Hormones tell us more about rapid adaptation of invasive Guttural Toads

Back in January 2019, the wonderful PhD student Adriana Barsotti visited Stellenbosch together with Dr Carla Madelaire (both from Fernando Ribeiro Gomes' lab in USP), to add some endocrinological studies to our ongoing work on invasive Guttural Toads in Cape Town (see blog post here). Within no time at all, the fab duo set to work on sampling invasive toads in Cape Town's exclusive Constantia suburb, and from there they travelled to Durban to sample native toads with MeaseyLab MSc student, Carla Wagener (see blog post here). Along the way, the two Braziliaras taught us some some useful caipirinha skills (see here). 

Now Adriana has published the paper resulting from all of her work in South Africa:

In this great paper, we learn:

Invasive toads have lower body condition and tend to become dehydrated in the more arid conditions of Cape Town;
Invasive toads have the highest BKA and N:L ratio which could favor dispersal in their novel environment;
Dehydration is a stressor for native and invasive toads;
BKA remains comparatively higher in invasive toads even after acute stressors.

...and all this after only 20 years of invasion!

Carla published her findings earlier this year, showing us that invasive Guttural Toads have changed the way that they think about water (see blog post here).

The expertise from Fernando's lab is a great example of how our understanding grows through collaborations. Not only that, but it was great fun to host Adriana and Carla in the MeaseyLab, and we look forward to hosting more of Fernando's brilliant lab members in the future.

Read the papers in full here:

Barsotti, A.M.G., Madelaire, C.B., Wagener, C., Titon Jr, B., Measey, J., Ribeiro Gomes, F. (in press) Challenges of a novel range: water balance, stress, and immunity in an invasive toad. Comparative Biochemistry and Physiology,https://doi.org/10.1016/j.cbpa.2020.110870 pdf

Madelaire, C.B., Barsotti, A.M.G., Wagener, C., Sugano, Y., Baxter-Gilbert, J., Ribeiro Gomes, F., Measey, J. (2020) Challenges of dehydration result in a behavioral shift in invasive toads. Behavioral Ecology and Sociobiology74: 83. https://doi.org/10.1007/s00265-020-02866-5 pdf

Natasha graduates at small ceremony

The global pandemic has meant that Stellenbosch University cannot hold the large graduation ceremonies that we've seen in the past (e.g. see here). Instead, small ceremonies of a handful of graduands have taken place this week, allowing PhD student to graduate in person. 

One MeaseyLab member graduating this week is Dr Natasha Kruger. Read more about Natasha in this blog post written for her defense in Lyon, France.

Also graduating this week were the MeaseyLab's two honours students: 

Dan van Blerk & Emily Rippon

Congratulations to you all! You make us very proud.

Shrinking toads attract lots of news coverage...

The publication of our Biology Letters note has garnered lots of press coverage all over the globe. The story that Guttural Toads introduced to Mauritius in 1922 have shrunk by nearly a third from their original size has led to a lot of interest. It ties into the fascination that people have with the role of islands in both dwarfism and gigantism. After all, Mauritius is probably best known for the evolution of a huge pigeon, commonly known as the Dodo, Raphus cucullatus.

Our finding that an invasive population of Guttural Toads had so quickly shrunk now raises questions about these other instances of gigantism and dwarfism. Is there a possibility that they also happened in only hundreds of years, instead of tens or hundreds of thousands, as previously thought?

There was another swathe of articles published after James' press release hit the web: read here

Animali Il record del rospo delle Mauritius: Focus.it, 03 Dec 2020

Miniature guttural toads on Mauritius and Réunion stun researchers: Agenparl, 08 Dec 2020

Morphological reshaping in guttural toads in Mauritius in a short time: The Hindu, 28 Nov 2020

Miniature guttural toads on Mauritius and Réunion stun researchers: Scienmag: Latest Science and Health News 08 Dec 2020

Miniature guttural toads on Mauritius and Reunion stun researchers: Phys.org, 09 Dec 2020

Los sapos africanos se miniaturizan en casi un siglo en las islas de Mauricio y La Reunión: LaSexta, 13 Dec 2020

Volverse enano en una isla: el caso de una especie de sapo: NCYT - Noticias de la Ciencia y la Technologia, 15 Dec 2020

Read the blog post about the paper here

Or read the original paper in Biology Letters here:

Baxter-Gilbert, J.H., Riley, J.L., Wagener, C., Mohanty, N.P., Measey, J.  (in press)  Shrinking before our isles: The rapid expression of insular dwarfism in two invasive populations of guttural toad    (Sclerophrys gutturalis). Biology Letters     http://dx.doi.org/10.1098/rsbl.2020.0651 pdf

Responding to reviewers’ comments with a rebuttal

Whether the decision you receive is Minor or Major Revision, or even Reject and Resubmit, you will be required to respond to the reviewers’ comments. There are several points that it’s worth bearing in mind as you do this. 

Reviewers’ comments can come across as harsh, upsetting and even rude and arrogant. While it isn’t ok for reviewers to be rude, it does sometimes happen. Remember that the reviewers are humans, and they have sat down and given freely of their own time to read your work. The most important thing to be aware of is that all they had was what you had written. No background information, and possibly no information about the species or the system involved. They will be experts at some level, but perhaps not the type you might expect. Importantly, the editor asked them because they thought that their opinion would be of importance in helping them make their decision on your paper. This means that you also need to respect their opinion and comments, even if you don’t agree with them or find them to be offensive, arrogant or even rude. Remember also that some apparent rudeness may just be a reviewer who has a sense of humour that you don’t understand. There are lots of examples of this oneShitMyReviewersSay.  So no matter what you think of each comment, you should respond to it in a professional and courteous manner that shows that you are a professional scientist. 

Why do scientists make disparaging or unprofessional remarks to their colleagues in peer review? Whenever two or three scientists get together, you hear tales of recent woes associated with peer review. The retelling of such stories is all part of the collective, cathartic unburdening of what can be a traumatic experience especially when we put so much effort into each piece of work (see Hyland & Jiang 2020). Reading through a lot of these reviewers’ comments, I can see that there is an attempt at humour  (seehere). This humour is not appreciated by those who receive the reviews. Perhaps I understand the humour, because I also come from that same culture that dominates STEM, but that is not understood or even recognised as humour by others. Writing humorous reviews is unprofessional, especially if it is used to accentuate negative aspects. Needless to say, we could all do without unprofessional reviews. But this problem with peer review is illustrative of the problems at our meetings; we need to be more inclusive.

What to do when you receive your reviewer comments

Your reviewer comments will arrive in an email when you are busy doing something else. If you have time to read them the same day, then my suggestion is that you read without trying anything further. Remember to forward them to your advisor as soon as possible. Simply read the comments and then close the email and mark it for further attention the next day. Your writing is very personal to you, and you might be surprised at just how hurtful it can feel to have someone critique your writing (and your experiment) without holding back. If you’ve not experienced this before, then prepare yourself. No matter how much effort you put into your text, sending it out for peer review is a really high bar. Make an appointment with your advisor. Whether good, bad, or bizarre, it is best to set aside some time to read through the comments carefully, so that you can respond. 

Once you’ve found the time in your week, sooner is better than later, sit and read the comments again. Normally, they will sound much better, and less harsh, on the second read. They will seem far more approachable than when you first read them. Most reviews will have a set of major (when applicable) and minor comments that you need to address from each reviewer. Try sketching a few responses down to the major revision comments before your meeting with your advisor. The easiest way to do this is to copy all of the comments from the email (together with those of the editor), and paste them all into a fresh document.  Use a different colour text or a clear set of symbols (e.g. >>>>) to indicate which text is your responses and which is the reviewers or editors. If it isn’t clear, then the editor may well get confused about what is the comment and what is the rebuttal. One of the best ways I’ve seen of doing this was to make a table with all the comments in one column (each on a separate row), and the author responses in a new column. 

Sketch out your responses to the major comments, and use a tick if you are happy with making the suggested minor comments. If there are comments that you don’t know how to handle, simply leave them with a question mark. By making this start before you meet with your advisor, you will have an idea of what is likey to be difficult to tackle in the revision.  Even if you’ve received a rejection with reviewers’ comments, it’s well worth having this same meeting with your advisor so that you can decide together what to do next. At the end of the meeting with your advisor, you should have a clear idea of how to handle all of the comments, or where to go, what to read or who to talk to (perhaps another co-author), to sort out those you don’t know. Together with your advisor, decide whether you need to send out the journal decision to co-authors now, or wait until you have your rebuttal ready to circulate. For me this decision is largely based on how much time the revision is likely to take: if it’s quick, rather send the revision and rebuttal together with the decision. 

Next, when you sit down to write the rebuttal and revise the document, you need to make sure that you have pressed “track changes” on the submitted version of the manuscript. I find it easiest to have both the rebuttal letter and the revised manuscript open side by side on the screen. As you revise the manuscript in response to the comment, make a note to mark that it’s done in the rebuttal letter. Mark any comments that you don’t do. Your revision is written as a rebuttal to the editor. While you don’t write your comments back to the reviewer, it is worth bearing in mind that the reviewer is likely to read them. 

• Do make a note of the line number where the revision is made (note that these can shift around in the revision
• If you have reworded the text, do copy and paste that rewording into the rebuttal using quotes and corresponding line numbers. 
• Simply use a word like “done” to indicate changes on minor comments. 
• Do be polite with your responses, but you don’t get any extra points for wordy thankfulness or praise. So keep it succinct and to the point. 
• Signal that you agree with the comment and that you have made a change to the text. 
• Do bear in mind that your reviewer is a human, and was likely operating under less than ideal conditions when reading your manuscript. They could have been getting constant interruptions. They could have been reading it after having read another three manuscripts. They could suffer from insomnia and read it in the middle of the night with no sleep for a week. Give the reviewer the benefit of the doubt. 
• Do thank your reviewers and editors in your acknowledgements. They’ve been working and doing the best for your manuscript without any thanks other than what you will give them. So give them a boost and help make their day that much brighter. 

What if you don’t agree with a reviewer?

Most of the time, reviewer comments are sensible, helpful and genuine attempts at improving the quality of your contribution. If you don’t agree with particular points, try skipping them and moving ahead with the easy points or those that you do agree with. Discuss any points that you don’t agree with your advisor. Try to get another perspective on the comment. Do your best to try to see the comment from the reviewers standpoint. 

For example, a reviewer might ask for details on a point in the methods, but they are mentioned in another section of the methods. This is a cue for you to add a flag to that point in the manuscript. For example, write “see section 2.2.3 for an explanation of how this was done”. 

If a reviewer has made a comment that says that they don’t understand something, this means that you need to make a change in your text so that the text is easier to understand. If they don’t understand, then it could be that more people don’t understand and you want your text to be understood by all people that are reading it, so make a change. 

If you and your advisor both don’t agree, then make it clear what exactly you don’t agree with. Again, try to see it from the reviewer’s perspective and write a courteous and clear explanation of why they might have misunderstood or misinterpreted what was written. Remember that the reviewer is likely to read exactly what you write in your rebuttal. Your job is to professionally explain why you don’t agree. Forget any of the emotion that you might believe to be there. Revert back to professionalism, because you are a professional.

When reviewers don’t agree

Normally, you will have two reviews (possibly three depending on the journal policy) and comments from the Associate Editor (AE). The AE acts as a judge given the opinions of the reviewers, and so if the reviewers disagree, the AE should suggest the correct direction for you to take. Sometimes this means that the AE will consulta third reviewer(and occasionally even more reviewers). See the chapter below on why it is important for editors to read your work. If the AE gives you no direction (as is increasingly the case) then make this decision with your advisor and indicate to the AE the conflict between the reviewers and the reason why you’ve chosen the direction you have.

What if you feel that your reviewer is being unprofessional?

If you really feel that a reviewer is being unprofessional, it is worth flagging this with the editor. I would say that I’ve never had to do this myself, but I am aware that there is some unprofessional behaviour out there (I’ve seen it on ShitMyReviewersSay). Discuss it with your advisory, but here are two alternatives:

1. If it’s just one or two comments, then simply state that you don’t feel that the comments are worthy of a response. Ask the reviewer to try again, or ask the editor to interpret the comment for you.
2. If it is every comment from one reviewer, write an email to the handling editor and ask for their guidance. They will flag it with the editor and come back with a solution for you. 

Appealing against a decision that you think is unfair

From time to time, a decision comes from an editor that is clearly unfair. I’ve had a few. As I’ve mentioned before, scientists are humans and humans do have biases that manifest into their professional lives. This is the reason for double-blind review. Scientists in STEM are predominantly white and male, and express the views of this minority but powerful group. Their prejudices do manifest in their decisions, and it is important to push back against this when you feel that this is the reason for a decision.

Most (good) journals will have an appeals process and you should look this up and see what’s involved. While doing this, it is worth reviewing the journal’s policy on how they handle manuscripts; again good journals should have a clear policy. Of all the rejections and poor decisions I’ve had on my manuscripts over the years, I’ve only felt that decisions were unfair and worth appealing less than a handful of times. 

Normally, an appeal is made to the editor in chief. Be very clear about why you are appealing and what in the decision does not tally with the journal’s own policy. Remain professional and detached from the decision itself, and instead appeal on how the journal’s own policy was not followed. For example, a journal may have a policy that the editor will sum up the reviewers’ comments and use this as the basis for their decision. If the editor seems to have sided with one reviewer while not considering others, this can be the basis of an appeal.

Any appeal should be agreed with your advisor and the other co-authors before sending it. 

Further Reading

Hyland, K. and Jiang, F.K., 2020. “This work is antithetical to the spirit of research”: An anatomy of harsh peer reviews. Journal of English for Academic Purposes, 46. 

Making sure that you don’t plagiarise

Why is a plagiarism a problem?

Essentially, plagiarism is when you copy somebody else's work. We're most commonly familiar with plagiarism of writing, and these days this is especially easy with the copy and paste function (Ctrl c & Ctrl v). Most people are not even aware that they have plagiarised because sometime in the past they copied and pasted the work of somebody else into a document and this later became incorporated into their text without them being aware of it. 

Plagiarism is a problem because essentially you are taking somebody else's work without attributing it to them. Like other forms of taking without permission, you can think of this more simply as theft.

How do we know whether we have plagiarised or whether we've simply written something that's very similar to somebody else?

Today there are several pieces of software that are used to compare submitted text with text that's written and available on the internet in order to discover plagiarism. One such example is TurnItIn. TurnItIn is used by Stellenbosch University. One of the outputs of TurnItIn is to highlight text that matches other text already on the internet. As almost all journals publish on the internet TurnItIn can accurately determine if text has been copied from another article or website.

I usually set TurnItIn to determine plagiarism with five or more consecutive words.

Remarkably it is very difficult to come up with exactly the same words that someone else used to describe a phenomenon. most people when they think about it feel that it wouldn't be that surprising if they came up with exactly the same words as somebody else.

When caught plagiarising most undergraduates claim that they simply read an article and then later happen to write the same words that were in the article. They categorically deny that they ever copied or pasted text from the article into their work. Proving to them that this was not the case is facile. But it's also a really useful exercise that teaches you a lot about plagiarism:

Try it. By trying it you'll learn what plagiarism is all about. 

1. Read an article, or even just one paragraph

2. Then try to write text using exactly the same words in the same order with the same syntax as that in the article: verbatim. Importantly, you must not look back at the article itself.  

3. Unless you have an eidetic memory you will fail at this task. 

This is not to say that no 5 or more words can ever be the same as someone else's. There are many situations in which this happens. Think of addresses, quotes, certain laboratory equipment or protocols, and certainly references at the end of your paper. There will also be the occassional coincidence (see example below). So there are many times when TurnItIn will come back with matching text. This is not what we're looking for in plagiarism.

If plagiarism is detected in your work what can you do about it?

It's remarkably easy to remove plagiarism from your work. 

Here's what you do:

1. Read the sentence that has been plagiarised several times to yourself. 
2. Now without looking at that sentence, write another sentence that has the same meaning. Because it's very hard to replicate somebody else's words without copying them, what you should find is that you've written a fresh plagiarised sentence. 
3. This can now be added to your text, changed as appropriately to fit your existing text. And that should be the end of your plagiarism worries.

Here's what not to do:

1. Take the sentence swap out some of the words for synonyms and pass it off as your own. 
2. The sentence will still have the same structure that you copied and essentially this is still somebody else's work. Moreover TurnItIn will still recognise this as plagiarism.

How can I make sure that I never plagiarise?

Quite simply if you never cut and paste, you won’t plagiarise. It’s that easy. I understand why people copy and paste as a way to get started, or because someone else has written something so well, it’s hard to believe that you could ever write it any better. But actually, you can write it just as well, and writing it in your own words is worth so much more. There are also very dire consequences for plagiarising other peoples' work, that it just isn't worth it.

Don’t forget that the penalty for plagiarism in your thesis might well be that you fail. You cannot submit a thesis with plagiarised text.

It still seems amazing to me when I submit a student manuscript to TurnItIn and see that it is completely free of any plagiarism. And I should say that this is usually the case. There are so many words in English and so many different ways of putting them that you really can have your own writing style. Your writing style will be as unique to you as a fingerprint, and it will be entirely free of plagiarism. It's something you can celebrate.

Is there a grey zone in plagiarism?

I would maintain that there is not really any grey area in plagiarism. So what are people talking about when they refer to a grey zone? The nominal grey zone within plagiarism comes when you copy your own text: "self-plagiarism". Essentially this is really just the same as plagiarism but obviously if you are the original author then if you use your own text it's not the same as using somebody else's, because the work is still yours.

However this is frequently complicated by multiple authors on a paper. For example, if I wrote a paper with five other people, even though the words were mine, if I use them again they would actually be attributed to all six authors and not just to me. Thus, if I use them again with five different authors it would still be plagiarism. This is further complicated by having different publishers for your papers. Let's say I wrote a paper, I was the sole author and it was published by a journal that retained the copyright. If I use the same text again in another paper where again I was the soul author, but it was published in a different journal and they retained the copyright, that would be a breach of copyright to the first journal. It would be regarded as plagiarism. 

Obviously, this situation really shouldn't occur because if you are the author of your own work then you should retain the copyright it should never be given to a publisher or a journal. The fact that many journals want to obtain copyright on work that they don't pay for is a complete disgrace but it's something that we're not going to go into right now (you can see rantshereandhereabout science publishing scandals). 

The simple way around this problem is not to plagiarise any of your own text or any of anybody else's. This is, as I've explained above, relatively easy because as long as you don't copy and paste any text you'll find it very hard to actually use somebody else's words. However it can get a little bit tricky when you are writing the materials and methods section of a paper, and especially when that paper uses exactly the same materials and methods as a previous paper. The temptation is great to go and copy the text that you've written before. But be aware that, however gray, this is plagiarism and you should not do it.

The likelihood is that because you're using the same names and their relationship is staying fixed as shown in the example above in materials and methods you are more likely to come up with text that a piece of software likeTurnItIn will show is plagiarised even when it isn't.

Concerned about whether or not there is plagiarism in your work?

If you are at Stellenbosch University, here are the links to use TurnItIn:

Staff:https://learn.sun.ac.za/course/view.php?id=8432&section=10

Postgraduate students:https://learn.sun.ac.za/course/view.php?id=24317

Want to read more about plagiarism to understand what it is?

Louw (2016) https://doi.org/10.20853/31-5-580

Read the Stellenbosch University policy on plagiarism here, and see what else Stellenbosch University has to say about plagiarism here:https://libguides.sun.ac.za/c.php?g=742962&p=5316900

If you want to know more about how TurnItIn works, there are lots of videos out there on YouTube that can help you. However, watch out for the ones that try to teach you how to cheat with TurnItIn. Trying to cheat this system is far more difficult that writing your own work. Cheating simply doesn't pay, so don't go there.