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Table Mountain Ghost Frogs need cold water

11 August 2020

New study looks at requirements for Table Mountain Ghost Frog tadpoles

In a new study, published today by MeaseyLab alumnus Zishan Ebrahim and colleagues, they determined the requirements of the tadpoles of Table Mountain Ghost Frogs, Heleophryne rosei. The iconic Table Mountain Ghost Frog only lives in the streams and kloofs around Table Mountain and nowhere else on the Cape peninsula (or anywhere else in the world). Previously, researchers had determined that the tadpoles require perennial flow (streams that don't dry) in order for the tadpoles to inhabit them. This then is the reason why Table Mountain is the only massif on the peninsula with the frogs. However, in a paper published today, Zishan Ebrahim shows that the frogs also have a sweet spot of temperatures above (and presumably below) which they can't tolerate. 

Zishan monitored physical parameters of Table Mountain's stream water for many years finding that tadpoles don't inhabit all of the streams with perennial flow on the mountain. The warm water that flows down some of the streams could be influenced by the complex hydrological installations on top of the mountain that were originally installed to supply fresh water for the city. Now much of the water on top of the mountain sits in dams where it heats in the sun and may influence the temperature in the streams. There are other problems on Table Mountain, most notably invasive trees, that are also likely to change the hydrological properties of the water and impact on the Ghost frogs and their tadpoles. 

Read more about the conservation relevance of this work in this recently published paper:

Ebrahim, Z, de Villiers, A. and Measey, J (2020) Assessing water conditions conducive to tadpoles of the Table Mountain Ghost Frog (Heleophryne rosei) and the relevance to their conservation Koedoe Vol 62 (1): a1581 DOI: 

  Frogs  Lab

Writing your abstract

14 July 2020

Writing the abstract

A good abstract is very important as, like a good title, it advertises the content of the paper and draws readers in. In a world where the quantity of scientific literature is increasing (see here), it is more likely that someone will read your abstract but not your paper. Actually, it’s far more likely that someone will read your title and use that to decide whether or not to look at the abstract. Moreover, when you submit your work to the journal, your editor may decide whether or not to immediately reject your manuscript based on the content of the abstract (see here). Therefore, it had better be good!

What is the abstract?

The abstract is a concise paragraph that sums up the major points of your manuscript so that the potential reader will be able to assess whether or not they want to read the entire paper. It is an abstract of the entire document. It should not be abstract!

So what would a good abstract contain?

A good abstract is a summary of the highlights of the paper. You can’t hope to include all of the results, but you should include relevant statistics that support your major finding. You must include the broader subject area that your study fits into, and show how your results are relevant to this.

None of this is easy, and you should not expect to write your abstract in a single sitting. It will likely require multiple iterations, and some intense word-smithing to make it as good as it can be. Abstracts almost always have a word limit, and that makes it challenging and means that you have to be concise (see here).

Increasingly, you’ll hear that a good abstract is citable. This means that it contains enough information that someone knows that it can be used to cite for a specific fact. Of course, these people should download and read the entire study. 

Where do you start?

Just like planning your writing in general, I’d suggest starting your abstract with an outline. Use bullet points to make a list of things that you feel that you should include. Rearrange your list until you have all the introduction points at the start, results in the middle and discussion at the end. 

There’s no need for detailed methodology, but it is useful to know the approach. For example, ‘we used a common garden experimental approach’ or ‘we sampled 85 animals from three invasive populations’. 

Although many abstracts are provided as a single paragraph, some are structured into the sections of the paper (like this), or as numbered points (like this). Using this formula is a good way to get disciplined about boiling your paper down into a small amount of concise words. It’s worth keeping a copy of any abstract that you compose like this in case you decide to submit to a journal that requires it. 

Starting with this framework will ensure that the abstract is well balanced. 

At this point, I’d circulate it to your advisor to ask whether there are other key points that should be included. As a rule, it’s easier to start with everything present, and only then cut the words down to something within the abstract word limit. If you wordsmith your abstract and then try and add a key point later, it’ll never come out so well.

When do you write your abstract?

Although the abstract comes on page 1 of your manuscript, only try to write it once you’ve got to the end of the process of writing your manuscript. 

Do abstracts for conferences differ?

Yes. It’s likely that an abstract for a talk will not be the same, unless you have already published paper: but even then it’s probably worth re-writing it. I’d suggest that your conference abstract be more descriptive and thought provoking. Pose questions that you will answer in your talk. 

Where do people go wrong in writing the abstract?

  • The most common mistake is getting the balance wrong. I often see an abstract that gets to the results, runs out of space and simply stops. It is important to have a statement about what the results mean. 
  • Another common mistake is to have a very simply worded abstract that conveys very little information. There is definitely going to be a lot to put in, so expect to write something too long with too much, and then discuss what can be left out.
  • Text from the main document is copied into the abstract. I’ve written about this elsewhere (see here), but you should never copy parts of your writing. You could start like this, but wordsmithing must change the words and their order substantially. Otherwise, when the first sentence of the abstract is the same as the first sentence of the manuscript, it will really turn off your readers.
  • Too many statistics or no numbers are also common mistakes. Often numbers can leave you with more space for other information. 
  • There is only time for one or two comments on the discussion, so pick out something important. Look through your written discussion and rank the points that you make in terms of interest to others. Can you combine two or more points into a single sentence?
  • The introduction of the abstract must frame the bigger question, and the discussion must show how your data responds to this. 
  • Finish with something conclusive and strong, preferably how this study changes the understanding, and not a caveat or suggested further study.
  Lab  Writing

Getting the low down on predatory publishing

01 July 2020

What are predatory journals?

Predatory journals are publications that purport to be from scholarly publishing houses, but have little or no editorial oversight or peer review. They exist in order to extract the Article Processing Charge (APC) that is so ubiquitous in Open Access journals. They continue to exist because publishing is moving towards APCs, and there is little difference between what they do and some supposedly ‘legitimate’ journals. For example, some definitions of predatory journals include that their APCs far exceed their publishing costs, but this can now certainly be said of some legitimate journals (see here).

If the line is so grey, how is it possible to tell whether or not a journal is predatory?

This is a surprisingly difficult question to answer. Predatory journals have become so sophisticated at what they do, that it can be very difficult to determine whether or not they are legitimate. Moreover, their electronically published journals can create new titles faster than the time that it takes to check that they are legitimate. An example of a publisher in the grey zone is Hindawi, that were once considered predatory but were later removed from Beall’s list (seearticle here). However, Hindawi still have some questionable practices and I’d suggest continuing to avoid them. 

At the same time, legitimate journals have become increasingly predatory in their habits, and it’s difficult to tell them apart from predatory journals. For example, there was a time when it was possible to categorically state that no journal will ever approach you with a general mailshot that invites you to contribute. However, there are now several legitimate journals that do do this. And there are many more predatory journals that also do it: this now constitutes most of my spam! 

Realistically then, in the current publishing world, there is a continuum from predatory to legitimate. It was not always this way, and that means that as an emerging researcher you are facing difficulties not faced by your advisor or other more senior academics. Not only do you need to avoid publishing in predatory journals, but you should also avoid citing their articles.

However, help is at hand. There are some definite ways that you can determine whether you are choosing a legitimate journal. Here are my 5 steps that you can take to safeguard your submission. I suggest that you use the following list in a stepwise fashion. 

  1. Use an index.Web of ScienceandScopusboth curate contents of legitimate journals. If your journal of choice appears in one of these, then it is very likely to be legitimate. Note that Google Scholar includes many predatory journals, so please never use this to determine whether or not a journal is legitimate. Note also that it takes a journal several years to gain enough kudos to get accepted onto Web of Science and/or Scopus. Therefore, it can still be legitimate and not be there. We have previously written about how to choose the right journal for your publication, and I refer you back to this posthere(you could also take a look at thisBot Zoo post). If the journal you want to publish in is not inWeb of ScienceorScopus, then proceed to the next step.
  2. Ask your librarian. Librarians are fantastic sources as well as custodians of information (see here), and journals are one of their key knowledge areas. Don’t hesitate to get in touch with your librarian and ask their advice (here’sa link to ours). They are likely to be very well placed to respond to your request. They may also be guardians of granting APCs at your institution, so it is in their interest to make sure that these valuable monies don’t fall into the wrong hands.
  3. Ask your advisor or an experienced colleague. It’s worth doing this with them so that you can see the steps that they follow. Given that steps 1 and 2 have already come back with uncertain answers, spreading your net more widely will help with step 4. However, be warned that there are increasing numbers of senior scientists that have been caught out by predatory journals, so checking their contributors is now no cut and dry way to differentiate between them and legitimate journals.
  4. Who is on the editorial board?Journals publish names of their editors, associate editors and the editorial board. Look through these lists and see whether there are names that you recognise. If you know any of the people, you (or your advisor) can contact and ask them about the journal (they should be happy to respond). Be warned that it is easy to place someone’s name on a website, so unless they have personally told you, keep away.
  5. Check against a known list.In the past, this might have been the first thing to do, but the number of predatory journals is preliforating so quickly that it’s hard for any list to keep up.Beall’s listretired in 2017. The next best list now has more than 3 times that. Seehere for an interview with the keeper of the new list,Simon Linacre. Sadly Simon’s list isbehind a paywall, so you can’t expect to access it. One of the reasons why Beall gave up is that the new tactic for these publishers is to produce lots of new journals. Curating a list is real work and has implications for the publishers on it, hence you now need to pay to access an up to date list. There are more lists:Cabell's Predatory Journal Blacklistand Jalalian's list of hacked journals.

Take a look at this excellent infographic from Rutgers University library, where they have a whole lot more information about predatory publishing.

If predatory journals are becoming more like legitimate journals, where’s the harm in publishing with them? 

Your reputation is important. As an emerging researcher, your publishing record is what many people will see first. It is all that is shown in your Google Scholar or ResearchGate profile. It’s your shop window or showroom. What prospective employers will want to see is that there are plenty of publications (appropriate for your career stage), and that they are in appropriate journals with good reputations. You might confuse having a good reputation with a high impact factor. The two need not be the same. High impact factor journals don’t accept all types of submission, and you may have data that simply doesn’t fit into one of their mandates. I would say that it’s still important to publish this, and there are many journals with good reputations where you can do so. Let’s leave discussion about the impact factor for another blog post.

The other reason why you would be best to avoid a predatory journal is that they attract very little in the way of scientific impact: few people will read or cite them (see article here). One thing that you definitely want for your work is for people to use it. To do this they must read and cite it. If you publish in a predatory journal, many scientists won’t even consider reading the content as it has not been, nor will it be, peer reviewed. Thus, unlike a preprint, it is not being openly offered to the community for review (seehere for a blog post on preprints). 

Due to the ambiguity of whether or not these papers have been peer reviewed, I would also suggest that youdo not cite publications that you think may be from predatory journals. You can use the same steps (above) to determine whether or not what you want to cite is from a legitimate journal.

What do you do if you have already published in a journal that others consider predatory?

  1. The first step would be to write to the publisher and withdraw the article. Whether or not you paid an APC, having it on their website is not good for your reputation. Beware, these journals don’t adhere to an ethical code, and so they might refuse to withdraw your paper. Or they may want to charge an additional fee to remove it (remember that they are in it for the money).
  2. Do not cite the paper, or put it on your CV. You can easily remove such articles from your Google Scholar profile or ResearchGate. Don’t put it in your showroom.
  3. Prepare a statement that explains how it happened. You may not have been responsible for the submission, or aware that the publication was from a predatory publisher. However, in time you are likely to forget the exact reasons. It would be a good idea to prepare a statement, so that if you are asked (for example in a job interview), you can explain how it happened. People can be very understanding when provided with an explanation, but if you say that you can’t remember or can’t give any details, then you may sound evasive.

The local viewpoint

Predatory publishing is a big problem in South Africa where 4246 papers have been published in 48 predatory journals: take a look at this article (Mouton & Valentine 2017). The NRF has also issued a formal statement on predatory publishing that you might want to look at (see here). And it’s not just publishing where the predators are lurking, they are also waiting to invite you to a conference (see here). Your work is valuable to you and to your advisor, so please try to make sure that it doesn’t end up in the hands of a predator!

Still want to read more? Take a look at this article byMonica Berger: Everything You Ever Wanted to Know About Predatory Publishing but Were Afraid to Ask

  Lab  Writing

Prize winning Jenicca

26 June 2020

A big congratulations to Jenicca Poongavanan who won best poster at the first virtual International Statistical Ecology Conference 2020

Some of you may remember that Jenicca did her MSc with Res Altwegg, Ian Durbach and myself in SEEC at UCT. Jenicca used aSCR (generated by Marike Louw) to investigate the spatial distribution of densities of the Peninsula Moss Frog, Arthroleptella lightfootii.  To read more about Jenicca's thesis, and aSCR in general see here and here. Jenicca has since moved to a lab in Florida where she now studies sea-birds (see here).

Poongavanan, J., Altwegg, R., Durbach, I. Measey, J. 2020 Modelling the range-wide density patterns of the Arthroleptella Lightfooti using acoustic monitoring data. (Poster) International Statistical Ecology Conference  (virtual): June 22-26, 2020.

  aSCR  Frogs  Lab  meetings  prizes

Writing concisely

17 June 2020

Writing concisely

So far on this blog, I have put an emphasis on a writing formula in order to get started writing. Many students have a problem in knowing where and how to get started with what seems to be a daunting prospect: writing a proposal or writing the entire thesis. I still feel that getting started quickly and efficiently with some confidence is one of your most important steps. But once you've made it through your first draft, you'll begin to find that you need to start refining your writing. That is saying what you need to say in less words and space.

In an ideal world, what goes into your thesis will be of the same quality as the accepted manuscript. The reality is that the thesis is often more wordy, with the result that reviewers and/or editors will ask you to be more concise. How can we achieve this?

I'm prompted to post this blog simply because someone else has written a great essay with 10 top rules to help you be concise. The essay is Open Access, so you can all find it here, and there's no need for me to repeat the words of Scott Hotaling. However, I am going to write some comments of my own on his rules, and I may build on this blog over time. There are some other posts that are also worth a second look along with this one: see here and here.

Here, the rules are Scott's, the comments are mine.

Rule 1. Take writing seriously

It is likely, that like me, you chose to do science at school instead of useful subjects such as English and/or other languages. It might have also occurred to you that it was a really bad idea not to have done more earnest work in languages now that you are expected to write like a professional. Certainly, if you did pay more attention in languages in school, you may not be suffering with the rest of us now. Personally, I never received tuition in the grammatical construction of English. Thus I'm left in the dark most of the time about exactly what is wrong. Instead, I simply try to rework a sentence into what I know is correct [and I often don't achieve that]. The lesson then is that should you come across an opportunity to learn more about writing, do take it. 

Although we talk about writing science here, the grammatical rules of writing (in English) are fairly universal (with some local exceptions), so do practice your writing. Maybe write a letter (or long email) instead of making a call sometimes. It'll also help you to read (see here). If you are a keen reader, then you could do worse than reading some Kurt Vonnegut. Scott provided this link  to an article I hadn't seen before. Go on, give it a read!

Rule 2: Identify and stick to your message

We've talked before about avoiding distracting your reader. Your aim is to be thorough, which will mean including all relevant information, but don't allow your writing to sideline them into taking the wrong direction. When Nitya won the prize for the best popular science article at the ARM, the editor of The Conversation said that he had established his narrative and stuck to it like a highway. The highway analogy is useful as although you will see signs to other places that you can point out, you shouldn't turn off the highway. The best of highways will also be free of traffic jams (think long, complex sentences here). 

This will mean that you may need to delete some of what you've written, and that can be hard (especially when they are the best bits). You can always keep a file with all the best bits that you've never used. Maybe one day you'll use them. Or maybe one day you'll see that they weren't quite as good as you thought they were.

Rule 3: Get to the point

If the highway is 'your message' then getting to the point is the big sign that states the destination. 

Some of the best papers I've read manage to encapsulate the whole point in the first sentence, or better still in the title. Our formula has you getting to the main question in the last paragraph of the introduction, but you should have already 'got to the point' in the first paragraph - i.e. the point that is the bigger picture. 

Rule 4: Keep your Methods and Results contained

You can find a guide to writing your methods here. This rule is about not allowing the methods to creep out of this section and into the results, or even the discussion. Similarly with the Results. There are some specific times when this is permitted (such as a post-hoc test), but generally you shouldn't expect to do this. 

Rule 5: Do not repeat yourself (too often)

Redundancy is often rife in proposals, theses and manuscripts. If you've produced a table with all of the results, then they don't need to be in the text. The same with a figure, especially Figure 1 which is often a descriptive map or diagram of apparatus. Have it once, but you don't need it twice.

Copy and pasting is very easy, and a good way of suddenly producing vast quantities of text. But repeated text is quickly recognised by the reader and appears very boring and cumbersome. This is likely to happen in the Methods and Results sections. If you find yourself deciding that you can simply cut and paste this paragraph while changing the variable names and the numbers, then you are wrong. Don't ever do it. 

Also, please don't cut and paste sections of methods from one part of your thesis to another. Just don't do it.

People also have a tendency to build the abstract by copying and pasting text from the main sections. Don't do it. The reader will quickly see the repetitions and become bored. Similarly, the conclusion/summary section is also often copied from lines above. If it's not worth writing again, then it wasn't worth writing before. Make it fresh, and keep it interesting!

Rule 6: Avoid unnecessary or inefficient “lead‐ins”

Interesting. I'd say that you need some practice and a critical eye to spot these kinds of errors. Having your advisor help or someone who has edited a lot of text. Scott's got some great examples, and so I'll let you peruse them here. Maybe the academic phrasebank is full of things to avoid, maybe not but it might help you get started!

Rule 7: Use first‐person, active voice

For some reason, most students avoid this at all cost. There appears to be the idea that saying "I" or "we" isn't correct for scientific writing. In fact, it can be the easiest way to avoid the passive voice. I've written more on this elsewhere... see here.

Rule 8: Remove unnecessary words

This is really getting down to the nitty gritty. It's hard to do this yourself. It's much easier for someone else to show you. Typically I only do this level of word-smithing for abstracts or when the imposed word limit means that you really need to remove excess words. However, Scott is correct that if you can learn to do this yourself, it will improve your writing. 

Personally, I like to slip in the odd 'as well as' instead of 'and', just to ring the changes. Scott would remove them, and you can see where he'd edit out other examples. Do we really have to be so hardline? I'd say that there are times when it helps.

Rule 9: Simplify your language

This is always a good idea. Making three short sentences instead of one very long one is much better. It also helps you avoid complicated grammatical clauses. 

Rule 10: Seek and embrace feedback

If you feel that you've given it 110% and no-one could ever have anything to say, then you're at the wrong starting point. There are very few people who get to the point when their writing doesn't benefit from asking for feedback. Certainly, if you can't take criticism coming from advisor[s], then you are unlikely to fare any better during peer review. 

I spend a lot of my time reading and commenting on the writing of my students. Every comment made is given to improve the document. I get mad when comments are ignored. It could be that you have a really good reason for not changing something, but if you don't explain why you then you aren't embracing the feedback. 

You should have noted by now that it's all about being flexible, and being stubborn about anything you've written isn't going to work (see comments from Kurt!). 

Rule 11: Read it yourself

Here's a rule that Scott didn't have. Perhaps it should have been inserted higher up the list. As I've said elsewhere (here for example), it would help you to have your work read through by one of your colleagues before you give it to your advisor. But above all, you must be prepared to read ALL OF YOUR WORK  yourself. Not just the first time you write it, but for EVERY version. Please don't ever expect me to read something through when you can't be bothered to read it yourself. Or see the next top tip!

***Top Tip***

Do you hate reading your own work? Unless you are very unusual, the answer is probably yes! 

Before handing anything in, or sending it off to examiners or reviewers, you can have your word processor read it back to you. Many word processors (and even browsers) now have this facility. Not only will they find sentences that sound weird (or too long), but they will mechanically respond to your punctuation. This will help you with excessive or missing commas, full-stops, colons, etc. Try it!

This top tip comes to you from the Baxter-Gilbert-Riley school of robotic reading

Being concise is a great way to good writing, and the abstract is a case in point

I've yet to write a blog post about the abstract, but when I do, I'll try to remember to link to these 10 rules of being concise.

Please don't forget to read Scott's 10 rules as written by Scott. You can get them here: 

Hotaling, S. (2020) Simple rules for concise scientific writing. Limnology and Oceanography Letters  doi: 10.1002/lol2.10165

  Lab  Writing
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