Growling Grass Frog Metapopulations

Growling Grass Frog metamorph (photo: Geoff Heard)

The Growling Grass Frog (Litoria raniformis) is a great example of a species that can be modelled as a metapopulation. The dynamics of Growlers (as they seem to be known to those who study them) seem to be dominated by relatively frequent extinction and re-colonization of wetlands depending on their condition and arrangement.

Geoff Heard, who presented today’s lecture on metapopulations in Environmental Modelling, has been studying Growlers for years, particularly around Melbourne where they are threatened by urban development. You can learn a little more about them at Geoff’s website.

Population dynamics

Michael Bode has just covered population dynamics in Environmental Modelling. So it is excellent timing that we’ve just published a post by Brendan Wintle about population viability analysis on qaeco.com. You can read it here, or a recent short synopsis on population viability analysis here by Hugh Possingham and me, which has just appeared in the Encyclopedia of Environmetrics.

Unloved biodiversity and coextinction

In the Global Environmental Change lecture today, I spoke a little about how invertebrates are often under-represented in scientific research, and also about some interactions among species. Extinction of two or more species species because of their relationship to each other is known as co-extinction. Such co-extinction is related to one of Jared Diamond’s “evil quartet” of biodiversity threats. Here is a blog post touching on co-extinction, particularly for under-appreciated species.

And just to prove that karma exists, if you make a joke comparing the appearance of a species and the person it was named after, you might expect payback. I hope you all campaign to save McCarthy’s plant louse, a co-threatened species in Western Australia – yes, it is a sapsucker…

Conservation decisions and reserves

The last few lectures in Environmental Modelling have tackled the issue of conservation decision making. Here I will link to a couple of interesting pieces about Australia’s new system of marine protected areas. These new marine protected areas cover a massive area of ocean. But it has been criticized because it is not representative, and it doesn’t address threats. Authors of these critiques are some of the world’s foremost experts on systematic conservation prioritization. The critiques show how systematic conservation planning could lead to better outcomes.

And, as an aside, Heini mentioned the SLOSS debate. You can read a little about my own take on it here.

Edit: And here is a paper about six common mistakes in conservation priority setting.

Research Assistant job at Monash University

Applications for a research assistant position (full-time for 12 months) close tomorrow evening (27 March). Associate Professor Melodie McGeoch, who is highly recommended by Carly Cook of my lab group, is seeking an RA with skills in GIS and plant identification. More information here.

How to structure your writing

This week in Environmental Modelling, we tackle models of noise and sound propagation. Part of this examines impacts of traffic noise on species. You can access a just-accepted paper that models effects of traffic noise on bird communication here. However, rather than write about that (Kirsten Parris will do that in the future), I decided to extend the previous post on direct writing, and discuss how to structure paragraphs, using a relevant review paper as an example.

Here I show how a piece of writing essentially should aim to be a story that follows a series of steps. Each step is a paragraph. Summarise the main point of each paragraph, and then order them. You should see that the steps follow a logical path.

In the following, I deconstruct a review of effects of noise on species (Barber et al. 2010; if you can’t access the paper from the journal due to the paywall, you might be able to get a copy here). I do this a paragraph at a time, illustrating how I see this review constructed. Let’s go:

  1. The first paragraph is an abstract that summarises the content of the review. Being able to write an informative concise abstract is a good skill to learn.

Anthropogenic noise and masking

  1. This broad introductory paragraph notes where noise sits in relation to other major threats to biodiversity. It could conclude with a brief overview of the structure of the review, just to help the reader understand where the argument is going.
  2. Why is noise possibly a problem, touching on the topic of masking.
  3. Some details about masking.
  4. Some information about the response of species to anthropogenic noise.

This section finishes here. It is largely introductory, touching on some of the main ideas that will appear throughout the rest of the review. Aside from content, these first few paragraphs are very important for engaging the reader, making them want to read more.

The scale of potential impact

  1. This paragraph is a change of tack, so a sub-heading is used. The main point of the section is that noise is ubiquitous. This paragraph notes that transport is a major source of anthropogenic noise.
  2. Noise intrudes into natural areas
  3. Roads are a major source of anthropogenic noise. This paragraph might have followed on better from para 6: transport is a major source of noise, roads are a big contributor to this, and the noise that is produced intrudes into natural areas. It flows better that way, doesn’t it?

Acoustical ecology

  1. Another change of tack, so another sub-heading is used. Acoustic signals in animals are important for reproduction.
  2. These signals are also important for a range of other reasons.
  3. There are also cross-species roles for acoustic signals.
  4. Examples of how sound, other than acoustic signals, is important for species.
  5. The acoustic environment is complex, so masking from anthropogenic noise could have surprising and important effects.

This section provided background material and examples of how sound is important for species.

Separating anthropogenic disturbance from noise impacts

  1. A new section, devoted to distinguishing effects of anthropogenic noise from other disturbances, is introduced. It opens by noting that anthropogenic noise is correlated with changes to species, but the noise is confounded with other changes caused by humans.
  2. More on the difficulty of separating the effects, focusing on quiet disturbance by humans.
  3. The need to control for these other effects, noting a step towards doing that.
  4. And another step toward doing that.

Recent findings…

  1. Another new section, on recent literature, including how to deal with the confounding through experiments. The first paragraph of this section describes an experiment in the field, and one in the lab.
  2. Describing a similar experimental design to the one in the previous paragraph. This one had some unexpected results, which actually make sense when considering the complex auditory environment (links back to the previous discussion of the complex auditory environment).
  3. Another section really starts here, I think. This paragraph covers the types of changes in acoustic signals that have been observed, across all sorts of species.
  4. Some more on responses to noise, noting that some species might not be able to compensate for the noise.
  5. More on about how species respond to sound – a bit of a grab bag of examples.

These last three paragraphs are really about the response of species to noise. They would fit under a sub-heading of that name. “Recent research” isn’t really a good heading – it doesn’t convey a useful story, certainly not in the middle of a review, and given that the review doesn’t cover material chronologically but rather by topics/themes. The first two paragraphs of this section really relate to the question of noise being confounded with other changes, so they could have been better placed in that section, and focusing this section on responses of species.

Adapting to a louder world

  1. A new section about adaptation to a noisier world.
  2. This paragraph covers more about evolutionary selection in noisy environments.
  3. Covers the ability of species to adapt to noisy environments, which is likely to be constrained.

Conclusions and recommendations

  1. A concluding section. What does this all mean? The influence of anthropogenic noise is important, and the authors also promote the importance of behavioural ecology for conservation (a bit of a plug for their research field in one of the highest profile ecology journals).
  2. Evidence of effects of noise is not particularly convincing in any of the single studies (e.g., due to confounding, and other reasons as noted previously), but taken together, they suggest important impacts. Experiments in this situation are important.
  3. The final paragraph. Noise might need to be managed to assist conservation. Note how this concluding paragraph links directly back to the topics raised in the first paragraph – that is ideal. We start with an issue, present some evidence, finish with a conclusion. So, actually, they did foreshadow where the review was going. It sought to convince the reader that anthropogenic noise was important for conservation. The authors could have lit the review’s path a little more clearly.

If you look at the section headings (or at least if you include my suggested headings), you will see a story:

  • Anthropogenic noise might be important for species that communicate acoustically.
  • Anthropogenic noise is just about everywhere.
  • The acoustic environment is important and complex, so a range of influences of noise on species might be expected.
  • It is hard to separate effects of anthropogenic noise from other changes caused by humans, but…
  • There are lots of studies across many different organisms that suggest effects.
  • Species might be limited in their ability to respond to compensate for anthropogenic noise.
  • So anthropogenic noise may be an important for conservation, especially given all the other threats faced by biodiversity.

This is a very nice review. If you look at the above structure, it makes sense as a way of constructing an argument; the review follows from one topic to the other. The review itself simply expands these basic points, gives extra details, notes weaknesses, and provides evidence to support these claims, using an impressive amount of literature from a relatively wide range of fields. The review also suggests the research field’s future direction.

So when writing anything, you should be able to summarise it as a series of steps. Each step will require more details and supporting evidence. You might note contradictory evidence, and how that might be resolved, or some other suggestion about where the topic is headed.

In any writing, think of the main point you would like to make. Then construct the basic steps required to argue that point. Fill in the details and supporting and contradictory evidence, and you are done.

Reference

Barber JR, Crooks KR and Fristrup KM (2010) The costs of chronic noise exposure for terrestrial organisms. Trends in Ecology and Evolution 25: 180-189.

Writing, writing, writing, …

Phil Gibbons, a  colleague from The Australian National University, told his class “undergrads are crap writers“. Now, that won’t endear you to your students, unless you have Phil’s lovely wry humour.

But everyone can improve their writing, undergrad, postgrad or seasoned scientists alike. How can you write well? David Salt, a professional editor and writer in the environmental arena, recommends using plain English and active voice, keeping things short and simple, varying sentence and paragraph lengths, and being enthusiastic. And you will need to practise.

In my Grad Seminar class, we examine tips to improve writing. Try writing as if telling a story to help structure your paragraphs and order material within your paragraphs.

Also, simplify your sentences. There was a time when it was seemingly usual for people to prepare written scientific material using extremely long-winded passages that might have been unnecessary, but were thought by some to cast a certain air of importance, especially with the use of passive voice*. It was mostly hot air of course. Write succinctly using active voice. Your readers will thank you**.

Measure your writing’s girth with The Writer’s Diet test, which will highlight problem areas. Jargon makes some science writing heavy on large nouns (e.g., nomilizations), so some highlighted problems might be fine, or at least unavoidable. Otherwise, this test is very helpful.

Results of the Writer's Diet test for a slightly earlier version of this blog post. See http://www.writersdiet.com/WT.php for details of the test.

Results of the Writer’s Diet test for a slightly earlier version of this blog post. See http://www.writersdiet.com/WT.php for details of the test. As an aside, an even earlier version rated as “Flabby”. Some of my previous writing has achieved “heart attack territory”. We can all improve.

Writing succinctly improves communication. Similarly, good grammar is important. Some might claim that poor grammar is unimportant when the meaning is still clear. However, poor grammar takes longer to read, and everyone has a finite life, so it takes away time from doing other things; effectively, your poor grammar is killing your reader.

Just as good grammar is a matter of following convention, scientific writing has other conventions. Here I list a few common issues I encounter regularly:

1. Know the difference between a figure and a table. A figure is a diagram or graph. A table displays tabulated data and information. Avoid presenting the same data in both figures and tables.

2. Place a figure caption under each figure. The caption should make the figure interpretable without reference to the main text. Cite all figures in the main text. Number them in the order in which you cite them. Identify the units in axis labels of graphs.

3. Place a table heading above each table. They serve a similar purpose to figure captions, with sufficient detail that the table can be understood without reference to the main text.

4. Use units appropriately by separating the number from the unit. For example, write 5 kg, not 5kg. If using the units as part of an adjective, you could use a hyphen between the number and unit (e.g., a 5-kg mass).

5. Make sure the labels on figure axes are readable. Remove items from figures that do not communicate important information (e.g., grid lines and 3-d effects are often unnecessary).

Want more pointers? Click here for some examples of succinct writing. And please suggest other tips via the comments.

*As a task: re-write this sentence more simply in active voice.

**A previous graduate emailed me recently saying that she hoped I still taught succinct writing skills because she uses them frequently in her job.