Write it right, part 2

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?

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.

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!).

Keywords

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/.

Write it right, part 1

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.
Example
It is the scope of this paper to determine which..
becomes
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”.
  Example
  In order to access information it is necessary…
  becomes
  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
  Example
  Do not make it longer than..
  becomes
  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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• 11 Smart Tips for Brilliant Writing (copyblogger.com)
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Crans-Montana, part 2

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.

Winter Doctoral School, Crans-Montana

This week (15-18 February) I’m attending a Doctoral School in Crans-Montana, a ski-resort in the Swiss alps. The topic is Studying Biomolecules by Experiment and Theory : a Biophysicist’s View, which I thought would be connected to my research project (I was invited by my supervisor, so he knows better where I should or shouldn’t go).

Up to today, Wednesday, I am proven so wrong: this is all about but my research (DNA, its mechanical properties, and how it aggregates to form chromatin: all from a purely theoretical point of view). Not that this makes the things less interesting: it just shows me how much more there is in biophysics than what we’re doing in our group, Theoretical Physics of Life Processes.

For example the talk by Joel Sussman (Weizmann Institute, Israel) was about intrinsically disordered proteins, i.e. proteins which have domains where there is no fixed structure, but something more spaghetti-like. This proteins could have the advantage of being able to perform more functions thanks to the flexibility of the disordered regions, which would/could get ordered in different ways for different functions.

Of course the speaker was extremely good, and that made the talk followable and enjoyable. The same can’t be said about, for example, Eileen Lafer, which told us about Protein assemblies, aggregates, and the role of chaperones. Her talk was extremely long, complicated for me and she was talking fast, trying to say a lot of interesting things, but which were, unfortunately, too much and too complicate for the audience (or just for me). Shame, because this lady has been publishing articles for about 30 years, which means she knows what she does. Moreover she’s a very nice person (I had dinner already two times with her, Rui Sousa and Ignacio Fita, and we had a lot of fun together, even if I’m 20 to 25 years younger than the youngest of the three) and therefore I feel that she could have delivered a great presentation. But swadly enough, being scientifically good, doesn’t mean you can communicate your ideas easily. And this is extremely true for me and this blog

Anyway, I’m learning a lot, by going to a school whose topic has nothing to do with my everyday duties. I know what is a synchrotron, how to correct for its outcome, I know how electron microscopy works, and how to get 3D imaging out of that, and a entire bunch of this exciting stuff. Only drawback: the school should also be theoretical, but up to know only experimentalists have shared their works. Let’s hope for the better.

Web Of Science, Papers and Leiden University

at least for me Papers and Web Of Science were not working together
when I was at home, since the ezproxy of Leiden University was not
properly configured. Yesterday I managed to indirectly contact the
administrator of Leiden ezproxy, and now Papers and Web Of Science
work together. Here’s how I did it:

Open with TextEdit the file

~/Library/Application
Support/Papers/PlugIns/SearchEngines/WOSSearchEngine.searchengine/Contents/Resources/gatewayurl.txt

replace the address there with the followin

http://wok-ws.isiknowledge.com.ezproxy.leidenuniv.nl:2048/esti/soap/SearchRetrieve

Then fire up Papers. Go to Preferences (⌘ + ,) sources, and as
Authentication URL use

http://wok-ws.isiknowledge.com.ezproxy.leidenuniv.nl:2048/esti/soap/SearchRetrieve

Check the box "Go to this page when paper is started". As library proxy use

http://ezproxy.leidenuniv.nl:2048/login?url=%@

Restart Papers. You should be prompted for the Leiden University
username and password. Fill them in. You should now see something that says

SearchRetrieve
Hi there, this is an AXIS service!
Perhaps there will be a form for invoking the service here...


This means that things work. You can now use the Web Of Science search
from within Papers.