illuminating science

On a vaguely related note, I was watching a little caterpillar bungy jumping down from a tree at Uni the other day. It descended down on a silk thread it had spun, then was slowly working its way up. It was really quite impressive - it held onto the thread using a few of its middle legs, while using the front pair of its (many) legs to reach up and grab the silk. Then it would pull down hard, swing its body up and capture that thread it had been holding onto with its front legs in its second front legs. It then would wrap that thread into a little ball which it would work down to its middle. Then, it would repeat the whole thing and move a little higher. It was really quite incredible, and it moved relatively fast up the thread.

Then, after it had gone about one metre up (I was still watching, enthralled!) from out of nowhere, this bird swoops down right in front of my face with its beak wide open, scoops up the caterpillar and is gone, leaving me startled out of my wits. I’m sure there’s a moral to this story, but I can only salute this poor, brave, little caterpillar.

Also, the title of my last post (”Don’t like snails? Try caterpillars!“) was supposed to be about using caterpillars to get rid of snails in the garden, perhaps with a slightly ironic twist given that both eat leaves…Well, you get the idea. Anyway, it was not suggesting that you should eat caterpillars if French food doesn’t agree with you. Although, if you’re really into insects try scrolling down a little way on this page! Mmm-mm!

Today’s guest post comes from Jenny Riesz, a PhD student in Physics at the University of Queensland. Her research is in the field of biophysics; she studies the biological pigment melanin. Read on to find out more! - Joel

Melanin a dark pigment that colours your hair, eyes and skin. It’s found in a huge range of species, from plants, to bacteria, to mammals. There are many different types, but we’re mostly interesting in those that colour skin – eumelanin and pheomelanin. Eumelanin is very black; squid ink consists mostly of eumelanin, with some protein. If you have dark colouring, you have a lot of eumelanin in your skin and hair. Pheomelanin, on the other hand, is red-yellow (red-heads have a lot more pheomelanin than eumelanin). You can see me in the picture in our ‘wet lab’ with a black melanin sample. This will be diluted down until it is almost transparent for spectroscopic measurements.

Melanin is also found in the inner-ear and brain stem, and no one really knows what it does there. We do know that it does something, because melanin deficiencies have been linked to Parkinson’s disease, and white cats (with low melanin levels) are often deaf.

Melanin acts as a photoprotectant in your skin. This means that it’s very good at absorbing light from the sun and dissipating that energy harmlessly (particularly the most dangerous high energy UV light). What’s really interesting is that some people think that melanin can also become carcinogenic, and actually cause the cancer that it is supposed to protect us against. We’re interested in working out why and how this happens, and eventually, how to prevent melanomas.

To study melanin we do spectroscopic measurements: we shine light of different wavelengths (colours) into a sample of melanin and watch how it interacts (does it fluoresce? How quickly and brightly?). We’ve discovered that melanin does fluoresce a little bit of light, but most of the energy is dissipated as heat – about 99.9%! And it does this very quickly – it only takes about 12 picoseconds (that’s 0.0000000000012 seconds!). We’re still trying to understand how it does this by doing calculations and building theoretical models.

I am also particularly interested in the structure of the melanin molecule. Unlike DNA and many proteins that have well understood structures, melanin is very hard to characterize. We know the basic building blocks that form it, but we really don’t know how they connect together to form the black pigment. Knowing the structure is very important if we want to build models to understand how melanin absorbs and interacts with light. Even though melanin has been studied for decades, it remains a most mysterious molecule!

Fascinating article on speciation on BBC news at the moment. It’s about how separate species actually form, something which I’d never really thought about before.

As you probably know, the basic idea of Darwinian evolution is that with each generation, random mutations or interesting combinations of genes give the individuals different abilities. Those with the best abilities are most likely to survive and breed, hence passing on their abilities to the next generation. In this way, eyes gradually develop from small llight sensitive cells to the amazing things we have today.

But if evolution is always moving forward, why do we end up with different species? Different enviornments is of course important - like fish moving onto the land to avoid the competition from other fish. Or, if you get two groups of animals separated (by say a river, mountains, etc) then each undergoes their own random changes, and develop differently. When they finally meet up, they might no longer be able to breed.

But what about species of, say, butterflies? They all eat the same thing (basically), live in the same places, etc. So why should they end up as different species which can’t interbreed - why not just one species, the best, winner takes all?

What researchers have found is that when closely related species of a certain type of butterfly live nearby, they develop different markings and tend to mateonly with those butterflies who have the “right” type of markings (i.e., of their species). It seems that mating with closely related butterflies produces strong offsprings, whereas mating with close species, although possible, produces weedier offspring that are less likely to survive. In this way, they can concentrate their gene line, and eventually become two separate species!

The article has quite a bit more detail, and is very readable, so go and check it out for more details.

Well, it looks like NASA is ready to give it another go - the shuttle launch is scheduled for two days time, even if the same fuel sensor malfunction occurs. After thorough checking it seems they can’t find anything wrong, so they’re going to monitor everything carefully and then away they go.

Fingers crossed! There’s less than week left before the launch window for this month closes, and they’re forced to wait until September. I’ll probably be off exploring Japan, so I’ll probably one of the last online to know - but here’s hoping. Good luck, guys!

Well, tomorrow I’m off to Japan! The choir that I sing in, Canticum auditioned and was accepted to sing at the World Choral Symposium in Japan. This is a gathering of choris from around the world, including both concerts and workshops. I’m not so excited about the workshops (most don’t really interest me) but the concerts should be great! It’s pretty cool to be going to sing for about 2000 people…! We’re then going on a little tour of some of the nearby towns (singing at places as we go!) and then finally singing at the Australian pavillion of World EXPO. So that should be great fun! Finally, my partner and I are going to take a few days off and explore some of the nearby mountain villages, including one that has been preserved in its “Edo period” look, with no cars, powerlines or aerials allowed to mar the illusion! Supposed to be a lovely place to visit, even beyond that.

I’ve been singing for ages, and although my favourite style is jazz and barbershop quartets, I do enjoy classical music too. As part of our tour we’re singing a wide variety of music, including a fabulous piece mundanely titled “Three Australian Bush Songs” by Ian Grandage. It has three parts called Dawn, Birdsong Chorus and Sunset, and they all brilliantly capture the Australian outback! I’m normally very cynical of Australian bush songs (let alone the hideous Austrlian Christmas carols…with the possibly exception of Aussie Jingle Bells which is so accurate it’s actually good!) But this piece really captures the sound of bird calls in the morning (done by choir members!), cicadas and the molten sunset…It’s great fun to sing to!

So, the upshot of this is that my posting may be a little sporadic over the next two weeks. I’ve been writing a few posts in advance about various things I’ve found interesting which I’ll post during my time away in case I can’t do anything else, and hopefully I’ll still find time to keep up to date on things and post about what I read as well.

Oh, and just in case you’re interested in my career as a Barbershop performer, I found the old webpage of my barbershop “The BS“, which includes a terrible recording of us singing at Government House in Queensland. We couldn’t hear each other at all because of the way the microphones were set up (we got all this distorted reflected noise which even overpowered hearing the person beside you…) but it at least gives you an idea. “When I’m 64″ was our signature piece Anyway, you can’t see our facial expressions and actions which was always half the fun! Barbershop has got to be my favourite vocal style - I really like jazz and male a cappella too. But I like classical music as well (and hence Canticum choir)!

Well, I submitted my paper today. Finally! Fingers crossed that I get good reviewers (My supervisor and I recommended several which I hope will like the paper…) From here, my paper gets sent to the Editor who makes sure that it’s relevant to their journal and has at least some chance of being published. Then, they select several reviewers (possibly using my recommendations, or possibly not) and sends a copy of the paper out to each of them. The reviewers read it, comment on it, and eventually decide whether they think it’s worth publishing. Finally, the paper gets sent back to the editor, who makes a final decision based on the reviewers’ comments, and passes it on to me. If they say yes, then it gets published! If no, I might have a chance to argue my case (and discredit their arguments against me!) and try again. We’ll see.

For this journal particularly it was quite a lot of work to get it into a form they could handle. I, like most physicists, write my papers in LaTeX, which is vaguely like HTML, in that instead of just selecting italics and typing, you actually tell it: \emph{some stuff in italics}. Then, you “compile” your paper, and LaTeX converts all those things you told it into the correct visible interpretation. While it might sound like a lot of extra work, it means that you don’t have to stuff around with Microsoft Word’s fonts or picture layout ridiculous paragraph indenting procedures. You just type your text, tell it what what different things are, and then it makes it look right. (E.g., I tell it that this is a new section called “Results”, and it automatically starts a new paragraph, does the right indenting, and heads it “Results” in bold.) It’s also great for maths - you write out your maths in “English”-style language, and it converts it to the proper symbols. Cool!

Best of all, you can very quickly change the entire look and feel of your document - every publisher has their own “style file” which tells LaTeX how it should typeset section headings or paragraphs, whether it should be one column or two, etc. So to switch journals, simply recompile your writing with that new style file! I can’t recommend LaTeX enough - I only use Word now for when I’m knocking up really quick documents that don’t need to look good.

Anyway, the point of all this was that this Journal made me jump through ridiculous hoops to get a single LaTeX file I could upload (for those in the know, I had to put my extra style files and my bibliography file all into the one…gah!) Then I had to separately upload separate files containing info about my paper, who I’d recommend as reviewers, a cover letter telling them they should definitely publish my work because it’s wonderful (ahem)…I’m exhausted!

And on that note, I’m going to go home, have some dinner, and then head out for some dancing! (Swing dancing, that is, for those of you who’ve just joined us…) Looking forward to my weekend…

There’s a neat little story on Nature News today about measuring the speed of electrons. Apparently, this group has done sensitive X-ray measurements of the movements of electrons in and around atoms. It’s pretty cool - it takes about 150 attoseconds (150 billion billion billion billion billion billionths of a second. I think.) for it to “orbit” around the nucleus, and 320 attoseconds to jump from a sulphur atom to a ruthenium (a typle of metal) surface nearby.

What I don’t completely understand is how they track the movement of the electron. See, in quantum mechanics electrons aren’t solid little cricket balls or anything like that - there’s uncertainty in where they are, and even how fast they’re moving. You really need to think of them as little “clouds” of electrons, where the electron is actually everywhere within the cloud at once. (Don’t worry - three or four (or five or six) years of quantum mechanics will make that a lot more understandable… :)) So they actually had to watch for the whole probability cloud to move between atoms, by looking at how the X-rays they sent in were absorbed. So it’s pretty neat!

You might be wondering why they were doing this. Well electron movement is critical for many (all?) chemical reactions, and if we can better understand how the electrons move we might be better placed for designing new compounds that perform a specific task (e.g., catalysts to speed up reactions, or perhaps certain drugs). They’re also trying to look for differences between electrons with different spins (think of it as a basketball spinning clockwise or anticlockwise). This is working towards a spintronics where computers run not on 1s and 0s but on spin “up”s and “down”s. The hope is that this would lead to faster, smaller and more efficient computers. (Note that it’s also different to quantum computers that you may have heard of. These will be classical computers, that do what our current computers do now, just better.)

A supposed “artist” is going to leave a tap running for a year, wasting 15 million litres of water, in an attempt to promote water conservation. While it’s a vaguely interesting stunt, it’s painfully clear that that’s all it is - a stunt, designed to garner publicity for the artist. While it may raise awareness of water conservation, and how much is actually wasting while running the tap, I can’t believe that it’s anything but incidental. No-one seriously committed to conservation would pull a stunt like this.

It’s happening in London, and Thames Water is considering issues a “stop waste” order to the artist, which would result in prosecution if he continued. I think he’s made his point now, he’s got his publicity, and so stopping now would be an excellent idea.

NASA is still looking for the glitch responsible for the shuttle launch cancellation last week. So far, they’ve been unable to find the problem, and it seems more and more unlikely that it’s going to launch this month. That means a delay until the next window in September (after the last disasterous launch, they’re requried to do daytime launches, so that cameras can pick up any potential problems.)

It all raises some interesting questions about “acceptable risks”. There are always risks with going into space, and, terribly and unfortunately, things do go wrong. NASA has been seeking to have the restrictions loosened, particuarly the daytime launch requirement, so that they can do more, sooner. I’d be really curious to know what the astronauts themselves think? After all, they’re the ones with their lives on the line. Where would they draw the line on safety?

Spoilers follow - but I have a candidate for the mystery at the end of book 6! (Don’t read if you want to try and work it out for yourself!) (Update: Comments show that I’m not even the first on my own site! Oh well! )

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At around 10pm last night, cureld up in bed, I finished Harry Potter! I can confidently say it’s an awesome book, probably my second favourite, after book 4. I’m going to comment on some things below (click “More” to see them) but there’s spoilers, so be warned!

There’ll be spoilers in the comments, too, so don’t read them if you don’t want to know! (And you don’t!)

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Well, I bought my copy of Harry Potter on Saturday morning, and as the book progesses I’ve been becoming more and more engrosed in it! So far I like it better than 5, and probably just below 4 (which is my favourite so far). But as the pace picks up, it’s starting to edge ahead as a winner

What’s tough is that I have a hundred and one things I need to do this week, and I just “relaxed” for 10 minutes (=30 minutes) by reading “one” chapter (many chapters…). Highest priority is to submit a paper we’ve been working on. It was unfortunately rejected from the first journal we submitted it to (we had one positive review, one negative, and two ambivalent reviews, which translates to a rejection). I’ve got to make a few minor changes and then submit it this week. This will be my second first author paper (the authors on a paper are usually listed first by the person who actually wrote the paper, then in decreasing order of contribution, with the exception of the last author, which is usually the person in charge of the research group. In my case, that’s my supervisor, Ross McKenzie. For a sligthly more cynical (but surprisinly accurate!) description, check out PhDComics.)

I’m also working on a third paper, and I need to edit it into a form that will be suitable for publication. I’m not great at this yet (I still find writing introductions a killer!) but I’m getting better - I’m a lot more capable than I was 2 years ago when I started my PhD. And that’s nice to know!

Anyway, I should get back to working on these papers.

So, I’ve just finished running a week of workshops for high school students visiting UQ (hello to all those visiting!) It’s been quite an enjoyable week - I’ve met some really interesting students, and had some good discussions, which is always the highlight for me, and hopefully they got some useful information out of it as well.

The activity which we ran was to build capcitors out of film canisters. (A capacitor is a device which is able to store charge - they’re the cylindrical things you’ve probably seen inside computers!) We then charged them up using static electricity, and discharged them to get a spark. Each capacitor can store about 5000 volts (yes, really!) but because it’s such low current (so few electrons) they’re not actually dangerous to use. When we had time, we then went and set off our Tesla coil, which can produce sparks of up to a metre in length, and reaches a couple of million volts. It’s pretty darn cool, and was one of the things that got me hooked into physics (or at very least, doing demos!)

Perhaps the only thing which was a bit disappointing about the week were the few students who really didn’t want to be there. I know that the workshops (not just ours! ) were all booked out, so it seems really unfair for other, interested people to miss out on going while these guys (& girls) can just have the day of school, and distract other people. I guess it’s unavoidable, but it’s still unfortunate.

For those who were there, did you have any feedback? I know you did survey forms, but they were pretty limited. Did you find the activity interesting? Was there somthing you would have preferred? E.g., would you have preferred us to do a talk on, say, black holes or quantum mechanics? Would you have preffered lab tours? What could we do to make the day better for you? I’d appreciate any feedback, and you’re welcome to be anonymous

As per my last post, it’s not long to Harry Potter so I doubt I’ll have time to post anything over the weekend. I might post my first thoughts about HP on Monday

I have to admit it - I’m a huge Harry Potter fan. When the lines open at 9:01am Saturday (Australian local time) I’m going to be there with the, er, youthful readers, then rush home, ignore my PhD and start absorbing this wonderful world. Of course, I have to go out at 10:00 or something ridiculous, but I’ll make a start at least!

I don’t know what it is about the books that are so appealing - I confess that part of it’s the way that the magic really is like science, and yet magical at the same time. It has rules and restrictions, but it doesn’t get bogged down or restricted by it, like it otherwise might. I also just love the wizarding world J.K. Rowling has created, and all the brilliant little quirks in it, and the way she translates “real life” problems into their wizarding world equivalents - some things are simpler, some are not.

But perhaps the best thing is that feeling like it could almost be true - it’s just possible that there really are wizards out there, and you might wake up tomorrow to discover that you’ve got an invite (however late) to Hogwarts…well, maybe not, but it certainly contributes to a ripper story!

That said, however, the secrecy surrounding the Book 6 release is reaching epidemic proporitions! After the accidental (?) sale of a couple of books before Saturday, a courty order was actually issues prohibiting the lucky book holders to distribute, talk about or even read the book! That’s pretty full on! Still, as someone said, this is the book equivalent of Star Wars - and we all know the kind of stink the movie industry kicks up over leaked movies. So why not books, hey?

Anyway, what with the new release, with just rereading the series (I finished book 5 on the plane back from Townsville) and all these trips, I’m going to have to really nuckle down to my PhD!!!

Well, I’m back in Brisbane! Sure, I’m going to be leaving again for Japan in a couple of weeks, but we’ll cross that bridge when we come to it!

Big thing in the news (at least science news!) at the moment is the upcoming shuttle launch in the U.S. Scheduled for Wednesday (i.e., yesterday) it was postponed until Monday after one of the fuel sensors (that measures how much fuel is in the tank) malfunctioned. The astronauts were actually strapped in a ready to go, about two and a hfalf hours before the scheduled launch - can you imagine how that must have felt?! Being all psyched up to go into space, and then having it cancelled on you at the last moment.

Still, with something as complicated as this, it’s far better to be safe than sorry. Scarily, on Tuesday a window cover fell off the shuttle and damaged one of the heat resistant tiles. As far as I can find out, no-one was working on it - it just decided to drop off. Everything has been fixed, but it’s still a little nerve wracking…

Hopefully, though, by Monday everything will be sorted out. The shuttle is to rendezvous with the International Space Station, in orbit around Earth, but due to the position of the launch site and space station they only have until the end of the month to launch, or they’ll have to wait until September before the two line up correctly again. That means I imagine there’s a bit of pressure to get everything working right before July 31!

We’ll see what happens on Monday!

Well, Jen and I are back from out outback trip to Mt Isa! We had a great time, visiting schools in Cloncurry, Richmond and Mt Isa itself, including Mt Isa School of the Air, talking to students who are on properties well away from any town and can’t go to a “real” school. We had a fabulous trip, and met some great people - both students and teachers. I’d like to say hi to everyone from Mt Isa who are (hoepfully!) reading this, and thank you all for your enthusiasm and making this trip so rewarding for us. I really hope you got something out of it, and I’d love to hear from you if you’ve got your hands on an Airzooka or measured someone’s lung capacity with our B.A.G.!

Next week, I’ll post about some of our fun experiences (and not so fun, like the 5 hour night drive, dodging kamikaze kangaroos in a car that weighed less than most of the roos! Tomorrow, however, Jen and I are flying off again, this time to do workshops in Townsville, at Kirwan High’s Thinkfest. We were there last year, and there was a great bunch of students, so we’re really looking forward to doing it again. This year, we’re going to be bringing lasers, polarisers and fluorescing minerals (one of which we actually bought straight from Mt Isa!) We don’t get back until Tuesday night, so I’m probably going to be out of contact again until Wednesday. Oh, and I’ll be able to show off my new fossil collection…it’s probably rather dull to anyone who’s ever owned fossils, but it’s quite cool for me - I collected them myself

Tonight, however, we’re just going order some Chinese, and plonk ourselves down in front of the TV and watch some episodes of Andromeda (a Sci-Fi series which has good and bad moments…Season 4 is supposed to be much better, so we’ll see how we go tonight!) Stay tuned, and see you next week!

Hi all! I’m writing from a slightly dodgy terminal in Richmond, which is a rather small town in outback Queensland. In the rush to get ready on Monday I didn’t have time to post, but I’m spending this week touring the outback doing science shows at various schools, including a “school of the air” in Mt Isa where (with Jenny) I’ll talk to students on remote properties who don’t go to regular schools.

This is part of World Year of Physics, and so far has been a fabulous trip - a lot of driving, but we’ve done two great days so far!

I’ll be back on Saturday and I’ll give some more details about what I’ve been up to then, but I may not be able to post again this week - so check back in on the weekend to hear what’s been happening!