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.

Pedagogy and a Pint

bar-406884_1280Academics have many draws on their time: research (grant applications, writing papers, speaking at conferences), teaching (planning lectures and workshops, delivering teaching, marking), and administration (committees on all of the above and more – admissions, marketing, student education, research, outreach). Most of that is just keeping things afloat, and so we sometimes lack the time to develop new ideas and discuss interesting and novel ways of working. Over the past couple of years I have been the “Academic Champion for Blended Learning” in the Faculty of Biological Sciences at the University of Leeds, and that has meant that I have spent a fair amount of time horizon scanning for teaching technology and working with early adopters. However, trying to roll-out big initiatives (like our brilliant new lecture capture system) can be hard because staff have limited time to engage. Recently, I tried something new to give colleagues an opportunity to talk about teaching: “Pedagogy and a Pint”.

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Online computer programming courses

Computer programming is becoming an increasingly important part of biology (my own discipline) and a range of other subjects.  Programming allows the analysis of data, the creation of software and the building of online resources and interfaces.  There are a range of online courses that you can take to develop these skills, and use as teaching aids for students, that cover a lot of different languages with different applications:

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Codeschool offers four key “paths” composed of sets of modules in different programming environments: Ruby and JavaScript (two different methods for online application building), HTML/CSS (web design), and iOS (for Apple apps).  However, they also offer “electives” alongside the main paths, looking at R (an open source programming language), Git (a method for version control in the development of programming), and Chrome Developer Tools (for apps in the Chrome browser).

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Codecademy, much like Codeschool, offers a wide range of programming languages. However, all courses through Codecademy are free of charge.  The focus is on web programming using HTML, CSS and JavaScript, and application building using Ruby, APIs, and Python.  Codecademy also allows people to generate their own courses, meaning that there are many smaller sets of tutorials designed to teach specific principles.

An Example of Use
CodeSchool runs a course called “Try R“, which offers a few hours of interactive training in the R environment.  For those of you not familiar with theR language, R is an open source programming language that is mostly built around data manipulation and analysis.  The course itself loads within the website, with a simulated R environment within which the student can work.  The content covered includes: syntax, vectors, matrices, summary statistics, factors, data frames, and “working with real-world data”.  At Leeds we teach our MSc Biodiversity and Conservation students in R for a short period, but this is the kind of tool that the students can use to familiarise themselves more completely with the language.  It could also be a gentle introduction to some of the R-based MOOCs that are run by Coursera.

Twitter in teaching

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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.

Student blogging

I don’t get many readers, but some people do find my blog and that has led to over 70k views for the past few years. I’m quite pleased with that, and it gives me the encouragement to carry on through the dry spells. However, I remember starting out and not knowing who would ever read (or even find) my blog. Now I have students who are setting out into the blogosphere and writing great material so I thought I would do my bit to send some traffic their way. Here is a quick list of their blogs, vlogs, radio shows and documentaries that I have come across recently:

EcoSapienLogo

EcoSapien – my former student David has been busy working on a number of projects. EcoSapien is a YouTube show dedicated to spreading awareness about conservation and biodiversity, as well as providing resources for teachers to educate school pupils about wildlife.

North Ronaldsay Logo

North Ronaldsay – David was also the mastermind behind a three-part documentary on the Orkney Island of North Ronaldsay. The show covers the history, wildlife, and people of the island with some beautiful nature shots.

Eye On Wildlife Logo

Eye on Wildlife – Emma produces blogs and podcasts focused on wildlife biology and biological conservation. You can also see her talking about How the Internet Can End Global Poverty, from the University of Leeds TEDx event in November 2014 (video should be available here soon).

Simon the Scientist Logo

Simon the Scientist – a mixture of science writing looking at a wide range of (pretty diverse!) topics.

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In Search of Ancestors – Simon (a different Simon, just to confuse us) is currently – at the time of writing – working as a field assistant in South Africa working on a fossil hominid project. This blog catalogues his ideas on hominid evolution.

Roaming Researcher Logo

The Roaming Researcher – Dan and I worked together on his MSc dissertation project. Since finishing his MSc, Dan has been travelling the world working on a wide range of field projects and shares his experiences on his blog.

Weekly Wildlife Watch Logo

Weekly Wildlife Watch – Tania and Gabriella have been running a student radio show on wildlife ecology and conservation for some time and have managed to get some fascinating folk in for interviews. Go listen and share!

If I have missed anybody then please do let me know and I am happy to update!

Why I blog (occasionally!)

There has been a lot of discussion over the merits of academics blogging (see here, here, here, here, here and here). The positive arguments seem to be that:

  1. It’s good outreach, allowing a flexible platform for communication of science
  2. Blogs allow rapid responses and reporting on research
  3. Online profiles are important and blogs can be a strong foothold in internet-space
  4. Writing for a non-technical audience is good practice for science communication

The negative arguments seem to be that:

  1. It doesn’t count in academic terms (it’s not a paper, a grant, or a lecture)
  2. Sometimes tenure panels might see blogging as a waste of time
  3. There’s the danger of “upsetting” people.

Well I think it counts (even if my colleagues disagree), we don’t have tenure in the UK, and I don’t mind upsetting people, so there’s no good reason for me not to blog! I was letting it drop off a bit, but all this discussion has encouraged me to start up again. One of the problems is that I lacked a blogging strategy, which meant that I only shared what I (A) found interesting, and (B) found time to write about. Most of my problem was that I found interesting topics and spent too much time on too few, too niche issues. That’s going to change. Here’s the plan:

  • I’m going to post lay summaries of each of my publications.  That’s 25 to start with, and I’ll add more as I go along. I see that as a vital part of science communication, and I’ll link them back to my publications page on my website.
  • I have recently been immersing myself in Twitter which has led to my discovering a lot more interesting (and sometimes plain weird) papers and articles. This will be a key (near-bottomless) source for new ideas, but I’ll try to keep to a theme.
  • The main topicsare going to be
    • General science things
    • Entomology news and views
    • Education and technology
    • Specific posts about my research
  • Finally, I’m going to write in short form now – no more monthly long reads. 500 words max, and always with an image or video. It was the length and detail that was killing my productivity, and nobody reads those longreads, anyway!

I am hoping that that is going to provide a sustainable flow of content over the next few months, and I’ll reevaluate at Christmas.  Happy reading!


Image credit: Cortega9, CC-BY-SA 3.0, http://bit.ly/1oiVIwr

iPad apps for academics (Part 2)

I wrote earlier about a few apps that I had found useful in my first weeks of owning an iPad. Well I’ve been actively pursuing opportunities to learn more about the learning applications for tablets like the iPad and wanted to share some of what I have found. A lot of this comes from a workshop by the brilliant Joe Moretti, who came to my university to run a workshop on iPads in education. I hope these are useful to you, too:Read More »

Flipping the classroom – how to make lectures engaging and interactive

I’ve been taking a teaching course that requires me to change the way that I teach to explore new techniques. At first it seemed like it was going to be a lot of effort, but it turned out to be a fascinating and enjoyable experience.  I was experimenting with a type of teaching called the “flipped [or inverted] classroom“.  Here’s how it works:

Flipped vs traditional teaching models

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Funding for academic outreach in biology (and other sciences)

I recently heard a keynote talk by Sophie Duncan, the Deputy Director of the National Co-ordinating Centre for Public Engagement, and was really impressed by her enthusiasm for embedding outreach and engagement at every stage of research. Sophie pointed out that there are a number of problems with public engagement as it stands:

  1. There can be a lack of support and reward for good engagement within departments.
  2. Outreach tends to be centred on the academic, rather than on the public.
  3. Groups outside of academia tend not to pro-actively seek academic collaborators.Read More »

Peer instruction – interactive teaching in a large lecture class

I attended a webinar before Christmas that was hosted by Eric Mazur, a well-known Harvard physics professor.  Setting aside how exciting it was to have a guest speaker talking live and taking questions from his office in the US, the subject of his talk was really fascinating.  Mazur has developed a series of techniques that can change the way we teach and here he was discussing “peer instruction”.Read More »