Basic elements of scientific papers

The basic elements of virtually any scientific paper are as follows (Introduction, Methods and Materials, Results, and Discussion and Summary):

• Introduction:  This section always appears in a paper. At the beginning of the Introduction is where you motivate your work (ie; why should anyone care?).  Start from a broad motivation, and move to focus in on the particular motivation of your work.  For instance, let’s assume I was writing an Ebola paper that describes a compartmental modelling analysis I did to assess the effects of isolation and/or quarantine on the spread of the disease:
  1. At the very beginning of the introduction I’d start off talking about the number of people killed in past outbreaks, and the wide geographic spread of outbreak locations, and the ever present risk that Ebola cases can be imported to other areas of the world due to modern air travel (the point being that no matter where you live, you should care about Ebola).  Then I’d talk about the high mortality of the disease. These would be among the first few sentences in pretty much any paper written about Ebola.
  2. For my particular paper, I’d then mention that the lack of current treatment options (like vaccines or medications) leave better hygiene, quarantine, and isolation as the only options available to slow the spread of disease.

  After motivating the project, you then move on to describing the objective of the paper. This is where you present your research question. And where you give a very short overview of what you did in your analysis, and how it advances the body of work in the published literature on the subject. In the Ebola paper case, I would add some sentences saying that mathematical models are being increasingly used to assess the efficacy of disease intervention strategies (and I would cite a few well known seminal publications on that topic).  Then I would state that in this work we use a mathematical model to assess the efficacy of isolation and quarantine, and I would state that no one has ever done that before for Ebola (as of August 2014, this was true).  In this part of the paper it is very important to state what is new and novel about your work.

  Once you have described your motivation and objective, it is a good idea to end the Introduction with a sentence or two that gives a road map for what the reader should expect in the following sections.  Something like “In the following section, we will describe the data sources and mathematical and statistical modelling methodologies used in these studies, followed by a presentation of results and discussion” (this is assuming your analysis uses data, a mathematical model, and statistical methods).

• Methods and Materials:  This section always appears in a paper. if you are using data in your analysis, the first subsection in this section should be Data.  The Data section should thoroughly describe your sources of data.  If you collected it, what were your laboratory or field protocols?  If it is time series data, what time steps are used?  What, precisely, is the data measuring?  If you got the data online, give a reference to the source.  Even if you didn’t collect the data, you need to describe the collection procedures of the person or group who did collect the data.
  If you are using a mathematical or computational model, the next subsection should be Model.  In this subsection, you will describe what kind of model you are using, and give citations to relevant related publications in the field.  You will describe what is new and interesting about your model (if relevant… sometimes it is the data that are new and interesting, and what is novel is applying an old model to new data).  Here you will give the model equations and compartmental flow diagram (if using a compartmental model), or other details about your mathematical or computational model.  You need to give enough details that anyone could reproduce your work based on this information.If you are using statistical methods that are fancier than your usual statistical tests based on Student T, Z scores, Spearman rho, etc etc, you need to have a subsection under Methods and Materials called Statistical Methods.  This subsection would be appropriate, for instance, if the statistical methods you use are so esoteric that they are either new, or very rarely used in your field.

• Results: This section always appears in a paper. Here is where, without discussion, you give the results of your paper, often in tables and figures, and accompanied text.  Do not discuss the results here!

• Discussion: This section always appears in a paper. Never put results that you haven’t discussed in the Results section here…. they should be in the Results section!  In the Discussion section, you talk about notable things revealed by your results and how this fits in with (or contradicts) the published literature.

• Summary:  This section is sometimes called Conclusions, and sometimes is lumped in with Discussion (and called Discussion and Summary).  It depends on the journal.  If there is a separate Summary section, you start off with a little paragraph describing what you presented in the paper, and why it is new and novel.  In the summary you detail limitations of your study, possible future work, etc, and usually end with a “feel good” sentence about the utility of studies like yours.

Lacum et al rubric for identifying seven key elements of scientific papers

In 2014, Lacum et al published a study where they trained students to look for seven key elements when reading or writing papers.  As I discussed above and in this post, where I describe what sections need to be in a scientific paper, these elements are integral in the sections of a paper:

1. Motive: Statement indicating why the research was done (e.g., a gap in knowledge, contradictory results). The motive leads to the objective.  The motive should appear in the Abstract and Introduction.
2. Objective: Statement about what the authors want to know. The objective may be formulated as a research question, a research aim, or a hypothesis that needs to be tested.  The objective should appear in the Abstract and Introduction.
3. Main conclusion: Statement about the main outcome of the research. The main conclusion is closely connected to the objective. It answers the research question, it says whether the research aim was achieved, or it states whether the hypothesis was supported by evidence. The main conclusion will lead to an implication.  The main conclusion is often the last sentence in the Abstract, and is of course also described in the Discussion and Summary.
4. Implication: Statements indicating the consequences of the research. This can be a recommendation, a statement about the applicability of the results (in the scientific community or society), or a suggestion for future research. This may appear in the Abstract, and certainly appears in the Discussion and Summary.
5. Support: The statements the authors use to justify their main conclusion. These statements can be based on their own data (or their interpretation) or can be statements from the literature (references).
6. Counterargument: Statements that weaken or discredit the main conclusion. For example, possible methodological flaws, anomalous data, results that contradict previous studies, or alternative explanations. Counterarguments are sometimes presented as limitations. They are placed in the Discussion and Summary.
7. Refutation: Statements that weaken or refute a counter-argument.  Refutation appears in the Discussion and Summary