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Who gets their APC fees waived?

21 May 2020

Who gets a fee waiver for publishing Open Access? 

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):

Together with some colleagues from middle-income countries, we are trying to get a handle on how the world of scientific publishing has become very fee based. My interest in receiving data from PLOS is simply that as the world's largest journal, you are likely to represent the others. As a not-for-profit, I'd presume that you are at the better end of the exploitation scale.

For example, from what I can tell, in 2016 PLOS published 26,397 papers. Of these only 897 were from countries in your Group 1 (full waiver). However, of this total only around one third conform to your stated 50% rule (50% or more of authors are from the Group 1 country). This means that around 1.1% of papers of all papers in 2016 were published for free from Group 1 countries. Most of these are from Bangladesh, Ethiopia and Kenya. 

Thus, the waiver PLOS waiver policy looks laudable until one realises that it amounts to around 1% of all papers. 

Your financial declaration (link for 2016) suggests that your waivers amount to nearly 5.5% of publication fee income. Thus we might presume that your Group 2 countries account for a much larger proportion of your waiver (which seems unlikely simply eyeballing members of this group) or that a lot of the fee waivers are generated for other reasons (e.g. editors don't pay fees, authors who appeal, etc.). It would be really nice to get some clarity on this. What is the policy for the 4.4%? From what I can tell, it is unstated but I know from colleagues that editors are regularly exempted from fees.

Given the large disparity between the 1.1% (my calculation for Group 1 waivers) and 5.5% (your declared waiver assistance), my opinion is that PLOS should rethink their fee waiver country groupings, specifically to expand to more countries. In addition, my opinion is that PLOS could easily afford to provide up to 10% of revenue in fee waivers. Once developed countries are excluded, such a policy would open up the potential for those without publication funds to receive more waivers. PLOS leads the way. If your non-profit fee waiving status is only 5.5%, we might expect that other publishing houses are giving even less (many have Group 1 country waivers which appears to be equivalent to only 1% of income). It would be fantastic if PLOS could take the lead in this and set a precedent for other for-profit journals. Similarly, if the majority of your fee waivers are actually discretionary, your stated policy is hardly honest. Policies are all about honesty, and as a not-for-profit organisation I'm sure that you'd prefer the honest option.

My own situation is similar to that of many of my colleagues from middle ranking countries. We receive little or no support and simply find it immoral to dip into research funds to pay for publication fees. The fees charged appear to be far in excess of what could reasonably be assumed to cost a publisher (I speak here as someone who has been involved with publishing at many levels). Yet, the options on publishing without fees are diminishing. This trend has come about as a result of the success of PLOS-ONE. Decisions by many first world countries to pay for all open access publications has firmly tilted the balance away from those of us in countries where such luxuries are not available. My university library continues to pay the fees to access many journals, whether or not articles are OA. Our research funds come from the taxpayer for research, but we are increasingly having to choose whether they be allocated to research or disseminating that research. 

Back to my original request, if you are able to provide me with details of PLOS publications that received partial or full fee waivers, I would be very grateful. If not, I will calculate the data and continue with my analyses unaided. Of course, it'd be nice to write that PLOS was totally open to providing the data requested, and not that I calculated it all myself because my requests were turned down.

I did get a response from Susan Au at PLOS:

“PLOS is unable to provide further information than what is already disclosed in our audited financial statements, which we make publicly available.  As disclosed in our financial statement footnotes, the fee assistance totals are aggregate activities from our Global Participation Initiative and Publication Fee Assistance program.  Please refer to provided links for program details.  Publication decisions are based solely on editorial criteria.  Output on resulting fee assistance activities recorded reflect published manuscript population, not submission population.”

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. 

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. 

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. 

  Lab  Writing

Submitting your work for publication

21 May 2020

Submitting a paper for review

In this week's lab meeting, we discussed the process of submitting a manuscript to a journal, and what happens once this is done. Here, I’ll briefly summarise some of the points that were made in the meeting:

  1. Targeting journals for submission: there are a lot of journals out there, and you need to make sure that you are submitting your paper to a journal in the right subject area. Your advisor should help with this, but if you are starting from scratch you can list journals in areas such as ecology or evolution using Web of Science or Scopus and rank them according to impact. This gives you a proxy list to discuss with your advisor and co-authors when preparing a manuscript for submission. Keep the agreed list, as if you are rejected from the first journal you’ll know where to go next.
    1. Take special note of journals that require fees (Article Processing Charges: APC), either for Open Access or as page charges (some US journals). See blog posts about Open Access and APCs here, here and here.
    2. The MeaseyLab policy is not to use research funds to pay for publishing, so you’ll need to make special provision for finding this money if you really want to submit to a journal that has an APC. 
  2. Prepare your manuscript (ms) according to the journal guidelines: this may require a lot of work especially if the journal requires full formatting on first submission. Some journals require additional items such as graphical abstracts, so make sure that you know what is needed. 
    1. Very important to note are any word limits (including for the abstract), and potential caps on number of citations.
    2. After approval from your supervisor, circulate this final version among your co-authors. This is a good time to gather the needed meta-data for submission. 
    3. You’ll (usually) need a letter to the editor, key-words, recommended (or opposed) reviewers, and addresses (with ORCID) for all authors. These should all meet the approval of your co-authors.
  3. Uploading your ms to the editorial management software requires time and preparation. Give yourself a good couple of hours for this process, as it can be frustrating.
  4. Once submitted to the system, your manuscript is usually checked before being passed to the editor. You may get it sent back if the meta-data is wrong.
  5. Inside the management systems, there are various workflows, and here I’ll describe something typical, although others do exist. Once the editor (often Editor in Chief) has your ms, they will decide which associate editor (AE) will handle it. 
    1. The AE should read the ms and may reject it if they feel that it won’t make it through review. An AE rejection isn’t great as they don’t always have the best experience in knowing what will and what won’t make it through. The editor usually has more experience. Hopefully, this won’t have taken long (1-2 weeks) and so won’t be very painful. This rejection may be fair or unfair, but it’s hard luck and there’s nothing much you can do except return to step 2 (above).
    2. Normally, your ms will be sent out to review and you can expect to wait 4-6 weeks (good), but sometimes up to 3 months, for a decision. If it’s away for over 3 months, you should definitely make a query on the editorial management system.
  6. Once back from review, you’ll get an email from the editorial management system with the decision.
    1. If it’s rejected, take the comments of the reviewers on board. Think about it for a couple of days, and then set about revising the manuscript. However unfair you think the reviewers have been, there should be some important messages for you to consider carefully and discuss among the co-authors before going back to step 2.
    2. Reject and resubmit: This is a category that means you need major revision, but the journal doesn’t want the time that it takes to do this on their stats. In many journals, this result has replaced ‘major revision’. Back to step 3 with a track changes manuscript and response letter to reviewer comments.
    3. Major revision: essentially the same as 6b. Both 6b and 6c result in your ms being reviewed again. You’ll need to carefully prepare both the ms and the response to reviewers as the reviewers will see both. Back to step 3 with a response letter.
    4. Minor revision: is unusual at this stage, but your ms should now only be assessed by the AE, so you should address your responses to them.
  7. If you are resubmitting, aim to prioritise this to get it done in 2 to 3 weeks if possible. 
    1. The reason is that the same reviewers are likely to be willing to look at your ms again within a month, and will remember all the points that they made. Similarly, the AE will remember all of the issues that they had. It’s hard to stress how valuable this is, as keeping it all fresh will result in a swift response.
    2. If you don’t or can’t manage to get your responses back quickly, you might expect a rocky ride through the review process when you go back for the second round. The reviewers you had before might not be available, but the AE will be obliged to have at least 2 reviews again. This means that you may get new reviews. New reviewers are likely to throw up new issues, and could result in your ms getting rejected at this stage, or that you’ll have another major review decision, sending you back to step 3 with a track changes manuscript and response letter to reviewer comments. This drags the whole process on for much longer and reviewers and AEs are likely to look less favourably at your ms. 
    3. A better result is when there are only minor revisions. In this case the ms is simply bouncing between you and the AE and even if this happens more than once, it’s fine as long as you can keep the response time reasonable (within a couple of weeks).
  8. Hopefully by now your ms has been accepted, and you are entering the last stages of the process. Your accepted ms should be sent to the publishers for typesetting, and you can get the proofs back very quickly (for some publishers). Most demand that the proofs are returned very quickly (often within 48 hours), and you should try to prioritise this if you can. If you can, please also send it to the co-authors. The more eyes the better at this stage for spotting errors. Don’t expect to be able to change a lot in the proof process, it’s really just for catching errors. Carefully check all figures, tables and legends. It’s not unknown that typesetters cause problems when they make proofs (tables can be disasters). 
    1. Check the acknowledgements again and make sure that your funders are included. You should always acknowledge:DSI-NRF Centre of Excellence for Invasion Biologyfor their support. I also suggest adding in the reviewers (even if anonymous) for their help in improving the ms.
    2. If you (or a co-author) spot a fundamental error with your data or analyses at this point (or any of the other steps above), you should discuss it with all co-authors and decide what to do. It’s better to withdraw the ms than to have to retract it later.

The peer review process is not ideal, but it is worth remembering that it’s there to help improve your manuscript. Different reviewers have different styles of review, and these tend to be culturally distinct around the planet. You should be aware that apparently ‘rude’ comments by reviewers might simply be attempts at humour. Try not to be disheartened by anything that you read in a reviewer’s comments. You never know the conditions that they were in when they read your manuscript, or what their day was like. This is also a point to consider when writing a review for a paper, but let’s tackle that in another blog post.

  Lab  Writing

What is needed for your research proposal?

12 May 2020

What is needed for your proposal?

In the Faculty of Science at Stellenbosch University, you need to have your PhD or MSc approved by a group of 3 independent staff members (i.e. not including supervisors) in your department (Botany & Zoology). The department requires that your written proposal is publicly available to everyone in the department to look at (normally deposited in the secretary’s office) at least 7 days prior to the oral presentation of your proposal. 

Your proposal is a collection of documents, where each document is a chapter of the thesis, and is roughly equivalent to a published paper. Ideally, these should be bounded by an introduction, which gives the bigger picture of how the thesis is placed, and a time-line at the end that demonstrates how you can complete the thesis within the two or three years for your MSc or PhD, respectively. Note that your project proposal is placed on your permanent file within the department.

Simply planning a study that results in two (MSc) or five (PhD) chapters equivalent to publications is not that hard. So what turns the collection of chapters into a thesis? Remember that the requirements for MSc and PhD are not the same. 

I think that it is useful to know what the examiners are asked to respond to when reading your thesis. 

When reading your MSc thesis examiners are asked:

  • Have the study objectives and the problems that were investigated been formulated satisfactorily?
  • Does the thesis show conversance with and a critical attitude towards the pertinent literature?
  • Is the material presented in a clear, systematic and logical manner?
  • Does the thesis show that the candidate is sufficiently familiar with the relevant research techniques and methods and have the research results been interpreted correctly?
  • Does the candidate show signs of independent, critical thinking or other signs of originality?
  • Does this investigation contribute to the knowledge of or insight in the relevant field of study?  Are new aspects in the field of study, if any, clearly identified?
  • Is the linguistic, stylistic and technical editing of the thesis acceptable?
  • Is the work acceptable for publication?

Note here that for an MSc, the examiner is asked whether the investigation contributes “ the knowledge of or insight in the relevant field of study”, and requires independent, critical thinking and originality. The Master of Science is done to demonstrate mastery of an existing body of scholarly work within the subject area. That is, you show that you are competent to do it: a Master of Science.

When reading your PhD thesis examiners are asked:

  • Has the motivation for the objectives of the study been formulated satisfactorily?
  • Do the research results constitute a meaningful contribution to the knowledge of and insight into the relevant field of study?
  • Does the dissertation distinguish clearly between own, new contributions to, and known results in the relevant field of study?
  • Is the candidate capable of evaluating the scientific meaning of his / her results and of placing this in context within existing knowledge in the field of study?
  • Does the candidate show signs of independent, critical thinking or other signs of originality?
  • Does the candidate show that he / she is sufficiently capable of doing independent research?
  • Does the dissertation show that the candidate is sufficiently familiar with the relevant research techniques and methods?
  • Does dissertation show conversance with, and a critical attitude towards the pertinent literature?
  • Is the material presented in a clear, systematic and logical manner?
  • Is the linguistic, stylistic and technical editing of the dissertation acceptable?
  • Are the research results acceptable for publication?

The critical difference with the PhD requirements is that you are now required to produce a “meaningful contribution to the knowledge of and insight into the relevant field of study”, and show that you are “...capable of doing independent research”. This degree prepares you to be an independent researcher, and so you are expected to have a critical attitude toward other research.

Thus for your PhD research, your work needs to be novel. This means that you are not simply applying the same experiments to another species or another scenario. But you are genuinely using your study system to generate new knowledge in an approach that is original. 

Given that all this will be needed in your final thesis, the academics that are reading your proposal will be asking whether or not the proposed work is going to meet all of these requirements. For both types of proposal, the assessing academics will be asking themselves whether the proposed work is practical and feasible (especially within the allotted time-frame), and they will ask whether or not the studies undertaken are posing testable hypotheses (see here). You can see how many of the questions for the final thesis can also be asked of the proposal. 

For the PhD work, the thesis needs to fit together preferably within a framework. I like students to draw how their chapters are interlinked, and to present this in the introduction of their proposal. A useful concept to be aware of is the 'Hierarchy of Hypotheses' (Heger & Jeshcke 2018 - see blog entry here). In this approach, you are encouraged to consider the 'bigger question' in your research area, identifying both what studies have produced evidence and identifying gaps from a theory driven approach. Generally, it is only possible to consider these types of concepts once you are familiar with the literature (both theoretical and experimental).


The Department of Botany & Zoology has an online postgraduate handbook (here) that contains a lot of useful information. It is updated annually, and you should make sure that you are looking at the current version. The department, faculty and university are prone to changing the requirements for these degrees, and these changes should appear within the handbook. If you find anything that concerns or worries you in the handbook (or elsewhere), don’t sweat it, but come and talk to your supervisor.


One of the best ways to learn about what is a good research proposal is to look at some examples. You should have already been sent some recent examples, and if you haven't please ask for one. Don't worry if it's not exactly the same subject that you are doing. Remember that the academic staff that assess your proposal are similarly removed from the subject area of the content. Instead, they have more experience about science in general and about what is practical and feasible to do.

Oral examination

For MSc marks, the department has a 80% to 20% split for thesis and oral presentation. The final mark will be written on your degree certificate, and you need to have >75% in order to get a MSccum laude

A PhD also requires an oral defense. The regulations surrounding this are more murky than for a MSc as it does not contribute toward your final mark: for a PhD you do not get a final mark, it’s simply pass or fail (hopefully pass!).


We expect that your final thesis will be a set of papers (data chapters sandwiched between an introduction and discussion), and so we ask you to prepare the proposal in the same way. That is, you will have two (MSc) or five (PhD) data chapters. In the proposal, each chapter will consist of three parts:


I’m not going to go into what’s inside the introduction here, as it’s already been done in other blog posts on formulaic writing (here) and specifically about the introduction (here).

Methods & Materials

What’s in the M&M section is also covered in the blog post on formulaic writing (here). At some point, I’ll write a specific post about this, but essentially you need to:

  1. Introduce important aspects of your study organism and/or study site
  2. Describe exactly how you’ll set up your experiment and/or collect your samples
    1. You must explicitly state how each of the variables (introduced in the introduction) is collected
  3. (If necessary) Describe how you’ll turn your collected data into the variables needed for your analyses
  4. Data analyses (how you’ll test your hypotheses). This should include a description of the statistical or analytical techniques. It’s useful to structure this section by each of the questions/hypotheses that you are posing

Hypothetical Results

It’s a very useful exercise to imagine how results will show that you have (or have not) accepted your hypothesis. You can’t show results that would cover every eventuality, but give some typical scenarios that you think may happen if you accept and reject each hypothesis. This could be a bar chart, a map, a scatter-graph, etc.

Your Proposal - what is it good for?

Once you’re done with your proposal, you might feel that you’ve done an awful lot of work without having added anything towards achieving your PhD or MSc. However, it’s actually a really useful document that you can use in a number of ways:

  1. Copy and paste directly into your thesis. One PhD student estimated that she pasted 60-70% of her proposal text directly into her thesis. This included nearly all of the methods and materials section verbatim.
  2. Use it to raise money to do your studies. Writing grant proposals is essentially the same as your thesis proposal, and so you can use this document (with some modifications to taylor it to the grant objectives) to raise money for your work. 
  Lab  Writing

Keep productive during lockdown

03 April 2020

Making a schedule of work to do...

Lockdown has come to us all. At the time of writing, we (in South Africa) have just completed our first full week of lockdown due to the emerging Covid-19 pandemic. Almost everyone has returned home to self isolate. Some lab members are back with their families, others are in their accommodation in Stellenbosch. The university has closed its doors during this period, and all experiments and practical work has stopped. 

Whether we wanted it or not, we now have an opportunity to write up completed projects, or plan the work that we want to do. While the lockdown might come with many unwanted restrictions, it does allow all MeaseyLab members to concentrate on analysis and writing.

But how should we remain productive, or (for some of us) how do we even start getting into a productive cycle? 

Try to enjoy your lockdown period, and make it as productive as you can. Everyone has their own way of working, but if you are struggling here are some tips that I find useful:

Schedule your work & mix it up

There are some tasks that we have that are more fun than others, and it's nice to have something that you can look forward to. Thus, making a simple schedule for your work where you indicate what you are doing and when can really help.

  • Know when you are more productive, and plan accordingly
    • some of us work better first thing in the morning, and others in the evening. Get to know yourself and plan to do the difficult stuff when you're fresh - or warmed up!
  • Make a "To Do" list
    • this will help you know what some of the little tasks are as well as bigger blocks.
    • If you really only have one thing to do (e.g. write PhD proposal), then break this up into smaller workable chunks so that you can start ticking them off
    • don't underestimate the importance and satisfaction of ticking off items on a to do list. Put it up on your wall, use coloured pens. Anything that makes it more satisfying for you
  • Don't become a slave to any schedule that you make
    • when you are being really productive, don't stop just because your time is up. 
    • conversely, when you're failing on a task don't stay with it when its time is up. Move on and come back to it soon. Even when you aren't doing this task, your brain will continue working on the problem.
    • Some problems do much better after a nights sleep, so if something is really bugging you then distill it and read this summary before you go to bed. Let your brain work on it overnight and reflect on what you think in the morning. It's worth having a go!
  • Be aware of what eats into your time (e.g. social media!)
    • if you really need to do this, then put it into your schedule for a less productive time when you know that you'll be flagging. 
    • When it's not scheduled, keep it off your desktop and avoid having alerts on your phone
  • Be logical in what you choose to do when. 
    • Don't plan to write your results when you haven't analysed your data.
  • Include items that are non-work into your schedule: 
    • such as coffee/tea breaks, social media fixes or exercise slots, and communicate these with anyone that you are in lockdown with (especially if they are prone to interrupting your most productive periods).
    • and include little things like writing or updating your profile for this website or the CIB website. Part of remaining productive is achieving little things on your to do list, as well as the really big items.
  • Plan meetings with other lab members (on zoom, skype or whatsapp), and keep communicating with your advisor, even if it's just to check in. It does help to chat about what you are doing as it helps you to verbalise and forces you to put it into another perspective. 
  • Don't spend too much time in this scheduling - it could end up eating all your time!

Don't forget that there is information on writing elsewhere on this website: 

The book is published!

11 March 2020

Published: Biological Invasions in South Africa

In what is actually a big event for the Centre for Invasion Biology, and invasion biologists all over South Africa, our book "Biological Invasions in South Africa" is published today! Moreover, it is Open Access and therefore free for anyone to download.

With 104 authors contributing to 31 chapters, there are nearly 1000 pages of text in this volume. The idea is that this book represents an encyclopaedic approach to covering all aspects of invasions in South Africa.

I wrote 2 chapters in the book that cover the invasive vertebrates in South Africa, as well as the invasive animals that have been donated from South Africa to the rest of the world. I also contributed to seven more chapters that cover many different aspects of invasions. Below you'll find the citations to my chapters, but I recommend downloading the entire book and looking through it all.

Byrne MJ et al. (2020) Education, training and capacity building in the field of biological invasions in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin, pp 731-755.

Davies SJ et al. (2020) Experience and lessons from invasive and alien animal control projects carried out in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin, pp 629-663.

Measey J, Hui C, Somers M (2020) Terrestrial vertebrate invasions in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin, pp 115-151.

Measey J, Robinson TB, Kruger N, Zengeya TA, Hurley BP (2020) South Africa as a donor of alien animals to other parts of the world. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin, pp 787-830.

Potgieter LJ et al. (2020) Biological invasions in South Africa’s urban ecosystems: Patterns, processes, impacts and management. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin, pp 275-309.

Richardson DM, Abrahams B, Boshoff N, Davies SJ, Measey J, van Wilgen B (2020) South Africa’s Centre for Invasion Biology: An Experiment in Invasion Science for Society. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological Invasions in South Africa pp 879-914

van Wilgen BW, Measey J, Richardson DM, Wilson JR, Zengeya T (2020) Overview of biological invasions in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin pp 3-31.

Wilson JR et al. (2020) The role of environmental factors in promoting and limiting biological invasions in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer, Berlin pp 355-385.

Wilson JR, Measey J, Richardson DM, van Wilgen BW, Zengeya TA (2020) Potential futures of biological invasions in South Africa. In: van Wilgen BW, Measey J, Richardson DM, Wilson JR, van Wilgen BW (eds) Biological invasions in South Africa. Springer,  Berlin pp 917-946

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