Category: Science

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

Schrodinger’s flippin’ cat!

There comes a time in a blogs life when a bit of a rant is called for, here’s mine or at least the first one. To be honest it’s a fairly discrete, civilised rant – because that’s the sort of chap I am. It’s about cliches in science.

Quite some years ago, Stephen Jay Gould wrote an essay entitled “The case of the creeping fox-terrier clone”, published in “Bully for Brontosaurus“. In it he describes how he was writing a piece on evolution using the time-worn example of the horse, and in particular an animal named hyracotherium also known as eohippus or “The Dawn Horse”. The problem for Professor Gould was that he found himself on the point of typing that eohippus was “the size of a fox-terrier”, the thing is he had no idea how big a fox-terrier was! That’s right, Prof Gould (who I think writes very nicely) was about to commit a cliche to paper, and rather admirably he stopped and had a bit of a think instead. Now the reason he was about to write this was that he’d read it many times before, it’s a very standard story in evolution. He wasn’t alone, many writers have written how “eohippus was the size of a fox-terrier”, and doubtless many of them had no idea how big a fox-terrier was. Many readers have, no doubt, read those words, nodded sagely to themselves and said “All is well, I know that eohippus was the size of a fox-terrier”. It’s not really the cliche that’s the problem, the problem is that we’ve gone through the motions of communicating an idea, but sort of failed. Just in case it was bothering you, a fox-terrier is about the same size as eohippus, or roughly 40cm at the shoulder ;-)  I reckon that’s about the same size as a large lamb.

This isn’t an isolated example, science writing (and education) is riddled with cliche, not just cliche in word, but cliche in thought. My own bugbear is Schrödingers cat, of whom surely everyone must have heard. Erwin Schrödinger was one of the fathers of quantum mechanics.

 (I have a bit of a weakness for lolcats)

Briefly, Schrödingers “thought experiment” is as follows: take one quantum mechanical system (a radioactively decaying material is common), one cat, one diabolical system to kill the cat based on a random event from the quantum mechanical system and one opaque, cat-proof box. Combine ingredients and wait…now open the box. The argument put is that prior to opening the box the cat is in an uncertain state between dead and alive (which is true of the quantum system, atoms in the radioactive material could be said to be decayed and undecayed simultaneously). 

However, Schrödinger prefaces this thought experiment thusly: “One can even set up quite ridiculous cases.” Schrödinger didn’t think his cat was genuinely in some weird half-way house between dead and alive he was quite clear that it was very definitely one or the other and the problem was that for systems obeying quantum mechanical rules this wasn’t the case. That’s the useful point in this thought experiment: “There’s something weird that goes on between the quantum and the classical and we don’t know what it is”. Yet time after time you see this experiment described without the critical proviso. People go away with the false impression that undead cats exist!

oh dear I can feel my self getting a bit incoherent now… special relativity, I’ve taught special relativity, it’s genuinely a marvelous intellectual leap that solved a couple of serious problems in physics. It has some real world applications (understanding my old friend the synchrotron, GPS satellites, lifetimes for relativistic muons in the atmosphere etc). But the text book examples we give to students are rather worn, nope, “worn” is the wrong word. “flippin’ ridiculous” gets a bit closer. Here’s one:

“You have a 10 meter long ladder, and a 5 meter long shed. How fast must the ladder enter the shed in order for it to appear to fit inside to a stationary observer?”

I can tell you the answer: it’s “really fast” – some large fraction of the the speed of light. To put it another way, a ladder travelling at the requiste speed could travel the length of the equator in something under quarter of a second, that’s probably a little faster than your reaction time and I’m sure you have an intuitive feel for the length of the equator. My point here is that (1) You’re going to struggle to get your ladder going that fast (2) if that ladder’s going past you that fast, the absolute last thing on your mind is going to be “ooo…look, the 10m ladder is fitting into the 5m shed”. If your shed is in a vacuum then you won’t get killed by massive plasma shockwave, but how many sheds have you seen in a vacuum? For part 2 of this experiment one may find some halfwit has placed a concrete block at the back of the shed to check the ladder really is fitting into the shed by bringing the ladder to an instant standstill inside the shed. Once again, when ladder hits concrete whether ladder fits into shed is the least of your worries. Assuming that you were in a vacuum, your ladder/concrete collision is going to release “absolutely loads” of energy – fusion bomb scale. There you go, I’ve lost it completely now. Special relativity teaching is full of everyday objects (trains and rulers are typical) traveling at implausible speeds, and it really winds me up!

Don’t get me started on “Alice and Bob“, the quantum cryptographers and if one more string theorist tells me that all the extra dimensions are “curled up very small”, there’s going to be some hurtin’.

And relax… I feel better now that I’ve written it down.

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!

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.

The Mock Magnetic Resonance Imaging Machine

One of the images above shows a real magnetic resonance imager (MRI) and one is a mock one – can you tell which is which?*…. I’ve been visiting another lab where they do medical imaging, I’m not a medical physicist myself but a few years ago I did some work using a magnetic resonance imaging technique called STRAFI[1,2] – so I’ve had some contact with the nuclear magnetic resonance tribe.

(Nuclear) magnetic resonance imaging is used for non-invasively looking at a person’s giblets and as such is really useful for doctors. Unlike x-ray imaging it is best for looking at squishy bits, x-rays are best used on bones.

The core of the technique is to put your subject in a VERY BIG magnet. The magnets used for medical imaging are typically 1.5Tesla or 3.0Tesla, this is hundreds of times the strength of a little bar magnet and approaching 100,000 times the strength of the earth’s magnetic field. A big nmr spectrometer will have a field of up to about 20T.

I’m not going to try explaining magnetic resonance imaging or nuclear magnetic resonance, the linked wikipedia articles look pretty good. It’s worth noting that you can make a good guess that someone is explaining nmr to a neophyte by the distinctive waving of their arms. nmr scientists seem inordinately fond of acronyms (DANTE, ADEQUATE, INADEQUATE, WEFT, NOESY, GRASE…) and I have the sneaking suspicion that they spend more time inventing their acronym than designing their experiment.

The idea with the mock magnet is that patients find the fairly confined space of the MRI machine a bit claustrophobic, but you can get them used to the idea using the mock magnet. Also if you’re doing experiments in the machine you can check your bits and pieces are going to fit in offline.

I enjoyed my time with the high field magnet, they’re clad in a shiny cryostat and they’re fond of ferromagnetic materials (like steel), this means they tend to stand alone in the middle of the lab. You can make the owner of a high field magnet very nervous by casually waving a screwdriver around in the presence of his “precious”. Even at a distance of 3metres a reasonable size magnet exerts a very noticeable pull. Once you’ve got the screwdriver stuck to the magnet it’s rather difficult to remove. Have a look on YouTube for a whole pile of videos on introducing metal objects to MRI machines.

Magnetic resonance imaging is a development of chemical shift nuclear magnetic resonance (nmr) spectroscopy, which has been keeping chemists happy for years. People are inordinately scared of the word “nuclear”, so for presentational reasons the “nuclear” is dropped from the name of the imaging technique.

An exciting aspect of nuclear magnetic resonance (and other areas involving big magnets) is the “magnet quench” phenomena, this is the problem that has caused so much trouble at CERN recently. High field magnets work by putting a large current (tens of amps) into a superconducting coil (or solenoid). The superconductors used in magnets have to be cooled by a combination of liquid helium (really cold) and liquid nitrogen (not quite so cold, but cheaper). Whilst superconducting, everything is fine – the current can flow for ever producing a magnetic field. However, if by accident or design, the superconductor stops superconducting then it heats up it’s liquid gas jacket, which vapourises potentially very rapidly. Here’s another video of  a controlled magnet quench, featuring a pretty, shiny magnet. The first minute is best, the venting helium sounds like a strange musical instrument.

I’m idly wondering whether a magnetic resonance imager embodies the most Nobel Prizes of any device you’re likely to meet in everyday life. Heike Kamerlingh Onnes won the 1913 physics prize “for his investigations on the properties of matter at low temperatures which led, inter alia, to the production of liquid helium”. Bardeen, Cooper and Schrieffer got the 1972 prize for their theoretical work on superconductors. Lauterbur and Mansfield received the 2003 prize for medicine for the development magnetic resonance imaging. There’s a whole bunch of other nuclear magnetic resonance prizes, arguably you could include Marconi for his development of “wireless telegraphy”.

*Actually, they’re both the same – I couldn’t take pictures of the machines I saw.


1.    Hopkinson, I., R.A.L. Jones, P.J. McDonald, B. Newling, A. Lecat, and S. Livings, Water ingress into starch and sucrose:starch systems. Polymer, 2001. 42(11): p. 4947-4956.
2.    Hopkinson, I., R.A.L. Jones, S. Black, D.M. Lane, and P.J. McDonald, Fickian and Case II diffusion of water into amylose: a stray field NMR study. Carbohydrate Polymers, 1997. 34(1-2): p. 39-47.

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.