Impact factors, Colossus and the Wakefield retraction.

(Graphs from The Independent (London), 21 June 2008)

Today was one of those days where lots of interesting stuff turns up. On the BBC, there was 2 very good pieces about the flaws in the scientific process, specifically closed peer review and impact factors.

I also notice that the BBC are running a daily piece about the history of computing in the UK this week, parts one and two have already been published. Today’s article about Colossus is especially good.

Also, after last week’s excellent, and damning, judgement from the GMC –

– regarding Andrew Wakefield’s reprehensible behaviour in his research into the ‘link’ between MMR and autism, today The Lancet finally pulled the paper in which his findings were published 12 years ago. Wakefield et al (1998) (doi:10.1016/S0140-6736(97)11096-0) has now been retracted from the public record after the Lancet concluded that the claims made by the researchers were ‘false’ ( – apologies for paywall).

Summary of the BBSRC Systems Biology Grant Holders’ Workshop 2010

You could be forgiven for thinking that this meeting was doomed from the outset, heavy snow across the UK making travel very difficult, even for those already in Edinburgh. Those of us in Newcastle just about managed to arrive on time, but there were plenty that didn’t. Despite this, a high proportion of posters still made it, and all but one talk was delivered, though admittedly not by the intended speaker in all cases. Indeed, the first day was like an extended and cruel session of Powerpoint karaoke at one point, with people delivering talks having never seen the slides.

What emerged was a healthy picture of a vibrant systems biology community in the UK, although one tinged by an uncertainty lurking in the not too distant future. Talks from the Centres for Integrated Systems Biology (CISB) directors on the first afternoon gave a flavour of the kind of research being done, and more detailed talks over the following day and a half filled in the picture.

Talks of note (to me at least)
I really enjoyed the keynote, from Peter Smith, of the University of Aberdeen. He is certainly doing systems biology, but not in the way most people first think of it. The ‘system’ he is concerned with is not a cell, an organ, or even a whole organism – it’s a whole ecosystem, or sometimes maybe even larger than that. Systems biology on a continental scale. He painted a very interesting picture of how taking biological factors into account in warming models can make a real difference to predictions. There was also an interesting story of using ecological models to predict bioenergy crop yield, and how this can feed into efforts to introduce certain traits into plants, in order to increase their yields in desirable parts of the globe.

The MCISB talk was great, a really good example of how modelling and ‘omics technologies can dovetail really nicely in a properly integrated project. They’re studying metabolism in yeast, looking at metabolite flux and the reactions that best control it. Flux Balance Analysis, metabolomics, proteomics and ‘traditional’ bioinformatics all combine nicely to illuminate different parts of the process, with data being deposited in many public repositories along the way.

The talk from the PRESTA project was also very impressive. Using lots of microarrays in interesting ways to investigate the stress response of Arabadopsis . Examining at more than just the changing expression of genes in isolation, but looking for patterns of genes that change together in interesting ways, in opposition, or a subset that react to the change in another subset, etc.

The BBSRC systems biology initiative is coming to an end. It was intended to kickstart large-scale systems biology research in the UK through a number of large grant awards, including the CISBs and the Systems Approach to Biological Research (SABR) projects. It was clear from some of the discussions at the workshop that some people are concerned that the winding up of these big grants, coupled with the looming shadow of considerable cuts, means that there is little future for the posse of systems biologists who have been produced over the last few years. ‘Too generalist’ was the major complaint, suggesting that systems biologists are jacks of all trades but masters of none. I would disagree. Systems biologists are masters of systems biology (I know this sounds rather obvious, but bear with me). Traditional biologists tend to be scared by maths, and modelling, and don’t really know where it fits in with what they do. Mathematicians and computing scientists tend to not know anything about biology. There is a large cohort here that knows a great deal of both. Mathematicians who are biology literate, and biologists who aren’t afraid of mathematics and computers. These are skill sets to be prized, not shunned. Systems biology is a discipline in its own right now, and I would be shocked to discover that these researchers do not have a life beyond their Centres.

P.S. I took a poster along, as a part of my role on the Ondex project, it’s on SlideShare, and I’ve embedded it here.

5 Best Data Visualization Projects of the Year – 2009 | FlowingData

The top visualization project of the year, according to FlowingData, is a project by Ben Fry, which shows changes to the theory of evolution over time. The project takes advantage of the publication of the full works of Darwin online to trace changes in the text of On the Origin of Species over time.
A deserved winner, and very apt, considering the batch of anniversaries that have gone by this year.

Google Acquires AppJet – are there any live, functional alternatives to Etherpad?

We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team.


The EtherPad site will stay online through March 2010 with some restrictions.


No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted.


Etherpad was a nice little tool, very effective at what it offered, I’m sure the guys who developed it will bring a lot to the Wave party. But seriously, Wave is nowhere near functional yet, it’s confusing, and glacially slow. So is there a decent alternative to Etherpad that is usable – right now?