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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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

The 2018 VBC PhD Symposium

One little side project I’ve been involved in since last year has been organising the Vienna BioCenter (VBC) PhD Symposium. I’ve attended and helped as a volunteer every year since 2015, though I only wrote about the 2016 symposium on my blog. For those who are not familiar with it, the symposium is held at the Vienna BioCenter in Austria and organised by a group of PhD candidates. We select a theme, invite speakers from across the world, co-ordinate and organise everything. This year’s theme is Metamorphosis – Transforming Science.

The symposium is going to focus on science and change; that includes topics like cutting edge technologies which will change the way science is done, environmental science which can change (and help save) the world we live in and the changing ways that we can communicate in science. So why am I writing about it now? I want anyone who is interested, to hear about it, sign up and attend. Continue reading

I finally finished reading The Fact of Evolution

A long time and still no proper blog post, just a brief summary of a book for my 2018 reading list.

coverThe Fact of Evolution (2011) by Cameron M. Smith

I finally finished this one! I started reading this about four or five years ago and finished four chapters. Then I went to Austria to do my PhD and left it behind in South Africa. After one of my trips home, I brought it to Vienna with me and read a little more before taking a break to read The Adventures of Peter Gray and De Vita Beata. I can now finally say I have finished reading it!

On the negative side, due to the multiple year time lapse and many gaps, I can’t clearly recall all of the book. All I can say is comes from the ending chapters. That is that the book was quite clear and well-written with several illustrations or tables to help explain things. Each chapter covers a particular aspect of evolutionary theory and it should make a good introduction to those who know little about evolution.

Assessing Scientists By Publications And Impact Factor Is One Of The Most Harmful Scientific Practices

I have a blog post titled Assessing Scientists By Publications And Impact Factor Is One Of The Most Harmful Scientific Practices on the OpenUP Hub blog.

OpenUP is a European Commission project for explaining, discussing and sharing information about open access. The website is not very well set out and difficult to navigate, with some information seeming to be missing completely, but it has good intentions. In any case, I decided to enter their blog competition since there’s an opportunity to win a trip to an open science conference in Brussels which could be nice.

My entry relates to just some of the problems in scientific publishing that are due to the practice of evaluating scientists according to publications and the impact factor. But I will direct your attention there to read more.