Tag: autobiography

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 22 2009

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.

Sep 29 2009

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.

Sep 21 2009

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.

Sep 20 2009

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.