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Publicity for Biological Invasions in South Africa

05 June 2020

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. 

You can listen to Brian's interview on this podcast


Funding

03 June 2020

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?

  1. Databases. There are many databases, but here we’ll mention 3 that are easy to use. 
    1. Mendeley:https://www.mendeley.com/

This is probably my favorite. It’s easy to use and apply or remove filters. You can use the same login that you have for the referencing software and SCOPUS. 

  1. Stellenbosch University Open 4 Research:https://www.open4research.eu/stellenbosch

For this you’ll need a sun.ac.za email address to register, but you’ll get access to their research database. It is nice and logical to use, and you’ll find local and international funding opportunities. 

  1. Research Professional:https://www.researchprofessional.com/ 

You’ll need to create a login for this site, although you might get an in with your university address. This provides you access to what could well be the same database as those above. This is a slick database and relatively easy to use.

If you are South African, or studying in South Africa, the NRF has a lot of opportunities to get funding. They have travel funds specifically for attending workshops and conferences, and students from our lab have a good track record of getting money for this. It’s well worth applying. You’ll need a login for the nrf, but you must have this if you are a student in South Africa. 

  1. Opportunities in your department or societies:

Probably the most likely place to get funding is where you already have an “in” (where you are already known). This will include professional societies where you are a member, or your department or university. These places also have prizes, so it’s good that you know what is on offer in order to benefit the most. 


  Lab  Writing

INVAXEN video now out

27 May 2020

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.

  Frogs  Lab  Xenopus

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
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