Torfinn Nome - Life as a …

I actually did it. I defended my thesis last week. Believe it or not. I certainly do not. At least not yet.  A summary of the thesis can be seen in the above picture (courtesy of Wordle).

Now what?

Lately, being part of an academic environment, I have increasingly been aware of the insufficencies we face as human beings. Not that I don’t gape in astonishment of what is being achieved in both medical and technology related research advancements these days. But we have the potential to achieve so much more. And I feel, more than a little, annoyed by the way we seem to deliberatly waste resources on obviously counter productive projects. Productive projects that eventually would make, pardon the cliché, our lives better. Pouring billions of dollars into military operations is obviously an easy way to make friends with people running the military industry. But it’s not much affecting the way we deal with treating cancer, enhancing ways of expoiting alternative energy sources, speeding up the making of a space elevator, or understanding the complex ways of gene transcription interactions. And I do believe those extra billions could make an impact. However, thankfully, we are making progress nonetheless. And the progress is gaining speed in a way only J.B.S. Haldane and H.G. Wells could dream of (while Ray Kurzweil knew all along…). But it’s not enough. Professors and other scholars, with life long knowledge and experience, do retire. And even tho they are able to share their valuable knowledge through their companions and peers before leaving academy, much is lost. I want humanity to be able to pass on this knowledge in a new way. I want us to be able to share everything. Knowledge. Experience. Not in writings. Not in teachings. The process is too slow. But in a way numerous scifi story writers have been telling us for years. My new boss, Stig W. Omholt (director of Centre for Integrative Genetics), showed me not long ago an article in New Scientist. About researches involved in technologies “extending human capabilities“. We don’t have time waiting for evolution to make human brains inter-connect, sharing intelligence, knowledge and experience, vastly improving our scientific progress. We need to understand the way the human brain store information, and its nearly endless creativity. And be able to reproduce it. Thankfully, The Singularity Is Near. And it will change everything.

Our lab environment is polluted by not only cancer inducing chemicals like ethidium bromide and the neurotoxic polyacrylamide. Even more disturbing is the frequent usuage of the radio. Or, to be more precise, the lack of a radio station that does not suck. Here in Norway we have a couple of commercial nation wide channels in addition to some channels provided by the public broadcasting institution. I can’t stand commercial channels, with the non stoppable annoying advertisements. But, even worse: The channels we listen to (we switch a lot) have one thing in common that annoys me the most. The repetition rate of some of the music. I mean, I don’t want to listen to the same tune 9 times during just a few hours.

Anyway.

Lately I have started wearing my trusty old DAP, which luckily carries an endless number of hours of music. After a few weeks I have come to the conclusion that I prefer some kind of jazz inspired music while doing lab work. Even tho my favourite band this week has been Gotan Project, which is a fusion of tango and electronica.

(Yup, Nat King Cole works pretty darn good for me.)

The confocal microscopy wasnt’ the blast I was hoping for. Not because 3D visualization using laser and fluourescence isn’t fun and impressive. But, mostly me having high hopes: Looking at living mammal cells. Manipulated proteins with different stains, interacting, colourful images… Oh well. Instead, we watched a dull image of some cells involved in the breaking loose of the leaves of the flower Poinsettia. There are times I really dislike studying at an agricultural university, one of them being now. :)

I’m attending a 3 week long course teaching different microscopy techniques. We are 8 people. Yesterday, I fell hopelessly in love. With their brand new scanning electron microscopy! I was kind of suspecting this to happen, having wanted to work on a SEM for along time, but I was really blown away. I definetly need to integrate it in my thesis. I have a hunch the confocal microscopy might not be too disappointing either…

Using intense lobbying (I believe), two … collegues (Lasse and Marthe) of mine got me a job at the Norwegian Institute of Public Health, all July and most of August. Thanks!

Initiating a new transformation process this Friday, I spent most of the weekend in the lab. Mostly … waiting. This evening, at 19:30, looking at the result (after restriction enzyme cutting): The transformation was successfull! Nothing to write home about, really… But. After a week of feeling crappy. Lacking results. Nothing going the way you want them to. Finally looking at a successfull result materialising in front of your eyes somehow makes it all worth while, and then some!

You have probably heard the phrase functional food. In Norway, the government have quite strict rules of what modifications are allowed to food and beverage. I don’t know the details, but so far I’ve only seen orange juice with artificially added calcium, milk with vitamin D, yoghurt with the probiotic Lactobacillus rhamnosus GG (LGG), etc.

One of my colleagues in the protein engineering lab, our resident super star (as in music), Lasse Fredriksen, is taking this a step further. His master thesis will aim towards finding a way to use one of these lactobacillus bacteria as vaccine carriers to our intestines, where our immune system will create antibodies, hopefully giving us immune resistance to the specified disease. And all you ladies out there, the vaccine he will try to incorporate is against the HPV type 16! (Associcated with cervical cancer.) Interesting stuff. I’m sure the future will bring loads of these specialised functional modifications. Maybe even directly linked against your own, personal, genome.

Oh, and btw, check out his band: Sanguine

That is, lack of successfull transformation. I got my colonies on the LB agar, and was happy, everything going on as planned. But, darn, something wasn’t right. Using restriction enzymes to cut the new plasmids, checking if my genes actually had been incorporated, showed … nothing. I’ve spent the last days trying to find out what went wrong. My PCR products seems all right. The plasmid we’re using for transformation has a “suicide” gene which gets transcribed if there is no successful gene incorporation, inhibiting growth. But, I got my colonies, the bacteria did grow. I even tried several different restriction enzymes, and restriction buffers, just to be sure. But, nothing, nada, my gene is not there. Weirdness. I will probably end up doing the transformation from scratch. Albeit I really want to know what went wrong…

I’ve learned a lot these first weeks. And the feeling of being totally lost is gradually fading. Still, talking about green fingers, my head definitely feels green sometimes… Anway. I got the primers. I did PCR. I did gel electrophoresis, isolating the genes I multiplied. Today I started the transformation progress, using the Zero Blunt TOPO technology. Tomorrow I will know if my first GMO (Gene Modified Organism) experiment was successfull or not. And later this week I will know if I actually managed to insert the correct sequence into the E. coli or not. Looking forward to checking out the agar plates tomorrow! My other life: Weekend; at our cabin in Valdres. The weather was absolutely perfect. Blue sky, no wind, -5 celcius. I spent the days enjoying cross country skiing, reading a norwegian classic horror book (”Døde menn går i land”), and listening to the Olympics on the radio.

So. I’m installed in the lab. I’ve done my initial share of mixing up buffers and LB media for the E.coli bacteria (the ever-present lab workhorse). I’ve created a (tiny) stock of vectors (pRSET based), and should work out the primers for PCR amplifying the two chitin binding proteins I will work on. Trying not to drown in protocols and all kind of information these first weeks, I’ve set up a wiki, and I think it will be quite useful. Actually, I think the whole lab should switch to the OpenWetWare system. My supervisor seems to like the idea, at least. But I guess the management is sick and tired of this happening every year, with new students trying to change the lab… (I know I would!) Today, I spent most of the day playing around with PyMOL, which provides “real-time visualization and rapid generation of high-quality molecular graphics images and animations“. It will definitely help trying to understand the chitin binding processes. Oh, and by the way: PubCrawler. “It goes to the library - you go to the pub(TM)”. You gotta love it.