Dr Administrator

Author's posts

Apr 12 2010

Why I’m voting Liberal Democrat

In a change from usual service I’m writing a political blog post, to cut to the chase: Vote Liberal Democrat! This post tries to explain why.

I’ve been a member of the Liberal Democrats since I was an undergraduate at Bristol University, 20 years ago. As a student I attended a party conference, did a bit of canvassing and I was also a “teller” a couple of times. Since then I’ve been in cover, very deep cover, I pay my monthly membership and a bit extra at election time and that’s pretty much the limit of my activism.

As a casual Liberal Democrat I don’t keep a close eye on party policy, essentially I rely on them being my sort of people and doing the right thing, it’s with some relief I can report that I agree entirely with Nick Clegg in his interview with The Observer this week. The whole interview is well worth a read, but I’ll pick up on one point: there’s a real value in a hung (or balanced) parliament with no party in overall control. Reducing the national debt will be a priority for any incoming government, this is likely to be at least a bit painful and I think it’s very obvious this is better done with a government that holds representatives from more than the 40% or less of the popular vote that a majority government is likely to get.  Many other issues will be with us for years to come: care for the elderly, climate change, pensions, the shape of our democratic systems. The solutions that politicians come up with should be robust, and have cross-party support, on recent evidence they need to work on this cooperative aspect of politics. Across the world and the UK, in devolved government and European elections we use a form of proportional representation, the sky has not fallen in. I’m fed up with the “smack of firm government” that first-past-the-post gives us.

The expenses scandal has had a big impact on politics in the last year, the Liberal Democrats came out well on this with relatively few outrageous claims and a very definite plan on how to address the problem which unfortunately was not picked up by the other parties. MPs had an expenses system which begged to be abused, I’m sure that with the same system at the place I work we would see a similar range of behaviour.

I’ve written in the past about the science policies of the Liberal Democrat, Labour and Conservative parties based around a debate organised by the Campaign for Science and Engineering in the UK. In summary, science has done fairly well by Labour over the last 13 years, with a noticeable wobble at the end over the science advisers, particularly on drugs advice. The Tories seem rather uncommitted to science, and look like they would do no better over science advisers. In the Liberal Democrats we have a champion in the form of Dr Evan Harris, who I really wish was my MP. He has done sterling work on the Science and Technology Select Committee, as well as campaigning on libel reform.

I vote in the City of Chester constituency, pragmatically there is absolutely no point in me turning out to vote. It will have no effect on the outcome, come May 7th not one particle of an MP in parliament after will have my electoral support.

Often party X will tell Liberal Democrats to vote for them to prevent party Y getting in, my response is in the form of an analogy: if I want chocolate cake for pudding the offer of an apple or a plate of cheese and biscuits will not satisfy, and may cause offence and derision. Vote for chocolate cake, vote Liberal Democrat!

Apr 10 2010

Experiments for obsessive compulsives

It feels like I’ve not really been writing about science very much recently, so I thought I’d return to some work on which I spent a few years, with my former PhD student, Pietro Cicuta.

We looked at the properties of a protein from milk (β-casein) spread on the surface of water: principally the effect that it had on the surface tension as a function of amount of protein. Experimental variables were the acidity and saltiness of the water. We did this using a Langmuir trough which I’ll describe below. b-casein is what’s known as a random coil protein: in contrast to many proteins, which curl up into a well-defined, unique shape, β-casein flops around like a piece of string. This work is directly relevant to people working in the food industry, and more generally interesting to people who work with polymers (chemists) and proteins (biologists).

β-casein acts as a surfactant which helps stabilise fat globules in milk. Surfactants are common type of molecule, the name is a contraction of “surface”, “active” and “agent”, unsurprisingly they are found at surfaces: typically between one liquids, like oil and water, but also at interfaces between liquid and air. Surfaces are important, they keep the inside in, and the outside out. Surfactant molecules help with this important process by stabilising surfaces (the natural tendency of liquids is to form big blobs, surfactants stop this process). Some examples: the cells in your body are surrounded by surfactants, mayonnaise contains surfactants from egg which keep the oil suspended in the water, all manner of cleaning products for clothes, hair, work by using surfactants to stabilise dirt in water, and foams are formed using surfactants.

To achieve this magic surfactants share a common feature: part of the molecule likes oil and part of the molecule likes water, so to keep both parts happy they hang around at interfaces. Most surfactants are like little tadpoles with water-loving heads and water-hating tails. β-casein is a bit different, parts of the string like water, so they try to stick into the water and parts don’t like water so they head for the air. However changing the acidity and saltiness of the water changes the strength of the love for water.

In most cases substances love water because they have an electrical charge, and this is why salinity and aciditiy are important in this experiment: if you change the acidity of the water the electrical charge on the protein changes because of the chemistry of the protein, if you change the salinity then how well the water can see the charges changes. It’s a bit like fog, when there is no salt in the water it’s as if the electric charges are seen through clear air and their influence spreads far and wide, adding salt is like a mist reducing the visibility of charges until ultimately the electric charges can’t be seen at all.

A Langmuir trough is a way of probing surfactant properties. It comprises a shallow trough made of Teflon, a barrier made of Teflon (which can be swept across the surface of liquid in the trough) and a surface tension sensor. Teflon is used because water sits on top of it forming a proud meniscus rather than spreading out, damply. The sensor is nothing more than a bit of filter paper attached to a force measuring device, dip it into the water and feel the pull – that’s surface tension. The idea with the barrier is that you place the barrier at one end of the trough, drop your molecules on the surface and then slide the barrier along, the molecules on the surface have few places to go so the decreasing the area amounts to increasing the concentration of the molecules at the surface. It’s really the 2D version of compressing a gas with a piston. I tried to find a picture of a trough with a single barrier, but couldn’t – the principle of the two-barrier trough shown here is the same, the black tower in the middle is the surface tension sensor.

Langmuir trough experiments are ideal for obsessive-compulsives: before you start your actual experiment you have to get the surface of the liquid you’re using absolutely clean. To do this you clean your trough, add in the ultrapure water, compress the surface, hoover (with a glass pipette connected to a vacuum pump) contaminants off the surface if there was an upturn in the surface tension, then go back to compressing the surface, hoovering the surface etc. Some times it just doesn’t work and you spend a morning trying to get your trough clean. Doing this for an oil/water interface is difficult, much more difficult actually I never succeeded. The core of the problem is that you don’t need much material to make a surface dirty, imagine painting a ball – the amount of paint required to cover the surface is much smaller than the volume of the ball.

The Langmuir trough was developed by Irving Langmuir, building on work by Agnes Pockels done towards the end of the 19th century. You’ll often see references to the Langmuir-Blodgett trough, the two terms seem to be used interchangeably but my understanding is that the Langmuir-Blodgett device is used to deposit surface active molecules onto a surface (which is not what we were doing). The Blodgett is Katherine Blodgett, who was the first woman to be awarded a PhD in Physics from Cambridge University.

From the surface tension data we extracted two things: firstly, how the protein molecules interact with each other – this comes from the early part of the compression data when the molecules are just starting to touch each other. Secondly, we get some idea of the innards of the protein from what happens when we squeeze the molecule harder and it starts to deform. Think of it like a bunch of eggs if you’re bouncing them around in a basket you find out about how bouncy they are, if you grab hold of one and squeeze it really hard you first discover that it has a tough outer shell, then you discover it has a soft squishy inside, then you discover you have egg all over your hands and you forgot to get the kitchen towel out before you started.

We find out this information about interactions and internal properties as a function of acidity and salinity, which we can then compare with theories of charged polymers. This comparison turned out to work quite nicely, and Pietro came up with a neat way of illustrating how bits of the molecule appeared to plunge into the water as the surface layer was compressed.

This is pretty much my most cited piece of work, with just less than 30 citations. So there you go, several years in the lab condensed into just over a 1000 words, although I didn’t mention the Surface Quasi-elastic Light Scattering (SQELS).

Reference
Cicuta, P., and I. Hopkinson. “Studies of a weak polyampholyte at the air-buffer interface: The effect of varying pH and ionic strength.” Journal of Chemical Physics 114(19), 2001, 8659-8670. (pdf)

Apr 04 2010

Caerwys – a breezy spring walk

Off to Afon-wen and Caerwys today for a brisk walk featuring steep walking through woods, spring flowers, llamas, highland cows and a newt. You can see the route here:


View Caerwys in a larger map

It’s a walk from “Walking in the Clwydian Range” by Carl Rogers, real men make up their own walks from OS maps and scouting missions but I’m lazy. A cool spring day today, in the distance we could still see the odd patch of snow on the hillsides. The trees were bare but the flowers had started to come out:

Clockwise from top left: Primrose, violet, wood anemone, and celandine
There were many birds out, singing away enthusiastically. I was going to show a picture of a woodpecker which we heard tapping away very close by, but we didn’t see it so it would really have been a conceptual piece so I’d like you take that conceptuality one step further and imagine a picture of a tree with an unseen woodpecker in it. Caerwys is the home of llamas, which I also treat with a degree of respect, since they spit if you offend them:

Although it’s a very rural location there are both signs of modern industrialisation in the from of quarries and sandpits and also the remnants of older work, including this lime kiln:

And also this rather creepy corrugated iron building which put me in mind of “Jeepers Creepers” or “Deliverance“:

With a vivid imagination, a walk in the countryside is never boring! We walked through the village of Caerwys, which is quite pretty – many of the houses seem to be well-made from the local limestone. No photos though, mainly because the streets were full of parked cars which are an aesthetic abomination and I don’t like photographing people’s houses in close up – it seems rude. However, I had no qualms about photographing this fine house across Ysceifiog Lake which was created for fishing by the Earl of Denbigh in 1904:

We next passed through a small nature reserve: Y Ddol Uchaf, which is a designated Site of Special Scientific Interest (SSSI) whose information board promised newts, and lo – I saw that there were newts and it was good:

On the final stretch back to the car we were treated to these handsome chickens:

And some Highland cows, we first sighted some of these in the distance across a field then we passed close by to another group behind a photography unfriendly fence then eventually coming to some easily accessible ones in photogenic mud:

This one, is the bull in the group, I’m a country lad and was easily able to identify him as such by dint of his sizeable testicles (which I refrained from photographing):

So there you go, a memorial of our Easter Sunday walk immortalised for when I am old and incapable of leaving the house.

Apr 03 2010

A brief history of gadgets

This is a post about gadgets and my relationship with them, spurred by my purchase of the latest gadget: an HTC Desire smartphone aka “Shiny”.

I have a suspicious relationship with telephones, basically I consider talking to people at a distance a form of devilry and if you expect me to type messages in a 26 letter alphabet using a 12 key keyboard you’ve got another thing coming. Telephone use at SomeBeans Towers is simple: most nights Mrs SomeBeans rings her dad, once a week on Sunday my mum rings me, roughly once a month my dad rings me with a list of computer problems for solution and once every three weeks I ring Majestic to arrange wine delivery : “Simples”. All phone calls beyond this are a cause for chaos, consternation, confusion etc. I appreciate this makes us “anomalous” but I’m too old to care.

Mobile phone use is even more occasional, whilst skiing we sometimes arrange slope side meet-ups via mobile phone. Mrs SomeBeans was reduced to hysterics watching me typing a text message, moving my lips as I did it and eventually giving up because of cramp. When buying a house use of the devil’s mobile speech-horn is inevitable. At the start of the last house purchase I sat on the train with my mobile phone ringing from my pocket thinking: “Why isn’t that person answering their phone? It sounds an awful lot like mine (I think)”, on the previous house buying occasion I attempted to recharge my phone via it’s headphone socket, it died.

My last trip to the phone shop was rather embarrassing for all concerned, I bought a Samsung E250 slider phone. I completely missed the point of the “slider” bit and asked the phone-geek whether it was a touch screen phone: “No, sir”. I expressed a desire for a phone embedded in an SLR camera lens, at which point the phone-geek claimed that the picture from some phone was as good as an SLR, so I like to think I wasn’t the only one to come away from the experience looking like a complete idiot. The Shiny was bought over the internet to avoid embarrassment.

I did wonder about the touch screen aspects of the Shiny, I believe there a two types of people in the world: those that are happy to smear their horrible, greasy fingerprints across displays, and those that wish to kill them. I fall into the second group, so there was some risk I would have a touch-screen phone which I was psychologically incapable of touching. Fortunately this has turned out not to be the case, whilst transferring over numbers from the old Samsung I repeatedly tried to use the screen as a touch-screen, to the chagrin of all involved.

Why the HTC Desire? I do a bit of programming and the Android operating system on which it runs is relatively straightforward for me to program on (the iPhone requires you to use a Mac). Android has such magic software as Google Goggles which carries out picture based searching – it works too: it successfully recognised “Luncheon of the Boating Party” by Renoir on our wall, as well as a rather more obscure photo, and Tasty by Kelis (front or back cover). It has a radio too (you notice phone functionality is pretty much the last thing on my mind here). Chatting to friends of a more phone-friendly nature I got the impression that the Desire was the way to go. Blackberries looked a bit serious and business-like (and don’t have radios).

The predecessors of the Shiny are my Psion 5mx, a fabulous PDA with a lovely almost proper keyboard and built-in software which did not need to be supplemented, I gave it up after many years because the connector between screen an keyboard started to break regularly, I followed this with a Dell Axim x51v which I never really loved. My phone history is completely unmemorable, my first mobile phone looked like a toy bone for a dog, and made young people laugh. I’ve had two other phones since then but I scarcely used them. In other gadgets I got a bluetooth GPS to talk to my PDA so I could geotag my photos, then I got a Garmin GPS60 which did it rather more robustly.

I joined the digital camera revolution rather early with a Kodak DC210, this was a revelation to me since previously my photography experience was limited to taking a few shots on film in a weeks holiday, finally filling a film after 18 months having completely forgotten where I was or what technically I had done to achieve the effect I had. After the Kodak I got an Olympus C750UZ, in parallel I also had a Casio Exilim S20 for it’s extreme compactness, then I went SLR picking up a Canon 300D from my father-in-law on which I became completely hooked, upgrading to a 400D shortly thereafter. The reason for going to the SLR was that even with a reasonably good point-and-shoot I was finding there were photos I knew I just couldn’t take because I couldn’t control the camera. An SLR gets round this problem by having a decent set of real controls, like a focus ring on the lenses, rather than some buried menu options and octopus-friendly button pressing. The thing with an SLR is that the camera body serves the function of a gateway drug, your dealer makes the real money on the lenses*. There’s probably a business model in giving away SLR camera bodies and making your profit solely on lenses and accessories. I’ve subsequently got a second Casio Exilim S10 to fill my dinky camera needs, this camera will take photos when people smile and claims that it can recognise different people and prioritise snapping according to your preference. This seems like a new way of offending friends and family, is making your wife anything other than top smiling priority grounds for divorce?

Returning to the HTC Desire: it’s fantastic! It can replace phone, pda, GPS and dinky camera: all in a beautiful package. The interface is a joy to use, wave your finger around on it and you go skittering off to different parts as if you’re skimming across the surface of a large desk. My old PDA felt like you were peering into a tiny fixed porthole on it’s innards. Tapping buttons on the screen gives you a touch of vibration feedback. Even the internet is pretty usable, as is the 200 page PDF manual.

I have a bit of a mixed attitude to gadgets: things that are nice to use like the Psion, Canon 400D and Shiny, I really like. Things with crap interfaces, I can’t abide: programming video recorders and central heating systems I hate for their horribly kludgey 20 random keystrokes with no user feedback nastiness.

And now, if you don’t mind, I will return to fondling Shiny.

*For the camera fans I have the 10-22mm, 50mm f/1.8, 18-55mm kit, 28-135mm, 100mm macro, EF 70-300mm lenses.

Mar 28 2010

Bug-eyed monsters from the planet Tharg

In a shameless piece of idea stealing I thought I’d write about how fiction informed my enthusiasm for science. Lucy Inglis at Georgian London started it, with her post on historical fiction had fed her enthusiasm for history. The Gentleman Administrator added his own thoughts, which are a little different. Then Jon Butterworth, a fellow scientist, mentioned sci-fi over on his blog so I thought I better get on with it before I was scooped!

Over the years I’ve read a huge amount of science fiction, from a huge number of authors but it’s always felt like something you don’t admit to in polite company. It’s always felt like a genre to be looked down upon by literary society. I think it’s the most imaginative writing there is.

Science fiction is a broad church ranging from almost entirely impersonal such as Last and First Men by Olaf Stapledon, to the very intensely human such as The Time Traveller’s Wife by Audrey Niffenegger.

Sometimes science-fiction is simply a back drop for a story: a thriller, a horror story, a romance – the fact it takes place on another planet, or in a whole different universe is entirely unimportant to the story. Sometimes science-fiction is about reflecting the fears of the day: the end of the world through nuclear war, a jingoistic enthusiasm for conquering new territories, or a reflection of a socially liberated society. Sometimes science-fiction is about a scientific idea, a what-if question. The best science-fiction mixes all three of these elements.

I can’t resistant adding in a few of my favourite ideas based science fiction here: Brian Aldiss’ Helliconia Trilogy is about a planet with century-long seasons, and how this impacts the animals, and “people” that live on it. Babel-17 by Samuel R. Delany is a classic science-fiction of ideas: what if there were a language, the knowledge of which let you think and act much faster? The Forever War by Joe Haldeman considers seriously the problems of fighting an interstellar war with combatants “lost in time” through the effects of time-dilation achieved by travelling at speeds approaching that of light, no doubt also influenced by his experience of the Vietnam war. Against a Dark Background by Iain M. Banks is about an isolated planet, subject to civilisation for many thousands of years, whose inhabitants have never left the planet surface in contrast to most science fiction where heading off to the stars is an early achievement. Kim Stanley Robinson’s Mars Trilogy is a detailed exploration of the mechanics (and sociology) of how we might really colonise Mars.

That’s just a tiny selection of the ones I can remember, there are so many other ideas from science fiction for which I just retain fragments. In writing this I’ve really struggled to keep the number of references to reasonable levels.

The attraction of science fiction for me are dreams of where we’re heading. Science in the lab can take years to work its way out into the real world, and often the impact of any particular experiment is rather small. Science fiction leapfrogs all that tedious waiting for an effect: it gives you the future, now.

Sometimes it can be surprisingly difficult to work out the potential impact of a new technology, who’d have thought that the ability to send 140 character text messages would be such an important use of mobile phone technology? To take an older example, in the late 18th century there was an enthusiasm for hot-air and hydrogen balloons but imagining their applications turned out to be surprisingly difficult task: principle amongst the proposed applications seemed to be the idea of using balloons to lighten terrestrial loads, not lift them entirely into the air. Search around a little and you’ll find people stating that they couldn’t see any reason why someone would have a computer in their home. Science-fiction gives you permission to loosen some of the bonds of strictly logical thinking, and say “Ignoring a couple of little problems, what really could it be like?”.

There are links to the historical novel from science fiction, for example The Difference Engine by William Gibson and Bruce Sterling imagines a past where Charles Babbage’s mechanical computers really took off. And the fabulous Baroque Cycle by Neal Stephenson is set in the period around the founding of the Royal Society and features many of the scientists of the day.

Science fiction has given me dreams of living in space, around the solar system, amongst the stars, in virtual worlds, with an augmented mind, with an augmented body. As I grow older, I realise that many of these dreams will forever be unfulfilled but I’m glad I had them.