Impact factors, Colossus and the Wakefield retraction.
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 Wakefield et al (1998) (doi:10.1016/S0140-6736(97)11096-0) has now been retracted from the public record after the Lancet concluded that the claims made by the researchers were ‘false’ (http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2810%2960175-7/fulltext – apologies for paywall).
Wildlife photographer stripped of award
The winner of the Wildlife Photographer of the Year award has been disqualified after judges ruled that the featured wolf was probably a “model”.
It is tough to imagine how you would go about getting this photo of a wild animal. The story given by the photographer on winning the prize was reasonably convincing, however.
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
via flowingdata.com
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?
A test post
I’ve been writing my blog for about 15 months now. In that time I’ve created a grand total of 33 posts. It’s mostly original content, and I don’t have much time for creating original content. I’ve been trying to think about ways of increasing my posting frequency, and there’s basically 2 things I can do – 1) find more time to generate content, or 2) post stuff that takes less time to generate.
Option 1 is basically an impossibility, given our current understanding of the laws of physics. That leaves option 2.
So I’m going to try cross-posting the content of my Posterous blog to my main site. I generate more posts at Posterous, mainly because it is recycled content, and the barrier to creating posts is so low, I just send an email, or use the bookmarklet that grabs content right from webpages.
Step 1 – stop auto-posting Posterous content to Friendfeed. I’ll let my blog propagate there, and not double-post.
Step 2 – enable XMLRPC posting on my Wordpress site.
Step 3 – Turn on Wordpress cross-posting on Posterous.
Step 4 – Write this post, and see if it propagates properly.
Feeling a bit stupid…
I really should have read this and this before trying to upgrade my Slicehost slice to Ubuntu Karmic last night.
Wondered why the darned thing wouldn’t mount the filesystem properly. After half an hour stressing with a read-only filesystem, I finally decided to check out what Slicehost themselves have to say about upgrading Ubuntu. The real problem discovered, the fix took all of 30 seconds. It was because of incompatible kernels. Luckily I could upgrade the kernel of the slice post hoc, and reboot, and everything works again.
Now, time to go and turn on those backups…
Defining absolute protein abundance
At the heart of Systems Biology is a vast hunger for measurements. mRNA abundance, metabolite concentration, reactions rates, degradation rates, protein abundance. This last measurement has long been problematic for researchers, mass spectrometers get increasingly accurate and powerful, but are still hindered by the simple fact that observed signal intensity does not necessarily correlate directly with the abundance of that peptide in the sample. Factors such as peptide ionisation efficiencies, dominant neighbour effects, and missing observations all give rise to erroneous estimates of peptide quantities. Until recently, the best way to get close to measures of protein abundance was to use a peptide tagging methodology, but these are typically expensive, and provide only relative quantification (useful for expression proteomics studies, less useful if you need to know the absolute levels of a protein for a Systems Biology study).
Recently, a three step method has been proposed for determining the absolute quantities of proteins in the cell, on a proteome scale. Step one is isoelectric focussing of tryptic digests of whole cell extracts. Step two, calculating the absolute abundance of a small group of proteins by Selective Reaction Monitoring (SRM). SRM uses spike in, isotopically labelled peptides of known concentration as references to calculate the actual abundance of peptides of interest. Finally, step three uses these abundances as reference points to calculate the abundance of all proteins in the sample, using the median intensities from the 3 most intense peptides for each protein.
Leptospira interrogans (Wikimedia Commons)
Using this methodology, the abundances of >50% of the proteome of a human parasite (Leptospira interrogans) have been determined to an accuracy of ~2-fold. These abundance measurements were confirmed by almost literally counting the number of flagellar proteins present in a cell by cryo-electron tomography.
Although current hardware probably limits this technique to a few thousand proteins, that is still a big step forward on what was previously possible. If whole proteome scale absolute abundance measurements become an achievable reality, maybe proteomics can finally take on microarrays as the dominant technique in the post genomics world.
Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E., & Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans Nature, 460 (7256), 762-765 DOI: 10.1038/nature08184
Testing feed-buster
I have been looking for a way to get the images in my blog posts included in my FriendFeed, because I think it makes it more interesting and eye-catching. Recently I found a tool called Feed-Buster, which exists purely to make RSS imports into FF more interesting. By replacing the URL of your feed with a feed-buster URL (http://feed-buster.appspot.com/mediaInjection?inputFeedUrl=FEED_URL), the images in your feed should be injected into the FriendFeed post. This post exists purely as a test of feed-buster, so I’d better include an image:
Sunderland Air Show
If feed-buster works as advertised, then that picture should be included in my FF stream. (Hey presto – though I had to use the Atom version of my feed to get it to work, RSS2 never updated in Feed-Buster).
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