illuminating science

26/10/2006

Honey bee genes give clues to social behaviour

Filed under: — Joel @ 1:28 pm

Honey bees are fascinating insects - they work together for the good of the hive, even at the expense of the individual. They communicate by dance, giving the direction and distance of a food source to the other bees. Queens are made by feeding the larvae protein rich “royal jelly”, which somehow triggers different genes. And they’re able to do all of this despite having only a million neurons in their brains (humans have about 100 billion!).

All of this makes them fascinating insects to study, and things just got better - researchers have succesfully sequenced the honey bee DNA, as published (subscription required) in the prestigious journal Nature today. This means we, in principle, know everything that makes up the bee - and if we can understand how all those genes fit together to produce the complex hive behaviour we might be better able to understand our own brains, too.

So far, they’ve already found some fascinating things, some of the bee genes are closer to verterbrates than insects, particularly circadian rhythms (our internal “biological clock”), the honeybee genmoe evolved much more slowly than the fruitfly, and there are many “molecular switches” called miRNAs which can turn other genes on or off, and it seems that these are responsible for the bee choosing different jobs. So that means genetics plays a key role in the bees behaviour. The next step is to really explore how all these basic rules provided by the genetics fit together to create the incredibly complicated behaviour seen for the whole bee society. How is the bee’s “waggle dance” encoded in its genes? And how did these behaviours actually evolve?

Most interestingly, they want to explore whether there’s similarities between a bee and human behaviour. For instance, some bees go off to hunt for food, while others wait to be told where the food is before going off to get it. Do the scout bees have the same genes that make humans do crazy stuff like bungee jumping? And by exploring the way bees respond and change after being red royal jelly we might learn more about obesity in humans.

23/10/2006

Philosophy Time

Filed under: — Joel @ 3:26 pm

So, as part of the weekly physics lecture series at the University of Queensland, we had a talk on Friday from a philosophy lecturer, talking about the philosophy of time. He was asking questions like, does time flow? Does the past and future exist? And how are these theories if, as general relativity theoretically permits, we think about “closed time-like loops”? That’s where you basically allow for time travel, in some “consistent” way. For example, I find plans for a time machine on my desk, decide to build it, discover it works, and then travel back in time to put those prints on my desk for me to find. Who actually made the plans?! Einstein’s theory of general relativity (and I don’t know too much about this, actually) allows, at least in principle, for such things to occur - but I’m not really sure of the details.

I went in the hope of an interesting lecture on the nature of time, implications for the universe, and so on. I have to confess, however, I was quite disappointed. In contrast to David Chalmers talk on The Matrix, which was rigorous and very logical, I found that the philosophy presented here was more of semantics and language than of real substance. What does it mean for the past to “exist”? How do you define “now”? If you say “only the present exists”, what are you implicitly assuming doesn’t exist? I confess I really couldn’t follow much of the talk - I just wasn’t up on the jargon - but I really didn’t see how any of this contributes to our understanding of the universe, or consciousness, or our minds.

As one questioner pointed out, none of the predictions of these theories could be tested, or would ever produce “different” outcomes in experiment. In fact, that means they’re not theories in the scientific sense, any more than theories of “intelligent design” (a supreme being/god/alien guided our evolution) because if you can’t test it, it’s not scientific. Sure, we’re producing theories of physics which we can’t test - yet. The key is that, in principle, you could test them - and we’re already working toward the next generation of equipment which can help confirm (or, even more exciting, disprove!) our cutting edge theories.

Basically, I guess I can’t see the point in this sort of research. I’d welcome some debate from philosophers, but it really seems a bit “wishy washy” - I want to see some meat! Some definitions! Maybe that’s just the physicist in me, though. That’s why I liked David Chandler’s work - he had real definitions, real conjectures, and really worked with it.

Anyway, two final neat things: we had our obligatory wacky question (along with condescending remarks to students), and I got again to hear philosophers’ habit of saying “sympathetic”, meaning (I think): “I understand where you’re coming from; you’re wrong, but I do see your point of view”. It’s usually in the context of “I’m sympathetic towards Bob’s Theory of Everything, but…” or “I’m sympathetic with people who have trouble believing Jane’s Axiom, but…”! :)

20/10/2006

Pollute to preserve? Artificial volcanos to beat global warming

Filed under: — Joel @ 2:36 pm

There’s a pretty interesting, if controversial, article in the latest edition of Science, on a proposal to deliberately pollute our atmosphere to counteract global warming.

Global warming refers to the recent increase in temperature of our planet, and all of the indications are that it’s because of human activities, most notably the emission of lots of green house gas, particularly carbon dioxide. The rise in temperature of our planet, far greater than has been seen in many thousands of years, coincides very closely with the industrial revolution, and there’s almost no question now that humans are responsible for it. The outcomes are many, but include the destruction of our reefs, change in world climate, droughts, storms, and rising sea levels wiping out costal areas. Unfortunately, because of the costs involved with reducing our CO2 output, many governments (particularly the U.S.) are reluctant to take any action.
Mt Pinatubo eruption
One highly controversial proposal is some sort of “geoengineering” strategy, whereby we change our planet in some other way to counteract these effects. In this case, the basic idea is to replicate some effects of a volcanic eruption, which spews millions of tons of sulfur into the atmosphere. This sulphur (and other emissions?) act to form more clouds, which in turn blocks out sunlight, producing cooling. It’s conceivable that by appropriately injecting compounds like sulphur dioxide into the stratosphere, we could cool the Earth enough to counteract the rise in temperature predicted by global warming. Apparently, after the Mount Pinatubo explosion, there was measurable short term cooling afterwards, so there is at least in-principle evidence that this could work.

The recent article (subscription required) presents climate models which suggests that this type of cooling might actually work, and hold off the effects of global warming indefinitely. It would involve somehow duplicating a massive Pinatubo-level contribution every two years, and the practical difficulties in actually doing this enormous (suggestions include using balloons, giant guns or massive planes), but according to researchers from the National Center for Atmospheric Research, “all the simulations have suggested it would basically work”.

Other scientists are not so impressed - they worry that instead of addressing the real problem (our greenhouse gas emissions) we’re coming up with bandaid solutions. Biogeochemist Meinrat Andreae of the Max Planck Institute for Chemistry in Mainz says “You’re papering over the problem so people can keep inflicting damage on the climate system without having to give up fossil fuels.” Carbon dioxide emissions also produce effects such as acid rain and increased acidity of the oceans, which seemingly wouldn’t be addressed by such a scheme. There’s also the issue that although “the Mount Pinatubo eruption…did not seriously disrupt the climate system”, this is a frightfully complicated system we’re messing with. It’s worth noting, however, that we do currently have very good models of our climate which are able to reproduce most of the the large scale climate effects we currently see (which is why we trust their predictions of global warming), and these models should, thefore, be trusted for this new scenario too.

Obviously, a lot more modelling needs to be done before real conclusions can be reached (a number of conferences and workshops are scheduled for next year, and I suspect this will increase). I’m not sure how I feel about the idea - current models of global warming suggest that we’ve already done irreversible damage to our planet which will destroy at least half our reefs, for example, over the next 50 years. If a “global shading” program like this could actually counteract that, then that could be a good thing. But surely it’s not a good solution for the next thousand years? I just can’t help but think with fossil fuels running out anyway that we’re better to look towards a sustainable economy rather than ways of maintaining our bad habits. The cost and time required for such an operation might be better spent on developing solar power technology (similarly, the massive amounts of money going into finding ways of storing carbon or making fossil fuels cleaner is disturbing). I’d also worry that just when everyone’s starting to take notice of the issues of climate change, if an easy solution like this is suddenly on the table, that people will just thank science and ignore the issue. Besides, I like sunshine!

19/10/2006

The rings of Andromeda

Filed under: — Joel @ 12:09 pm

The Andromeda galaxy, also known as M31, is the closest galaxy to Earth. It’s a spiral galaxy, like ours, but has an unusual property - a ring of stars surrounding the galaxy, and no-one was quite sure of its origin. There’s also strange warping of the the outer edges of the galaxy.

Now, in today’s edition of Nature magazine, new observations (subscription required, unfortunately!) have revealed a second, smaller ring of dust. According to the researchers’ analysis, the most likely explanation for all these strange properties is that a nearby galaxy M32 plunged through the centre of the Andromeda disk about 200 million years ago! Space.com has some cool pictures.

To back this up, they ran computer simulations on Andromeda - starting with basically a spinning clump of stars, they lett it run for a billion years (!) over which time the good old galaxy spiral arms formed. Then, they smashed a small galaxy (M32) into the centre of it. After letting everything settle for another couple of hundred million years, they got a galaxy which looks a lot like Andromeda - it had the two rings, and with the right brightness, and various other key points. The rings themselves are “density waves”, like ripples in a pond, caused by the gravity of the M32 galaxy. It’s not clear cut, but it’s pretty suggestive that at some time on our past, the two galaxies collided.

Beyond solving this particular mystery, while colliding galaxies may have been common in the past, it doesn’t happen so often today. To have a (comparatively) recent collision right next door to us would give us a great opportunity to understand more about galaxy formation and structure. Incidentally, it’s possible (though by no means certain) that Andromeda itself is on a collision course for the Milky Way - but don’t worry too much. Even if our paths do line up, it won’t be for about 3 billion years into the future! :)

Evolution extreme

Filed under: — Joel @ 11:20 am

There’s a rather silly article on BBC at the moment describing one scientist’s idea that in the future humans will evolve into an elite, physically perfect upper class and a troll like lower class. Basically, his idea is that as people become more and more choosy about their partner’s physical (and mental?) attributes, the “best” will only marry the “best” leading to further division. For the most part, I’ve got to think this is downright silly. I think pretty few relationships are based on purely physical looks or fitness, and environment is at least as important as genetics for intelligence, so it seems pretty unlikely we’re really going to see an evolution into Eloi and Morlocks like in H.G. Wells’ Time Machine. And given the report was for “men’s satellite TV channel Bravo”, I think we can safely take it with a grain or fifty of salt.

I would be interested to know, however, whether there really is evolution gonig on with humans anymore - it seems that, at least to a large degree, everyone has the opportunity to find a partner and a family, and so selection pressure (”survival of the fittest”) doesn’t really seem to be a significant effect. There’s some suggestion of evolution over our brains over the last 10,000 years, but whether that’s still going on today? I would wager that the more likely route forward is technological advances - cyborgs, brain-computer interfaces, etc.

On a vaguely related note, there’s a great article in New Scientist about “swarms” of robots which are capable of moving an object too heavy to move for a single robot. The movies are far and away the best part! The behaviour of the robots was tuned through simulations and “genetic algorithms”, where you basically let the program parameters evolve - instead of telling the robots what to do, you give them some basic ideas then keep the best programs, “breed” them, and keep exploring. This kind of emergent phenomena is fascinating; check out NetLogo for some more great simulations you can run yourself!

18/10/2006

The Solar Future

Filed under: — Joel @ 3:10 pm

I went to a great talk on Friday from Prof. Andrew Blakers from Australia National University (ANU), in Canberra. He was talking about their new method for manafacturing solar cells, which makes them very cheap and yet have good efficiency (around 20%, which is apparently about average). The key step was a clever way of slicing up blocks of silicon very thinly and precisely so that they can be layed out onto the solar panel. the cells are also double sided, so if you put a mirror behind them, then light that doesn’t get picked up the first time has a chanced to be used on the way out.

He had some of the solar cells with him - they’re actually flexible! You can bend them (at least to a point :) ), and they keep working just fine! What was particularly interesting was that in his opinion that the solar cells they’re producing will be economically viable alternatives to fossil fuel for energy production - it will cost less to install a solar panel on your roof than to buy regular electricity. Of course, he was a little hazy on the actual timescale, but something on the order of 10 years seemed reasonable, if I recall correctly. Another interesting point was the “energy payback” time - how long do the cells need to function to have produced more energy than was required to make them - is about 1.5 years, shorter than the average of around 3 to 5 years. This is actually an important measure - in the early days, solar cells took so much energy to make, they would have had to run for 30 years before repaying that energy!

One of Austrlia’s energy companies, Origin Energy, has licensed the technology and is in the process of commercialising it, so hopefully we’ll see Sliver Solar Cells coming to a roof near you!

Also today came an announcement from that company I love so very much, Google, that their headquarters (the Googleplex!) will be installing solar panels to provide about 30% of their office power consumption. Producing 1.6 megawatts, it’s enough electricity to power 1000 homes, and their announcement says they expect it to be a cost saving move. Incidentally, Google is also building a new, huge data centre in Oregon, where numerous dams provide cheap and renewable power. Yet again, kudos to Google for being at the forefront of technology.

17/10/2006

Not-quite wave/particle duality

Filed under: — Joel @ 2:42 pm

So what inspired yesterday’s post on wave-particle duality (recommended reading before this one :) ) was a post on Physics Buzz about “wave/particle duality with a droplet made of trillions of molecules”! Recall that the best double slit experiment looking for wave-particle duality clocks in at about 100 atoms, and while experiments have demonstrated various other quantum phenomena at large scales, I think trillions of molecules would be a record for any type of experiment.

Intrigued, I read the actual article (which requires a subscription to read more than the abstract). The experiment describes an oil droplet that’s bouncing on a pool of oil. When you vibrate everything at the right speed, you create a “walker” - the waves created by the bouncing droplet actually propel the droplet forward. Damp the waves, and the drop stops moving; get rid of the droplet, and the waves vanish. It’s a symbiotic relationship :)

What’s neat is that if you fire off this “walker” (droplet+wave) towards a pair of double slits, you get a sort of interference effect, much like you do in quantum mechanics. The wave part of the walker goes through both slits, interferes with itself, and the various reflected waves eventually push the droplet into one direction or another. The actual droplet only goes through one slit, but if you repeat the experiment many times and look at what directions the droplet goes after going through the slits, you see the same pattern as from QM interference.

The article points out this connection, and notes that it’s quite similar to the pilot wave interpretation of quantum mechanics, where the wave function is actually a separate wave that accompanies a particle and guides it to its destination. But the physics is completely different here - although there’s connection with the mathematics, there’s no fundamental relationship between this oil drop experiment and quantum mechanics.

I thought it was a fascinating experiment, and it was an interesting connection to the quantum mechanics formulae. However, the Physics Buzz post was quite misleading, mainly because of terminology. Although wave/particle duality to a non-physicist probably means just that (something which has both a wave and a particle component), inside physics it has very definite meaning - it refers to the quantum mechanical phenomena. So to say the experimenters “demonstrated wave/particle duality with a droplet” is a quite misleading statement! If you’re not a physicist, this probably sounds a bit pedantic, but the reality is that physics (like any other profession - think of law, or medicine!) assigns very special meaning to common words - “measurement”, “field”, “interference”, all these words have a lot of meaning besides the dictionary definition, just the same way that the language used in a legal contract is very important. Use the wrong language, and the meaning is skewed or lost. At best, there’s a lot of head scratching. At worst, you end up with a movie like What the Bleep.

All that said, Physics Buzz has some good stuff, and is worth a read. :)

16/10/2006

Wave/Particle duality

Filed under: — Joel @ 2:34 pm

This post was motivated by an article I just read, and which I’ll comment on at the end, but was also a good opportunity to talk about one of the Big Ideas in quantum physics - something called “wave particle duality”. Normally we think of waves and particles as being very different things. A particle is something like a billiard ball, which has a position, a speed, a mass, etc. It bounces of walls in a very predictable way, bounces off other balls, and is always there. A wave on the other hand is something like sound or a water wave. It’s spread out - it can bend around corners or objects, overlap with itself and even cancel itself out. That last bit is called “destructive interference” and you can sometimes see it (hear it, actually) when listening to music from stereo speakers - as you walk around the room, you might find that at some points the sound almost disappears, while in other places the sound is quite loud. That’s because the sound waves from each speaker take slightly different times to reach you, and sometimes can be “out of phase”, cancelling each other out. (It only works well with good speakers, though, because otherwise the sound waves from each speaker are different enough that they don’t cancel out.) A very cool application of this is noise-cancelling headphones, where a circuit creates a new sound wave to cancel out background noise.

Wave/particle duality, however, is a part of quantum mechanics which says that all of matter - light, atoms, you, me - is both a wave and a particle. The most famous example of this is the “double slit experiment”, where a beam of light is shone at two narrow slits in a screen and projected onto the screen. These slits work just like the speakers I mentioned above - they’re putting out two copies of the same light. If light was a particle, the two beams of light would just go on their merry way and we’d see two bright patches on the screen. But because light is a wave, we instead see this strange banded pattern where sometimes the light waves have destructively interfered with each other. A picture (courtesy of Wikimedia) demonstrates this best:

The double slit experiment, which shows light interferes with itself and so is a wave.  Courtesy of Wikimedia.

What’s odd, though, is that I can repeat this experiment for electrons - firing single electrons, one at a time, towards a pair of slits, and looking where they hit a photographic plate. Since my gun isn’t perfectly accurate, the electron might go through the left slit, or it might go through the right slit. If electrons were particles, as we expect, then we would gradually see bright dots building up in two patches behind each slit. But, amazingly, we see the same pattern:

Check out this awesome movie of the pattern building up. It’s from an experiment by Hitachi, and that site’s a good read. There really are individual electrons hitting the screen, one at a time, in specific spots - just like particles. But the pattern says that somehow, that single electron can still interfere with itself and cancel itself out - just like if it was a wave. Whoa! And it also works with heavier particles, atoms, molecules - and even porphyrins, which are biological molecules. This really is a fundamental property of matter. Other experiments, such as the photoelectric effect explained by Einstein, also show that light sometimes acts like a particle.

Therefore, we conclude that all of matter acts as both a wave and a particle. The resolution is something called the “wave function”, which is a like a wave of probability that describes the position of a particle. It tells us the probability of finding the particle at any given position in space. There’s some probability of the electron going through each slit, and so a wave of probability flows through both, interferes with itself, and eventually reaches the screen. When it comes time to hit the screen, the electron must “choose” where it will strike according to those probabilities - the bright spots are high probability, the dark spots are low probability. You can apply exactly the same interpretation to the experiment with light - and we have a unified explanation for the double slit experiment.

Of course, I’ve glossed over heaps of details here, both the mundane and the exciting (although both are probably relative terms!). I didn’t discuss the mathematics of constructive and destructive interference, exactly how the wave function is tied into probability, or what the wave function looks like, which are all well understood topics. But I also didn’t touch on why or how the electron chooses a given position, which is still the subject of some controversy, or whether these double slit experiments will continue to work for bigger and bigger molecules or even objects like ping-pong balls, a subject of even more “discussion”. Practically, the answer is no (the experiments would be impossible to perform) but would there be intereference to see if we could? There’s the question of why we don’t usually see this wave particle duality, and other quantum effects, in our day to day life. These are really fundamental questions, and while quantum mechanics as we currently understand it works brilliantly, it’s still not complete. These are important, fundamental questions and I think it’s exciting to think that there’s so much new physics waiting to be discovered!

I think I’ll leave it here, for now, and discuss my actual motivation for this post tomorrow!

10/10/2006

Back!

Filed under: — Joel @ 1:47 pm

So as my last post indicated, I have successfully submitted my PhD. It now gets sent to two reviewers who (theoretically!) have two months to read, review and comment on my thesis. After that time, they send it back with their recommendation. This can be either:

  • The thesis is brilliant - congratulations! (Okay, “satisfactory” the is official adjective in use)
  • Once you correct a few minor errors - congratulations!
  • Several sections need reviewing, but once this is done - congratulations!
  • The thesis is insufficient for a PhD, but if you revise it you can resubmit it.
  • Do not pass go, do not collect $200 - the thesis is no good, never will be any good, and you don’t get a PhD. Full stop. End of story.

Clearly, the final option is pretty rare - if you get to the point of submitting, it’s a pretty crummy supervisor (let alone student!) that hasn’t picked up on a thesis that bad before now. Most theses need minor corrections or revisions - you make them, show it to a “chair of examiners” that works at your university, and you’re done. My aunty, Jennifer Gilmore, is one of the few I know who required no corrections at all (and put her on the Dean’s List of Outstanding PhD Theses!). Of course, I won’t mention how many years she’s actually been working on it!

I now have a position doing science outreach at the University of Queensland, which I’m really looking forward to getting stuck into. I’ll have lots of opportunities to visit schools and work with students, as well as other public outreach ventures. And I’ll be putting a lot more into my blog, too!

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