Category Archives: Blog

Journals, Publications, Science

Molecular epidemiology and phylogeny reveals complex spatial dynamics of endemic canine parvovirus.

Leave a comment

J Virol. 2011 May 18. [Epub ahead of print]

Clegg SR, Coyne KP, Parker J, Dawson S, Godsall SA, Pinchbeck G, Cripps PJ, Gaskell RM, Radford AD.

Canine parvovirus 2 (CPV-2) is a severe enteric pathogen of dogs, causing high mortality in unvaccinated dogs. After emerging, CPV-2 spread rapidly worldwide. However, there is now some evidence to suggest that international transmission appears to be more restricted. In order to investigate the transmission and evolution of CPV-2 both nationally and in relation to the global situation, we have used a long range PCR to amplify and sequence the full VP2 gene of 150 canine parvoviruses obtained from a large cross-sectional sample of dogs presenting with severe diarrhoea to veterinarians in the UK, over a two year period. Amongst these 150 strains, 50 different DNA sequence types were identified, and apart from one case, all appeared unique to the UK. Phylogenetic analysis provided clear evidence for spatial clustering at the international level, and for the first time also at the national level, with the geographical range of some sequence types appearing to be highly restricted within the UK. Evolution of the VP2 gene in this dataset was associated with a lack of positive selection. In addition, the majority of predicted amino acid sequences were identical to those found elsewhere in the world, suggesting CPV VP2 has evolved a highly fit conformation. Based on typing systems using key amino acid mutations, 43% of viruses were CPV 2a, 57% CPV 2b, with no type 2 or 2c found. However phylogenetic analysis suggested complex antigenic evolution of this virus, with both type 2a and 2b viruses appearing polyphyletic. As such, typing based on specific amino acid mutations may not reflect the true epidemiology of this virus. The geographical restriction we observed both within the UK, and between the UK and other countries, together with the lack of CPV-2c in this population, strongly suggest the spread of CPV within its population may be heterogeneously subject to limiting factors. This cross-sectional study of national and global CPV phylogeographic segregation reveals a substantially more complex epidemic structure than previously described.

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Activism, Coding

George Monbiot: Robot Wars II

2 Comments

George Monbiot recently raised the issue of automated online astroturf campaigns, in this article for the Guardian, repeated on Monbiot.com. For those that don’t know, this involves a special interest group recruiting a team to create and maintain multiple digital personas (Facebook accounts, etc). This army of virtual ghost warriors can then be used to create the impression of mass support (a.k.a. ‘grassroots’ support – geddit?) for a given cause or campaign.

Now, while this might be used for what you or I might term ‘good’ causes, the truth is that as always, those with more money and other resources (usually, the baddies) are more likely to exploit it. If ‘one person: one vote’ is the apex of democracy, then the possibility that faceless corporations or governments (or even NGOs) can use the methods of geniune campaigners to further their aims is distinctly chilling. Especially so when you consider the spread of slacktivism – the tendency for individuals’ political/social engagement to stretch no further than the online petition or the Facebook ‘like’ button..

But… a thought occurred, and I wrote to St. George. Here’s what I said:

Dear George,

read your article on astroturf campaigns with interest – had noticed it going on subliminally, but your article suggests it’s more widespread than I could possibly have imagined. A big problem, especially in the age of slacktivism…

How to deal with it? I had a quick idea, possibly seeded by Blade Runner (which I saw last night):

An online standard, or score, authenticating online personas as real people. Volunteers could specifically query individuals in what would amount to a Turing test; and/or some interaction algorithm could assess a persona’s authenticity. Of course in the latter case interested malign parties could easily (especially if the algorithm was open-source). Why would people participate? Because a

I wonder a) whether it’s worth doing, and b) if it would catch on.

I personally think that anonymity online is a bit of a curse – fine to protect political dissidents from reprisals, but an open door for abusive cowards. More and more of my generation (b:1981) place more faith in identifiable online personas, linked to either personal websites or managed through Disqus, etc.

And of course philosophically it’s an incredible moment if we’ve arrived at a point in history where a majority of human communication is online, but we can no longer even tell human from machine, let alone friend from foe!

Anyway from a quick straw poll of programming friends it seems an interesting idea to explore, so I’d love to know what you think.

Cheers,
Joe

Ideas, anyone?

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Blog

Bury me at sea

1 Comment

I hate hot weather, being burnt generally and cremation in particular. So I’ve always wanted to be buried at sea since I heard about it: Bagged up in sailcloth, with some lead shot at my feet and the last stitch through my nose. The North Atlantic, ideally. But how to go about it? There’s a few bits and bobs online (and here), which Tom Cutler summarises:

If you want to bury a person off the English coast without incinerating them first, you should let them know when you register the death and… get hold of an Out of England form (Form 104) from the coroner. You must also apply to DEFRA for a free licence under… the Food and Environment Protection Act 1985. Include a doctor’s certificate with your application, confirming the body has no fever or infection (embalmed bodies may not be buried at sea.)

… burials are restricted to:

  • The Needles Spoil Ground, west of the Isle of Wight;
  • Somewhere off the Northumberland coast;
  • Somewhere near Newhaven.

You can arrange the burial through a funeral director, or you can do it all yourself. It’s common sense mainly: weight the coffin properly – not forgetting to drill a few holes – make sure the top won’t come off and get hold of a willing boatman… You also need to weight the corpse with chains and secure a metal tag around it in case the worst happens and the body has to be returned to you.

Cutler, T. (2006) 211 Things a Bright Boy Can Do. HarperCollins, London.

Clarity. Although for the full trad burial treatment, I’d have to be lobbed overboard in my hammock. Only I don’t own a hammock.

Been getting into the swing of planning the whole thing, in fact. The Anglican prayer book has a special bit for burials at sea, which I reckon would sound pretty awesome at the time:

UNTO Almighty God we commend the soul of our brother departed, and we commit his body to the deep; in sure and certain hope of the Resurrection unto eternal life, through our Lord Jesus Christ; at whose coming in glorious majesty to judge the world, the sea shall give up her dead; and the corruptible bodies of those who sleep in him shall be changed, and made like unto his glorious body; according to the mighty working whereby he is able to subdue all things unto himself.

(1928 Book of Common Prayer)

… All of which has got me thinking about music. One way or another there’s going to be a massive party, too!


Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Music

Recording.. aftermath

1 Comment
A pile of music gear
54kg WizzAir luggage really worked against us at 3AM. Thanks, TfL

So…

  • 1 producer,
  • 2 engineers,
  • 3 countries,
  • 4 animals/toddlers,
  • 5 musicians plus a Katy and a Rysia,
  • 12 days,
  • 15 tracks,
  • 32 transfers and
  • countless bottles of Shumenska (cheap Bulgarian Beer)

later, we’ve finally finished tracking what will end up as my debut LP. It will be an incredible record with some unbelievably good songs played by amazing musicians sounding great and some gifted production…

If it seems strange reading that, well, it’s weirder typing those words, believe me. But that really is what’s happened, somehow. We’ve come so far in a few months from the midnight scribbles, to the 3am jams and demos, to the rehearsals, the fire and the fury in the studio. Listening back to the very, very rough tracks I can’t come to any other conclusion: this record is REALLY good.

I think I’m only able to write that without cringing because so many other people other than me have taken this project on now. Tom and Rysia have built an amazing complex out there at Furnace Studios, and he and Ben Startup of Valley got some wicked lush sounds. While with every passing day we’ve got more and more excited about the production James Ewers is injecting into the record.

4AM face
4AM face

There were some blood and guts on the studio floor but James got some incredible performances out of Dave Wade Brown and Dave Miatt (TT), I think it sounds to me like the guitar of Dave’s life. On the last day he sat there nailing take after take for 30 hours straight, while Dave WB’s perfectionism/power/passion on the skins actually scared me. Jimmy Hatherley and Mike Anderson also did really well to get their heads round the material so quickly. Even Startup got on the credits!

I think you’ll be surprised in the extreme by the tracklisting, so we’ll keep that under wraps for now, but we should be releasing an EP of the Falmouth stuff ASAP, then tracks from these sessions (including the odd Hicks remix) later in the Summer. Not sure when the whole LP’s gonna be done. There’s some bits and bobs left to do (string, brass, harp, BVs) before the main vocals but we’re basically there. Shock.

More to come including a (late) diary (sorry, slow internet + busy actually doing the job when we were out there). Bye for now x x

PS: We’ve got some dates coming up, might turn them into a minitour if we can bolt on London and Bristol either side:

  • April 29th Secret gig, Laines, Brighton (email for deets)
  • April 30th Sotones Spring Social, Hobbit, Southampton

PPS: Thanks to Katy very, very, very much for helping us not degenerate (totally) into moon-howling freaks.

More PS: Woke up this morning to find the garden had burst into technicolor while we were away:

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Blog, Music

Hjaltalín – rare UK appearance

Leave a comment


Big treat for everyone in London tomorrow, as Icelandic septet Hjaltalín come to visit us for a rare gig, the culmination of a national tour (so they should be super-tight). Last year’s Terminal was full of unexpected arrangements and quirksome hooks (think Neil Hannon producing a Björk LP with a brass section in tow) and one of my favourites.

Have a quick listen now, on Spotify. Words like lush, cinematic and winsome all apply, but I think there’s enough Skandinavian willfulness there to keep it interesting, too. See ‘Hooked on Chilli’ or ‘Feels Like Sugar’. Great, isn’t it? So I’ll be seeing you at the Slaughtered Lamb in Shoreditch (MAP – tube Farringdon or Old St – one of my favourite venues for this kind of complex-arrangement music) tomorrow, 7pm on Tuesday 8th March. Oh, it’s a God Don’t Like It-curated show too, so the support act are going to be ace.

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Blog, Coding, Music, Science

Barcelona, LP preparations and some (lap)topless coding…

1 Comment

LP prepppppp

The nearer we get to recording the LP (2 weeks to go, and counting..) at Furnace, the more I seem to listen to PJ Harvey, Pulp, Pavement and (cat) Power. Obsession with all things ‘P’? Will we have a plethora of parping polyphones all over the place? I THINKK SO>

Barcelona

Well. A very kind person took me on a weekend trip to Barcelona to see the sights. The sights in question being the excellent capital of Catalunya herself, but mainly mates Nathan, Bobby (The Beaux Hardts) and Paola. Not been there since 2000, and since I was drunk then and drunk now I can’t really claim any deep Theroux style observations on the ephemeral nature of change in the world’s great cities, or the permanence of poverty, or anything like that, beyond the usual ones everyone makes about Barca.

These are:

  • The girls in Barcelona are all REALLY HOT
  • Why is Park Güell so far from the centre of town?
  • Supporting Barca (a winning team) is (whisper it) lots more fun than supporting one that is slightly less than triumphant like Saints [but see 1].
  • Yes, the girls in Barcelona really are all REALLY REALLY HOT [2].

Oh, and their Boris bike system (or ‘hire bike’, as they quaintly put it) works with a lot less fuss than ours. Anyway, here’s some quick crappy sketches:

Sun. Drenched. Rooftop. Morning. Coffee. MMMMMMM
... because every dickhead has to have a go at drawing it...
MEGA quick sketch from the top of Park Güell. FYizzle...

Laptopless coding

Years and years of touring experience, science fieldwork and sofa sofing mean I am a seasoned and unflappable traveller. ‘Seasoned’ like a piece of rotten wood is…

So having nearly missed my flight out, I also managed to leave my laptop charger in London. Instead of doing something sensible like getting pissed in the sun I decided to wireframe all the code for the next HADPACK iteration on pen-and-paper. WHOOOOAH!

Yes, it is oldschool, but it really is true what the textbooks say: working on paper first really helps you to think clearly about your code, especially if you’re working with complex class inheritance structures (oh, yes…)

Coding HADPACK (HIV Antigen Determining PACKage) from the ground up
More HADPACK work - thinking about how the UI interrelates to the experimental design process

OK, so there’s a bit of work left to do still. Back to the laptop…

Footnotes

1 – Although Bob informed me that Bilbao (one of the earliest Spanish teams ever founded) first played in red-and-white striped shirts that they got from which South Coast port’s city team? That would be  Southampton St. Mary’s, known nowadays as Saints. And Athletico Madrid followed suit. So Saints can at least claim the credit for kitting out the first ever Spainish football teams.

2 – No, I’m not being silly. Bob & Paola’s is just a tennis ball’s boff from the Ramblas, where Orwell (nearly) had a shootout with the Facists in la Guerra Civil. My guess is it wasn’t a lack of munitions that stopped them firing (as claimed) but the beauties of Barcelona. Make love, not war…

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This

Activism, Cycling

Bike Kill .. literally

2 Comments

Check this out, a motorist loses their rag with a Critical Mass demo and ploughs through them as if they were snow, not fellow humans (0:45 in):

For those of you that don’t know, Critical Mass is a great protest movement worldwide. They peacefully promote cycling as a sustainable replacement for motor transport in cities, as a way to get fit, and lower carbon emissions.

Most of the major cities of the world celebrate a monthly day where massed bicyclists ride together. They stop traffic along the way, but this is not the aim – in fact as in normal traffic, the massed cyclists tend to move as quickly – or slowly – as cars in congestion do. However by riding together they reinforce each mutual confidence on the road, and remind other road users that bikes are not invisible nonentities, but real people.

I’ve never seen any physical violence on any of the 30+ Masses I’ve been on in London or NYC, and most cars can proceed on their way after a few minutes’ delay: not dissimilar to being stuck in traffic as usual, and the campaigners have made their point. This time, however, the driver loses it. Disgusting, inhuman and inexcusable.*

*Coda: the BBC report that the driver ‘felt intimidated’ by the bikes. If you’ve ever ridden in a major city, you’ll know what a sick joke this is. If you’ve known riders who’ve been killed, as I do, you might be tempted to concluded that the driver in question should be taken off the road and examined by a psychiatrist…

Post to Twitter Tweet this Post to Digg Digg Post to LinkedIn Post to LinkedIn Post to Slashdot Slashdot Post to StumbleUpon Stumble This