Take me out is a Dutch program in which a guy sits in front of 30 girls. While he presents hiself, these girls can press a button; that means they are not interested in the guy. Once the presentation has finished, one of the left girls (usually none, sometimes one, rarely more than one) “gets” him, and she take him out. If more than one is left, then the guy chooses the girl. If none are left, he goes home and that’s it.

While the program is very funny, my wife made a good point the other day: the opposite game would not be possible. In fact the girls push the button while the guy says what he likes, what he does, and so on. Now imagine the opposite: if 30 guys would judge one gal, they would just look at the external parts (so to say), and never, ever push the button if they like that, no matter what the gal does or likes. Ain’t she right?

Write it right

As written previously, here’s the second post about writing scientific articles. So the objective is to have people read, remember and cite our work. What makes an article a good articles?

Writing an article

Thanks to stilleben for the photo.

Good title

When scrolling through the new articles of the day, or through the results of a search engine, we see only the titles of the papers. If the title is boring, unattractive, or if it doesn’t explain what you have accomplished, we will have a hard time clicking on it. The title has to lure the readers inside the paper, the same way carnivorous plants lure insects in their traps. Once inside, as opposite to plants traps, the readers are still free to go, so we need to write it right to keep them inside. But they have to get in, so spend some time on the title, brainstorm with your colleagues, take a walk, a ride, whatever: find a good title!

First and last sentence

The first and last sentence of the article are the most important. The first says in which area the article is and connects it to our everyday life. The last says what you have accomplished and state which implications your work will have for science and for the rest of the world. Writing them right is extremely important. It just so happen that one of the teacher found my first sentence beautiful (I’m not picking this adjective up, that’s what he wrote), so here you go

Every cell in our body, whose typical size is 10 micron, contains DNA which, if stretched, would be approximately two meters long.

The sentence is very simple, short, yet states the problem very clearly: the DNA cannot fit in our cells if not compacted in some way. Body, cells, length, they are all things people understand, or feel connected to.

If after these two sentences the reader is still there, then probably the abstract is the next chewed thing.

Good abstract

The abstract has to contain your whole article in short. State the problem, why do we care about it, how you solved the problem or a part of it, the consequences for the world and future works. It is kind of shrank, but that’s how people want it. If the results are clearly stated, then they may cite you without even reading the rest of the paper (this is not a good practice but, alas, so it happens). So in general you may write the abstract for people who only read it, skipping all the rest (except first and last sentence). So don’t refer to figures or equation: the abstract should be self-contained.

All the rest

After the first sentence, make things more and more specific, but let all the technicalities outside the introduction. Explain here the 3 letters acronyms you will use later, except if sure everyone knows them (for example DNA or, maybe, LHC).

You can use a friendly style when writing, but do NOT write a diary, like: the first day we found this and that, and that he came along saying this, so we changed the method, etc. No one care about it. If you want to write a diary, use MacJournal or OrgMode or whatever suits you. Do not waste journal space.

How to structure the article

How much introduction (I), how much calculations and results (R), how much discussion (D)? Well, something like in the picture below. And what about the methods and the algorithms we are so proud of? They may just go in the Appendix, or, if space is an issue, a complementary materials pdf. If someone is really interested about your work, they will look it up, don’t worry.

How to schematically structure your paper

All the article should follow the basic principles of storytelling, which is create a tension inside the reader so that he want to finish the article, is curious about the end. Every writer, from Andersen to Bulgakov, knows that. You tell something to the reader, but not all, you make him curious, let him experience some tension, and, at the end, but only at the end, you give him what he wants. That’s a long story made short, because story telling needs years to be mastered and books to be learned. If you want to know more about it, you can begin here: writing a good story is very similar to writing a good article or delivering a great presentation, because inside every scientist there once was a kid who once heard Snow-white, Hansel and Gretel, etc. (I’m not kidding!).


Spend some time on keywords, because this is how your article is going to pop-up when searching for its contents. Keywords are word which are relevant to the paper and are not in the title (they are already indexed, so don’t repeat yourself). Try to think what would you search if you wanted to find your article. Monitor the article in your field to see what the others used as keywords. And use this neat trick if there is a paper very similar to yours, already published and very good: if you think those who read that paper should also read yours, copy some keywords of that paper: when searching for them, both will pop up; and if you listened to what I said and therefore have a title sexy enough, people will read your paper too!

That’s it

Well, this was basically what I learned from the course. If it happens that you will have the opportunity to follow it, just do it! The webpages of the write it right course is at, rare enough, http://write-it-right.org/.

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Write it right

As a PhD student for FOM I’m offered to follow some soft-skill courses during my career. These included the ‘Art of Presenting Science’ and ‘Write it right’. The latter ended Friday, 16 of April, and it was a two days course teaching how to write better papers. But why should we write it right? There are several reasons. But probably we care just about one. Publishing! If we want to make a living out of our scientific career we have to publish as much as possible. This means to convince one editor and two referees that our work is worth! But how? First we have to lure them into our articles. Then the articles have to be enough sexy to keep them reading, understanding and agreeing.

This is not only true for the referees: you also want the other readers to keep reading, to understand and to agree. Only in this way they will cite your papers, they will make you famous and eventually they will offer you a job.

Well, let me tell you, it surely seems like a hell of a job. But reading on will help you getting things done.

Keep it simple

Although good in English, we are not native speakers. The simpler we keep it, the less mistakes. Furthermore, most of the readers have an english level lower than ours: so KEEP IT SIMPLE! Use the Gunning fog index if unsure about a passage. This index is designed to keep your sentences short and without complicated words. You do not have to show off your English: you will impress your referees with your results, so keep the English simple and out of the way.

There is another reason to keep a sentence short: our attention-per-sentence vanishes after 30 words. Then try to avoid anything longer than 15: in this way you will not only keep your audience, but they will also feel smart: they’re understanding this difficult bosonic nuclear reacting stuff paper with little effort! And if the introduction in the article is well written, they will cite your clear and easy (yet complete!) paper when writing their own. Another free lunch that comes if you stay away from long sentences, is that they are more difficult to keep coherent and to construct.

Speaking of construct, avoid all unnecessary constructions! Don’t use
It could be noted that: just replace it with Note. The same holds for In order to: a to will make the same job, for less typing. If is possible to shorten a sentence while preserving the sense, then go for it! The two examples above are, well, just examples, there are many more cases where this applies.
It is the scope of this paper to determine which..
Here we determine which..
This was a personal mistake I did in my exercise (before taking the course), and the correct form looks 1000 times nicer than the original.

Another advice is to use the active form instead of the passive one. The passive one seems more formal, more objective, but keeps the reader away from the subject and it is longer reading and using it. It is archaic in the blog and twitter era. If everywhere around passive is less and less used, reading a paper all written in passive form feels weird. Do we want our readers to feel weird? No we want them feeling comfortable with us, we want them citing us! But this is not the only reason: writing passive sentences without mistakes is more difficult, so keep them active!

There are however cases where you need the passive form: use it, but not too much (they advised us to write the article 2/3 in the active form, and 1/3 in the passive one, so keep these proportions in mind).

All the above should contribute to a shorter paper, which is good for three reason
– journals have a limited amount of pages per year, therefore editors like short articles;
– referees do not care about journals space limit; they care however for their time limit: the shorter an article, the more time they have for their things
– if a reader can learn about your results in 4 pages, he will not be happy when reading about them in 10!

Better technical English

Journals do not publish articles poorly written. The first thing a referee has to say is whether the article is clear and written in correct English. So in addition to what said above

  • avoid the to + verb form: it is better the verb + ing, because often the infinite is wrongly used.
  • the pompous it, or pit: when you find a it in your paper, ask yourself “To what does it refer?”. If you can answer the question, keep it, otherwise “off with his head”.
    In order to access information it is necessary…
    To access information is necessary…
    Not only the it is gone, but also In order to is replaced by to. Without changing the sense of the sentence.
  • use inverted commas around a word only when is used in a novel way or uncommon context
  • avoid repetition we said that we would like to see whether we are able to convince you that we…
  • do not use abbreviations like don’t or he’s: they are a bit slangy and they may be ambiguous: does he’s mean he has or he is?
  • Avoid double negation to say a positive thing
    Do not make it longer than..
    Make it shorter than..

All this was just a part of the course. I’ll try to publish the next (even more interesting) part on one of the following days. So stay tuned!

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I wrote a page on how to create a script which does, in Linux, something very similar to what LaTeXit does for Mac


Tomorrow Macheist nanobundle will end. As written in the previous entry, they were able to put together 10 applications worth together 342$ for just 19.95$, 5 of which goes to charity, i.e. 14.95$ instead of 342$.

How do they do that? Paying an average of 1.49$ per app feels like buying iPhone applications. Furthermore the bundle organizers get a living out of it, so the developers will get more or less one dollar per sold bundle (plus free attention from the whole Mac world, which usually doesn’t come for free).

Rules of the game

The basic rules of any Macheist bundle are the following:

  • it only lasts for few days (a week in this case)
  • it is not very often
  • some apps are very good (pricey and well coded) and some are very cool (i.e. people want them even if cheap)
  • some applications get unblocked if you spread the word on twitter or facebook
  • some applications get unblocked if there are at least n buyers.

Each rule is the trick. Read on to learn it.

n is a big number

Yes: if they knew the bundle would be bought by 100 people, then if wouldn’t make much sense: giving away your app for 100 person in a week for 100$ is probably less than what they usually get in the same amount of time. But if n is 50000, they’re getting much more. Of course, to a broader range of people. But in a week.

Who’s the developer who gets so much money in a such short amount of time? Even Rapidweaver, which costs 79$, would need to sell 100 copies per day (which I doubt they do) to get the same amount of money (but then, probably, Rapidweaver developers get more than 1$, since they represent the very expensive app). Of course this can’t go on forever, they would lose money in the long run, but since it only last for a few days (ehi, that’s the first rule)..

..if you really need the app..

you probably already own the app you need, and you bought it when you needed it, not waiting for the bundle. So the developers lose only few potential “real” clients (i.e. clients which would have bought the full price app), because the percentage of this “real” clients who get the discount, is very low, compared to n.

If you don’t really need the app..

then probably you would never get it without discount. You would search for a free alternative, otherwise you would end up using Emacs, like real men do. But if they’re so cheap, for just a week, and there is that very cool app you always wanted, with just a bit of good advertising is probable that you will end up buying, because they’re almost free, and in the end you think you needed it. And, afterall, …

…it doesn’t happen very often

Either you do it, or you’ll lose this great deal forever. It last only few days, and it happens once in a year or so. It means you can afford it! This is great way of making customers desiring things, which could be called..


Yes, they’re good in advertising: they make you spread the word, by twitter and facebook, to get bonus apps, meaning they’re doing the best kind of spam: mouth to mouth (so to speak).

“Hey, my friend Brian [not a scam bot somewhere in Asia] told me Macheist has a great deal for 20 bucks, let’s check it out!”

And Brian friend will eventually buy the bundle.

Yes, this is how it works: at the end it will increase even more the number of sold bundles, i.e. the money the developers (and organizers) get.  And, worth noting, Macheist also has a quite populated forum, where people can exchange ideas about everything, from apps, to things which could get unlocked, and where the developers hang around to listen to feedback from users.

Why putting the n limit in the first place? Are we not going to get those blocked apps?

If you would get everything, without waiting, user powered advertising wouldn’t work, because people would see no point in reaching n sold bundles, and so they would see no point in spreading the word. And without this word spreading, they would sell much less.

But what does this means? Would we get all the apps anyway at the end? Yes, not giving them before, was just tactics. And which other tactics they use? Well,  sometime they..

..play dirty

This time they announced, in the last moments, to boost the bundle, that Tweetie would have been part of the bundle. Not only. It’s months that people are waiting Tweetie for Mac 2.0. There were also rumors its developer was not going to release it anymore, rich enough thanks to Tweetie for iPhone. But, here it is they say: bundle buyers will not only get Tweetie 1, they will also get Tweetie 2 when it comes out, and they’re also going to participate to the Tweetie 2 beta program. This really made a lot of people crazy about the bundle: people who were sceptic, bought it. People who weren’t interested in anything but Tweetie, bought the bundle (which costs as much as Tweetie alone). In shorts, a lot of people bought the bundle in the very last day, and the were way over n=500000 before the end.

Speaking about it, at the end, “the perfect con is one where everyone involved gets the thing they wanted”, as they say in “The Brothers Bloom“. Developers get money and attention, organizers get money, and we get the app. Only this ain’t a con, because the organizers have created a rewarding job doing what they like to do, working with Macs and Mac users; they had great ideas (the rules) and used them wisely to get what they wanted. In shorts, they really did something worth imitation: create a business out of nothing, have fun while doing it, and get rich enough to live with it! Bravo!

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10 great applications for 19.95$ (something like 15€) at Macheist: if you would need only one of them (except for Tracks), it would be worth buying the whole package. I bought the bundle the first day, and I have to say I’m extremely satisfied with most of them. And there is Tales of Monkey Island included!

And, as a nice side effect, 5$ go to a charity!

The very first Apple Computer logo, drawn by R...
Image via Wikipedia

Today I stumbled upon a Lifehacker article which explained how to change the background color in Adobe Reader, when displaying PDF (which could alleviate the eyes’ stress if reading a lot). Well, it turn out that the same can be accomplished with my favorite OS X pdf reader, Skim (from version 1.3.4 on). Just open Skim, then fire up Apple Script editor, and paste the following code

tell application "Skim"
set theColor to choose color
set page background color to theColor
end tell

It is not a great hassle to do it once, but if you plan to do it more frequently, you can save the script as an application, and then drag it to the Finder toolbar, so that you will always have it available.

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  • While leaving Amsterdam behind me, driving, I was listening to Radio 1. They were interviewing Jos Baijens, high-school teacher in Eindhoven, whose popularity recently increased for wearing a muslim scarf in public, as a protest for a proposal by Geert Wilders, which would like to introduce a 1000€/year tax for women who wish to wear such a scarf for religious reasons in public. Baijens was so contrary to such a proposal, that he decided to wear the scarf in the same way muslim women wear it, in public.
  • Besides agreeing or not with the proposal or with the protest, I was impressed when the presenter asked Jos what his children had to say when they saw him “scarfed” like a woman. Being Italian, I expected the children to say whether they agreed or not with his father. No. They said (roughly translated) “Dad, if you think it’s important to do so to express your opinion, you should do it”. They didn’t say “Dad, you could be a wal-creature.” or whatever; instead they expressed all the Dutch tolerance by simply saying that he could do as wished. No support, or lack of support of his idea. They simply don’t care, do they? They simply mind their business. It’s all very Dutch, you know.
  • And you, any experience with the Dutch spirit?

when two weeks ago I left for Switzerland, I asked to neighbors to turn on the heating the day before our arrival. To save energy, during our absence it was set to 10˚, and we expected to find the house at 19˚ when coming back.

So at 5am, the day of our arrival, we were kind of surprised to, well, find that the house temperature was 9˚. The heater was broken. I have no skills whatsoever in fixing home appliance, so we went to sleep, with the baby sleeping between me and my wife: concentrating human heaters in one place seemed like a good idea.

But there was something else disturbing our sleeptime: not only the cold air of the house (you could see moisture exhaling!), but a letter arrived the day after our departure: we had to find a new energy supplier, otherwise electricity and gas would have been cut out the day… before our arrival! It wasn’t happened yet, but we suspected it would have, very soon. So quickly, before falling asleep, we picked up a new energy supplier through internet, not knowing if it was soon enough.

Soon enough I wake up and called the landlord, which, after a short visit to determine whether he could fix the heater, called a technician to fix it. Being weekend we had to wait some hours, that I spent doing the wrongest thing in case of a cold house: thinking!

What was I thinking? Why was I thinking? Well, I wasn’t able to perform any other activity, so worried for my 5 months old daughter and my pregnant wife. That, and the cold.

I had a couple of sweater, warm socks, but still I felt the coldness of the house. It was like being trapped. I couldn’t sleep, waiting for the technician. I couldn’t use the computer, because my fingers were too cold to type. I could just think.

How did they overcome this cold centuries ago? Smaller room, smaller windows, more people, and fire. We didn’t have any of those, except the kitchen fire. But still, outside the smalle room with fire, what were they doing to prevent themselves from freezing? They were working, keeping them busy, not thinking. The thinking and listening was restricted to the small room, in the evening, arond the fire, when the elders woud tell some tales. They had an easy time keeping the people listining, because when the stories were over, it meant it was time to get outside the small, warm, room. They still were able to get to bed, probably warm at the beginning, but cold in the morning. Moreover, more people used to sleep in the same room, still small and with small windows. In practice, they had way to keep theirselves warm, at least in some places. We didn’t. Eventually, while I was thinking, the techincian came by, and fixed the thing. It was like rediscovering the fire, again, in 2010. Everything began to change. I could get under the blankets again, and get some warm, coveted sleep. Finally.

The take home message is: get some portable eletric heater: it will be useful to warm the smallest room of your house, where you’ll be able to tell tales and to think. And no one will interrupt.

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Today at the theoretical school in Crans-Montana, I heard the talk of Ignacio Fita, a crystallographer based in Barcelona who gave a talk about Xray Crystallography, the theoretical bases and the techniques used to get the most out of the data, how to correct it, and how to interpret it.

In general Xray crystallography is used to determine the structure of molecules and proteins, structures which generally need high resolution to be observed with precision. This high resolution can be achieved either with electron microscopy, or with Xray crystallography, but the latter is usually preferred (up to now) because by creating a crystal of the sample we want to observe, diffraction can enhance the precision of the measurements. It may sound complicated, but the way Ignacio explained the theory, made the comprehension very simple for everyone. (oh, and he took advantage of slides to make the concepts easier to grasp).

After that he explained a couple of ways to get the phase of the scattered rays out of the data. All we get in fact, with this type of crystallography is the amplitude of the scattered waves. This mean that the most important information (phase) is lost. Luckily enough, a lot of physicists elaborate clever and conceptually simple ways in order to get the lost information back. At least they seemed simple to me the way they were presented.

Then somehow time was running out, and the last part, probably the most interesting for the one already acquainted with Xray crystallography, was faster and sloppier: he wanted (as Eileen yesterday) to explain the experiments he thought as important, but for the little time remaining it was to much, and he had to rush. Probably he too would have had a benefit by timing his presentation and picking only the most important things, instead of saying more but with less art. But anyway, I should stop whining! Great work Ignacio.