Animals

Many biologists grew up liking animals. That’s why they became biologists. Not me. I never had a particular interest in animals, never had pets, never brought in animals from outdoors. My interest in the local wildlife only emerged after I had been working as a (molecular and computational) biologist for some time. Walking to and from the lab, you start to notice things.

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“I am interested in data visualisation.” – “Great! Try this cupcake.”

Imagine the following situation. You are at a party and chat with someone you’ve just met. You start talking about what you do and what you are interested in. You say something like “I like statistics, and especially how it applies to solving biological problems.” The person you are talking to smiles brightly and then says: “Fantastic! Have you tried braiding your hair?”

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Dear Sir …

“Excellent”, said an e-mail I received recently from a collaborator, “talk to you soon, Stephanie!” This happens to me a lot, in professional contexts. I have been called Stephanie by colleagues and teachers, bosses and students. I have been introduced to a full lecture theatre as Stephanie, I have been invited for job interviews as Stephanie.

I don’t like it.

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How my coffee shop solved my research problem

A while ago I told you I was stuck with my research beccause I could not afford to build a library on the moon. Yes, it’s a long story, but it comes down to the fact that the proteins that transmit and store information in our body do this by undergoing changes to their function, shape, chemistry, location etc.

Here, for instance, is my favourite protein, CaMKII, and some of the things that can happen to it:

CaMKII_monomer_states_anno

Actually, this picture does not show all of CaMKII, only about one twelfth of it (well, one twelfth of what matters). But even for this little part of a protein, there are a lot of options: Is a phosphate group attached to it or not? Is it active or inactive? Bound to another protein called calmodulin or not? That’s already 8 possible states that little protein subunit can be in. With each new possible modification, the number of possible states doubles, and soon you have a mindboggingly big number of possibilities (what we call “combinatorial explosion”). This makes those proteins difficult to model using a computer.

Unfortunately, modelling proteins using a computer is what I do for a living. Hence the dilemma. What did I decide to do? Go for a coffee, of course. But this turned out harder than I thought.

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Stuck with your research? – Kaffeehaus

Remember the time when I was stuck with my research on combinatorial complexity in multi-state proteins, because I could not get the money to build a massive library on the moon? (Don’t you hate it when that happens?)

So, what did I do to solve the problem? I will answer this question in a minute, but let’s look at some poetry first.

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How my research got stuck because I couldn’t afford The Moon

“OK,” I said, “we can do this. All I need is a librarian, an architect, and a planetary scientist.”

But let’s start from the beginning.

Proteins. They are awesome. In the human body, proteins do all the work. They hold things in place, they move things, they make things, they destroy things. They can store and transmit information (and those that do are my favourites). But how might a protein store information?

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The problem with Australia

I am not good with small talk.

See, I am Austrian. We are grumpy people. Not only am I Austrian, I am also from the Western part of Austria. Here is what the CIA World Factbook has to say about this:

[…] population is concentrated on eastern lowlands because of steep slopes, poor soils, and low temperatures elsewhere.

No wonder than that we are not often in the mood for idle chit-chat.

In addition, I am a scientist, and like many other scientists deeply suspicious about small talk. We like novel insights and interesting thoughts. We don’t always understand what small talk is for. So, traffic this morning was horrible, you say? The weather has been lovely this June? Thank you, but I don’t need to be informed about the bloody obvious.

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Not my superpower

I have long had a secret theory that everybody has one very specific and mostly useless superhero power. For instance, I have met a woman who, for years, has always woken up at precisely the same time every day (without using an alarm clock). I know a man who can sound exactly like a trumpet (without using a trumpet). And then there are several people dear to me who have an uncanny ability for finding four-leaf clovers.

My secret theory goes on to say that one day, when evil aliens from outer space attack Earth, circumstances will magically fall into place such that each of us gets to use our very specific superhero power and together, we will save the planet, thus proving that our superhero power wasn’t that useless after all. (Well, I don’t actually really believe that. But wouldn’t it make a great movie?)

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Say it in a sentence

I recently came across this very awesome site called “lol my thesis”. The site challenges people to summarise the content of their dissertation in one sentence. The one-word thesis summaries range from the somewhat surprising (“Irish cultural history is defined, before and after, by one school teacher’s crazy lifelong dream of becoming a martyr, because druids.“) to the somewhat less surprising (“If you take an obscure mathematical object and encode it into another obscure mathematical object, the result is an obscure mathematical object.“) to the somewhat depressing (“We will never know what a long dead writer wanted us to know about his work.“) Reading the entries on lol my thesis reminded me of a rather traumatic experience I had as a young grad student. 

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