Writing Materials & Methods

Previously, we have covered writing a paper as aformulae, theintroductionand thediscussion. There’s no real reason why I haven’t covered Materials & Methods or the Results sections, other than they tend to be easier than the rest. Here I am going to share some ideas to get you started on your Materials and Methods section. 

You should start writing this section in your proposal, and you may have to alter parts of it when turning it into your thesis later (if you change your methods). For most people, it’s a relatively simple exercise, but here are some pointers to get you started.

The Materials and Methods section should be citation dense, especially if you have used standard methods that have been written up elsewhere. If there are different methods, you should also explain why you used one over the other, as reviewers or examiners may require this. 

If you are introducing new methodologies, then you can expect to write a lot in this section about exactly how this was done, as well as the background to the reasons why the new approach to the methodology was taken.

Your aim is to produce a coherent methodology that anyone in the next 200 years can pick up and follow in order to replicate your study. 

Sections or subheadings

As ever, I’m going to recommend inserting section headers into your Materials and Methods to help you break it up into bite sized chunks. These are principally for the reader, but will also make your job easier.

Study organism or study system

Having already written the introduction (see here), you will know that there isn’t too much space to write a lot of information about your study organism. However, often there is important background information that is needed on the species, which would be distracting or lose the flow of the introduction. By having a ‘Study Organism’ section at the start of your Materials and Methods, you can add in all relevant information in a paragraph or two. 

For example, if you are working on African clawed frogs,Xenopus laevis, this would be the section where you can explain their distribution, that they are principally aquatic, or that they are invasive on four continents. You probably won’t need all of these points, but just the aspects of this species’ biology that is relevant to your study. You should make sure you know whether or not the journal requires the taxonomic authority. If you are not sure, include it now -see here for an explanation. 

Similarly, if you are working on Guttural toads,Sclerophrys gutturalis, you can write in this section the known dates when they were introduced to Mauritius and Reunion, and how we know that those animals came from Durban. You can also give details of their natural range in sub-Saharan Africa. 

If you are working on a community of animals, or it is the geographical region that is more important than any single species, you should explain the study system here. For example, if your study is about the fynbos, then you should provide some background information about this kind of vegetation here. 

If relevant, you may need to provide a map with the location of samples that you used in this section. My preference is to try to provide a composite figure that will also include an image of your study organism (if relevant). 

Animal husbandry

If you have kept animals in the lab in order to do experiments, then here you can provide details of their welfare: housing, feeding, light:dark cycles, temperature, etc. If you bred animals to produce your study life-history stage, all relevant information is needed here. All this information should be available from your ethics application. Some journals will want you to include the details of your ethics permission here.

Repetitive methodology

If you’ve used the same methodology for each part of your data collection (like DNA extraction, sequencing, etc.), you should have a section that explains all of this prior to any experimental manipulations done. It’s best to go to look to see what other people have reported on in order to know what level of detail to include. For example, 20 years ago it would have been important to include detailed information of how you extracted DNA from tissues. Today, you can probably say that you used a standard extraction kit or salt extraction without saying more. 

Experimental manipulations & data collection

If you have done more than one kind of experiment, it’s probably a good idea to give each a separate subheading. Be consistent with these subheadings between the Materials and Methods and the Results.

One very important point here is to fully explain the collection of all of the variables that are used in your analyses. Remember to use exactly the same names for your variables here, as you have in the introduction (and will use in your graphs, figures and Results sections). It’s very important that the reader gets this consistency across sections. Please also remember to include all units that you collect data in (there is a space between numbers and units!), and the accuracy of the measuring equipment used. 

Equipment: Many journals require that you name the company that you bought equipment from as well as the town and country where it was made. This is to help others that might want to buy the same equipment (although it’s a bit outdated in these days of multinational companies). You should try to get all of the model numbers of equipment as you do the work, so that you are not scrambling later on to find out what they were. It’s really quick and easy to take a picture of this at the time. 

If you have built or designed new equipment for your Materials and Methods, you can expect to make a diagram of this here, if it can’t be adequately described in a paragraph. 

Data analysis (or Data analyses if plural)

This section is getting increasingly longer as people do ever more fancy statistical manipulations. As above, it’s very important that you use the same names for the variables as you have introduced and collected them. In addition to explaining the specific tests that you performed, you should explain what roles the variables have as dependent, independent, or random variables in your model.

Any transformation of any of the data that you collected (e.g. log, ln, cosine) should be mentioned here, along with tests that you performed to ensure that they adhere to the conditions required for the statistical test that you conducted. 

Give the name for each package in R that you use, together with its citation. Also give a citation to R as well as the version that you used in your analysis. If you don’t use the latest version of R, then your reviewers may want to know why, so always remember to update your version of R when you do your analysis.

Did you leave anything out?

By following your Materials and Methods, anyone else should be able to repeat your work. If there isn’t enough detail for someone else to conduct the same experiment or survey, then you will need to add this information somewhere. For example, a list of sampling points or a database of sequences might be needed in Supplementary Information.

TheMaterials and Methods section can often get overly long, and is relatively easy to edit to make it much shorter. In journals where there is a word count limit, you may want to move some of the Materials and Methods into a supplementation information section. 

Publicity for our new book: Biological Invasions in South Africa

Today is Environment Day, and to celebrate, Brian van Wilgen has been given interviews to journalists about our new book: Biological Invasions in South Africa. Since the book was released free online in March (see blogpost here), the chapters have been downloaded 154 thousand times! 

Some of the great information shared in this book is about alien trees that consume ~5% of our scarce water resources, in South Africa. Invasive species pose a direct threat to the survival of almost half of 1 600 native species listed in South Africa’s Red Data List. The book provides information on 1 422 alien species including plants, birds, mammals, fish, reptiles & amphibians. 

A newpaper article in the Witness:

You can listen to Brian's interview on this podcast or this radio interview.

Funding databases

Funding is one of the most important aspects of doing science, and something that different emphasis is placed on in different parts of the world. In North America, in particular, graduate students are expected to be able to demonstrate that they are able to raise their own funds, as this is expected of them in their jobs as academics. No matter where you are, your CV will be greatly improved by showing prospective employees (or labs) that you can generate your own funding. North America has a lot of opportunities to apply for funding for all sorts of reasons. There are less opportunities elsewhere, but the pool of people applying is also smaller. There are now so many opportunities, that several databases exist to help you find appropriate funding for your particular situation.

Our focus today is to have a look at some of these portals, and to quickly consider some of the major reasons why you might want to apply for funding.

Reasons you might want to apply for funding:

1. To improve your CV. Even if it’s only a small amount of funding that you apply for, it will make your CV look better. You might also want to search for prizes. Academic prizes carry both money and that feel good, look good feeling that CVs need.
2. Your project is unfunded. If you are completely unfunded, or you have a bursary but no running expenses, then you are going to need money to do your work. The more work (particularly field work) that you want to do, the more money you’ll need to raise.
3. Your project is funded, but you want to do more. Although CIB bursaries come with running expenses, if you want to do a lot extra (like side projects or paying assistants to collect extra data) then all of this is possible if you can raise some more money to do it. 
4. You want to attend a conference or workshop. There are great opportunities for travelling around the world, but they cost money and international conferences are often very expensive.
5. Publishing in Open Access journals. I find the idea of putting cash into the pockets of publishers abhorrent, but you may have little choice. There are some opportunities to get funding for OA publishing. 

It is clear that without making an application, you won’t get any funding. But where do you start?

BiodivERsA has officially released the INVAXEN video

Yes, it's the moment that you've been waiting for so long. The INVAXEN video was the result of winning a competition to publicise the outcome of the project. The output was a collaboration between INVAXEN researchers, BiodivERsA and the company Squarefish. It was quite illuminating to see the process of the script, storyboard, animation and then hiring the voice-over and music. 

Here's the finished product:

And the blurb underneath:

This animated movie shows the results of the INVAXEN project (“INVAsive biology of XENopus laevis in Europe”) which studied the biology, ecology, and impact of the highly invasive African clawed frog (Xenopus laevis). The scientists developed models to predict future invasion patterns and passed on their scientific findings to local stakeholders to collaborate with them on conservation actions. The video shows how BiodivERsA-funded projects not only excel in their scientific research, but also how relevant they are at societal level, and how they can help with management practices on the field. ~ This research was funded by the ERA-Net BiodivERsA, with the national funders ANR (France), BelSPO (Belgium), DFG (Germany), FCT (Portugal), part of the 2012-13 joint call for research proposals on invasive species and biological invasions. The Belgian Biodiversity Platform & BiodivERsA led the production of this video, along with the INVAXEN researchers and the animation & motion design studio Squarefish.

Who gets a fee waiver for publishing Open Access? 

The cost of publishing Open Access (Article Processing Charge or APC) is excessive, far outweighs the actual costs of type-setting, promotion and distribution, and is increasingly excluding scientists from publishing. If you don't believe me, consider the graph below from (Grey 2020). Grey clearly demonstrates a relationship between impact factor and the OA publication fee (APC).

Now ask yourself whether the cost can really increase with the Impact Factor (IF), or (as even publishers admit) the fee to publish is based on what academics can afford to pay. That is, publishers allow the cost to be set by the market. Because if you have your paper accepted in a journal where the IF is 13, you are likely to find the money to pay for it - even if this is 5 times the cost of the journal with an IF of 2.5. Yes, they may be in exactly the same publishing house. They may be distributed on the same platform. But when the IF went up, the value to your career and reputation also went up. Those publishers know it and they are going to exploit you willingness to pay for it. 

Getting a waiver for the >$1000 cost of publishing OA is therefore very important, if like me you can't afford to pay. So how do you think the waiver system is administered? 

Read the journal websites and you'd be forgiven for thinking that journal waivers are provided for the poorest academics who can't otherwise afford to publish. That's what publishers want you to believe. But actually, like elsewhere in life these freebies are actually given out to authors in order to get them to come back. Yes, just like getting that free can of coke at the supermarket, publishers are using the same tactics to get us to change to publishing OA in their journals. Why? Because they make so much more money, that they are laughing all they way to the bank.

The case of PLoS

Some time ago (31 July 2018), I wrote to PLoS to find out about their fee waiver system. At the time, I saw that waivers for publishing (largely in PLoS-ONE) were being handed out to people all over the world, irrespective of their financial status. This appeared to jarr with their stated policy, so I wrote asking for data on this and asked them to explain their process (my email slightly edited):

I did get a response from Susan Au at PLOS:

I pushed further and was told that PLOS simply doesn’t retain data on who gets waivers. If my figures (above) are typical, this means that PLOS is not being entirely honest about their stated waiver policy (in their financial declaration) and where waivers are actually given. They make it sound good, but actually they are using it as a hook to pull customers in.

More recently, I questioned the policy of another journal in this regard,Neobiota. In that blog entry, I showed that Neobiota have a policy very similar to PLOS, providing waivers for (potentially) one single author (seeblog post here).

The bottom line here is that fee waivers are being given out that PLOS declares in their financial statements as being to the benefit of authors that can’t afford to pay fees. However, the majority of waivers are actually being handed out to unknown authors, but likely not those from poorer countries. If PLOS keeps no records, does any APC charging journal? 

Should we make a fuss about getting fees waived? Or simply get fees waived when we can and keep quiet?

My view is that an open and transparent system should be compulsory. There would be no shame in the acknowledgements stating that APCs were waived. Indeed, I suggested this some years back (see blog entry here), but apparently to no avail. 

And if the system isn’t transparent?

It would be fair to assume that some people are profiting at the expense of others. This is the time-honoured tradition in the publishing business, and relates back to the power of privilege. 

Indeed, I'd suggest that now these people have started sucking the financial blood out of our academic sytem, the only real way to move fowards is to get rid of the publishers altogether. 

Grey RJ (2020) Sorry, we’re open: Golden open‑access and inequality in non‑human biological sciences Scientometrics (2020) 124:1663–1675