The impact of climate-induced distributional changes on the validity of biological water quality metrics [paper summary]

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “The impact of climate-induced distributional changes on the validity of biological water quality metrics”, was published in the journal Environmental Monitoring and Assessment in 2010. You can find this paper online at the publisher, or on Figshare.

Background: Water quality is measured in a number of different ways: measuring levels of chemicals and pollutants, measuring temperature and other physical parameters, and monitoring the animals and plants that are living in the water. The theory is that the animals and plants living in the water have certain requirements of their habitat (particularly a need for clean water) and so you can use the presence of certain “fussy” animal groups as a proxy for water quality. The problem is that, under climate change, species are moving around as environmental conditions – especially temperature – changes.  This means that changes in the animal and plant communities at a given site might give the appearance of an increase in water quality while actually the arrival of new species is simply the result of climate change.

What we did: I analysed an extensive dataset of British dragonfly and damselfly (known collectively as the “Odonata”) sightings to look for a pattern of geographical movement since 1960.  Dragonflies and damselflies are an important group in biological water quality monitoring, as they are particularly sensitive to pollution.  I found that the patterns of water quality that would be detected using Odonata at a generic site would appear to change over time with the changes in Odonata communities, independent of any changes in water quality.

Importance: Biological communities are used extensively in the monitoring of freshwaters and this research emphasises the need to take distributional shifts that occur as a result of climate change into account when using this method. It is likely that water quality is improving, with better treatment of wastewater and better enforcement of environmental regulation, but accurate monitoring is the key to continuing improvement. Secondly, this paper demonstrates once more the fact that Odonata are responding to climate change.


Image credit: Tambako the Jaguar, CC BY-ND 2.0, http://bit.ly/1v8EGcK

Massively Online Open Courses (MOOCs) in Higher Education

I have written before about the fact that massive open online courses (MOOCs) can play a complementary role to that of traditional teaching within higher education. There are a number of platforms offering these courses now, and academics should certainly consider including components of MOOCs in their teaching. Here are a few of the platforms:


My own institution, the University of Leeds, has partnered with one of the newer MOOC providers: a UK-based group of universities called FutureLearn. These courses represent the most recent evolution of MOOCs, away from simply posting standard lectures and quizzes online and towards the production of MOOC-oriented materials that make the most of the distributed learning environment. This includes a lot of great multimedia content, auto-graded quizzes, animations, discussion boards, and a whole lot more.


PictureAs of April 2013, Udacity offers 24 courses.  The platform grew out of a highly popular engineering course that was run out of Stanford University by Sebastian Thrun.  In 2012 Udacity launched with just two courses (one in building search engines, and the other on programming robotic cars).  Courses involve watching recorded lectures and then answering quizzes on the material.  This is supplemented through homework which encourages the application of the techniques that have been learnt.  One course is currently accepted for credit at some universities.


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EdX was founded by MIT and Harvard, but now includes a wide range of institutions from around the world.  These institutions began by offering 12 courses in 2012 but that number is projected to increase considerably.  EdX charges for certificates of completion, and their courses are not yet recognised as credit-bearing at universities.

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Coursera is the largest of the MOOC providers.  Backed by venture-capitalists, rather than by universities, in May 2013 Coursera contained 70 partners who contributed 374 courses.  At present it isn’t clear how Coursera will make money, and they work individually with each of the partners to provide individual agreements.  Five courses are currently considered as credit-bearing in the US.

An Example of Use

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As part of a core section of a university programme, students are required to attend “key skills” classes.  These are fairly common in UK universities, involving small group discussions based around research skills, careers, and any other topics that the tutor decides to cover.  As part of one of these sessions, a tutor decides to focus on critical thinking.  Rather than doing huge amounts of research on an area that is not her/his speciality, the tutor decides to use a Coursera MOOC as the starting point.  S/he asks the students to enrol on “Critical Thinking in Global Challenges“, a MOOC run by the University of Edinburgh.  This MOOC lasts five weeks and requires 3-5 hours of work per week.  After each of the MOOC classes, the tutor discusses the session with the students.

Phenology determines seasonal variation in ectoparasite loads in a natural insect population [paper summary]

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “Phenology determines seasonal variation in ectoparasite loads in a natural insect population”, was published in the journal Ecological Entomology in 2010. You can find this paper online at the publisher, or on Figshare.

Background: Parasites drain resources from their hosts in order to survive and reproduce.  The effects that this has on the host have been shown to be substantial in some species of dragonfly and damselfly. However, in order to assess how serious these effects are, we need to know something about patterns of parasitism: how many parasites does a host carry and how does that number vary throughout the year?

What we did: We had a two year study looking at a single population of the azure damselfly, Coenagrion puella, at a single site in southern England.  All the damselflies (1036 in total) emerging from the pond were caught, marked individually, and the number of parasitic mites that were clinging to them were counted.  We had a number of hypotheses as to what might drive variations in parasitism: higher temperatures might increase the effectiveness of mites at finding and latching-on to hosts, larger animals might have more parasites, or there might be a difference between sexes in parasitism.  We found that most of the variation in parasitism was related to the animals emerging in the middle of the season having the most parasites, while animals emerging early or late had fewer parasites.

Importance: The seasonal pattern suggests that variation in parasitism is the result of ecological interactions where parasites have evolved to take advantage of their hosts’ patterns of development. Given that dragonflies and damselflies have been shown to be emerging at different times in response to climate change, it remains to be seen whether mites will be able to track these changes.


Image credit: Brad Smith, CC BY-NC 2.0, http://bit.ly/1q6YTeA

Empirical evidence of senescence in adult damselflies (Odonata: Zygoptera) [paper summary]

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “Empirical evidence of senescence in adult damselflies (Odonata: Zygoptera)”, was published in the Journal of Animal Ecology in 2010. You can find this paper online at the publisher, or on Figshare.

Background:  Ageing is thought to be one of the most widespread biological phenomenon, though it has often been said that insects do not live long enough to experience it. Experiments with insects in laboratories under ideal conditions have shown that ageing does occur, but there are very few studies that have demonstrated this in the wild.

What we did: We used two extensive datasets of sightings of the azure damselfly, Coenagrion puella, to look for an effect of “demographic senescence”.  What this means is that the chance of an animal dying on any given day increases as it gets older.  Hundreds of animals were marked and followed for their whole lives over two summers.  The damselflies live for, on average, 7 days after marking and that follows a period of around 10-12 days of maturation.  What we showed was that, even over so short a lifespan, there was a detectable signal of age-related mortality.  We also demonstrated that there were a number of other variables, principally weather and parasites, that also influence the chance of a damselfly dying.

Importance: Ours was only the second study that comprehensively demonstrated ageing in a wild insect population.


Image credit: Tim, CC BY-NC-SA 2.0, http://bit.ly/1vvSVWl

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.

Accounting for recorder effort in the detection of range shifts from historical data [paper summary]

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “Accounting for recorder effort in the detection of range shifts from historical data”, was published in the journal Methods in Ecology and Evolution in 2010. You can find this paper for free online at the publisher.

Background:  Climate change is causing a range of effects in plants and animals. One of the most noticeable is the colonisation of new areas as the environment warms to a point where animals are able to persist where once they could not. However, the sources of data used to detect these kinds of patterns tend not to be systematically collected and so present unique challenges during analysis.

What we did: I analysed a series of different methods that have been used to control for the effects of recorder effort bias in the detection of range shifts.  This recorder effort bias occurs when there are far more recorders looking for animals in a later period and so the chance of discovering those extreme populations increases. Thus range shifts could simply be an artefact of increased sampling. I demonstrate that the methods that have been used before vary in the detection of range shifts and that some make more sense than others. I follow this up with a case study on range shifts in British Odonata and make recommendations concerning the most appropriate methods.

Importance: Climate change is an important issue and we need cutting-edge analytical tools if we are to properly assess its impacts on the world. I hope that this paper has contributed to this aim.


Image credit: Ken Slade, CC BY-NC 2.0, http://bit.ly/1qAae4a

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.