No matter what type of paper you write, it needs to have a clear thread through it, and sections need to clearly link. One of the challenges is that writing is linear – it has a start point and an end point. By contrast, much academic content is complex – more like a website, where things are related in many different directions. The challenge of writing is to turn the multi-facetted nature of the content (where everything is related and linked to everything else, like the internet) into a simple, one-directional argument.
Some general principles hold. At the most general level, it’s a good idea to start your paper broad, have specific aims at the end of your introduction, and then have a detailed ‘meaty’ part in the middle. Towards the end, you need to get back to the big picture, preferably the same context that you started with. The other general principle is that you must not assume background knowledge beyond the obvious in your discipline. In other words, your chain of argument must not leave out steps that are actually important for the reader. Ask yourself how you would need to explain the general gist of your paper to your friend who studies a different discipline, or to your aunt. A good structure tends to make sense even to ‘uninformed’ people. If they don’t get the basic structure you’re proposing, it’s likely that you have left out important steps in your logic.
I distinguish between a few different types of papers. Standard empirical papers tend to follow a standard structure: introduction, methods, results, discussion, conclusion, acknowledgements, references. Sub-headings are common (and useful) within methods and discussion, in particular, but sometimes also in the results section.
Essay papers are fundamentally different. They have no set rules, which makes it even more important that they follow a logical, and clearly understandable thread. Often, it’s a good idea to outline what this thread is specifically at the end of the Introduction. Also, even though it’s an essay, sub-headings can be immensely useful. Check your subheadings – if, without any further information, they tell a logical story, you’ve probably worked out a useful structure.
Review papers are different again. Again, there is a lot of flexibility for how exactly those are prepared, and it depends a lot on which journal you’re writing for. It’s worth noting that in ecology and conservation science, journals are increasingly keen on quantitative reviews or meta-analyses (a statistical approach to extract patterns out of multiple case studies).
No matter which kind of paper you write, headings are critically important. Typically, you will want to use 2-3 heading levels. You need to clearly differentiate these in style, so that it’s easy for readers to see what you’re doing. E.g. use a bold 15 point font for main headings, a bold 13 point font for subheadings, and an italics 12 point font sub-sub-headings. It’s a good idea to match the journal style.
See also:
- What type of paper are you planning to write?
- What is a logical sequence of headings?
Writing a journal article 
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