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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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

Profit > Humanity?

This is a bit of a weird post because, in one sense, I’m actually criticising a journal publisher for making articles open access but, the bigger point, is that it is for a limited time and reveals a very troubling mindset. First, let’s talk about what sparked this. Scientific publisher Springer Nature is currently holding its Change the World event. It’s chosen about 180 of the best scientific articles it published in 2016 and is making them available for free. That’s great! But… at the end of this month, those articles will no longer be free unless they were originally published as open access articles.

I am using Change the World as an example but what I’m going to say here applies to all scientists that promise to improve people’s lives then publish behind a paywall. Springer Nature is framing its event as being a huge benefit to the world. I trust science, I’m sure that what is in those papers really can make a difference to the world. But lets just assume we really believe it when they say: Continue reading

Isolation of Ustilago bromivora strains

I published a new article in Bio-Protocol this week describing how to isolate strains of Ustilago bromivora from the spore material that forms on infected plants. It’s certainly not all my work; the protocol is a modification of a published protocol and has been worked on by many people in the Djamei lab, as indicated in the acknowledgements. I just happened to be the one who chose to write it up.

After the publication of our previous paper on the U. bromivora/Brachypodium pathosystem, we were approached by Bio-Protocol to publish certain protocols in full in their journal. You would think that people would be eager. It’s a lab protocol and writing it up takes very little work yet you get an article published. I was the only one that expressed an interest in writing this up. I imagine it’s because it’s not a “sexy” paper but that mindset neglects something very important. Science is not just about findings; it’s a way of discovering how the world works which can be applied to any situation. At the foundation of that is the idea of sharing one’s methods so that, at least in principle, anyone with sufficient skill can repeat what you have done. Continue reading

Elsevier, you suck!

Remember when I wrote about the need for open access? I mentioned that some publishers have very high profit margins. Elsevier’s was 37%. Elsevier also has faced years of criticism for its policies, including a long term boycott, which has probably had little effect. You want to know why this happens?

A friend of mine shared a photo on Facebook from Insufferably Intolerant Science Nerd which showed this picture.

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It’s an article about Sci-Hub, a site which allows anyone to bypass paywalls and access research articles for free, hidden behind a paywall. That’s irony. But it doesn’t stop there.

EDIT: This contradiction has since been fixed. I guess since the author found out about it.

I don’t necessarily trust things I see on the internet so I go looking for this paper and find that it indeed costs $35,95 IF you access it through Science Direct, Elsevier’s own research portal. However, if you access it directly from the journal’s page it is free! Not only is it free but it includes this text.

A bizarre and frustrating dissonance exists between what content is routinely made free by scientific journals and what is not. For example, News and Perspective articles such as this one are published free online by Elsevier.

Yes! Annals of Emergency Medicine is published by Elsevier and News and Perspectives are free to access through the journal’s website but access that same article through Elsevier’s own research portal will cost you $35,95. Now, if that isn’t bizarre and frustrating, I don’t know what is. Elsevier, you suck!

The case of Diego Gomez highlights the need for open access

It was in November 2014 when I first wrote about Diego Gomez. Tomorrow will see a court, in Colombia, decide his fate. (Article in French) He is facing a fine of up to $327 000 and four to eight years in prison for the sharing a scientific article with a colleague. This is something that many scientists do and which is sometimes necessary for our work. This case highlights the need to move to a world where all scientific articles are open access, i.e. free to read. Continue reading

Science: Behind the scenes

I’ve collected a few weird stories from the world of science that are interesting. They’re not science stories about discoveries and research but they’re science stories about what goes on behind the scenes.

Spam and mailing lists

Let’s start with an amusing tale. We’ve all got spam before and scientists are no exception. Fed up with the constant spam from one particular journal, Dr. Peter Vamplew submitted a fake article, originally written by David Mazières and Eddie Kohler, that expressed his frustration. The article was 10 pages long and merely consisted of the sentence, “Get me off your fucking mailing list” repeated throughout. Continue reading

Science: DIY, peer review and problems

DIY science seems quite interesting, especially if you have an interest in science but are following a different career path. There are various ways to get by without the usual instruments, although I’m not sure how successful they are, but this guide to turning your smartphone into a microscope seems pretty good. I’ve actually got a busted laser pointer (the battery compartment doesn’t shut) so I might try this at some point.

The following is a story I heard about at the Southern African Society of Human Genetics conference. According to a news article published in Science magazine a series of obviously fake papers were created and sent to 304 open access journals.

By the time Science went to press, 157 of the journals had accepted the paper and 98 had rejected it. Of the remaining 49 journals, 29 seem to be derelict: websites abandoned by their creators. Editors from the other 20 had e-mailed the fictitious corresponding authors stating that the paper was still under review; those, too, are excluded from this analysis.

It’s a worrying result but a useful one. For example, it shows that peer review works at PLoS One and BioMed Central. In addition it told me that there is poor peer review at Dove Press and the OMICS publishing group, which is worrying because I had been getting Dove Press alerts (though never read their articles) and had heard senior scientists mention OMICS as a possible place to publish. Needless to say I cancelled my subscription to Dove Press alerts and will advise against publishing with OMICS.

The main problem with the experiment, and it is at least mentioned in the article itself, is that there’s no control group. It describes this as an open access issue but doesn’t give us the data to say that it doesn’t happen in subscription journals. This issue has been raised elsewhere, like here and here, the latter with further criticisms.

Lastly, we have a sad story about the many problems currently plaguing science. While I would suggest reading at that link and the two articles it references, if you only have time for one I would recommend this one. There are many scary things included, lack of replication of studies, problems with peer review and poor use of statistical significance to name a few. Many I’d already heard of but it’s distressing to see it all laid out in one place. But it’s only if we know about it that we can start addressing it.