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ArrestAD

The ArrestAD team had its kick off meeting in Paris on 5 January 2017. This was held on Paris, the base of our coordinator, Dulcé Papy-Garcia and was hosted by the APHP in the Espace Scipion. Team members from outside Paris stayed at the Hotel La Demeure  situated nearby and though on the Boulevard St Marcel, nice and quiet.

The kick off meeting started with a presentation form our coordinator, which provided the backdrop for the day. Science presentations from the participants then followed. These provided an overview of the position of the field of the participant and then summarised research plans. In a multidisciplinary project, one cannot be fully up to speed with the other fields, so we all learned a lot. The more technical part of these presentations gave us an opportunity to discus the nuts and bolts of our research plans and how these fitted together. It…

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A little late this year, but then there are many calendars, so it is surely the start of the New Year for someone, somewhere, today.

Three years ago I made a simple resolution for the New Year, which was not to review for commercial closed access journals. I developed this in 2015 (and here) when I decided to change my publishing priorities and avoid commercial closed access journals.  This was pretty much already happening, so painless. My two caveats relating to publication are important, if you collaborate extensively, simply because many colleagues live in countries where Impact Factor rules their lives. Thus, when I am not the PI and in editorial control of the work, but merely a contributor, then I suggest alternatives, but I do not dig my heels in. For my students and postdocs who originate from these many countries the Learned Society and Open Access alternatives have pretty much solved the problem, in that they have decent impact factors, and their career progression will not be impeded.

I have also been experimenting with preprints for some time and now, along with Open Data. So the 2016 resolution adds preprints and Open Data. All papers where I am sole PI and have, therefore, the full decision-making power on publication (and also full responsibility for the paper) will be first submitted as preprints and data will be fully accessible.

What is interesting is the development of the change in publication culture. There are still many wedded to the notion that the “Top” journals are those with the highest impact factor, despite the fact that there is no evidence to support this conclusion. Witness the article in Nature reporting the excellent decision by the Gates Foundation, which stipulates that worked funded by the Gates Foundation cannot be published in journals that are not properly open access and open data compliant. To paraphrase the Nature headline:

“Shock Horror, Gates stops researchers publishing in Top journals aka ours”.

The implication that a paper in Nature is worth more than one in The Biochemical Journal or PlosOne to name two other good journals of many is ludicrous. Only when the paper is read can one decide whether it is excellent, good or poor, and then it takes time (=years) for the full scientific impact to be recognised. There are plenty of papers in ALL journals that are worse than poor, ample evidence is provided by a quick scan of Pubpeer; Nature for one has a lot to do to put its house in order.

So preprints and Open Data it is. I would encourage all my colleagues to follow suit.

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I made my first New Year’s resolution on December 31, 2013: to only undertake reviews for open access and learned society journals.  This I have stuck to well, as I noted a year later for the simple reasons that it makes sense and it frees up my time.

Today I had a request to review a manuscript for Nature Publishing Group’s Scientific Reports, and I realised that I need to clarify my position.

I am on strike. (more…)

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This is a question raised at the end of the excellent article by @Amy_Harmon regarding Open Access and preprints is can biomedical scientists evaluate each other without journals?

The short answer is a resounding yes.  Physical scientists and mathematicians have been posting much of their research as preprints on arXiv for a few decades, with no prejudice to their ability to evaluate the quality of work or of individuals.

The counter argument raised by many in biomedical sciences, from scientists to some journal editors can be boiled down quite simply: We are special and cannot possibly do this.

Various arguments are put forward, from competition (=fear of scooping) to intellectual property. These arguments are heard in many biomedical/biology departments, sometimes leading to quite heated discussions. It is also interesting to note that the defenders of the status quo are not necessarily the older members of the community.

There is a simple answer. Yes you are special, but not in the good sense of the word. (more…)

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A tweet brought me to a PeerJ blog post on the uptake of open peer review. The post is worth reading. At PeerJ open review is an option – authors and reviewers can opt in or out, and only if both opt in is the reviewing history of a paper published.  One thing that caught my eye was that while 80% of authors opt in, the total number of paper with open reviews is just 40%, which indicates that reviewers are more reticent. (more…)

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This post assembles various comments I have posted and other thoughts on sci-hub and access to the scientific literature. It finishes with some ideas about what we should consider keeping and some of my better experiences, as a consumer and producer of the scientific literature.

Some time between clay tablet and the PDF

Once upon a time manuscripts were hand written, double spaced (fountain pen as ever outperforming all other tools), graphs transferred to tracing paper using a rotoring pen and Letraset (also alive and well) used for symbols. (more…)

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During a quick scan this morning of the “recent” comments on Pubpeer, an activity that I pursue regularly, as part of my reading, there seemed to be a lot more author responses.  So I counted.

70 articles featured with comments.

10 of these had an author response.

This is progress. I have no data, but my impression is that a year ago author comments were far rarer, maybe 1% or thereabouts. Now we are at 14%. Let’s hope this is not an anomaly, but a trend, and maybe in a few years papers without author responses will be in the minority.

Regardless of arguments about anonymity, etc., post publication peer review is growing, which is a sign of health in the scientific enterprise.

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