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Selecting key-words

03 September 2021

Selecting appropriate key-words

Key-words are very useful in your studies, because if you have a good selection, they can help nail down a good proportion of the literature that you will need to read during your studies. Moreover, if you have the best selection of key-words, then you can set up some automated notifications for when new items are published. The only problem then is pulling together the correct key-words. 

When you submit a conference abstract, or a paper for publication, you will also be faced by a demand for key-words. This is when I often draw a blank. What will be the appropriate key-words for my study? I can often think of one or two, but regularly journals want at least five. 

A method for finding key-words

Here is my method for finding appropriate key-words. It’s quick, but it does require a piece of free-ware:VOSviewer, which for me has become an invaluable research tool.

  1. Go to yourliterature databaseof choice (i.e. Web of Science, Scopus, PubMed, Dimensions.)
  2. Search for documents using the key-words that you are sure are appropriate
  3. Constrain the results to ~500 documents. 
    1. You can either do this with the search date (e.g. the most recent 5 years)
    2. Or you can simply take the first 500 documents that are found
  4. Download these ~500 documents in a tab delimited text file.
  5. In VOSviewer
    1. Press the ‘create’ button
    2. Create a map based on bibliographic data
    3. Read data from bibliographic database files
    4. Select the file that you downloaded in the appropriate tab
    5. Type of analysis
      1. Co-occurrence
      2. All keywords (you can choose here)
      3. Full counting
    6. You should see the total number of key-words in your downloaded file now
      1. Change the minimum number of occurrences of a key-word so that you have ~100 results (again you can choose what suits you)
    7. Press finish



You should end up with a network like the one below. Here I have used the key-words “invasive” and “fish” (following previous exampleshereandhere). 

In VOSviewer, you can highlight any one of these key-words and see exactly what combination they have been used in. I have selected examples that occur 10 or more times in my downloaded file. This means that I can be fairly sure that these are relatively common key-words to use in combination with the ones I know are good.

The larger the panel in this network, the more frequently the word is used. This should help you when you select your own key-words. For example, even though I had used the keywords “invasive” and “fish” to generate this network, one of the first things I noticed is that the term “invasive species” is far more common than “invasive”. Hence, the first thing I should do is to change the first of my key-words.

Some of the key-words relate to specific taxonomic groups. Others include the habitat in which the fish were sampled. Now I have a shortlist from which to pick the remaining 5 key-words that I need in order to submit my abstract or manuscript. Once you’ve made your selection, you can go back to your literature database, add this combination of key-words into a search and see what comes out. If you’ve done it right, you should see some familiar papers on similar topics to your own. 

If you found this article useful, then read more helpful tips about writing and publishing in these free OA online books written for biologists:

How to write a PhD in Biological Sciences

How to publish in Biological Sciences

  Lab  Writing

How to stand up to science deniers

24 August 2021

Talking to science denialists & the post-truth clan

I think we’ve all been in the situation where you are stuck in a room at some social event where you have to be on best-behaviour. But the person that most wants to talk to you is someone who just wants to tell you that everything you do is wrong and meaningless, and actually they hold the truth. They then proceed to tell you about some YouTube video that they’ve seen that convinced them that xxx (insert as applicable with moon landings, round earth, global warming, UFOs, all science or - especially these days - vaccines) are all bogus and/or are part of some conspiracy theory. You may get the feeling that the reason they’ve picked on you is that they know you are a scientist, and they basically want to sparr because they are sure that they can beat you. If you haven’t been in this position yet, it’ll happen to you someday soon, and in my experience is coming round more and more frequently.

Of course, the reason why this person thinks that they can beat you, is that they are planning to use the techniques that they’ve now trained themselves for using their ‘research’: i.e. watching whatever YouTube suggests now that its algorithm knows they are interested in this kind of thing. Their tactic will be to rattle off any number of tropes that if you have any inkling of an argument about why any one can be shown to be incorrect - they are ready to rattle off another. One of the major problems is that if you have an audience, especially an audience that is already sympathetic towards the denier, then your attempts to rebuff this person might actually backfire and reinforce the trope in them. 

This blog article is based on the ideas that Philipp Schmid and Cornelia Betsch put forward in their 2019 paper (get ithere). They concentrate on the types of message content that are safe to pursue as a science advocate when in public discussion with a denier. Note that they do not cover two other important points: characteristics of the sender (you) and receiver (them). You should probably not expect the receiver of your argument to publicly change their minds, or admit they are wrong. What you can hope to do is to bolster the audience’s belief in science as a way of pursuing truth.


Topic rebuttal

Topic rebuttal is to have a set of facts on a subject to hand that refute or respond to the claims of the denier. This is tough for a lot of us, as we are often not conducting research in the particular area of interest of the science denier. Yet, many of us are aware of some basics that can at least slow down some of the more outrageous claims. In order to use topic rebuttal on your denier, you should be well prepared on the topic of the debate. But the way deniers take on scientists is by constantly switching to new topics until they find one that you aren’t aware of how to rebut. This might make it look to an audience as if they know more than you do. Once they find the topic that you can’t rebut - what then?

The other string to their bow is for every topic that you can rebut, just to claim that this is your opinion - making it look to the audience like that topic was an even draw - while they move onto the next topic. By pitching your response as equal to their claim, they can keep slipping through the topics until you get stuck, and then they will end up scoring one more than you. Or this is how it will seem to the audience.

This is when you can turn to technique rebuttal. 

Technique rebuttal

Technique rebuttal will stand you in much better stead with an audience, because it will allow you to explain why the argument of the denier is wrong - not simply that they are wrong. Doing this, the audience will learn more about the nature of science, the need for evidence and that each topic is not an even score, but that you are the one who is scoring. Moreover, when the denier reaches a topic that you are not familiar with, you can explain that you don’t know the facts, but still go on to challenge the technique of their basis. 

What we can be sure of is that your science denier will not be challenging you on the basis of a scientific study. This means that their argument needs another technique from which they can make their argument. Let’s look at each of these techniques in turn, and discuss how to spot and rebut them:

Selectivity

Observational selection, or cherry picking studies, has come up a lot during the pandemic as the media (and science deniers) have turned their attention to articles being posted on preprint servers. These are studies that have not even met the silver standard of peer review (see why I call Peer Review a silver standard and not a gold standardhere), and yet are touted by deniers as good evidence when ten other studies that do not show any effect are simply explained away as bad studies (also conspiracy theory - see below). 

There are any number of reasons why we might expect good science to come up with a spurious results (i.e. Type I or Type II error, seehere). You can explain how science counters this with a consensus of studies. Importantly, is the concession that scientists will change their minds on topics if they find that their findings, or the consensus of findings of others, shows them to be wrong. 

Impossible Expectation

Any argument that has an expectation that is unrealistic. As scientists we know that absolutisms are not real. Whenever someone tells you that something is 100% safe or 100% effective, they are (1) wrong and (2) their logic is questionable because there are no such extremes in safety or effectiveness. For example, vaccines are neither 100% effective, indeed many vaccines have quite low efficaciousness. Nor are vaccines 100% safe, there are usually a small proportion of people who will have adverse reactions. What is important though is exactly how small that group of people is. For vaccines in public circulation, adverse reactions are likely to be less than 1 in 10 000 or less than 1 in 100 000. This will be similar for other common medications (like the contraceptive pill that turns out to have quite a high level of adverse reactions that many people are prepared to accept). This is one of the easiest arguments to spot among denialists, and you can explain to most audiences in simple terms what an unrealistic or impossible expectation is.

Conspiracy Theories

Spotting a conspiracy theory is quite easy. When deniers claim that there are scientists who are being paid to publish their findings, and that the overwhelming majority of scientists are simply being paid off (typically by big pharma, governments, tech industry, etc.) - then you know that they are resorting to a conspiracy theory. Sadly, there are conspiracies out there. They are regularly perpetrated by big pharma, oil and tobacco companies - and these commercial interests are prepared to pay tame scientists to publish, often in inhouse journals. Governments too are known to ensure that their scientists publish studies that reinforce their views. 

Hence, once you’ve spotted a conspiracy theory, you need to be careful how you respond. But you can go back to scientific consensus and work on how widespread results are unlikely to be the result of a conspiracy, and that these are more likely to be akin to cherry observational selection (see above).

Misrepresentation / False Logic

Denialists often fall into traps around faulty logic. You can find a list of thesehere. The most common errors are that one statement does not logically follow from the first. 

Another common mistake is that ‘something happened after, so it was caused by’ argument. This is a surprisingly common explanation, but fails to take an objective look at total evidence. This is especially common in people’s personal insight. For example, they took a vaccine, and then got sick. Therefore, the vaccine made them sick. Of course, there are lots of levels of this debate, including that there is a small chance that they really did have a reaction to the vaccine, but this doesn’t make the vaccine unsafe, because it is expected and experienced by a great many people.

Deniers will often eschew statistics, as being a way that lies are told. Again, there is some small amount of truth here, but large effects cannot be explained by faulty statistics, and once again the scientific consensus here is a valid response.

Fake Experts

The last technique that deniers often use are fake experts. Fake experts are real - and by this I mean that there really are people who are employed by universities that pedal bullshit (seehere for how to spot a bullshiter). When I worked as a post-doc for University of the Western Cape back in the late 1990s, there was a Professor employed in their Department of Zoology who had a career giving talks on alternative medicine. His experiments would never get published, because he failed to conduct controls or had very few replicates. But this did not stop him peddling his untruths around the planet. He would be invited to give talks to more people in more places than any scientist I’ve ever known. There is another retired Senior Lecturer from Stellenbosch University that sells fake kits to repel invasive polyphagous shot hole boring beetles. No doubt he has made a packet from claiming to be from the university. 

An argument built on a fake expert is rather like a naive version of observational selectionism (see above). They are relatively easy to spot, and then simply invite a discussion with the fake expert. Ask about specific studies that the fake expert has conducted, their results and where they are published. Expect to hear more connections to observational selection and conspiracy theories.

How to know when what you smell is bullshit

Carl Sagan wrote a great list that he called his ‘baloney detection kit’ (and I have renamed above). This is well worth reading because it is something that you can help teach a public audience into how not to get duped by a science denier again. 

Do take a look at the paper by Schmid & Betsch (2019) and read about experiments that they conducted on technique rebuttal and how effective the approach is with science denialism.

Schmid, P. and C. Betsch (2019) Effective Strategies for Rebutting Science Denialism in Public Discussions.Nature Human Behaviour3: 931–39.https://doi.org/10.1038/s41562-019-0632-4.



  Lab  meetings  Writing

Publicity for Nolwethu's work on Volunteers

20 August 2021

Volunteers get a well-deserved boost with a write up in the Cape Times

Nolwethu's study on how volunteers was written up in a piece for the Cape Times today. 

Nice to see this work getting the attention it deserves!

Jubase, N., Shackleton, R. & Measey, J. Help Heroes Fight Invasive Alien Plants Cape Times  20 Aug 2021

  Lab  Writing

IPCC confirms SW Cape is getting warmer and drier

19 August 2021

The southwestern Cape is getting warmer and drier - bad news for frogs

Many of you will be aware that the extreme southwestern Cape of South Africa is a frog biodiversity hotspot. There are four endemic genera and 36 endemic species that occur in the fynbos alone (see Colville et al.2014). It is also a hotspot where many species are threatened, as shown in the following image from Angulo et al. (2011). Reasons for the threats include habitat transformation and invasive species, but new data from the IPCC suggest what many of us have been thinking that the climate is getting worse for amphibians in this area.

Frogs from this area breed in seasonal temporary vernal pools, puddles or have direct-developing tadpoles that rely on seepages and moist environments. A combination of reduced rainfall and increased temperatures in this region is therefore bad news for frogs. 

This area of the world is also under high anthropogenic pressure. The City of Cape Town has expanded to include ~4.6 million people, all of whom require food grown in the lowland areas North and East of the city. Species in the mountains are generally impacted by invasive plants such as pines and acacias. 

The new IPCC WGI interactive Atlas (https://interactive-atlas.ipcc.ch/) with regional information allows users to plot mean temperatures and mean precipitation per decade from 1980 to 2015. The trended data demonstrates that this region of the world is getting warmer and drier. This is within living memory, and chimes with comments from the community that frogs are becoming generally less abundant when walking in the mountains. According to Barry Rose, who as a boy in the 1950s collected frogs for his grandfather, when walking in the mountains of the Cape peninsula he saw an abundance of frogs that would jump out of his path as he moved through the fynbos. Now they seem to be far fewer.

We have also seen this trend in our research on toadlets from the genusCapensibufo. Cressey et al. (2015) that are no longer in many of the places where they were found in the 1970s. We have also seen general analyses on the assemblage frogs in this area from Mokhatla et al. (2015).

Is climate to blame for enigmatic declines?

It is very hard to know whether climate change alone is reducing the overall numbers of frogs in the fynbos. But this does underline the importance of monitoring populations of the species that remain. Very few areas are being monitored, but we appreciate that there is a need for long term support for initiatives that are collecting data (Measey et al.2019). 

See the recent blog posts (hereandhere) to find out more about how the MeaseyLab is attempting to monitor populations of frogs by usingaSCRto quantify the density of calling males.



Literature

Angulo, A., Hoffmann, M. & Measey, G.J. (2011). Introduction: Conservation assessments of the amphibians of South Africa and the world. In: Ensuring a future for South Africa’s frogs: a strategy for conservation research. (ed. G.J. Measey), pp. 1-9. SANBI Biodiversity Series 19. South African National Biodiversity Institute, Pretoria. 

Colville, J.C., Potts, A.J., Bradshaw, P.L., Measey, G.J., Snijman, D., Picker, M.D., ProcheŞ, S., Bowie, R.C.K. and Manning, J.C. (2014) Floristic and faunal Cape biochoria: do they exist? In: Fynbos: ecology, evolution, and conservation of a megadiverse region. (eds. Allsopp, N., Colville, J.F., Verboom, G.A.) pp 73-93. Oxford University Press. 

Cressey, E.R., Measey, G.J., & Tolley, K.A. (2015). Fading out of view: the enigmatic decline of Rose’s mountain toad Capensibufo rosei. Oryx, 49, 521–528.https://doi.org/10.1017/S0030605313001051 

Measey, J., Tarrant, J., Rebelo, A.D., Turner, A.A., Du Preez, L.H., Mokhatla, M.M., Conradie, W. (2019) Has strategic planning made a difference to amphibian conservation research in South Africa? African Biodiversity & Conservation - Bothalia  49(1), a2428.https://doi.org/10.4102/abc.v49i1.2428

Mokhatla, M. M., Rödder, D. & Measey, G.J. (2015) Assessing the effects of climate change on distributions of Cape Floristic Region amphibians. South African Journal of Science;111, 2014-0389.https://doi.org/10.17159/sajs.2015/20140389

  aSCR  Frogs  Lab

Volunteering to remove invasive plants

13 July 2021

Impacts of volunteers on invasive plants

As a volunteer, it can sometimes be very disheartening to work clearing alien invasive plants, because they pop back up so quickly and the task seems so much bigger than you are. But, in a recently published study by Nolwethu Jubase, we show that not only do volunteers make a significant impact on the problem, but they get a lot more from it than just cutting down aliens. 

Being faced with a never ending barrage of invasive plants might seem enough to get your spirits down and give up. But in the Western Cape, volunteer groups are strong and derive great satisfaction from ridding the area of invasive species. Nolwethu estimated that their work amounts to nearly 5 300 ha of land cleared of aliens per year with labour costs equivalent to ZAR 5.1 million! This is a significant input into the fight against invasive plants, but the groups could do with better support. Currently, volunteers put their own monies into work needed at the sites, but need training for many of the aspects of removal and use of herbicides.

Of the many problems that the groups face, support from authorities seems particularly lacking. There is a great need for coordinating the groups so that their activities fit into the bigger picture. This role needs to be taken on by a national authority, such as SANBI. Particular problems faced by the groups included the movement of governmental organised alien clearing. Sometimes land cleared by volunteers is then cleared by government workers the next week. 

On the up side, volunteers get a lot out of their time spent removing invasive woody aliens from the fynbos of the Western Cape. They learn and get inspiration from others in the group and receive feelings of satisfaction, happiness and a sense of achievement. 

Read more about the study:

Jubase, N., Shackleton, R.T., Measey, J. (2021) Motivations and contributions of volunteer groups in the management of invasive alien plants in South Africa’s Western Cape province. Bothalia - African Biodiversity & Conservation 51(2), a3. http://dx.doi.org/10.38201/btha.abc.v51.i2.3 pdf

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