Apr 20 2010

Book review: Joseph Banks by Patrick O’Brian

Once again I venture into my own idiosyncratic version of the book review: more reading notes than review. This time I’m reading the biography of Joseph Banks by Patrick O’Brian. Joseph Banks has popped up regularly in my recent reading about the Royal Society and the Age of Wonder. He was on Captain Cooks trip to Tahiti, and then went on to serve as President of the Royal Society for 42 years – the longest term of any President. The Inelegant Gardener has been reading about Kew and various plant hunters, and Sir Joseph crops up there too. Despite his many talents, there are relatively few biographies of Banks, and he is relatively unknown.

Sir Joseph was born of a wealthy family from Lincolnshire, he was educated at Harrow, Eton and then Oxford University. At some point in his school years he became passionately interested in botany, and whilst at Oxford he went to the lengths of recruiting a botany lecturer from Cambridge University to teach him. The lecturer was Daniel Solander, a very talented student of Carl Linnaeus, who would later accompany Banks on his trip around the world with Captain Cook, they would remain close friends until Solanders death in 1782.

Sir Joseph’s first trip abroad was to Newfoundland and Labrador in 1766. The area had been ceded to Britain by France, but there was an international fleet of fishing boats operating in it’s waters. Banks made his trip as a guest Constantine John Phipps on HMS Niger, which was sent to the area to keep an eye on things. It seems fairly common for gentleman to travel as guests on navy ships of the time: this was broadly the scheme by which Charles Darwin would later join HMS Beagle on his trip around the world.

1768-1771 finds Banks circumnavigating the world on Captain James Cook’s ship, HMS Endeavour, in Cook’s first such expedition. This voyage was funded by George III following an appeal from the Royal Society for a mission to Tahiti in order to observe the transit of Venus. Banks paid for the contingent of naturalists from his own funds. The stay in Tahiti is much written about largely, I suspect, because they remained there some time. Following their stay in Tahiti, they continued on to New Zealand, which they sailed around rather thoroughly but seemed to land on infrequently as a result of hostile responses from the inhabitants. They then sailed along the East coast of Australia, stopping off on the way at various locations but most particularly Botany Bay. At the time the the existence of Australia was somewhat uncertain in European minds. There’s a rather fine map of their course here and Banks’ journals are available here.

Through the chapters on both these voyages, O’Brian makes heavy use of the diaries of Banks, quoting from them extensively and often between block quotes further quoting Banks’ own words. This may work well for those of a more historical bent, but I felt the need for more interpretation and context. It often feels that O’Brian is more interested in the boats than the botany.

The next episode is somewhat odd: Banks was planning a second trip around the world with Captain Cook but he never went. At almost the last minute he withdrew on the grounds that the Admiralty would not provide adequate accommodation for him and his team scientists. The odd thing is that, despite what appears a fractious falling out, Banks appeared to remain very good friends with both Cook and Lord Sandwich, First Lord of the Admirality at the time. I wonder whether Banks, remembering the 50% mortality rate of his previous voyage with Cook, understandably got cold feet. As a consolation he went off to Iceland in 1772 for a little light botanising, where he scaled Hekla.

Despite recording an extensive journal, collecting a considerable number of anthropological, botanical and zoological specimens as well as a large number of drawings by his naturalist team Banks never published a full report of his Tahiti voyage. He showed the artefacts at his home in Soho Square and prepared a substantial manuscript, with many fine plates but seems to have lost interest in publishing close to the end of the exercise. Throughout his life he produced relatively few publications, this may be a reflection of his dilettante nature: he was skilled in many areas but not deeply expert and so published relatively little.

Banks was elected to the Royal Society whilst on his world tour, and later become President for a 42 year term, until his death in 1820. He made some effort to improve the election procedures of the Society, at the time of his election being in the right social class appeared to be more important than being a scientist. As part of his role as President he was heavily involved in providing advice to government including a proposal to use Australia as a colony for convicts. He was also heavily involved in arranging the return of scientists and others caught up in the wars following the French revolution. In addition to his work at the Royal Society, he also helped found the Africa Association and the Royal Academy.

Kew gardens was created a few years before Joseph Banks became it’s unofficial superintendent (in around 1773) and then director. He had a pivotal role in building the collection: commissioning plant collectors to travel the world, all backed by George III. I must admit that my recent reading has led me to see George III in a new light: as an enthusiastic supporter of scientific enterprises, rather than a mad-man. George III and Banks also collaborated on a programme to introduce merino sheep from Spain, which had potentially huge commercial implications. Banks was seen as a loyal courtier.

Through his life it’s estimated that Banks wrote an average of 50 letters per week almost entirely in his own hand, although they were fantastically well organised during his life, on his death they were rather poorly treated and dispersed. Warren R. Dawson produced a calendar of the remaining correspondence. I’ve not found this resource online but a treatment like this Republic of Letters would be fantastic.

I suspect a comprehensive biography of Joseph Banks is exceedingly difficult to write; this one seemed to cover voyaging well but I felt was lacking in botany and his scientific activities at the Royal Society. Perhaps the answer is that a comprehensive biography is impossible, since he had interests and substantial impacts in so many areas. There was simply no end to his talents!

Footnote
In the style of a school project I have made a Google Map with some key locations in Joseph Banks’ life.

Apr 17 2010

Lasers go oooooommmmmmm

In a previous post I mentioned, in passing, surface quasi-elastic light scattering (SQELS). SQELS is a fancy way of measuring the surface tension of a liquid using light, it has some advantages over the alternative method: sticking something into the surface of the liquid and measuring the pull but it is technically challenging to do.

The basic idea of SQELS is this: if you take a liquid surface, even in the absence of breezes or shakes, it is perturbed by tiny waves the properties of which tell you about the surface properties of the liquid. These waves have frequencies of 10kHz, wavelengths of 0.1mm and amplitudes of only a few angstroms. They are driven by the thermal motion that means everything, on a small enough scale, is jiggling away incessantly. To measure these waves laser light is shone on the surface, most of the light is scattered elastically that’s to say it stays exactly the same colour. However, some of the light is scattered inelastically (or quasi-elastically since the effect is small) – it changes colour slightly, the power spectrum of the surface waves is imprinted onto the laser light in terms of shifts in its colour. So all we need to do is measure the power spectrum of the light reflected from the surface to find out about the surface properties of the liquid.

It turns out I don’t have any photos of the SQELS apparatus in all its glory, so I shall describe it in words. The whole thing is found on an 8 foot by 4 foot by 1 foot thick optical table. A fine, very solid table whose top surface is a sheet of brushed steel, pierced by a grid of threaded holes 25mm apart. The apparatus is in the form of a large U covering two long sides and one short side of the table. A laser is bolted at the start of the U; light heads from the laser along the table through a set of lenses, polarisers, a diffraction grating, then upwards through a periscope before being directed down onto the liquid in Langmuir trough. The Langmuir trough is protected by a cardboard box, decorated in the style of a Freisian cow with holes cut roughly in the sides to allow light in and out. Captured after reflection from the surface of the liquid, the laser light is directed back down to the table surface by a second periscope from where it passes back along the long side of the table into a photomultiplier tube – the detector.

The cardboard box is there to stop air currents disturbing the surface of the liquid, vibration is the enemy for this experiment because the liquid in the Langmuir trough picks up the slightest disturbance and wobbles around. Sitting on an optical table weighing a large fraction of a tonne isn’t enough – it needs to be on the ground floor too because buildings wobble and in this instance the Langmuir trough sat on an active anti-vibration table – a bit like noise cancellation headphones but the size of a small coffee table. You can manage without active anti-vibration if you’re willing to do your experiments in the dead of night.

The cardboard box is emblematic of a piece of research apparatus: much of it is constructed from pre-fabricated components, some of it is custom-made in the departmental workshop but then there are the finishing touches that depend on your ingenuity and black masking tape. I did have plans to get the cardboard box remade in perspex but the box was just the right size and if I wanted more holes in it I could easily cut them with a knife so it was never worth the effort. I seem to remember a bit of drainpipe being involved too. As an experimental scientist you get your eye tuned in to spot things just right to add to your apparatus.

The laser is a single mode solid-state laser producing light of 532nm wavelength – a brilliant green colour. Three things are important about lasers: firstly, they are fantastically bright; secondly, they produce light of a very pure colour – a single wavelength. Thirdly, lasers go “oooooooommmmmmmmm”, whilst conventional light-sources go “pip-pip—-pip-pip—pip”. Technically this is described as “coherence”, we’re using a laser in part because we want something to compare against and a conventional light-source isn’t going to work for this. If you’re measuring a small change, it’s very handy to have a “ruler” close at hand, and in this case the elastically scattered light is that ruler.

You’ll notice that I’ve not said anything about the results we obtained using the SQELS; truth be told, despite all the hours spent building the apparatus, doing the experiments and analysing the data the results we obtained told us little more than that which we could get by easier and simpler means that I described in my earlier post. I also had the sneaking suspicion that it would have helped if I knew more about optical engineering.

(I got distracted in the middle of this post, browsing through the Newport optical components catalogue site!)

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 12 2010

Why I’m voting Liberal Democrat

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

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

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

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

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

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

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

Apr 10 2010

Experiments for obsessive compulsives

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

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

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

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

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

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

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

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

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

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

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

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

Apr 04 2010

Caerwys – a breezy spring walk

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


View Caerwys in a larger map

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

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

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

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

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

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

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

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

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

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