A hat-full of academic how-tos

Dipping in and out of the stream of tweets, there are always fascinating links to excellent resources for academics at all stages of their careers. I just spotted another, and thought it might be about time to aggregate some of these for posterity. Here’s the quick list (to which I will add if people suggest links), and details are below

  1. “How to find a postdoc”
  2. “How to get started with R”
  3. “How to use Github and RStudio”
  4. “How to use Github effectively”
  5. “How to respond to reviewers’ comments”
  6. “How to write a literature review”
  7. “How to help fight sexism in academia”
  8. “How to make your publications more accessible”
  9. “How to make your work reproducible”

Read More »

How to write a scientific paper

writing-427527_1280When we teach students how to write papers, we take it for granted that they have already absorbed the basic format of a scientific article from their reading of the primary literature. They should be familiar with abstract-intro-methods-results-discussion-references, for example, and the content that goes into each section in order to lead the reader through the work. However, it is easy to see how students might fail to grasp the general structure of a scientific paper. For example, we often hold up the high impact journals as models of scientific research, but journals such as Nature, Science, Current Biology and PNAS have a structure and a style that is really quite different from other journals (referenced abstracts, methods at the end, extremely brief structure). I have been teaching undergraduate and postgraduate students how to write scientific papers and theses for a few years now, and I thought I would share my personal method (I think I can credit Phill Watts, now at the University of Oulu, for suggesting this to me years ago):

I hope it’s useful and please do let me know if it helps, either in the comments here or on the YouTube page. The video is released under Creative Commons.

Why has the blog been so busy recently…?

typewriter-407695_1280For the two or three people who actually pay any attention to what I get up to here, you might have noticed a bit of a theme over the past couple of months: large numbers of posts (an anomaly in itself!) summarising some of my papers. I set myself the task of writing these lay summaries to try to make my work a little bit more accessible to people who might be interested in the topic but who might not have access to the paper, have the technical skills needed to interpret the findings, or who simply don’t have time to go and read a 7,000 word scientific article.

I’m pleased to say that I am (nearly) up to date now, and you can see the fruit of my labour here or click the green links labelled “lay summary” next to each of my papers on my publications page. There are 30 summaries in total, with a couple missing for the most recent papers. Trying to make research more open and accessible is a personal passion, and so I’d love to hear what you thought of this. Is it useful? Is anything still unclear? Drop a note in the comments and let me know.

One simple way to increase visibility of your scientific publications

Background: As well as publishing in ecology and evolutionary biology, I am also interested in how that publishing industry works. There is a clear need to disseminate information as widely as possible in order to accelerate the rate of testing of new theories and discovery of new information. However, some publishing models (and some publishing companies) hide scientific research away so that most people do not have access to that work. Self-archiving is a way for researchers to make available certain forms of their research without breaking copyright (which is almost always handed over to the publishers).

What I did: I reviewed some of the literature on the benefits of self-archiving, in terms of the access to the general public and what has become known as the “open access advantage”: papers that are more openly available are cited more. I also show that over half of all ecology and evolution papers could have been archived in a format that was almost identical to their final, finished format without breaking copyright. I then highlight key methods that researchers can use to self-archive their work: publishing through institutional repositories, third party websites, or self-creation of online portfolios using online tools.

Importance: Self-archiving has the potential to open up research (often funded by taxpayers) to a far wider audience, and this is an important step towards making research more accessible to the general public.

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled ““Going green”: self-archiving as a means for dissemination of research output in ecology and evolution”, was published in the journal Ideas in Ecology and Evolution in 2013. You can find this paper for free at the publisher.

My first preprint submission

My last post was about open access – making sure that your work is freely available after publication. However, I have also been experimenting with preprints – posting articles prior to publication for open peer review. PeerJ is one publishing model that has been gaining traction recently. They also offered free publication for a trial window and have a monkey as their mascot, so how could I resist? My paper, “Continental variation in wing pigmentation in Calopteryx damselflies is related to the presence of heterospecifics” is available now (with all the data used in the paper) at the PeerJ preprint site, while the manuscript is in review at the PeerJ journal. I thought it worthwhile reflecting on the experience and my growing support for this idea.Read More »

Be sensible about open access, but it’s still a good thing!

In a recent paper published in Trends in Plant Science, Anurag Angrawal presents a few “reasons to be skeptical of open-access publishing” (Angarwal, 2014) in order to stimulate debate over the current open access (OA) publishing model. Ironically this is behind a paywall so I thought I would summarise the content, which is more reasonable than the title suggests. Here is the gist of the four problems:Read More »

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.

Read More »

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 »