OK, here’s a little taste of what I usually do, rather than some random ramblings… I have a PhD student who is running enzyme-linked immunosorbent assays, or “ELISAs” to the initiated. This is a standard technique for measuring (in a semi-quantitative way) the amount of a given substance in a sample. Basically (and this is a pretty basic description), you stick an antigen to a surface (like the bottom of a plastic tray) and then add an antibody that sticks to the antigen. The antibody has an enzyme stuck to it and when you add the substance of interest the enzyme catalyses a reaction that causes a change in the intensity of a colour. You can shine a light through the sample to see how much the colour has changed and that gives you an idea about the concentration of your sample.Read More »
Category: Open source
An example of progressive peer-review in a scientific journal
Almost all scientific papers are peer-reviewed. This means (typically) that between one and three researchers from the same field as the paper’s topic offer (sometimes constructive) criticism and a judgement as to whether or not the paper merits publication. There is a strange ritual to it, whereby the authors submit, the reviewers critique, then the authors rebut or acquiesce to the reviewers’ demands, while the editor acts as ringmaster and makes the final decision. The main problems are that (i) there is a lack of dialogue (you only get a very small number of opportunities to engage), and (ii) your manuscript is in the hands of a very small number of reviewers with their own particular foibles and hobby horses.
A solution to this is to have either (i) open pre-publication peer-review, or (ii) open post-publication peer-review. This means that the paper is discussed by more people and in a medium which encourages dialogue, such as a blog comments section. Even better, each element of the dialogue can feature as a subsection of the paper itself, making each section citable in its own right. This encourages reviewers and commenters alike to produce high-quality criticisms and has been implemented in some journals. Here’s an example of the process in action in a particularly controversial climate paper at Atmospheric Chemistry and Physics:
This is certainly the way forward for open science.
One quick trick to increase visibility and citations of research papers
Since I’m “young” (whatever that means) I sometimes get asked to advise on how to disseminate research outputs through new-fangled doohickies like “the social media” (like writing click-baity headlines). This came up in a School Management Group meeting today, in the context of trying to increase visibility and citation rates for papers published by our faculty. It was something that I was quite interested in, so I spent about an hour doing some quick literature searches and then implementing some of what I found. Here’s the gist:Read More »
Community Collaborative Science (CoCoSci) as an alternative model for scientific collaboration?
I went to a fascinating talk by a colleague at Leeds, Dr Mark Davis, a few weeks ago. Mark works on Alternative Finance (“altfin”), which involves a shift in economic thinking away from traditional big banks (with low interest and risky investments) towards peer-to-peer and community-based lending. You can read more about Mark’s ideas in his recent Conversation article: “How alternative finance can offer a better banking future“. Mark had a lot of fascinating insights which (to a lay person like me) resonated strongly. The notion that banks are inherently risky and create the circumstances for economic collapse, and the idea that all of our money that we give to banks ends up going far away into large, complex economic systems, rather than helping closer to home. Mark also made the point that there is a parallel between the “Big Society” notion promoted by the UK Conservative Government under David Cameron, and the Alternative Finance concept that he promotes. Under the Big Society, it is assumed that everybody has a little bit of spare time here and there and that we can volunteer that time to solve social problems. This means lower investment from the government because we are (in theory) capable of taking over from public services. Some people are skeptical… Altfin, on the other hand, takes the same approach to capital: almost everybody has a small amount of capital sitting around that is doing nothing productive, and if we pool our spare capital then we can do good things with it. This got me wondering whether the same thing was true for research…
Keeping them engaged – tech solutions for in-class quizzes
When I joined my current institution in 2012, I was offered the role of “Blended Learning Champion” – basically I had to promote a combination of the best pedagogical tools, including in-person techniques and digital technology. As soon as I started, I learned about what became known as “the clicker fiasco”. There was a time, you see, in the halcyon days of 2010/11, when all students in my faculty were given little devices that could be used to respond to questions during the class. It looked a little bit like the one on the right here, and worked extremely well. Lecturers would embed questions in their lectures, the students would answer using the clickers, and everybody was happy. At some stage some inconsistencies in the software versions, or possibly some old hardware (the exact cause is unknown), caused the whole system to come crashing down. What was frustrating about this situation is that there was substantial buy-in from academics to use these technological tools to enhance their pedagogical practice, but the failure of the clickers deprived them of both their favourite tools and their enthusiasm for blended learning. Now, I think I have found the solution: Socrative.Read More »
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 ResearchGate, Twitter, Slideshare, LinkedIn, Figshare, Google Scholar, Academia.edu, Flickr, 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:
- ResearchGate: 2,106 reads, 454 profile views,
- Twitter: 976 followers
- Slideshare: 2,386 views
- Figshare: 20-200 views per article, but full stats require institutional subscription
- Academia.edu: 484 views, 35 downloads
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 »
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.
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:
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).
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.
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 »
Katatrepsis 