Just so I don’t get all rusty and completely forget how to post in this blog, I thought I’d share a cool new tool I’ve discovered- thinklink.
This is the background: I am currently assembling an online course about disease in nature and am looking for ways of getting students to work with the material in a series of small-ish assignments. Our students get plenty of practice writing essays, but with scientific information, text is not everything. It has always struck me in student dissertations and literature reports that very few include custom-made figures. Of course for anything other than reports of their own research, it is perfectly fine to borrow published figures, as long as they are correctly attributed. By comparison, it is a lot of work to prepare figures from scratch, but it’s the thinking, not the doing (as in graphics design) that takes so much time. You don’t know if you really understood something until you’re made to draw it (try explaining how a toilet cistern works!). This is why I am going to include a small number of “creative” tasks in the course.

fungal life cycleOne specific example in my online course was the reasonably complex topic of pathogen life cycles. Both fungi and oomycetes (aka “water molds”, including such lovelies as potato late blight, sudden oak death and crayfish plague) tend to have alternative sexual and asexual life cycles (see pic). There are all sorts of variations on the themes of plasmogamy (cells from separate hyphae fuse, but the nuclei stay separate), karyogamy (nuclei fuse), meiosis (nuclei split) and spore formation. Not all species include all steps.

I’m going to ask students to research the life cycle of one pathogen of choice and then to annotate the generic picture (above) with info on what each stage/ event/ process looks like for the particular pathogen they have picked. Here’s where thinglink comes in:

Life cycle of Phytophthora infestans (Potato Late Blight)

Life cycle of Phytophthora infestans (Potato Late Blight)

Rather than producing really complex composite graphics, or simply reproducing an existing pic (see example for potato late blight; M. Piepenbring via Wikimedia commons, CC BY-SA 3.0), I’ll get them to insert information tags and/or hyperlinks into the template via thinglink.


When I tried to do that for wheat stem rust, with admittedly one of the most complex life cycles of all fungi, I realised quickly that I hadn’t completely understood it. This pathogen does not quite fit into the general scheme, and I had to get a bit creative while thinking how to map the different types of rust fungus spores and hyphae onto the scheme. (For nerds: the “problem” is that like many basidiomycetes, rust fungi spend much of their life as dikaryotic mycelium. Karyogamy and meiosis occur a long time after plasmogamy, and crucially, after a host switch from barberry to a cereal, before going back to barberry. I know, right?) Below is my annotated scheme for stem rust. This would be provided for students as an example of how it could be done, but also with a note that pretty much any other pathogen is less complex than this one. Simply hover over the pic for long enough to see pics and text. I think that’s pretty neat.

I have not completely worked out how to make this work for students. If they like, they can get their own accounts and just share a link with me, much like I’m sharing my thinglink here on this blog. If I can bring myself to shell out $35/year for the “edu premium” version, I can set up student groups that don’t require them to sign up, and in addition I would unlock many new features.

Speaking of which, in the free version there is a limited choice of tags (five coloured dots, or letters A-E) and (I think) only text, online figures, web links and links to youtube videos can be included. I’ve not really needed anything fancier yet, so currently for demonstration the free version is fine. There are some bugs though; when I tried to copy and paste text I had written in MS Word, it wouldn’t let me. Bizarrely, only pasting into the for the URL box worked, from where I could drag it into the free-text box. There was also an issue with moving the tags (dots) around. Rather than allowing simple dragging, any click and drag on a tag would resize the tag itself. Using opposite corners to enlarge and then shrink the tag, it’s possible to move tags elsewhere- but what a drag. Perhaps this is sorted in the “edu premium” version, and they are testing users’ patience by making the free version buggy? Might upgrade after all…

On the thinglink website, many of the featured examples are just randomly placed links on fun pics. Once I had a closer look at what’s possible, though, it really struck me that this could work fantastically well for science education; both as a didactic tool and (as described above) to get students to assemble interactive graphics as an assignment. Thinglink provides an embed code that has worked well in our virtual learning environment. Here are two more examples I’ve put together in relatively little time:


I am a MOOC dropout

Let me confess. Yes, I am among the majority who have signed up for a MOOC and didn’t have the determination/ time/ interest to stay on and complete the course. That’s why the carcinogenic molecule (or is it a splinter of graphene?) that is the icon of Coursera’s “Introduction to Physical Chemistry” is hanging over my notes like an angry rain cloud.

mooc dtced


Massive Open Online Courses are one of the most talked-about recent developments in universities. Are MOOCs the future of higher education? Will they put us all out of our jobs? Nothing but hype? I wanted to see for myself. In the words of a colleague, I signed up to see what it’s like being a MOOC student, and to steal their best ideas.

Being a part-time distance learner on a “proper” credit-bearing, award-winning MSc course means that it would have been difficult for me to devote a lot of time to additional online learning, so it was always going to be more skimming than deep diving. I decided to have a look at one of the first four MOOCs offered by colleagues at the University of Manchester. As an undergraduate I studied Physical Chemistry for four semesters, and I developed a grudging fondness for the subject- it was all equations and calculating stuff I didn’t much care about with those equations, but the bigger picture made sense and everything came together in a satisfying way. Would my colleagues pull off an inspiring online course in what can be an extraordinarily dry subject? If it can be done for Physical Chemistry, anything is possible. (This comment of mine on the “Introduce yourself” discussion board won the approval of the course organiser!) On the lookout for courses closer to my own subject, I found “Introduction to Biology- The Secret of Life” from MIT and “The Chemistry of Life” from Kyoto, both hosted by EdX.

Rather than the actual content, it was the ideas for online pedagogy that interested me. What would take the place of 50 minute lectures? How would assessment and feedback work? Is there contact with staff? And considering that experimental lab work –the experience of actually doing science rather than just hearing about it- is central to our on-site degree programmes, what would happen instead in cyberspace?

In the event, while there was little mindblowing innovation, I did take away many good ideas. All three courses unsurprisingly had video lectures, typically between 5 and 15 minutes long. Some were narrated PowerPoints that must have come straight from the original lecture, some were Khan Academy style. Eric Lander, human genome pioneer and high-profile MIT professor, was filmed delivering “Introduction to Biology” to what must have been a select studio audience –surely more than 50 MIT students normally take this introductory class? Motonari Uesugi of Kyoto University talked straight to camera about “The chemistry of Life” in front of a SMART Board. I can’t say it made a huge difference; all lectures were clearly very well planned and delivered enthusiastically. With Lander’s extraordinary charisma and energy, the “live” experience certainly added to the enjoyment of watching the videos. I hadn’t expected to get inspiration from a MOOC for improving my delivery of traditional lectures!

One feature of the EdX courses that I liked a lot was the navigation through a series of alternating short video lectures and two-question self-test quizzes. “Introduction to Physical Chemistry” had longer self-tests after between five and ten short lectures. Here, the volume and complexity of didactic teaching made the whole course feel surprisingly conventional; a real throwback to my undergraduate days when formula after formula and definition after definition fell from the heavens. The majority of self-tests in all courses were multiple-choice, which makes sense because it offers instant feedback. The two EdX courses also had drag-and-drop questions and quite a number of interesting interactive plug-ins for manipulating molecular structures. However, in the biology course the later bits on genetics are largely MCQ. The most innovative assessments were used in the “Chemistry of Life course”: several peer-reviewed exercises where students were asked to e.g. come up with a research project proposal. These exercises came with very detailed and useful guidance for the peer reviewers. The most charming and original of these tasks was to re-draw a drug structure and “read” it like a star constellation (a “drug constellation”) or a molecular Rorschach test: this structure looks like a child with a balloon; the drug will make the patient cheerful like a child. Only the Japanese could come up with that. “The chemistry of life” emphasises the need for innovation and originality in science, and this task hits the spot in a playful way.

I was too late to participate in those exercises and so unfortunately could not see what students came up with, but peer reviewing seems a valid answer to the dilemma of the enormous student:staff ratios on MOOCs.

It is difficult to assess how many participants there were on the courses; the “Introduce yourself” forums had around 150 posts for Physical Chemistry and around 1100 for Introduction to Biology. Clearly there were many more students on the course who never posted anything, and the number of actual scientific discussions was very limited. In Physical Chemistry, the Professors and PhD students were astonishingly engaged in the forums, both for science and banter (by far the most lively thread was “Scientific Songs”), and this was very much appreciated by the core of most dedicated participants.

Another feature of Physical Chemistry was “lab work”. Not quite as hands on as in this physics MOOC, but still- a demo experiment was filmed and participants had to read changes in temperature or gas volume over time from the screen. These readings needed plotting so that physical constants could be calculated. Another experiment involved a Flash simulation of a spectrometer that allowed a reading of hydrogen emission wavelengths. Good experiments with excellent instructions. I think science can’t be taught without at least some experience of the scientific process of experimentation because equations and constants do not, in fact, fall from the heavens. They are the fruit of hard work.

Judging from the introductory discussion posts, MOOCs largely reach an audience of current (or soon-to-be) university students and older graduates who want to branch out or tap into nostalgia like me. Not quite a revolution in HE there. Nor did I see any truly novel pedagogy (except perhaps the creative “Drug constellations” task with its own Flickr site). But maybe I’d need to take part in a cMOOC for that. Still, I’ve learned a great deal and found these MOOCs a treasure-trove of neat ideas for the online part of my own teaching. I am cautiously excited about MOOCs.

Lecture flipping- part 3

film strip


On to the geeky bit- the technology behind the flipped lecture. I haven’t uploaded the videos (yet) to youtube so an icon will have to do…

Even before I decided to volunteer for the biochemistry lectures and before I planned “lecture videos”, I was fascinated by science videos on YouTube- asapscience, Earth Unplugged, Minute Earth and especially Minutephysics, Myles Power, Periodic videos, PHD comics, SmarterEveryDay, thebrainscoop, Veritasium, Vihart and Vsauce. Creating something, merging science with a little bit of art and creativity sounded like fun, and I wondered if I wanted my own science channel. Trouble is, all of the above “content creators” (as YouTube calls them) make videos with pretty high production values –read: recorded under semi-professional conditions with very good cameras and lighting. My first attempts at creating videos the way Henry Reich does for Minutephysics (time-lapse recording of hand-drawn doodles on paper, a beautifully simple version of professional videoscribing as e.g. seen in RSA animate) were not encouraging. Much easier to start from animated Powerpoints and record screencasts. Without a vast amount of research, I settled on Snagit to do the screencasting. It’s very easy to use and cheaper than the full Camtasia studio. Snagit does not include editing, so I decided to subscribe to Adobe Creative cloud as well (affordable with educational discount) so I can use Premiere Pro, although chances are Camtasia studio would have been cheaper in the long run. It’s a shame that Adobe decided to exclude their screen capture tool (part of Captivate) from the Creative Cloud.

Having watched a few traditionally recorded lectures done with screen capture technology, I found them unbearably slow compared with the snazzy YouTube channels above. For a succinct style, I scripted the videos and created the Powerpoints alongside the script. I created those ppts based on the previously existing lectures, but soon found I wanted my own style and needed to include way more animation than would be practical for a classical lecture. After a while I found that I needed to make those animations move slowly (or fade in/out over eg 2 seconds instead of 1) because the 10-15 fps recording rate of Snagit otherwise made things jump awkwardly. For the voiceover I recorded my reading the script with Audacity on a Rode Podcaster microphone, using a fleece jumper around the mic (and myself!) to achieve a reasonably dry sound. This was good fun and surprisingly easy. Some room for improvement though- I’d like the sound even drier, and I’d prefer to speak standing up rather than hunched over the desk mic. Should be easy to fix. Having recorded the screencast (just clicking my way through the ppt), I spliced video and voice together in Premiere Pro to make text or images appear just at the right time. It took a while to get the hang of it and arrive at a routine for cutting, moving, rate stretching etc, but in the end this was a very satisfying thing to do. In some of the other videos I edited in other clips, for example of molecular dynamics animations that I found on the web. I’ve yet to learn how to produce animations of rotating protein structures but that’ll come.

Making these videos was very enjoyable, but also extremely time consuming –about 2-3 full days of work per lecture-, and having started production on the first one I realised I would only be able to convert 3 lectures to videos this year. Probably just as well because this was a trial run, and it makes sense to learn from the first round before rolling out the flipped approach to all of my lectures in the unit.

Each of these videos shrunk the 50 minute lecture down to 15-25 minutes split into two videos or just one. This was intentional, so students would be able to go through material for revision more quickly, but it also meant that I had to talk quite fast. I would have to wait for student feedback to see if they agreed.

Lecture flipping- part 2

communication cycles

Moving on to the design of my flipped lecture experiment. So here are the principles I wanted to apply in my flip teaching experiment: As a resource for self-paced learning, I would make videos available that would replace the teaching of “stuff” in classical lecture format. Having individually worked through the videos at their own pace, the students would be able to do simple exercises via Nearpod (next post) and submit them online. In the original lecture time slot, I would discuss the solutions to exercises, spending more time on those that seemed more problematic. There would then be a second round of Nearpod quizzes during the lecture, this time (as in Eric Mazur’s classes) allowing peer-to-peer discussions, and again online submission of answers from mobile devices. These pub quizzes would be more challenging and more real-world, thus hopefully more interesting or even inspiring, and perhaps answering the question “why do we have to learn all that stuff?”.

The two rounds of quiz would result in two cycles of learning, articulation of understanding and feedback, which should mean –for those who actually take part- in much better learning.

This pedagogical side is summarised it in the illustration above. The chart analyses the different elements of this flipped lecture according to Diana Laurillard’s Conversational framework (Rethinking University Teaching: A Conversational Framework for the Effective Use of Learning Technologies, Routledge 2001, or more recent publication). Showing off what I’ve learned in my DTCE course last semester…

The left hand side shows what Laurillard calls the Teacher communication cycle. Traditionally, the first arrow (here: video) is the lecture, and the two following arrows are the exam (“students articulating their conceptual understanding”, or just ticking boxes in MCQ) and the exam mark as feedback. In fairness, we have a lecture-by-lecture online quiz as well as an end-of-term exam here, but both are summative (marked). Additional cycles of exercises with formative feedback were something my “focus group” had also requested- last summer I quizzed my personal advisees what they thought might improve this lecture unit. The peer communication cycle on the right is new and hasn’t been tried in this large lecture unit before.

Lecture flipping- part 1


So, I’ve very recently learned (from a student!) about the ADDIE model for instructional design, and I think it makes sense to follow that model here. Let’s talk about the analysis phase!

Much of this actually happened more than half a year ago, so this account is probably edited with a bit of hindsight. Last summer I volunteered to take over the first half (10 lectures) of our 1st year introductory biochemistry lecture. As a biochemistry graduate I had a rush of nostalgia thinking about topics like lipid structures that I had not come across in my research for a while. Apart from the desire to go back to my roots, as well as to be seen to be taking on more teaching while I had the opportunity to choose what interested me, I was also keen to try the lecture flipping approach discussed in an earlier post.

The class is compulsory for all but a handful of our year 1 life science students and this semester had about 530 students enrolled (not that one ever sees that many). About 100 of these are biochemists “by name” while the rest vary in the degree of enthusiasm about chemistry and molecular life sciences in general. When I first met the students I asked who disliked chemistry or felt very insecure about it, versus who thought it was a piece of cake. There were many more in the first camp. It is safe to assume that for the majority biochemistry is something they grin and bear somehow rather than expect to enjoy. Some, but not many, brought very good A-level chemistry knowledge. For the purposes of instructional design, it’s safe to consider them novices. There was my challenge!

The unit has been very well run for years and I had an experienced colleague to guide me. Having looked through the material and the six-page list of detailed learning objectives (just for “my” half of the course!), it struck me how much factual “stuff” has to be learned. Of course it was no different in my student days. Somehow the memorization of amino acid structures and metabolic pathways is a character-building rite of passage. The dilemma is that there’s only time to teach the “stuff”, and we keep our fingers crossed that deep understanding of concepts and the ability to apply that conceptual knowledge to new problems come as a byproduct.


Twiddla: online interactive Whiteboard

first twiddla


But before that, a brief interlude. I had long been looking for a sort of collaborative whiteboard that allows students to annotate and comment on a single document such that each comment would be immediately visible to all participants. I’m aware of shared documents in eg Google docs or Dropbox, but I wanted something a little freer where students could circle around stuff, add notes etc. I think I first came across Twiddla in this post on emergingedtech. As the post says, these kinds of tools tend to come and go, and it’s one of the frustrations in this business that any online tool that works well this year might not be around next year.

Anyhow, Twiddla is pretty uncomplicated and allows you to upload documents, pictures or webpages as background to a whiteboard that can then be annotated by everyone who is sent the URL for that particular “meeting”. Everyone can highlight stuff, draw lines and boxes around text or images, and add notes. In this case the learning objective was to understand the conventions of writing a lab report. A colleague had written a very nice “bad example” lab report which I had turned (crudely) from a pdf document via screenshots into images. It is possible to upload a regular pdf as background but I didn’t have the “proper” Acrobat software to trim the pages I didn’t want off the original document.

Having inserted text and images as background, I sent the link to the 8 students with minimal instructions and invited them to annotate “everything that was wrong” with the “bad example”. One issue I had to explain is that the “erase” function needs to be used judiciously- comments, highlights and background are erased together, so all would be lost. However, anything in the “comment layer” can be selected and moved or deleted individually, and Ctrl+z for “undo” works in the whiteboard.

As the figure shows, the students had no trouble finding their way around the whiteboard and annotated heavily but in a very orderly way. They also used individual colours for underlining and freehand highlighting (I think- don’t know who did what), but it’s a pity that text boxes can’t be colour-coded. Instead I suggested using the initials. One student got in very early and added loads of comments, which made it less rewarding for the rest of the group. But I suppose there’s no straightforward way of encouraging a more synchronised collaboration unless it’s really essential for the task.

I think this worked well as a preparation for a face-to-face discussion, but it was a bit tricky in the tutorial session to work from what had turned into a very complex annotated document. Calling on the individual students to explain their comments did not seem a particularly intelligent way to go about it. Maybe I’ll invite the group, or smaller groups of students, to summarize the take home messages instead of trawling through the whole whiteboard myself with everyone watching. I think there is plenty of potential for other kinds of collaborative tasks with this tool.