Dec 17 2009

The Professionals

Lecturing is a tough business, and half the job is largely ignored.

This post is stimulated, in part by an article in Physics World on the training of physicists for lecturing, and how they really don’t like it. It turns out it is rather timely since Times Higher Education has also published on the subject, in this case highlighting how universities place little emphasis on the importance of good teaching in promotion.

I taught physics at Cambridge University: small group tutorials and lab classes – I was a little short of a lecturer. I also taught physics as a lecturer at UMIST. I should point out that the following comments are general, I think they would apply equally to any of the older universities.

Mrs SomeBeans is a lecturer in further and higher education, the difference between the two of us is that she had to do a PGCE qualification whereas I was let loose on students with close to zero training.

I did spend an interesting day in lecturer training at Cambridge, a small group of new lecturers, and similar, spent a fairly pleasant day chatting and being video’d presenting short chunks of lectures. I learnt several things on that day:
1. Philosophy lecturers use hardly any overheads.
2. Most of us found lecturing pretty nerve-wracking, one of our number wrote out her lectures in full in longhand to cope.
3. Drinking as a cure for pre-lecture nerves doesn’t work well
4. I spoke like a yokel and was slightly tubbier than I thought!

Round two at my next employers was a bit more involved. I can’t remember much from the two day event, but many of the points from the Physics World post came out. Scientists are typically taught how to lecture together as group, and their point of view is somewhat in collision with those of educationalists who seem to be able to throw out three mutually incompatible theories before breakfast and not be interested in testing any of them.

I have an insight which may help scientists in these situations: outside science the idea of a “theory” has quite a different meaning from that inside science. This paradox is also found in management training. Non-scientists use a “theory” as a device to structure thought and discussion, not as a testable hypothesis. Therefore multiple contradictory, or apparently incompatible theories, can be presented together without the speaker’s head exploding. They’re not generally tested in any sense a scientist would understand, very few people attempt to quantify teaching Method A against teaching Method B. The thing is not to get hung up on the details of the theory, the important bit is being brought together to talk about teaching.

I enjoyed parts of teaching: physics tutorials for second years at Cambridge was something of a steeplechase with the not particularly experienced me, hotly pursued by rather cleverer undergraduate students over problems for which the lecturers did not deign to supply model answers. Exceedingly educational for all concerned. Practical classes were also fun: the first time a student presents you with a bird’s nest of wires on a circuit board it takes about 15 minutes to work out what the problem is, the second time you immediately spot the power isn’t connected to the chip – and students think Dr Hopkinson is a genius.

Lecturing I found pretty grim, except on the odd good day when I got an interesting demonstration working. I was faced with 80 or so students, many of an unresponsive kind. I ploughed through lecture notes on PowerPoint which I found interesting when I was writing but in the lecture theatre I found painfully long winded. Lecturing is the most nerve-wracking sort of public speaking I’ve done, and I suspect many lecturers find it the same. I remember one of my undergraduate lecturers was clearly a bag of nerves even in front of the small and friendly course to which I belonged (and I’m not good at picking up such things).

In a sense lecturing is a throwback, there are so many other ways to learn – and I fear we only teach via lecturing because that’s what we’ve always done. Nowadays it’s easy, although time consuming, to produce a beautiful set of printed lecture notes and distribute the overheads you use: but is it really a good use of time to go through those overheads (which I am sure is what nearly everyone does)? Nowadays I learn by reading, processing and writing (a blog post) or a program.

There’s another thing in Physics World article:

At universities the task is often performed by academics who are much more interested in research and therefore regard teaching as a chore.

This is absolutely true, in my experience. I’ve worked in three universities post-undergraduate, I’ve been interviewed for lectureships in a further six or so. And in everyone the priority has been research not teaching, which is odd because if you look at funding from the Department for Innovation, Universities and Skills something like £12billion is directed at teaching and something like £5bn at research.

So why did I write this post: perhaps it’s a reflection of opportunities missed and a time spent chasing the wrong goals. If I did it all again there seem to be so many more ways to talk to other lecturers about teaching. On twitter, in blogs.

Dec 13 2009

Drowning by numbers

I am not a mathematician, but physics and maths are intimately entwined. I suspect I stumble on a deep philosophical question when I ponder whether maths exists that has no physical meaning.

On a global scale I am moderately good at maths, I have two A levels* in the subject (maths and further maths), long years of training in physics have introduced me to a bit more. However, beyond this point I realised I was manipulating symbols to achieve correct results rather than really knowing what was going on. A lot of my work involves carry out calculations, but that’s not maths.

I did intend decorating this post with equations, I didn’t in the end, wary of a couple of things: firstly the statement by Stephen Hawking that every equation would half sales; secondly I discovered that putting equations into Blogger is non-trivial. Equations, statements in mathematical notation are the core of maths and much of my journey in maths has been in translating equations into an internal language I understand.

So here’s a pretty bit of maths, the Mandelbrot set, the amazing thing about the Mandelbrot set is how easy it is to generate such a complex structure. We can zoom into any part of the structure below and see more and more detail. Mathematics is the study of why such a thing is as it is, rather than just how to make such a thing.

Image by Wolfgang Beyer

I remember playing with Mandelbrot sets as a child, before I understood complex numbers, to me they were a problem in programming and a source of wonder as I plunged ever deeper into a pattern that just kept developing. Have a look yourself with this applet… *time passes as I re-acquaint myself with an old friend*. There is something of this towards the end of Carl Sagan’s novel Contact, where the protagonists discover a message hidden deep within the digits of π.

I fiddle with numbers when I see them, and I suspect mathematicians do too. So my Girovend card showed 17.29 recently which, without the decimal place is 1729 = 13+123 = 103+93, the smallest number that has the property of being the sum of two different pairs of positive cubes, it’s also a very common piece of numerology. The numbering of the chapters of “The Curious Incident of the Dog in the Night-time” by Mark Haddon, with consecutive prime numbers also appeals to me.

It’s become a tradition that I find ways to annoy the people I visit, and there’s no escape for mathematicians here. It seems like the best way is to annoy a mathematician is to assume they can do useful arithmetic, like a calculating a shared restaurant bill. Interestingly though, this may be a poor example, since fair division methods for important things, like cake, are an area of mathematical research.

It’s true that some mathematicians are a bit odd, but then so are some physicists and to be honest if reality TV has taught us anything, it’s that the world is full of very odd people in every walk of life. So if you meet a mathematician, don’t be afraid!

*A levels are the qualification for 18 year olds in the UK, when I was a student you would study for 3 or 4 A levels for 2 years.

Update: Since writing this I’ve discovered a couple more interesting sites for fractals, and for want of a better place to put them I record them: here you can find a pretty rendering of the quaternion Julia set, and here is an in depth exploration of the Julia and Mandelbrot sets (1/1/10).

Dec 09 2009

Wordless Wednesday

Dec 06 2009

A jigsaw not a House of Cards

This is the blog post I was never going to write, its about climate change.

This post will contain pretty much no science, if you’re interested in that then I’ve put some references at the end. Instead this is a post about my personal journey with anthropogenic global warming (AGW).

So why did I decide to write this now? A couple of reasons really: the Copenhagen Climate Summit is next week but mainly climategate, the publication of leaked e-mails and data from University of East Anglia Climate Research Unit. I was listening to the Today programme Radio 4 in the UK in the gym, I was so frustrated by their climategate piece I had to turn the radio off and start to compose this post in my head. It’s the mindless spouting of John Humphrey’s about something of which he clearly has no understanding which is frustrating.

My journey begin in 2007 when “The Great Global Warming Swindle” (TGGWS) was broadcast. Ben Goldacre wrote about it on his blog. People I knew started talking about it and the balanced view it presented: yet it was utterly at variance with what I knew about global warming. I still haven’t seen “The Great Global Warming Swindle”, nor have I see it’s antithesis Al Gore’s “An Inconvenient Truth“. Subsequently OFCOM ruled that several scientists had been treated unfairly by TGGWS, and I decided that I was going to treat any further science broadcast by Channel 4 (the broadcaster) with overwhelming skepticism.

I say my journey began in 2007, but actually it began long before then. I’ve been reading New Scientist for the last 20 years, New Scientist is a popular science news magazine; I’ve also been reading Nature for quite a few years. Nature is a general scientific journal, with science news – getting a paper in Nature is like winning a gold medal at a national sporting event for a scientist. So by 2007 I had absorbed the conventional scientific view of on AGW via stories in the scientific press, In much the same way as I have conventional opinions on continental drift, evolution, the big bang, and mass extinction.

“The Great Global Warming Swindle” stimulated me to action, here was purportedly a scientific question which should have a scientific answer. First stop was the Intergovernmental Panel on Climate Change (IPCC) 3rd Assessment report published in 2001 succeeded closely by the 4th Assessment report published 2007. I focused on the Physical Science Basis (WG1): the Summary for Policymakers for this report is short (18 pages) and written in a pretty accessible style, the following chapters filling out the detail and referencing the primary peer-reviewed literature. This is the coal-face of science, it’s where I publish my professional work. Ultimately I also got myself an undergraduate textbook on atmospheric physics and Spencer Weart’s book on the history of climate science.

So how does a scientist get on outside their field? Well, the IPCC reports are no problem for me to understand. I can get on fine with understanding the abstracts of most the papers in the primary literature, but I would really struggle to contribute to this literature and I would not be able to pick out subtle errors, or judge between opposing expert views. This is unsurprising, because these papers will have passed peer-review and this means in most cases anything obviously wrong would have been weeded out.

I also plunged into the blogosphere, reading both contrarian and conventional sites. The only one I’ll cite here is realclimate.org, a blog by climate scientists which reports on new papers in the literature – I still read this. It was in the blogosphere that I came to my conclusions on the contrarian view: it’s wrong. I’ll expand on that slightly, there’s a huge bunch of stuff that’s just rubbish from the scientific point of view, there’s a smallish bunch of stuff where people from other areas of science have published work on climate science that may well be accurate for their field but the climate science looks a bit wobbly, there are a very few academic climate scientists who think that IPCC AR4 exaggerates the problem but on the other hand there are quite a few academic climate scientist who think AR4 was overly optimistic.

Thus armed with knowledge I set out to argue the scientific case for the existence of anthropogenic global warming… I think I gave up on arguing about AGW when, in an exchange on a discussion forum, I suggested reading an undergraduate text in atmospheric physics was a useful thing to do in understanding climate science and the response was “Just goes to show what you know”, it seemed knowledge was counting against me – blind prejudice was what was required. I had mistakenly believed I was arguing a scientific case, when in fact most other people were having a political argument dressed up as a scientific one. Which is odd really because it never occurred to me that global warming was a political question.

It seems to be a characteristic of contrarians that they view climate science as a house of cards, that if they disprove the contents of a single scientific paper then the whole edifice will fall. Hence there are very long arguments about single papers such as the original hockey stick controversy. However, science is a jigsaw, not a house of cards: to test a piece of science you look at the pieces of science around it to see how they fit, rather than staring very hard at the one piece. This view of science also makes it less personal, nothing in science depends solely on the work of one person. If they didn’t exist someone else would independently come up with the same result before too long.

People are naturally political, democratic animals. They like to consider both sides of a dispute and come up with what seems like an balanced solution. Science is not democratic, there is not a middle ground. If we vote on science, nature will not accommodate to match the outcome.

References

Intergovernmental Panel on Climate Change 4th Assessment Report (know as IPCC AR4 published 2007)
Copenhagen Diagnosis (an update the IPCC AR4)
Physics of Atmospheres by John Houghton
The Discovery of Global Warming by Spencer Weart

Dec 03 2009

Confocal microscopy

Back to stuff I should know, in theory, at least.

I had my first microscope as a child, it was a small one but I had a great time looking at little creatures that lived in dirty pond-water. I remember spending a long afternoon trying to see transparent single celled animals, and finally getting the lighting just right to see an amoeba. I also remember trying to immobilise a tiny worm with white spirit – it exploded, but I like to think it died happy.

This week I shall mostly be talking about ‘confocal microscopy’, this is a type of light microscopy (as opposed to electron, infra-red, x-ray, scanning tunnelling, or atomic force microscopy). The smallest thing you can see with a light microscopy is about 1 micron across, that’s a thousandth of a millimetre – a human hair is about 80 micron in diameter. A normal light microscope gives you a nice focused picture of a slice of you sample at the “focal plane”, but it also lets in loads of light from parts of your sample away from the focal plane which leaves you, overall, with a bit of a blurry picture. Microscopists get around this problem by slicing their samples up very thinly hence no bits to be blurry, but this is a fiddly procedure and leaves your sample very dead even if it started alive.

Confocal microscopy is a technique by which the slicing of the sample happens virtually, you can put a big fat sample in the microscope and by the use of cunning optics you only get an image from the focal plane which is lovely and sharp. You can build up a 3D picture of the sample by moving it up and down in front of the lens. Marvin Minsky was the original inventor of the confocal microscope in about 1955 but was somewhat held back by the lack of lasers, computers and stuff. Things picked up again in the 1980’s as these things became readily available. Oops, I think that might have been some cod history ;-)

An interesting feature of the confocal microscope is that if there’s nothing in the focal plane, you don’t see anything (unlike a conventional light microscope where you can always see a big bright something, even if it’s blurry) this can be disconcerting for the learner – you can’t find your sample!

Every microscopy needs a contrast mechanism, a way of separating one thing from another. In confocal microscopy by far the most popular contrast mechanism is to use fluorescence via the use of a fluorescent dye to label bits of your sample.  If you illuminate a fluorescent dye with light of one colour it emits light of another colour (making it stand out particularly well). If you ask an organism nicely (okay – genetically engineer), you can get it to make Green Fluorescent Protein (GFP) which is a protein that fluoresces green (duh!).  All that remains is to find a way of  sticking the fluorescent dye to the thing in which you’re interested.

In each post about science I like to add a little fact to help you wind up / avoid winding up practitioners in that field. So to wind up a microscopist: project an image onto a screen for a presentation and claim “x800” magnification (or whatever). The problem is: to what does “x800” magnification apply? Is it what the microscope told you when you looked through the eyepiece? Is it the magnification on the printed page, the computer screen or on the wall? We really doubt you know. It’s scale bars all the way.

For several years I was proud keeper of a confocal microscope. I, and my students, had great fun with the microscope and it had fun with us. The pointy end of the microscope is the objective lens, the bit closest to the sample. A fancy microscope like our Zeiss LSM 510 had 5 or more objectives mounted on a turret (see the image at the top of the post), each objective gives different magnification. The Zeiss LSM 510 was fully motorised, and too clever by half. It would assume that you wanted to stay focused on the same part of the sample when you changed objectives (or it changed them for you, with it’s motors). Now the problem is that for a x10 objective the focal plane is about 1cm from the front of the objective lens, and for a x40 objective lens it could be only a tenth of a millimetre. Now imagine I’ve just focused deeply inside my sample using an x10 objective, I switch to the x40 object on the computer….. and the microscope mashes the x40 objective lens into the sample, blithely ignoring the sound of £6000 lens smashing glass coverslip and covering it in sticky sample!

In later posts I’ll show some of the results from the confocal microscope in non-mashy-lens-into-sample mode.

Here are some images, these are all slices through solid objects. I didn’t really think this through in terms of explaining what’s in these first three images, roughly they’re what you get if you add a small amount of salt-water to Fairy liquid (although I would prefer you to use Persil washing up liquid). First up is a cross-section through an “onion-type micelle”:

And these are the structures you see in a similar system but with a different concentration of water:

This is a false colour image, bit lurid – don’t know what I was thinking at the time. These are known as “myelin”:

Pollen-grains are always popular – I stole this one from here. Each of the images is a slice, and the inset bottom right is the result of adding all the slices together.