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Doctor Do-It-All (11.10.06, 08:31)

He can picture himself growing old here, and he actually looks forward to winter! Surely, Polish people have a positive attitude towards Norway. This one is nature-loving, thirty-something, and one of our PhD students. Waclaw Kusnierczyk is a young MD who has set out to re-design Gene Ontology, but not until he explains us what on earth that is!

So here we are. Gene Ontology is a representation of what is general in the domain of molecular biology, broadly speaking. It says, for example, that a cell wall is a cellular component. Waclaw explains that it is quite typical that two databases, created by two different teams for the purpose of storing the same kind of information, use different names for the same things, causing misunderstandings and extra work.

"In brief, an ontology is a representation of what is general in a particular domain—e.g., that a human is an animal, that a woman is a human, but not that this particular human here, say me, is silly. This may be true, though.”
- Ontologies are supposed to help here. Building ontologies is also a good test of our knowledge: we often discover that our knowledge is incomplete only when attempting to express that knowledge in a formal language. Gene Ontology is very simple in structure, though it includes some 20,000 terms. It is widely, if not wildly, used to annotate experimental data and scientific publications. It is now being substantially restructured, and I hope to contribute to this process.”

In other words, these people are creating the common computer language for all researchers working on genes and their products. Biologists, computer scientists and philosophers all have something to communicate, and now they are getting a common language.


The earth would still be the centre of the universe, if it weren't for/if not for Copernicus. Marie Sklodowska Curie opened up the science of radioactivity. Polish scientists have altered the way we perceive the very large and the very small things in life. And the way we eat. The next time you check something for vitamins, remember Kazimierz Funk. He is the pioneer in the field of dietary disease.

Remarkable Polish scientists can be found everywhere. Now, why would four of them choose Trondheim? Surely, it cannot be the weather. Could it be love?

People from Poland is a new, short series in Universitetsavisa, leading up to POLEN 2006.

Not happy with the food
- And your average day at work?

- Teaching ... but the main purpose of my stay here is research in knowledge representation in the biomedical domain. I work in collaboration with computer scientists, biologists, and philosophers – it is a very interesting and involving field. A day at work is just a day at work. I wish the canteen served better food.”

- Do you have any recommendation for the cooks on campus – a tip of the day?

- Ha! Of course, it is not that the food is generally bad or the like. But it sometimes lacks taste. On other occasions it is really good. Some time ago the canteen in Realfagbygget served very tasty meals, but the cook has left. I wonder why?

The canteen in the newly built hotel for patients at St.Olav hospital serves excellent meals.

Tip of the day? No, rather tip for the whole year. More fresh vegetables, more variation in the spices used, if any. No pizza Grandiosa, please. I have recently spent some time at the University of Saarbruecken, Germany. Canteens there are smaller, but serve 5 or 6 different dishes every day.“

The philosophic child
He has always been intrigued by the surrounding reality. As a child, he was fascinated by the abundance of patterns in the things we observe and the events we participate in.

- Our knowledge about the world is so advanced that one can learn only a very tiny fraction of it, and yet so incomplete that it is quite easy to come up with a question that no one can answer with confidence. I always wanted to know everything about everything, and ended up with knowing nothing about nothing.”

Not sure I believe that. Like when Socrates said “I know that I know nothing”, we took it as a statement of a wise man’s understanding of the vastness of possible knowledge.

“Excellent! Even better: it has to do with knowledge about genes. Gene Ontology is the number one in the world of biomedical ontologies, at least in terms of its popularity in the community.
Beautiful background
Waclaw grew up in Wroclaw, a city three times the size of Trondheim in population. It is located by the border of the Czech Republic and Germany, in southwest Poland.

While Trondheim is a thousand years old, Wroclaw has a cathedral the same age. The city is at least two hundred years older. Historically, it has belonged to the kingdom of Bohemia, the Habsburgs, Prussia, and now Poland. It is also one of the major centres of the pro-democratic movement in Poland, where the Solidarity trade union movement began its work some 25 years ago. Architecturally, it looks like something Disney would copy.

They say a picture speaks more than a thousand words; maybe that’s why Waclaw cannot leave home without his camera. His many Norwegian sceneries at his website suggest that nature intrigues his eye the most. And that he has seen more of Norway than most Norwegians.

- Well, perhaps I have taken thousands of pictures of the few places I have been to. Photography teaches you to pay attention to details, and to grasp every moment. It is true that it is hard for me to leave home without a camera. The nature in Norway is fascinating. Here in Trondheim, both Bymarka and Ladestien are among my favourite places (ed. note: Bymarka and Ladestien are outdoor recreational areas in Trondheim).”

From Poland to programming
He completed his medical degree in Wroclaw, but the stethoscope never became his instrument. He became a doctor turned computer nerd.

After his studies, he went to Perugia in Italy on a one-year Tempus grant.

In 2001, he came to NTNU Department of Information and Computer Science. Waclaw’s humble goal is to finish his thesis, but right now he’s more occupied with teaching programming.

- It is a way of funding my work on my thesis, or it should have been. It started as just a temporary job, a means to survive, but now it takes up almost all my time. Actually, teaching is really rewarding. Often it is only when I teach that I have a chance to discover what I really do not understand.”

Disappointments turned into dreams
His first experience with NTNU could have been better, but now this is the place where he is hoping for a great job-offer.

- It was difficult at the beginning, though it could have been worse. A lot of crucial information for newcomers is available only in Norwegian, and I was given different and sometimes conflicting advice and hints on what I can and what I should or should not do. An especially disappointing experience was how little support NTNU gave me in finding a place to stay. But Norway is not a difficult place to live, once getting used to the cuisine. I already picture myself growing old here, and that might actually be a good reason to leave.”

Sweet snowy expectations
Temperatures are rapidly declining, and the daylight recedes gradually into the dark half of the year. I wonder how this one feels about our winter climate.

- Are you looking forward to winter?

- Which one? You claim to have two seasons: the green and the white winter. That’s not true, that’s marketing. The worst season is the grey winter, after the snow melts and before the nature wakes up for good. I wish climate changes removed that one from the schedule/calendar. But the white winter is fantastic, and yes, I am looking forward to it: this year, my two-year-old daughter will go skiing by herself for the first time. And next year, she will teach us how to ski.”

By Hege J. Tunstad

Waclaw Kusnierczyk