Monday, March 29, 2010

Gender Bender?

Gender I spent Saturday afternoon marking the Friendfolios our students have been creating this term. Overall, both the feedback and the marks are very good, but after a short while of systematically going through them, it became clear that females were contributing more than males. However, the picture is complex - for example, the top contributor is male. Does assessment based on social network activity favour one gender over the other? So while we will be doing more complete analysis soon, I had a quick look at gender influence for this assessment. The median marks for the Friendfolio component and overall module mark were:
Although females score higher marks than males, there is no significant difference between the marks (chi square, p 0.58), hence no evidence that assessment of social network activity has a gender bias. Why do males score less than females? Because they submit fewer assessments. If we want to worry about something, that's what we need to sort out. Let's start with why this is.

Thursday, March 25, 2010

Come the Revolution

Molotov cocktail You may not have realized it (lots of academic publishers still haven't), but we are in the middle of a revolution in publishing. Along the way, we may be at the start of a revolution in academia too. How do I know? Well it's pretty obvious when the BMJ exhorts us to:
be out there fighting to get peoples’ attention and to shape the world.
At the same time, Nature abandons the citation index and suggests:
alternative measures of creativity and productivity should be included in scientific metrics, such as the filing of patents, the creation of prototypes and even the production of YouTube videos.
At the same time, Nature quietly opens up it's prized content, making Nature News available to all, online, free, and slips in online commenting across the entire magazine. Of course, modern journals such as PLoS have had these features, and much more, for some time, but it's nice to see the pressure beginning to tell on the old guard.

The fight is not over yet. It now moves on to grant funding bodies, higher education managers and government to recognize our achievement in bringing these new channels of publication and digital scholarship to maturity. Their capitulation is inevitable. See you at the barricades comrade!


Tuesday, March 23, 2010

The Complexity of Cooperation

The Complexity of Cooperation Last week when I wrote about the importance of being nice, I was undecided where to place open notebook science (ONS) in terms of the prisoner's dilemma. Since then, I've read Robert Axelrod's follow-up to The Evolution of Cooperation, The Complexity of Cooperation. In this book, Axelrod moves on from the two-person prisoner's dilemma to consider situations much more applicable to the real world - multi-party interactions, significantly without the assumption that the parties involved will always take a rational approach (= noise). He also considers such influences as norms (behavioral expectations and cues within a society or group), and emergent properties of complex systems. Irrational behavior, societal norms, altruism? Suddenly we are into ONS territory.

Unfortunately, as Axelrod's simulations approach reality, the simplicity he was able to bring to The Evolution of Cooperation tends to evaporate. Most of what I know about Nash equilibria I learned from A Beautiful Mind. Nevertheless, Axelrod's landscape theory approach does have valuable things to say to those considering ONS, but on balance, it's more difficult to whole-heartedly recommend that everyone should read this book as I did with The Evolution of Cooperation.

Take home message? ONS is mathematically justifiable, but it's always going to be a risky pathway unless and until societal norms in science change. A good example of this are the ridiculous patent laws, which invalidate ONS discoveries from patent protection. In reality, few organizations have deep enough pockets to establish and defend serious patents, so the beneficial effect of openness is to deprive others of patents through prior publication. I'd count that as a win.

Monday, March 22, 2010

Tories buy Gordon Brown

on Google:

Open Notebook Science - The Chytrid Project

Open notebook science (ONS) is the practice of making the primary record of a research project publicly available online as it is generated. This involves placing the personal, or laboratory, notebook of the researcher(s) online along with all raw and processed data, and any associated material. The approach can be summed up by the slogan "no insider information".

Regular readers will know that I've been thinking and writing a lot about ONS recently. There are two reasons for this. First, it is a natural extension of the work I have been doing in education over the past few years. Second, over the past few weeks I have been discussing with my colleagues the possibility of setting up an ONS project. ONS is far from the norm of accepted scientific practice (I'll be writing more about norms here tomorrow), but over the last year of talking to some of the leading practitioners of ONS, notably Jean-Claude Bradley and Cameron Neylon, I have become convinced that I would like to try it myself. Based mainly on the experience of Jean-Claude, we have set up a blog as one part of our feasibility test of ONS, a space where out part-formed thoughts, ideas, planning, and general commentary on ONS stuff will appear. The other part is our open notebook on Wikispaces, where all the data will be posted. Anyone familiar with ONS will immediately recognize that this is a clone of the Jean-Claude's approach. I have discussed this with him and it seems sensible to carry out our first faltering steps in a tested format. If you want to follow our progress, subscribe to the RSS feed for the blog, or go to this page and subscribe with the feed reader of your choice. If you prefer, you can receive updates via your email account.

Open or closed? It's not that simple. There are many flavours of ONS, and it's not clear yet which one(s) we want or are able to pursue. Indeed, our style of "open" is one of the first things we need to work out about this project. For a variety of reasons, not all of the research done in our laboratory will switch to ONS. Initially, we intend to try it out with a new chytrid project we are developing (which I'll describe in a subsequent posts on the new blog). Thus our approach to ONS is itself an experiment. Only time will tell if we are able or willing to continue in this format. Apart from funding, this depends whether this idea wins hearts and minds - not only in our lab, but beyond it - at the University of Leicester and in the wider scientific community. In part, that depends how much interaction we receive from colleagues, near and far. The project we are beginning is a new field for us, so we don't expect the world to be queuing up to help us, but to be successful, the downside risk of ONS needs to be balanced by the upside of helpful positive interactions from interested observers. Without the generosity of my colleagues, who have been prepared to entertain my madcap ideas about open science, I would not even have got this far.

My institution will judge the success of this project in terms of grants and publications, so that must be our yardstick too. On a purely personal basis, I also have other, possibly more important, criteria for judging the success or failure of this venture: openness, collaboration and the advancement of science. Judge us on these criteria.

Friday, March 19, 2010

Begin the Beyond

BeyondGoogle Over the last few weeks, with the assistance of my librarian colleagues Sarah Whittaker and Keith Nockels, we have rolled out the new information literacy component of our second year Biological Sciences "Research Skills" module. This consists of four components:
Each of these except Refworks has an associated assessment, which for the first two consists of online MCQs. The CiteULike assessment is designed to give students practice at writing critical appraisal of scientific papers as well as using CuL. Based on our experience with students using delicious as part of their PLEs, we asked students to:
  • Briefly describe how they found the paper they bookmarked: 10%
  • Write a critical appraisal of around 500 words: 50%
  • Relevance to degree stream: 20%
  • Descriptive one-word tags used (including a degree-specific tag): 20%
Students bookmark and annotate (at least) one paper a week for three weeks - in our previous experience, three is the magic number of repeats needed to maximize the "light bulb moments" in student social media use. So far, the results are encouraging, but judge for yourselves at the links above.


Wednesday, March 17, 2010

Oh, Sir Jasper

On the importance of being nice

share Since I wrote Why would I want to share? and Sharing is a selfish act, I've been thinking about this topic. Practically, this has consisted of reading Robert Axelrod's excellent book, The Evolution of Cooperation. This has influenced my thinking significantly, and I have come to believe a thorough understanding of the prisoner's dilemma is key to social behavior. Fortunately, it is possible to summarize the book in three simple rules:
  1. In a classical prisoner's dilemma (i.e. a one-time interaction), always defect.
  2. In an iterated prisoner's dilemma (i.e. repeated interactions by the same partners), use Tit-For-Tat (respond in kind).
  3. Be nice, i.e. do not defect on the first move. After that, use Tit-For-Tat. The more interactions there will be, the more important it is to be nice.
In the book, Axelrod provides abundant evidence to support these rules and examples of where they can be seen in operation in the real world. So how would we apply these rules to:
  • Teaching students: (Iterated) - be nice but firm, sticks are needed as well as carrots.
  • Open notebook science: It's not clear to me whether this is iterated or not, which makes a big difference.
  • Online identities: (Iterated) - be nice but stand your ground on principles.
You can fill in more cases for yourself - but only if you've read the book, which I strongly recommend.


Tuesday, March 16, 2010

Thought Experiment

Thought What I want:
  1. A way to aggregate all the disparate bits and pieces I write online across many services - tweets, status updates, comments, etc.
  2. Visual representation of this data with a semantic format - something like a non-random Wordle.
  3. Auto text generation based on these themes to produce a semi-coherent narrative for final manual polishing.
I'm not sure how practical this is at the moment. The aggregation part is not unduly taxing, and the visualization part is clearly possible. Generating meaningful analysis is the hard part, but I'm not asking for a tool to write finished papers for me, just something to produce a rough draft and take the slog out of the early stages.

Let us be social - lessons learned from The Digital Researcher #DR10

It is a common misconception that in Leviathan, Thomas Hobbes said that life was nasty, brutish, and short. In fact, what he actually said was that life is the state of war of every man against every man:

solitary, poor, nasty, brutish, and short

Let us be social.

Over the past couple of years I've been involved in a number of Web2.0 training events. All have suffered from the same difficulties: too big a differential between the least and most experienced attendees, and a multiplicity of tools leading to information overload. It's not entirely clear to me how you avoid these problems, but of all the events in this area I have participated in, The Digital Researcher shindig at the British Library yesterday was probably the most successful:

I think the main reason for this was that overall, in spite of the difficulties listed above, the content was well structured enough not to let the Why? get buried in the How? This may have meant that some of the less experienced participants went away with somewhat restricted view of what to do next, but at least we didn't drown them in information (although there was a lot for everyone to take in on the day). And hopefully, the more experienced attendees got something out of the day too.

Wednesday, March 10, 2010


Peel eased the black Toyota Prius off the M11 and continued on across Essex. Thank God he didn't have to make this journey regularly like in the old days, before he started doing his programme via ISDN from Peel Acres. Still, it had been fun to visit some of the old watering holes in London. Walters would have enjoyed it. No-one had recognized him. Being dead had its compensations. Heart attack on a walking holiday in Peru? He'd thought no-one would ever believe that, but Pig said they would, and of course she was right. And no-one was going to look for him in the Essex badlands.

Pig would be asleep when he got back, but he'd get up early tomorrow and cook her breakfast. Couldn't afford to sleep in tomorrow anyway, had to get the March edition of Dandelion Radio online before the weekend. The music was the main thing of course, as always. All those new bands straining to be heard. But it was fun pretending to be all the different DJs, especially the occasional fake Dutch accent. A heck of a lot more fun than working for the BBC, that was for sure. It had just got worse and worse over the years. Home Truths was the killer, nice idea but eventually he just couldn't take the BBC bullshit any longer, and "death" had been a relief. Dandelion Radio was just about doing what he liked. A bit like the pirate days really, but totally legal. Of course, it didn't pay, but radio had never been about the money. And no more Top of the Pops bollocks either, although it had paid for the original Peel Acres. Yes, he wished he'd discovered this internet thing years earlier. It might have kept him alive.

This is a work of fiction and any resemblance between the characters and persons living or dead is purely coincidental. Well, sort of. Oh, and Dandelion Radio, that's real too.

Tuesday, March 09, 2010

I say Pub, you say Quiz

logo After dinner at the CFB Reps Forum last September, Peter Klappa gave us a practical demonstration of how pub quizzes can be used in an educational context. In spite of the hangover next day, I decided that this was still a good idea and that I wanted to try it out on one of my own courses.

In a nail-bitingly close finish (nineteen and a half point to nineteen), AIDS & Co managed to hold off a late push from the Vacant Virologists to unexpectedly claim the confectionery prize. The whole thing was clearly very engaging, and I will certainly be using this format again, although like all such interventions, it clearly needs to be used sparingly to remain effective.


1. Have you done this type of exercise before (if so, when)?
No (All)

2. Was this session useful?
I found it very useful - learnt a lot. I will be using the quizzes on blackboard more since doing questions has proved helpful. Very useful form of revision. I learned more than I expected to from it. It was a nice overview of the past few weeks (and it doesn't hurt that we had fun doing it).
It was quite useful to have it brought all the lecture material that you had taught together. It was also quite fun.
It was useful to see what small details we knew and it was also very enjoyable to take part in it.

3. Any other comments?
Can we have a copy of the answers please.
Very enjoyable. Would be nice to have a copy of the Q&As.
It would be quite useful to have the questions and answers. Or just the answers for use in revision.
[problematic - writing good questions is time consuming and I need to be able to reuse them]
Probably the best tutorial in all the 3 years I’ve had.

Sunday, March 07, 2010

Where's the Open Science?

share Since there are clearly too many hours in the day and I have nothing to fill most of them, there's a faint possibility that I might become involved in some laboratory science in the mid-future. Of course, this is dependent on funding (sigh), but there is some seed corn money available, so it's not just a pipe dream.

Two weeks ago I had what I thought, at the time, was a barnstorming idea, but after a two hour brainstorming session on Friday, things don't look so clear any more. We do though have two ideas which seem highly feasible, plus a number of other fainter prospects. One problem to be overcome is that to make at least one of these projects viable, we would need to set up a strategic collaboration with someone who has expertise we lack. The reality is that to attract any funding, we also need to work collaboratively to overcome our lack of track record in the specific area we are trying to apply our existing expertise to.

Musing about this on Saturday, my thoughts turned to open science. I haven't discussed the prospect of running any projects in an open way with any colleagues or funders, and I suspect there would be major difficulties, but there's no harm in thinking about it at this stage.

My first port of call was OpenWetWare (information), but I couldn't see much there that we would be usefully able to contribute to in the foreseeable future. That set me thinking about open notebook science, but the list of "active" practitioners on the Wikipedia page is discouraging - not exactly a vibrant field. Of course, there may be many projects not listed there, but it's not exactly encouraging or likely to convince my colleagues. I wonder if the slightly disorganized field of biological experiments fits into the exemplary model of Jean-Claude Bradley's UsefulChem wiki? I'm hoping that someone leaves me a comment saying that there's lots of relevant open science projects I've missed. I wonder. Open science is an iterated prisoner's dilemma, which is a messy and unpredictable business. Too unpredictable for most people to try to build a career on. Thinking about strategies which are likely to be successful leads me towards the concept of an open science community rather than unilateral complete openness - a long term multiplayer collaboration. Does such a community already exist? If not, how do we build one?

Friendfeed discussion:

Friday, March 05, 2010

Peer Review - A Love Poem by Google

Peer Review - A Love Poem

Every here is the process of subjecting your
work and your ideas to your peers in other
words people
with the same level of qualifications that
you have
they've already done something to review about
essentially what's happening when you're doing
group work
but they refused recorded by almost everyone
I was in the central part all the scientific
process and certainly
if you're going to have a scientific career
you will be subjected to peer review annual
city taking part in peer review of other people's
work on a regular basis
throughout the course of the next week
what we'd like you to do
these two engaged in some the reviews
all of the work that's going on here on friend the
and what i'd like you to do to take to or
three all the people that you follow on friend feet
and to subject
their call for the haitians to
the review in other words
we want you to look at their coleman's
on their status updates and the like
and that pattern of activity over the past
few weeks old friend the
I want to right for them
your impressions old how they're getting
a loan compare it with
hello everyone else is going on for a fee
the reason we want you to do things
it's because by engaging in this process
you will inform yourself of have you were kidding
because peer review process or of mutual benefit
don't you think
we don't want is to just degenerate into
a from of on what people thought the bus
because that doesn't really have any value
that just wasting your time you could be spending
doing something useful
but on the other hand of this movie sins of
the room or the abrupt
so as with professional career years
a little bit of time and diplomacy
the school for which the oldest when you take
part in this process or it really doesn't
have any value
so take some of your
about the fortunate that face our friends
he doesn't call them friends that a printed
refers to the people you follow as the subscriptions
take some of your subscriptions
and I didn't hear review over the next week.

Caption Competition

You may have read that Google has turned on automatic "English language" captions on YouTube. Hmm. Watch the video above and read the captions below. "A video owner can download the auto-captions, clean them up, and upload a corrected transcript." Not that automatic then. How do you turn this option off (or, since we're talking Google here, can you)?

every here is the process of subjecting your
work and your ideas to your peers in other
words people
with the same level of qualifications that
you have
they've already done something to review about
essentially what's happening when you're doing
group work
but they refused recorded by almost everyone
I was in the central part all the scientific
and certainly
%uh if you're going to have a scientific career
%uh you will be subjected to peer review annual
city taking part in peer review of other people's
on a regular basis
throughout the course of the next week
what we'd like you to do
these two engaged in some the reviews
all of the work that's going on here on friend
and what i'd like you to do to take to or
all the people that you follow on friend feet
and to subject
their call for the haitians to
the review
in other words
%uh we want you to look at their coleman's
on their status updates and the like
and that pattern of activity over the past
few weeks old friend the
I want to right for them
%uh your impressions old how they're getting
a loan compare it with
hello everyone else is going on for a fee
the reason we want you to do things
it's because by engaging in this process
you will inform yourself of have you were
because peer review process or of mutual benefit
don't you think
%uh we don't want is to just degenerate into
a from of on what people thought the bus
because that doesn't really have any value
that just wasting your time you could be spending
doing something useful
but on the other hand of this movie sins of
the room
%uh or the abrupt
so as with professional career years
%uh a little bit of time and diplomacy
the school for which the oldest when you take
part in this process or it really doesn't
have any value
so take some of your
%uh about the fortunate that face our friends
he doesn't call them friends that a printed
refers to the people you follow as the subscriptions
take some of your subscriptions
and I didn't hear review over the next week

Thursday, March 04, 2010

Interesting times

I had an interesting meeting recently with representatives from the Annals of Botany regarding social tools and publication channels. The plan is that we will collaborate to try to achieve some commercialization knowledge transfer involving aspects of the education research I have been doing for the past few years.

AoB Plants

What I didn't know before the meeting is that AoB has recently spun out an online, open-access plant science journal, AoB Plants:
  • No open access fees to authors for an initial period
  • Double-blind refereeing
  • Published minimum acceptance criteria
  • Fast publication of accepted papers
and all that good stuff we like about open access. Although I was already interested in AoB, reading about the new journal has made me even more enthusiastic about working with Annals of Botany as a partner.

Wednesday, March 03, 2010

Highwater Mark

Engineering To my shame, before today I had never set foot inside James Stirling's iconic 1959 Engineering Building here at the University of Leicester. I'm not proud of that.

It's even better on the inside than on the outside, reflecting the confidence and optimism of higher education in the 1960s.

50 years later, it feels like this was the highwater mark for UK higher education, from which we have been in constant retreat ever since.

The Digital Researcher #DR10

British Library You know how it is. The meeting goes quiet, then you unexpectedly hear yourself volunteering to give not one, but three presentations at the Digital Researcher event at the British Library on March 15th.

The next thing you know, it's a couple of weeks before the event and you're trying to work out what you should say to a group of postgraduate researchers dipping their toes into the digital world, possibly for the first time.

I feel fairly confident about my first session, introducing the audience to microblogging, talking about networks and doing the housekeeping, such as the #DR10 hashtag we hope is going to hold the day together.

I'm a little more scared about my second session on social bookmarking, not because I don't have enough to say on the topic, but because I was the idiot that suggested we should run these info sessions in PechaKucha format, and I don't have much experience of presenting in this demanding way.

OK, I don't have any experience of presenting in this demanding way :-|

The session that worries me most is my last one on intellectual property (meaning, as far as I'm concerned, Open Access, Creative Commons and Open Source). Even though I have 30 minutes for this one, I'm worried that I'm going to leave important stuff out. Which is why, apart from the fact that if I believe in social tools I should crowdsource these sessions anyway, I'm asking for your help. Given 30 minutes, what would you tell postgraduate researchers about intellectual property, and what resources would you point them at?

Tuesday, March 02, 2010

Dear Old Bruce :-)

Plagiarism of online material may be proven using the Internet Archive Wayback Machine (
Med Hypotheses. 2009 Dec;73(6):875
Many writers and researchers are reluctant to publish online for fear that their work will be plagiarized and used without attribution elsewhere. For example, junior or freelance researchers may worry that their ideas will be 'stolen' and published under the name of professional or senior researchers; and that then it could be hard to convince people that in fact the idea had originated elsewhere. However, if this happens, plagiarism may be objectively proven by a service called the Internet Archive Wayback Machine ( permits clarification of the issue of dates and allows the reader to draw their own conclusions about authorship, whether charitable or otherwise. In sum, is a little known, freely available and potentially very useful mechanism for defending intellectual property rights.

PMSL - Bruce discovers the interwebs :-)

Redundancy Notice

Friendfeed has wormed it's way so deeply into my consciousness that I can't have a f2f conversation any more without trying to click the Like link that isn't there.
What do you mean, get out more?
By the same token, I no longer wake up sweating at 3am wondering if I'll have a job next month. Right now it's, What is Facebook going to do to Friendfeed? This results in an irresistible compulsion to investigate alternatives to Friendfeed, hence recent interest in BuddyPress, and huge disappointment that a company with the resources of Google could turn out a piece of crap like Buzz (which is not to say that Buzz won't improve with time).

Fortunately, the fact that lots of other people (such as Cameron, Neil and others) are going through the same thing means that I have no doubts about my sanity. Still, I find myself jumping from site to site asking, Could this be the replacement for Friendfeed? So far, the answer is no. The closest I've come so far is probably Cliqset, although at present it falls short of Friendfeed.

That isn't crucial at this time, what matters is multiple tool redundancy, so that if one goes down or becomes unusable, another takes it's place. What is far more problematic is the fragmentation of the community which has built up around Friendfeed. Since we're all unlikely to agree on the same tool to migrate to, that's where decentralized semantic microblogging comes in, although that's even further away than a replacement for twitter at present. The future holds more and more of this redundant approach to online technologies, as any parent of a PS3-deprived teenager will currently tell you. With Friendfeed, I can switch to another service, with a PS3, I'm stuck. iPad? No thanks.

In the meantime, another day, another tool...

Monday, March 01, 2010

Derek Bok

Derek Bok In 2000 I was asked to give a plenary talk on microbiology education to the Australian Society for Microbiology about this new-fangled internet thing. I did, and as a concluding slide while I wittered to a gradual halt, I put up what has since become the strapline of this blog (ha, that'll sort the RSS subscribers out :-)

At the time, it was an original, though possibly not very, statement, but several years later someone said to me that that it was a quotation. In spite of searching, I couldn't find the source, but Steve Wheeler's post this morning finally led me to it's origin - Derek Bok.

Except that it didn't. I've never heard of Derek Bok before, and his famous quote is similar but not identical to my strapline. Now since Derek has date priority on me, I might have some difficultly in trademarking my strapline. Which is fine, because I don't want to. It's just a case of great minds thinking alike.