PubMed Commons is a huge leap forward

For me, PubMed Commons came out of nowhere.  I was aware of some innovations in publishing (check out journals like Cryosphere for examples of progress in academic publishing) but to have a huge group like PubMed involved in pro-actively pushing boundaries is a real game-changer. Here’s why it’s so important: academic publishing as it currently exists is broken. We have been using a model for publishing that is built around a century-old method for the dissemination of information.  This involves (i) the submission of articles to an editor, (ii) the selection of a small number (usually 2-3) of referees to review the paper and make sure it is adequate, and (iii) a judgement made by the editor and the referees as to whether or not the paper should be accepted.  At that point, the paper is either published (in which case it becomes a matter of record) or rejected (in which case it is never heard of unless published elsewhere).  What this means is that ENORMOUS amounts of scientific information is never seen, and that information that is released in given a sometimes-cursory review by a small number of people who may not be experts in the area.  The internet should already have changed that in a number of ways:Read More »

“Camouflage on the edge” – a new paper on concealing colouration

In 2012, the US Government cancelled a $5 billion camouflage project under which it had already supplied uniforms to soldiers in Afghanistan.  The pattern of camouflage, called the “universal camouflage pattern” (UCP) was supposed to allow soldiers to blend in equally well in forests, deserts, and urban environments but had been deployed but never properly tested to ensure that it provided proper protection.  When this testing was finally carried out, it demonstrated that the camouflage performed poorly, and was actually putting soldiers at unnecessary risk.  It got so bad that US Army soldiers were trading their uniforms with locals so that they could wear something with appropriate colouration.  What this goes to show is how poorly we understand the mechanisms underlying camouflage, even while we spend enormous amounts of money attempting to exploit the phenomenon.  A new paper that my colleagues (based at Carleton University) and I published today in the Royal Society journal Biology Letters adds a key piece to the camouflage puzzle by illustrating for the first time the mechanism behind “disruptive colouration“.  The paper can be viewed for free at the journal homepage, as can all Biology Letters articles, until 30th November 2013 – go browse, it’s a fascinating journal with short, varied, interesting papers.

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Four reasons to publish during your PhD, and how to go about it

A graduate student yesterday told me that they were despondent over not having published more during their PhD. I was just pleased that they were considering it at all, because the British PhD culture is still (to a certain extent) fixated on the production of a thesis (which nobody will read) rather than academic journal articles. I thought I would take a few minutes to lay out the reasons that I think you should be trying to publish whatever you can whenever you can:Read More »

A nice review of the demands of open science

The journal Psychological Inquiry has just made an issue on open access science open access.  I’ve flicked through a couple of articles and they look like a thoroughly interesting combination of pros, cons, and speculations.  In particular, the opening article states the needs of an open science movement very clearly in its abstract:

We call for six changes:

  1. full embrace of digital communication;
  2. open access to all published research;
  3. disentangling publication from evaluation;
  4. breaking the “one article, one journal” model with a grading system for evaluation and diversified dissemination outlets;
  5. publishing peer review; and
  6. allowing open, continuous peer review.

I think these six principles sum-up the needs of the research community quite well.  We are working in an out-of-date and horribly expensive system that is not benefitting scientists or those who use the science.  There has always been pushback against these kinds of measures (see the response in the same issue of Psychological Inquiry by the editor of a different journal), mostly along the lines of “it’s too hard” or “that won’t work”.  However, those sorts of arguments are undermined by a number of journals which are doing precisely these things extremely well.  I’ll mention Cryosphere as an example that I have had experience with.  A few small changes could go a very long way towards improving the system, and we cannot let the editors and publishers try to convince us that it cannot be done!

While we wait for the open access revolution, self-archive!

I’ve just had a paper published on open access in ecology and evolution, so I thought I would let you know what it’s all about.  I wrote a few weeks ago about how you can often post more of a scientific paper online without violating copyright than you might think.  I went through a couple of journals in which I had published articles, and tried to work out what I could self-archive.  The answer was usually “quite a lot”!  Then someone in the comments popped up and mentioned the SHERPA-ROMEO website, which allows you to search for the name of the journal in which your paper has been published and then shows you the policy on self-archiving.  Well, being the data-lover that I am I decided to check out the rest of the journals in ecology and evolutionary biology (all 165 that were listed on Thomson Reuters Journal Citation Reports).  The results were pretty interesting…

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How much of an academic paper can you post online? Most of it!!

Edit: As was pointed out in the comments, you can find self-archiving info for most journals at http://www.sherpa.ac.uk/romeo/ [h/t Laurent]

I have been a bit frustrated about scientific publishing, as you might have been able to tell if you read some of my earlier posts on open access in academia.  I posted earlier this week about Aaron Swartz and the legal predicament in which he found himself when he downloaded huge numbers of scientific papers.  I was frustrated at the lack of access that most people experience to academic publishing, but didn’t want to resort to breaking the law to remedy the situation.  However, a certain amount of that frustration could have been relieved had I just taken the time to figure out where the boundaries lie in the copyright documents that I sign when I publish papers.  I decided to have a look to see how many of my rights remain, and I was quite interested to find out that I can post a reasonable amount of information on the web without breaking any laws.  As ever, this isn’t legal advice.  However, there do seem to be a few generalities that others can use to guide the release of their publications depending upon the publisher that owns the journals within which their papers are published:Read More »

The (current) limits of open access and #PDFtribute

EDIT [18/1/13]: At almost exactly the same time as I was posting about how the revolution was coming, the revolution started.  Mathematicians are setting up community-run, open access journals independent of larger publishers.

I had never heard of Aaron Swartz before he died.  Swartz was 2 1/2 years younger than me and spent his life working on, with, and around the internet and its various limitations.  I have a lot of respect for what he accomplished, not only in terms of the technical progress that he was a part of, but also because of his philosophy about open access to information.  In the wake of his death, supporters took to Twitter to post free copies of their publications, whether or not the material was in the public domain.  This reflects Swartz’s actions in downloading millions of academic papers from the MIT network which precipitated the court case that he was fighting when he chose to end his life.Read More »