Tag: autobiography

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 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 13 2010

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.

Dec 29 2009

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.

Dec 23 2009

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!