Category Archives: Blog

Befi-BaTS v0.1.1 alpha release

Long-overdue update for beta version of Befi-BaTS.

Software: Befi-BaTS

Author: Joe Parker

Version: 0.1.1 beta (download here)

Release notes: Befi-BaTS v0.1 beta drops support for hard polytomies (tree nodes with > 2 daughters), now throwing a HardPolytomyException to the error stack when these are parsed. This is because of potential bugs when dealing with topology + distance measures (NTI/NRI) of polytomies. These bugs will be fixed in a future release. The current version 0.1.1 improves #NEXUS input file parsing.

Befi-BaTS: Befi-BaTS uses two established statistics (the Association Index, AI (Wang et al., 2001), and Fitch parsimony score, PS) as well as a third statistic (maximum exclusive single-state clade size, MC) introduced by us in the BaTS citation, where the merits of each of these are discussed. Befi-BaTS 0.1.1 includes additional statistics that include branch length as well as tree topology. What sets Befi-BaTS aside from previous methods, however, is that we incorporate uncertainty arising from phylogenetic error into the analysis through a Bayesian framework. While other many other methods obtain a null distribution for significance testing through tip character randomization, they rely on a single tree upon which phylogeny-trait association is measured for any observed or expected set of tip characters.

Numerology!

Yeah, I’m not talking about the famous Lemmings level, unfortunately (anyone know a good Flash implement of that btw?), but the tendency for certain dates to be kickass.

By kickass, I mean:

Kickass (n) (cic-aze). A sequence of date and time digits of spurious yet substantial numerological significance.

A great one happened a few weeks ago, on the 10th October, better known to you and me as:

10/10/2010

Or, if you get really anal and look at the time as well:

10/10/10 10:10:10

I think I’ve always collected these most excellent dates since I noticed 6/7/89 as a kid. Obviously 09:09 on 9/9/89 was a date of seminal excitement to me (not shared by my junior-school teacher, unfortunately), and at the same time on 9/9/99 I went completely wild. 01:01 on 1/1/2001 sadly passed me by as I was busy drunkenly drying my bricklike mobile phone off with a hairdryer, having fallen into a pool soon after midnight.

Being born on the 11th December, I’m particularly looking forward to a quarter-past two on my birthday in 2013, and both 11/11/11 11:11:11 and 2012/3/4 05:06:07 should be special too, as will 3/14/15 09:26 (using US dates) and 2/7/18 02:08. I’ll probably end up missing 22/2/2222 2:22 though…

Why?

Being ever-so-slightly OCD, I am more excited by these numbers than is possibly healthy, but from experience most people have a bit of a soft spot for these dates, the study of which is known as numerology, and is especially popular in China, apparently. Whole organizations have based mass-action days around them.

Without wanting to cod-psychoanalyze too deeply (I’ll save that for the pub) I wonder if the (fairly) modern obsession with significant date combinations has anything to do with our need to mark the passing of time in a relentlessly-changing world. ‘Never mind that you can’t even remember what you had for tea yesterday,’ this argument runs, ‘at least you had that tea on a date of cosmic significance.’

The fact that said dates are measured from the (arbitrarily-defined) birthday of a largely fictionalized individual in Judea 2000+ solar orbits ago is immaterial. Perhaps this need to mark the passing of significant chunks of our life is primal; we’re not so different from our Stonehenge-building, mushroom-eating proto-hippie ancestors after all…

About this new site

As you can see, I’m running a new site now. Some content will be loaded pretty soon (old blogs, lyrics, music, software etc) but the design I want to do is pretty complicated, especially as the client-side stuff, so I want to wireframe it first somewhere else offline. Might get it done in a couple of months, so look out for a bit redesign after Christmas!

This is partly an ego trip, but mainly because I’m pissed off with Facebook / Myspace and all their popularity contests and formulaic box-filling shit, and want to get back to the good old Netscape days of the 1990s, when a personal website really was just that, and you could put whatever you liked up, however you wanted to.

I’ve installed plugins for Twitter and Soundcloud, and will get flickr in there too soon. Also, for commenting, I’ve activated the really-pretty-cool DisQus engine, so that those of you on social networking sites that want to comment, can.

In the meantime I’m going to slowly let the Facebook and Myspace accounts die. Just as a little piece of me dies every time I login to those damn things.

1,313: A Sotones Sampler

STCD037'1,313: A Sotones Sampler' - Artwork by Billy Mather IllustrationReleased 04/11/2010

CD | MP3 | Spotify

Buy now: iTunes | Amazon | All stores

‘1,313: A Sotones Sampler’ is the second Sotones Records compilation, featuring some of the best music from across the south coast, spanning indie rock to dubstep, folk to electronica. Featuring smash singles by Moulettes, Moneytree, Haunted Stereo, Peter Lyons and Fresh Legs, as well as new works by artists including rude_NHS, nato, Ann The Arc and Jeffisalive. Artwork by Billy Mather (billymather.co.uk)

Tracklisting:

  1. Moulettes / Horses For Hearses / Horses For Hearses EP (Licensed from B.alling The Jack)
  2. Fresh Legs / Julian / Julian EP – Deluxe
  3. Moneytree / Medicineland / The Great Indoors Part III
  4. Haunted Stereo / Lock The Doors / On A Pin/Lock The Doors
  5. Anja McCloskey / Newton / Turn – Turn – Turn
  6. Jackie Paper / All The Wine / What’s Wrong With Broken Glass
  7. Peter Lyons / Old Friends / Old Friends
  8. Jeffisalive / Sunlight’s Yellow Dress / Sunlight’s Yellow Dress
  9. rude_NHS / Roy Orbital / Roy Orbital
  10. JayEtAl / Feather / Where No City Lights
  11. nato / Missing Song / Eating Clouds
  12. Ann The Arc / Buttercup (Single) / Buttercup (Single)
  13. The Beaux Hardts / Hey, Who Turned Up The Gravity? / Leisure (B-Sides & Rarities Special Edition).
  14. Lonely Joe Parker / Brooklyn / What’s Wrong With Broken Glass
  15. Bobby Wade & Cristof Certic (4TK De Nada Demo) / Tax For Sure / Double Barreled

Buy Now direct from Sotones.co.uk

Guest Art Curators: Lonely Joe Parker – Bike Art

(Originally posted on The405.com)

October 15, 2010 – Edited by Will Slater

Yes, we said yesterday’s piece was the last of the guest art contributions for this month, but it turns out that Lonely Joe Parker sent us one that got lost! So here is the actual final article from A Badge of Friendship:

I wanted to write about Weimar-era George Grosz, the scabrous illustrator and cartoonist whose utterly irreverent attitude and DIY aesthetic predated punk rock by a good decade or five. Unfortunately some staffer in a Sunday supplement went and dedicated a centerfold to him the other week, so instead I’ll have to ramble uninformedly about bikes instead.

Image and video hosting by TinyPic

I’ve loved bikes since I was small – I don’t know when I got my first one, but a yellowing picture my gran has shows her pushing me and smiling while I try to reach the magical speed of eighty-eight miles per hour on a sky-blue minimountain bike with stabilizers. In wellies. As it’s got a basket and streamers I think it’s probably a girl’s bike, and secondhand, but it had me hooked. Now whenever I see a toddler tottering along, legs flailing, I think of that sunny afternoon in the eighties on a small bike with a big golden flower in the background.

Bikes have a direct, visual appeal – from quaint sit-up-and-beg bikes that suggest their penny farthing ancestors; to purebred 70s racers sinewy like their riders, gleaming like an Arabian stallion in the sun; to sleek, space-age recliners, more like rocketships than pedal-powered commuter bikes. Then there’s the workbikes (gutterpunk couriers on their squat bastardized MTB / fixie hybrids; delivery trikes; and the ambulance riders on their cute mini lifesaver-mobiles with their dinky lights and sirens).

And the art inspired by bikes – notably a slew of Art Deco Tour de France posters and their imitators, but also cinematic depictions – fascinates me, as well as art made *by* bikes, such as city-painting, where teams of riders fan out dribbling paint (sometimes unwittingly) to create citywide tracery of wobbling lines that only the pigeons (and a few heliborne execs) can fully appreciate.

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For me bikes’ real beauty lies in movement, and it’s in zipping around the city that they come to life in a balletic dance that is half human, half mechanised. I think you can read some of riders’ characters and lives in their style, and so watching other bikes is a bit like a soap opera, or a succession of interpretive performances – and my own riding tells my story, too.

There are the couriers, the new ones flying along panting on piecework as they bash through the traffic, the older, crustier ones seemingly seeping effortlessly through, plotting their path miles ahead down the road. The long-distance commuters and triathletes, hurtling along red-faced and steaming in their own personal Tour. The hipsters, gliding along obliviously like swans on a lake, and of course the beginners, easily picked out on their Boris Bikes these days, wobbling along nervously like ice-skaters.

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‘Old Faithful’ was built at home by Graeme O’Bree using parts from a washing machine – he broke the world Hour Record on it in 1993

As a kid in a shit suburb in England I loved riding out round the houses looking for enemies to gun down, whether that was Maggie Thatcher, the Soviets, Messerschmidts or maybe Kevin from the other class at school.

The bikes in style at the time were mountain bikes with about 65 gears and for a while I only had a shitty old BMX frame. Then just as I got a normal mountain frame, everyone started getting spinner disc wheels like Gold Medalist Chris Boardman. Only they weren’t carbon-fibre aero-discs; just bits of heavy plastic that covered the spokes – what a gyp. You could put cool patterns and stuff on them though; WWF was pretty popular I think. I tried to make one from a bin lid and it nearly killed me when it stuck through the forks.

But, the freedom… I wore through a succession of shitty old mountain / really old town bikes until but I learned to fix bikes pretty well though.

One night after scouts my mate Chris Baker let me have a go on his racer. It looked like a heap of geek-junk from the Seventies – everything was all spindly and rusty – but, even on the shingly beach outside the hut in Hythe, it went like a train. I *needed* one of these speed machines. off I went. But racers were *definitely* the least cool kids on the block at the time, as no-one had invented fixies or skinny jeans.

Then – all at the same time – I outgrew all my MTB bikes (puberty hit) and BMX came back into vogue. So I got a shonky old Raleigh from some relative of my step dad, and I discovered that I could ride all the way into Southampton in only about an hour. So I decided fashion was just a way to sell you crap you didn’t need, discovered The Clash and started ignoring people who talked rubbish.

Resume

Hey.

Been a little while… summer involved a lot of busyness and general running-about. Apart from anything else there was a lot more work to do on the Ann The Arc record than I knew.

Good news is, the demos have been flowing for new LJP stuff pretty freely for over a month now – up to about 40 tracks. About 10 of these made it into my set at the Sotones showcase at The Old Queen’s Head last month, and I went to Bulgaria to put that set down with the lovely and talented Tom and Rysia at Furnace Studios.

I’m gonna slowly polish a couple at a time and stick them up on Soundcloud, I’ll let peeps know when I do.

In the next month or so I’ll be doing a few one-off gigs about the place while we work out the kinks in the new set before we record – so stay tuned!

Till then, laters xx

Generation of neutralizing antibodies and divergence of SIVmac239 in cynomolgus macaques following short-term early antiretroviral therapy.

PLoS Pathog. 2010 Sep 2;6(9):e1001084.
Ozkaya Sahin G, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spångberg M, Thorstensson R, Achour A, Fenyö EM, Stewart-Jones GB, Spetz AL.

Neutralizing antibodies (NAb) able to react to heterologous viruses are generated during natural HIV-1 infection in some individuals. Further knowledge is required in order to understand the factors contributing to induction of cross-reactive NAb responses. Here a well-established model of experimental pathogenic infection in cynomolgus macaques, which reproduces long-lasting HIV-1 infection, was used to study the NAb response as well as the viral evolution of the highly neutralization-resistant SIVmac239. Twelve animals were infected intravenously with SIVmac239. Antiretroviral therapy (ART) was initiated ten days post-inoculation and administered daily for four months. Viral load, CD4(+) T-cell counts, total IgG levels, and breadth as well as strength of NAb in plasma were compared simultaneously over 14 months. In addition, envs from plasma samples were sequenced at three time points in all animals in order to assess viral evolution. We report here that seven of the 12 animals controlled viremia to below 10(4) copies/ml of plasma after discontinuation of ART and that this control was associated with a low level of evolutionary divergence. Macaques that controlled viral load developed broader NAb responses early on. Furthermore, escape mutations, such as V67M and R751G, were identified in virus sequenced from all animals with uncontrolled viremia. Bayesian estimation of ancestral population genetic diversity (PGD) showed an increase in this value in non-controlling or transient-controlling animals during the first 5.5 months of infection, in contrast to virus-controlling animals. Similarly, non- or transient controllers displayed more positively-selected amino-acid substitutions. An early increase in PGD, resulting in the generation of positively-selected amino-acid substitutions, greater divergence and relative high viral load after ART withdrawal, may have contributed to the generation of potent NAb in several animals after SIVmac239 infection. However, early broad NAb responses correlated with relatively preserved CD4(+) T-cell numbers, low viral load and limited viral divergence.

Safety and immunogenicity of novel recombinant BCG and modified vaccinia virus Ankara vaccines in neonate rhesus macaques.

J Virol. 2010 Aug;84(15):7815-21. Epub 2010 May 19.
Rosario M, Fulkerson J, Soneji S, Parker J, Im EJ, Borthwick N, Bridgeman A, Bourne C, Joseph J, Sadoff JC, Hanke T

Although major inroads into making antiretroviral therapy available in resource-poor countries have been made, there is an urgent need for an effective vaccine administered shortly after birth, which would protect infants from acquiring human immunodeficiency virus type 1 (HIV-1) through breast-feeding. Bacillus Calmette-Guérin (BCG) is given to most infants at birth, and its recombinant form could be used to prime HIV-1-specific responses for a later boost by heterologous vectors delivering the same HIV-1-derived immunogen. Here, two groups of neonate Indian rhesus macaques were immunized with either novel candidate vaccine BCG.HIVA(401) or its parental strain AERAS-401, followed by two doses of recombinant modified vaccinia virus Ankara MVA.HIVA. The HIVA immunogen is derived from African clade A HIV-1. All vaccines were safe, giving local reactions consistent with the expected response at the injection site. No systemic adverse events or gross abnormality was seen at necropsy. Both AERAS-401 and BCG.HIVA(401) induced high frequencies of BCG-specific IFN-gamma-secreting lymphocytes that declined over 23 weeks, but the latter failed to induce detectable HIV-1-specific IFN-gamma responses. MVA.HIVA elicited HIV-1-specific IFN-gamma responses in all eight animals, but, except for one animal, these responses were weak. The HIV-1-specific responses induced in infants were lower compared to historic data generated by the two HIVA vaccines in adult animals but similar to other recombinant poxviruses tested in this model. This is the first time these vaccines were tested in newborn monkeys. These results inform further infant vaccine development and provide comparative data for two human infant vaccine trials of MVA.HIVA.

Voting: Intentions

“A fair society starts with a fair election”
Billy Bragg

So tomorrow we will go and cast our votes to try and pick a government. The Election has come at last.

Except there’s not one single election where we all pick our favourite to be the leader. Instead there are really 650 separate elections for local representatives. If your vote doesn’t end up backing the winner in your area, it looks a lot like a wasted vote**.

If you live in a safe Labour or Tory seat you’re effectively unable to vote: no matter what you do, the party you support won’t win in your area unless you’re very good at persuading 10,000 people to vote the same way you do. So how do you get heard if you’ve got a minority viewpoint?

Like most people, I’ve had real trouble making up my mind who to vote for this time.

This is basically because there seems to be very little difference between the parties on most of the important issues: everyone wants to get the national debt under control while protecting hospitals, schools and police, and trying to cut greenhouse emissions. In a way that’s a good thing: consensus on these really important issues means we ought to be able to take the decisions we need to take, even in a hung parliament.

On the other hand, there are lots of small issues where only one party really represents my views. In my particular case, that’s the Greens, but you may be different. This is a reflection of modern societies really – the big questions about healthcare and the budget are more-or-less matters of small policy tinkering that most people agree with, while other concerns are raised by NGOs and smaller parties (what you might call ‘single-issue’ parties).

In France, Germany, Japan, South Korea and Spain – all rich, perfectly functioning, healthy modern democracies about the same size as the UK – they have a system of elections that allows for larger parties to govern based on a common consensus, while ensuring minority rules are also represented: proportional representation (PR), where MPs are elected according to the exact number of votes cast for their party. Every vote really does count.

For the first time in over 80 years we have the chance to reform our electoral system and finally make it truly democratic. Here the parties actually are different. The Tories oppose PR because they think that we (the plebs) can’t be trusted to elect a capable government if we’re allowed to vote directly, and because they worry that Britain is somehow a weaker or more indecisive country than Germany, France or Japan. This is, in a word, bollocks – the British people aren’t idiots, and last-time I checked, patriotism entailed pride in your country, not fear that it might fuck up where others have had no problems. Labour only dimly support PR, because they stand to lose a lot of power as the current setup massively favours them (in 2005 they won a double-digit majority with around 1/3 of the votes cast).

Only the Liberals support PR completely, and have pledged to hold a referendum to introduce it. Yes, this is because they have the most to gain of the 3 main parties, and yes, some of their policies I disagree with, and yes, a vote for them might in some cases be a vote for the Tories BUT we need to reform this rotten, outdated system (nearly 200 years old) and we may not get another chance in our lifetime.

To those who say that we need a Tory majority to deal with the economic crisis, here’s what I think: All the parties want to cut the deficit. The measures they’re all taking are basically the same in that they don’t go far enough. And most importantly, the best way to avoid a repeat of the mistakes that lead to that crisis (and others to come), ultimately, is to have a better-functioning democracy that represents us.

So. I live in Hythe, which is a Tory seat. Tomorrow I’ll be voting Lib Dem because the more votes and seats they get, the more likely it is that we’ll get a PR, a voting system where our votes actually count directly. And then in future I can vote Green, or UKIP, or whoever I damn well want, safe in the knowledge that this time, my vote really will count.

**The maths behind this is simple but pretty unsettling. Imagine there are only 10 constituencies (areas), of 10 voters each, and only two parties. Party A win 4 of the constituencies outright, with all 10 votes in each. In the remaining 6 constituencies, they come second with 4/10 votes. Party B, who win those 6 constituencies with 6/10 votes in each, have won a total of six of the available ten seats, and win the election. BUT only 36 people voted for them (6 votes in each of 6 constituencies) out of 100, compared with 64 votes cast (10 in each of 4 constituencies, plus 4 in each of 6 constituencies) for Party A. If this seems like an oversimplification, well, the results of the 2005 election pretty much exactly match these ratios.

Recording report

ello

just a quick note to say what’s going on at the moment…

recording-wise, i’m meant to be finishing leila, brooklyn and shanty to go on this split EP for Oxjam with Dave Miatt. unfortunately we’re doing it all on tick, and its going really frustratingly slowly.. hence the shitty demos on myspace at the moment, sorry about that. the idea is to do some more tracking of the current sessions (produced by Izaak Bullen a.k.a. The Scarlet Letter Union) very soon. we’ll see.

longer term at least we’ve got round to putting this page up which took longer to sit down and do than you might imagine.. “will people fan me?” “should it be just me editing it or should i let someone else do it?” “why am i such a massive cunt?” etc.. but we figured it was better to have these pages up and going rather than spend ages waiting for some mythical ‘jump off’ moment. so there you go.

in the summer months lots of fun happening – will be doing another bike tour like last summer, but this time it’ll be longer and (hopefully) a few bigger venues. also the legs will be shorter and planned longer in advance – this time i REALLY want loads more people to come along for the ride!

then sometime towards the end of the summer, depending on everyone’s commitments, we’re spending a few weeks at Furnace Studios – a residential studios in Bulgaria – to jam out an LP proper for an autumn release on Sotones. Also all the back catalogue is getting slowly re-issued on digital too – stay posted for that.

in the meantime, take care of each other xxx
joe

ps: don’t put tipex on the keys of your computer to tell black notes from white ones in garageband.. really bad idea…