Monthly Archives: May 2013

A day in the life

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Today is Monday, 20 May 2013 (yes, sorry for the delay in posting)

I am working at Caltech as a postdoctoral fellow in the Division of Biology and Biological Engineering

This is a day in my life.

  • 8 am – It is a sunny morning in California.

    palm_trees

    I get up, shower, have breakfast and walk to work, admiring the blooming jacaranda trees on my street.

    jacaranda

  • 10 am – Work is underway.

    desk

    I spend the morning trying to install a new software package which will eventually allow me to do some cool modelling and parameter analysis of biochemical reaction systems. This bit of software requires some other software, which in turn requires some other software. After spending nearly all morning googling exotic error message, I finally manage to install all the required packages.

  • 12:15 pm – I check my e-mails and reply to some of the more urgent ones.
  • 12:45 pm – I go for lunch, enjoying the beautiful May weather outside.

    Campus

  • 1:15 pm – Back in the office, I read a paper draft my work study student has sent me, and start adding my own sections and figures to the paper.
  • 3 pm – As part of the “Women Mentoring Women” programme at Caltech, I have this year been mentoring a grad student. This afternoon, we meet for coffee to discuss her plans for medical school, books, and cats.

    coffee

  • 4 pm – Back working on my paper draft.
  • 4:30 pm – My boss just came in to schedule a meeting for tomorrow. I take some time to prepare for the meeting and e-mail relevant documents to both my boss and my co-worker.
  • 5 pm – Back to working on the paper draft, and finally get it into a state that I am happy with. Will it be Ice Cream Day soon?
  • 5:45 pm – Do some reading.
  • 6:45 pm – It’s evening on campus. Get a sandwich for dinner.

    evening

  • 7 pm – Back at work, wrap up, update my lab notebook, make plans for tomorrow.
  • 7:30 pm – Choir rehearsal on campus. At the moment, we are learning bits of Beethoven’s 9th for commencement. Good fun.
  • 9:45 pm – Home from choir, I spend half an hour doing some housework, while listening to an audiobook (Bring up the Bodies, part 2 of Hilary Mantel’s trilogy about Thomas Cromwell). Listening to audiobooks is literally the only way I can trick myself in doing any household chores at all. (The rest of it is handled by my robot vacuum cleaner. Yay robots!)
  • 10:15 pm – I make myself some tea and tackle my final exam for my EdX Statistics Course. Longer than I expected, but fortunately not hard.

    stats

  • 11:30 pm – I skype with by boyfriend in London. It is the last thing I do before I go to sleep and the first thing he does after waking up. I am insanely grateful to be living in an age where technology allows us to do that. Where it is possible for two people, across an ocean and a continent, across an entire night on earth, to connect.

Say it in ten hundred words

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One thing I like a lot is languages. In fact, I have started taking Dutch classes at the beginning of the year, and it has been very enjoyable. Recently, my teacher has introduced a new kind of homework: Writing short essays. The first one involved describing my work.

Now, this is hard. First of all, I haven’t learned a whole lot of words yet. Second, they are words from my Dutch textbook, so they are chiefly intended to help people go about their day-to-day lives in the Netherlands. (“Hello. My name is Joop. My bicycle is broken.”) Nothing there (at least not in lessons 1-15) about, say, computational neuroscience. Or synaptic plasticity. Or Calcium signalling. At first, I was a bit frustrated, because my limited vocabulary does not allow me to say the things I want to say.

But thinking of it some more, I was reminded of several things at once: My early days of learning English, the Up Goer Five and Oulipo. Bear with me, I’ll explain.

At age 10, I started learning English in school. On one of our first written tests, we had to translate into English a little dialogue where someone tells a friend about his new cat. The friend asks: “Is it male or female?” Now, “male” and “female” are difficult words, and most students could not remember them (or even remember that we’d learned them in class). A few got it right. But they were not the most impressive. The most impressive students were those who had forgotten the words, but still found a way to say what they wanted to say. A few wrote: “Is it a He or a She?” and one, rather ingeniously, asked: “Is it a Mr or a Mrs?” What I learned that day was that not having the necessary words is not an excuse. You just have to find another way of saying it.

This is exemplified rather marvellously by this xkcd comic, where a Saturn 5 rocket is described using only the one thousand (or, as the comic says, “ten hundred”) most common words in the English language. It is fantastic! If you want to try this kind of stuff yourself, there is an Up Goer Five Editor you can use: Enter any text, and words that are not in the most common 1000 will be highlighted, so that you know to replace them with simpler words. You can also read texts other people have posted. Some describe their work, some give synopses of movies, some even re-work poems or songs. Some of these texts are absolutely awesome, as if restricting the authors to a limited vocabulary had unlocked an enormous creative potential.

This is not a new idea, of course. In the 1960s, the French literary movement Oulipo did exactly the same thing: Authors invented rules or constraints, and then tried to write texts following these rules. At the height of the movement, Oulipo superstar George Perec published “La Disparition”, an entire novel without the letter e. (You should read it, it’s fun! If you can’t read French, fret not. There are at least seven translations into other languages, all of them without the letter e. The English translation is titled A Void).

So, if limiting yourself to a restricted version of the language is good enough for my middle school class mates and for xckd and for George Perec and his friends, if it even made them better, more creative writers in some way, then I should stop worrying about not knowing much Dutch and just embrace the creative challenge.

I am sure Mr Cat would agree.

Ice Cream Day

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So, apparently the Japan Ice Cream Association has declared 9 May to be Ice Cream Day. Or, as they say in Japan, アイスクリームの日. I am not even making this up, you can read about this here. It’s even mentioned on Wikipedia, so it must be true.

Let me take this opportunity to tell you about my own little Ice Cream Day tradition. It is to do with publishing scientific papers and originated in collaboration with my former fellow PhD student, the Most Delightful Lu Li.

Our job as scientists is to find stuff out. But once we have found something out, our job is also to let the world know about it, so that other scientists can build on it. Now, you would think that the “finding stuff out” part is long and tedious and that the “telling the world about it” part is easy. Well, it’s not. It’s long and tedious as well.

Here is how it usually works: After having found stuff out, the scientists involved in this particular project get together and start drafting a paper. The paper describes what they have found out, how they did it, why it’s important and how it fits into the bigger picture. This in itself can take a while, especially if several authors are involved. At this “writing up” stage, it might turn out that further analysis is needed, or that some experiments need to be repeated or that additional data might have to be collected in order to make the scientific argument stronger. Once the final paper draft is ready and approved by all co-authors (including agreement on where all the commas and semicola should be, which can take weeks), it is submitted to a scientific journal. At this point, I think it’s time for ice cream.

At the journal, an editor will send the paper to other scientists working in your field to review it. This is called “peer review” and typically has one of two outcomes: a) your peers reject the paper or b) they accept it, pending a few changes (e.g. doing further analysis, repeating some experiments, collecting more data, or removing the second comma on page 3). If most reviewers think the paper is acceptable, the editor will get back to you with a list of required or suggested changes. You make these changes (which, again, can take a while) and re-submit the paper. At this point, it’s time for ice cream.

There can be a bit of back and forth between the editor and reviewers and the authors (e.g. reviewers get to review the revised version of the manuscript to check that the changes have been made to their satisfaction), and this … can take a while. But if all goes well, the paper is finally accepted for publication in the journal. At this point, it’s time for ice cream.

Once a paper is accepted, the journal has to publish it, which includes correct typesetting, sending copies to authors for final proof-reading and all sorts of whatever else it is journals do, which – you guessed it – can take a while. But one fine day, the paper will be published, at which point, it’s time for ice cream.

All in all, the process can take a considerable amount of time. For instance, a recent paper I worked on with the Most Delightful Lu Li took more than three years to go from initial draft to publication. So, a couple of Ice Cream Days along the road are probably in order.

To recap, here are the rules:
1. You submit a paper: it’s Ice Cream Day
2. You submit revisions: it’s Ice Cream Day
3. The paper is accepted: it’s Ice Cream Day
4. The paper is published: it’s Ice Cream Day
5. (Extra bonus rule courtesy of the Japan Ice Cream Association) It’s 9 May: it’s Ice Cream Day