An important part of science is to share your results in the form of papers. Perhaps, even more important is to make those results understandable and reproducible in the Methods section. This week, Adina E. Pusok, Postdoctoral Researcher at the Department of Earth Sciences, University of Oxford, shares some very helpful tips for writing the Methods in a concise, efficient, and complete way. Writing up the methods should be no trip to fantasy land!
For my occasional contribution to the Geodynamics blog, I return with (what I think) another essential topic from The Starter Pack for Early Career Geodynamicists (see end of blog post): how to write the methods section in your thesis, report or publication. Or using the original title: “Writing up the methods should be no trip to fantasy land”. Don’t get me wrong, I love the fantasy genre, but out of an entire scientific manuscript that pushes the boundaries of knowledge (with additional implications and/or speculations), the methods section should be plain and simple, objective and logically described – “just as it is”.
The motivation for this post came some months ago when I was reviewing two articles within a short time interval from each other, and I felt that some of my comments repeated – incomplete methods sections, assumptions let to be inferred by the reader, and which ultimately made assessment of the results more difficult. But I also consider it is not ok to write harsh reviews back (for these reasons), since again, there is little formal training for Early Career Scientists (ECS) on how to write scientific papers. Moreover, even when there is such formal training on academic writing, it is often generalized for all scientific disciplines, ignoring some important field-specific elements. For example, a medical trial methods section will look different from an astrophysics methods section, and within Earth Sciences, the methods section for a laboratory experiment on deformation of olivine will contain different things compared to a systematic study of numerical simulations of subduction dynamics.
A common approach by most students (especially first time) is to dump everything on paper and then hope it represents a complete collection of methods. However, with increasing complexity of studies, this collection of methods has neither heads nor tails, and is prone to errors. Such pitfalls can make the manuscript cumbersome to read or even question the validity of the research. Generally, journals do have guidelines on how the methods should be formatted, how many words, but not necessarily what to contain because it varies from field to field. I believe there should be a more systematic approach to it. So in this post, I aim at describing some aspects of the Methods section, and then propose a structure that (mostly) fits the general Geodynamics studies.
1. The scientific Methods section
The Methods section is considered one of the most important parts of any scientific manuscript (Kallet, 2004). A good Methods section allows other scientists to verify results and conclusions, understand whether the design of the experiment is relevant for the scientific question (validity), and to build on the work presented (reproducibility) by assessing alternative methods that might produce differing results.
Thus, the Methods section has one major goal: to verify the experiment layout and reproduce results.
It is also the first section to be written in a manuscript because it sets the stage for the results and conclusions presented. So, what exactly do you need to include when writing your Methods section? The title by T.M. Annesley (2010) puts it perfectly into words: “Who, what, when, where, how, and why: The ingredients in the recipe for a successful methods section”.
- Who performed the experiment?
- What was done to answer the research question?
- When and where was the experiment undertaken?
- How was the experiment done, and how were the results analyzed?
- Why were specific procedures chosen?
Across sciences, the Methods section should contain detailed information on the research design, participants, equipment, materials, variables, and actions taken by the participants. However, what that detailed information consists of, depends on each field.
2. The Methods section for numerical modeling in Geodynamics
I propose below a structure for the Methods section intended for numerical simulations studies in Geodynamics. I want to mention that this structure is meant as a suggestion, especially for ECS, and can be adapted for every individual and study. Geodynamics studies may have different aspects: a data component (collection, post-processing), a theoretical (mathematical and physical) framework, a numerical framework (computational) and an analog component (laboratory experiments). The majority of studies have 1-2 of these components, while few will have all of them. In this post, I will focus primarily on studies that use numerical simulations to address a question about the solid earth, thus having primarily a theoretical and numerical component.
Before I start, I think a great Methods section is like a cake recipe in which your baked cake looks just like the one in the photo. All the ingredients and the baking steps need to be explained precisely and clearly in order to be reproduced. We should aim at writing the Methods with this in mind: if someone were ‘to bake’ (reproduce) my study, could they succeed based on the instructions I provided? There are many ways how to write your Methods, my way is to break it into logical sections, going from theoretical elements to numerical ones.
- Brief outline – A general paragraph describing the study design and the main steps taken to approach the scientific question posed in the Introduction.
- Theoretical framework – Any numerical simulation is based on some mathematical and physical concepts, so it’s logical to start from here. And from the most important to the least important.
- 2.1 Governing equations – Section describing the conservation of mass, momentum, energy.
- 2.2 Constitutive equations – Section describing all the other elements entering the conservation equations above such as: rheology (deformation mechanisms), equation of state, phase transformations, etc. Each of these topics can be explained separately in subsections. For example,
- 2.2.1 Rheology
- 220.127.116.11 Viscous deformation
- 18.104.22.168 Plastic deformation
- 22.214.171.124 Elastic deformation
- 2.2.2 Phase transformations
- 2.2.3 Water migration in the models
- 2.2.1 Rheology
- Figures and tables:
- Table of parameters – for quick definition of parameters used in equations.
- Computational framework – Section explaining how the theory (Section 2) is solved on the computer.
- 3.1 Numerical methods – code details, discretization methods, programming language, solvers, software libraries used, etc. If you are using a community code, these details should be provided in previous publications.
- 3.2 Model setup – Section describing the layout of the current experiment.
- 3.2.1 Details: model geometry, resolution (numerical and physical), parameters, initial and boundary conditions, details on rheological parameters (constitutive equations), etc.
- 3.2.2 Must motivate the choice of parameters – why is it relevant to address the scientific questions?
- Figures and tables:
- Table of parameter values, rheological flow laws used.
- Table with all model details (to reduce text).
- Figure illustrating the model geometry, initial and boundary conditions.
- *NOTE: If you are testing/implementing a new feature in the code, you should allocate a new section for it. Also, spend more effort to explain it into details. Do not expect many people to know about it.
- Study design – Section describing the layout of the study.
- 4.1 What is being tested/varied? How many simulations were performed (model and parameter space)? Why perform those simulations/vary those parameters?
- 4.2 Code and Data availability – code availability, input files or other data necessary to reproduce the simulation results (i.e., installation guides). Many journals today only accept for publication studies in which data and code availability is declared in standard form (i.e., AGU journals). Some other questions to answer here: where were the simulations performed? how many cores? can I reproduce data on laptop/desktop or do I need access to a cluster?
- Figures and tables:
- Simulations table – indicating all simulations that were run and which parameters were varied. When the number of simulations is high (i.e., Monte-Carlo sampling) you should still indicate which parameters were varied and the total number of simulations.
- Analysis of numerical data – details on visualization/post-processing techniques, and describe how the data will be presented in the results section. This is a step generally ignored, but be open about it: “visualization was performed in paraview/matlab, and post-processing scripts were developed in python/matlab/unicorn language by the author”. If your post-processing methods are more complex, give more details on that too (i.e., statistical methods used for data analysis).
Before you think you’ve finished the Methods section, go over your assumptions, and make sure you’ve explained them clearly! Geodynamics is a field in which you take a complex system (Earth or other planetary body) and simplify it to a level that we can extract some understanding about it. And in doing so, we rely on a physically consistent set of assumptions. It is important to bear in mind that this set of assumptions may not always be obvious to the audience. If your reviewers have questions about your methods and interpretation of results (that you think is obvious), it means that something was not clearly explained. Be pre-emptive and state your assumptions. As long as they are explicit and consistent, the reviewers and readers will find less flaws about your study. Why that choice of parameters? Why did you do it that way?
3. A few other things…
It’s good practice to write a complete Methods section for every manuscript, such as one following the structure above. However, some journals will ask for a short version (1-2 paragraphs) to be included in the manuscript and have the complete Methods section in a separate resource (i.e, Supplementary Data, Supporting information, repository) such that it’s made available to the community. For some other journals, it will be difficult to find a balance between completeness (sufficient details to allow replication and validity verification) and conciseness (follow the guidelines by journals regarding word count limits).
To master the writing of the Methods section, it is important to look at other examples with similar scope and aims (especially the ones you understood clearly and completely). It is also a good idea to keep notes and actually start writing up your equations, model setup, and parameters as the study progresses (such as the mandatory lab notebook).
Finally, some tips on the style of writing of the Methods section:
- be clear, direct, and precise.
- be complete, yet concise, to make life easy for the reader.
- write in the past tense.
- but use the present tense to describe how the data is presented in the paper.
- may use both active/passive voice.
- may use jargon more liberally.
- cite references for commonly used methods.
- have a structure and split into smaller sections according to topic.
- material in each section should be organized by topic from most to least important.
- use figures, tables and flow diagrams where possible to simplify the explanation of methods.
The Starter Pack for Early Career Geodynamicists
In the interest of not letting the dust accumulate, the growing collection of useful Geodynamics ECS posts (from/for the community):
- Writing your own press release
- Software development guidelines
- https://blogs.egu.eu/divisions/gd/2018/12/05/get-conference-ready/ (collection)
- Peer-review process
- Oral and poster presentations
- Work-life balance
- Scientific color maps
References: Kallet R.H. (2004) How to write the methods section of a research paper, Respir Care. 49(10):1229-32. https://www.ncbi.nlm.nih.gov/pubmed/15447808 Annesley, T.M. (2010) Who, what, when, where, how, and why: the ingredients in the recipe for a successful Methods section, Clin Chem. 56(6):897-901, doi: 10.1373/clinchem.2010.146589, https://www.ncbi.nlm.nih.gov/pubmed/20378765