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Formatting your thesis

21 August 2020

Formatting your thesis

Let’s face it, after spending so much time writing your thesis, having it formatted so that it looks very smart for submission is gratifying. Try to make it a fun event by listening to your favourite music very loudly or having some of your banned tipple (do both if you dare!). It doesn’t require the same level of creative concentration required when writing your thesis, but it does need great attention to detail. 

Your university will have their own stipulation for exactly how they want the thesis formatted. In this very short blog post, I’ll point you to the relevant links for Stellenbosch University and provide a check-list for last things to do before you submit.

Here are the Stellenbosch University library guidelines on thesis submission. Ultimately, your thesis will be deposited to the library, so their guidance is golden:

This link has really useful guidance for formatting in your word processor: 

This is the link for the SU writing lab; apex/f?p=105:1:8087869729856:: NO::: . You can ask them to go over your MS drafts or chapters for spelling/grammar etc.

Your faculty will have their own requirements. Make sure that you consult the student handbook for your department of faculty:

Many of these final formatting requirements are also useful for journal submissions. Note that these all require time. If you don’t have the time, then please make your advisor aware what has and what has not been done so that you can prioritise what must be done before submission.

The following points are based on what may irritate or annoy your examiner (and you really don’t want to do that!):

  • Spell check - yes, it sounds obvious but doing a final spell check is a good idea. Not only this, but take the time to have your word processor ignore or add all of the special words (e.g. species or site names) that it doesn’t otherwise recognise. This will ensure their consistency throughout (within and between chapters).
    • Make sure that your language settings are set to ‘South Africa’. 
    • Look out especially for words that have different accepted spellings like those ending in -ise or -ize. Decide which you want and be consistent
    • Capitalisation of common names, place names and not adjectives. For example, ‘South Africa’ has two capitals, but ‘southern Africa’ only has one.
  • Grammar check - always good to take a final look, especially for chapters that you wrote some time back. 
    • Use the word processor automated options to help you. 
    • Have your computer or another device read the text so that you can hear anything obviously wrong.
    • Pay attention if you have used “we” or “I” and make sure they are consistent in your thesis. As a rule I encourage “I” in a thesis, unless the chapter is also a manuscript, in which case “we” is usually correct.
  • Page layout. Really important to get this right in your template. Make sure that your template has:
    • Correct paper size (A4 and not US letter)
    • Margins
    • Line spacing
    • Page numbers
    • Line numbers (really helps your examiners)
    • Headers & Footers. If you can manage a chapter specific header, it’s useful to show your name and a short chapter title.
  • Sections and subheadings. I’ve encouraged you to use subheadings throughout your thesis. Here you have a chance to number them sequentially. This is very useful for your examiners and may be a requirement for the university. Using the word processor’s built in functions will make this task consistent and easy.
    • I dislike writing within a formatted document (as word processors can start getting weird), so my preference is to cut and paste written text into a template at the end. 
    • Remember to give them a check through before handing it in. If you’ve done the sections correctly, then the contents page will come out right.
  • Title page - prescribed very strictly by the university. The librarians place the SU watermark after final submission to the library.
  • Content page - word processors can do this automatically if your thesis is formatted correctly throughout (see sections & subheadings above). 
    • You can check this to make sure that you’ve done all of your sections and subheadings correctly.
  • Acknowledgements - this is your time to say thank you to all the special people that have helped during your study. There are probably more than you realise, but in addition to your friends and family (who most people don’t forget), think about the people who administered the work, lab mates (past and present) who were always there to help, and people who gave permission at study sites. 
  • References - probably one of the most dreaded sections of any thesis preparation, but they do have to be done. If you’re one of these people that has everything in a database, then you’ll be laughing or cursing your database throughout. While it might be tempting to only look through the data within the database, spend some time to see how it’s displayed in the thesis. A mistake in the reference database will be multiplied many times in the thesis. Remember that examiners love to take a random look through the reference section to make sure that it’s all good. After years of painfully entering references themselves, they know just what to look for. 

Mistakes people make:

Other than the obvious things all mentioned above, here are some of the mistakes I’ve seen.

  • Submitting the wrong version (yes this does happen!). Probably worse if having a mixture of right and wrong versions for different chapters (worse because it takes longer to sort out)
  • Last minute additions to text with incorrect spelling and or grammar
  • Two correctly spelled synonyms sitting next to each other when only one is desired (probably came about when editing)
  • Leaving the ‘mystery sentence’ added by your advisor to make sure that you read your thesis one last time. When I’ve given the final nod to my students that their thesis is ready for submission, I always ask them to read it just one more time. I’m well aware that given how many times they’ve read it, they are unlikely to do it again. So, to give some incentive, I add an unflattering remark to the thesis in a random position aimed at the examiners. I reason that students are unlikely to want to insult their examiners, and so this extra push will be enough to have them read it one more time. 
  • Comments and or edited text (especially when it’s marked as being by someone other than the student).
  • Page numbers that start again and again at different sections
  • Lots of blank pages or spaces (avoid blank pages if you can, and try to limit the amount of blank space (never >half a page).
  • Leaving important people out of the acknowledgements (e.g. advisor, administrators, funders, etc.)
  Lab  Writing

Fearful of handing in work

14 August 2020

Fear of submitting written work

Are you fearful that your work won’t be well received? 

Is it really up to the standards that are required?

Could you do better if you just spent some more time?

These are all really common thoughts, and they go along with ‘imposter syndrome’ for a lot of early career (and even older) academics. There are some important points to think about here:

  1. Everybody has these ideas and you aren’t alone
  2. Handing in work and getting feedback is part of the learning experience
  3. The fact that you care so much about your work and how it is perceived is a good thing. If you didn’t care, then this would be a problem. 
  4. If you never hand anything in, you won’t get your post-graduate degree

Think of it this way

The process of writing is part of your learning process, and you aren’t learning alone. That’s why you have an advisor. While you think that there may be a great intellectual gap between you and your advisor, I can promise you that there isn’t. But your advisor is an experienced reader. Hopefully, there have been many students who have benefited from learning with your advisor (talk to them about their experience). They already work with a lot of students and help those people to bring their writing to a level where it can be accepted by an academic community. There's no reason why your work would be any different. 

Like other members of the academic community, your advisor also has experience of receiving critical feedback about their written work. Sometimes it is painful and sometimes it feels personal. But getting feedback (or peer review) is a fundamental part of the publishing process. Talk to your advisor and other lab members about this process. Ask people how they overcame their fear of submitting written work.

What can you do to help yourself overcome the fear of submitting written work?

1. Give it to a friend or colleague to read

Remember that most of what you write should be understandable to the majority of people who can read (think of The Conversation as a reasonable reading/understanding level). This means that you can give your written work to fellow postgraduates and postdocs and ask for feedback.

2.  Annotate your text with places where you are particularly unsure.

If there’s a certain part that you are struggling with, annotate it (add comment in word) and point out that you are struggling with this particular section

3. Ask for a meeting with your advisor

You can sit down together with your advisor and discuss the points where you are uncertain before handing in the work. Or, after you’ve written it you can ask for a session when you are given verbal feedback

4.  Produce a checklist

If you specifically worry that there may be errors in what you write (grammatical, spelling, plagiarism), then make a checklist that you can tick off prior to submitting. Once your check list is done, don’t mess with the written work again (or you could add more errors), just hand it in!

5.  Set a deadline for yourself

If you don’t already have one, having a set of deadlines that you give yourself to give your writing to work to colleagues and hand in to your advisor. If you know that you aren’t good with deadlines, share them with as many people as you can!

6.  Tell your advisor about your fears

There’s nothing like honesty. Your advisor may be able to cut you some slack, or might sit down with you and look at how the two of you can overcome this difficulty.

7.  If you have more than one advisor, there may be one who you are more confident to read your work, and you can suggest that reading is done in series (instead of in parallel - actually I’d advise this).

8. Talk to your advisor about what really gets you the most upset. If you can’t do this face to face, then you could annotate it in a reply to their comment. The chance is that your advisor doesn’t know how upsetting it is and you’ll be helping them in their future interactions with students.

9. Ask your advisor about their fear of handing in and get them (and others in your lab) to share their stories. You might find that you have common ground to start sharing how these problems can be overcome.

At the end of the day, this is teamwork. Either you and your advisor are a team, or there are a bunch of advisors helping you. It is in everybody’s interest that the job gets done. Getting a line of dialogue moving with your advisor is essential, even if you have to arrange a meeting about a different subject and then introduce the problem later in the meeting. You need to find a way of getting through the fear, and if it’s going to be a persistent problem, you’ll need to work out what works best for you.

  Lab  Writing

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
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