This blog post is a compilation of information, and my personal experiences on the process of writing a scientific paper. The tips here contained exist only because I think they could be useful, and not because they have been extensively tested by me.

Starting from scratch

At some point after certain amount of work, you may end up with a message to share which is telling something potentially new and interesting. If it makes a full story, which could be potentially interesting for others, then it is likely to be ready. Ideally, at this point you would have some colleges to share it and receive feedback:

  • What do you think about this?
  • What other point of views my be explored?
  • What can be improved?

But this is very unlikely in most situations.

One should decide the paper’s theme (subject) and two or three points the reader should get home.1 If something you write isn’t needed to help the reader understand the theme, then it has to be omitted. Once you open the LaTeX blank .tex document to start your paper, the first thing to write should be the message you want to transmit. This will be a lighthouse for you when lost, and for the collaborators, which are going to be on the same page from the beginning.

I have found that the loss of perspective once you dive into the writing is what results in sentences and paragraphs with zero contribution to the discussion. I plan for my next draft to write down the ideas I want to transmit in each section, and then build the paragraphs from them.

Structure of the paper

Structuring from the beginning the paper will for sure facilitate a lot the process. Structure the sections with bullets, and then the ideas to transmit with dashes. Answering “What did you do?” is the key to finding the structure of a piece 2. Every section of the manuscript needs to support that one fundamental idea.


The introduction may be the most important part, because you have to make the reader want to know the answer of your question.

Of course, this is somhow easy when you are also excited to share your work, when you find it meaningfull. It may be, on the other hand, very difficult when you do not like your research, and you are only doing it as a mean to an end.

A good Introduction should answer the following questions.

  • How did I get to this question?
  • Why is that important?

Remember, while you still have the perspective, use it to define the key ideas to transmit. For example, a regular Introduction could follow this line of thinking:

  1. Why is the field of your work important?: This is normally the opening sentence or paragraph showing what interesting applications have the phenomena your work is framed in. It should be simple, direct, and create curiosity in the reader.
  2. Which is the state of the art?: This introduces the previous work that has been developed in the field, and ends by identifying the problematic.
  3. Which are the tools available to solve this problem?: This is dedicated to present the available tools to tackle the problem, specifying which was selected and justifying why.
  4. Which is the objective?: Clearly state the objective of the work. This usually involves explaining that the selected method will be applied expecting to obtain some result.
  5. How is the publication structured?: Describe what information is presented in each section. It is not necessary to mention the number of the sessions. Something similar to the following example should work: “First are discussed the methods and techniques employed. Then the results are presented. Finally, the work ends with a set of conclusions and further opportunities.”


This section presents the methods selected to solve the problem.


The results sections should show how I structured my work and answered the questions presented in the Introduction.

  • This is what we did, and
  • This is what we learnt.

All sentence which is not contributing to that core message should be removed.

This section is not only to report your results. Its value increases considerably when you are capable to put in the context of the field why are those results important, and how they affect a wider understanding of the topic. Generating new hypothesis and proposing further investigations to carry out is also important.


Finally the Conclusions are a mean to show what does this all means to the story presented in the introduction. However, there are some researchers who prefer to simply summarize the results obtained. I personally prefer the first approach.

Importance of the sections of the paper

  • When people first see your paper, it is the Title what they look at. A good title will attract the attention of the reader, a weak one will kill the interest on keeping reading your paper.
  • The abstract is probably the second most important section to attract the attention of the reader, as it is what we all read after the title.
  • Then, figures are also critical, as is more likely the third element people normally look at. Having a set of figures which to some extent tell the story by themselves is key to a good paper.

Real life case

I started writing my third scientific paper (second in English) on February 17th. It was finally ready after four revisions of my supervisor, and a month of work. It is a relatively small work, but anyway it consumed enormous amounts of my time. Specifically, I spent 48h and 23min of active work during the last month to conclude the submitted manuscript. Further corrections from the referees may require additional time.

It is considerable how the manuscript improved from what it was in the first version and what it is in the last. Based on what I have learned I made some corrections and additions to the post this post.

The greatest learning I had was to realize the importance of perspective (zoom out). Write everything having in mind what its purpose is in the text, and how it relates to previous and forthcoming paragraphs. Writing unintentionally, just following the flow that came to my mind, lead me to produce paragraphs and sentences which supported nothing of my research.

For example, take in consideration the following opening paragraph. This is how it was in the first version

Mono- and bis-(thio)urea chiral catalysts have received strong attention as hydrogen-bonding organocatalysts, being the Takemoto catalyst, the cinchona catalyst, and the Jacobsen catalyst maybe among the most famous. However, chiral aliphatic N,N’-linked oligoureas, a class of helical foldamers previously reported to catalyze enantioselective C-C bond-forming reactions, are increasingly attracting interest as chiral organocatalysts because, on the one hand, they are modular and scalable and, on the other hand, they may retain some key features of enzymes such as high reactivity and stereo-selectivity but also chemo-selectivity and site-selectivity. This is particularly true for synthetic alpha-peptides which were found to be well-suited as chiral catalysts for a broad range of asymmetric transformations.

and this is how it ended

Enantioselective C-C bond forming reactions are of fundamental importance in modern chemistry, and their understanding at the molecular level is key for identifying improvements and new niches in the production of everyday-use materials, cosmetics, drugs, etc. This proves true whether the application is tailored to the pharmaceutical industry where each enantiomer have specific biological functions (for example the (R)- and (S)-Thalidomide), to the production of specific properties in renewable, biomass-sourced, biodegradable, and petroleum-alternative materials (for example polylactides (PLA)), or to any other field.

What is important to notice is that the first version was extremely technical, using lots of jargon, large and complex sentences, boring, and did not showed the importance and possible applications of the work. The correct approach to start the manuscript is by attracting the attention of the reader, and showing why are these results important. Otherwise, everybody will get bored and lost interest in the work.

This is what I refer as perspective, knowing that the first thing to do is show the importance and the work and create curiosity in the reader, after show what has been done regarding the subject, etc. (as described for the Introduction a few sections above).


First, build the lighthouse:

  1. Write down the main idea you want to transmit, this will be the paper’s theme.
  2. Write down two or three points the reader should get home.
  3. Write down the sections, and the main ideas to you want to expose in each of them.

Have in mind that:

  1. Telling a story is more joyful for you and the reader.
  2. The objective is to show what you have found new and compelling.
  3. Do not write defensively, think in the reader and not in the criticism.
  4. You need to explain with your manuscript why your results are interesting, and how they affect a wider understanding of the topic.
  5. Try to reassess the existing literature and consider what can your findings be used for in the future.
  6. Also make sure to consider alternative explanations when pertinent.

Finally, take into account the following rules for improving the writing product:

  • Limit each paragraph to a single message: do not try to fold multiple ideas into a single block of text.
  • Write in short, simply constructed and direct sentences.
  • Know what you are saying, otherwise it will be difficult to comunicate it to others.
  • Avoid a lot of jargon in sentences, try to put your work in simple words.
  • Avoid the use composed sentences, and transitional words like “however” or “thus”. Their use may deviates the reader from the main message.
  • Avoid saying what you will not do. For example, don’t say “We will not consider…”

Other references

  1. Nature’s publication Working Scientist podcast: How to write a top-notch paper.
  2. Nature’s publication Publish like a pro, although this is not that useful.


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