Play the lottery day

A few weeks ago, I submitted a grant proposal, the first since starting my new job at the University of Edinburgh. This is how research works: You have a great idea for a project, but in order to do that project, you need co-workers and lab space and equipment. So you apply for a grant where you explain what you need the money for.

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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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