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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

Changing their behaviour

15 June 2020

Behaviour change and a hormonal link

Who could forget the fantastic visit or Carla Madelaire and Adriana Barsotti to the MeaseyLab back in January 2019 (see here)? The two spent only a few months in the lab, but worked super hard on a few experiments that drilled down into the relationship between hormones and behaviour of guttural toads when they are dehydrated.

Today sees the beginnings of all the fruit of their labors with the publishing of Carla's behavioural paper in Behavioral Ecology and Sociobiology!

This paper represents a significant step forwards as we show that after only 20 years of invasion into the dry conditions of Cape Town, Guttural Toads have changed the way that they think about water. When you find it, you stick with it! In this paper, Carla shows a link between this water finding behaviour and the hormone corticosterone. Adriana has another manuscript (submitted) that further investigates this phenomenon also with Guttural Toads. 

It was a great pleasure working with both of you and we look forward to more work and celebrations in the future (there will be cake & cachaça!). Last January, we celebrated their arrival (see here).

The intrepid duo catching toads in Durban with the all important yoghurt pot!

To read more about Carla and Adriana and their adventures in South Africa, see blog posts here, here, and back in Brazil here.

Madelaire, C.B., Barsotti, A.M.G., Wagener, C., Sugano, Y., Baxter-Gilbert, J., Gomes, F.R., Measey, J. (in press) Challenges of dehydration result in a behavioral shift in invasive toads. Behavioral Ecology and Sociobiology pdf

Publishing your natural history observations

12 June 2020

Publishing Natural History Notes

Traditionally, all accounts of the world around us were natural history observations. Early biologists had other jobs and practiced their natural history in their spare time. Professional natural historians were very often landed gentry for whom actually earning a living wasn’t a daily occupation. Philosophical clubs where these gentlemen (as at the time they were usually men - a trend that has thankfully changed) met and discussed their observations, and sometimes published the talks in pamphlet form for general circulation. These observations are at the core of the first publications in the first ever journal (see herefor some juicy examples). 

Accumulating natural history observations over time is a very powerful means of conducting science. However, this has largely fallen out of favour, due in part to the professionalisation of science and the proliferation of scientists who need to remain publicly accountable for their work. You can decide whether the demise of the monied classes that used their privilege to observe natural history was a good thing. But you can’t deny the power of the accumulation of many observations over a lifetime, which can be extremely important when you look at what cumulative observations can lead to, such as that of Charles Darwin and “The Origin of Species”. For a longer read on the interaction of ecology and natural history, have a look at this article in American Scientist.

In this series of blogs on writing and publishing, we have been mostly interested in hypothesis driven research (seehereandhere). But when you trace back the literature on which many of the original big ideas are founded (see here), they are almost always natural history observations. Hence, publishing natural history observations is important, and the recognition of this can be seen in the increasing number of journals that are prepared to accept manuscripts to accommodate these. 

What are natural history notes?

Natural history notes are accounts of novel information, once-off or multiple/methodical observations and range from a short paper to a few structured paragraphs. There are some observations that you know do have value, but are not necessarily in your line of enquiry or even direct interest. They expand our natural history knowledge, specifically with biological information not broad or detailed enough for a paper. But by growing the records of these published observations, we increase our understanding of behaviour, biology, and ecology. 

How do you decide whether your observation is worth a note?

Knowing what does and what doesn’t make a natural history note is probably related to your experience in the field, or down to how well read you are on a given topic. If you don’t know, and can’t easily find out (yes, google scholar is a good place to start -see here) whether or not your observation is important to record, then write and ask someone who would know. It is easy to communicate these days, and you might find someone that can help with relevant literature. You can always start by asking your advisor for some names. 

Of course, you may know (as soon as you make the observation) that it is noteworthy. So in this case, what should you record?

What should you record?

  • Time, date, location (preferably with GPS coordinates)
  • The species involved (and any potential interactions with any other species)
  • Environmental data (if you have it - remember that temperature and weather is very important for ectotherms)
  • Context and a description 
  • A picture, video, or sound recording of the observation (if at all possible)

Be aware that especially if you are in the field, it may not be possible to get some of this information again. So it’s really important to save as much as possible, even if you don’t use it all.  

Older biologists will likely tell you that there is no substitute for writing everything down in a field notebook. Actually, there is and you can record everything digitally, including dictating field notes. It’s then up to you to make sure that this is all backed up so that you don’t lose anything and light the touchpaper on the smug notebook holding oldies. Yes, your phone can do all this (and more), but you do need to keep your phone safe.

Whatyou must not do, is to try to remember anything in your head! This simply won’t work. It may be several years before you realise the importance of your observation, and by this time your head will have erased all of the important details. Notebooks are more fun to go back through, especially when they preserve some of your feelings at the time and often (for me) squashed invertebrates between the pages, that remind you of the genuine atmosphere. It becomes a kind of professional diary, and likely something that you’ll only ever be able to share with your future self. But it’s nice to share!

Where to publish your natural history note?

As you should know by now, my preference is for you to publish your work somewhere where it can be found by others. If at all possible, submit to something indexed in Web of Science or Scopus (see why here). 

Here are some ideas of places where you could submit your natural history note. Note that not all are equivalent, and you’ll only get very important observations into American Naturalist or Ecology, while nearly anything goes in Biodiversity Observations! In every case, you’ll need to consult the instructions to authors and make sure that your observation has what it takes. 

Indexed in Web of Science / Scopus

Not indexed

Herpetology Notes

African Herp News

American Naturalist

Herpetological Review

African Journal of Ecology

Urban Naturalist

Austral Ecology

Herpetological Bulletin

The Scientific Naturalist

(within Ecology)

Tropical Natural History

Bioinvasion Records

Biodiversity Observations

Once you’ve decided where you want to submit, I suggest that you download some of the published observations that will give you a good idea of the style that you will need to use. 

What needs to be in your natural history note?

Rather like any scientific publication, your natural history note needs to have some context for the observation. If the total note is only a paragraph, then this might be only a sentence or two. But if your contribution is going to be several pages, then you’ll likely need several paragraphs that provide enough background information for the reader to know why your observation is significant. Include sufficient citations to previously published records where relevant.

The observation itself!Try to include as much of the information that you collected at the time as possible. The journal will likely have specific ways in which each of these is to be provided, so make sure that you follow their instructions. You can include links to videos or recordings that are archived somewhere formally (either at the journal or there are plenty of collections for this stuff). Most journals will allow you to publish a picture if you have one, and for some you will have to have a picture in order to publish. 

Lastly, provide some discussion about why you think the observation is significant. Does it provide new insight into this taxon? Does it allow you to make management recommendations? What further lines of enquiry should be made now that this observation has been recorded? How does your observation fit into the bigger picture?

Some examples

I have published a few natural history observations (certainly not as many as Martin Whiting), and I will publish more. I store these in a special place (see here). 

An example of a favorite isMeasey & Turner (2008):

This is the amusing tale of what happened when Adrew Turner decided to put a live caecilian into his mouth! Yes, sometimes your friends do odd things to amuse you, and it kinda backfires. Andrew suffered greatly, and as soon as he started reacting I got out my notebook and started recording his symptoms. I sat and watched him for several hours as he spat repeatedly out of the taxi window on our way back to the hotel. Yes, there was great mirth in the entire episode, but I knew immediately that there was important significance as there had been no publications on the subject of caecilian toxins at that time.

[once I’m back in the office I’ll upload an image of the notebook page]

According to Google Scholar, this note has been cited 3 times, so it wasn’t all for nothing! However, I still regret not having got to my camera fast enough to get the picture of Andrew with a caecilian in his mouth!

Thanks James!

Many thanks to James Baxter-Gilbert who originally gave a presentation for the MeaseyLab that inspired this blog post. James also edited this post - so thanks again!

  Lab  Writing

Writing the Materials and Methods section

09 June 2020

Writing Materials & Methods

Previously, we have covered writing a paper as aformulae, theintroductionand thediscussion. There’s no real reason why I haven’t covered Materials & Methods or the Results sections, other than they tend to be easier than the rest. Here I am going to share some ideas to get you started on your Materials and Methods section. 

You should start writing this section in your proposal, and you may have to alter parts of it when turning it into your thesis later (if you change your methods). For most people, it’s a relatively simple exercise, but here are some pointers to get you started.

The Materials and Methods section should be citation dense, especially if you have used standard methods that have been written up elsewhere. If there are different methods, you should also explain why you used one over the other, as reviewers or examiners may require this. 

If you are introducing new methodologies, then you can expect to write a lot in this section about exactly how this was done, as well as the background to the reasons why the new approach to the methodology was taken.

Your aim is to produce a coherent methodology that anyone in the next 200 years can pick up and follow in order to replicate your study. 

Sections or subheadings

As ever, I’m going to recommend inserting section headers into your Materials and Methods to help you break it up into bite sized chunks. These are principally for the reader, but will also make your job easier.

Study organism or study system

Having already written the introduction (see here), you will know that there isn’t too much space to write a lot of information about your study organism. However, often there is important background information that is needed on the species, which would be distracting or lose the flow of the introduction. By having a ‘Study Organism’ section at the start of your Materials and Methods, you can add in all relevant information in a paragraph or two. 

For example, if you are working on African clawed frogs,Xenopus laevis, this would be the section where you can explain their distribution, that they are principally aquatic, or that they are invasive on four continents. You probably won’t need all of these points, but just the aspects of this species’ biology that is relevant to your study. You should make sure you know whether or not the journal requires the taxonomic authority. If you are not sure, include it now -see here for an explanation

Similarly, if you are working on Guttural toads,Sclerophrys gutturalis, you can write in this section the known dates when they were introduced to Mauritius and Reunion, and how we know that those animals came from Durban. You can also give details of their natural range in sub-Saharan Africa. 

If you are working on a community of animals, or it is the geographical region that is more important than any single species, you should explain the study system here. For example, if your study is about the fynbos, then you should provide some background information about this kind of vegetation here. 

If relevant, you may need to provide a map with the location of samples that you used in this section. My preference is to try to provide a composite figure that will also include an image of your study organism (if relevant). 

Animal husbandry

If you have kept animals in the lab in order to do experiments, then here you can provide details of their welfare: housing, feeding, light:dark cycles, temperature, etc. If you bred animals to produce your study life-history stage, all relevant information is needed here. All this information should be available from your ethics application. Some journals will want you to include the details of your ethics permission here.

Repetitive methodology

If you’ve used the same methodology for each part of your data collection (like DNA extraction, sequencing, etc.), you should have a section that explains all of this prior to any experimental manipulations done. It’s best to go to look to see what other people have reported on in order to know what level of detail to include. For example, 20 years ago it would have been important to include detailed information of how you extracted DNA from tissues. Today, you can probably say that you used a standard extraction kit or salt extraction without saying more. 

Experimental manipulations & data collection

If you have done more than one kind of experiment, it’s probably a good idea to give each a separate subheading. Be consistent with these subheadings between the Materials and Methods and the Results.

One very important point here is to fully explain the collection of all of the variables that are used in your analyses. Remember to use exactly the same names for your variables here, as you have in the introduction (and will use in your graphs, figures and Results sections). It’s very important that the reader gets this consistency across sections. Please also remember to include all units that you collect data in (there is a space between numbers and units!), and the accuracy of the measuring equipment used. 

Equipment: Many journals require that you name the company that you bought equipment from as well as the town and country where it was made. This is to help others that might want to buy the same equipment (although it’s a bit outdated in these days of multinational companies). You should try to get all of the model numbers of equipment as you do the work, so that you are not scrambling later on to find out what they were. It’s really quick and easy to take a picture of this at the time. 

If you have built or designed new equipment for your Materials and Methods, you can expect to make a diagram of this here, if it can’t be adequately described in a paragraph. 

Data analysis (or Data analyses if plural)

This section is getting increasingly longer as people do ever more fancy statistical manipulations. As above, it’s very important that you use the same names for the variables as you have introduced and collected them. In addition to explaining the specific tests that you performed, you should explain what roles the variables have as dependent, independent, or random variables in your model.

The independent variablehas variation that does not depend on that of any other measured. These are usually measured by you during the experiment.

The dependent variableis usually the one that you are testing to see whether any of the independent variables explain it.

Random variablesare subject to variations outside of your experimental control but that you want to make sure do not influence your interpretation of the dependent variable. Examples of random variables might be the order in which you did the experiment, or the position in your experimental setup).

You should be familiar with the terms above from when you formulated your hypothesis (see here for a refresher). 

Any transformation of any of the data that you collected (e.g. log, ln, cosine) should be mentioned here, along with tests that you performed to ensure that they adhere to the conditions required for the statistical test that you conducted. 

Give the name for each package in R that you use, together with its citation. Also give a citation to R as well as the version that you used in your analysis. If you don’t use the latest version of R, then your reviewers may want to know why, so always remember to update your version of R when you do your analysis.

Did you leave anything out?

By following your Materials and Methods, anyone else should be able to repeat your work. If there isn’t enough detail for someone else to conduct the same experiment or survey, then you will need to add this information somewhere. For example, a list of sampling points or a database of sequences might be needed in Supplementary Information.

TheMaterials and Methods section can often get overly long, and is relatively easy to edit to make it much shorter. In journals where there is a word count limit, you may want to move some of the Materials and Methods into a supplementation information section. 

  Lab  Writing
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