ELISA analysis in R

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 »

“The New Education” by Cathy Davidson

51dYKk9sOsLFirst of all, this isn’t a commissioned review – I bought The New Education by Cathy Davidson myself and am (sort of) reviewing it because I found it extremely thought-provoking. In fact, on a recent trip to the States with a few colleagues, I nattered on about it almost non-stop so I feel that I should probably share a few insights from the book. It is worth noting that the book is very USA-focused and so not everything is going to be applicable for everybody. However, there are more than enough shared issues among higher education institutions that the book resonated with me in a lot of different ways. Below, I pick out a few of the sections that I found particularly interesting, and share some of the ways in which they might affect the way that I try to influence teaching at my university:Read More »

What works in higher education: active learning

university-105709_640When I advocate for pedagogical research (an area in which I try to maintain an active interest), I am often told by colleagues that the quality of the research is poor. As a result, it is difficult to evaluate what actually works in higher education and so there is no real impetus to change what we already do. Indeed, I remember one academic colleague squeaking through a teaching qualification by the skin of their teeth because they steadfastly refused to cite any pedagogical literature. I wanted to write a quick post to make the case that this is not always true.

Specifically, the article I want to mention is this one:

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Published in the Proceedings of the National Academy of Sciences (PNAS) – a highly reputable journal in which many of my colleagues would be delighted to publish their work – the paper describes a review of an approach known as “active learning“. This method is very simple: students should be actively engaged in the learning process rather than being a passive audience. From the article:

The studies analyzed here document that active learning leads to increases in examination performance that would raise average grades by a half a letter, and that failure rates under traditional lecturing increase by 55% over the rates observed under active learning. The analysis supports theory claiming that calls to increase the number of students receiving STEM degrees could be answered, at least in part, by abandoning traditional lecturing in favor of active learning.

The authors compared 158 active learning studies to 67 traditional lecturing studies to find these rather startling effects. Unsurprisingly, those studies that used a typical lecturing style had significantly greater failure rates. This likely stems from the student’s lack of evaluation of their own learning during the course, which is only revealed when the exam marks are returned at the end of teaching. Through active learning, students gain a greater appreciation of their progress through a continued self-reflection on progress made. Similarly, the increase in performance is not surprising: students who have errors in their understanding discover those errors and can take steps to remedy them when engaged in an active learning environment.

So why aren’t we all doing active learning? The simple answer is that active learning requires an investment of time and a different perspective on teaching. Most university lecturers have never actually been trained as teachers, and their only experience of teaching was the old-fashioned exposition style of didactic lecturing. They are doing what they know. Workloads are at such a level that retraining and refocusing efforts on new ways of teaching is occurring piecemeal, rather than through large-scale redesign of teaching based on empirically validated methods.

So what is the solution?

For me, there has to be a community of practice that allows academics to help one another to enhance teaching. Since teaching in higher education tends to be relatively siloed into modules, academics often develop their own teaching style with relatively little input from colleagues. A greater awareness of best practice and learning from one another could bring about considerable enhancements, with support and guidance (and, sometimes, copying wholesale if appropriate!) in the implementation of new techniques. I’d be interested to hear whether anybody has found a solution to this problem and any interesting case studies where the transition from exposition to active learning has been achieved successfully. Feel free to drop a note in the comments below.

Overassessment, stress, and university education

homework-2521144_640On 1st August 2018, I took on a new role as Director of Student Education in my department and that has got me thinking more practically about the higher education teaching stories that I read. Since I now have a position where I can effect change, are there positive steps that can be taken? The first story I came across was this from the Times Higher Education Supplement:

The modular structures of degree programmes have resulted in a stressful assessment environment for students in UK universities, according to a recent study. It is not just the volume of assessment but also the ways that students are evaluated that is hindering meaningful learning…

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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:

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This is certainly the way forward for open science.

One quick trick to increase visibility and citations of research papers

digitization-of-library-3068971_640Since 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 »

Tweeting over the Great Firewall

Wow, six months without a post is the longest I have neglected the blog for a while! I’ve got a couple of posts to write now that the summer is over, but I thought I would start with something that was a bit of a challenge for me over the summer. I spent a couple of weeks in Beijing in August, including five days attending the International Congress on Ecology (INTECOL). Usually, I like to try to promote the work that is going on at conferences and contribute to the general online science community by live-tweeting. The only trouble is that in China Twitter is banned… I came up with two solutions:

Solution 1: VPN

I used a virtual private network to bypass the firewall. That worked pretty well, and while VyperVPN cost about $12 for a month it gave me regular access to the web for the duration of my stay in China. Not bad value. However, part of my reason for going to China in the first place was to exchange ideas with Chinese researchers, and that’s tough if they can’t see what you are tweeting.

Solution 2: Weibo

My second solution, then, was to take to Chinese social media to try to communicate. There is a fair amount of guidance on Twitter and conferences, but I couldn’t find anything on Weibo and conferences. Also, Weibo is very much Chinese (as opposed to global) and so there wasn’t much hope of me communicating in the local language. Still, I tried my best and punted most of my first day of tweets (in English, unfortunately, and one as an experiment in Chinese via Google Translate) out through Weibo as well.

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The results were not that surprising…  I got a bit of interest on the Twitter feed (interestingly, many many bot accounts, which has never happened before), but very little on the Weibo feed. In fact, I got absolutely no interaction whatsoever. The Twitter feed was completely out of sync with the rest of the planet (or so it seemed), but at least a few people both saw and understood them!

So, what I learned here is that social media is tough to crack in China, even when trying to use local tools. It’s also tough to sign up for Weibo because the authentication uses Chinese mobile phone numbers… Aside from that, the hashtags are a little different (note the “#” at the beginning as well as the end of the hashtag above) and I really never got to grips with finding profiles of people who might be interested and trying to add them to “Weibos”. Has anybody else had any success? Are there academics using both Weibo and Twitter in their social media arsenal?

PS: If you are interested, here’s a quick run down of the conference via my tweets and another from another attendee.

Update on Community Collaborative Impact

A few months ago I wrote a short blog post about “Community Collaborative Science” as a model for impactful teaching and research in UK universities. As I mentioned back then, this kind of “service learning” is a core part of the curriculum in many US universities, but has not taken off in quite the same way in the UK. I was discussing the idea with my partner and we ended up putting together a pitch for a NESTA seed grant. The grant would have been used to build the system and pilot a few projects through an online collaborative workspace. Here’s the pitch:

Unfortunately, the pitch wasn’t successful, but there seem to be other people thinking along similar lines. If you are interested in this kind of topic then please do drop me a line and we can discuss this in more detail.

Help us understand mimicry!

Picture1I have written about mimicry before, describing why most mimics are imperfect and how some mimics imitate not only the appearance of other animals but also their sounds and behaviour. Now, I need your help with an ambitious experiment to test theories about the evolution of mimicry. Most people know that there are harmless animals that have yellow and black stripes to look like stinging bees and wasps. But did you know that there are many thousands of such species, all with different degrees of “bee-ness” or “waspiness”? The new experiment is designed to compare 56 harmless hoverflies with 42 wasps and bees to measure how similar they are. That’s 2,352 unique comparisons! This information will allow us to test exciting new ideas about the evolution of mimicry. There’s only one catch…

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With his beard and odd dress sense, Uncle Sam would have made a fine entomologist!

This particular experiment will use the human brain as a processing tool and the power of the crowd to generate data. It’s a bit like “Strictly Come Mimicking” (or “Mimicking with the Stars“, if you’re in the US): you just need to rate how similar you think the two insects appear out of 10. I’d appreciate it greatly if you could take some time to run through the experiment below. Don’t do it thinking that there is an end, though – there are 2,352 combinations, remember, and the images are randomly paired on each screen! You can access the experiment here:

www.mimicryexperiment.net

My goal is to reach 10 ratings of each pair of insects. That means a total of 23,520 ratings. I know this is a long shot, but that’s the aim, people! Please do share it far and wide! I’ll share regular updates on the blog as the ratings come in (however many or few there are!).

“Noble nature”…?

20161231_184514Walking home after a few drinks on New Year’s Eve, I spotted a small sign in a shop window. The text says:

“As the bee collects nectar and departs without injuring the flower, so should a man behave in his village”

– Dhammapada (1st Century BC)

Two things sprang immediately to mind. The first was the tendency that we have to attribute greater emphasis to quotes from older civilisations, despite the fact that those civilisations are less developed. Older civilisations are not wise like older people – they are actually younger in an absolute sense (as pointed out by Eliezer Yudkowsky). It is as if being from a time far distant to our own confers wisdom that we perceive lacking in contemporary society.

However, the second thing that occurred to be was that “that’s not how bees work”… Pollination is a mutualism most of the time, but not always. By offering a nectar resource in exchange for the transfer of pollen, flowers have evolved relatively straightforward paths to that nectar for their respective pollinators. Sometimes that is a big, open flower that can be accessed by many species, but other times the flower has a peculiar shape or the nectar well is particularly inaccessible. The latter cases often result in very specific species that are able to access the nectar using particular behaviours or very long tongues.Read More »