Julien defends his thesis

19 September 2017

Julien Courant defends his PhD thesis 

Congratulations Julien! Doctor Invaxen Courant defends his thesis infront of a jury of amphibian experts from around the world. 

Invasive biology of Xenopus laevis in Europe: ecological effects and physiological adaptations

Julien has already published a lof of papers from his thesis, but there are still some great ones to come...

Courant, J., Vogt, S., de Villiers, A., Marques, R., Measey, J., Secondi, J., Rebelo, R., De Busschere, C., Ihlow, F., Backeljau, T., Rödder, D. & Herrel, A. (2017) Are invasive populations characterized by a broader diet than native populations? PeerJ 5:e3250 DOI 10.7717/peerj.3250 pdf

Rödder D, Ihlow F, Courant J, Secondi J, Herrel A, Rebelo R, Measey GJ, Lillo F, de Villiers FA, De Busschere C, and Backeljau T (2017) Global realized niche divergence in the African-clawed frog Xenopus laevisEcology and Evolution 2017;00:115. pdf

Ihlow F, Courant J, Secondi J, Herrel A, Rebelo R, Measey GJ, Lillo F, de Villiers FA, Vogt S, De Busschere C, Backeljau T, and Rödder D. 2016. Impacts of climate change on the global invasion potential of the African clawed frog Xenopus laevis.  PLoS ONE 11(6): e0154869. doi:10.1371/journal.pone.0154869 pdf

De Busschere, C., Courant, J., Herrel, A., Rebelo, R., Rödder, D., Measey, G.J. & Backeljau, T. (2016) Unequal contribution of native South African phylogeographic lineages to the invasion of the African clawed frog, Xenopus laevis, in Europe PeerJ 4:e1659 

Louppe, V., J. Courant and A. Herrel (2017) Differences in mobility at the range edge of an expanding invasive population of Xenopus laevis in the West of France? J. Exp. Biol. 220: 278-283.

Courant, J., J. Secondi, V. Bereiziat and A. Herrel (2017) Resources allocated to reproduction decrease at the range edge of an expanding population of an invasive amphibian, Xenopus laevis. Biol. J. Linn. Soc. DOI 10.1093/biolinnean/blx048

  Frogs  Xenopus

Writing a paragraph

17 September 2017

Writing a paragraph

Last month I wrote a blog about writing a scientific paper in a formulaic style, as well as the advantages that this has over starting from scratch each time. The suggestion was that once the data is collected, and the analyses are complete, you sketch out your paper in a 'bullet-point' outline. This outline will give you an idea of the subject in each paragraph, as well as how the paragraphs fit in with each other. The other suggestion was to assign citations to this outline to help you remember those main ideas.

Writing paragraphs has a skill all of its own, and the aim of this blog is to go over the basics of how to put a paragraph together.

In the paragraph above, the topic sentence is red, the supporting sentences are green and the clincher is blue.

Topic sentence

A topic sentence allows the reader to understand quickly the idea/topic you are putting forward in the paragraph. It must be in the context in which you are going to develop the same topic. There’s no point in just mentioning a topic in passing or using it in a different way than you will later.

Make your topic sentence relatively simple. Don’t be tempted to add multiple clauses. If the topic sentence is too complex, you’ll lose your reader right at the beginning of the paragraph.

Supporting sentences

Supporting sentences convey all the relevant information to the reader. They are going to be statements that are well cited, showing readers where the original ideas came from. Be sure to keep these sentences on topic, and regularly refer back to your outline to make sure that you keep to the original objective of the paragraph. These are the meat of the paragraph and it’s really important to get them right.

If you are writing about differences, then state which way the difference is. If bullfrogs are larger than leaf litter frogs, then say this. Telling your audience that something is different than something else only ends up leaving them guessing about the way in which the things are different. There’s no point in drip dripping this information through. Set it down in as little space as possible so that your reader doesn’t get bored.

Sentences within the meat of the paragraph interact, and there’s a great example to show how this is done here. These interactions usually dwell around pertinent variables (such as those that you are going to deal with in your paper). By using the same or similar words within the paragraph, you are able to demonstrate to the reader how those different points interact.

While repeating the names of the variables, or their abbreviations, can be helpful, repeating descriptive words becomes quite tedious to the reader. Repeatedly reading the same ideas repeated over and over quickly bores the reader (yes, I'm repeating myself - boring isn't it). It will also give the reader the impression that your vocabulary is very limited. These days you can do a quick right click on highlighted word to get a drop down list of synonyms. This can allow you to go back and replace your repeated word with: recurrent, frequent, recurring, repetitive, constant or continual. That’s more than enough to spice up the paragraph. However, if you’re not sure whether a word is correctly replacing another, ask a friend to read it.

Use an example

Examples are a very powerful way of conveying ideas in a short amount of space. Don’t replace your paragraph with an example, but do use an example if it shows the reader just what you want. You should be able to do this in a sentence (or two), but if you’re tempted to go on, it’s probably not a good example. Because the first paragraph sets out ideas, it's unlikely that an example there will be a good idea.

Avoid lists

I’m not a big fan of paragraphs which are simply a long list with little or no thought offered. The worst ones are where there are so many citations along the way that it’s really hard to pick out what is sentence and what is citation. I understand that it’s important to show precedent and that there is merit in showing how widespread an idea is over taxa or in different disciplines. You never find these lists in journals where words and/or citations are limited, which suggests that you can dispense with them.

Don’t bamboozle

It’s easy to use jargon. The whole point of jargon is to convey a (usually complex) idea in a short amount of space. Using a word (or two) instead of using several sentences clearly has some advantages. However, there is such a thing as too much jargon. Simply put, it’s unnecessary to use jargon when you can use plain English in the same amount of space. My old tutor at Liverpool University, the late, great Brian Moss, shared the following example of too much jargon, when plain English would have been much shorter. The fact that it gave Moss a chance to write about moose wasn’t lost on anyone!

Brian was so unhappy after reading the above that he felt compelled to write the following letter that was published in the BES Bulletin.


The last sentence of the paragraph: the clincher

Once you’ve conveyed all of the information that you planned to impart in your outline, it’s time for the last sentence. This should conclude the evidence that you’ve provided on your topic. Try not to make it lame. For example: “This shows that little work has been done.” Instead, make it a real clincher about why the topic is important, or how and why you will tackle it. Instead (or as well if you can), you may want this sentence to link on to another paragraph (topic), especially if flow is important at that part of your outline (see below). Either way, make sure that your last sentence is on topic, and one that sticks in the readers’ minds.

Above all - read it!

Your paragraph is not finished until you've read it. Reading is an essential part to writing that cannot be emphasised enough. If your paragraph and any other text doesn't make sense to you, it sure won't impress anyone else. If you can't bear to read it through immediately, then do it after you've written two or three paragraphs. I suggest that you don't wait until you've finished the manuscript. Rather get the text right as you go along.

How does the paragraph fit into the flow?

So now we’ve gone over the formula, it’s time to take a step back and look again at the paragraph in the context of your outline. Remember that the paragraph represents a single subject, but that it is still just part of the manuscript as a whole and you need that to flow from beginning to end. This means that it’s not enough to write each paragraph in isolation, but to think of the way in which they link together as a whole.

I am very fond of ending a paragraph on a linking sentence. Essentially, this shows how two ideas are connected in the last sentence. This really helps with getting the flow of an introduction or discussion, but linking sentences are not always the best way to end a paragraph. Sometimes there’s no option but to change the subject completely, and then you should go for the clincher idea (see above). For example, you may want to end the paragraph by seeding a new twist on the paragraph’s idea.

Seeding ideas

The introduction sets out the established literature in order to put your study in context, but your discussion provides you with an opportunity to present new ideas, or to turn and twist existing ideas in a new way. Once you’ve got a good idea what these are, I like to seed the introduction with hints as to what these might be. Sowing seeds early in a manuscript will provide the reader with hints as to where you are going. Writing these seeds as questions is a really good way of sowing them into an introduction. You can then go on to answer them (if only partly) in the discussion. Beware though, there’s no point in asking a major question in the introduction to which your data has no relevance!

Breaking the rules

Just as in the other blog post on formulaic paper writing, when writing a paragraph you shouldn’t feel totally constrained so that you can’t break the rules. Breaking the rules can set you free, and much of what you read that really stands out will do this. However, it’s much easier to break the rules and get it wrong, than break them and get it right. The idea of this blog was to help you get started, not to communicate with those who are already writing great stuff. So if you're already great, don't break it by doing any of this!

  Lab  Writing

Why are we disinterested in animal invasions?

08 September 2017

Why are we disinterested in animal invasions?

Invasives in the Cape Discussion Group is a regular discussion group focussing on invasions that are happening within the fynbos. Hosted at the CIB (and usually led by John R. U. Wilson) the group consists of representatives from SANBI, City of Cape Town, CPUT, UWC, ARC, DAFF, DEA, CapeNature, and the CIB. 

Agreeing to cover for John while he was away, I posed the question: Why are we disinterested in animal invasions? The Cape is replete with animal species which we appear to ignore, or prefer not to think about. Can we define why so many animal invasions are not important to us - or define how and when we would definitely do something? This month's meeting will focus on the current suite of animal invasions in the Cape and ask which we should be doing more about.

Despite having a circulation list of 105 people, we were only 6 for the meeting (from left to right): Nitya Mohanty, Florencia Yannelli, Marike Louw, Phil McLean & Sarah Davies. 

Our numbers spoke volumes about the disinterest in invasive animals. 

Nevertheless, we made a list of Cape invasive animals and the reasons why they were not controlled or eradicated. Note that the list isn't exhaustive but gives some indications about why animals are so hard to tackle. First, control of many species were found to have ethical or economic conflicts (C). Invasions of many species were considered to be to far advanced to be feasible to control (F). Whether or not research was needed before a decision on control/eradication could be made (R). Lastly, many of the species are utilised, potentially causing further conflicts with their control.

  Lab  meetings  News

Fossil frog bone publicity

01 September 2017

Not just old bones

Publicity for Thalassa's publication about Ptychadena  fossils from Langabaanweg in the SANParks Times.

In this article, Thalassa explains about the significance of the finding of Ptychadena  bones from close to Cape Town in South Africa's winter rainfall zone. 

Read the original paper published in the South African Journal of Science here:

Matthews, T., Measey, G.J. & Roberts, D. (2016) Implications of a summer breeding frog from Langebaanweg (South Africa): regional climate evolution at 5.1 Mya. South African Journal of Science J Sci. 112(9/10): 20160070

  Frogs  News

Formulaic writing?

29 August 2017

Is it worth writing a paper to a formula?

Sometimes it seems that every paper I read is just repeating the same formula over and over again. I even tend to forget that it's there until someone breaks the mould. Breaking the mould produces papers that really stand out, captivating the reader straight away. So why aren’t we writing those manuscripts every time we write a paper? Moreover, why don’t we teach students to write standout papers that will captivate everyone. Should we really be teaching formulaic writing?

Here I argue that not only is writing to a formula good practice, but it’s the best way to learn scientific writing. When you look to see who is writing those knock-out articles (i.e. "broken mould"), the answer is that they are really experienced researchers who have written hundreds of papers, and (unlike some of us) in doing so have learnt the essence of great writing. Such greatness is not innate and comes rarely to any researchers (even those who have written hundreds of papers). That's why I suggest to my students that they follow the formulas that are by now well recorded in many blogs and websites on scientific writing.

There is another reason why writing to a formula is recommended. Not only is it easier, but because it is so common and widespread, it also gives the reader a familiarity which to read your work. This means that editors are able to skim through and find exactly what makes your work worth publishing, and it means that those who are only semi-interested are more likely to cite your work.

So what is the formula?

At this point in the meeting I usually go to my white board and start drawing funnels (as a metaphor) and blocks. However, others have much better diagrams and here I’ve adapted an idea from Brian McGill’s blog, which you can find in full here. But you can also find other useful material here in a paper by Sheela Turbek and colleagues, and here in a paper by Kevin Plaxco. If you are of the Twitter persuasion, you get lots of useful tips and links from @WriteThatPhD and @Write4Research.

The diagram below is supposed show the movement of a liquid medium from one vessel to another. This is to make you think of your readers' understanding moving fluidly from one section to another. The introduction concentrates the ideas into your particular approach, while the discussion allows the reader to understand how your results fit into the larger body of knowledge. 

But what goes into the top, and perhaps more importantly, what comes out of the bottom? I'd like for the discussion to end in a greater understanding of the system for the reader. But maybe if we could also inspire the reader to read more, that would be a great result.

Once again, I should stress that this is not the only way of writing a scientific manuscript, but it has two really important qualities which I recommend to my students: i) it makes writing easier, and ii) readers will be familiar with the style and this will help them understand your work.

So now that you've got the idea that writing to a formula is a good idea, what next?

If you are reading this because you have to write a thesis chapter, a grant application or a proposal, I'd suggest that next you go and read 5 other relevant papers in your field and annotate them to see how well they fit into the formula described above. This will give you a practical idea of how the formula is put into practice. 

Next, I suggest that you begin to plan out your formula as a bullet-point outline. Start by writing a general sentence for the subject of each paragraph. Then use sub-points to plan each sentence within the paragraph. Lastly, annotate these with citations that you want to use. 

Now, it's time to start writing. But before you put finger to keyboard, I'd suggest that you read some more about writing paragraphs. You can find some really good advice on how to write a paragraph here and here

And if that's left you feeling like you can't even start. Remember that the best way to start writing is to do just that. It's unlikely that your first effort will be the one that you will finally submit. But by starting to write, then going back and polishing, and polishing you will achieve your goal. 

When is it good enough to submit to my advisor?

Firstly, I'd prefer to see the bare and then fleshed outline before you start the writing proper. This would mean that we are on the same page and that you will submit something that is planned and thought out. Once you've read and revised the draft text three times yourself, and you feel that you can't really improve it any more, hand it over. If possible, hand it to an office mate or other friend first. Your reader shouldn't have to be an expert in your field, but only a loose grasp on scientific writing is required to follow any paper.

When you get your critique back, remember that if they couldn't understand it, you have to change it. Don't blame the reader! But perhaps we're straying into another area of academe here...

  Lab  Writing