Choosing to die

Terry Pratchett was recently diagnosed with Alzheimer's disease and has made a programme, Choosing to die, about his enquiries into assisted suicide. It's pretty difficult viewing: Pratchett visits the widow of a Belgian writer who, like him, had Alzheimer's disease and had chosen to end his life. He visits a former taxidriver in a hospice with motor neuron disease, who had chosen not to die. The bulk of the programme is spent with two men who went to the Dignitas clinic in Switzerland, where they were helped to die. Andrew, only a couple of years older than me, with multiple sclerosis and Peter, born in 1939, with motor neuron disease. The death of Peter is shown in full. It's not this that is my abiding memory though, that will be of the courage and dignity of the wife and mother of these two dying men. Neither woman wants their loved one to go.

The striking thing for me was how both men appeared to be heading off to Switzerland before their time, for fear of not being able to go when they felt they had to. The current legislation seems to be wilfully sadistic, obliging early death for those that chose whilst holding out the threat of prosecution to the family.

The Swiss are allowed to be helped to die at home, whilst foreigners go to die in a small blue apartment in an industrial estate. Incongruously the shallow steps to the front door are protected by black and yellow safety tape: because if you're going to die you don't want to fall over and crack your head open. This seems a great pity since in the background you could see the snow clad Swiss Alps, a glorious place to die.

A number of members of my close family have died over the last ten years. I don't think we're an unusual family, we've discussed assisted dying, often in the aftermath of a death. My paternal grandparents both died in their nineties in retirement homes, very much reduced from their previous vigorous selves, moving gradually to death. My maternal grandparents both died at home, quite suddenly. My stepfather died at home in a hospital bed, cared for by my mum with the support of nurses. He'd known he was going to die since cancer stopped him eating a couple of months earlier. Mum is the bravest person I know.

The consensus in the family appears to be for assisted dying but I think we all know privately that as the law stands now it will not happen. We will be left to face what lingering or sudden deaths nature serves up to us, in the knowledge that modern medicine has got so much better at keeping us alive but not necessarily living.

This is one of the few places where my atheism collides with the established church: any time the right to die is discussed it appears to be a Christian or one of the Lords Spiritual who is called upon to make the case against: often citing the idea that my life is a gift from God, and that I have no right to dispose of it. Clearly for an atheist this is an argument discarded in a moment.

I may die in an accident tomorrow. I may hang on to the absolute end waiting to see what is over the the next ridge. Or maybe, when I am old and have had enough, I'll want to go at a time and place of my choosing.

How I choose to die is none of your business - I won't presume to choose for you.

Obsession

This is a short story about obsession: with a map, four books and some numbers.

My last blog post was on Ken Alder's book "The Measure of All Things" on the surveying of the meridian across France, through Paris, in order to provide a definition for a new unit of measure, the metre, during the period of the French Revolution. Reading this book I noticed lots of place names being mentioned, and indeed the core of the whole process of surveying is turning up at places and measuring the angles to other places in a process of triangulation.

To me places imply maps, and whilst I was reading I popped a few of the places into Google Maps but this was unsatisfactory to me. Delambre and Mechain, the surveyors of the meridian, had been to many places. I wanted to see where they all were. Ken Alder has gone a little way towards this in providing a map: you can see it on his website but it's an unsatisfying thing: very few of the places are named and you can't zoom into it.

In my investigations for the last blog post, I discovered the full text of the report of the surveying mission, "Base du système métrique décimal", was available online and flicking through it I found a table of all 115 triangles used in determining the meridian. So a plan is formed: enter the names of the stations forming the 115 triangles into a three column spreadsheet; determine the latitude and longitude of each of these stations using the Google Maps API; write these locations out into a KML file which can be viewed in Google Maps or Google Earth.

The problem is that place names are not unique and things have changed in the last 200 years. I have spent hours transcribing the tables and hunting down names of obscure places in rural France, hacking away with Python and loved every minute of it. Cassini's earlier map of France is available online but the navigation is rather clumsy so I didn't use it. Although now I come to writing this I see someone else has made a better job of it.

Beside three entries in the tables of triangles are the words: "Ce triangle est inutile" - "This triangle is useless". Instantly I have a direct bond with Delambre, who wrote those words 200 years ago -  I know that feeling: in my loft is a sequence of about 20 lab books I used through my academic career and I know that besides an (unfortunately large) number of results the word "Bollocks!" is scrawled for very similar reasons.

The scheme with the the Google Maps API is that your program provides a place name "Chester, UK", for example, and the API provides you with the latitude and longitude of the point requested. Sometimes this doesn't work, either because there are several places with the same name or the placename is not in the database.

I did have a genuine Eureka moment: after several hours trying to find missing places on the map I had a bath and whilst there I had an idea: Google Earth supports overlay images on its maps. At the back of the "Base du système métrique décimal" there is a set of images showing where the stations are as a set of simple line diagrams. Surely I could overlay the images from Base onto Google Earth and find the missing stations? I didn't leap straight from the bath, but I did stay up overlaying images onto maps deep into the night. It turns out the diagrams are not at all bad for finding missing stations. This manual fiddling to sort out errant stations is intellectually unsatisfying but some things it's just quicker to do by hand!

You can see the results of my fiddling by loading this KML file into Google Earth, if you're really keen this is a zip file containing the image overlays from "Base du système métrique décimal" - they match up pretty well given they are photocopies of diagrams subject to limitations in the original drawing and distortion by scanning.

What have I learned in this process?

• I've learnt that although it's possible to make dictionaries of dictionaries in Python it is not straightforward to pickle them.
• I've enjoyed exploring the quiet corners of France on Google Maps
• I've had a bit more practice using OneNote, Paint .Net, Python and Google Earth so when the next interesting thing comes along I'll have a head start.
• Handling French accents in Python is a bit beyond my wrangling skills.

You've hopefully learnt something of the immutable mind of a scientist!


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Review of the year: 2010

In a heroic attempt to be timely, I am writing a “Review of the [my blogging] year” post - it’s the first full blogging year for me.

A new feature after my first few months of blogging are book reviews: my house is full of books, and although I’ve read (nearly) all of them I can’t remember the contents. I don’t really consider my book posts to be reviews: they are notes on books for my own future edification. I generally only post on non-fiction although I did write more generally about science fiction. You can see all my reading for the year on Shelfari. The focus of my non-fiction reading is very broadly the history of science, I think my favourite of these was “The World of Gerard Mercator”; this is the story of mapmaking from a time when the full extent of the world was just being discovered. I’ve also read a lot about the Royal Society; this is their 350th anniversary year and, in Britain at least, it was at the heart of the scientific revolution. It’s through the Royal Society that I did my first bit of original source reading: “The History of the Royal Society of London by Thomas Sprat”, published in 1667. A strange experience stimulated by the people I have met on twitter.

Every so often I do a bit of hunting out of data; for example “A sceptical look at the economy” pulled together numbers on the deficit, the debt and how they have changed over time - a useful learning experience and something I refer back to. I also quite like “Occupations of MPs”, which shows that MPs are overwhelmingly barristers. News reports often fail to provide context to stories, and these posts are my attempts to find that context. At one point I even combined fiddling with data and the history of science in one post, extracting membership of the Royal Society data and plotting it: “The Royal Society and the Data Monkey”.

As a continuation of the data monkey thoughts, I did some blogging on computer programming which is my modern equivalent of fiddling about with projects in a shed. “That’s nice, dear” is an overview of programming and some pretty maps I made with election data, the title from my wife: it’s her usual response to me excitedly displaying my latest achievement! I also made “A set of blog posts on SQL” about which I kept very quiet. The hunting out of data and programming run together really, several of my data posts have been the result of significant amounts of programming, for example: “Yields from income tax”.

When I started blogging my intention was to blog about science, in a way that people who were generally not so interested in science might read. I’ve enjoyed doing this, my blog post on the periodic table is one of the most frequently accessed, possibly due to students doing their homework! Some of the scientific posts are on work I’ve done, such as “Understanding mayonnaise”, some are on things I simply find interesting: like “Fun with fluids” which features video of dolphins playing with vortex rings and others are about the life of a scientist, such as: “Publication, publication, publication”.

I’ve also done quite a lot of current affairs blogging, some of this is straightforward rant brought on by newspaper articles but some of it is party political. At the beginning of the year you wouldn’t have known I was a Liberal Democrat party member – I think everyone knows now! Amongst other things I did a post election summary here, and more recently I wrote a slightly more philosophical post. Perhaps most entertaining is my doom-laden post election “I was up for Evan Harris”, my most visited post for the year - I think because of graph, showing the inequities of the first-past-the-post electoral system, was linked from the comments in a Guardian “Comment is Free” article.

Personally the year was slightly eventful: alongside the usual holidays (Westendorf for skiing and the Lake District) I had a little operation after which, somewhat surprisingly, I was confined to the house for 6 weeks in September and October. It was an odd time, ultimately I found I got on quite well confined to the house reading and doing little things in programming disturbed only intermittently by the fear that, health-wise, things weren’t going to plan. I still struggle to understand where my blog lies with regard to personal and private, for a while I kept a diary which was like a blog. My diary was never particularly personal: it recorded facts and where I was when, with the odd diversion into slightly longer entries on books I had read.

Somewhat less common this year for me were photography blog posts, aside from the photos for a calendar, the holiday posts above and a solitary walk post, I don’t seem to have done many this year. Mrs SomeBeans aka The Inelegant Gardener has been much more active on the photography front.

This September we installed photovoltaic(PV) solar panels, to go with the thermal solar panels we got a couple of years ago. PV solar is made economic by the feed-in-tariff, which is exceedingly generous, on our East facing roof we generate approximately the same amount of electricity as we use during the late summer. Now, with the panels covered in snow, we generate nothing. This was also the year of Shiny, my new HTC Desire: not really used as a phone but more a laptop replacement for the home and I also got myself a Kindle ebook.

I’ve enjoyed reading through my blog posts; they provide reminders of my mental activities. I like to maintain the facade that blogging is just for me, but in truth I’m pathetically happy to see the viewing stats rising on a post.

Happy New Year to you all!

A diversion in my life

In the past my blog was my diary, which was entirely private. I kept a diary on my Psion for a number of years before the feeling that I should make a daily, or at least a regular, entry on the minutiae of my life became oppressive and I gave up. More recently I resumed as a blogger, and rather than writing down minutiae I wrote in a more formal, extended style on things that were happening, or on my mind, for a more public audience. It still provided a record of what I thought when.

This post is difficult in the sense that it is somewhat private: I had a minor operation on the 23rd September and only now am I about to go back to work. My minor operation turned out to be a little more complicated then expected. The aftermath has taken up a significant portion of my time and dominated my thoughts for the last 6 weeks. I hasten to add that at no time has my life (or any part of my body) been at serious risk and I have only occasionally been in minor, localised pain and been a little inconvenienced. This is all a storm in a tiny little teacup, but it is my teacup and I have had some sort interesting experience along the way.

I will be circumspect about the exact nature of my affliction. I started with a visit to a GP, who packed me off to the consultant at my local hospital. This is where I had my “unexpected prostate examination”. *That* wasn’t the affected part! A useful experience really, because at some point later in my life a semi-regular prostate exam will probably be a good idea and to be honest, there’s nothing to it. Warning signs: men, if you are semi-clad and a doctor asks you to roll on your side and pull your knees up to your chest – ask him why first!

I have medical insurance as a taxable benefit of my job. My initial intention was to stick with the NHS – my local hospital is over the road from where I live, whilst the private hospital, I believed, was many miles away. It turned out the private hospital was closer, and the wait was shorter and the consultant clearly thought me mad for not exercising my insurance. My initial private consultation was just 4 days after I raised the issue, on a Saturday morning, with potentially my operation the following Thursday. As it was the operation was delayed a few weeks because I had visitors at work on the Friday coming from Sweden – and it seemed wrong to bounce them and then my surgeon was going on holiday, to Sweden, for a couple of weeks. Compare this with initial consultation wait of 1 month, and operation scheduled for almost three months later on the NHS. I don’t see this as a criticism of the NHS: to provide fast service requires that you have more capacity than you strictly need – we choose not to fund the NHS to that level. I’ve been very happy with my local NHS GP service, and the quality of the medical care they provide – I’m sure that the quality of the medical care I would have received from the local hospital would be similarly excellent.

The nice things about private medicine are: it happens pretty quickly (and conveniently), the surroundings are nice and you’re better separated from your fellow man.  The people who join you in private medical care may or may not be more pleasant than those with whom you are treated with in the NHS but they do not generally share a room with you!

I didn’t sleep the night before my operation: I’d never had a general anaesthetic before and to be honest I was a little bit scared – it didn’t help that I’m passingly familiar with historical pre-anaesthesia tales of operations for bladder stones and a mastectomy: I had a minor fear that I would be fully conscious but unable to communicate. I was also scared I wouldn’t have my operation, because to be honest things were getting a bit difficult. My final fear was that I would wake from my anaesthetic with caffeine withdrawal – I’d been fasting for the previous 18 hours or so.

To start the day of my operation properly a wasp stung me on my toe!

General anaesthesia is extinction: there is consciousness, there is nothing, there is consciousness. Chatting to the anaesthetist as I went under I discovered I was getting propofol. I suspect the porters tasked with returning post-operative patients to their rooms have a collection of the most utter gibberish known to man. For my part I supplied them with the prime factors of my room number: 2 and 13, thank you for asking.

The first week or so after my operation passed easily, I’d expected to be off work for a week and I had some books to read. I even made a new website for the Chester Liberal Democrats. The next week or so it sort of dawned on me that the consultants slightly sweaty brow after the operation and the advice that I would take “a long time to heal” did mean something and I was indeed going to take “a long time to heal”. So here I am 6 weeks later during which I’ve largely been confined to the house.

Somewhat surprisingly I’ve done OK: I’ve read a lot, I’ve fiddled around with various computer programs, blogged a bit, shredded many old bills, re-organised things and not watched daytime TV and not even listened to the radio a great deal.

A visit to the consultant at about week 3 was somewhat surprising – I didn’t things were going too well, he thought they were going great! He has always appeared somewhat disdainful of patients, GP’s and a willingness to prescribe antibiotics for imaginary infection. He said mine was one of the more difficult operations of my type that he’d done. I suspect he wanted the medal I claimed for myself on that one.

The doctor (and consultants) views on the solubility of soluble stitches are quaint – their reported view is that they dissolve in 10-14 days. I started off with 20 stitches, six weeks ago. Number of stitches which have disappeared through dissolution: 3; Number that I’ve helped out: 12. Number remaining: 5. The nurse seemed a bit more clued up and said they “took ages”. I suspect the problem is that patients assume that they shouldn’t tell the doctor they’ve been fiddling with their stitches, so the doctor continues in the happy belief that stitches dissolve.

So that’s the story of my last 6 weeks, the funniest thing in all this is something my dad said; unfortunately it makes it pretty much absolutely clear what my operation was, and so I might leave it to an ephemeral tweet.

A piece of land

I am the under-gardener to The Inelegant Gardener, more specifically I am the under-allotmenteer. For those outside the UK, allotments are standard sized vegetable gardens enshrined in UK law. We took possession of our first half allotment plot on 1st October 2006.  I remember our visit to the colony to see the allotment; we’d taken our traditional Saturday morning wander around town when The Inelegant Gardener mentioned, apparently in passing, that she’d like to look at an allotment (or rather a half-plot). I was instantly wary of this idea, I remember watering and weeding on my dad’s allotment as a child, back breaking and boring work. But when I stood at the foot of the overgrown plot I was instantly converted. A strange feeling came over me, of land, food, honest toil and soil – it was like my own Soviet propaganda film. Here I could work the land and provide!

The half-plot on possession, October 2006

But more was to come: walking back to the car some months later, after working on the half allotment, I pointed and laughed at the risible start someone had made on digging a neighbouring whole plot. A sheepish Inelegant Gardener admitted to being the owner of the risible start and a new whole plot. It turns out she was an aggressive territorial expansionist, albeit a pathetic digger. The Inelegant Gardener did her best “feeble female” look, and I agreed to dig the new allotment. A task I was to complete some 18 months later, almost exactly two years ago.

A risible start to the digging of the whole plot, April 2007

As under-gardener my principle tasks are digging and construction: sheds, paths, compost bins and the like. It’s rather satisfying work compared to my day job, which mostly concerns generating abstractions inside a computer. Allotment work produces tangible output: an hours digging produces a patch of turned soil and a bucket of roots. Construction produces sturdy, useful structures of which a man can be proud. As a result of this toil I am able to identify perennial weeds purely from their roots: dock, bindweed, nettles, couch grass, horsetails, ground elder. I sometimes worry that The Inelegant Gardener will pimp me out to other allotmenteers for digging work.

The Inelegant Gardener is still subject to unrealistic fancies, having directed me to spread about a ton of farmyard manure on the potato-patch-to-be she seemed to believe the worms would quickly incorporate it into the soil. Bollocks would they, not in two weeks, not without the aid of little squad of wormy JCBs! It was muggins wot' dug in the manure. I still think potatoes are magic though, turning over the soil with a fork and white egg-shaped edible things appearing – it’s magic. More realistically the potatoes came out all manner of shapes and sizes, several years they suffered from blight.

For us allotmenteering is a bit of fun, if a crop fails it doesn’t matter. Seeing the blight-wilted potato-tops and unearthing the rotten, stinking tubers gives an insight into what it is to rely so closely on the vagaries of nature for your livelihood. Seasonality becomes much more obvious; despite being relatively clued up about agriculture in truth I had little sense of when what vegetables were in season. Now I know, and it’s cabbage for most of the winter. Currently in season are courgettes (bloody hundreds of them), carrots, sweetcorn, potatoes, mangetoute, French beans, raspberries, beetroot. It’s fair to say we haven’t entirely cracked planting appropriate quantities, to start with we had one or two exemplars of any particular vegetable per meal, now we have massive, short-lived gluts.

We achieved a crop on our second visit to the allotment or rather Henry, a fellow allotmenteer, gave us some produce to keep us interested. He has continued to provide advice ever since, but now we swap vegetables and fruit. When we started only a small fraction of the plots on our colony were in cultivation, and Henry seemed to be keeping the place alive. These days most of the site is cultivated, it’s a friendly sort of place – most people will stop to say a few words as they pass on their way to their own plots. I can do a passable impression of a someone who knows how to grown stuff, if interrogated.

Our other neighbour at the allotments keeps chickens, at one point they had free range across the whole site they would come and supervise digging, jumping into the trench at inopportune moments to pluck out a tasty grub. Nowadays they are behind chicken wire, but still come to the fence if you’re digging or weeding by them, making approving clucking noises. There is something very reassuring about this companionship.

These days the allotment is looking almost ship-shape, at least it does when we’ve caught up with all the weeds. I continue to be proud of my construction efforts.

New paths! June 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)

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.

On being a fellow of Pembroke college

For a period in my life I knew that if I ever ended up in the news the item would have started "Cambridge don, Dr Ian Hopkinson..." because I was a fellow of Pembroke College, Cambridge.

Oxford and Cambridge universities in the UK, are structured somewhat differently from other universities. In addition to the normal university departments that you would find in any university there are the colleges. The colleges have their own independent, and in many cases, very long existence. They are responsible for the housing and pastoral care of students (and academics), as well as teaching involving small groups. In some subjects they employ full-time lecturers but this is not generally the case in the natural sciences. Each college has a mixture of fellows and students from all subjects, in some ways the parallel is with members of a club. Other universities have apparent equivalents in their Halls of Residence and 'colleges' although these things are actually quite different in character.

Clearly Pembroke is the best of the colleges by any rational evaluation! Whilst I was in Cambridge it celebrated its 650th anniversary, although little if any of the original physical structure remains. The college features a chapel designed by Christopher Wren, behind some panels in one of the parlours are the scribblings and sketches by the workmen involved in the building. The ceiling of the Old Library is a fabulous, intricate 17th century plaster construction, I spent many long college meetings admiring it. Alfred Waterhouse was involved in some substantial re-building of the college in the late 19th century demolishing, with dynamite, the pre-existing medieval main hall in the process.

The list of alumni is rich with comedians (Peter Cook, Tim Brooke-Taylor, Eric Idle, Bill Oddie) and writers (Clive James, Ted Hughes), a little light on scientists although it does feature George Gabriel Stokes, Ray Dolby (inventor of the Dolby noise-reduction system) and John Sulston (Nobel Prize winner). Historically, there's William Pitt the Younger, and Nicholas Ridley (martyred by the old enemy in Oxford). The wiki page gives a summary of the history, and an extended list of alumni.

Pembroke college was somewhat different from anything I had experienced previously and it introduced me to a whole range of social gaffes. From my initial purchase of my MA gown, where I hastily thrust my arms down the sown-up sleeves rather than out through the exit slits; to confusing the Master of Pembroke, Sir Roger Tomkys, former High Commissioner to Kenya with my pointless statement that I had bought my cutlery from Argos (he thought I meant the Greek island); to turning up one summer evening in very crumpled linen for dinner only to discover that it was a celebratory meal for the Drapers' Company and I was under-dressed by at least an order of magnitude. Fortunately, as a fellow, I was allowed to walk on the grass, the public aren't. There are no signs to this effect, because senior fellows thought they looked untidy.

As a fellow I received little in the way of cash, I was employed by the university as an Assistant Director of Research* and paid by the college to do a few hours small group teaching each week. Pembroke mainly paid me in food, drink and company. A fairly elderly medieval scholar was the college wine buyer and did an excellent job. Dinners were particularly fine after college meetings, starting in the parlour, for pre-dinner drinks, five courses with a different wine with each course after which we returned to the parlour for port and so forth, Bath Oliver biscuits (Oliver was a former fellow) and fruit eaten with silver knives and forks.  Most junior fellows seconded to serve in the parlour.  For a long period I never drank port that was younger than I was and I got a taste for Sauternes which I can no longer support. Mrs SomeBeans has never forgiven them for the goat's cheese profiteroles.

As part of my job as fellow I was engaged in admissions interviews: one nervous fellow (me) interviewed fifteen nervous potential students for the Natural Sciences course. I remember having wet feet for most the morning, since I'd cycled in to college in a downpour. All but a couple of the students were predicted at least four A grades at A level, ultimately we were to take one or possibly two of the group I interviewed.

The colleges go to some length to make the admission system fair in relation to the background of the student, but to be honest the problem starts well before application. A vignette: my flatmate at Bristol University went to Harrow he was one of very few in his year *not* to apply to Oxford or Cambridge (Oxbridge), to the displeasure of the masters. I, from my respectable state comprehensive, was one of a handful to apply to Oxbridge. For my school, entry to Oxbridge was not a key performance indicator, it didn't really have the knowledge or background to support applicants.

In a way the debate on access to Oxbridge misses the point: it takes outstanding students, has excellent resources in terms of cash and people and it produces excellent output. What can you learn from this setup? As a measure of pre-university performance it's not great, we depend on written record and a few brief interviews. A real challenge would have been to take average students and see what we could do with them.

The best thing about college was my fellow fellows: they were bright, passionate about their work, always keen to talk about it. We met for lunch: classicists, modern linguists, historians, computer scientists, chemists, physicists, biologists, naturalists, engineers, English scholars talking about our work, the world and the etymology of the swearing of the American students over for summer schools. And in the usual college way we could wine and dine in our departmental colleagues colleges where the circle widened. It's an oddity of most modern universities that the scope for meeting colleagues from different departments is actually rather limited. The college system in Cambridge satisfies that need in some style.

Footnotes
Top image from Wikipedia: http://en.wikipedia.org/wiki/File:Pembroke_College_Cambridge.JPG
*The Assistant Director of Research is no where near as grand as it sounds, it is a position that lies between postdoctoral research assistant and lecturer and is filled in Cambridge by people who will be unrequited in their desire for a permanent position.

What kind of scientist am I? (audio version)

My earlier "What kind of scientist am I?" post is now available as a podcast: http://bit.ly/6EA17H - Posterous allows the easy posting of audio. I'm not sure I'll do it again but it was fun to try. I used a basic Logitech headset microphone, Audacity to do the capture and editing with the Lame plugin for MP3 export.

What kind of scientist am I?

Following on from my earlier blog post on the tree of life, this post is about the taxonomy of my area of science: physics. I should point out now that I'm not too keen on the division science in this way. These divisions are relatively recent, as an example: the Cavendish Laboratory, the department of physics at Cambridge University, was only founded in 1874.

I am an experimental soft-matter physicist.

So taking the first word: experimental. This is one of the three great kingdoms of physics, the others being  computer simulation and the theory. "Experimental" means I spend a large part of my time trying to do actually experiments on objects in the real world, this may involve substantial computational work to process the output data and should generally involve some comparison to theory when published, although serious development of theory tends to end up in the hands of specialists. Computer simulation is distinct from from theory: simulation is like doing an experiment in a computer - give a set of entities some rules to live by and set them at it, measure results after some time. Theory on the other hand attempts to model the measurements without the fuss of explicitly modelling each entity in the collection.

Next to the physicist bit: In a sense theory is the essence of what physics is about: building an accurate model of the world. The important thing with physics is abstraction, to take an example I'm interested in granular materials; from a physics point of view this means I'm looking for a model that covers piles of ball bearings, avalanches, sand dunes, grain in silos, cereals in a box and possibly even mayonnaise all in a single framework.

And so to the final division: soft-matter. Physical Review Letters, which is the global house journal for physics, has the following subdivisions (in italics):

• General Physics: Statistical and Quantum Mechanics, Quantum Information, etc; Domain of Schrödingers cat, Alice and Bob exchanging secure messages, and Bose-Einstein condensates.
• Gravitation and Astrophysics; Physicists go large. Stephen Hawking lives here - black holes, the big bang.
• Elementary Particles and Fields; down to the bottom, with things very small studied by things very large (like the Large Hadron Collider at CERN). Here be Prof Brian Cox.
• Nuclear Physics; The properties of the atomic nucleus, including radioactivity, fission and fusion. This is Jim Al-Khalili's field. 
• Atomic, Molecular, and Optical Physics; Stuff where single atoms and molecules are important, things like spectroscopy, fluorescence and luminescence go here.
• Nonlinear Dynamics, Fluid Dynamics, Classical Optics, etc; Pendulums attached to pendulums, splashes and invisibility cloaks!
• Plasma and Beam Physics; Matter in extreme conditions of temperature: fusion power goes here.
• Condensed Matter: Structure, etc; Condensed matter is stuff which isn't a gas - i.e. liquids and solids, and is acting in a reasonable size lump. 
• Condensed Matter: Electronic Properties, etc; This is where your semiconductors, from which computer chips are made, live. 
• Soft Matter, Biological, and Interdisciplinary Physics; Soft-matter refers to various squishy things, plastics, big stringy molecules in solution (polymers), little particles (colloids, like emulsion paint or mayonnaise), liquid crystals, and also granular materials (gravel, grain, sand and so forth).

So there I am in the last division, studying squishy things.

Since I've provided a means to wind up most sorts of scientist in previous blog posts, I thought I could provide a few here for me. Theoreticians can wind me up by assuming that experiments, and the analysis of the resulting data, are trivially easy to do and if they don't fit their theory then I need to try again. Simulators I have a bit more sympathy with, simulations are experiments on a computer, however when you're writing a paper perhaps you should say in the title you ran a simulation, rather than did a  proper experiment like a real man ;-)

Update: I made this post into a podcast: http://bit.ly/6EA17H - it's on Posterous because uploading of audio is easier. I used a basic Logitech headset microphone, Audacity to do the capture and editing with the Lame plugin for MP3 export.  I'm not sure I'll do it again but it was fun to try!

Confocal microscopy

Back to stuff I should know, in theory, at least.

I had my first microscope as a child, it was a small one but I had a great time looking at little creatures that lived in dirty pond-water. I remember spending a long afternoon trying to see transparent single celled animals, and finally getting the lighting just right to see an amoeba. I also remember trying to immobilise a tiny worm with white spirit - it exploded, but I like to think it died happy.

This week I shall mostly be talking about 'confocal microscopy', this is a type of light microscopy (as opposed to electron, infra-red, x-ray, scanning tunnelling, or atomic force microscopy). The smallest thing you can see with a light microscopy is about 1 micron across, that's a thousandth of a millimetre - a human hair is about 80 micron in diameter. A normal light microscope gives you a nice focused picture of a slice of you sample at the "focal plane", but it also lets in loads of light from parts of your sample away from the focal plane which leaves you, overall, with a bit of a blurry picture. Microscopists get around this problem by slicing their samples up very thinly hence no bits to be blurry, but this is a fiddly procedure and leaves your sample very dead even if it started alive.

Confocal microscopy is a technique by which the slicing of the sample happens virtually, you can put a big fat sample in the microscope and by the use of cunning optics you only get an image from the focal plane which is lovely and sharp. You can build up a 3D picture of the sample by moving it up and down in front of the lens. Marvin Minsky was the original inventor of the confocal microscope in about 1955 but was somewhat held back by the lack of lasers, computers and stuff. Things picked up again in the 1980's as these things became readily available. Oops, I think that might have been some cod history ;-)

An interesting feature of the confocal microscope is that if there's nothing in the focal plane, you don't see anything (unlike a conventional light microscope where you can always see a big bright something, even if it's blurry) this can be disconcerting for the learner - you can't find your sample!

Every microscopy needs a contrast mechanism, a way of separating one thing from another. In confocal microscopy by far the most popular contrast mechanism is to use fluorescence via the use of a fluorescent dye to label bits of your sample.  If you illuminate a fluorescent dye with light of one colour it emits light of another colour (making it stand out particularly well). If you ask an organism nicely (okay - genetically engineer), you can get it to make Green Fluorescent Protein (GFP) which is a protein that fluoresces green (duh!).  All that remains is to find a way of  sticking the fluorescent dye to the thing in which you're interested.

In each post about science I like to add a little fact to help you wind up / avoid winding up practitioners in that field. So to wind up a microscopist: project an image onto a screen for a presentation and claim "x800" magnification (or whatever). The problem is: to what does "x800" magnification apply? Is it what the microscope told you when you looked through the eyepiece? Is it the magnification on the printed page, the computer screen or on the wall? We really doubt you know. It's scale bars all the way.

For several years I was proud keeper of a confocal microscope. I, and my students, had great fun with the microscope and it had fun with us. The pointy end of the microscope is the objective lens, the bit closest to the sample. A fancy microscope like our Zeiss LSM 510 had 5 or more objectives mounted on a turret (see the image at the top of the post), each objective gives different magnification. The Zeiss LSM 510 was fully motorised, and too clever by half. It would assume that you wanted to stay focused on the same part of the sample when you changed objectives (or it changed them for you, with it's motors). Now the problem is that for a x10 objective the focal plane is about 1cm from the front of the objective lens, and for a x40 objective lens it could be only a tenth of a millimetre. Now imagine I've just focused deeply inside my sample using an x10 objective, I switch to the x40 object on the computer..... and the microscope mashes the x40 objective lens into the sample, blithely ignoring the sound of £6000 lens smashing glass coverslip and covering it in sticky sample!

In later posts I'll show some of the results from the confocal microscope in non-mashy-lens-into-sample mode.

Here are some images, these are all slices through solid objects. I didn't really think this through in terms of explaining what's in these first three images, roughly they're what you get if you add a small amount of salt-water to Fairy liquid (although I would prefer you to use Persil washing up liquid). First up is a cross-section through an "onion-type micelle":

And these are the structures you see in a similar system but with a different concentration of water:

This is a false colour image, bit lurid - don't know what I was thinking at the time. These are known as "myelin":

Pollen-grains are always popular - I stole this one from here. Each of the images is a slice, and the inset bottom right is the result of adding all the slices together.

Who Dr.?

After the big and shiny experience as an undergraduate I went off to do a PhD., to make me into a Dr. This was something I'd intended to do since a visit to the Campden and Chorleywood Food Research Centre as a school student; there we were shown around the labs and I was convinced that a career in science without a PhD. was going to be a serious uphill struggle involving the cleaning of much lab glassware.

The exact nature of a PhD. varies from country to country and from subject to subject. In the UK a PhD. in physical chemistry is typically 3 years long and the supervisor will usually have a big say in what the student does.

I did my PhD. at Durham University in the Interdisciplinary Research Centre for Polymer Science, supervised by Prof. Randal Richards. Prime motivation for this particular PhD. was the cash, it was funded by Courtaulds Plc and paid a research assistant salary. It also got me back to more big and shiny science, in the form of the neutron source at the Rutherford-Appleton Laboratory  (RAL) and with the added benefit that a very skilled technician made my polymers for me. This was good because I've never been "at one" with synthetic chemistry, the untidiness of the process didn't suit my temperament. Apocryphally the start of polymer science was a bit slow because the early polymer synthesisers couldn't crystallise their material, this led to much derision from other synthetic chemists who made lovely crystals from their materials, rather than black sludge that polymer scientists made. The molecular nature of polymers wasn't appreciated until the 1920's which is really rather recent.

So for 3 years I slaved away: I prepared samples - spinning thin films onto lumps of shiny flat silicon, I went down to the RAL for 48 hour experimental runs, I wrote FORTRAN programs do do data analysis, I read journal articles, I attended conferences, made posters and gave presentations. I observed, from a small distance, the activities of synthetic chemists.

The chap over the desk from me was a historical re-enacter, I watched as he made his own chain-mail.

It was whilst I was writing my thesis, entitled "Surface composition profiles in some polymer mixtures", that I first met with the elephant of despair. The elephant of despair lived in the library, he was made of a transparent material so you could scarcely see him and he was only about 6 inches tall. He stood in the gaps between the journals, waiting for when I would arrive to find an article and discover on the way a paper published 10 years ago which captured most of what I'd slaved over for the last three years. His plaintive trumpeting has haunted me on and off through the years.

I think the day I decided I wasn't going to make an effort to get "Dr." onto all my paperwork was the day I was in the bank the man in front of me was having a lengthy discussion with the cashier because the printed numbers in his saving book did not line up with the ruled lines. After he'd left the cashier turned to her colleague and said: "He had to complain, he was a doctor". As it stands the only people who call me "Dr Hopkinson" are my parents, one of my credit cards and the odd polite student.

For reasons I don't understand medical doctors appear to refer to PhD's as "proper doctors", whilst I've always considered myself a bit of fraud since I was not a "proper doctor" - who could potentially save your life. Perhaps they're just being polite.

And now I'm nearly a PhD. grandfather, I supervised three PhD. students of my own and one of these has a student who is about to do her viva. I don't have children, but I feel very 'parental' about my students - I'm immensely proud of them and their achievements.

Talkin' about my generation

My generation have all been wallowing in nostalgia at the Electronic Revolution strand on BBC4, in particular Electric Dreams - the 80's and Micro Men - the story of Sinclair and Acorn computers. We grew up in a golden age for programming, the generation before us had no hardware and the generation after us had no need to write their own software. We programmed because we had to.

I had a Commodore VIC20, cheaper than the BBC Micro, more classy and substantial looking than the Sinclair ZX81, available slightly before the ZX Spectrum. All of these lovely old machines available for your viewing pleasure at Centre for Computing History, along with many others. Look around the internet and you can also find all manner of emulators and manuals for these early machines. We wrote our own programs, or we typed in games from magazines - this was often a rather lengthy process and a bit prone to error.

I found the "VIC20 Programmers Reference Guide" here re-typed by Asbjorn Djupdal. Here's snippet: a program which allows you to enter the scores in each quarter for an American football game and then prints them out on screen in a table:

100 DIM S(1,5), T$(1)
110 INPUT "TEAM NAMES";T$(0),T$(1)
120 FOR Q = 1 TO 5
130 FOR T = 0 TO 1
140 PRINT T$(T),"SCORE IN QUARTER" Q
150 INPUT S(T,Q)
160 S(T,Q) = S(T,0) + S(T,Q)
170 NEXT T,Q
180 PRINT CHR$(147) "SCOREBOARD"
190 PRINT "QUARTER";
200 FOR Q = 1 TO 5
210 PRINT TAB(Q*2 + 9)Q;
220 NEXT
230 PRINT TAB(15)"TOTAL"
240 FOR T = 0 TO 1
250 PRINT T$(T)
260 FOR Q = 1 TO 5
270 PRINT TAB(Q*2 + 9) S(T,Q);
280 NEXT
290 PRINT TAB(15) S(T,0)
300 NEXT

Oh, this brings back memories!

To me programming and science (or at least physics) are intimately linked, almost the first programming I ever did was to visualise beat frequencies. To this day, if I want to really understand a scientific paper I'll implement the equations in a program, as often as not a few typos in the equations are revealed in this way and I'll have learnt exactly what the paper was on about. Teaching a student is a fantastic why to learn something, teaching a computer is almost as good.

Most the programming I do is of a workmanlike nature, it drives machines for measurements; it processes data; it analyses results; it computes equations, but there is scope in programming for a deep elegance, a pared down beauty which is difficult to describe - it's like finding the answer to a cryptic crossword clue - perhaps for an artist it's like finding just the right line to give a character personality. It's an algorithm that does what it has to do with the least effort required. I still program a lot for my work (relatively small stuff that only I will use), and it's not unknown for me to waste an hour doing something elegantly rather use the quick, dirty and obvious approach.

Programming is in my genes, in two ways really - my parents were both programmers from the sixties. We once found a leaflet advertising the Elliot 503 in our loft, 400sq ft of '60s computer with substantially less processor power than the most lowly of today's devices - this is the computer on which my mum learnt to program. Dad started on an early Ferranti of some description in the late 50's.

Earlier programming for me pretty much amounted to shouting verbs at things, possibly because I used FORTRAN which at the time was ALL IN CAPITALS. Programming today feels very different, it's more like visiting a library to get a book of spells to cast or the singing of a choir. I still enjoy doing it, in fact I'm writing a twitter client in C# just so see how to do it.

You might get the impression from all of this that programming is for the mathematically minded, but it isn't - it's really for the logically minded, for some mathematical applications maths is required but otherwise it isn't.

I taught the basics of programming to first year physics students a few years ago, and the thing that really shocked me was that, out of a class of fifty, only one had any real programming experience. There is hope though, I suspect programming still holds a fascination - my single data point: father and son sitting down to program the BBC Micro on Electric Dreams.

An introduction to the big and shiny

So off to university I skipped, with paternal instructions to "blossom". I did BSc Chemical Physics at Bristol University. This is a fine course for the indecisive, such as myself who couldn't decide whether they were chemists or physicists. There were only 16 students in my year, we could all fit in one lift in the physics building. The chemical physics degree involves most of the first year chemistry and physics courses, but in later years you drop organic chemistry, particle physics and astrophysics to make space to do courses in the rest of chemistry and physics. This training means I'm less bemused by molecules than the majority of physicists.

It was at Bristol that I was introduced to big, shiny machines for doing science: for my final year project I worked on Extended X-ray Absorption Fine Structure (EXAFS) at the Daresbury Synchrotron Radiation Source (SRS).

I was using EXAFS to discover something about the structure of molecules in solution, and the arrangement of a glass around metal ions. This is typical of the sorts of study done at synchrotron sources: finding exactly where the atoms in a particular material. Where the atoms are helps you understand the properties of the material: what reactions does it catalyse, how well does it conduct, how strong is it, and so on.

The synchrotron radiation source is a device for producing huge quantities of light all the way across the spectrum from x-rays to ultra-violet light, passing through the visible spectrum on the way. To do this you make electrons go round and round in circles really fast inside an evacuated tube, as they go around they emit electromagnetic radiation: here's a practical application of relativity - the electrons are traveling at a substantial fraction of the speed of light, so to calculate (and control) their behaviour you need to include relativistic effects. X-rays are actually emitted when the electrons pass through the intriguingly labelled wigglers and undulators - sets of cunningly arranged magnets around the evacuated tube.

The SRS was a pretty big machine - 30 metres in diameter, it closed at the end of 2008 to be replaced by Diamond which is substantially larger. You can see SRS, along with Diamond (near Harwell) and the ESRF in Grenoble, which is even bigger still, on this Google Map. The ring shape of SRS is just about apparent, Diamond and ESRF are very obviously rings.

I've worked in several big science facilities (all of them either neutron or synchrotron sources), they have  some common features. Separate instruments cluster around either a ring shaped source or a central point - a beam line (usually an evacuated metal tube) runs from the source to your experiment. The instruments have been built for different consortia by a small team and then used by scientists from around the world. The instruments are scattered around warehouse-sized sheds, filled with a wide range of machinery (which generally contribute to rather high background noise). The control stations for each instrument may be in portacabins, or small corrals. For neutron and x-ray facilities there are a lot of really big concrete blocks around to block harmful radiation.

The deal with working on these instruments is that they run 24 hours a day, and you apply for time on them. If your application is successful then you get to use the apparatus for a block of time, typically a couple of days or so. Some users are lucky: their experiments take days or hours to run, so they can pop off to the pub between runs. I've always been stuck doing experiments which last 20-30 minutes per shot. Normally you try to get a team of three or four people to work in shifts, through the night you survive on machine coffee, cantankerous vending machines and possibly loud music. You try to do data analysis as you go, to make sure nothing is going wrong and to help pick which samples to run next. These are one-off research machines, so the data analysis process may be a bit convoluted, and not very user-friendly.

It turns out I have some pictures from my visits to Daresbury (as part of my small obsessive streak I digitized my old photo collection a few years ago)

This is me looking really very boyish at the control station for the EXAFS machine, that's the back of Sue's head. Sue was a PhD student working in the same lab as me.

I'm pretty sure this is the EXAFS station I worked on, John is pointing at a polysytrene vessel containing liquid nitrogen (not quite sure why). John was another member of the research group.

This isn't the equipment I was using but see how shiny it is, how many bolts hold it together and how many unexplained protruberances it has. Who can but fall in love with such things?

All in all it was a rather exciting introduction to the world of research science. My rather small contribution to the measurement of cobalt ions in glasses (which were subtle shades of blue and pink) led to my first paper[1] in the scientific literature!

Reference

1. Harrison, C.C., X.C. Li, I. Hopkinson, S.E. Stratford, and A.G. Orpen, Ultraviolet-Visible-Near-Infrared and EXAFS Study of Co-Ii Coordination Chemistry in Post-Doped Silica Sol-Gel Glasses. Journal of the Chemical Society-Faraday Transactions, 1993. 89(22): p. 4115-4122.

57 varieties

At the end of the last post I said it wasn't important what sort of scientist I was. This isn't entirely true, once you leave school you have to make a fairly definite decision as to what you will study at university. In fact, in the UK, you narrow down your options quite significantly at the age of 16, when you chose which A-levels to do.

This is a rather timely post since across the country thousands of students will be exchanging information on A-levels as they start at university, and it's a pretty safe topic of conversation.

For my A-levels I did chemistry, physics and a double helping of maths. To be honest it's a very long time ago that I decided to follow this path, so some of the thinking behind this choice has left me. I like playing with numbers (and computers) which explains the maths. Chemistry was just fun: involving fire, fumes, pretty colours, fragrant solvents and other cool stuff - okay cooking peas in different salt solutions and processing cabbage to measure vitamin levels and the thing with the liver and the apple were a bit unpleasant but at least gripping - I can remember them 20 years later. I don't remember greatly enjoying physics at school, but it seemed to have great potential (astronomy, Einstein, gadegts and so forth). I really wish I'd done biology as well, I think I was put off by the "naming of parts" and the fact that most of the specimens for dissection had gone off a bit.

Of course as time passes the broad division of science into three areas (physics, chemistry, biology) seems awfully crude and as I progressed through academia I seemed to end up in ever smaller silos - hence the 57 varieties. Back in the good old days scientists ranged freely over vast areas, nowadays it feels like we struggle to find an ever smaller niche to call our own. I don't really want to be master of one tiny corner, I want to be a welcome visitor all over town.

The Scientist

So I announced my scientist-ness in my profile to the right. Why did I do that?

It's the tribe I belong to, the people I feel kinship with across the world, the badge I'm proud to wear, it's the single word that says the most about me.

I'm told my first words were "oooo...look!", this to my mind is the first half of the mindset of a scientist. Mark Carwardine has just illustrated this nicely on the rather wonderful TV programme "Last Chance to See", they're on Madagascar. He's wandering around crying out "oooo....look", pointing things out to Stephen Fry: a leaf-tailed gecko, a pygmy chameleon, sifaka... Okay, so he is varying his vocabulary a bit, but that's the gist.

"Why?" is the other half of the mindset. In the case of Madagascar, it's that way (rich in unique wildlife) because it split from the rest of Africa long ago. And in the glorious recursive way of it all those few words "...it split from the rest of Africa long ago" lead into another story of how the continents we stand on are gliding across the world (albeit very slowly).

To me it doesn't really matter the type of scientist, it's an artificial division. "oooo...look" and "why?" are the important things. Perhaps everyone thinks this way, but some of us have just had the fortune to get paid for it.

Ritual purposes

But why blog? The obvious answer is that everyone else is doing it, so why shouldn't I? There's a dynastic element to the exercise as well: it's important that my thoughts should live beyond my head ;-) A fact brought home to me as I cycled along the busy A41, amongst the juggernauts.

In years to come perhaps a 24th century version of Time Team will be rummaging through the lower strata of the internet and find this blog. Tony Robinson will ask Mick Aston: "What was it for?". Mick will reply "There were an awful lot of these written at this time, we believe they were for ritual purposes". "They don't serve any useful purpose then?".

Tony Robinson also plays a part in the naming of this blog. When I first went online socially, some years ago, it seemed common to have a nickname rather than using a real name. After much head-scratching I came up with "SomeBeans" as my favoured nickname. The origins lie in a Blackadder sketch in which Blackadder attempts to teach Baldrick the intracies of "Adding". At the time I was a lecturer and the link to teaching seemed appropriate.