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

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.
2. 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. 
3. 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. 
4. 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.
5. 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.
6. 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.
7. 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. 
8. 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.
9. Once back from review, you’ll get an email from the editorial management system with the decision.
10. 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.
11. If you are resubmitting, aim to prioritise this to get it done in 2 to 3 weeks if possible. 
12. 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).
13. 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). 
14. 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.

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 “...to 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).

Handbook

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.

Examples

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!).

Structure

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:

Introduction

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
3. 1. You must explicitly state how each of the variables (introduced in the introduction) is collected
4. (If necessary) Describe how you’ll turn your collected data into the variables needed for your analyses
5. 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.