Monthly Archives: June 2007

And the nominations for “Worst acronym for a biomedical standards groups” are:

I’ve been told recently that I am doing a lot of ranting in this blog.  My argument is that if I do it here, I don’t subject you to it verbally ;)

There’s a plethora of rubbish acronyms going around in the biomedical world.  I work on a couple of projects with tenuous acronyms (CISBAN – the Centre for Integrated Systems Biology of Aging and Nutrition and CARMEN – Code, Analysis, Repository and Modelling for e-Neuroscience), but I think this one really takes the biscuit:

“EMERALD (Empowering the Microarray-Based European Research Area to take a Lead in Development and Exploitation) is a project to establish and disseminate quality metrics (QC), microarray standards and best aboratory practices (QA) throughout the European microarray community. ”

You can just tell someone thought really hard about how to shoehorn EMBREALDE into EMERALD, and I can pretty much guarantee they weren’t entirely happy with the result.  They should have aimed for EMBROILED instead I think.

A disturbing open letter on the future of Physics

At least at GCSE

I remember my final GCSE physics exam.  It was the easiest exam I ever sat.  Our (we thought at the time slightly sadistic) teacher had trained us for 2 years on O-level papers (we were the second year to have GCSE’s inflicted upon us).  Needless to say we were more than adequately prepared for the GCSE.  I still remember smiling broadly when I opened the exam paper and saw all the relevant equations written down on the inside of the paper.  I think it took about 20 minutes.  I’m convinced to this day I got 100% (back in those days you didn’t get your marks back, just a grade).  It seems these days even the equations are optional, and from that open letter, the questions are bugger all to do with physics.  Shocking read.

You keep using those words. I do not think they mean what you think they mean…

A classic excerpt of complete nonsense from a work bulletin:

“A group from IRES, the Energy Systems Analysis Group, are working with Newcastle City Council and Eldon Square shopping centre to help the centre identify potential areas of reduction in their usage of electricity, gas and water.

The shopping complex, in Newcastle city centre, has identified that the amount of electricity it uses annually could light up the North East, London, the South and the Midlands combined.”

Of course, this kind of stuff coming out wouldn’t be so bad, if it wasn’t coming out of a Institute squarely focused on science.

Bank Charges IV

So I decided today after umming and ahhing about filing a small claims action against NatWest last night (the 14 day deadline for their response to my last letter expired a while ago) to phone them up and see what the situation was.

Interestingly they now have a charges dispute number set up (08000154212 – Dial 1 for complaints and then 1 again for bank charges). I called them at 9.01am this morning, got through to a human about 9.06 am (not bad!). They acknowledged my complaint and after taking my details said that they were prepared to offer me £1520 of my £1666 claim (ie they dispute my interest calculations, but not the unlawful charges) and that I would receive a letter to this effect by 13th July.

I could still drag them into the small claims court, which would probably end up costing them £1900 so I’m not surprised to have them try and settle this early. I think I will wait till the 13th July and see this paper letter before deciding whether to file against them, but it’s very good to know that there is the prospect of regaining at least £1500 of my money back in the near future.

Mmm motorsport

Whilst I do like the occasional footy or cricket game, snooker match or other non-participatory sport on the box I guess my heart really lies with things that involve engines. Particularly engines that makes things go *really fast*. If there was a better day for motorsport in general than today I’d really like to know when it was.

First of all we had the Spanish leg of the MotoGP. Now I never really liked bike racing as a rule, and even Superbikes never really captured my imagination, I’ve always been more of a F1/touring cars/rally kind of guy. In the last 18 months or so I’ve developed a real love of bike racing though, and that’s probably due to the realisation that in MotoGP at the moment there is a real star of the scene at work. Valentino Rossi is the Michael Schumacher of the MotoGP world, except with bucketfuls of charisma and a tendency to play fair (I never did like Schumacher). Watching Rossi hurl a bike through a race is quite fascinating to watch as you can never discount a race win from him no matter what position he starts in. Like Shumacher his strength is in the corners, coming in hotter than anyone else can seemingly manage and getting on the throttle sooner. Today, hot on the back of a win in Italy, he had pole position. The fact that he came in second to Casey Stoner (his real challenger this series) is almost irrelevant as the last 8 laps fighting between the leading 3 (Stoner, Rossi and Pedrosa) was simply the most exciting thing I have seen in years. The fact they can drive these bikes at F1 speeds with barely a hairsbreadth between them is just fascinating and come the end of the final lap my heart was pounding at a rate only previously seen during exercise.

Great, I thought to myself, I haven’t got that worked up about F1 in years, probably not since Damon Hill won his world championship. Could I even be bothered to watch the Canadian Grand Prix? I’d already fallen asleep during the qualifying repeat.

To be honest my interest in F1 waxes and wanes. Shumachers domination started to bore me, I didn’t like a lot of the rules changes in the last few years, and it just didn’t feel like a competition at times. However I think had I missed today’s race (again, possibly one of the best races I’ve seen) I would have been gutted. Lewis Hamilton – the great new hope of British motorsport, led from pole in a gripping race that suddenly made me think that a World Championship in his rookie season is not out of the question. Alonso was full of mistakes, seemingly far more interested in the grass than the track at times, and as the race shook out in a series of crashes and mishaps Hamilton remained possibly the most composed man on the track. Normally with the safety car deployed multiple times in a race it kills much of the excitement, but we had cars black flagged for jumping pit lights, drive through penalties for dubious use of the pits under safety car conditions and one of the most horrific accidents I have ever seen in F1 (Kubica briefly becoming an airborne missile rather than car which I’m still amazed he survived). Thinking about it the Canadian Grand Prix is rarely dull, but this was exceptionally good viewing. Clearly however, hearing the British national anthem for the 1st place driver (haven’t heard that since Button got his first win in 2006) was the icing on the cake. I’ve always followed drivers rather than teams in F1, I think Jensen is a great driver stuck with a team whose performance is sadly degrading, but it’s so, so good to have a real prospect of a Brit in with a chance of unseating Alonso…

I can’t say I was surprised to read this

So J C Venter has applied for a patent on a minimal genome

As I was sat at the computer wondering why I dont read Slashdot anymore I came across the story here.  This confirmed that the reason I don’t read Slashdot anymore is because they are now the internet equivalent of the Daily Mail, only with patents, instead of political correctness as grist to their mill.

I don’t even know where to start with their byline.  First of all there is barely a mention of synthetic biology in the patent application, and certainly doesn’t really tie in with our current view of that field.  There’s the merest suggestion that this minimal genome could be, maybe, one day be constructed from ‘synthetic DNA’ – but there is certainly talk of stitching things together from natural sources.  Importantly there’s actually no suggestion that such an organism actually exists in the Venter labs.  It’s a long way away from a synthetic cell (when you can drop synthetic DNA into a nice rich soup of mush and have it auto-assemble an organism around it I might take notice).  And to suggest that the project to describe a minimal genome was a ‘philosophical exercise’ is spurious – it’s entirely a scientific one.

Personally I can’t stand patents on basic genetics, I have far less concerns about patents on software.  The system is broken, it will eventually fall down, and patent applications like this will end up looking foolish.  But knee jerk reactions to it are unhelpful, as they are to any issue.  Give the patent system enough rope and it will hang itself.  That’s not to say that synthetic biology will not throw up some interesting test cases.  When you have designed a de novo system that does something biologically novel, I think you might actually want a patent.  You might have done something.. $DIETY forbid.. non-trivial and non-obvious.

Blog downtime

What you don’t see behind the scenes is the amount of spam signups I have to fight on this blog. Whilst I’m running the latest version of Nucleus (the CMS behind the site), providing I allow people in the configuration to sign up for an account, then I get 100’s of signups a week, no matter what steps I take to prevent them from doing so. Clearly there is a little loophole in Nucleus that allows this, and I don’t like it much, nor after having a look around the modules can I see a solution to this problem.

So I’m going to try to migrate the site to WordPress. Whilst I like Nucleus at the back end (a lot) I think it’s actually lacking some more standard blog features that I’d rather have in the core distro, rather than rely on plugins for. WordPress seems to be a de facto standard amongst my friends (although I did seriously consider using Drupal given how much we rely on it in work), and I guess this will make it my 3rd CMS backend for this site..