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”

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Messing about in boats

I realise that this is the second eulogy that I have posted on the blog in the last couple of months (which is all the more striking due to the low frequency of posts), but there was one passing recently that I simply have to mark. I was devastated to hear that Professor Brian Moss died recently. You will find a number of obituaries written by people who are better qualified to comment on his scientific work, and who knew him better as a person. However, while I was not as close to him as some, I did have the honour and privilege of learning from him as an undergraduate, a postgraduate, a postdoc, and as junior faculty, and so I feel the need to share some of the affection and deep respect that I felt for Brian. There have been a number of leading academics who have influenced my work and career (Dave and Tom in particular) and without them I would not have the collaborations, publications, or career that I enjoy today. However, I think it’s fair to say that Brian had the single largest personal influence over me from anyone within the academy, and shaped the academic that I have become. Other people watch David Attenborough on television, but I had the privilege of being taught by and working alongside my very own Attenborough who inspired me to think in different ways across disciplines. Read More »

The man who played with dinosaurs

We had some sad news in the department earlier in the week. We heard from his son that Professor R McNeill Alexander FRS had passed away at the age of 81. I didn’t know Neill very well, but we had chatted a few times over coffee in the department, which he still visited regularly until a year or two ago. We also lived in the same area of Leeds and I saw him often at the local farmers market. However, there was one particular encounter with Neill that I remember vividly, and I wanted to share the anecdote:

dinosaur-470161_960_720I was at a local Cafe Scientifique in 2013 when I saw Neill give a short presentation and demonstration of some of his world-leading research on dinosaur locomotion. However, rather than this being in front of an auditorium full of people (as would befit a Fellow of the Royal Society, former President of the Society for Experimental Biology, former President of the International Society for Vertebrate Morphologists, author of countless books and articles, the list goes on…), Neill gave an informal presentation to a group of four young children, their parents, and me. Sat in the cafe at Leeds Museum, Neill quietly explained to the small audience the history of his discoveries: how dinosaur models could be used to evaluate mass and centre of gravity, how dinosaur tracks could be used to infer gait, stride, and speed. I don’t recall him taking any personal credit, although it was his to claim, but rather he discussed the ideas as having been a communal advance. Then, at the end of the talk, Neill sat with the children and played with them using the same toys from which he had drawn such inspiration as a researcher and through which he had revolutionised so much of what we know about animal biomechanics and locomotion. I don’t know who the children were, and I don’t know whether they or their parents were aware that they were sat playing with dinosaurs alongside one of the greatest scientists of his generation, but for me that is perhaps the purest example of science communication that I have ever witnessed.

RIP Robert McNeill Alexander (1934-2016)

Avoiding Attack! (a classroom kit)

I blogged some time ago about a Cafe Scientifique talk I gave on the topic of “Avoiding Attack” (broadly mimicry and camouflage in animals). I stole the title of the talk wholesale from the excellent book of the same name written by former colleagues Mike Speed and Tom Sherratt along with Graeme Ruxton). After giving that talk, I was asked to contribute to the Leeds Festival of Science – a great initiative where University of Leeds staff engage local people (particularly schools) with their research through on-campus and external events. As part of that event this year I took part in the “schools roadshow” where researchers go out into schools to teach about their work. I thought I would post the resources that I used here with some notes so that teachers can make use of the materials that I produced. Everything here is released on a Creative Commons license (CC-BY 4.0).

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Making my research more open using Kudos

I’ve always tried to make sure that my academic work wasn’t tucked away on a dusty shelf (or paywalled in an obscure academic journal, which is the equivalent in the digital age) and that has meant that my digital footprint is huge. I have accounts on ResearchGateTwitterSlideshareLinkedInFigshareGoogle ScholarAcademia.eduFlickr, and Google+ (as well as probably a few more that I’ve forgotten!). I don’t think I have lost anything by “scattering my wild oats” across a huge swathe of the internet, because I assume that it increases visibility. Indeed I get a few views across all platforms:

However, what I have been looking for is a service that allows me to aggregate all this content. Ideally it would have (i) a single page per publication, where I could bring together all the bits of information relating to that paper (data, preprints, press coverage, and a lay summary), and (ii) a personal profile page that brings all of those publication pages together under my profile. Well, I think I’ve found it!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.

Do dragonflies give birth to live young?

Heliocypha perforataSomething strange seems to be happening in one particular species of damselfly, the common blue jewel Rhinocypha perforata (pictured right). Or at least it has been caught on video for the first time… Aside from being a particularly attractive species of damselfly found in China, Thailand, Laos, Malaysia and Vietnam, the common blue jewel seems to adopt a rather unusual form of reproduction (for an insect, at least). Read More »

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.

Some hoverflies look like stinging wasps and bees – some even act the part!

Picture1Background: Animals and plants can benefit by resembling other species. For example, some plants have spots that look like ants to deter herbivores, cuckoos look like hawks to frighten smaller birds from their nests, and harmless snakes have striped bodies that resemble highly venomous species. However, there are other modes of resemblance: animals and plants can smell, sound or act like another species in addition to (or instead of) having visual resemblance. However, we don’t know much about how different types of mimicry interact in the wild.

What we did: Heather Penney, a MSc student at Carleton University, collected individuals from 57 species of hoverfly. Hoverflies are famous for having some examples of very close visual mimicry of stinging wasps and bees, but in some species this mimicry is “imperfect”. It is also known that hoverflies can exhibit behaviours that are characteristic of wasps and bees, and so Heather tried to elicit these responses from each of the species that she caught. She found that only 6 out of 57 species exhibited behavioural mimicry, and that these species belonged to only two genera (i.e. they were all closely related). Furthermore, there was some evidence that only animals that looked a lot like wasps also had behavioural mimicry.

Importance: While behavioural mimicry has been described a number of times in the wild, it is rarely surveyed using such a comprehensive approach – Heather tested every species in a community so that we know that there are a range of species that do not exhibit these behaviours. Also, we show that the behaviours are constrained to relatively few high quality visual mimics which suggests that behavioural mimicry acts to enhance morphological mimicry where that morphological mimicry already exists.

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “The relationship between morphological and behavioral mimicry in hover flies (Diptera: Syrphidae)”, was published in the journal American Naturalist in 2014. You can find this paper on the publisher’s website or for free at Figshare.

Image credit: Photos by Brent Lamborn, used with permission.

Twitter in teaching


Twitter is known as a “micro-blogging” site, in the sense that communication through Twitter is restricted to 140 character “tweets”.  Probably as a result of this slightly unusual nature, it is rarely adopted in a teaching framework, but that doesn’t mean that there are not opportunities to use the platform to help students.  Uptake has not been helped by the fact that a relatively small minority of academics are currently using the service, meaning that there is a lack of familiarity.  There is also some jargon that you will needto be familiar with to interactthrough this medium:

  • Hashtags – these are tags denoted by the “#” character that group tweets according to particular topics.  For example, a recently published paper on avian phylogenies might be tagged as #bird #evolution.  This makes it easier for users to find and share relevant content.
  • Retweets – rather than generating all of your own content on Twitter, it is common practice to spread the content created by others.  If someone has posted something you found interesting, you can retweet (designated “RT” within the tweet) to push that back out to your followers.
  • Followers – the people who subscribe to tweets from your account are known as “followers” and you will see the option to “follow” other users on Twitter.  This is the audience for your tweets.

The good thing about Twitter is that there is a lot of information. The bad thing about Twitter is that there is a lot of information. Using Twitter effectively means being able to take what you can from the stream of data without feeling too bad about letting a lot of it slide past. This can be helped by managing lists of users of particular interest, and by using programmes that interface with Twitter, such as Tweetdeck and Hootsuite.

An Example of Use
As part of a tutorial on research methods, a class of eight second year undergraduates are given the table of contents to three leading ecology journals from the past few weeks and are told to find a paper that they are interested in and engage with one of the authors on Twitter.  The exchange should involve questions related to the content of the paper or the authors’ similar work and should fit the format of the medium (140 characters).  The students should submit the Twitter exchange, along with a reflection on the experience and the information that was gathered, as an assignment for marking.  This kind of activity helps the student explore a medium of communication that is rarely emphasised within university education, as well as developing their online personae and potentially networking with important researchers.
Also think about:

  • Using Twitter as a communication tool with the rest of the class (e.g. posting assignment deadlines)
  • Using Twitter in-class, by incorporating a Twitter stream on a screen while teaching.  Students can then interact in real-time.