down to choosing between being a student or a (young) adult. London will give me plenty of social activities, much more than Basel can offer. Basel however will come down to a more independent project, where I would be able/have to make most of the project's decisions myself. It may sound a bit simplistic, but I now have a rough idea and have yet to sort things out. I'll say UK:7, Basel:9. Tomorrow morning, we'll get an envelope at the reception saying whether or not we are in the next round. Pretty exciting, isn't it?

--

OK, second day is over, and what a day that was. In fact I should have an answer to the ultimate question by now (and believe me, it isn't 42...). This is at least what I imposed on myself. Now I'm not so sure anymore. There are plenty of thoughts crossing my mind right now. For one thing I think maybe I just want to take a quick decision for Basel to evade the possibility of failure. After all, some 6 others have also applied for it and received their interviews today, and I couldn't face the fact of deciding for them and then being dumped. Even more, I wonder if I'm afraid of a bog change in my life, taking a chance and a risk. London would be very different from Basel in many ways, both positive and negative. Am I just afraid of the choice and want to go with the obvious one? I don't think so. Prof. Isacke managed to eliminate one of my bigger doubts about the project, namely being able to make certain decisions on your own instead of having to follow a narrow line drafted by you group leader. In fact, it was more of the opposite. However she also reassured another doubt, which is the fact of living in a big city such as London. I grew up in a city as well, but London is huge, and I'm not 100% convinced that I would feel at ease in the long run. It is all very exciting and freaky, but I'm not sure if it's really that what I want.

I never met so many nice people in such a short period. I'm sure, from the point of PhD student organisation and activities, nobody can top what they offer you here. Considering the project itself, I think I would certainly be able to publish a paper or two here. I'm not sure if the overall importance of the Basel project is higher than this one. This one certainly has many interesting translational aspects, meaning the more or less immediate use in clinics, as they are working very closely with a hospital. I'd like to think that the mTOR project has nevertheless a bigger potential, but of course also a bigger risk. It is however more one the basic research side.

Finally, I think it comes down to the following question: Which subject am I more interested in? Regardless of the techniques, the nice people, the surrounding and location, I will be working on a more or less focused subject for 3-4 years, and it'd better be interesting to me. Many of the researchers I've met these last days told me that they were in fact a bit scared by the TOR pathway. It all was so complex, unclear and nevertheless tightly regulated and crucially important. I must say, during the last year, the subject has completely sucked me in, and it's complexity is really what fascinates me about it. I know that if I choose it now, I'm probably going to digest it for a couple of years, and I'm not talking about the PhD. And I think I am ready for this step. UK:8, Basel 9. I just couldn't find this last point, making the draw.

I must say this has probably been one of the most difficult decisions I had to take so far. I tried to judge my decisions considering both my guts and my reason. It was an amazing experience, and I recommend it to everybody who's reading this (congrats if you actually made it that far!). In the end, it helped me to write this down, because decisions and ideas change so quickly over one day, and you loose yourself in asking the same questions over and over again. I think I gave London a fair chance. I really hope so, because they certainly deserve it. I'd warmly recommend this institute to anybody interested in great research in a nice network of high quality labs. Who knows where I'll end up one day, if the right time has come?

--

Today is Friday, and as I have not yet received any news from them, I'm pretty sure that they did not select me for the project. I'm both glad and sad, as you may imagine from my previous writing. I could very well imagine why they would choose somebody else: I've no background in breast cancer research; the know I have an offer for a PhD position in the area I have a background in, on top of that in a very good lab; I've selected only one single project, and from what I could tell they wanted me to do the PI3K one in Prof. Workman's group. But I did my best, and learned a lot, and had a good time on top of that, so there really is no need to worry. And that is the story how I decided to do my PhD in Prof. Mike Hall's lab in Basel, Switzerland.

You probably know how it feels in the darkroom, waiting for that darn Western blot to come out of the developper. So here's a list of things you can do to pass the time:

1. Try so hard to look if you can see your HRP bands by eye that you start to see funny circles
2. Spin with you chair until you get sick
3. Count 60 seconds in your head and see if you're faster that the chronometer (chances are you will be)
4. Wash your hands until you get bored (happens rather quickly)
5. Count the amount of money you got in your pocket just be touching the coins
6. Think, in a chronological order, about the last 5 meals you had
7. Try to imagine that the whole institute had been evacuated due to a fire but they forgot you
8. Imagine what it will be like playing Spore
9. Try for the first time to play a game on your mobile, then realizing the light from the display will kill your film
10. Write a really really really boring list of things to do in the darkroom while waiting for your Western Blot

Seems like I got that list covered today!

Prof. Mike Hall was one of the examinators during my thesis and exam. The is one of the leading scientists in the field that covers my project. This is not only because he discovered the TOR gene, which turned out to be a central player in cellular growth regulation (from yeast to men). Yesterday he offered me a PhD position in his lab, if I were to decide not to go to the UK, which indeed would be a wonderful alternative as well.

I've just been asked by Prof. Seck, President of the Section des Sciences de l’Institut Grand-Ducal, Uni.Lu, to give a conference in the cycle of the Researchers from Luxembourg abroad. Since I'll be in the US starting in January, I'll give the lecture probably somewhen between October and December 2008, so stay tuned;-) Quite an honor I must say!