The Science Of Scientific Writing    Set E     Scientific Sections    Methods: Frame of Reference + Elaboration      Methods: Coherence         Exercise 1       Final Page .

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OVERVIEW: The way to well-written science

How to do the Course


PART I: Paragraphs and Sentences

SET A: Paragraphs: The Maps Behind Them

SET B: Paragraphs: Using Maps to Meet Readers' Expectations

SET C: Paragraphs with Something Extra: Points and Tails

SET D: The Generic Section: Expectations and Maps as Blueprints

SET E: Scientific Sections: The Methods and Results

SET F: Scientific Sections: The Discussion

SET G : Scientific Sections: The Introduction

SET H : Sentences

SET I : The Paper as a Whole



PART II: The Paper and its Sections


SET 1: Argument Parts

SET 2: Indicator Words

SET 3: Refining Claims

SET 4: Locating Arguments in Prose

SET 5: Rationale's Essay Planner

SET 6: Evidence in Arguments: Basis Boxes

SET 7: Assessing

SET 8: More on Assessing

SET 9: Analysis Maps

SET 10: Assessing Again

Synthesis 1: Position-Early Paragraphs

Synthesis 2: Position-Final Paragraphs

Synthesis 3: Writing a Discussion I

Synthesis 4: Writing a Discussion II

Materials and Methods (1): Frame of Reference + Elaboration

The Methods section is usually considered the easiest of all to write, and is often the first part taken on by an author. The apparent ease of writing is due, I believe, partly to the fact that its organising principles draw heavily from real-world systems; and partly to the fact that, being the least frequently read of the sections, there has been less "selection pressure" to make the Methods more generally intelligible.


The Methods does not generally have any Frame of Reference paragraph/s (but it could do with some!)

With regards to the basic two-part structure expected of a generic section (Frame of Reference (FOR) + Elaboration) the Methods section is the most atypical in that it rarely has any introductory paragraphs. To the extent that the role of the FOR is to provide a map of what is to follow, this function is accomplished to a degree by the heavy use of sub-headings in the Methods - they are used here more frequently than in any other section. Thus a reader can quickly scan the sub-headings, and if they are suitably descriptive, and the reader reasonably acquainted with the field, he or she should be able to get some idea of the section's overall plan.

The need for an FOR is also reduced by the fact that as noted above, the Methods usually adheres to real-world frameworks, and the sequence of its sub-sections typically follows a natural chrono/logical order (explained in more detail below). Thus one could even imagine that all Methods sections have an implied FOR paragraph, telling us, as it were, that the steps described are ordered in the sequence they were performed, and that they involve a gradual shift from the general (e.g. the choice of a study site) to the most particular (e.g. how the data acquired at the study site were analysed).

The main other role of the FOR part of a section (in a multi-section text) is to provive a conceptual bridge to any previous section/s. For the Methods this is a function that is often sadly lacking by virtue of there rarely being any FOR paragraph/s. There is often an enormous conceptual "gap" between the superficial reference to the overall experimental approach in the Introduction (if any, it will usually be in the final paragraph) and the highly sophisticated accounts found in the Methods. Non-specialist readers will often be mystified as to how the multitude of steps described in the Methods are related to what was mentioned in the Introduction. This is an obvious negative consequence of the compartmentalisation of the scientific paper: The weakness of the conceptual connectivity is not as explicitly obvious as it would be if the paper were written in a linear fashion.


How to bridge the Introduction and Methods

The conceptual "bridges" needed between the Introduction and the Methods can be provided in various ways:

(1) Devoting one or more paragraphs in the Methods to addressing the rationale of the methodology. In some disciplines, especially those more statistically inclined (e.g. ecology, sociology), there is a stronger tradition of including a Methods sub-section called "Experimental Design" or similar; it would be wonderful for science if this strategy were more universally employed.

(2) Adding introductory sentences to individual paragraphs (in the Methods) that clearly link back to Methods-related content in the Introduction

(3) Bulking up the description of the experimental approach in the Introduction. This was a favoured approach of mine when writing papers, for example, see how the following final paragraph of the Introduction of this paper lays the groundwork for a more detailed description in the Methods:

In this study, we investigate the response of the vacuole system of P. tinctorius to GTPgS and GDPbS, Brefeldin A (BFA), and aluminium fluoride. These compounds are well known for their ability to alter the vesiculation/tubulation equilibrium of animal cell endomembrane compartments [Gilman, 1987; Klausner et al., 1992; Robinson and Kreis, 1992; Takei et al., 1995]. By using these perturbing agents, and monitoring their effects on vacuolar behaviour in living hyphae by use of fluorescein-based dyes, we aim to determine if vacuolar tubule formation requires GTP-binding proteins, and if so, to gain some insight as to which class or classes are involved.


The role of a paragraph's Framing Sentence is often fulfiiled by a sub-heading

As mentioned above, sub-headings are used more heavily in the Methods than anywhere else, and they often precede a single paragraph and fulfil the role of a Framing Sentence for the paragraph, e.g. as shown below(from this paper),

Incremental place-learning task. Rats were trained to a constant platform location with eight trials a day, ca. 10 min (±3 min) apart, for 5 d (i.e., 40 trials altogether). Trials 2 and 6 of each day were run as rewarded probe trials. Start positions changed between trials, to discourage egocentric strategies. An additional rewarded probe trial was run on day 6, to assess incrementally acquired memory unconfounded by within-day learning.

If a sub-section has several paragraphs, then it is probably advantageous to provide a one-sentence paragraph that provides a guide to the entire sub-section; at the very least the sub-section heading should allude to each of the methods mentioned in the paragraphs: e.g.

Culturing, Dye Loading, and Mounting of Hyphae


What content should (and should not) be elaborated

Deciding the appropriateness (or otherwise) of content for the Methods section is usually not hard for young scientists and I will only make some brief comments here about some more difficult decisions.

(1) What level of detail is required?

It is often said that the role of the Methods section is to allow someone to repeat your experiment, and this is true, but that "someone" is expected to already have almost the same own familiarity with the methodology as you do, or access to someone who does. As such, you do not need to include details that a competent experimenter in the field would be assumed to know. Compare these two versions of the same report (from this site)

"Each plate was placed on a turntable and streaked at opposing angles with fresh overnight E. coli culture using an inoculating loop. The bacteria were then incubated at 37 C for 24 hr."

"Each plate was streaked with fresh overnight E. coli culture and incubated at 37 C for 24 hr."

For the readerships of many journals, the second version provides sufficient detail.

Given that very few if any of your readers are likely to actually repeat your experiments, the more important roles of the Methods are:

  • to explain the rationale for your approach, looking back to the Introduction (as explained in the previous sub-section of this page)
  • to lay the groundwork for understanding the Results

Therefore, rather than including every detail (the what), it is much more important to focus on including some of the gist (the why).

(2) Can I include any Results?

Simple answer: yes. One of the motivations for the evolution of separate Methods and Results sections is to allow readers to focus more easily on what they generally consider to be more important, i.e. the Results. Taking this a bit further, readers want to focus more on those results that are more, rather than, less "important". You can help your readers to do this in various ways, e.g. by strategic structuring of the Results section, or by shifting some less important results out of Results section (e.g. into an appendix) or in the case of what could be categorised as "preliminary results" into the Methods section itself. In the later case, these are generally the results of early experiments that led to some refinement of the methodology, or confirmation of its validity.