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Retrieving loggers from KZN

14 March 2022

Downloading data from Hobo loggers

Sometimes you have to take a leap of faith and leave expensive equipment in the field in order to get much needed long-term data. This is what we did last February in a trip to KZN where we made an elevational transect while collecting African clawed frogs for Laurie (see Blog Post here). We placed four loggers at sea level, 1000 m, 2000 m and 3000 m asl. Sadly, the logger at 3000 m asl disappeared very soon after we placed it in a deluge of floods that hit Lesotho in March 2021. That meant that there were still three more loggers out in the field that needed to be retrieved. 

Fortunately, with the help of Bongani Ntloko from Letseng mine, we were able to redeploy another Hobo logger into a pond with Xenopus at ~3300 m asl. The results after one year (March to March 2022-23) are amazing.

Firstly, note that the scale on the y-axis only goes up to 20 C, and the water never gets that warm. For most of the year, the water is below 10 C. Only from around mid-October to late-March is the water above 10 C. This means that the frogs in Lesotho are more than half of their year in water less than 10 C. Even in summer, the water still regularly dips below 10 C on a daily basis.

Happily, the logger from 2000 m asl at the Fat Mulberry was retrieved by Marggie and she brought it to Stellenbosch where we could download the data.

This month I made a trip back to KZN to retrieve the outstanding loggers from near Dalton and at Bonamanzi:

The temperature of the water in a dam near Dalton never went below freezing, but it did get quite cold (as well as getting hot in the summer). 

Meanwhile at Bonamanzi, the temperature was nearly always above 10 C, and even went above 40 C! Contrast this with Lesotho when the water temperature rarely went above 10 C!

You may remember that Bonamanzi was where we had our traps vandalised by crocodiles. Happily though, you can see that the logger (right) didn't come to the same fate. The logger near Dalton (left) was still tied to the same stone sunk in the dam. 

Thanks to friends in Lesotho, we redeployed one of these Hobo devices there. Because you can replace their batteries, they are fantastic and just carry on working. We are hoping that the new logger won't go AWOL!

Now with stats from downloads, we can see who uses Sci-Hub

15 February 2022

What is Sci-Hub?

Sci-Hub is a file sharing website that allows anyone to access to ~95% of all scientific articles that normally sit behind a paywall. While publishers see Sci-Hub as a pirate site that disseminates content that they own illegally, many of the world's scientists have come to rely on using it to quickly gain access to articles that they would otherwise be charged to read. Read more about Sci-Hub and its Kazakhstani founder Alexandra Elbakyan on Wikipedia

At first sight, this does seem to be a lawless exercise, but remember that none of the knowledge or content are paid for by the publishers. Indeed, many scientists are increasingly viewing the publishers' paywall as immoral, while sites like Sci-Hub are akin to a Robin Hood dissemination of knowledge already funded by civil society. To read more about the issues with publishing science, see How to Publish in Biological Sciences (Measey 2022). 

Who uses Sci-Hub?

Today, Alexandra Elbakyan gave us the stats on who uses Sci-Hub. What struck me most is that we might expect scientists from poorer economies to use Sci-Hub proportionately more because they lack the economic power to access the papers. 

What Alexandra revealed is that it is the more wealthy economies (who publish more) that use Sci-Hub the most. In other words - everyone uses Sci-Hub.

Here I have graphed on the x-axis GDP (Purchasing power parity; international dollars from IMF for 2021) of the top 50 countries downloading Sci-Hub (data taken 15-02-2022), while on the y-axis the number of papers each country has published so far in 2022 (from Scopus 15-02-2022). Size of bubbles are proportionate to the number of Sci-Hub downloads. Both axes are on log scales.

Although we might expect the bubbles to get proportionately bigger as the economies get poorer, what we see is that it is mostly the largest economies who are accessing Sci-Hub the most. 

Is this a mistake?

Surely, rich countries such as the USA and France (#2 and #3 on the Sci Hub download list) don't need to access Sci Hub as all of their institutions can subscribe to all content? This is how it might seem from afar, especially if you work in a low or middle income country. However, the idea that all academics work at wealthy institutions in rich countries is a fallacy. Countries, such as the USA, have very large numbers of tertiary institutions and most of these are not at all wealthy. Those who conduct research there need to obtain research from behind paywalls that their institutions don't subscribe to. Their only option is to use Sci Hub. I say that this is their 'only' option as paying $30-$50 for each article that they need to read is not really an option. 

Let's not forget that the better educated public in rich countries might also be more likely to try to access scientific articles, although I doubt that many will know of the Sci Hub option.

These same people (i.e. the vast majority of scientists in the world, even those from rich countries) suffer from the new price ticket on gold Open Access publications. Like those scientists from middle income countries, they cannot afford the prices that publishers charge and so have to look for alternatives. 

There are also some oddities in the list. As Alexandra Elbakyan points out, many places in the UK do not allow access to Sci Hub, and so there people might be using proxy servers to access it via the USA (also inflating their figures). But this is speculation. 

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Sam defends his MSc thesis from a comfy chair in Mauritius

12 February 2022

An unusual MSc defence setting

Defending your MSc with an oral presentation can be a harrowing experience. The assembled crowd is anticipating the results of your research study, you are aware that your presentation counts as 20% of your final mark (in South Africa at least). It is time for your best performance. However, with COVID comes challenges and also opportunities. For Sam Peta, being able to present his MSc thesis defence online allowed him not to miss the opportunity of a lifetime with fieldwork in Mauritius. With the island closed to visitors (from South Africa) for nearly two years, Sam's only opportunity to go came around the same time that he needed to defend his thesis. 

An hour before the defence, the heavens opened and torrential rain fell on Mauritius. Undeterred, Sam continued to prepare to give his talk. The, about 30 minutes before the defence was due to start, the power to the house failed and we were thrown into the gloomy darkness of a power-cut in a storm on a tropical island. Quickly we devised a plan, we could use the mobile network and hope that the laptop battery would continue to work for the full talk. Just as we got it all set up, around 10 minutes before the start, the power popped back on again and we breathed a sigh of relief.

Sam settled into presentation mode, making himself comfortable as much as he could while he talked to the congregated academics. The talk went well but now it was time for the inquisition. Sam responded to all questions in his usual detailed response, and after nearly an hour the defence was over.

I took Sam out for dinner at the Flying Dodo to celebrate this final hurdle of his MSc studies. We will remember this MSc defence for a long time to come.

Fieldwork for Sam in Mauritius

11 February 2022

Sam Peta - In Mauritius at long last

The COVID-19 restrictions have been tough on most people, but for MSc student Sam Peta they turned his international fieldwork for his MSc studies into a very local affair. Sam was supposed to be investigating diet and trophic levels of invasive and native populations of the Guttural Toad (Sclerophrys guttuarlis) using a suite of quantitative methods. Those invasive populations include Cape Town, and the Indian Ocean islands of Mauritius and Reunion. 

However, the COVID lockdowns started only 3 months into Sam's thesis, when he had only managed a single trip to the native range in Durban. At the time, we thought that we'd still get Sam into the field to work on the island populations before the end of his thesis. But back then we were not familiar with the course of the pandemic, the waves and the variants that would see those in southern Africa become the new pariahs of the rest of the world. 

Although the trip was postponed, happily for Sam he managed to make it to Mauritius and conduct the planned field work on their tiny toads. Sadly, this work is too late for his thesis, but it'll be a great addition to his existing work on Guttural Toad diet. Reunion remains closed.

Racism in science

01 February 2022

Racism in Science: take away lessons from the E. O. Wilson debacle

Racism is still a persistent reality in 21st Century human societies. Those societies include scientific and academic institutions, even though we all would rather that those labels could never be associated with us or our approach to the world about us. Like other problems in academia (seeMeasey 2022for a miscellaneous group of issues from bullying to fraud), our best approach is to be aware of issues with racism and not to pretend that they don’t exist.

This blog post is written to highlight the lessons that we need to learn from the recent (and not so recent) revelations about the racist beliefs of E. O. Wilson. There is no doubt that E. O. Wilson was a great ecologist. His ideas and ecological insight will continue within the scientific literature many decades into the future. But following new revelations in an article by Farina and Gibbons (2022), we can no longer have any doubt that E. O. Wilson was also a racist, and actively used his influential position to promote his racist views albeit through third parties in order to avoid exposing himself. 

The article by Farina & Gibbons (2022) is well worth reading, as they provide the evidence for E. O. Wilson’s views and also the way in which he corrupted the academic system, through publishing gatekeepers, to promote ‘scientific racism’ of those who espoused it, and defended them when they were threatened. 

Take-away lessons

It is all too easy to admire scientists (and others in society) who lead their fields and achieve levels of greatness in their own lifetimes, and sometimes beyond. Today, that global admiration and recognition often results in those individuals reaching levels at which they are unassailable in their societies. Such was the case with E. O. Wilson. Following his death in December 2021, a critical article in New Scientist by Monica R. McLemore (2021) was lambasted by many scientists on social media for suggesting (again) that E. O. Wilson was a racist - a claim that they considered baseless. But this wasn’t the first time that E. O. Wilson had been called a racist, and it was something that he was acutely aware of and did his best to hide from colleagues and the public (Farina and Gibbons 2022). The importance of the article by Farina and Gibbons (2022) is that they demonstrate the evidence for E. O. Wilson’s activities, and his complicity with others who shared his beliefs. 

This is not the only example where our current academic system has become corrupted by those who reach the highest ranks of their profession. Those individuals become so highly regarded by their colleagues and institutions that they are cocooned and protected against any accusations of wrong-doing. This is mostly as these positions come with such power and influence that they command an income to their institutions that cannot be threatened. Another prominent example is that of academic fraud (seeMeasey 2022for examples). Even when individuals are exposed by their colleagues and former students, their institutions continue to protect and defend them because they represent a source of income that is unparalleled by their less controversial and lower income colleagues. Indeed, for as long as we promote the winner-takes-it-all attitude to funding science, we can expect that there will be individuals that use and exploit the system for their own gains (seeHeard 2015for a nice perspective on this problem). Sadly, those who exploit the system to the highest level, will also be protected by their institutions. 

In a nutshell, as scientists we are all human. There are those among us who will have bizarre and ugly beliefs, including racism. We cannot pretend that these prejudices will go away with an old generation, they will continue to morph and change as time goes by. What we can do is to remove the professional inequalities that currently exist in hiring and publishing science, and be aware that no matter how high our colleagues reach in greatness within their own fields, it does not mean that they cannot be wrong. 

Further Reading

Fainra S. & Gibbons M. (2022) The Last Refuge of Scoundrels. Science for the People Magazine 25. 

Heard, S. (2015) Why grant funding should be spread thinly. Scientist Sees Squirrel Blog Post:

McLemore, M.R. (2021) The Complicated Legacy of E. O. WilsonScientific American, 

Measey, J. (2022) How to publish in Biological Sciences: a guide for the uninitiated. CRC Press, Boca Raton. ISBN: 9781032116419 

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