This post was going to be a rant about Barclays and how I hate them. Then I was distracted by these two things and I realised they're not worth it. Sourced, like so many nice things, from Fabulist again.
I went to Sefton Park Library for the last time today, returning the penultimate book in Stephen King's Dark Tower series. I'm going to miss it, it's a tiny library, but perfectly formed. I'm going to try and save the final book for San Francisco.
Thursday, May 29, 2008
Tuesday, May 13, 2008
Big Changes
A short post, but there's lots going on at the moment and I haven't told lots of friends what I'm up to.
I'm getting married on Friday, to someone I've actually been with for ten years, so it's strange (and wonderful) to be finally doing it! It's all been a bit of a rush and is a tiny wedding with only our immediate families, not the way we'd envisaged it, but hopefully lovely all the same. Wish us luck!
The reason for the swiftness is another big change, I've got a job in San Francisco at UCSF and we wanted to be married with our families before we went as we might not get another chance in quite a while.
We leave Liverpool at the end of this month to stay in London until the beginning of July when I officially start, visas willing. Very exciting, very stressful, and hopefully all over soon! I am looking for temping in London for June as I finished my current job at Liverpool last week - so please let me know if you know of anything, I have a weird bunch of skills and have done everything from office work and lab work to making sandwiches in the past. CV on request ;)
Will update with news here when I'm able to, and also with more details of the move. The best way to keep in touch will probably be Twitter, not knowing what sort of internet access that we'll have when we first move.
I'm getting married on Friday, to someone I've actually been with for ten years, so it's strange (and wonderful) to be finally doing it! It's all been a bit of a rush and is a tiny wedding with only our immediate families, not the way we'd envisaged it, but hopefully lovely all the same. Wish us luck!
The reason for the swiftness is another big change, I've got a job in San Francisco at UCSF and we wanted to be married with our families before we went as we might not get another chance in quite a while.
We leave Liverpool at the end of this month to stay in London until the beginning of July when I officially start, visas willing. Very exciting, very stressful, and hopefully all over soon! I am looking for temping in London for June as I finished my current job at Liverpool last week - so please let me know if you know of anything, I have a weird bunch of skills and have done everything from office work and lab work to making sandwiches in the past. CV on request ;)
Will update with news here when I'm able to, and also with more details of the move. The best way to keep in touch will probably be Twitter, not knowing what sort of internet access that we'll have when we first move.
Thursday, May 01, 2008
Penguins, Spies, Clay and Plato
I've been too busy to follow much of We Tell Stories, Penguin and Six To Start's online narratives and ARG, which is a terrible shame. I have tried to dip in and out though (I particularly enjoyed my fairy story about the poor peasant girl Cellulitis), but it means I won't be winning the entire Penguin Classic back catalogue.
A little while ago I signed up with Penguin to review a pre-release (and as it turned out, pre-cover and pre-typo-removal, there's probably a term for that) copy of Clay Shirky's Here Comes Everybody. I did it, to put not to fine a point on it, for shits and giggles. At some point I was supposed to blog about the book and maybe send them a link to the blog post. I'm ashamed to say that I never have. Luckily being shambolic and unreliable as an individual is a characteristic of the blogosphere, I can console myself as being an insignificant part of something much more effective as a collective. The effective collective.
Clay Shirky is now popping up everywhere (that host is worse than Jonathan Ross - does he need a guest?) and his book seems to be being well received. Which is great, because it's a really interesting book. It's primarily about user-generated content and social networks on the internet, with examples ranging from flash-mob protests using Twitter to Wikipedia. He should get into ARGs, there's some lovely fodder there.
This is something particularly of interest to me right now because we're making an ARG, which I sometimes view as making a place for people to play and seeing what happens. Analogous to designing Twitter or Facebook, but with less defined networking. The players will play us almost as much as we play them, and creating somewhere where this can happen with ease that is also appealing and fun is not easy, but I think there are relevant lessons from Here Comes Everybody. The concept that stuck with me is that persuasion is better than prescription when it comes to making the game, perhaps exemplified in the book by Wikipedia, starting as a place for experts only to contribute and being improved by becoming a place for everyone.
Another example of this that's been recently discussed at Unforum is player recruitment. If you want to bring more players to the game making "going out and finding new players something that players want to do because the game's cool" is much better than the Facebookesque "recruit me 20 players and I will give you something lacklustre and piss off your friends". Better because it doesn't piss people off and better because our players are doing us a favour, never the other way round. Puppet Masters or Court Jesters?
Speaking of making an ARG, we had our second meeting with Cancer Research UK a weekend or two ago, I got up at 5 am and got home at 5 pm for a two-hour meeting, that thankfully, was really worth it. Our Cancer Research UK liaison was incredibly enthusiastic about everything. Obviously a man of taste. He also thinks we can make money, which is even better.
Below is our motley crew outside MI5 headquarters. Do we get hung for taking a photo there? Let's see whether I'm duffed up in an alley and the post mysteriously corrupted o_O .
So, because I'm a scientist and every figure must have a legend, this is The Legend of the Vauxhall Six; mysterious strangers with an enigmatic purpose. Shane, with pockets that are infinitely large on the inside and quite large on the outside; Izzy, who cannot look into the camera directly for fear of bewitching you with her enthusiasm; Juliette, that's not just a belt on her coat, it's a dark grey belt, probably with a concealed laptop; Adrian, our own disembodied Mimir, notable for 'lurking at the back'; David, who has accomplished terrible things with that thumb; finally Mark Haymes, whose abilities are simply to look less like a student than the rest of us. And to liaise, which he does with aplomb. My own ability is overuse of; the; semicolon.
I promise next time I'll take a better picture. Is this one even level? I have terrible trouble with horizons.
Anyway the point of this post was that after enjoying Mr Shirky's book quite a lot (it wasn't one of these weird, preachy, trendy evangelist books, neither was it dry as old bones - just nicely thoughtful and a little compelling) I was suckered into going for another Penguin blog offer. Their Facebook group has offered a Penguin Classic to bloggers who want to review one of each of the 1300 (or was it 1400?) Classics. Unlike last-time they specify that six weeks after receiving the particular, randomly assigned classic, they expect a review. Mea culpa. The things I do for a free book.
My randomly assigned classic? The Symposium. I should have gone for Puffin Classics shouldn't I? I could have done a lovely review of Black Beauty. I guess I'm not going to get pin badges with this one?
A little while ago I signed up with Penguin to review a pre-release (and as it turned out, pre-cover and pre-typo-removal, there's probably a term for that) copy of Clay Shirky's Here Comes Everybody. I did it, to put not to fine a point on it, for shits and giggles. At some point I was supposed to blog about the book and maybe send them a link to the blog post. I'm ashamed to say that I never have. Luckily being shambolic and unreliable as an individual is a characteristic of the blogosphere, I can console myself as being an insignificant part of something much more effective as a collective. The effective collective.
Clay Shirky is now popping up everywhere (that host is worse than Jonathan Ross - does he need a guest?) and his book seems to be being well received. Which is great, because it's a really interesting book. It's primarily about user-generated content and social networks on the internet, with examples ranging from flash-mob protests using Twitter to Wikipedia. He should get into ARGs, there's some lovely fodder there.
This is something particularly of interest to me right now because we're making an ARG, which I sometimes view as making a place for people to play and seeing what happens. Analogous to designing Twitter or Facebook, but with less defined networking. The players will play us almost as much as we play them, and creating somewhere where this can happen with ease that is also appealing and fun is not easy, but I think there are relevant lessons from Here Comes Everybody. The concept that stuck with me is that persuasion is better than prescription when it comes to making the game, perhaps exemplified in the book by Wikipedia, starting as a place for experts only to contribute and being improved by becoming a place for everyone.
Another example of this that's been recently discussed at Unforum is player recruitment. If you want to bring more players to the game making "going out and finding new players something that players want to do because the game's cool" is much better than the Facebookesque "recruit me 20 players and I will give you something lacklustre and piss off your friends". Better because it doesn't piss people off and better because our players are doing us a favour, never the other way round. Puppet Masters or Court Jesters?
Speaking of making an ARG, we had our second meeting with Cancer Research UK a weekend or two ago, I got up at 5 am and got home at 5 pm for a two-hour meeting, that thankfully, was really worth it. Our Cancer Research UK liaison was incredibly enthusiastic about everything. Obviously a man of taste. He also thinks we can make money, which is even better.
Below is our motley crew outside MI5 headquarters. Do we get hung for taking a photo there? Let's see whether I'm duffed up in an alley and the post mysteriously corrupted o_O .
So, because I'm a scientist and every figure must have a legend, this is The Legend of the Vauxhall Six; mysterious strangers with an enigmatic purpose. Shane, with pockets that are infinitely large on the inside and quite large on the outside; Izzy, who cannot look into the camera directly for fear of bewitching you with her enthusiasm; Juliette, that's not just a belt on her coat, it's a dark grey belt, probably with a concealed laptop; Adrian, our own disembodied Mimir, notable for 'lurking at the back'; David, who has accomplished terrible things with that thumb; finally Mark Haymes, whose abilities are simply to look less like a student than the rest of us. And to liaise, which he does with aplomb. My own ability is overuse of; the; semicolon.
I promise next time I'll take a better picture. Is this one even level? I have terrible trouble with horizons.
Anyway the point of this post was that after enjoying Mr Shirky's book quite a lot (it wasn't one of these weird, preachy, trendy evangelist books, neither was it dry as old bones - just nicely thoughtful and a little compelling) I was suckered into going for another Penguin blog offer. Their Facebook group has offered a Penguin Classic to bloggers who want to review one of each of the 1300 (or was it 1400?) Classics. Unlike last-time they specify that six weeks after receiving the particular, randomly assigned classic, they expect a review. Mea culpa. The things I do for a free book.
My randomly assigned classic? The Symposium. I should have gone for Puffin Classics shouldn't I? I could have done a lovely review of Black Beauty. I guess I'm not going to get pin badges with this one?
Open Source Sequencing and Colossal Squid
The Polonator has a really cheesy name (Arnie dressed as a giant bee?) , but it's a really important step in molecular biology. It's a DNA sequencing machine, there are lots of these around at the moment as people have managed to make systems that beat the traditional dideoxy Sanger-sequencing method (which was used to sequence the human genome) in speed and in the bulk cost of sequencing. Examples include 454's pyrosequencer and the dubiously capitalised SOLiD system. Both produce substantially shorter reads, single sequences of DNA, than the ABI 3700's used to sequence the human genome (though I've heard rumours that a new 454 machine that can do 500 bp reads is on the cards), but do millions at a time.
If you want to run one of these systems, you purchase them for hundreds of thousands from the manufacturer, get trained how to run them by the manufacturer and buy the consumables from the system from the manufacturer. You don't necessarily know what the reagents are in these consumables and therefore all the trouble-shooting you do involves the manufacturer too. This is because these machines are expensive to make, not many people buy them and they become defunct very quickly. It ties labs to the machine, probably long past the time when they're cutting edge.
In some ways it's silly to keep these reagents secret. I worked for AstraZeneca for a year as an undergraduate (which was great experience - companies are much stricter about lab protocol than universities and you pick up good habits!) and they purchased a machine for typing bacteria that I was involved with validating for use - the RiboPrinter Microbial Characterisation system. We bought their kits and never knew what was in them, but myself and another student, frustrated by the fact that we had to write a report for university that would contain no science at all as we didn't know what was in these kits, sat down and attempted to work out what they contained. Judging by the comments from the sales reps from Dupont who make the system, we were pretty close in our estimation. If two undergraduates can work out what's in the various solutions (which is a long way from making a working machine, but at least would mean we weren't reliant on buying inevitably more expensive proprietary reagents) what's the point in the secrecy anyway?
The Polonator is different in that the system is open source. They give you full specs of the machine, they give you full details of the reagents required: what's in them and the concentrations. You can get the machine and make your own protocols for it and share them with other users. According to the article in Technology Review (via Digg) users are already collaborating to improve the chemistry.
Surely this is how science should be done? The philosophy is that scientists share their work and it's peer-reviewed before grants are rewarded, after papers are written and discussed by the community at conferences and after publication. This should allow everyone to build on each others' work and mean that resources aren't wasted - molecular biological research is not cheap to do. This isn't in reality what happens. Labs have their own protocols for performing experiments that might be shared amongst collaborators, but more rarely with the whole scientific community unless it's a more ground-breaking achievement. Minor improvements to protocols that could save time and money are shared perhaps by word-of-mouth. Negative results are generally not reported, meaning that identical experiments could be performed again, perhaps many times, in another lab, wasting resources again.
There are good reasons why some information shouldn't be shared, perhaps to allow a patent to be taken out on the intellectual property to prevent someone nicking the idea for their own gain. But I believe that there are more benefits in the majority of cases for sharing results. There's not a lot of truly open source science going on out there currently. Another example would be the OpenWetWare project, which aims to make sharing of information and protocols amongst bioscientists easier - to the extent that they encourage lab notebooks to be kept online on their wiki. It takes brave souls to get involved initially, posting up their failed and frustrating experiments along with the successes, but then once more people are involved I reckon the benefits will speak for themselves.
Hopefully more projects like this will be initiated and we can have a truly open, more productive scientific community.
On a completely different topic, a group of scientists at the Museum of New Zealand Te Papa Tongarewa have been investigating three Giant Squid (Architeuthis dux) and one Colossal Squid (Mesonychoteuthis hamiltoni, it's bigger, I reckon they're reserving the name Ginormous Squid for the next bigger one they find) that they've had on ice. The blog is fascinating, with pictures of the biggest eye in nature and some clips of them during the dissection. I like squid, and own a T-shirt to prove it - linky.
If you want to run one of these systems, you purchase them for hundreds of thousands from the manufacturer, get trained how to run them by the manufacturer and buy the consumables from the system from the manufacturer. You don't necessarily know what the reagents are in these consumables and therefore all the trouble-shooting you do involves the manufacturer too. This is because these machines are expensive to make, not many people buy them and they become defunct very quickly. It ties labs to the machine, probably long past the time when they're cutting edge.
In some ways it's silly to keep these reagents secret. I worked for AstraZeneca for a year as an undergraduate (which was great experience - companies are much stricter about lab protocol than universities and you pick up good habits!) and they purchased a machine for typing bacteria that I was involved with validating for use - the RiboPrinter Microbial Characterisation system. We bought their kits and never knew what was in them, but myself and another student, frustrated by the fact that we had to write a report for university that would contain no science at all as we didn't know what was in these kits, sat down and attempted to work out what they contained. Judging by the comments from the sales reps from Dupont who make the system, we were pretty close in our estimation. If two undergraduates can work out what's in the various solutions (which is a long way from making a working machine, but at least would mean we weren't reliant on buying inevitably more expensive proprietary reagents) what's the point in the secrecy anyway?
The Polonator is different in that the system is open source. They give you full specs of the machine, they give you full details of the reagents required: what's in them and the concentrations. You can get the machine and make your own protocols for it and share them with other users. According to the article in Technology Review (via Digg) users are already collaborating to improve the chemistry.
Surely this is how science should be done? The philosophy is that scientists share their work and it's peer-reviewed before grants are rewarded, after papers are written and discussed by the community at conferences and after publication. This should allow everyone to build on each others' work and mean that resources aren't wasted - molecular biological research is not cheap to do. This isn't in reality what happens. Labs have their own protocols for performing experiments that might be shared amongst collaborators, but more rarely with the whole scientific community unless it's a more ground-breaking achievement. Minor improvements to protocols that could save time and money are shared perhaps by word-of-mouth. Negative results are generally not reported, meaning that identical experiments could be performed again, perhaps many times, in another lab, wasting resources again.
There are good reasons why some information shouldn't be shared, perhaps to allow a patent to be taken out on the intellectual property to prevent someone nicking the idea for their own gain. But I believe that there are more benefits in the majority of cases for sharing results. There's not a lot of truly open source science going on out there currently. Another example would be the OpenWetWare project, which aims to make sharing of information and protocols amongst bioscientists easier - to the extent that they encourage lab notebooks to be kept online on their wiki. It takes brave souls to get involved initially, posting up their failed and frustrating experiments along with the successes, but then once more people are involved I reckon the benefits will speak for themselves.
Hopefully more projects like this will be initiated and we can have a truly open, more productive scientific community.
On a completely different topic, a group of scientists at the Museum of New Zealand Te Papa Tongarewa have been investigating three Giant Squid (Architeuthis dux) and one Colossal Squid (Mesonychoteuthis hamiltoni, it's bigger, I reckon they're reserving the name Ginormous Squid for the next bigger one they find) that they've had on ice. The blog is fascinating, with pictures of the biggest eye in nature and some clips of them during the dissection. I like squid, and own a T-shirt to prove it - linky.
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