Monday, August 31, 2009 - interesting tool

PMSL @timeshighered

MicrobiologyBytes For more than three years (since April 2006) I've been experimenting with weekly podcasts covering all aspects of microbiology. I decided to have a break over the last month, and during that time I have been thinking about the future.

On balance, I don't feel that the audio format of these podcasts adds much value to the content beyond what could be achieved with text and images in the style of standard posts on MicrobiologyBytes. In some circumstances though, a video can add significant value, so I have decided not to post any more audio podcasts for the foreseeable future and to invest the time in producing occasional videos which you will be able to view on this site. All of the old podcast files will remain available on

Having taken this decision, the next thing I read in THE was Academics must wise up to Web 2.0 marketing – and the answer is high-quality podcasts. Laughable. YouTube? Yes. Twitter? Yes. Facebook? Yes.

Another example of "experts" telling academics how to do their jobs. Wake me up when you've actually got some experience of the technology you're talking about.

Sunday, August 30, 2009


Just worked out how to add captions (e.g. URLs) to screen captures via YouTube annotations:

Thursday, August 27, 2009

Document Repositries


Is risk-averse fear of failure the biggest problem facing science?

Fear of failure I was more than a little surprised (but gratified) at the response to yesterday's post Why are scientists so dull? When I wrote it, I didn't consider it any more than reportage of a paper I'd stumbled across on PubMed, but the tweetage throughout the day made me think more about the subject.

On Saturday, I spent most of the day sitting in the Faraday Lecture Theatre of the Royal Institution at Solo09. Even then I was thinking about how much scientific careers had changed since the Royal Institution came into existence, but yesterday's comments made me think about this again.

When I was trained as a post-doc, my big boss told me always to have one banker project and (at least) one punt into left field. From where I sit right now, I can't see much blue skies thinking going on. Why not? Well the chances of getting "speculative research" funded are so slim that it's not worth investing the time in grant applications you haven't already got all the "supporting data" for. Hypothesis-driven research? Don't make me laugh. How is it hypothesis-driven if the penalty for "failure" is so high?

YMMV. Let's hope it does, or we're really in the sh*t.

Wednesday, August 26, 2009

To RSS or not to RSS, that is the question

RSS I was pondering RSS in the small hours of the night (ya gotta do something if you're a chronic insomniac), so the latest chapter in the Is RSS Dead saga struck a chord with me:
ZDNet's Sam Diaz called RSS a "Web 1.0 tool" and voiced the opinion that "there are better ways now".

Twitter and Facebook are great for content discovery; RSS is one of a number of tools that can be used for content aggregation. Comparing them is like comparing apples to oranges.

The real question is who is RSS hurting? Nobody.
Well that rather depends on whether you're relying on RSS as a major strategy for delivery. While RSS uptake is still rising among the people who read what I write online, it is rising slowly and will never be the dominant means of delivering my outputs. Personally, I'm a big RSS fan, but most of the people I talk to admit that they rarely or never read their subscriptions.

So what is the answer? Fortunately, I've figured that out :-)

Redundancy. Publish on every available channel - paper, blog, RSS, Twitter, Facebook/Friendfeed, YouTube.

This takes some effort, but not as much as generating high quality original content.

So now you know :-)

Why are scientists so dull?

QUESTION: why are so many leading modern scientists so dull and lacking in scientific ambition?

ANSWER: because the science selection process ruthlessly weeds-out interesting and imaginative people. At each level in education, training and career progression there is a tendency to exclude smart and creative people by preferring Conscientious and Agreeable people. The progressive lengthening of scientific training and the reduced independence of career scientists have tended to deter vocational 'revolutionary' scientists in favour of industrious and socially adept individuals better suited to incremental 'normal' science. High general intelligence (IQ) is required for revolutionary science. But educational attainment depends on a combination of intelligence and the personality trait of Conscientiousness; and these attributes do not correlate closely. Therefore elite scientific institutions seeking potential revolutionary scientists need to use IQ tests as well as examination results to pick-out high IQ 'under-achievers'. As well as high IQ, revolutionary science requires high creativity. Creativity is probably associated with moderately high levels of Eysenck's personality trait of 'Psychoticism'. Psychoticism combines qualities such as selfishness, independence from group norms, impulsivity and sensation-seeking; with a style of cognition that involves fluent, associative and rapid production of many ideas. But modern science selects for high Conscientiousness and high Agreeableness; therefore it enforces low Psychoticism and low creativity. Yet my counter-proposal to select elite revolutionary scientists on the basis of high IQ and moderately high Psychoticism may sound like a recipe for disaster, since resembles a formula for choosing gifted charlatans and confidence tricksters. A further vital ingredient is therefore necessary: devotion to the transcendental value of Truth. Elite revolutionary science should therefore be a place that welcomes brilliant, impulsive, inspired, antisocial oddballs - so long as they are also dedicated truth-seekers.

Tuesday, August 25, 2009

One simple idea

Simples While I was away on vacation, I was reading when a phrase popped into my head, seemingly from nowhere:

One simple idea

Reflecting on this, it occurred to me that part of the reason for the failure of some of the projects I've tried to run over the past year has been complexity - trying to do too many things at once. Perhaps a one simple idea approach (which could later be elaborated on) might be more successful.

At the time, I was pondering what to do this year with my first year key skills module, I.T. & Numeracy Skills for Biologists. The immediate problem is that it's difficult to present this as one simple idea - two would seem to be the minimum requirement. All this was still circulating in my brain last week when I read:

I’ve stuck to the path I’m afraid: exploring student non-use of blended learning. Kate Orton-Johnson. (2009) British Journal of Educational Technology 40 (5): 837–847
This paper draws on qualitative data from a study of student use of blended learning as part of a conventionally taught undergraduate Sociology course. Findings from an early evaluation questionnaire highlighted an overwhelming pattern of non-use of the materials and subsequent research with a group of 16 students evidenced limited and inconsistent engagement with the resources. In an analysis of the category ‘non-use’, the students’ rejection of the materials is seen to be closely related to a trust in traditional texts as authentic academic knowledge and an instrumental and strategic approach to study. Blended learning resources are shown to challenge existing learning patterns and practices, reconfigure existing understandings and expectations of academic scholarship and reconstruct academic boundaries in new spaces.
"This instrumental approach to scholarship is not a new phenomena. Becker, Geer and Hughes (1968) in their study of college students, highlighted the conflict between grades and learning and argued that rather than acting as autonomous intellectuals in the pursuit of knowledge, students are primarily concerned with finding out what is required of them in order to obtain good results... The blended learning environments afforded students the flexibility and freedom to balance their academic and wider responsibilities; however, engaging with the resource in more depth was seen as an additional layer of work and in its non-compulsory and nonassessed form was avoided."

How do we boil down these complex online-offline interactions into one simple idea? Should we? And if we don't, how many students do we lose along the way?

Monday, August 24, 2009

Friendfeed and ALT-C 2009

Dashboard Looking at Matt Lingard's Netvibes dashboard for ALT-C 2009 prompted the question, is there a FriendFeed group for the conference? There should be, although I can't find one at present. Why?

Reason 1: Archiving of otherwise transient information.

Reason 2: Threading of discussions - as at Solo09.

Reason 3: Plays nice with mobile devices.

Reason 4: I've just built one - and here it is.

(and here's the F-Alt group Friendfeed group - OK now Josie? ;-)

Unpacking Solo09

I spent Saturday at the Science Online London (Solo09) conference, and a very interesting day it turned out to be. Much has been written elsewhere about the actual content (also well covered in the Friendfeed group), so I'll restrict myself here to reflecting on my personal reactions to the event.

I'll start by getting the irony out of the way. In the building where Faraday invented electricity (stretching the truth only slightly), why was it so hard to recharge a mobile device? Thankfully, speculation that Solo09 was an plot by Susan Greenfield to lure all the science bloggers to the Royal Institution so that she could arrange an "accident" to befall them was unfounded (surprisingly, she didn't put in an appearance).

I didn't physically attend the meeting last year, but I did participate actively online, and it was noticeable that after a brief flurry of activity on Twitter in the morning, almost all the activity switched to Friendfeed. This year, there was probably more online activity than last, involving both physically present and remote participants, and much more evenly split between Twitter (which had a more casual, chatty feel) and Friendfeed (more of an archive from the physical participants). This was in spite of a request (which was observed as far as I could see) not to comment on the content of the first talk of the day, which consequently also derailed the Second Life stream (which people had paid £10 for). In general, the performance of Second Life through the day confirmed my opinion that SLIsPants, and I felt that remote participants would have been much better served by a video + slides stream, such as an Eluminate-type interface.

Overall though, the meeting was a great success and much kudos is due to the organizers, sponsors and speakers. it is planned to hold a similar event next year, which I would very much like to attend if I am able to, especially if the idea of a science education strand comes to fruition.

Saturday, August 22, 2009

Science Online London (Solo09)

Science Online London Today I'm going to be at Science Online London (programme). I wasn't able to attend in person last year, but I followed the live streams online and gained a lot from it. You can follow @soloconf on Twitter, hashtag #solo09, but judging from last year, most of the action will be in the Solo09 FriendFeed Room:
The Web is rapidly changing the communication, practice and culture of science. Science online London 2009 will explore the latest trends in science online. How is the Web affecting the work of researchers, science communicators, journalists, librarians, educators, students? What can you do to make the best use of the growing number of online tools? This is the follow-up conference to last year's Science Blogging 2008: London conference. The name of the event was changed to reflect the variety of science-related activities happening online today. Topics include blogging and microblogging, online communities, open access and open data, new teaching and research tools, author identifiers and measuring the impact of research.

See you there, or see you online.

Friday, August 21, 2009

In Cloud We Trust

Cloud over Blackboard Ya gotta feel sorry for Blackboard (but not very much). After all the fuss about upgrading to Bb9, apparently, it's not going to happen because a "significant" issue has been discovered. Significant eh? What's the p-value and how many degrees of freedom? ;-)

Moving to Blackboard version 9 at this time would present an unacceptable risk to the University's Virtual Learning Environment (VLE) given the proximity of the new academic year. In addition, Blackboard themselves are unable to give any guarantees as to when a fix for the reported issue could be made available.

Remind me again - how much are we paying them each year? Sigh, when will people learn?

RSS is like advertising

Nothing happened Sigh. The holiday is over, and of course, back to work begins with clearing inboxes. The email inboxes weren't too bad, the spam filters having taken care of much of the dross. As ever, email brought me no good news, only work needing to be done (which can wait until Monday), and a huge amount of messages I didn't really need to receive (easily deleted).

The RSS backlog was more interesting. It would have been easy to declare RSS bankruptcy and delete the backlog, but because the information I get via RSS is much more valuable than what comes through the email channel, I didn't want to do that. If I had done, I would have missed some of the interesting things which happened while I was away, such as the changes to Google Reader, being able to send items directly from Google Reader to CiteULike, and Friendfeed turning into Facebook (possibly).

So I slogged through the subscriptions, deleting half a dozen which had failed to add any value while I was away, by which time it occurred to me that I could probably delete half of the feeds I subscribe to without damaging the quality or diversity of the information I get via RSS. Like advertising, 50% of RSS is ineffective. The snag is, it's impossible to tell which half until after the event.

Friday, August 07, 2009

Playing with Diigo, but not enjoying it

I'm still trying to get my head around Diigo after our chat about Tagginganna yesterday.

Diigo makes any document on the internet a social object by allowing any Diigo account holder with the correct privileges to annotate and comment on the content. For the following demonstrations, you'll need to be logged into Diigo, then, if I've set the permissions right, you should be able to see the examples.
I'm still finding Diigo frustrating and complicated to use - the interface is awful - and I'm not convinced this is the best way to approach the issue.

I much prefer inline comments, so I knocked up a quick demo wiki. This is only a short text, for longer works it would be necessary to balance the tension between continuity of the text and breaking it down so that tagging becomes useful.

To me, the best solution at the moment is looking like CommentPress, an open source theme for the WordPress blogging engine that allows readers to comment paragraph by paragraph in the margins of a text. With CommentPress you can annotate and debate at paragraph level, turning a document into a conversation, as in this example. The comment interface is very familiar and should encourage good participation.
Problem: The Commentpress theme is not available at, so it would mean a self-hosted installation (which would then be able to serve more than one text). Maybe something after the design of StatsBytes would be an acceptable compromise?

Tuesday, August 04, 2009


CiteULike Tricky things, notifications. Overdo it, and you get bacn (not quite spam, not quite ham). But undercook it, and it's impossible to sustain online discussions because people don't know there are messages waiting for them. Consequently, I'm please to report that CiteULike has just (officially) implemented for:username tags, which can be used to alert users with whom you share a connection that something interesting is waiting for them. Users still need to visit the site to be notified, and won't get hassled by email (unless you send them one). In contrast, delicious's new share features veers dangerously close to bacn.
Kudos to thegoose.

In addition, CiteULIke now also has "private" tags, though I haven't quite figured out what you'd use those for yet (cue for Fergus to leave a comment explaining their function):-

Why can't we all get along?

UoL Computer Centre Yesterday I (and a bunch of other people) attended a consultative meeting organized by UoL IT Services to discuss ... well, I don't feel I should publicize what was discussed at this stage, not because it's particularly secret, just out of courtesy. (It's really not a big secret, if you buy me a coffee, I'll tell you about it :-)

Yes, I'm being nice about IT Services. It's true that in the past I have occasionally had somewhat negative feelings about my colleagues in the pointy house, but the truth is I've always respected them as hardworking individuals even when I've disagreed with official policy.

After we finished our discussions about the stuff I'm not going to tell you about, the meeting turned to future plans, spending limits and how to persuade senior management budget holders to do the right thing. Turns out the academic staff present were only too willing to work closely with ITS to get to where we both want to be. Turns out, we're not in competition with each other and have many shared interests. Turns out that we both get more out of working together than we do by being locked in entrenched positions.

It may be that the time-honoured dept reps system has had its day at UoL, and that there's a lot more traction (for both sides) to be had from IT Services working with interested stakeholders rather than people who, in some cases, may be doing something because they've been told to do it by their head of department rather than because they have any particular interest. It could be that there are interesting times ahead. Fingers crossed.

Monday, August 03, 2009

Living in the Post-Internet Age

Shortly after noon today, large sections of the internet went dark across many UK higher education establishments. The outages were patchy and seemed to depend, in part, on location, but most services were unavailable, including institutional services.

My first thought was "How do I survive without the Internet?", followed seconds later by "What still works?". The answer to that one was Google and all the associated properties (including GMail), Twitter (via the API but not via web), Posterous, Wikipedia, and a patchwork quilt of external services.

Within minutes, I was up and running again, although having to use a little ingenuity to route around some of the blank spots. Those who were tied to institutional services ... had a long lunch break (presumably).

So the moral of this story is:

Spread your love around, and if you love your users, set them free.


Anna Karenina Last week I was chatting to @stujohnson and he mentioned that @nosnilwar was interested in developing online discussion formats for various texts. For the purpose of tinkering, we decided to play with the Project Gutenberg version of Anna Karenina.

Stuart had suggested using diigo for the purpose. I had never found a use for diigo before, so I installed the diigo bookmarklet (rather than the toolbar, which can't be installed on Macintoshes or on CFS) and had a play. A nice feature of diigo are the sticky notes other users can see on annotated pages:

diigo note

What I really like about this is that the discussion is inline with the text. However, the amount of text which can be placed in a note is limiting and if many people are commenting on the same text, it would get messy, so it may be necessary to use the diigo groups for extended discussion:

diigo groups

I thought it might be possible to use CiteULike for similar purposes. By manually bookmarking a passage of text it's possible to build up a dataset, although this is relatively laborious since the process is not automated. However, it does provide access to the nice features of CiteULike such as tagging and RSS everywhere. There is no direct way to have inline discussions around the selected passages, although each CiteULike group has its own message board, discussion forum and blog:

CiteULike group

The last thing I tried was a shared Google document. However, at 1.9 Mb, the text is too long (500 MB limit), but by splitting it into the the eight component parts - not ideal - I was able to upload each one. Google Docs allows those with editing permission to add inline comments and footnotes to the text:

Google docs

To try to promote discussion, it would be advisable to notify the people who can edit the document when annotations are added:

Google document
All of these solutions could work, so I guess you pays your money (or not) and takes your choice. What have I missed?