How to start writing a paper, the order of things to do

The work is not done until the paperwork is finished.  A paper, i.e. a collection of texts, figures and tables, summarizing the work for a masters, bachelor or diploma degree, presents your various efforts in a form that can be comprehended by others.  This post provides an idea on how to start, how to go ahead and how to complete such a paper.

The paper

The components of the paper and their order should be: title, affiliation, keywords, abstract, introduction, results, discussion, summary, outlook, acknowledgements and references.  This, however, is neither the order in which a paper is written nor the order in which most people read the paper.

I have to be attracted by the title, I then read the abstract, glance over the figures, check the references, have a more careful look at the tables and start reading the summary.  At any stage, I might either decide it is not worthwhile to continue or I decide I should read the entire paper.  In the latter case, I will probably have another very good look at the summary of the data (figures and tables) before I start reading the entire paper from beginning to end.

The order of its components is certainly not the order in which the paper is written.  This post concentrates on how to write a paper and that means, in which order the components of the paper should be created.

The canonical order

  1. Data, figures, graphs, tables, charts, formulas
  2. Message of the paper
  3. Introduction
  4. References
  5. Results
  6. Discussion
  7. Summary
  8. Outlook
  9. Abstract
  10. Title
  11. Acknowledgements

Data, figures, tables, formulas

Collect the data that you created in the process of your work during last few days, weeks or even months.  Create a first version of all figures, tables and mathematical formulas.  Make sure to write long legends that explain everything in reasonable detail.  Do not refer to text that you have not written yet to explain details in the figures.  Include no conjectures, implications or interpretations: concentrate on the data.  You will continue to work on the figures and tables and formulas and their legends until you submit the paper.

Message of the paper

Now that you know, what you have achieved during the past period of time you can develop a message.  This means, you create a consistent story line by sorting the data and figures for the results and the discussion sections.  The order in which you present the data in your paper does not have to be chronological, i.e. it does not have to follow the order in which you created it; it should be logical and comprehensible.  You are not writing a novel, you do not have to capture anybody’s imagination; rather, you should make sure that the facts are laid out in a correct order for one of your peers.

In many institutions you have to give a talk.  The graphs, figures etc. form the basis for your slides and your verbal presentation provides you with an an excellent opportunity to test their comprehensibilty as well as the general story line.

This is also the right time to realize that some data, experiments and/or evaluations are missing.


Science in a very general sense is a vast field.  You work in a particular discipline on a very specific subject.  Most of the work you have done will be a repetition of what others have done before you.  Most of your conclusions have already been concluded by others.  Accept it, other scientists will have come up with similar data and similar conclusions by similar means.  Phrased positively, you confirm their findings and prove that you are a capable person in a laboratory.  Through a combination of hard work and good luck you might have been able to extend the knowledge in your field.  With even more luck you  might have even been able to extend our knowledge on science in general.

Place your contribution

Where in the world of science is your contribution?

The introduction you are about to write embeds your contribution in what we know, with details of what you know in your discipline and it embeds your discipline in science in general.  This is confirmed by the references to papers by other laboratories, papers by other members of the laboratory you are working in and papers decscribing your own work.  You tell the rest of the world where your contribution fits into the general framework of your discipline and that of science in general.

It is usually a very good idea to write a very detailed and long introduction.  It might be too long for the paper you intend to submit, so you will shorten it later, but if you intend to publish more than one paper or intend to continue in this field or on that subject your generic introduction will improve over time.  You will find more references, you will refine the references and you will understand the part of the message of some papers that actually concerns you better.  You will adapt your generic introduction to the paper you are writing.

The very last paragraph of your introduction explains what the reader can expect from this paper.  You define the questions you intend to answer and you explain the results in broad terms.  Again, you are not writing a novel and you do not have to generate any element of suspense.  It is much more important that the reader knows what to expect.  The idea is to connect to the message and not to the medium.

The introduction and the legends are special in the sense that you will most likely be able to re-use them later in your career.


Most of the references in your paper are required in the introduction.  You will probably refer to many of them in the discussion.  Maintain a list of references and make sure you know what the main messages of these papers are.


Since you have all the data in your figures, tables, graphics and collection of mathematical formulas as well as an outline of the message of your paper, i.e. your story board, writing the results section should be relatively straightforward.  Make sure you restrict yourself to facts.  Avoid any interpretations of your data.  It should start to become clear why the different experiments were required and how they relate to each other.  The results section should contain very view references since most if not all the material you present is originally yours.


The discussion embeds the results into the common line of science.  It essentially addresses the issues you raised in the very last paragraph of your introduction.  You answer the questions you have posed and you explain why and how you filled in the various gaps in our knowledge.  If you have come up with a new model or a  significant change to a currently accepted model here is the place to present it and to illustrate it with some figures of your own.


The summary should contain no new information.  It simply summarizes the paragraphs mentioned above for those who do not intend to read your complete paper.  If the paper is short you can obviously skip it, but if your paper is somewhere around 80 pages long do not hesitate to invest 2-3 pages in a very well written summary.


The outlook should be devoted to future work.  In particular, you should point out, which
questions remain un-answered, which new questions came to your mind and which different approaches you would recommend for future experiments.  If you wish to speculate, here is the place to do it.

Abstract and keywords

The abstract summarizes your paper.  It embeds your paper within your discipline, it points out what you have done and which techniques you used.  It says explicitly why your paper is important.  The abstract outlines your various findings and indicates their novelty.  Your abstract should definitely contain the specific facts, numbers or relationships that you regard as important.

Make the effort to write the abstract from scratch and do not copy phrases from the other text fragments to describe the content of your paper.

Consider that only the abstract and the title are guaranteed to be available online and will be indexed by specific keywords and phrases.  Therefore, most scientists will only find your paper it if you have phrased the abstract using the commonly applied terminology.

The choice of keywords is important to make sure that your paper is correctly indexed.  Continue to use the same keywords for book chapters, conference abstracts, conference
proceedings and reviews.


The title is obviously extremely important since it will attract most readers.  Use the allowed number of characters and make absolutely sure the title contains your sub-discipline’s keywords and the main message.  Do not worry if it changes several times while you review the paper.  Use a simple running title while you write the paper and do not worry about it until now.


Do not hesitate to acknowledge how others have contributed to your work.  However, concentrate on the professional help and mention details wherever this is appropriate.  Make sure that the acknowledgements are correct and well balanced.  Your project might have started quite a while ago and many who have helped you might not be on your mind anymore.

The bits and pieces

Your paper makes your work a part of the scientific literature.  It essentially consists of three parts: the introduction, the results and the discussion.  The introduction sort of positions the paper, while the discussion provides your opinions on how the results should be  interpreted, how they fit in with what is already known, what is new and how they contribute to your discipline and to science in general.

The introduction and the discussion have expiration dates.  They are the products of our
time.  The results section should, however, be timeless.  The results of your experiments should be the same in a hundred years.  The data you have produced should be exactly
the same if the experiments were reproduced elsewhere on this planet “or on the moon”.  This is one very good reason, why it is very important to distinguish between data and implications.  In the end, your paper will most likely be judged by the data it has produced rather than by your speculations.


In the very beginning, most of the effort should be spent on reviewing the data, re-checking the laboratory book, reviewing the methods & materials, collecting information on the machines, tools and kits that were used for the experiments and on summarizing the data in figures, graphs, charts, tables and collections of formulas.

In the end, most time should be spent on the abstract, the title and on the first one or two paragraphs of the introduction.  These may only amount to 2-3 pages of text but they are the most crucial parts of the paper.  They will be read by at least an order of magnitude more people than your entire paper.

Common mistakes

The most common mistake is that authors start with the abstract.  They summarize a paper that has not been written yet and simply produce a list of promises.  The importance of writing the abstract at the very end cannot be over-stressed.

Another very common mistake is that the legends are not complete.  It does not matter if the legends are too long you can always shorten them.  But it is very important that you have a set of complete legends in the very beginning of the paper writing process.  Once you have a first draft of figures, tables and formulas you will discuss the message of your paper with your boss and your peers.  Complete legends are essential, otherwise nobody has a chance to understand the exact circumstances under which the data had been gathered.  As long as you cannot convince your boss and your laboratory peers that your paper is worth reading it is very unlikely you will convince anybody else.

Do not be afraid to write too much and in too much detail.  Details that were left out while writing the text are very hard to fit in later.  It is usually much easier to shorten a text than to lengthen it.  You might also want to re-use some paragraphs in another paper.  Most likely you will place the emphasis a little bit differently, which means you will shorten the text differently and you can do so without having to write a new text from scratch if you considered the leeway in the first place.

Self-plagiarization is a misconception.  Your texts are yours.  Use your older texts, take advantage of good phrases and good ideas you have come up in the past, insert them into your new texts and then edit them and reshuffle their order to improve the new text and to adapt it to the current circumstances.  Whenever you write, consider the fact that you may be re-using the texts.

About ernsthkstelzer

Physicist, Scientist, Full Professor (W3) at the Johann Wolfgang Goethe Universität in Frankfurt am Main, Group Leader at EMBL (European Molecular Biology Laboratory) until February 2011, worked at EMBL for almost 28 years, use Mathematica in my research since version 1.0.1. Best known for my work in microscopy, in particular light sheet based fluorescence microscopy. LSFM, SPIM, DSLM, PFM.
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