Irresponsible City Press article credulously promotes psychics

I was rather dismayed, though not entirely surprised, to see a South African publication uncritically promoting the views of psychics to describe the coming year. This was particularly frustrating as it came just after hearing about how the UK’s The Guardian has recently been promoting the pseudoscience of astrology (see accounts here and here). At least in the case of The Guardian they published a letter from John Zarnecki, former president of the Royal Astronomical Society, which is clear that astrology should not be taken seriously. Just as with astrology, there is little to no scientific evidence to support the existence of psychic powers nor any supernatural ability to predict the future.

Claims of psychic powers are often debunked, particularly by magicians who are well aware of how to fool people, but more keep popping up all the time. The video below is of the late James Randi showing that James Hydrick‘s alleged telekinesis is not a psychic power but merely a simple trick.

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The problem with describing organisms as “higher” or “lower”

In my most recent publication, I was not happy with the use of the terms “higher” and “lower” when referring to various organisms but, despite my objections during draft editing, they were retained. However, I want to take this opportunity to state that these terms are the remnants of outdated beliefs, can lead to a poor understanding of biology and do not belong in scientific text. This issue has been addressed in blogs, online fora and the scientific literature (see references at the end).

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Reference managers: Migrating from Mendeley to Zotero

Today is Software Freedom Day and I thought it would be the perfect time to talk about a software migration I am currently making. I started using Mendeley back in my honours year and was happy enough with it to make a very positive blog post about it in 2012. I was less happy when it joined with Elsevier but continued to use it nonetheless. Now, I am switching to use Zotero as my reference manager in the future. Why?

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Overpopulation and the environment

It’s a weird feeling when you find people questioning something you would’ve thought was both obvious and widely accepted. That’s something that happened to me recently regarding the impact of human population on the environment, something we’ve been hearing is a problem from environmentalists for decades. That’s why I was surprised to read an article by Ketan Joshi talking about the problems in a recent film (which I haven’t seen) and being completely against the idea that we need to talk about population. In fact, he goes so far as to call population control “a cruel, evil and racist ideology.”

I had no idea how he had come to that conclusion, and I still don’t know how much of that was directed specifically at the film he was critiquing and how much was a general comment, but there was a Twitter thread by George Monbiot which is a good read and makes explicit a similar line of reasoning. His contention is that, although the majority of carbon emissions are by the, primarily white, ultra rich, people (particularly white people) prefer to blame population growth than the wealthy as it deflects responsibility from their own actions and that this is, intentionally or not, racist because those countries with the highest population growth rates have largely black or brown population. While I agree with several of his starting points, I think he makes several errors in reasoning as he builds upon them that undermines his conclusions and which I wish to address here. Continue reading

Tedious publishing: Preregistration can help

Imagine that an architect were tasked with building a house, came up with a design, had a team of builders construct the house and then asked the prospective owner whether anything needed to be changed. The prospective owner tells the architect that he doesn’t like a part of the house and would rather it were done differently. To please the owner, the architect knocks down that section of the house, rebuilds as directed and then repeats the process until the prospective owner is satisfied.

To any sane person, this situation would seem completely ridiculous. It would be stupid to go through all the effort of constructing a building without first confirming whether everything was acceptable at the planning stage. Strangely enough, this is not far off from the common practice in science. We design and perform experiments, collate and narrate the results and then send our write-ups to journal editors, who in turn distribute the manuscript among a coterie of our peers. These peer reviewers supposedly check the manuscript for publication-worthiness, advise us of errors in execution or interpretation, and recommend various changes and additions. Frequently, this turns out to be a prolonged exercise that incurs significant expense, but does not add much value to the central theme of the manuscript. Without a doubt, the scientific process can benefit from well-performed peer review. However, extant peer review processes are more wasteful than beneficial as in the analogy above.
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Final papers from my PhD

I am happy to report that the last two papers from my PhD are now available for everyone to read!

Two Is Better Than One: Studying Ustilago bromivora–Brachypodium Compatibility by Using a Hybrid Pathogen

This, along with the U. bromivora genome paper,  is probably the most important paper from my PhD. Those two papers formed the basis of my thesis. Although I did not manage to fully answer the question I set out to answer, this is a paper where most of the experiments, most of the analysis and most of the writing was done by me, so it is special to me. It’s also quite interesting! If you want to know exactly what we learned, you can read the paper itself but I will give you a brief summary of what we were trying to learn.

We knew there were two very closely-related fungal species which could infect different host plants. This told us that although they were very similar, there was something important about them that was different; we wanted to know what that was. Even more exciting, we could create a hybrid between the two fungi that was still able to infect one of the host plants. What I was trying to do was take the hybrid and breed it over and over again with the parent that couldn’t infect while making sure that the hybrid could infect. After enough generations, we should then find the hybrid would be genetically almost identical to the non-infecting parent but with just a tiny bit of the infecting parent inside it. That would tell us what the difference between them was and we could then try to figure out how that part of the genome led to interactions with the plant. Continue reading

How might science benefit from a world without journals?

I think it was in either 2017 or 2018 when I had lunch with a visiting speaker and mentioned that I was finding it hard to see any value in publishing in journals. With bioRxiv and similar projects, we could just get rid of journals all together. He said that journals still served an important filtering function in letting him know where to find the good research and, without journals, we would be overwhelmed by poor science. I now want to respond to that idea because I think there is a possible benefit to getting rid of journals and I think the problems that he feared can be easily overcome. Continue reading

Traditional scientific publishers have repeatedly undermined moves towards open access

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The Sci-Hub logo.

I recently read a profile of Alexandra Elbakyan and her pirate library, Sci-Hub. Sci-Hub provides free access to a huge number of scientific papers which would otherwise be locked away behind paywalls and only available if you paid a huge fee. The traditional scientific publishers are not happy with that, have sued her several times and continually try to take down her site. I think, given the current realities in science, that Sci-Hub is necessary until the publication process can be reformed.

I have a colleague with whom I talk about publication practices in science and that sort of thing and, while we generally agree, we do differ on our attitudes to traditional publishers. He has often said that he doesn’t want to drive them out of business and would like to work together with them to solve the problems. I have generally maintained that they are antiquated relics from the print age who serve no real purpose, add little to no value to the scientific enterprise and oppose necessary reforms in science. So, it was interesting for me to see some of these issues come up in the profile of Elbakyan. Continue reading