Why do I need to cite?

20 September 2017

Why do I need to cite? Standing on the Shoulders of Giants...

Have you ever wondered what the blurb on the front of Google Scholar means? Who is standing on whose shoulders?

Essentially, it's a recognition that all research is built upon research that has gone before it, and this is the basis for citations in the text of scientific papers. Interestingly, although the phrase is often attributed to Isaac Newton, it turns out that Newton got it elsewhere:

If we dwell a moment longer, we can look back at the World's first scientific journal: Philosophical Transactions 

You can download the first of those papers of 1665 and note that there are no citations (other than to books or letters) because there were no previously published articles from which to draw. However, even then authors noted that ideas came from previous authors and we can recognise that acknowledgement back to Aristotle.

Research is built on existing work and ideas

It would therefore be very unlikely that your idea/ideas has no basis in existing literature. If you can’t find it, the chances are that you haven’t looked in the right way. Try Google Scholar, Scopus, Web of Science and vary the search terms or try searching for articles citing something similar. There are lots of ways to search, but maybe that's another blog post for another day.

Citations demonstrate to readers where your ideas have come from. Citations can also be used to reduce what you need to write – especially with respect to methodology. If you (or others) have already provided the methodology in full then you can give a much simpler description and the citation.

Where to cite?

Automatically, I'd suggest that you cite whenever you write. Using citations becomes habit forming, and you’ll end up wanting to use citations everywhere. Popular scientific writings tend not to have citations, but they can still be there but subtly different. Have a look at this example from The Conversation.

Within a manuscript for a scientific journal or in your thesis, you can expect that your introduction and discussion sections are going to be full of citations. The methodology may also have citations, and these can often save you needing to write a lot of sections which would otherwise be very detailed (see above).

Where within a sentence should the citation come?

There are a number of different styles, and this is likely to depend on the journal that you are writing for. The standard way is to use the name and year in parentheses at the end of the statement to which the citation is relevant.

The impact of all invasive amphibians is similar to that of invasive birds and mammals (Measey et al. 2016).

You’ll see that sometimes the names are brought into the sentence and become the central agents of the text. The phrase et alii (often abbreviated to et al.), literally means "and others" referring to the other authors (typically used when there are more than two - but check the journal format!). 

Sometimes, instead of "et al." you can write "and colleagues" or "and others". This is something to do occasionally when you are looking to diversify some text. Don't over do it though.

Measey et al. (2016) found that the impact of invasive amphibians is comparable to that of birds and mammals.

This technique is very useful when you then want to add another sentence or two about this same study.

Measey et al. (2016) found that the impact of invasive amphibians is comparable to that of birds and mammals. They did this by constructing GISS scores for all individuals in all groups. 

Because the authors are the subjects of the first sentence, the citation becomes implicit in the second sentence.  Then you don’t need to use the same citation again within the paragraph.

What about page numbers?

Sometimes you'll see a citation with a colon and page number after. This really only needs to be used if you are quoting specific text on a particular page:

Measey et al. (2016: 976) proposed that using GISS scores could show that "some amphibians can have devastating impacts to the environment". 

What about citations as taxonomic authorities?

Taxonomists have special rules for this, and I'll do it in another blog post. These are not the same as regular citations (because they don't appear in the literature cited and you don't have to have read the descriptions), and only some journals ask for them. 

Is it possible to mis-cite?

Yes. One of the most common ways in which students mis-cite a paper is to use statements made in the introduction (or discussion) which were not the subject of the study. For example, in the introduction of their paper, Measey et al. (2016) make comments on amphibian decline.

Amphibian populations are currently declining across the globe (Wake & Vredenburg, 2008; Collins et al., 2009; Pimm et al., 2014) and alien amphibians are at least partially driving these declines through competition (Kupferberg, 1997), hybridization (Dufresnes et al., 2015) and introduction of novel pathogens (Berger et al., 1999; Daszak et al., 2003; La Marca et al., 2005; Martel et al., 2013).

However, it would be wrong to give a statement on amphibian decline and cite Measey et al. (2016). They did not study amphibian decline. Instead, you should read the papers that they cite (Wake & Vredenburg, 2008; Collins et al., 2009; Pimm et al., 2014), and read around those to find studies on amphibian decline that are appropriate for your context. This underlines one important aspect of choosing citations where the statement that you make relates directly to the study carried out in the citation.

Another common mistake is to forget which paper has which information. You can try to make sure that you don’t do this by taking better notes or a more accurate plan.

Should I cite without reading the paper?

No. When you are citing a study, you should be sufficiently familiar with the publication that you are endorsing the study in relation with the statement that you make (but see below). If you are not convinced by the nature of the study that you are tempted to cite, then rather don’t cite it and use another one. If you can't get hold of the paper, this is another reason why you might not cite it. This is a regular reason given for why Open Access journals attract more citations. 

What should I not cite?

This does depend on the journal you are writing for. Some journals don’t permit citations to unpublished data or web sites. My suggestion would be to avoid such sources anyway (with particular exceptions – see below), unless it is really important that you include it. Other examples of texts to avoid are: text books (use the original paper instead), newpapers or magazines, predatory journals (or any non-peer reviewed article).

One exception to the not citing websites relevant to our work is the IUCN Red List. Note that all entries on this site now have DOIs, and this might be a good guide for what is available to cite. The DOI is very useful as it means that there is a consistent record of that version. Otherwise, you could cite any website (even this one) and then the owner can go and change the site and it no longer says what you thought it did. The DOI removes this problem there will always be an archived version with that particular DOI.

Do I cite the review or the primary literature?

This depends on the space you have and whether the review contains all the information you need to cite. It’s preferable to use primary literature, but sometimes reviews (or meta-analyses) are actually more expedient to use, especially if they are not the focus of your study. You can even cite both when relevant.

How many citations is enough?

Some journals have a word limit, or even a limit to the number of references that they allow. Others do not, and you should probably use what is recently published as a guide to what is acceptable. For the chapter of a thesis, you should err on the upper end; from 50 to 100 references. Note that citations may well be more as you may cite a paper more than once.

Obviously, everything you cite needs to be in the Reference (or Literature Cited) section, and you may well need to spend time deleting extra stuff. You can get around this common issue by using a citation manager like Mendeley or EndNote. I’d always suggest that you use one of these tools as they can really help with your reading too. These days they are busy turning into a kind of scientific social network. They regularly make suggestions of what you could be reading based on what you read. This can be useful.

If you are looking for multiple examples of a statement that you’ve made and there are many possible, I’d suggest that you aim to produce three. Make sure that you use a suffix (like “e.g.”) to show that you are aware that these are examples of a widely reported phenomenon. You can choose these as you like, but may want to consider using what you consider to be ‘the best’ examples, and/or references that you are planning to use elsewhere in your paper/chapter. This can drive the total number down considerably, and helps to keep the citations more relevant to your work.

Should I cite myself?

If you are publishing relevant and appropriate papers, then there is no reason not to cite yourself. In many cases (such as with your thesis work), your own publications are likely to be more relevant to methodology and subject matter than much of the other work that is out there. However, if you’ve previously published on termite fungus and now you’re publishing on frog toes, it’s unlikely to be relevant.

I would avoid citing your thesis if possible, rather put it all into papers. There are times though when citing your thesis is unavoidable. Within your thesis, I would suggest that you do provide citations to different chapters as this will help the examiners see how the chapters relate to each other.

Take a look at this article on self-citation. They claim that self-citations in the Natural Sciences run at 33% (Centre for Science and Technology Studies, 2007). 

Should I cite my friends?

It may be easier to cite your friends if you already know their work well. You may have heard them talk and know that the subject is relevant. They may be encouraging you to cite them, but should you?

In these days of scientometrics, we do need to acknowledge that citations act as a kind of currency. They count towards your H-index and this can reflect on your prospects as a post-doc or employee. What’s also clear is that cited papers get cited more, so it could really help your friends if you cite them. Obviously, the inverse is also true, so beware of the politics of citing. However, the most important points have already been raised (above). The study must be relevant and appropriate before it gets included as a citation in your work.

Should I cite my advisor?

Yes!

Does the impact factor of the cited article matter?

Papers in journals with high impact factors are more likely to be cited because their contents are already thought to be of interest to a wide range of people. That is something that the editors of that journal will have considered even before sending the manuscript to review. Sometimes (but not always) the impact factor of the journal can be an indication of the quality of the study. But you should judge this for yourself when you critically read the paper.

I find that the first paragraph of a paper is more likely to contain citations of higher impact journals. This is in part as these are likely to be more cross cutting (as is often the case for the first paragraph). In the end, if you need to make a choice, choose the paper that is most relevant, irrespective of impact factor.

  Lab  Writing

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 venerable 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