Archive 2012

Happy Christmas Marcus Wilson Dec 17

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Blogging has ground to a halt in recent days, as I try to get other things done, such as research proposals, reviewing a PhD thesis, supervising a summer student, and attending numerous parties. I’m off on holidays very soon, but will be back early January.

I’m currently grappling with an ever increasing parameter space in one of our computer models. These parameters are for things associated with various neural processes – such as how quickly does release of a particular neurotransmitter occur, and under what conditions? There are a lot of things we need to know, but in some cases they haven’t been measured very well.

The solution is easy. Consult some friendly experimental neuroscientists. Which we did last week. But that didn’t help, because they didn’t know either. In fact, it made it worse, because they drew our attention to another raft of things that we should be considering, but didn’t have much data on either. Indeed, they looked to us to help reduce their parameter space through our modelling.

I get the impression that there is very little known at the cross-over between physics and neurophysiology. A good reason to study it, then.

Verification and Validation Marcus Wilson Dec 10

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I’ve worked on a lot of computer models of physics things for my various employers to date. Although I’d describe myself as primarily a physicist, I’m also a computer modeller – that’s what holds together my work on mould growth in grain silos, dispersion of dust within pig-sheds, infra-red sensors, radar propagation, electrical behaviour of neurons, etc, which on the face of it are rather different (and some not obviously physics at all). Note that I don’t claim to be a computer programmer – I don’t produce fantastic memory-optimized whizz-bang graphics apps – what I mean by modeller is being able to take a physical thing (like flow of air in a pig-shed), produce equations that describe the physics going on, and then write a computer programme that solves these equations to produce a result that should describe something physical.

A big part of doing this is answering the question "how do I know my computer is turning out a meaningful result?" There are basically two bits to this question.

1. Verification. This is ensuring that my computer programme is actually solving the equations that I think it’s solving, and doing what I think I’ve asked it to do. One small mistake – e.g. a bracket ‘)’ in the wrong place, two lines of code executed in the wrong order, etc., and the answer might be different. I need to be sure that I’m getting what I think I’m getting.

2. Validation. Here’s where we ask the question – "Is my physical model (my equations) really describing reality."

Verification is tedious but fairly straightforward. Validation is harder, and can be really costly. Often validation requires one to do some experimental work – set up a few test cases that can be accessible both to experiment and to the computer modelling – and see how close the two are.

A neat way of doing verification is to work out analytic solutions to the mathematical equations. By ‘analytic’ I mean exact solutions – using pen and paper. That’s often really hard in general – if you could do it you wouldn’t need to do a computer model of it – but often even when you can’t you can still work out certain properties that the solutions must have – e.g. what do you get when you set a particular parameter to zero, or to infinity, or what do you get when particular parameters are identical?

I’ve been doing a spot of verification with a summer student this morning, on a computer model we are putting together describing the response of neurons to Transcranial Magnetic Stimulation. The equations are complicated, but one thing we know is that if we set certain parameters to be identical, certain outputs from the model should be identical. More specifically, we get four graphs out – and all four should be identical. So when we had three that were the same, and the fourth that wasn’t, we knew that something was up with the code.

Of course, finding  the fault  is another thing entirely. Wilson’s law of verification states (from bitter experience) that the time taken to locate a fault is inversely proportional to the size of the fault. In other words, tiny little problems in the code take the longest time to discover.

In the case of this morning, we eventually tracked down the problem. It was really tiny. I’d titled one of the graphs incorrectly. Everything in the code was correct – in this regard at least – it was just that the plot that we thought was ‘plot 4′ was actually another plot – so it wasn’t surprising it was different to the other three. The real plot 4 was hiding elsewhere – once we found it we saw that it was, in fact, the same as the others. Cue hitting head against a wall.  Code verified then. Or, I should say, verified in this regard. Verification and validation never truly stops.




Celebrating Teaching Day Marcus Wilson Dec 04

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This morning we were treated to some talks by some of the award-winning teachers at The University of Waikato. It was a bit unfortunate that none of the talks were from the ‘scientific’ disciplines, but that’s not because none of the winners were from scientific disciplines. We have our good share of excellent teachers in this faculty. Here are a few things stood out for me.

1. Kirstine Moffat’s unquenchable use of theatre.  Granted, she lectures in English Literature, which makes putting on period costume and illustrating a point with a conversation between sock puppets less radical than in some subjects, but getting otherwise unenthusiastic students to pay attention has to be a good thing. I think if I pulled out a couple of sock puppets in an engineering lecture the room would empty faster than in a response to a fire alarm. So it would need to be a bit different, but I’m sure there’s room for some creative thinking.

2. Gemma Piercy (Labour Studies and Social Policy) pulled out this quote from one of her students

The mark you get for an assignment is more valuable to you than having the knowledge about the assignment topic itself."

I think a good many students will agree with that. The comment says a lot. First of all, it says that the student is after a degree, as in the final certificate. Whether or not he or she actually has any understanding of the topic is a secondary issue; what matters is the bit of paper, because it’s that bit of paper that gets them a job. Next it hints that there is something deeply wrong with the assignment. An assignment should link with a learning outcome – doing well on an assignment should be synonymous with learning. In my experience, if something is going wrong with your teaching, the first thing to look at are the assessments. And it also suggests that there is a failing to engage the students with the teaching and learning process. "Why are we learning this?" is a common question from a skeptical student. If the outcome at the end can’t be envisaged, then the motivation to learn evaporates.  Gemma’s done a wonderful job over the last couple of years of getting it right.

3. Then there’s Juliet Chevalier-Watts (Law). With her talk, what I got out was to have the courage to try different things. Some may not work first time, some may lead to cries of derision from one’s colleagues (and the students for that matter), but "if you do what you’ve always done, you get what you’ve always got." And that doesn’t help anyone to move forward.

As I write this, I’m also contemplating a meeting that I have in a few minutes to discuss the nuts and bolts of a particular third-year engineering paper that I’m teaching next semester. Dynamics and mechanisms is a deeply tedious topic (I think so) – and one with a few really hard bits in it. Last year I was a little bit radical with it (e.g. the test you could talk in – also here) – this year I think I need to go a bit further. Time to start making that sock puppet.

Undiscovery in physics Marcus Wilson Nov 28


With the recent undiscovery of Sandy Island I’ve begun wondering what other things might be ripe for undiscovery. Wasps, for example. Wouldn’t it be great if we realized that there wasn’t actually any evidence for the existence of wasps after all. Their discovery had been just a mistake made by an entomologist back in the depths of history. We can all tell our children not to worry about them – they don’t exist. Our chickens would love to see the neighbour’s cat undiscovered (as would we – at least from our garden).  I’m sure a variety of places might feature strongly too. Hamilton is bound to be on the list of some people; but, I can assure you, the last time I looked it was still there.

I don’t think in physics there has been a great deal of undiscovery in the last few centuries. I struggle to think of any real undiscoveries.  Sure, there have been changes to our thinking. For example, relativity superseded Newtonian physics, but it would be wrong to say that Einstein undiscovered Newton’s Laws of motion. The latter are still a cornerstone of physics – but their applicability has been reduced to the realm where things aren’t travelling close to the speed of light. That would be more like discovering the coastline of Sandy Island is a bit different to what the maps have it. One might say that the Michelson-Morley experiment undiscovered the aether, but in reality the aether had never been discovered – it was just a well-accepted hypothesis. Likewise Joule’s experiments with heat put pay to the idea that heat was a fluid, but since no-one had claimed (supported by real evidence)  to have observed this fluid, it wasn’t really an undiscovery either.

Underlying modern science (by which I mean Galileo and beyond) is experimental evidence. No change in understanding of science, in any discipline, is going to happen without well collected and well analyzed data. This makes undiscovery of something (by which I mean overturning of some knowledge, theory or principle that has been believed based upon evidence, as opposed to mere hypothesis) unlikely. There have been a few instances of reports of new things that have been made prematurely, with unreliable evidence, such as cold fusion and faster-than-light neutrinos, and these have been embarrassing for the groups concerned and undiscovered very rapidly.  But undiscovery here has happened because they were never properly discovered in the first place.

That said, neither was Sandy Island properly discovered. My spell-checker’s underlining of the word undiscovery may be for good reason.

I’d love to hear readers’ thoughts on this one. Is there any piece of modern science that has been genuinely undiscovered?





Seeing circular polarization Marcus Wilson Nov 22

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Physicsworld magazine is doing a ‘special feature’ this month on animal superheroes – those with rather unusual physical abilities.

The best of the lot (in my subjective opinion) is the featured-on-the-cover mantis shrimp. Not because of its ‘dactyl clubs’ that can produce a force of 700 N, but because of its eyesight.

The mantis shrimp can see circularly polarized light - something that no other animal is known to do. Polarization describes how the electric and magnetic fields in the light wave are oriented. For example, a horizontally-travelling light wave (say in the x- direction) might have its electric field pointing in the z-direction (vertically) and the magnetic field in the negative y direction. In an electromagnetic wave, the electric field, magnetic field and direction of travel are all mutually perpendicular. We could call that a vertical, plane polarization.

In circular polarization, the electric field moves in a corkscrew-like shape as the wave travels. The corkscrew can spiral one of two ways – hence there are two distinct polarizations which we call left-handed and right-handed. The mantis shrimp can distinguish between the two. It does this by using its own version of a quarter-wave plate – made of a birefringent material – one that has a different refractive index in different directions. That converts a circular polarization to a linear polarization, which it detects via more conventional methods. (There are several animals that can ‘see’ linear polarization – bees are a famous example. There are plenty that don’t distinguish one  polarization from another at all, such as humans.)

The mysterious question is why? Bees use linear polarization to assist navigation (light from the sky is linearly polarized), but what use is distinguishing left-handed and right-handed circular polarizations to a shrimp? There’s a cool research question for someone’s PhD thesis.


Validity in experiment Marcus Wilson Nov 20


Last Friday I was at the Waikato Science Teachers’ one day conference in Cambridge. There was a wide range of different material talked about, which made for an interesting day. One of the questions which was tackled (led by Simon Taylor)  was ‘When is an experiment valid?’ Or, what is ‘validity’ all about when it comes to science. Some thoughts from the audience were ‘When it does what it is supposed to’, ‘When it agrees with theory’, ‘When it is controlled’, ‘When it is repeatable’, ‘When it measures what it is supposed to’.

All of these I think are reasonable responses, depending upon the situation. f you are illustrating a physical principle to a class then you certainly want your experiment to behave – we all know that physics experiments are too often characterized by the fact that they don’t work – especially when they have a big audience.

But an experiment can never ‘not work’. It does what it does. The fact that it didn’t do what you wanted or expected could be for a variety of reasons – bad experimental design, poor control, statistical variation, or maybe because of some ‘new’ phenomenon. After all, where would science be if every experiment agreed with current theory? Major strides forward in science have usually been triggered through experiments that didn’t do what the experimenters were expecting.

I think a good definition of ‘valid’ would be ‘that the experiment measures what you think it is measuring.’ That, from memory, was basically Simon’s point. If we achieve that, then it doesn’t matter whether we find a new phenomenon, validate an existing theory, or just make a mundane measurement of electric current in the lab. We’ve done some good experimental physics.

Sorry – short entry this one – baby wants attention.


Pinhole cameras and eclipses Marcus Wilson Nov 15

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Well, the eclipse yesterday was fun. There were enough patches of sky between the clouds to get some good views. I was pleased that the pinhole cameras I made out of miscellaneous cardboard tubes, tins, paper and tinfoil worked really well. Also, the trees around the front of the sciences building gave some nice natural pinholes as the sunlight worked it’s way through the gaps between the foliage – we could see lots of crescents projected onto the wall of the building. Not something you see everyday.

The trick with the pinhole camera is to get the combination of length between pinhole and screen and size of pinhole correct. (Basically – the f-number in photography-speak) A long length means a larger image – but also a fainter one. To increase the brightness, we need to let more light through (a bigger pinhole) but the drawback of this is that it blurs the image. It takes a bit of experimenting – best done well before the eclipse that you want to see.

On the subject of which…if you live in New Zealand…you don’t have a lot of opportunity for a while. We northerners get an iddy-biddy eclipse next May (10th) – sorry Mainlanders – you miss out – and then it’s nothing for ages before we get a few more feeble partials in the 2020s. BUT, as I said earlier, it’s then non-stop eclipse mayhem from 2028, with THREE total and THREE annular eclipses before 2045, for those of us who are still alive to see them. Details are all here courtesy of RASNZ.

There are a few videos up already from the Cairns region – here’s one. However, video does not do an eclipse justice, partly because of the difficulty in video capturing parts of the corona at different luminances simultaneously. If you want to see the fainter, whispy stuff at the far edge of the corona, you end up well overexposing the brighter area nearer the moon.  The naked eye does a far better job of capturing the totality phase than a camera.

I note a fair amount of pink on the video – this is the chromosphere – a thin, cooler area of the sun, between the photosphere (the bright yellow bit that we normally see) and the corona.





In a not-quite symmetric world Marcus Wilson Nov 13


An interesting problem to ask students to think about is this: Write down a definition of ‘left’ (as in the opposite of right). It’s something every adult knows, but how do you define it. There’s little wonder that children take a long time to grasp which is left and which is right.

One might say: Well, if you are in the Southern Hemisphere, face the position of the midday sun and left will be the side of you where the sun sets. But that just shifts the problem to another: Define ‘south’. Then one could resort to physics, and look at the direction that a positive particle is bent under a particularly oriented magnetic field, but that muddies things further – we need to know about positive and negative and also left and right – so we are no better off.

In order to do it, you need some asymmetry in the universe. Fortunately, there are some we can draw from. For a start, the Earth isn’t symmetric – just by saying ‘in New Zealand’ we establish ourselves as being in the southern hemisphere, then we can apply arguments about where the sun sets etc.

There are also  other asymmetries. There is more matter than antimatter, for example. Why? It’s something that the Large Hadron Collider might give some clues about (It wasn’t built just to find the Higgs Boson). There are more subtle ones, concerning CP-violation in particle physics (this actually links back to the matter/anti-matter asymmetry) which suggests that there is a fundamental asymmetry about the universe. But why?

What got me thinking about this was the clockwise rotation of baby Benjamin at the weekend. Lying on the in-laws living room carpet, he seemed to be quite able to rotate clockwise (so that his head swizzled round roughly to where is feet were) but not anti-clockwise. So there is a preferred direction. It could be because one leg is stronger than the other, which is quite possible, but there may be other reasons – for example the ‘grain’ in the carpet might be an issue here.

One thing’s for sure – he’s living in an asymmetric universe.

 Postscript 22 November 2012

This news has just come out: An experimental measurement of time-reversal symmetry breaking. That’s allowed by our current physics understanding – what isn’t allowed is charge-parity-time reversal (CPT) symmetry violation.




A tip for the scholarship physics exam Marcus Wilson Nov 08

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My last entry gave a couple of tips for exams in general. Now, here’s a tip specifically for the NZQA scholarship physics exam. In part, it comes from an assessment of the interviews I’ve been doing with first year students and practising physicists on the way that mathematics is used in physics. 

One really strong theme that practising physicists emphasize, is the conceptual nature of physics. One of my interviewees, who works in a successful NZ science-driven industry said this:

The ability to discern the important from the less important is a paramount skill.

In other words, doing physics well is down to identifying what are the bits of physics that matter, and not getting carried away with the bits that don’t. When faced with a problem, the very first thing he needs to do is to get down to the basic, core science principles of what’s happening. He doesn’t start writing down equations, or doing calculations, or deriving formulae, until he’s sure what concepts are going to matter for his particular problem.

It’s also clear that my first year students don’t identify with this skill so strongly. There are hints in the interviews that some of them do, a bit, but it is not anywhere near as strong as for the practising physicists. It’s a difficult skill. And it’s one that often isn’t really taught – either at school or university. (I would suggest we try to change this – I would say it’s more important than knowing the technical content of the subject.)

Having looked at the scholarship physics questions for several years, I know that they are written to identify those students who grasp physics over those who can simply rearrange equations and plug numbers into them. Being able to do algebra alone isn’t going to get you scholarship (though not being able to do simple algebra will seriously harm your chances). What is going to help, above all else, is to be able to identify what parts of the subject are relevant to particular situations. This takes practice.

So, my tip is this: The first thing you should ask yourself is "What is this question about?" – i.e. what areas of physics is it going to draw from? (Read the title of the question  – it can give you some hints) Then, ask "What concepts am I going to need to draw together to tackle this?"  And "How do these concepts fit together?" Then, and only then, should you think about writing down equations.  Otherwise, you’ll get lost in a sea of irrelevant algebra.




My top two exam tips Marcus Wilson Nov 06

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Yes, it’s that time of year again that a sizable slab of the population dreads. Exams. University exams are in full swing here, and the school ones are creeping up. So, here are my top two exam tips to help you on your way. You might think they are very, very obvious, but it is surprising just how many students fail to follow them – especially the second.

1. Turn up to the right place at the right time. That means, make sure you know when the exam is, and where it is. If in doubt of the room’s location, find it beforehand. There’s nothing quite like the feeling of not being able to find the room when you’ve got 90 seconds before you need to be there. However, arriving late is better than not arriving at all because you thought the exam was in the afternoon when it was in the morning or that it was tomorrow. Don’t laugh – It happens. The consequence could be that a student has to be at university for an extra semester to complete a paper again. It pays to double check, and triple check.

2. Read the question, and answer the question, the whole question, and nothing but the question. Don’t answer what you would like the question to have been, or what you think it should have been, or what you read it as because you skimmed over it too fast, answer what it actually is. Too often when marking I see ‘brain-dump’ answers. A student thinks – "Goody – a question on XYZ – I know lots about this topic" and proceeds to write down the entire contents of their brain regarding this area, whether it is relevant to the question or not. And too often, they neglect to cover what the question actually wanted them to do.. Anything you write that isn’t relevant to the question, you get no credit for. That’s nought, zero, zip, zilch, 0. All you are doing is wasting your time.

And, if I can add in a third, remember there is light at the end of the tunnel. Exams (at least on this intensity) don’t go on for ever.


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