Category: Science

Science, usually research I have done or topics on which I have lectured

Nov 15 2009

The past is a foreign country

I’ve been hanging out with historians recently (both online and in real life), so it got me thinking about how scientists treat history. The 150th anniversary of the publication of “On the Origin of Species” is coming up too, so it seemed like a good time to write this post.

My impression is that historians are about the reading of contemporary material, and drawing conclusions from that material; a realisation I came to writing this is that historians seem to have the same sense of wonder and passion for historical minutiae as I have for nature and science. I remember talking to a historian of science who was working on an original manuscript of some important scientific work, it quickly become clear that this was much more exciting for her than me. To me the exciting thing was the theory presented in it’s modern form, I wasn’t very interested in the original.

In science it isn’t the original presentation that’s important: I haven’t read Newton’s Philosophiæ Naturalis Principia Mathematica, Maxwell’s A Treatise on Electricity and Magnetism, any of Einstein’s four “Annus Mirabilis” papers, Galileo’s Dialogue Concerning the Two Chief World Systems, Darwin’s On the Origin of Species, the list goes on…

And that’s not to mention the real contemporary material: correspondence, notes and labbooks. I have a sequence of about 20 labbooks in the loft from 15 years of research, supplemented by a hoard of files and e-mails stored on my computer, covering the same period. I’m not sure I even want to try to reconstruct what I was thinking over that period – let alone try it on someone else’s records! It’s not that I’m remiss as a scientist, we just don’t read original material.

The original presentation of an idea may not be the clearest, and it may well be that it makes more sense later to present it as part of a larger whole, and to be honest scientists can be a bit hit and miss: Newton’s physics is great but the alchemy was bonkers. Science comes in bits, these days the bits are the size of a journal article and it’s only when you’re doing active research at the cutting edge that you need to keep track of the bits.

Mathematical notation is an issue for original publications. For example, Maxwell’s equations, which describe electromagnetism (radio waves, electricity, light…) are a monster in his original presentation but can be squished down to four short lines in modern notation (actually a notation introduced not long after his original paper). There’s a rule of thumb that each equation in an article halves the number of readers, therefore I link you to Maxwell’s 1865 version on page 2 of this document with the modern version at the bottom of page 6…
impressive, no?

A bit of history is introduced into the teaching of science but it’s either anecdotal such as the apple falling on Newton’s head, Gallileo dropping things off towers, Sadi Carnot and his wacky exercises, or we might give a quick historical recap as we introduce a subject. But to be honest it’s really all window dressing, the function of this history is to provide a little colour and give students the opportunity to do some exercises which are tractible.

Are scientists losing out as a result of this historical blindness? History should certainly inform us of our place in society, and our future place in society (okay – I’m talking about cash here!). I’m less sure that it has something to teach us on the ‘craft’ of science, this is something that comes from professional training – perhaps it would help if we were not presented with such caricatures of our scientific heroes.

So that’s my view, how wrong can I be?

Nov 09 2009

Pretty molecular models

And now I leap off into a topic in which I am not properly trained: molecular biology!

You sometimes get the impression  that scientists lead dull lives because they over-analyse things, they’ve lost their sense of wonder. The thing is: the more you know, the more you wonder.

One step up from atoms, you find molecules – atoms bound together. Starting things simple, here’s caffeine:

As every chemist kno carbon (C) atoms are black, nitrogen(N) atoms are blue, oxygen(O) atoms are red and hydrogen (H) atoms are white. (Not really but those are their traditional colours in molecular models).  Isn’t it beautiful? You can play with an interactive version here. In real life chemistry is more messy than this which is why I’m a physicist rather than a chemist.

The caffeine molecule is about 1 nanometer across, 1 (US) billionth of a meter. To give you a feel for the size of a nanometre: think of a grain of rice – about 1mm across, now imagine a kilometre. Walk your kilometre with the grain of rice, I walk a kilometre in about ten minutes and it takes me past two roundabouts, a gym and a postbox. Now look at you grain of rice again. To a caffeine molecule, a grain of rice is a kilometre wide.

Molecular models of this sort are a representation of reality, the things they miss out are: (1) in real life molecules are not static, they’re jiggling away furiously through the action of thermal energy (2) generally they’re going to be surrounded by solvent molecules (often water, which are also zipping and wiggling around) (3) they’re sort of soft, fuzzy and deformable and different parts of the molecule will be sticky or slippery according to their chemical nature. Ten years ago a good question at any molecular modelling seminar was to ask about the solvent molecules, the usual answer was “there aren’t any” – this usefully puts molecular modellers in their place since we’re rarely interested in molecules without solvent. Perhaps things have moved on since those days.

Life specialises in bigger molecules than caffeine, exquisitely crafted into little machines. And the incredible things is that all of life (humans, mammals, reptiles, birds, snails, bees, tardigrades, sponges, plants, algae, bacteria, fungi, weird bacteria that live in hot underwater vents) share the same 4-letter DNA code, which codes for the same set of 21 amino acids which build all the proteins to make life. Many of the proteins themselves aren’t hugely dissimilar across all the plant and animal kingdoms, particularly those to do with the most basic operations (processing DNA, converting food to energy).

Proteins are strings of amino acids: each different type of protein has a different sequence of amino acids.
Protein molecules typically contain many (a hundred or more) amino acids. The amino acid sequence is known as the primary structure, next up is the secondary structure: alpha-helices and beta-sheets. Different amino acid sequences can produce alpha-helices and beta-sheets that look the same. These structures are represented using “ribbons”:

This is a model of lysozyme, the alpha-helices are shown in red and the beta-sheets are yellow, bits of “random coil” amino acid sequence are shown in green. Lysozyme is about 5 nanometres from one end to the other. You can play with an interactive version here. The amazing thing about proteins is that their 3D structure forms spontaneously and very rapidly when they are synthesised in the cell, this process is known as ‘folding’. Furthermore the folded, or tertiary structure, of the protein is the same every time – it has to be or the protein won’t do it’s job. One of the great challenges in molecular biology is that, despite knowing the amino acid sequence of a protein from the DNA which encodes it, working out the 3D structure is a question of measurement, or comparison with other sequences of known folded structure.

Lysozyme is a physicist’s protein, you can buy it in bottles by the gram. I’ve worked on lysozyme, looking to see how it unfolds on a surface when heated.

You can go see more protein structures on http://proteopedia.org/, the lysozyme model above is 132L. I could play on there for hours…

References
Green, R.J., Hopkinson, I. & Jones, R.A.L. Unfolding and intermolecular association in globular proteins adsorbed at interfaces. Langmuir 15, (1999), 5102-5110.

Oct 30 2009

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.

Oct 20 2009

Twitter, rumours and physics

The twittersphere avoided making a bit of a mistake this morning. Wikileaks had obtained a new version of the BNP membership list, which they released (the BNP claim this list is a fake). Prior to release it was claimed that a peer of the realm was on the list and immediately post release that peer was named. Only it turns out it wasn’t him, someone who styled himself Lord with a very similar name was the man on the list. Fortunately the released list was detailed enough that this could be checked, someone had the wit to check before blindly repeating the name. Once they’d done this they started correcting the false rumour (in what looks like quite a vigorous manual effort). It’s worth noting here that the fact-checker appears to be a trained journalist.

But it could so easily have been very different. It could have been very difficult to establish the rumour was false, it could have been that the diligent fact checker stopped to finish his cup of tea before tweeting his correction, the rumour could have been re-tweeted by someone with many followers. All of these things could have happened but didn’t, will this be true the next time?

On the plus side, twitter rumours do appear to be traceable back to source and it’s very easy to find the individual rumour-mongers and put them right. This is certainly true for non-malicious rumourmongering (that’s to say where people have not made a special effort to propagate a rumour, nor hide their tracks).

There is a scientific link here, modelling of all sorts of networks has long been a respectable scientific field. For example, there’s Per Bak’s forest fire model and work that follows on from there. More recently there’s been work focussing more explicitly on computer networks and social networks. To a physicist Twitter represents an example of a simple system which has nodes (with ingoing and outgoing links) and messages that are propagated between the nodes. The nodes could be trees in a forest and the thing passed could be fire, or the nodes could be computers in a network with the message being network traffic; the nodes could be scientific papers with the messages citations of other papers. The physics doesn’t care about the detail of these things, it cares about a small number of parameters in the system: how many links in and out of a node? What’s the probability of a message being transmitted from one node to the next?

So there’s an interesting bit of network analysis to do here. How fast can a rumour propagate on Twitter? What fraction of people refrain from tweeting a false rumour to stop it propagating? What’s the best way to squash a false rumour?

Having watched the no doubt frenzied activities involved in squashing today’s rumour. One useful tool would be an automated rumour-quashing robot. It would search for tweets containing the rumour (probably based on a manually selected keyword) and tweet the originator with a rebuttal.

Think before you tweet!

Oct 09 2009

Superconductivity

This is a little post about superconductivity, lecturing and liquid nitrogen.

The lecture I remember most clearly was when I first demonstrated the Meissner effect in a superconductor. You can buy a little kit to help with this. It contains a little powerful magnet, a disk of a high temperature superconductor and a polystyrene dish. Put superconductor in dish, add liquid nitrogen to dish, wait for bubbling to subside then drop small magnet onto superconductor and this happens:

(A video is better, see here)
The little magnet just sits there, suspended above the superconductor, if you give it a prod it’ll spin around on it’s axis. It’s magic! Now the first time I did this was live in a lecture theatre in front of fifty students. I’d not had a chance to try it out in advance, and I must admit I was a bit underwhelmed by the equipment provided. So I did the tippy-out-the-liquid-nitrogen and wotnot, and my first words thereafter were “Bloody hell – it works!” – the students seemed impressed too. Much poking of the little magnet with the plastic tweezers was done, and we also splashed around the liquid nitrogen for more fun. I did the demonstration the following year, but it wasn’t the same without my genuine surprise and excitement.

Lecturing is a bit of performance (quite literally), I struggled with the format because I found it hard to get meaningful feedback from a large group of students. If you do it passionately and enthusiastically it comes across to the students, but that’s difficult to sustain for lecture after lecture. If you get it spot on, it’s brilliant but usually its just a chore (for both student and lecturer).

Just to explain a little more about superconductors: a superconductor is a material which conducts electricity perfectly – it’s resistance is zero (not just small, zero). A light bulb, an electric fire or kettle would be utterly useless with a superconducting element, the electric current would flow through it without emitting any light or heat. Heike Kamerlingh Onnes discovered superconductivity in 1911 (having first worked out how to liquify helium to cool his samples). More recently a bunch of so-called high temperature superconductors have been discovered, the weird thing is these materials are ceramics – they don’t conduct at all at room temperature and yet cool them down to liquid nitrogen temperature (-196degrees centigrade) and they conduct really well. As I’ve mentioned in earlier blog posts, superconductors are used for the making of big magnets and there are also some applications in very sensitive detectors. In principle they would be great for electrical power transmission, but the requirement to cool everything down to at least liquid nitrogen temperatures has meant they’ve not been economically viable.

Laboratory scientists take liquid nitrogen for granted but it’s an utterly alien material, like furiously boiling water but at the same time deep-bitingly cold. It hisses as it’s poured into a new vessel, wreathed in clouds of condensing water vapour. Liquid nitrogen splashed on a laboratory floor will chase dust bunnies around with distinct droplets of fiercely boiling liquid, like tiny hovercraft. The droplets vanish without a trace.