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Writing the Methods Section

Writing the Methods Section

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!

Adina Pusok. Postdoctoral Researcher in the Department of Earth Sciences, University of Oxford, UK.

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.

Proposed structure:

  1. Brief outline – A general paragraph describing the study design and the main steps taken to approach the scientific question posed in the Introduction.
  2. 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
        • 2.2.1.1 Viscous deformation
        • 2.2.1.2 Plastic deformation
        • 2.2.1.3 Elastic deformation
      • 2.2.2 Phase transformations
      • 2.2.3 Water migration in the models
    • Figures and tables:
      • Table of parameters – for quick definition of parameters used in equations.
  3. 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.
  4. 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.
  5. 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):

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

Let’s talk about plagiarism

Let’s talk about plagiarism

Hey you! Do you have 5 minutes to talk about plagiarism?
Have you ever wondered if some parts of a thesis that you have supervised are simply a copy-paste from another thesis or article? This week, an anonymous guest author will tell us about their personal experience with plagiarism in science and what can be done against it.

Granted, it is not the most fascinating topic. Until recently, I really thought there was nothing to say about it. Everybody agrees that plagiarism is bad, and one shouldn’t do it, right? Plagiarism is just for a pair of lazy bachelor students or maybe one or two entitled old professors who believe they are untouchable, right? Right?! Oh boy, was I naive!

For me, it all started with reading a few words that do ring a bell on a master student thesis that I had co-supervised. After some more investigation, I realized that this student did indeed copy and paste sentences and even paragraphs from my PhD thesis, as well as from other articles. He did also plagiarize in former assignments and in a scientific article he published in a journal at the beginning of the year. Uh uh.  At this point, the student had already defended his thesis and just got his master degree validated. In the process, the thesis had been evaluated by two independent reviewers and also had been read by my two PhD advisors. Nobody suspected anything. And this happened at THE top Earth science research institution of a country which is renowned for the quality of its research. No problem, I think, I contact the co-supervisor and the director of studies. For sure they’ll know what to do. Hahaha. I spare you the details, but, to sum it up, the master degree had already been awarded, so there was no way whatsoever to change anything about it.

I didn’t make friends this past few weeks by insisting and playing the self-righteous scientist card. The student still got his master and will soon be enrolled in the PhD program of the same institution. However, my complaining seems to have had some effect. In the institution in question, they will buy the rights to a plagiarism scanner software and create a special commission to deal with plagiarism cases. From now on, master students will have to include a declaration of originality for their master theses, and they will have a course on research integrity. If the same situation arises, there will be official tools to deal with it, and hopefully the education the students will receive will help prevent plagiarism.

So yes, sometimes it’s worth it to be (a bit) annoying. Here are a few other things you might want to consider in order to avoid this kind of situation.

Plagiarism and “self-plagiarism” (also called text recycling) are not allowed by most journals, however, there is quite a large part of the scientific community that does not see the problem with self-plagiarism and does it regularly in articles. Some copy whole paragraphs from former articles of theirs and, sometimes, these articles pass the plagiarism scan that journals generally do. So it is really worth it to scan for plagiarism every paper you receive to review. That’s how I gave my fastest peer review ever: 5 minutes to scan the article, 5 min to realize that a whole section was a copy and paste from another article, and 5 min to write a rejection message.

Check every thesis, every draft and every paper you receive with a plagiarism software. You might have some surprises. If you do so, you’re making students/co-authors a favour. Had I done that check with my student prior to his thesis submission, he could have had the chance to make things right, avoided cheating on an exam, and got his master degree fair and square. Instead of this, he has to walk around with a master diploma he didn’t really earn. Not a good start in one’s professional life. Same with co-authors:  if you catch their plagiarism, you save all your team the embarrassment of getting your paper rejected by a journal because of this.

It might be a good idea to check the policy of your institution on plagiarism before you’re faced with the situation I described earlier. If there is nothing planned, urge people in charge to set up some procedure. You don’t want to be in the situation of catching a student after his master has been validated and not being able to do anything about it.

Finally, to people who practice text recycling: if you want to copy a sentence from another article because it is the best sentence to describe your thoughts… Why not putting quotes? If you don’t, you’re just being dishonest.

 

How the EGU works: Experiences as GD Division President

How the EGU works: Experiences as GD Division President

In a new regular feature, Paul Tackley,  president of the EGU geodynamics division, writes about his role as a president, and gives us an insider’s view on how EGU works and is preparing for the future. 

Paul Tackley. Professor at ETH Zürich and EGU geodynamics division president. Pictured here giving an important scientific talk, or maybe at karaoke. Your pick.

Stepping into the role of GD Division President has given me a big learning experience about how the European Geosciences Union is run and about how members are represented and can participate. Here I convey some impressions, give a quick overview of how EGU functions and the role of division presidents, and mention a few other activities you may not be aware of.

Firstly, I was impressed just how much a bottom-up organisation the EGU is – how it is run by members for the benefit of members. EGU employs only 7 full-time staff – very few compared to the 140+ employed by the American Geophysical Union! Thus, most of the organisation is run my volunteers, including the big jobs of President, Vice-President, Treasurer and General Secretary, and also the presidents of the 22 scientific divisions and members of eight committees. Of course, the fact that so few staff are needed is helped by the fact that Copernicus (the company) deals with publishing all the journals and organising the General Assembly (GA), and Copernicus has 54 employees.

Secondly, I now appreciate that EGU does a lot more beyond organising the General Assembly and publishing 18 open access journals. In particular, EGU is active in the areas of Education and Outreach, and supports various Topical Events, with each area coordinated by a committee. Additionally, a Diversity and Equality working group was recently set up. I encourage you to read more about these various activities on EGU’s web site.

What must a division president do?  The main tasks are to organise the division’s scientific programme at the General Assembly, and to attend three EGU Council + Programme Committee meetings per year: short ones at the General Assembly, and longer (2-3 days) ones in October near Munich, and in January somewhere warm (such as Nice or Cascais). Practically, this involves sitting in a darkened room for 2-3 days with a lot of other people (there are many other members in addition to the division presidents, including early career scientists) listening to information of variable interest level and discussing and making decisions (voting) when necessary. The EGU Council discusses the full range of EGU activities, so meetings consist of a series of reports: from the president, the treasurer, the various committees, the ECS representative, etc., often with much time spent discussing and voting on new points and developments that arise. Programme Committee meetings are focussed on the General Assembly, both discussing general issues and accomplishing the specific tasks of finalising the list of sessions (October meeting) and the session schedule (January meeting). Throughout all these meetings, I have found the council members to be very collegial and constructive in trying to do what is best for improving EGU activities and making optimal arrangements for the General Assembly (although of course, opinions about what is best can vary). Additionally, Copernicus is continually improving their online tools to make scheduling easier.

The President Alberto Montanari, Programme Committee Chair Susanne Buiter and Copernicus Managing Director Martin Rasmussen, celebrating the EGU General Assembly.

I am happy that there are several other people actively taking care of various tasks in the GD Division. Division officers stimulate sessions in their respective areas of the GA programme and judge the Outstanding Early Career Scientist Award nominations, while judging of the OSPP (Outstanding Student Poster and Pico) awards is organised by an Early Career Scientist (now Maelis Arnould). Our Early Career Scientists are incredibly active, maintaining this blog and the Facebook page, and organising social events at the GA. Finally, the Medal committee decides the winner of the Augustus Love Medal.

Changes are ongoing at EGU! In a multi-year process the finances are being moved from France to Germany, a complicated process as described by our Treasurer at the GA Plenary session. Moving the EGU office (where the 7 people work) from a confined space on the campus of Ludwig Maximilian University of Munich to a much larger modern office premises is happening around now and will allow some expansion of the staff and a suitable space to greet visitors. In the longer term, it may be necessary to move the location of the General Assembly from Vienna due to the ever-increasing number of attendees!

To conclude, EGU is our organisation and we can contribute to the running of it and the decision-making process, so I encourage you to get involved and to make your views about possible future improvements or other issues known to your representative (i.e. me, or our Early Career Scientist representative Nicholas Schliffke). And if anyone wants to take over as the next GD Division President, (self-)nominations can be submitted starting in September with the vote coming in November!

Programme Committee of EGU, which includes its chair, all the division presidents, the executive board, key people from Copernicus and Programme Committee Officers including the ECS representative and OSPP coordinator.

Conferences: Secret PhD Drivers

Conferences: Secret PhD Drivers

Conferences are an integral part of a PhD. They are the forum for spreading the word about the newest science and developing professional relationships. But as a PhD student they are more likely to be a source of palpitations and sweaty palms. This week Kiran Chotalia writes about her personal experience on conferences, and lessons learnt over the years.

Kiran Chotalia. PhD Student at Dept. of Earth Sciences, University College London, UK.

My PhD is a part of the Deep Volatiles Consortium and a bunch of us started on our pursuit of that floppy hat together. Our first conference adventure was an introduction to the consortium at the University of Oxford, where the new students were to present on themselves and their projects for a whole terrifying two minutes. At this stage, we had only been scientists in training for a few weeks and the thought of getting up in front of a room of established experts was scary, to say the least. Lesson #1: If it’s not a little bit scary, is it even worth doing? It means we care and we want to do the best we can. A healthy dose of fear can push us to work harder and polish our skills, making us better presenters. Overcoming the fear of these new situations takes up a lot of your energy. But it always helps to practice. In particular, I’ve always been encouraged to participate in presentation (poster or oral) competitions. Knowing that you’re going to be judged on your work and presentation skills encourages you to prepare. And this preparation has always helped to calm my nerves to the point where I’m now at the stage I can enjoy presenting a poster.

Regular work goals that crop up in other professions are often absent, especially when we’re starting out.  The build-up to a conference acts as a good focus to push for results and some first pass interpretations. At the conference itself, it makes sure people come to see your poster and you can start to get your face out there in your field. Lesson #2: Sign up for presentation competitions. AGU’s Outstanding Student Presentation Award (OSPA) and EGU’s Outstanding Student PICO and Poster (OSPP) awards are well established. At smaller conferences, it’s always worth asking if a competition is taking place as, speaking from experience, they can be easily missed. They also give you a good excuse to practice with your research group in preparation, providing the key component of improving your presentation skills: feedback. Lesson #3: Ask for feedback, not just on your science but your presenting too. If you’re presenting to people not in your field, practice with office mates that have no idea what you get up to. By practicing, you can begin to find your style of presenting and the best way to convey your science.

Me, (awkwardly) presenting my first poster at the Workshop on the Origin of Plate Tectonics, Locarno.

Sometimes, you’ll be going to conferences not only with your fellow PhD students, but also more senior members. They can introduce you to their friends and colleagues, extending your network, more often than not, when you are socialising over dinner, after the main working day. Lesson #4: Keep your ear to the ground. These events provide a great opportunity to let people know you are on the hunt for a job and hear about positions that might be right for you. At AGU 2018, I became the proud owner of a ‘Job Seeker’ badge, provided by the Careers Centre. It acted as a great way to segue from general job chat into potential leads. A memento that I’ll be hanging on to and dusting off for conferences to come!

One of the biggest changes to my conferencing cycle occurred last year after attending two meetings: CIDER and YoungCEED. Both were workshops geared towards learning and research, with CIDER lasting four weeks and YoungCEED lasting a week. Lesson #5: Attend research specific meetings when the opportunity arises. Even if they don’t seem to align with your research interests from the outset, they are incredible learning opportunities and a great way to expand your research horizons. By attending these meetings, the dynamic of my first conference after them shifted. There was a focus on catching up with the collective work started earlier in the year. Whilst the pace was the most exhausting I’ve experienced thus far, it was also the most rewarding.

Between all the learning and networking, faces start to become familiar. Before you know it, these faces become colleagues and colleagues quickly become friends. In our line of work, our friends are spread over continents, moving from institution to institution. They tend to offer the only opportunity to be in the same place at the same time. This also results in completely losing track of time and catching up into the early hours of the morning, so the next lesson is more subjective. Lesson #6: Know your limits. Some can stay out until 4am and rock up at the 8.30am talk. I wish I was one of these people but I have a hard time keeping my eyes open past 12.30am. Whatever works for you!

Me, presenting my most recent poster at AGU 2018 with my job seeker badge!

After the conference finishes, you are often in a place that you’ve never visited before. Lesson #7: Have a break. If you can, even an extra day or two of being a tourist is great treat after a hectic build-up as well as the conference itself. If staying for a mini holiday post-conference is not an option, make sure you take some time when you get home to rest and readjust before you get back to work and start planning for the next one.

Last but not least, Lesson #8: Don’t forget to have fun. The stress surrounding conferences and your PhD in general can at times be all consuming. Remember to enjoy the small victories of finally getting a code to run or finding time on the SEM to analyse your samples. At conferences, enjoy being surrounding scientists that are just starting out and the seasoned professionals with a back catalogue of interesting stories. And if you’re lucky enough to be at a conference somewhere sunny, make sure to get outside during the breaks and free time to soak up some vitamin D!

The Shanghai skyline after the Sino-UK Deep Volatiles Annual Meeting at Nanjing University.