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This is something I meant to post about ages ago, but forgot about. Via Denyerec, I read an article which suggested that going barefoot is healthier for your feet. It’s a long article, but an interesting one, and confirms a suspicion I’ve had for a long time that shoes — even sensible ones — constrain your feet and make you walk in an unnatural way. The conclusion seemed to be that heavily padded shoes make people plant their heels down much harder than they would with bare feet, thus placing more stress on all the joints of the leg. With no heel or sole padding — after a period of adjustment — people walk in a more fluid, softer way, placing the heel gently and rolling smoothly from the heel to the forefoot. Walking without shoes can also improve stability by allowing you to sense the form of the substrate, adjusting your balance and grip with small changes in the shape of the foot and the force applied.

I enjoy going barefoot when I can, because I love the sensation of the variety of textures under my soles. However, the local pastime around our way seems to be smashing glass bottles, so I usually only go barefoot at home or in the garden. When I first went to Brazil, I was amazed by the guides going barefoot in the forest, given that there were so many thorny branches and spiky leaves on the ground. Most people in the rural areas go barefoot most of the time, and our guide said he preferred to do so in the forest because he could move quietly. He did indeed move silently, while the rest of us clumped and rustled along like a herd of heffalumps¹ in our heavy boots, despite trying to walk quietly. His soles were as tough as leather from all the barefoot walking.

Denyerec linked to some ‘barefoot’ shoes made by Vibram called FiveFingers, which have an extremely thin, unpadded sole (just a thin layer of rubber to keep your feet clean and protect you from sharp stuff), and allow you to move each toe independently. They look intriguing, and I’d love to try a pair. I think that your feet would probably hurt like mad for a couple of days as they got used to the lack of padding and you changed the way you walked, then they’d feel wonderful. Has anybody got a pair? If so, what are they like?

¹ I nearly wrote ‘elephants’, but elephants move almost silently, except when pushing trees over. ↑

I’ve been trying to write another grant proposal recently (a seemingly Sisyphean task for academics), but I ended up a bit stuck. It was a collaborative idea that a colleague and I sketched out last year, but which — for one reason or another — ended up on the back-burner for a while. I was really struggling to pull it together. We had plenty of ideas, but I was having trouble rearranging and grouping them into a sensible structure and seeing gaps that needed to be filled. Finally, I decided to blow the dust of my copy of Tinderbox and try that.

I wish I’d done it earlier. I used to use Tinderbox a lot for writing notes and organising ideas¹, but newer, shinier applications have come along, and I’ve gradually turned to them. But Tinderbox is still a great tool, and it really excels at visual brainstorming. If you open a map view, you can just hammer out short notes containing all your ideas, then group them into similar themes later. With a linear outliner (a view which Tinderbox also has), you end up worrying more about where stuff should fit than what the important ideas are.

Once I’d got all the ideas down, I made some adornments (‘sticky notes’ on the page to visually group notes), and started moving notes around, first into similar ideas, then dividing them into aims, questions, hypotheses, techniques and random things to remember. Once that was done, I moved back to the linear outline view, and tidied things up, fleshing out the outline a bit as I went. It was really effective, and almost fun²! While Tinderbox can export notes quite easily as text (or HTML or XML), I probably won’t bother to do so in this case, because I was just using it as a tool for thinking rather than writing. I’ve started to write the final document with the Tinderbox outline view open to guide my writing, and it’s working really well.

¹ I even constructed, managed and wrote this weblog with it when I first started blogging. ↑

² Something which can make grant writing even almost fun is a miraculous tool, in my opinion. ↑

I took part in the RSPB Garden Birdwatch today, and spent an hour noting down the maximum number of each species of bird visiting the garden within the selected hour. As well as being quite fun, and a good way of encouraging people to notice the bird life going about its business in their gardens or local parks, it’s also a scientific exercise, gathering important data about the temporal and geographic changes in species numbers. While there is inevitably a small amount of statistical noise introduced because the participants are mostly not scientists, the enormous number of participants and broad coverage of the UK would be impossible without the participation of the public, so it’s a valuable exercise.

As I did my hour of observation, I was aware of a familiar non-scientific urge creeping in. Despite that fact that I know very well that a survey period in which few or no birds are observed is as scientifically valuable as one which huge numbers of birds are reported, you can’t help feeling disappointed and frustrated — if it’s your garden — when you get a pathetic avian turnout of a couple a few tits, two robins and a blackcap. I would never note down birds that weren’t there (as a scientist, that would rank alongside armed robbery in severity), but that didn’t stop me sitting there urging birds (in my mind) to come and visit the garden.

We get a good range of species visiting the garden, in reasonable numbers. Blue tits, great tits, coal tits, and small, bouncy puffball flocks of long tailed tits are regular visitors, along with a pair of robins, a pair of blackcaps (in the winter), blackbirds, dunnocks, wrens, chaffinches and occasional bullfinches. We also had groups of house sparrows (though sadly they seem to have reduced in numbers last year), the ubiquitous magpies and wood pigeons, and rare but startling visits from a sparrowhawk. Of course, that’s a cumulative collection of birds, over the course of hours or days, and in any randomly selected hour, we would be unlikely to see more than a small sub-set of those species, which is why my observation hour was so disappointing.

I did see a sparrowhawk flying over the garden during the hour, but the instructions tell you (sternly) to count only those birds actually in your garden. Curses.

On Saturday, we visited an exhibition at the Ikon Gallery in Birmingham of Japanese woodblock prints by Utagawa Hiroshige. Being a printmaker himself, Mr. Bsag is very interested in any kind of prints, and I love Japanese art of all kinds. It was a great exhibition, with some really stunning pieces of work in it.

Most of the prints were the kinds of compositions that you tend to associate with Japanese art: the paper is usually oriented in ‘portrait’ format, and often very tall and thin, with a view from above of a distant landscape. Many contain fields or forests in the foreground, a body of water of some kind in the middle distance, and mountains in the background. They are precise and beautifully composed, often with diagonal lines leading your eyes back and forth across the paper from the bottom to the top.

However, some of the pieces were very unusual in composition, and I loved them for their boldness. Hiroshige often placed a very large object right in the foreground of the picture, letting our eye travel past it to see the background. So, for example, there is one print in which a wooden pillar forms the left edge of the image, with a large paper lantern in the top right, and we can see a street beyond. Another print of a plum tree has the trunk and blossom of the tree almost filling the very near foreground, and you can just glimpse people walking past in the background. Van Gogh was evidently also an admirer of this print, and produced a version of it in oils.

A few prints show scenes of the interiors of houses, or holiday gatherings beside the sea, and in them Hiroshige places people in the frame so that they are literally cut off by the edge of the painting. It gives the prints an intriguing feeling, as if you are missing some of the story, and makes you keen to find out what is going on. They feel strikingly modern.

I’ve never been to the Ikon before (despite living in Birmingham for 3 years now!), but I liked it a lot. It has an old façade (Edwardian or Victorian, I think), but a very open, modern interior. There’s a glass lift inside a glass window on the outside of the building, so that you can look at the outside as you ride in the lift. There’s also an audio installation in the lift by Martin Creed. ‘Work #409’ is a piece “For lift and choir of bass, tenor, alto and soprano voices”, performed by Ex Cathedra. As the lift ascends, they sing an ascending scale, with a descending scale for the lift descent. We don’t normally travel in lifts for just a couple of floors, but it was so much fun listening to the choir providing a soundtrack to our short journey that we went up and down a few times. If you try it yourselves, I recommend descending from floor 2 to the ground floor for the best sonic experience!

I was less keen on another piece which is on the glass wall next to the lift. I forgot to note who it was by, but it’s called ‘Imaginary Landscape’ and is comprised of vinyl lettering on the window, with lines referencing objects or colours which do not exist. So there are lines pointing to invisible Herons (and their Latin name), or a particular shade of yellow. Like many conceptual pieces, I found that it was vaguely amusing for a couple of minutes, but once you’d got the joke, there wasn’t much more to say about it.

However, it did make me think that art is the only field in which you could get away with that kind of thing. I was fantasising about submitting a manuscript to a journal with the headings printed for each section (‘Methods and materials’, ‘Results’ and so on), but no text beneath the headings, and an empty figure with an arrow referencing “Highly significant result which will change the course of biology”. At the bottom would be the line:

I CAN HAZ NATUR PAYPR NOW?¹

¹ This is LOLCat language, in case you are wondering. ↑

I’ve got a secret liking for Heston Blumenthal’s ‘In Search of Perfection’ cookery show on TV. On the one hand, I’m somewhat appalled by his sheer profligacy with energy and ingredients in order to produce a very small quantity of fancy food. On the other hand, it’s hard not to be drawn in by his enthusiasm, and by his scientific approach to creating what he regards as the perfect dish.

Given the season, it was inevitable that this week’s programme was about creating the perfect Christmas meal. While most people feel pretty daring if they try cooking a goose for Christmas dinner, rather than the staid old turkey, Heston — as usual — took culinary daring to a new level. He was determined to have a first course (after the wafer that smelt of babies) containing gold, frankincense and myrrh, stubbornly refusing to accept (until the last minute) that myrrh actually tastes pretty awful, and is bitter as hell. Obviously he doesn’t pay attention to the lyrics of Christmas carols. He reluctantly admitted defeat on that one, and whittled the myrrh twigs into teaspoons to stir the frankincense tea with, but you could tell that he felt it was cheating.

Each of his dishes seems to take about a week to complete, in 43 easy steps, some of which require vacuum pumps, liquid nitrogen or an edible, heat-proof gel that sounds distinctly unappetising. He must have a carbon footprint the size of China: he travelled to Siberia (which, incidentally, looked absolutely ravishing) for 2 pints of reindeer milk to make into ice cream, and many of the 43 easy steps for each dish seem to require boiling something for 5 hours.

The funniest part (though not for the geese involved, I’m sure) was his attempt to raise geese in a calm, stress-free environment, feeding them on pine needle-laced food to impart a Christmassy flavour to the meat. I’m sure he’s right that meat from calm, unstressed animals tastes better, but I’m not so sure that chasing two geese around a field, holding them in a very awkward and unpractised manner, and then isolating them in an unfamiliar stable away from all their mates is the best way to produce a serene Anserine environment. When Heston ¹ placed the goose in a very flimsy enclosure within the stable, it evidently presciently decided that Something Was Terribly Wrong, and immediately bust out of the enclosure to make a break for the safety of the field and its flock mates.

¹ For some reason, he held his goose gingerly away from his body as if it was an unexploded bomb. ↑

Quantum mechanics blows my mind.

No matter how many times someone patiently explains (usually with the help of ping-pong balls) that it is possible for atom-sized objects to exist in two places at the same time, or to be both a particle and wave at the same time, I end up saying, “Wha… Bu…?” and looking gormless. Inside my head, my inner Scotty¹ yells into an intercom “The engines cannae take it, Cap’n! The dilithium crystals are gonnae blow!”, while being showered with sparks from an overloading console. I think of myself as a relatively intelligent person, and I do a fair bit of thinking about abstract things most days, but I can’t seem to get a mental hold on a theory that involves completely non-intuitive ideas that blow raspberries in the face of common sense. I do enjoy it though; it’s the intellectual equivalent of riding on a really intense rollercoaster — very scary, but rather exhilarating.

So I could sympathise completely with the look of terrified bewilderment on E’s face as various physics professors tried to help him understand quantum mechanics in the documentary Parallel Worlds, Parallel Lives. E (Mark Everett of the band Eels) was trying to find out about his father Hugh Everett III, who was the originator of the idea of parallel worlds (the ‘many-worlds interpretation’). Hugh died when E was quite young, and it sounds like he didn’t communicate much with his children when he was alive. E lost all of his immediate family within a relatively short space of time, so it’s understandable that he has — until now — found it quite painful to think about. It was a wonderful documentary, both from the perspective of the science, and the personal journey E went on. After talking to friends and colleagues of his father, he ended up feeling like he knew Hugh a bit better, and seemed to be more at peace with his past.

One of the bits I enjoyed most was when E was listening to some dictaphone tapes his father recorded, which he had never heard before. He wasn’t even sure that he would recognise Hugh’s voice, because he died so many years ago, and spoke so seldom in the home. In the end, he did recognise his voice, and was amazed to hear him sounding so talkative and enthusiastic, while chatting with a colleague. E had already said that his father was quite tolerant of his adolescent drum practices, and sure enough, half way through the tape, a loud drum solo comes in the background, and we know exactly who is responsible.

¹ What? You mean you don’t have an irascible Scottish Starfleet engineer in your brain? Just me then… ↑

There’s a really cracking documentary about photography on BBC Four at the moment, called Genius of Photography. The first programme looked at the historical origins of different photographic methods, and the social and artistic changes that it brought about. Like all good documentaries, it told me some things I didn’t know before, and made me think about photography in a slightly different way.

For example, they explained the process of making daguerreotypes, and showed some examples, both from the 19th Century and contemporary images. I knew the name, but had never really considered how they were made. You have to expose a mirror-polished silver plate coated with a layer of silver halide to light, and then you exhibit the original plate after developing and fixing the image. Daguerreotypes are really the antithesis of modern, digital photography. The equipment is expensive and cumbersome, the developing and fixing process is labour intensive, not to mention the fact that it involves mercury vapour, for added peril. It requires a lot of skill, and to cap it all, you can’t reproduce the image: the plate is the image, and cannot be duplicated or printed. But boy, are they beautiful.

I’d only ever seen still images of daguerreotypes, but watching film of people holding them, and seeing the images from different angles, you get a much better impression of their almost three-dimensional appearance than you do from a still reproduction. They also showed some contemporary daguerreotypes (you can see some lovely examples by Jerry Spagnoli here) which were really stunning, with a beautiful tonal range and an odd feeling of intimacy. Perhaps it’s partly their rarity, uniqueness and the craft that has to go into making them that makes them feel so special.

It’s the 50 year anniversary of the disastrous fire at the Windscale nuclear reactor, and there was an excellent documentary on BBC Two on Monday. I knew the basic story of the fire, but not the details, which — it has to be said — were fairly terrifying. It could easily have turned into a far more serious situation, but for the actions of staff at the site.

As they said in the documentary, because it was Britain’s first nuclear reactor, they had no idea what to do when the fire broke out. The deputy general manager, Tom Tuohy, described climbing up on top of the pile, opening an inspection hatch and seeing a raging inferno inside the graphite core. I can’t remember his exact words in the documentary, but he grinned and said something like, “I remember thinking, Blimey! What a mess.” Classic British understatement strikes again… They took the brave step of running water through the pile, without knowing at the time whether it would put the fire out or cause a massive explosion. In the end, it did neither; the fire still burned because of the air blown through the pile which was also supposed to cool the uranium cartridges. Again, they had another terrible decision to make about whether to leave the fans running and risk spreading and feeding the fire, or turn them off and risk further overheating. They chose to turn the fans off, and luckily the fire went out.

The whole situation seemed to have been exacerbated by corners which were cut in the Government’s rush to manufacture enough material to produce a H-bomb and convince the Americans that Britain was a genuine nuclear power, worthy of sharing their nuclear secrets. Parts of the aluminium cooling casings surrounding each uranium rod were trimmed to try to increase the output of plutonium, which probably contributed to the overheating problem. The safety measures also seemed laughable — the workers were poking the cartridges out with old scaffolding poles at one point (reminiscent of something Homer Simpson would try to pull off), and they were only protected by flimsy looking plastic suits and rudimentary breathing apparatus. Macmillan’s report covered up the poor decisions and pressure imposed by the Government, and blamed the fire on an “error of judgement”, which was grossly unfair on all those who risked their lives to try to get the fire under control.

It seems that I may have brought a little stowaway back with me from Brazil. A couple of weeks into the trip, I noticed that I had a small lump on the bottom of my left foot, between my big toe and second toe. That wasn’t very surprising, because I am — as I have said before — a mosquito magnet, and had gathered a impressive collection of bites by that time. However, this one seemed a bit different.

[Squeamish readers, please look away now.]

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I caught the end of a really dreadful Panorama programme on the supposed ‘dangers of Wi-Fi’ yesterday, and was glad that I hadn’t seen the rest, because I might have put my own health in danger by lobbing a heavy object through the screen of my TV. After a bit of calmer reflection later on, I wondered if I’d got an unbalanced view of the show by only watching the end. Perhaps they had presented the scientific evidence in a thorough and balanced way at the beginning, and it only degenerated into doom-laden narration and sinister, pulsing Wi-Fi router graphics at the end?

Judging by the write-up on The Register, the whole thing was uniformly bad. They managed to compare the radiation level tens of centimetres from a laptop with that hundreds of metres from a mobile phone mast, all without mentioning the inverse-square power law. ‘Evidence’ was talked about without giving any details of the methodology used, whether the studies were performed double-blind, or whether the levels of exposure used in animal studies were in any way comparable to normal exposure levels in humans.

People are bad enough at understanding and making decisions about risk and probability without presenting a one-sided account like this, unsupported by evidence. How many of those who protest that Wi-Fi in schools is harming their children drive their kids around in cars or let them play in the sun without sunscreen?

I’m tempted to use a recording of the programme as a teaching aid for my students. Their task would be to identify every instance they can find of scientific inaccuracies, distortions or subtle manipulations of the viewer, perhaps with a small prize for the person finding the most errors. At least then this Panorama programme would have some educational merit.

Lecturing is a strange thing. I’ve been doing it for a while now, but I’m still learning a lot. I gave my last undergraduate lecture for the academic year today, so I’ve been reflecting on the process.

Despite the fact that you are — ostensibly — just standing at the front and talking (with the occasional bit of laser pointer waving), it involves a surprising degree of parallel processing. I don’t use notes during lectures, but I do make sure that the text on the slides is detailed enough to prompt me with points that I might not remember on the spur of the moment (this also helps students on the handouts, or course). But typically, you’re trying to lead the audience through the points you’re making, linking ideas together to form a coherent story, sometimes between lectures or modules, and preparing them for a new idea, so there’s a lot of off-the-cuff improvisation around the bare content. I had an experience today when — as I was talking — I saw an acronym that I couldn’t immediately translate. As part of my brain was talking out loud about the first section, another part was fishing about for the expansion of the acronym. This time (it certainly doesn’t always pan out so well) it came up trumps just as I had to talk about the acronym, and slipped the speaking bit of the brain the right words very smoothly. Score!

I can’t speak for the students, but when this process works well, I find it extremely satisfying, almost like a mental/verbal equivalent of dancing. When it doesn’t work, it can be excruciating, stumbling over every idea and garbling explanations. Either way, it’s exhausting, so I’m glad to have a bit of a break before the next round.

A post by Jason Kottke about origami got me thinking about how we learn new skills and the role of instruction. By coincidence, I spent some time at the weekend trying to do some origami myself. The Saturday edition of The Guardian newspaper printed some patterned and coloured squares to cut out, along with instructions to create cranes, cicadas, penguins and sloths, among other things. I had a go in an idle moment, and did fine with some and got completely baffled by others. The sloth, for example, totally defeated me.

Even with step-by-step instructions, there are some folds that you just have to play or experiment with in order to understand them. It might be better if you had someone demonstrating the procedure live, but I still think that there are parts you have to understand structurally in order to be able to do them properly. Like many complex skills, the best an instructor can do is to draw your attention to the salient parts of the process so that you’re not randomly trying things, and to steer you back on course when you veer off it.

Thinking along those lines, the photograph of the incredible origami silverfish created by Robert Lang, and the staggeringly complex crease patterns that go along with his designs are even more impressive. The crease patterns only show part of the story of course; you still need to know the pattern of manipulating the creases in order to create the 3D structure, and that seems unimaginably hard unless you’ve got Jedi-level spatial visualisation skills. As Robert Lang himself says:

The creases all work together when they are fully folded, but it is often the case that there are no intermediate states — no subsets of the creases — that can be folded together, which would form the individual steps. For such a model, the only way to assemble the model is to precrease all of the creases, then gently coerce them all to come together at once with a minimum of bodging.

[…] Small wonder, then, that to many people, the concept of an origami crease pattern as a form of origami instruction is more than a little reminiscent of a famous S. Harris cartoon in which a scientific derivation is described by the phrase “then a miracle occurs…”

I’m in awe of his ability to produce these amazing origami pieces, when I have trouble with a very abstract, 2D sloth and step-by-step instructions.

Alan’s recent post about a crab spider reminded me that I never followed up on my promise to talk about Brazilian giant flattened spiders. True, I haven’t exactly been deafened by people wanting to hear the story, but since when did I write things that other people wanted to read? Despite the earlier billing, this spider wasn’t exactly giant, but it was big by the standards of British spiders. I should also say that, while I’m generally not frightened of spiders, invertebrates aren’t really my thing, and I don’t like spiders of unknown species and biting propensity creeping up on me¹.

My colleague and I had been working quietly on the balcony of the hotel room, when we suddenly saw this big, flat, grey, ghost-like spider. Our first instincts were solidly scientific — we took the photograph you see above, complete with carefully placed binoculars for scale (the diameter of the binocular is about 4cm). This was swiftly followed by a very non-scientific, big-girl’s-blouse moment when we flicked it gently but firmly off the balcony with a long ruler.

A few hours later, I turned my head slightly and saw the same species of spider (perhaps even the same individual, back for revenge!) a few centimetres behind my head, sitting on the wall of the chalet in the perfect position to hop onto my neck. Eeek. I didn’t scream, but I did move away from the wall fairly sharply. We stood at a safe distance and looked at the spider, speculating about its unusual flattened body plan, and coming to the unwelcome conclusion that it was perfectly adapted for slipping underneath closed doors. There followed a lot of activity in which ring binders, books and other stacks of paper where jammed into the gap under the closed door to form a spider exclusion zone. I spent the rest of the evening looking nervously over my shoulder at the spider on the wall, not sure whether I would be more relieved to find it still there (where I could see it), or gone to an unknown location.

Now that the memory is several months old — and the spider itself is safely several thousand kilometres away — I’d quite like to know what species it is, and whether I was worrying about nothing.

¹ Before anyone else points this out, yes, I do know that very few spiders will bite a human unless provoked or in imminent danger of death. It’s just that there’s something about a big, unfamiliar spider that tends to override this knowledge in a primeval way. ↑

I’ve been playing with a couple of new software tools recently which are designed to help with either the reading (Papers) or writing (Scrivener) process. Papers is available as a ‘public preview’ and so has a number of rough edges, while Scrivener has reached a highly polished version 1.0, and has been rightly lauded by many people including Merlin Mann.

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I sometimes amuse myself in idle moments by trying to compile a list of my ‘Desert Island Animals’ — those animals I would most like to watch (not eat!) if stranded on a desert island devoid of other life. It’s always very hard to choose, but collectively, Birds of Paradise often rank highly (choosing among the Birds of Paradise, however, is nearly impossible). So I was delighted to see some excellent footage of several species on the ‘Jungles’ episode of Planet Earth.

It isn’t just that they are brightly coloured: many birds are. Birds of Paradise¹ have so many pop-up crests, chest shields, cloaks and deely-bopper-like head appendages that they can change the outline of their body completely. They are the Transformers of the bird world. As if that wasn’t enough, they often accompany this visual transformation with an eccentric dance and an unearthly sound.

The Superb Bird of Paradise (Lophorina superba) is a great example of this principle. At rest, it looks like a pretty black bird with a striking metallic turquoise chest, but when it displays, which you can see in this clip, it erects a set of feathers to turn its whole front elevation into a vertical elliptical shield, with a huge turquoise segment. Just in case that doesn’t get the female’s full attention, he throws in a clicking sound like someone trying unsuccessfully to light a gas stove, and bounces up and down in a sexy fashion. If you haven’t seen it before, you’ll be staring and yelling “Whaaat!”. Even if you have seen it before, you’ll be wondering (in the original sense of the word) how the heck you turn something bird-shaped into something that looks like the Superb Bird of Paradise when displaying. Birds of Paradise: Birds in Disguise.

¹ That is, males do. The females are brownish and ordinary-looking. However, they are the architects of the males’ amazing displays through their choice of mates, so they are impressive in another way. ↑