Paper Writing for PhD Students, Part 4: Theatrical Cut, Or How To Konmari Your Paper

writing4

This post continues the paper-writing self-help series for PhD students directly from where the previous post ended.

Once you have decided the key point of your paper and have settled on its main conclusion, the next step is to choose what results go in. This choice should be made with care: now that you have a point to make, plan your paper so that everything else supports this point. The rest should go! The best papers are often quite minimalistic: they drive their point home with essential ingredients only. Papers that contain tons of unrelated results are difficult to comprehend, because the reader is left wondering where to focus her attention. Clutter reduces clarity. Always konmari your paper! Keep what makes it happy and discard everything else.

Continuing with the film industry analogy, the process of going through your results and deciding what to keep resembles the process of editing of a Hollywood movie. After the movie has been shot, the director and the editor start working with an abundance of raw materials that are to be sculpted into the final product, the theatrical cut. The goal is to assemble the film from the shots and scenes that best support the storyline, cutting out footage that is not essential and that doesn’t have the emotional impact that the director desires.

Your paper is your theatrical cut. Use only the elements it needs, and leave out the rest.

Cutting out material and deciding not to use some of your results may feel difficult and painful – you spent a WEEK on that plot! But, believe me, it is for the best. If you want your work to have impact, it has to be read and understood, which is greatly hindered if there is too much unimportant or unrelated information to absorb. Clutter draws attention away from the point that you want to make, and leaves the reader exhausted.

Perhaps it is because of the pain caused by discarding perfectly-good-yet-unimportant results that most journals nowadays allow for a extended special five-hour-long director’s cut in the shape of a Supplementary Information document with an unrestricted page count. You can dump all those raw materials that didn’t make it to the theatrical release to the SI, so that they can safely be forgotten and ignored by the rest of the world. But now your week spent making that plot means at least something.

But back to your cut – how to choose the results that are to be included and that support the key result?

Let us see how far we can push the film script analogy discussed earlier. A typical film script begins with the Setup phase where the characters and the setting are introduced, then moves on into the Confrontation phase where the characters are put in interesting trouble, and finally there is Resolution (epic fight in space followed by an exploding Death Star or similar). This may be followed by a brief Epilogue (with or without frolicking ewoks). If we divide our results into these four categories, Setup and Confrontation contain results that are needed for getting to the main result, for building up excitement and for leading the storyline to its climax. Resolution is the main conclusion that we discussed in the previous chapter. Epilogue shows what follows from the Resolution.

The Setup category contains plots and results that are required for the reader to make sense of the context, setting, your experiment, and/or your data (like, basic statistics, and so on). Schematic diagrams that visually explain the concepts that your paper works with also fall into this category; always include a schematic diagram or two!

The Confrontation phase brings the story closer to the final revelation that you aim to make; it highlights the open important question that you address. You can do this, for example, by showing empirical results that are surprising and cannot be explained by existing theories, and then providing an explanation as the Resolution of your storyline. You can also build up excitement by presenting a number of competing hypotheses or models, to be then shot down by your results (except for the one model that matches with your data and provides your Resolution). Or, you can begin by displaying some surprising system-level results or statistical observations and then home in on their detailed explanation in the Resolution phase.

The Resolution category should only contain your main result and key point; one to two figures.

The last category of results, the Epilogue, is more important than the last couple of minutes of a blockbuster film. These results are presented after the main result, and serve the purpose of highlighting its significance. One key technique is to think of some application or consequence of the main result, and to illustrate this with, say, a figure that plays the role of an example rather than that of an important stand-alone result.

If you look at some research papers published in the glossy magazines (Nature, Science, and so forth), you’ll see that great many authors apply this technique: out of the four or so plots in those letter-format papers, the first is about Setup/Confrontation, the second is the key result (Resolution), and the rest are there for showing why the key result matters, or what it means (Epilogue). For the kinds of journals that us mere mortals publish in, these figure counts may be larger–the important thing is to decide on clear roles for your results and figures and use them accordingly when telling your story.

Paper Writing for PhD Students, Part 3: The Importance of Focus

keyboard

[This post continues my “self-help” series on writing papers for PhD students; the previous episode can be found here. This series is an attempt to share some of the conceptual tools that I use with my students. Their point is to structure your thinking and focus your decision-making on a limited number of problems at a given time; having all options open at all times is an enemy of creativity.]

Scientific papers are stories, not just containers of information. The more focused and exciting the story, the more likely it is that it reaches someone. This is because that someone has to decide to invest their time in reading the paper, and as we all know, the world is full of papers, too many for any of us to read.

Thinking of papers as stories is something that doesn’t come naturally to most students or scientists. If we have been taught at all, we have been taught to write (boring) reports, certainly not to develop storylines, or to work with the kinds of higher-level conceptual elements that, say, journalists use.

Good writing starts with careful planning. I usually plan my storyline in three steps.

The first is defining the key point of the paper, the main conclusion that you want to tell the world. The second step is choosing the essential building blocks for the rest of the storyline, leaving out all results that are not necessary. The third step is taking these building blocks and arranging them into a condensed version of the storyline: the abstract of the paper. That’s right – I recommend writing the abstract before the rest of the paper. This is unconventional but it works.

Defining the focus of the paper – its key point and its main conclusion – is the most important step, as it lays the foundation for the rest.

In the best case, the key point is a single important result, but usually things are slightly more complicated than that. In any case, you should be able to explain your point and  main conclusion with one to three sentences. If you think that this is too little, consider these: the Earth rotates around the Sun, and not vice versa. Space-time is curved by mass. The salt of deoxyribose nucleic acid has a structure with two helical chains, suggesting a possible copying mechanism for genetic material. And so on. Clearly a sharp focus doesn’t mean that the result is simplistic – to the contrary, there is usually a lot of depth behind results that can be described with a few words.

Choosing a key point that can be condensed into a few sentences doesn’t imply that your paper has to be narrow in scope. If your work is of an exploratory nature your key result might be that you have mapped out a problem area and your paper provides the map, or perhaps your main conclusion is a broad synthesis of several sub-results that make up the bulk of your paper. The most important thing is that you can make it clear to the reader what your paper is about.

If you can compress your message into a package that can be easily communicated, the higher the likelihood that it reaches its intended target, the reader. This is not limited to primary transmission – say, the reader encountering your abstract on the arXiv and deciding to read on – but secondary transmission is important too: getting the reader to share your paper with colleagues, online or face-to-face. Whatever the type of transmission, it works best if the thing being transmitted is compact and focused.

Communication is always difficult and all communication channels are noisy – a tight focus helps your message to make it through in one piece.

Next: Theatrical Cut, Or How To Konmari Your Paper

Thou Shalt Not Smooth!

This is a very short post for those dabbling in the dark arts of network neuroscience. Everyone else, read this or this, they’re probably more fun anyway.

degree_new

[Figure from Eur. J. Neurosci, doi: 10.1111/ejn.13717]

Q: When building ROI-level functional brain networks from fMRI data, should I apply spatial smoothing to the voxel time series?

A: No you should not, what were you thinking? See above; it messes up your degrees and links non-uniformly, and in general has weird effects. In any case, you already average your voxel time series to get your ROIs, which is brutal enough. For more, see our recent (open-access) paper in the European Journal of Neuroscience, with @TuomasAlakorkko and @eglerean and @hpsaarimaki and Onerva Korhonen.