A Schooner of Science

Trojan atom

// January 27th, 2012 // No Comments » // Recent Research

What kind of control we can wield over atoms!

An electron orbiting an excited potassium atom has been confined with radio waves to mimic the movement of the Trojan asteroids of Jupiter.

The Trojan asteroids precede and follow Jupiter as it orbits the sun, like an entourage of bodyguards around royalty. Earth’s first Trojan asteroid was recently discovered, but it’s nothing to the group that Jupiter’s got, numbering over a thousand.

Resembling this comma-shaped group of asteroids, the electron was limited to a confined “wave packet”, say researchers from Rice University, Oak Ridge National Laboratory and the Vienna University of Technology.

How’d they do it? Lasers, radio waves and supersized atoms.

Here’s a video, with my explanation below it.

First they created a Rydberg atom using ultraviolet laser. That’s a highly excited atom, where the outermost electron has jumped up from its normal orbit into a much, much higher one.

As the outer shell electron jumps outwards, the atom becomes bigger. In this case, an unimaginably small potassium atom grew as large as a full stop! Say wha? I mean, that’s HUGE!!! That’s bigger than a bacteria, than a skin cell – from ONE ATOM?! Get out!

Locating that electron, even in a supersized Rydberg atom, is no easy task. Electrons, I was told at uni, wink in and out of existence. They can act as a particle or a wave. Instead of pinning down an electron, you just predict where it’s most likely to be – called a wave function. It’s a fuzzy way of looking at things.

The team could collapse the wave function with a sequence of electric field pulses, which basically limited where the electron would be. That created the comma-shaped wave packet that resembled the Trojan asteroids.

Next job – make it move! They made the localised electron move in an orbit using radio waves, which rotated the nucleus.

Brilliant!

But how can you check where the electron is, and measure your results, when you can’t see it?

The answer was to do it in snapshots. Each snapshots of the wave packet was made using another electric field pulse. Unfortunately, the process destroyed the Rydberg atom, so they had replicate the experiment tens of thousands of times to get enough data to complete the picture.

Seems like a lot of work to make something extremely tiny and wavy move like you want it, but who knows where research like this might lead. To have this kind of control over electons could lead to new types of chemistry, and quantum computing.

Mind blown.

Source: The press release and paper, published in Physical Review Letters this week.

Future floating laboratory, prospectus of the HMS Beagle Project

// December 2nd, 2011 // 1 Comment » // Science Communication

Yesterday afternoon I went to a prospectus to the HMS Beagle Project while founder David Lort Phillips is in Adelaide.

It’s a CRAZY exciting project which plans to build a modern version of Darwin and FitzRoy’s tall ship the HMS Beagle, kitted out as a floating laboratory.

Marine biologists could benefit from getting much-needed ship time. As it’s a tall ship, it can get closer to land than large cruise vessels, giving it an extra bonus to people studying tidal areas. Groups into DNA barcoding might find it useful too, as it can be tricky to get high quality samples for DNA testing – most are set in formalin which ruins the info. More on DNA barcoding soon.

Climate research can be done from the boat, the connection between biodiversity and climate change could be exploited in the project. There’s a collaboration of the HMS Beagle with NASA, combining observations from space with water samples in the ocean.

In 2009 the Brazilian tall ship Tocorime with the International Space Station, and they ran live hook-ups between scientists on the boat, an astronaut above, and school children in Paraty. Looks like Keven Zelnio from Deep Sea News was there! The students had questions written in English on paper which they screwed into a sweaty ball with excitement, according to Karen James, involved with the HMS Beagle Project.

Most interesting for me is the prospect of science communication on the high seas. We can take high-tech science to ports around the world, including remote areas that often miss out on science engagement events.

I’d like to see the online aspect of the beagle able to webcast and tweet from the deck, setting up chat sessions with classrooms and the public. Maybe people could watch the Beagle’s progress through the ocean, and be updated with the science we on the way. Oh, I gots ideas!

At the moment they have blueprints and some collaborations sorted out, but are still looking for funding to get it built and in the water. The first five years it would retrace the first voyage of the Beagle, including along the South American coast.

Chile are planning to build their own ship in connection to the project, possibly named after the Beagle support ship, the Adventure.

Darwin was 22 when he signed on with the Beagle, an amateur with an interest in science – mainly geology. What he saw from the ship and at port, particularly in the Galapagos Islands, lead him to a world-changing hypothesis.

Maybe the new Beagle will have the same effect on some young scientists. Good heavens, I just really hope they build this tall ship, and when they do, that I’m on it helping to share their discoveries online, in ports, worldwide.

Modelling catastrophic dam collapse and natural disasters

// June 24th, 2011 // No Comments » // Recent Research, Science Communication

One of the biggest dams in the world, Geheyan Dam in China holds more water than five Sydney Harbour’s, a massive 3.12 billion cubic metres worth.

What would happen if it failed?

Australian CSIRO scientists collaborated with China’s Satellite Surveying & Mapping Application Centre (SASMAC) to model the region and apply six different dam failure scenarios.

“Our simulations show where the water would go, how fast it would reach important infrastructure such as power stations and the extent of inundation in major townships downstream,” said Dr Mahesh Prakash from CSIRO in the press release.

Dam failure is a real possibility, as many parts of China are prone to earthquakes. We’ve seen plenty of natural disasters over the past year, highlighting the need to prepare for such events.

Modelling and data visualisation can inform emergency procedure development and ensure new infrastructure is built protected areas.

“The modelling technique we developed for this work is really powerful,” Dr Prakash said. “It gives us very realistic water simulations including difficult-to-model behaviours such as wave motion, fragmentation and splashing.”

This video shows a dam failure simulation, and explains how the model was created. I enjoyed the delicious hundreds and thousands demonstration to show how water acts as a group of particles. Yummy!

The same software has been used to model other catastrophic events, including tsunamis and volcanoes. They also modeled the 1928 St Francis dam break in California. The simulation was very similar to the real event, suggesting the technique is accurate.

Inspiring Australia and the barcode of life, conferences

// February 7th, 2011 // No Comments » // Science Communication

Couple of interesting conferences coming up this year. The first one is Inspiring Australia in Melbourne from March 28-29. ‘Tis a science communication conference, tackling topics like social media, politics, and a whole bunch of exciting sci-comm stuff. Registration opens today, and it will be good.

The second conference is the Consortium for the Barcode of Life which will be hosted in bonny old Adelaide in November this year. Adelaide Uni scored the gig after competition with 19 applicants from around the globe. Previously the event has been hosted in Mexico City, Taipai and London.

DNA code is a bit like a barcode to begin with: Information hidden in a mysterious pattern that only a computer can analyse. The barcode of life refers to specifically to a certain small section of DNA which can be used to compare species. The section changes between species, but stays the same within members of the same species, and is accurate for most mammals and bees.

The consortium is to discuss and co-ordinate how to take DNA samples from all the animals IN THE WORLD, and have them on a giant database. Then when future scientists find a weird animal, they can take a sample, scan it in and *beep*, one lemur for $9.99. It’s a neat idea, and totally exciting that Adelaide is hosting this International event.

Radioactive decay of teaspoons in the workplace

// January 30th, 2011 // 19 Comments » // Just for Fun, Recent Research, The Realm of Bizzare

Have you ever noticed a mysterious loss of teaspoons at your workplace? Maybe it’s not teaspoons, but some other cutlery item. At my old work it was forks, which dwindled even when I bought new replacement ones. At the Australian National University neither spoon nor fork were safe, causing some students to eat salad with two knives as chopsticks.

The same thing was happening at the Burnett Institute in Australia. Teaspoons were critically low, no matter how many new ones bought. Clearly it was time for science.

“Exasperated by our consequent inability to stir in our sugar and to accurately dispense instant coffee, we decided to respond in time honoured epidemiologists’ fashion and measure the phenomenon,” they said in the paper.

They numbered 70 teaspoons and placed them in tearooms around the institute. Lo and behold, they started to disappear. Every week they counted the remaining teaspoons, probably with a lot of suppressed giggling and delight.

After five months, 56 out of 70 teaspoons disappeared, that’s 80%. The half life of the teaspoons was 81 days.

Teaspoons in communal tearooms disappeared faster than those in tearooms specifically for certain projects. Expensive teaspoons disappeared no faster than cheap ones.

According to the study, “at this rate, an estimated 250 teaspoons would need to be purchased annually to maintain a practical institute-wide population of 70 teaspoons.” The cost? About $100. Extrapolate that to the workforce of Melbourne, some 2.4 million people, and you’re looking at quite a wad of cash.

And it’s not just economic loss, it’s also workplace satisfaction. “Teaspoon displacement and loss leads to the use of forks, knives, and staplers to measure out coffee and sugar,” the study suggested. Staplers? You know it’s a bad day in the office when you’re measuring sugar with a stapler. Indeed, nobody in the office said they were “highly satisfied” with the number of teaspoons in a survey they conducted at the end of the study. Yes, they even did a survey.

But why are teaspoons such hot property?

The study gives a few possible theories. Perhaps there are so many teaspoons, people don’t think it will matter if they take one home. Over time the small acts of thievery add up until there are no teaspoons left.

Alternatively, and I can say this no better than the authors, “Somewhere in the cosmos, along with all the planets inhabited by humanoids, reptiloids, walking treeoids, and superintelligent shades of the colour blue, a planet is entirely given over to spoon life-forms. Unattended spoons make their way to this planet, slipping away through space to a world where they enjoy a uniquely spoonoid lifestyle, responding to highly spoon oriented stimuli, and generally leading the spoon equivalent of the good life.”

Their final theory is les choses sont contre nous “things are against us.” “Resistentialism is the belief that inanimate objects have a natural antipathy towards humans, and therefore it is not people who control things but things that increasingly control people,” says the study. Think of all the time you spend cleaning, buying, repairing, using and selling things. Do items really control our lives, sending us on some materialistic goose chase for reasons we cannot yet understand? I can only assume Yes.

I want to hear from anyone who has experienced this phenomenon, be it spoons, forks or knives. What goes missing in your workplace, and why do they constantly disappear. And what is the spoon equivalent of the good life?

Lim, M. (2005). The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute BMJ, 331 (7531), 1498-1500 DOI: 10.1136/bmj.331.7531.1498

Massive hat tip to James at Disease Prone, who said my posts had slowed down and suggested this paper.

A Gingerbread Laboratory

// January 19th, 2011 // No Comments » // Just for Fun, Science at Home

Thought I’d share some pictures of this awesome gingerbread laboratory my dad made me for Christmas.

It’s a science and research lab. Unfortunately some of the roof caved in during transit.

The lab comes complete with helipad. You can see some of the decorations inside through the “sky light.”

Royal icing, smarties, jelly beans, mint leaves, marshmallows and licorice allsorts decorate the interior while icing sinks ensure proper hygiene. Here’s the view from the front door.

Connecting via common ancestors and Genographics – Interview with Wolfgang Haak

// December 8th, 2010 // No Comments » // Recent Research, Science Communication

At the Genographic Event at the RiAus I also interviewed Dr Wolfgang Haak, who spoke about Y-chromosome markers to determine paternal ancestry. He’s been involved in the Genographic Project for three and a half years.

What are the benefits of understanding ancestry?

It’s pretty much a personal thing, at the end of the day, because I suppose everyone’s interested in his or her own genetic history. This is my personal driving force, finding out more about myself. Where’s my place in this planet, in this world, where do I tie into the global picture? That’s a big motivation for me, and as I find out more as I work with people that it’s the same motor or driving force with them as well.

We share a common ancestry after all, there’s a common interest in our genetic history as well.

What first attracted you to the Genographic Project?

I have always been interested in genetics, but I actually come from an anthropologic background and genetics is certainly a part of that. I also come from an Ancient DNA lab. This was a step further into more modern population genetics. This is about getting both things together. Having a modern day perspective, plus adding a timely depth to that picture that we get from modern day diversity.

Tell us about your own ancestry, have you genotyped yourself?

Yes, I’ve done both. Mitochondrial, I’m haplogroup H, and I can further pin that down to group H1, so that is a Palaeolithic, Mesolithic one that might have come into Europe prior to the last glacial maximum, around modern day Spain or Italy or even a South Eastern refuge. It’s not entirely clear but we’ll find out over the next couple of years.

On the paternal side its even more enigmatic. I’m part of a North African lineage that probably originated around the Horn of Africa, so there’s that connection on the Eastern side of Africa where it connects to Saudi Arabia, and that has a high frequency there into the Nile Valley, and from it spreads into South Eastern Europe. Not entirely sure when it spread across the Mediterranean region, but probably historic times rather than prehistoric times.

Genographics, Neanderthals and Cannibalism, an Interview with Carles Lalueza-Fox

// December 8th, 2010 // 1 Comment » // Recent Research, Science Communication, Sex and Reproduction

After the event last night about the worldwide Genographic Project, I caught up with Prof Dr Carles Lalueza‑Fox, the first speaker on the night, for a quick interview. He’s an expert on Neanderthals, or Neandertals I think we call them now. Named after the Neander Valley where the first specimen was discovered.

What first sparked your interest in studying Neandertals?

When the first Neandertal sequence was retrieved in 1997 I had been working on ancient DNA for a while, but then Neandertals seemed to be something in a different league.

In the first ten years it was only possible to get mitochondrial DNA from Neandertals.

For me, I really liked Neandertals and human evolution as a child. Ancient DNA was something particularly difficult at the time, and the thing that brought me to the subject.

How human do you think Neandertals were?

How human?

Yes, tricky question.

Haha, yes. It’s a very long question, a very difficult question. One must always take into mind our tendencies are always fluctuating. We saw them as a very primitive human lineage in the early 20th Century, but I’d say that now we’re turning to the point where we see them as very similar to us.

Maybe the best thing to think about Neandertals is they are more different from us than any modern human to any other modern human. That’s the way we should think about them.

If we want to think of them as a different species that’s fine for me, but there is a range of difference between us and the Neandertals.

The cuts found along Neandertal bones you suggest are evidence for cannibalism. Could they just be an example of de-fleshing prior to burial?

Well, yeah, it might be right in some circumstances. But this is not only cutting, you know de-fleshing the bones. It’s also fragmenting the bones with small stone tools, very small fragments, and even the skull, and the faces. For me it’s very difficult to think that this kind of post mortem activity is something more because this is a complete destruction of the bones.

It’s very similar to what we see in other sites with fauna, the bones are broken to extract the marrow in the same way.

And it’s a pretty common thing, well, not common these days, but certainly we humans have our own history of cannibalism.

Yes, well there are several sites with the signs in Neandertals. But you almost think that life was very tough and they were structured in very small groups, so the fact that you find another one… I mean you’d say “hey, we are Neandertals all of us,” but I’d say that’s a modern conception.

Whereas for them it might be “hey, you’re not one of my family I may as well eat you.”

Yeah, the idea of humankind, in fact, is very recent. After the second World War, and the UNESCO thing. So even the idea of humankind is more recent than we might think now.

And what do you think of the possibility of Neandertals and humans mating?

I think it’s plausible with the data we have. It was probably something that was a minority, restricted in time and space, it was nothing important in my view. The thing is we can detect it now in non-African modern humans is because this was an expanding population, so even a small event of just a few, say it was, this was amplified later on.

Science that’s only skin deep

// December 3rd, 2010 // 2 Comments » // How Things Work, Recent Research, Science Communication, Sex and Reproduction

I’m a guest blogger for the RiAus, and this post also appeared on their fancy website. To tell the truth, I really wanted to call this post “Hormonally Yours” in homage to the Shakespeare Sisters (anyone?) but I’ll save it for another post.

Recently I was in Arnhem Land, visiting some Indigenous communities with a couple of friends. While I was there, I got pretty jealous of everybody’s darker skin. “It’s so well suited for Australia,” one of my friends lamented. “I should be in Norway or something.”

Pale skin like mine is not great for Australia. I tan pretty easily, but only after being burned bright red. While I was in the NT I slathered sunscreen religiously, but still managed to get a highly embarrassing burn on my lower back when I was building a sandcastle (an epic sand turtle, actually. Totally worth it.)

Anyway, enough about me and my weirdly tanned lower back (it’s been months! Why won’t it go away?) Let’s talk about Nina Jablonski, an anthropologist. In 2000 she suggested a new reason why skin colour varies so much. It’s not an adaptation to protect against skin cancer and sunburn, like I always thought it was.

It’s real job is to keep us highly fertile by maintaining a delicate balance between two key vitamins: Vitamin D and Folic acid.

Vitamin D is obtained through some foods, but mostly from drinking in sunshine. UV light turns cholesterol into Vitamin D, which then goes to either your liver or kidneys to be converted to an active form.

Once active it helps white blood cells like macrophages kill bacteria, and helps control levels of calcium and phosphate – important for building healthy bones.

Deficiency in Vitamin D causes rickets, a disease resulting in soft, easily broken bones and deformity which can lead to early death.

So getting enough UV (specifically UVB light) is important to not dying, and therefore having reproductive success later in life. It’s been backed up by Yuen, A. (Vitamin D: In the evolution of human skin colour DOI: 10.1016/j.mehy.2009.08.007)

Natural selection favours soaking up UV.

Folic acid is obtained in leafy vegetables and fortified cereals. Rather than being made by UV, the light can destroy folic acid by literally breaking it apart. (Jablonski, N. The evolution of human skin coloration DOI: 10.1006/jhev.2000.0403)

Critical for DNA synthesis, folic acid is essential during pregnancy when a lot of new cells are being made.

Folic acid prevents against 70% of neural tube defects in embryos. Its destruction by UV is bad news.

Natural selection favours avoiding UV.

So there’s an ideal amount of UV light that needs to get through the skin – enough to produce Vitamin D, but not too much to destroy all the folic acid. Getting the balance right for the environment you’re in means higher fertility, which drives natural selection

This is what Nina Jablonski thinks caused the evolution of skin colour through the sepia spectrum we see today. Dark skin, with high melanin, stops more UV light. That’s exactly what you want if you live in a place with a lot of sun, like places near the equator. Light skin lets more UV in, which is great if you live somewhere overcast and not very high on UV.

Understanding how your skin colour (NOT your race) influences these two vitamins is important in being healthy. It’s more important now than ever, because we humans travel a LOT.

Sadly, Australia is pretty high in UV and I am pretty white. Thank god for sunscreen.

Things are rarely that simple though, and I imagine there’s a few different things going on that connect UV light to skin colour.

On Tuesday the RiAus is holding an event called Skin Deep: Exploring human ancestry. They’ll be showing a preview of a new SBS documentary about skin colour scientific research, as well as results from the Genographic Project. Basically they took DNA samples from a lot of volunteers and some national identities, and now they’re giving us the goss on who’s related to who’s secret love child.

I’ll be there, I’d love to see you (though seats are limited.) I’ll be the one tweeting in the corner. Follow me @CaptainSkellett

Would love to hear from anyone who took part in the Genographic Project, and anyone who didn’t. Who would you most like to be related to? For me it’s David Attenborough, then I can dream of inheriting his voice.

Physics of lapping lets cats drink without mess

// November 24th, 2010 // 2 Comments » // How Things Work, Recent Research, Science at Home

First up, apologies on the lateness of my post. A whole week has gone past! Oh me! I humbly do beseech you to forgive this old salt and do throw myself upon the deck in penance. Me only defense is that I have just moved from Canberra to Adelaide, and me Schooner does need an awful lot of bubble wrap. To distract you from me own slackness, I have scoured the nets for the cutest science story evah. I ply you with kittens thusly:

.

Cats are a more delicate and refined animal than messy, smelly and drooly dogs. I’ve always been a cat person. I think they have higher standards. Turns out they also drink better than dogs.

Both dogs and cats lack the complete cheeks that humans have, which means they can’t drink water by suction like we can. Dogs get around this by using their tongues as a ladle, cupping the water from bowl to throat.

Cat’s do it differently. They lap water briskly, but not like a ladle. Instead, they DEFY GRAVITY and make the water lift up into the air like a glorious floating blob of refreshment.

Sounds crazy, but it’s true. When they dip into the dish, water adheres to the dorsal (top) side of their tongue. The surface tension (sweet, sweet hydrogen bondage) of the water drags a column of water into the air. The cat can thus pull water into its mouth using inertia.

The competition between inertia moving water up and gravity pulling it down sets the lapping frequency of the cat. Smaller cats with smaller tongues lap faster to drink, large cats lap slower. Observation of lapping frequency in big cats like lions shows the same kind of trend, suggesting they use the same physics as the household feline.

Cats might do this because it’s a neater, cleaner way to drink and it keeps their whiskers nice and dry. Whiskers have an important sensory function, so it’s worth the effort to keep them tidy.

The research was published in Science, and began when a researcher was watching his own cat drink. A video of the researcher and cat is below, and shows in super slow mo exactly how water defies gravity when a cat enters the equation.

Did you hear that? Did you? Not only is it physics, hydrogen bonding and gravity defying, plus, PLUS, the tongue could have implications for robotics of the future. Yeah. Robot cat tongues. It’s going to happen.

Actually tongues are very interesting. They obviously have no bones for support, so instead they have a muscular hydrostat system where support comes from muscles. The same thing happens in octopus tentacles, where muscles stretch in one of three directions: Along the tentacle (longitudinal), across the tentacle (transverse) or wrapping around the tentacle (helical.) When an octopus moves, one muscle contracts to become shorter which forces the muscles around to stretch, supporting the movement like a skeleton.

Cats and octopus. You know this post was worth the wait.

Reis, P., Jung, S., Aristoff, J., & Stocker, R. (2010). How Cats Lap: Water Uptake by Felis catus Science DOI: 10.1126/science.1195421