What does writing your PhD have to do with Shiny Apps? 

Shiny apps are R based interactive web applications that sit on a Shiny server. They make it easy for users to create plots and tables through a series of sliders or dropdowns. How to Write a PhD is already an interactive book in that readers can request alterations and additions (see here). But the book itself was static - until now. In the past 2 weeks, I have started to insert Shiny Apps into chapters where they might enhance content. 

The first example appears here in the chapter on Time Management. I know from my experience teaching students in my class on Writing Skills that although telling them that drawing a Gantt Diagram to plan their first year of studies sounds easy, they struggle with getting started. So here's a Shiny App that does just that: 

Don't take my word for it - have a go yourself!

The other Shiny App explains in set theory how Boolean Operators work. Here it is:

Perhaps more controversially, the last Shiny App shows you how you could get started on writing the first paragraph of your discussion. An oportunity to get input from AI is also provdided together with a caution: Please remember You may use the AI generated text to help and inspire you to compose your own text, but do not copy and paste it. A full explanation of why this is not acceptable can be found in an earlier chapter on using Artificial Intelligence. Here it is:

If you like these Shiny Apps, and have an idea about which app should come next in  How to Write a PhD or How to Publish Science, then let me know! 

Visiting the Chinese Academy of Sciences - Kunming Zoological Institute

The Chinese Academy of Sciences hosts many of the premiere research institutions in China, including the Kunming Zoological Institute which shares its grounds with the Kunming Botanical Institute, a few kilometers north of downtown Kunming. I was very interested in meeting Che Jing and her research group, who have received international acclaim for their groundbreaking work on amphibians. In turn, they invited me to visit KZI and give a talk.

It was a great pleasure to meet so many keen and enthusiastic early career resaerchers, and all interested in amphibians. It was a special pleasure to meet Alex Karuno, originally from the Kenyan National Museum in Nairobi. Alex studied with Patrick Malonza before he moved to China to continue his PhD studies. You can find Patrick's name at the top of a list on my CV page. 

Alex should finish his PhD by the end of this year, and we wish him all the best for doing that! 

Now an adjunct Professor in Japan!

Regular readers of this blog will know that I visited the Amphibian Research Centre at Hiroshima University in June 2024 (see blog post here). Since then, Profs. Takeshi Igawa and Hajime Ogino and I have been scheming for my return in 2025 when I will conduct a large experiment at the ARC. To make this all easier, I have been appointed as an adjunct Professor at the university. 

It is a great honour to be associated with such a great institution. I greatly look forward to conducting my research there.

Jonathan and Sasha graduate

Graduation time is a celebration of years of hard work. Today, it was the turn of Sasha Dines PhD and Jonathan Bell MSc. 

Sasha did her PhD on the use of acoustics to monitor populations of the Indian Ocean humpback dolphin (Sousa plumbea) - allegedly South Africa's most endangered mammal (other mammals may also be threatened). Her PhD worked involved years of deploying microphones into the sea in areas where the dolphins occur, and then trawling through thousands of hours of recordings listening for the occassional whistle or moan. Sasha found that acoustic monitoring might be a superior way of assessing the populations of Indian Ocean humpback dolphin as each individual has it's own signature whistle that can be recognised. 

Jonathan (aka JJ) spent several years looking into the perceptions of members of the public into how they perceived the right for access onto their properties to remove invasive species. Jonathan also looked into the best times in which to remove invasive Guttural Toads from urban properties. It turns out that the toads are most easily captured at night when the lights are on (not as simplistic as you might think!). 

We are very proud of the achievements of both Sasha and Jonathan and congratulate them again on their graduation. It has been  a privalege to have them as members of the MeaseyLab at Stellenbosch University. We look forward to hearing more about their achievements in future.

Dines, S. (2025) Applied passive acoustic monitoring of South Africa's most threatened marine mammal, the Indian Ocean humpback dolphin (Sousa plumbea). Stellenbosch University, PhD thesis

Bell, J.J. (2025) Right time, right place: a mixed method approach for invasive species management. Stellenbosch University, MSc thesis

Adding an important data point on African frogs

Big data syntheses need data, and the majority of scientific data still comes from the nothern hemisphere power houses of USA and Europe with China fast catching up. However, there is still a lot of the rest of the world out there. It is important that studies are made, especially in the southern hemisphere in data poor areas. Today, a new paper on the "Vulnerability of amphibians to global warming" was published in Nature. The article used physiological data from all over the world, but one continent had hardly any data available to the authors.

The African continent is especially data poor:

 

With only 4 data points on it, Africa is a notably large continent with a hardly any data. It is satisfying then that the one data point (shown in Cape Town) comes from the study of Carla Wagener (see here). This study looked at the physiological performance of tadpoles from high and low altitude locations of the African clawed frog, Xenopus laevis.

Obviously, Africa needs more data points, but we are very pleased that we were able to contribute to such an important study.

Literature

Pottier, P., Kearney, M.R., Wu, N.C. et al. Vulnerability of amphibians to global warming. Nature (2025). https://doi.org/10.1038/s41586-025-08665-0 

Wagener, C., Kruger, N., Measey, J. (2021) Progeny of Xenopus laevis from altitudinal extremes display adaptive physiological performance. J Exp Biol 1 April 2021; 224 (7): jeb233031. doi: https://doi.org/10.1242/jeb.233031