illuminating science

For those of you who’ve just joined us, I’m doing a PhD in physiscs at the University of Queensland in Australia. I’m in my third, and hopefully final, year, which means I’ve got to start getting ready to write up. Ultimately, I’m going to have a big, thick book of work which describes in great detail what I’ve been working on for the last three years. The actual details I’ll save for another post (can’t use up all my ideas at once!) but it’s about trying to make simple models to understand very complex biological systems. We’d like to use techniques from other areas of physics to understand things in biology like photosynthesis and how our eyes detect light. Believe it or not, there’s lots of interesting things there which aren’t very well understood at all!

Anyway, I made my first steps today when I completed the Table of Contents for my thesis. Basically, this meant deciding on what the chapters are going to be, and what sections and subsections are going to be in each chapter. It actually feels remarkably good to have done that - each section doesn’t look anywhere like as challenging as the thesis as a whole did.

Of course, I’m not quite telling the truth - I’ve actually been working on writing up my thesis in bits and pieces as I go - summarising one paper or another, writing an introduction to photosynthesis, or writing papers about my work for submission to journals. So I’ve actually got quite a lot of stuff written already - I just now need to start making it all come together.

And even if it’s 90% blank space, my official thesis page count is now at 21 pages!

Tomorrow and Saturday, I’m off to a conference in Sydney. I’m not sure if there’ll be internet there or not, so I may not be able to post for a couple of days, but if there is I’ll try and write about what interesting things I come across! Otherwise, have a good weekend!

Then again, hot on the heels of my last post (rant?) about bad reporting, the ABC News (Australia!) had on their front page about a neat astronomical planetary lineup that’s happening this week. Mercury, Venus and Saturn will be lined up nicely in the Western sky for the rest of the week - making a nice twilight display (yes, twilight!)
It’s been raining here the last couple of days, so I’ve yet to see them, but hopefully it’ll clear up soon!

Good on you ABC for deciding this was headline worthy Of course, it probably doesn’t compare to a tsunami or politics on the world scheme of things, but it sure beats the latest footy results or yet-another-celebrity-breakup - I think it’s great to go out and marvel at the universe every once in a while

This has got to be the worst piece of reporting, at least in the sensing of damaging science’s reputation, I’ve ever seen. Check out the headline: Boffins create zombie dogs. Intrigued? It’s about scientists working at the Safar Institute in Pittsburg on suspended animation, where someone who is critically injured and can’t get to the hospital in time might be able to be preserved in “suspended animation” for several hours until doctors can treat them appropriately. It’s actually quite ingenious - they drain all the blood from your body, replacing it with an ice cold saline (salt) solution, which effectively freezes your organs so that they don’t deteriorate from lack of oxygen. By the sound of it, your heart would actually stop - you’re clinically dead. Then, they replace your blood and give you an electric jolt with the paddles to restart your heart - and away you go again.

So what’s the report on about? Well, they tested it on dogs, keeping them frozen for several hours before reviving them - hence, zombie dogs. Good grief…Sure, it’s a neat twist - but couldn’t they have come up with something better than “Boffins” creating “zombie dogs”? Do they think people don’t care that this is a technique that could save countless lives? People who are injured in car crashes, in warfare, anywhere where the needed medical treatment isn’t readily available. I may be cynical at times, but surely the world’s population isn’t that bored with science that they won’t read an article like that…? Concerning to say the least…

Oddly, while I’ve heard about this before (it was a lot more theoretical at that stage) there’s only a couple of reports about this on the web at the moment - it makes me wonder if it’s entirely legit or not. If it’s not true, that’s disappointing, but the basic principles are sound, I think - at the very least, it’s being quite seriously researched by several trauma centres. Then again, IANAD (I am not a doctor)! As BrettW points out, the picture isn’t exactly encouraging either. Nonetheless, the way it was reported was shocking - and it it’s false, all the more shocking. (But not necessarily surprising.)

This would be a neat “real life” problem for a maths or physics class: a bunch of record breakers tried to erect a giant iceblock, but it melted faster than expected, and flooded the square with strawberry and kiwi fruit juice. (mmmm….) For 5 points, based on the power output of the sun, its distance from Earth and gueestimating 20% of the power reaches the iceblock (or just looking up the actual power incident on earth - it’s on the web) calculate the rate at which the iceblock would melt, probably assuming a latent heat equivalent to water. The dimensions probably aren’t really important for this calculation, although the block was 7.6m high so you could assume scaling if you liked.

And, I’m sure there are lots of extension questions which could be amusing as well

MIT is conducting a blog survey which may (or may not…) yield some interesting results. The questions aren’t really inspiring on their own, but put together they may form an interesting data set. If you run a blog, why not fill it in - only took me 10 minutes!

If you didn’t read the comments to that post about a guy selling Angelina Jolie’s air, then I highly recommend it - BrettW gave a very thorough derivation (though I haven’t checked his maths…We’ll assume he’s right though!) which suggested at least a few billion of Angelina Jolie’s air molecules would be in a litre bottle, and indeed in my lungs right now, while Luke Lea said this agreed with an earlier calculation they’d seen. Les, a meteorology friend of mine, also suggested that a more thorough answer would need to account for global air movements - how long would it take for air from America to reach us in Australia? Local diffusion is, I expect, quite rapid (think how quickly you can smell an open bottle of perfume or dried herbs) but I’m not sure how that translates to global distances.

I was also reminded of a similar, and scary, question - take a barrel of oil/polutant/contaminant/other-nasty-stuff and dump it into the sea [NB: This is a thought experiment only, thankyou!]. Mix it evenly across the whole planet’s oceans, then take one teaspoon of water out. How many molecules of polutant are in that water? The answer depends on what assumptions you make, but it’s in the 100’s or 1000’s of molecules. From just one barrel! Whoa! Of course, it’s easy to make impressive statements like this because “1000’s of molecules” sounds like a lot, whereas it really weighs next to nothing. But a fact is a fact…

In other good news, the final vote on commercial whaling, proposed by Denmark, was vetoed today, with only two countries supporting it. Further talks are planned over the next year to discuss the issue, but I’m not really clear what they hope to achieve. The IWC is anti-whaling at the moment, and unless more pro-whaling countries join, that doesn’t seem likely to change any time soon. However, with Japan threatening to quit the IWC, might the pro-whaling countries be tempted to support limited commercial whaling, rather than risk losing control altogether? That sounds perilously close to blackmail to me…but maybe that’s just politics! Time will tell, I guess.

Well, a string of good results from the IWC today. Japan lost their bid to resume commerical whaling, and by a decent margin (29 against, 23 for, with a three quarter majority needed to pass). They also lost a bid to resume hunting mink whales, and to remove a decade old whale sanctuary (no hunting, full stop, scientific or otherwise) in Antarctic waters. Finally, Australia championed a “non-binding resolution” condemning Japan’s “scientific whaling” program.

Basically, the commission is very much anti-whaling, and it seems unlikely that Japan (or other pro-whaling nations, such as Denmark) are going to be able to get the resolutions they want passed. This has lead Japan to threaten to withdraw, which would be a bad day for whaling. Actually, I don’t really understand why they’re still in/ever in the commission - what do they get out of it? Anyone know? I assume that international politics plays a role…

Another Japan sponsored vote was the introduce secret balloting (see Wikipedia) which would let countries anonymously vote without revealing their position - perhaps encouraging smaller countries to vote for whaling, an clearly unpopular decision. Again, it was rejected by the committee, and while I do appreciate the positives of secret ballots, I don’t think it’s appropriate here.

The bottom line is I can’t see how this can continue - Japan seems desperate to resume whaling, presumably at the behest of the rich/business types which have the money to afford whale and to have political clout. It would require the Japanese parliament to vote to leave the IWC, and we have to hope that there’s enough members who care about their planet not to let that happen.

If you’ve been following the news (and I’m sorry that I’ve been too busy to post about it the last few days!) then you might have heard that a new spacecraft designed to test solar sails was set to launch today. Fired from a Russian submarine (which had to get special permission to fire a missile that could potentially have contained a warhead, but in fact contained the solar sail set up!) it cost just $4 million (U.S.) and was to be the first test of the actual propulsion of the solar sails. The idea is that the gentle push of sunlight as it bounces of an object, completely negligible to us here on Earth, would slowly accelerate a light enough object with a large area.

Unfortunately, it seems things are not going well - the team has lost contact with the spacecraft. The Cosmos 1 Weblog, but Project Operations Assistant Emily Lakdawalla is a fascinating insight into what it must be like being involved in an operation such as this. I strongly recommend reading from the bottom up (in chronological order) so you can see their thought process and the chain of events. There’s a slow but depressing descent from the optimistic “but that’s not entirely unexpected” to “We don’t know.”

Earlier reports basically said that they were expecting to fail. Well, maybe not quite that (because if so, why waste the money?!) but they did say “It will be a not-surprising failure if it doesn’t [succeed].” It’s depressing, though not nearly so much as the various craft lost to the Martians on Mars. It’s not completely over yet, but I’d say it’s pretty close. Watch the above blog for more details.

Very positive news today, regarding whaling, with the Japanese losing a vote at the International Whaling Commission to restart commercial whaling (whale is a delicacy in Japan). All is not over, however, as there is still a vote to be had on “scientific” whaling, where whales are caught for scientific research, but as I understand it can still be eaten afterwards. Japan wants to increase the number of scientific catches each year.

Quite frankly, I’m appalled at some of the comments from Japanese spokespeople, such as MP Yoshimasa Hayashi who encourages other countries to “recognise cultural differences”:

“We would like to ask them to think about it in this way - that we agree to disagree,” he said.

“We are not asking them to eat whale, but we are asking them to understand that we have a eating way of culture and by some scientific management system we are trying to resume the commercial whaling.”

I’m very much in favour of being understanding and respectful of other cultures, but not at the expense of an entire species. If an animal is endangered, then that should be that - no questions asked, we do whatever is necessary to remove them from the endangered list. Hopefully, that doesn’t mean a dramatic change in lifestyle for us, but if it does, so be it.

In practice, that probably isn’t the case - but it’s great to see the Australian goverment getting out there and very actively campaigning against the resumption of whaling.

Would you buy a jar of air that supposedly contained molecules breathed by Angelina Jolie or Brad Pitt? Maybe - but would you pay $15,000 for it?! Some enterprising character was selling just that last week - a jar which he’d opened then shut as Jolie and Brad Pitt walked past, possibly (but with no guarantee!) trapping air that they’d breathed inside.

Okay, so this is a ridiculous (but effective…) money making scheme, but one has to wonder - how true was his claim really? This would be a great real-world example of a Fermi problem, named after famous physicist Enrico Fermi. A Fermi problem asks you to estimate something, that you couldn’t intuitively guess at, by making rough but educated guesses about a number of things and putting them together to reach a sensible answer. Examples might be “What is the mass of a fully loaded cement truck?” or “How many blades of grass are in a football field?” or even, “How far would the Earth move if everyone in China jumped at once?”

In this case, I can think of at least two interesting questions - “How many molecules breathed by Jolie and Pitt would likely be in that jar?” and “In any (open!) jar anywhere in the world, how many molecules are likely to have been breathed by Jolie or Pitt some time in their lives?” I haven’t done any guesstimations yet, but I’d expect that both answers are non-zero.

If anyone would like to have a go, a couple of starting points might be to estimate how much air our lungs hold (perhaps by large a single breath can inflate a balloon?), how many breaths we make in a minute/hour/day/year, and how old Angelina and Brad are. Then, estimate how much air there is in the whole world…and so on! Remember that all you’re going for is an order of magnitude estimate - round things to the nearest 100 or 1000 or whatever to keep it simple.

Let me know…

I was looking over yesterday’s post about our research group, which I wrote fairly quickly and in hindsight probably doesn’t tell the whole story. It’s all definitely true - we’ve got an amazing group of people with a diverse range of skills, and I really do think that this is where a lot of interesting research is going to happen, on the boundaries between disciplines.

But at the same time, it can be hard work. For example, when we talk to chemists, they rattle off a dozen compounds and how this compound or that oxidisation reaction is going to be important. Unfortunately, I know relatively little chemistry, so it can be pretty slow going to establish a common ground. Equally, it’s hard for me to talk to them about Hamiltonians and various quantum mechanical models, since they know comparitvely little on those subjects. And talking to a biologist is even worse, from both sides! We’re learning that finding a common language can be quite hard work - we even have different names for the same physical models!

But there’s also a more subtle issue, which I guess both helps and hinders, and that’s how we actually think. Physicists are trained to really think about the why and the how of things. They want to understand the big picture, the underlying laws which govern the system. Everything should be able to be derived from basic principles, and (in principle) you should have to remember very little to be able to build up a complete picture of what’s going on. In comparison, I think that chemists are a lot more about the “what“. They need to know what compound will bind with which other, which bond will break first and so forth, but, as I see it, they’re not so interested in the fundamental origins of these properties. And this isn’t necessarily a bad thing. That’s the approach that ultimately lets them be more productive. And after talking to Paul Burn this week, I’m totally blown away by how much a good chemist can tell so quickly about a system! (He was predicting our overnight computer calculations!)

But all this does mean that communications can be tricky. As a physicist, when I’m trying to understand some chemistry property, I find it really frustrating not being able to find a clear explanation of the why and how (this is particularly chronic in chemistry textbooks!). And I’m sure chemists get frustrated when we get bogged down in unimportant details!

I guess that if you’ve got no idea what “should” happen, it’s hard to proceed - you really need some chemistry knowledge to get started. But in the end, you want to try and develop some sort of coherent model and really understand the system, which is something physicists are really good at. In fact, that’s probably a physicist’s strongest attribute - the ability to capture the essential points of a problem and use them to really understand what’s going on.

Another big difference is that “Physicists think the details don’t matter, chemists think they do, and the truth is somewhere in between!” Physicists tend to assume spherical cows, and forget about whethere there’s a carbon or a nitrogen. Chemists, on the other hand, want to model every atom precisely. In the end, some of the details matter, but some don’t - and what my project is really about is working out which are which! I’m biased, of course, but I’ve had disappointing encounters with chemists who can’t see any value in what we’re doing - it’s the details or nothing.

You’ll notice that I haven’t talked about biology in this discussion. Partially, that’s because I know a lot less about biology, but I also see it as a bit polarised. Biologists really do spend a ridiculous amount of time memorising names and whatnot, things which I think you’d be far better just to look us in a book when you need them. This is completely about the “what”, since there really isn’t any “why”. And some biologists then go on and do equally “what” research, or think about things in equally “what” ways (which is still great research!). But others (e.g., genetics) really do focus on the “why”, if not in exactly the same way as a physicist. So it’s hard to classify biologists. (how ironic! :))

So, for my conclusion I feel I should be offering some sort of fundamental insight or advice. However, all I can suggest is that everyone needs to learn a little more about all the other fields and their strengths and weaknesses, and be tolerant of them. Going out on a limb, we need be open to the ideas of the other disciplines, even if they go against our basic “training”, and see how we can use them to do something spectacular. And some of this, I suspect, is a little controversial, but I’m certainly open to argument!

There’s a rather interesting article (with a neat picture!) on Carl Zimmer’s blog about the evolution of beetle horns. Everyone’s no doubt seen a variety of beetles with their quite impressive head gear, but I’d never before realised just how varied they could be. There’s lots of interesting discussion, but for me the most interesting was the picture of horn evolution about half way down, and the discussion of what evolutionary pressures might have caused it. Most interesting!

There’s an interesting article on Wired News about new miniature transistors that are made of only a single molecule, a few billionths of a metre across. Transistors are miniature control and amplification units that let you switch electricity on or off in a circuit, and also amplify a small signal into a larger one. Their absolutely vital for computers, and are a limiting factor on how small we can get chips.

One project has experimentally built a transistor which can be controlled by putting current through a nearby silicon surface. The big issue, of course, is whether you can scale this to the millions of transistors needed for a computer, but it’s certainly a step in the right direction. And, since they’ve actually got experimental proof, that’s a great step forward. One thing that’s interesting, though, is that the actual article doesn’t mention the word “transistor” at all, except in the references. I’m not sure if that’s significant, since I don’t know a lot about the field, but it’s certainly interesting.

The other proposal is much more intrinsically interesting for me, because the transistor runs on quantum mechanics - even at room temperature! Unfortunatley, as the article subtly mentions later, this project is just theory so far - but they have good models and computer simulations which are quite convincing, and the basic principles are well understood and experimentally verified. Even cooler, I looked at their preprint article, and I actually understood a lot of the theory! (See, I really am learning something!)

Basically, what they have are hydrocarbon rings - things like benzene, which is a ring of six carbon molecules, with hydrogens sticking off (hydro-carbons - get it?). They then attach miniature leads to carbon atoms onto the rings, at roughly the 12 o’clock and 3 o’clock positions, say. These are what you want the electricity to flow through, passing through the carbon ring. Now, here’s the beautiful bit - if you try and conduct electricity (which is just moving electrons) around the ring, you begin to see wave-particle duality - the electrons act as waves, which can interfere with each other. This is just like water waves that can combine or cancel each other out. If you set things up right, the electron waves will cancel each other out (”destructive interference”) and no current will flow. But, you can add a third “control” lead, whose voltage you can adjust, and mess up the interference - letting electricity flow. Hence you have a transistor which you can switch on and off, in response to this small signal from that third lead.

What’s cool is that this is completely quantum mechanical - the electrons are interfering with each other, and by controlling this interference you control how the circuit works. And it doesn’t need to be frozen in liquid nitrogen - they claim it will work even at room temperature! Cool!

What’s also neat, from a purely personal perspective, is that they’ve used a simple model to describe the system, which is quite similar to the models that we’ve been using here to describe completely different systems. And that’s the real beauty of these sort of techniques - someone can go and find all sorts of interesting results for one system, then realise that they can use all those results, at no extra charge, to find out stuff about a whole range of other systems!

Again, though, the real issue is whether they can produce it in large numbers. (And they haven’t actually made it for real yet!) But they do say that because it’s a simple chemical molecule, it can be produced by chemical reactions and so it should be relatively easy to make large numbers of identical transistors. So who knows? We might be seeing mini-computers in the not-so-distant future!

Had a quite satisfying meeting this afternoon. One of the things I’m involved with at UQ is a group which is trying to determine the structure of melanin, the pigment that colours your skin and your hair, is missing in albinos, and is responsible for melanomas. I might write about the physics and challenges later, but I won’t get into it now.

What’s really interesting about our group is the range of people we have working in it. On the one hand there’s experimentalists capable of synthesising a huge number of compounds - tell them the structure, and they can (probably) make it. That means we can look at all different variations on what we think are the basic units of melanin, and get information about them. Then, we’ve got experimentalists who take experimental data about these samples - absorption spectra, fluorescence, etc.

Next up, we have people working on simulating these molecules in the computer to predict their properties which can be compared back to experiment, and used to make predictions about what sort of structures we should expect. And finally, we have people (like myself) doing larger scale theory, trying to put some restrictions on what kind of models we should use, how we can interpret the data, and what sort of experiments would prove useful to do next. (Of course, everyone’s doing that last point together!)

It’s really cool being in a meeting with all these different people because there’s such a broad range of abilities - everyone has something to contribute, even PhD students like myself, since I’ve been involved in a lot of the ground work that my supervisor hasn’t. (That said, when the heavy weights talk, I listen! ) There are physicists, chemists and computational scientists (often with people doubling up on roles!) and it’s a really broad knowledge base to draw on.

I think that a lot more of the really cutting edge research is going to be happening in groups like this - mixing several of disciplines, looking at things from different directions, and most importantly not reinventing the wheel (e.g., physicsists trying to discover soemthing chemists have known for years!) And I certainly hope, and expect, that lots of good things will come of our group here!

I was browsing Nature News today, and noticed something rather odd - three of the article were about sex! Not that there’s anything wrong with this, you understand, but I haven’t recently seen any articles about sex recently, and then there’s three in one day.

Read on for a summary (just in case anyone’s a little squeamish!)
(more…)

I know I was going to write about Heron Island, but I haven’t had time to put thoughts to paper (electrons?) yet, as we’ve got a couple of international visitors, staying on after the conference, and that’s taking up quite a bit of time, as well as doing my annual review…blech. So that will have to wait. In the mean time, I overheard (okay, I was outright evesdropping) an amusing conversation (if you’re a physicist, anyway) on the train the other night. This guy was talking to a girl (who could be a poster girl for Clinique with the amount of make-up she had on…) and saying “My friend’s got this brilliant strategy for roulette - he can’t lose. On his first turn he bets $10. If he loses he then he doulbes his bet!” Uh oh. “He bets $20, then $40, and so on until he wins, and comes out ahead.” Ah, if only they’d read my blog…that’s the Martingale Strategy and doesn’t work in the long run - particularly when the house tips the bets slightly against you.

But what I found most interesting, was that he then said “Then, after he’s won, he goes back to $10.” The girl replid “Aaaah…and that’s because the chance of winning again straight away is less…isn’t it?” To which the guy replies “Ummm, yeah, I think so.” Of course, that’s not true - the roulette wheel doesn’t remember what numer it came up on last, and the past results can’t affect the future (in this type of game, anyway). It’s one of the most common misconceptions in probability. It’s hard to understand - if I’ve thrown 9 heads in a row, surely I’m more likely to get tails next? No! While it’s true that it’s highly unlikely to get 10 heads in a row, given that you’ve already thrown 9 of them, the probability of getting one more is 50%, just the same as tails. This is conditional probability, similar to what makes the Monty Hall problem so hard to understand.

I just found it interesting that even though we’re all forcibly taught probability at school, and especially things like this, that so many people don’t get it. Of course, I’m sure I’ve been taught basic things in history or geography that would inspire experts in that field to say the same thing, but I think that mathematics is involved in so much more of everyday life that people really do need to understand it. I wonder, and only half-jokingly - if we taught probability in terms of gambling, would people pay more attention? I mean pretty much everything is there - in roulette it’s easy to talk about average payouts and expectation values. Poker has combinations and permutations, and conditional probability… I suspect some people wouldn’t like it (as in, conservatives would want their children learning that) and there may be some validity to that (you don’t want to encourage gambling!) But then again, if people understood how bad the probabilities were, perhaps they’d never gamble at all!

Well, last week there was a big lack of posts. The reason for this was that I was on Heron Island, attending a conference on quantum materials. By quantum materials, we mean any sort of solid “stuff” where you need to use quantum mechanics to understand how it works. Examples are superconductors (both the traditional metal ones, and new “organic superconductors” made out of carbon, nitrogen, etc.) and OLEDs - organic light emitting diodes, which are set to revolutionise flat screen displays. But it also includes some biological molecules (like the rings of chlorophyll molecules in photosynthesis) which use quantum mechanics to achieve their purposes, and is the subject of my PhD.

Anyway, it was a fabulous conference - and I have lots of interesting things I want to write about as a result. The only stupid thing was that I forgot to post that I was going! (I had it written and everthing…) So hopefully you’re still reading (and, indeed, if you’re reading this, then you are) and will forgive this transgression.

From Slashdot comes news of a report on whether Americans believe in life on other planets. There’s some moderately interesting statistics, like that 60% do believe in life on other planets, and more of those are men than women, or that 46% of churchgoers believe in ET compared to 70% of non-churchgoers.

What I found most interesting, however, was what people thought about what intelligent life would look like on other planets, and what capabilities they’d have. Basically, the majority of people believe that the aliens would look similar to humans, that they’d be more advanced, and that they would have the technology to travel and communicate through space. I wonder how much of this is influenced by shows like Star Wars (or even sci-fi show Andromeda, which is critically guilty) where most aliens are human except for a furry head, or antlers, or whatever can be easily done by the make-up department. (And yes, I know there are many exceptions in Star Wars, but still most are bipeds…)

I’d be really interested to hear from an astrobiologist (someone who studies life on other planets) as to what the current lines of thinking are in science. My gut instinct is that they’d look nothing like us, unless you believe in some sort of convergent evolution, where having a head on a neck, standing upright with two hands and two feet, etc, provides a distinct advantage in some universal sense. (Perhaps life doesn’t require bipeds like us, but intelligent life does? Sounds kind of arrogant…)

A little digging on Wikipedia reveals astrosociobiology, the study of extraterrestrial civilizations and their social characteristics. It’s interesting to theorise, but I can’t help but be a little skeptical…

Anyway, the last interersting tidbit was whether we should respond or not - the vast majority (90%) of believers say yes, and still two thirds of non-believers agree. But some 20% of people would feel “nervous and afraid” if they learned that life existed on other planets - I wonder if there’s any justification for that? I’d like to think that we, as a species, wouldn’t go and wipe out or exterminate another planet. But then again, we do some pretty horrible things… Love to hear from anyone who has their own responses to this survey!