I found the below figure which I do not know the Author which I think can be useful to understand both what it is implied in writing a scientific paper and what is a theory, with respect to more simple analysis of data (or models, BTW). The first four arrangements of the data have some interest but, they do not capture much our interest. To do a gory example, is like to take an animal or a tree, separate them in parts and analyzing them from the point of view of the atoms it is made. This information is real but it does not say anything crucial about the living being. The being important think is realized when all the material is put together again (it would be great if the separation operation would be reversible) and it is analyzed in its “holistic” form and function.
So, it is for the topic of a paper. Usually we have a problem and we dissect it using a “reductionist” approach, but we are not able to put again the whole together and make sense of it. The reductionist action is usually not trivial at all, as the figure could, on the contrary, suggest, and the Authors are usually exhausted after having applied the techniques for doing it which could be experimentally and/or mathematically very complex. But writing the paper needs the vision of the whole, the story to tell, and the discovery, in the rough matter, of the sense. It is not a bottom-up action but more a top-down one, where hypothesis and deduction comes before than induction.