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.

Which animal has the longest tail?

// January 19th, 2012 // No Comments » // Just for Fun

I’m pretty fond of doing the Saturday quiz in the Adelaide newspaper, though I never keep score. I mean, who knows who won the Olympic backstroke in 1978? That was before I was born! I can’t let that drag down my credit rating, you know.

Anyway, last week it asked which land mammal has the longest tail. What do you think?

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Go on, have a guess.

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Got one?

If you thought a giraffe, congratulations. You got it, at least, that’s what the paper said. It’s so dang tall, even its knee-length tail breaks records.

But that’s not the animal I want to talk about. Pff, giraffes. Have you seen them drink? Gimme a break.

I want to talk about the giant anteater that has an almost equally long tail, and a far finer one IMHO.

Found in South and Central America, as far down as Northern Argentina. They eat a lazy 35,000 ants a day with their lovely long tongue and fearsome claws, which rip and tear into rock-hard anthills. They eat quickly for a minute, than meander off to the next anthill leaving the colony to recover.

Plus, they are MASSIVE! Giant anteaters can be over two metres long, roughly seven feet.

Three feet of that length is all tail baby. Long, hairy tail. Not quite long enough (by inches!) to rival that of the giraffe, sadly. Still… you know… I was pretty close.

Here’s Wikipedia’s image of the giant anteater. Notice anything weird?

How much does its front foot look like a panda? I had to look twice to make sure the animals weren’t cohabiting or something.

Made me wonder if there aren’t other, even more exciting tails out in the animal kingdom. Comment if you’ve got ‘em.

A little something something from a bluehead wrasse fish

// January 13th, 2012 // No Comments » // Just for Fun

I know, I know. It’s been awhile. Bad pirate! Post-holiday pillaging and plundering, time got away from me. Not to worry, I’ve harpooned it and got a handle on things now.

So, just a quick one to tide ye olde blog over ’till I’m properly back on decks.

Thought I’d share this rather funny column with you.

‘Tis McSweeney’s (hast thou heard of it?) called Dan Savage’s Wild Kingdom. Just quietly, it’s high-llarious!

This post includes various organisms calling a talk-back radio show looking for some late night dating advice. Here’s a sampler:

CALLER: Dan, I have a question for you. Why is it that when a female bluehead wrasse fish sleeps around, she’s a slut, but if she becomes a male through simultaneous hermaphroditism and sleeps around, he’s a stud? Double standard much?

Read Dan’s reply, and the other caller queries, here. Do click it, ye scurvy dog, there’s plenty of lols to be had.

Fond frolicking and frothy waters, the Captain.

Christmas chemistry, the science of holly

// December 21st, 2011 // 2 Comments » // Poisons

Green and red, classic Christmas colours, adorn the spiky holly shrub. A sprig may garnish puddings, but garnish nibblers like me must hold back on holly for it is poisonous in large doses – though some leaves can make a tasty beverage!

Holly includes about 400 species in the genus Ilex. The cultivated species is Ilex aquifolium, and about 20 or 30 of those bright berries can kill an adult. Poisonings are more likely in pets or children, and about five berries will make a kid feel sick.

It’s the usual suspects in symptoms – sleepiness, sore tummy, vomiting, diarrhoea. Larger doses cause paralysis, kidney damage and death.

Chemically, they contain a cocktail of active ingredients. Among them are the triterpenes, precursors to steroids which are cytotoxic (kill cells), steroids and a nitrile called menisdaurin.

Traditional medicines use holly for fever, gout and chronic bronchitis.

A couple of species native to North America, I. vomitoria aka yaupon and I. cassine, make caffeine and were used to make “black drink”, a stimulating brew also used as a vomit-causing emetic.

South American species I. paraguariensis contains as much as 1.6% caffeine (five times more than the above species) and some of the cocoa chemical theobromine in their leaves, and tasty tannins.

Also called yerba mate, I. paraguariensis is brewed to make mate tea, which is delicious. It’s pronounced MAH-tay, but be careful not to put the emphasis on the second syllable. Wikipedia says that makaes mah-TAY, which means “I killed” in Spanish.

So it’s fine to have a sprig of holly in the house for Christmas, just don’t make a holly pie out of it!

Vampire squid on Occupy Wall Street, biology of Vampyroteuthis infernalis

// December 14th, 2011 // No Comments » // The Realm of Bizzare

Occupy Wall Street protesters took up arms – eight of them – in their march on Monday. Carrying craftastic models of vampire squid high above their heads, in homage to Matt Taibbi’s description of the bank as “a great vampire squid wrapped around the face of humanity, relentlessly jamming its blood funnel into anything that smells like money” in Rolling Stones, 2008.

Harsh words, right? I mean, vampire squids are totally awesome!

The vampire squid inhabits the cold, high-pressure environment of the deep sea. Light is absorbed by the water, making it perpetually twilight. A vampire in twilight, that’s not horrifying, that’s dreamy, amiright? Don’t hit your head if you swoon.

We don’t know much about these little dudes because they dwell in that most mysterious of spots, the deep sea. Vampyroteuthis infernalis means vampire squid from hell, but it’s not even technically a squid. Or an octopus. It’s got an order all of it’s own.

They have a consistency similar to a jellyfish, quite gelatinous. Like many jellyfish, it swims by shooting out a jet of water behind it to propel it forward, but it has a couple of fins for manouvering. It has eight arms and two extra arms which hide in its ‘pockets’ and can extend the length of its body when needed.

This National Geographic vid is pure pirate gold for high quality images of the creature.

They hold the title for the largest eyes relative to their body. An individual about six inches long has an eye an inch across, about the same as a full-grown dog. All the better to see you with, my dear. They also have a receptacle behind their eye for spermatangia, the tough sac of sperm ejaculated from the specialised arms of a lover. Just imagine date night

The most brilliant behaviour is their bioluminescence. These guys glow!

When startled, squid may shoot out ink to confuse predators. That’s not much good when you live in twilight, so instead the vampire squid shoots out glowing balls that dazzle and confuse. Over a thousand discrete bright particles within a matrix of mucous. Picture that, you’re out looking for a snack late at night, feeling pretty hungry, you think you smell something good and suddenly there’s some wacko waving glowsticks and snot in your face!

Another defensive ploy is to go into pineapple pose. Turning their bell-shaped tentacles over them, they completely change their shape (going kind of inside out). They light up some spots on their head which animals may take for eyes, which glow and then shrink as if the animal has swum away. Even if you didn’t buy that the animal was gone, looking at the videos, you wouldn’t want to eat that.

Stephen Fry gave respect to these sweet deep sea entities in this clip from QI. Hat tip to Dr M at Deep Sea News.

Oh… and about that quote Occupy Wall Street are marching for. The vampire squid’s diet seems to consist of molluscs, fish and crustaceans. As far as we know, it’s not a blood sucker, and Tree of Life. describes the funnel as absent. That must make it hard to stick said metaphorical blood funnel into anything, whether it smells like money or not.

Recommended links

In the QI link, they say the bioluminescence explosion is like John Barrowman! You might know Barrowman as the immortal Captain Jack Harkness from Dr Who and Torchwood, but blow me down, that captain can dance!

Still got time for more videos? Here’s David Attenborough talking about the deep ocean.

The majority of this info was from Tree of Life.

Eyewear made by 3D printers, designed by you

// December 13th, 2011 // No Comments » // Science Art

Someone I met in the sci-comm scene in Canberra last year is making it possible for the public to use 3D printing to design eyewear.

A few companies give the public access to the technology, but I like that this one is all about the eyewear (you know… sea-glare.)

Three dimensional printing creates objects by building up layers of material like stainless steel or polyamide plastic, usually as a powder. Each layer is stuck to the other with a a hardcore high-powered laser. Some materials are laid down as a liquid, instead of a powder, and then hardened to a solid. Instead of cutting out a design, they build it up, making it easier to do very fine work and one of a kind items.

The technology has been pegged for such epic, borderline science fiction things as creating organs by building up layers of cells – which I don’t think anyone has actually done yet, though someone did print an ear out of silicone.

Beehive have started designing a user interface so people can design their own eyewear, and they’ll 3D print it for you. SO COOL!

They’re are crowd sourcing funds for the project, and asking for pledges. Each pledge gets a reward, including sunglasses made with their technology, and if they don’t get the necessary dough by the end, you get your money back.

I think a little cut-out molecule on the side would be pretty cool. Maybe of caffeine, you know, keeping it real the morning after a big party. Or the stages of mitosis along the sides, with the glass sections being the moment where it has split apart into two cells.

There’s heaps of possibilities, I can think of a few ace neurobiology and chemistry themes… What would you make?

Museum of South Australia exhibition on barcode of life

// December 9th, 2011 // 1 Comment » // Science Art

Joseph Rossano's artwork at the Museum of South Australia

For those of you who live in or around Adelaide, I recommend popping into the SA Museum and checking out a funky artwork by Joseph Rossano. It’s just in the foyer (past the security people, before the staircase) and features a set of big, blue butterflies behind frosted glass.

The butterflies look blurry – on purpose – but if you have one of those new-fangled iPhones you can scan in the QR code next to them and sneak a peek behind the glass to the species inside. The QR codes are a barcode symbolising the DNA barcodes, a short stretch of DNA written on the side of each of the frames.

My current work, BOLD, utilizes two-dimensional QR codes–a surrogate DNA Barcode– to link the viewer to the science behind the art. By scanning one of my sculptures–for example a colorful butterfly collected by Area Conservacion Guanacaste parataxonomists and hosted in the Smithsonian Institution’s collections–the viewer transports one’s self to Dr. Daniel Janzen’s natural history of the specimen and other collateral data. All of the specimens portrayed in this series are deliberately indistinct behind their window, thus making it difficult to discern the organism’s true identity. – Joseph Rossano artist statement.

It’s a fun way to explore and interact with DNA barcodes (if you don’t know what I’m on about, read this) and imagines a future when DNA barcoding devices are handheld for species identification on the fly.

Be quick though – it’s in the last weeks and will be returning to America after that. Keep an eye on this artist though, looks like there’s some great science art in the portfolio.

Science behind the headlines – beyond seven billion people

// December 9th, 2011 // 1 Comment » // Science Communication

We reached a big milestone last month as the world’s population exceeded seven billion people for the first time. Looking behind the headlines was Paul Willis at the RiAus and a panellist of scientists and journalists on Tuesday (event details here.)

In the 20th century we added five billion people to the Earth. Before that, we had only added two billion in total. Part of the reason is a decreased death rate, due to better medical facilities, coupled with an increase of food made possible by the Haber process that produces nitrogen fertiliser from nitrogen in the air. The chemistry makes it possible to, on some level, make food from air.

But population increase is not exponential. The UN expects the population to level off at 10 billion in the next fifty years, after a dramatic decrease in fertility, which no one anticipated.

“It is unconscionable to have a policy to increase mortality!” says Graeme Hugo, Director of the Australian Population and Migration Research Centre at the University of Adelaide. “The only way forward is to decrease fertility, that’s the only thing on the table.”

The world has done very well to reduce fertility, halving it since the 1970’s.

However, in some areas of Africa and isolated pockets in Asia it is not dropping as fast as expected. Two years ago East Timor each woman was having around eight children. The continued high fertility may be because we’ve taken our foot off the pedal when it comes to efforts like increasing contraceptives, women’s education and emancipation.

Beyond numbers

But it’s not all about the numbers, and that was the key point the scientists spoke about on Tuesday. Population is a complex issue, and has to be considered in connection to age and spatial distribution and consumption of goods.

The cost of looking after an aging semi-majority (the baby boomers) is a worry for some political movements. Balanced age groups are important to ensure the number of dependents and the number of workers is stable.

Migration may not change the global numbers, but it’s important for people are spread out in the right way. That means considering how many people a local environment can sustain in terms of food and water.

Consumption is also critical. One baby born in the United States consumes the equivalent of 30 babies born in Africa according to Udoy Saikia, School of the Environment, Flinders University (here’s a relevant link.) “People in developed countries should limit their consumption,” says Hugo. “In many developing countries, consumption needs to go up because they’re not consuming enough to be healthy.”

One way for more developed countries to limit consumption is to go vego. A more vegetarian diet is able to support more people for the same number of resources. Bring on the lentils!

This Tedx talk on the topic, I can’t recommend it enough.

Magic bullets

Scientists agreed that coverage of the seven billion people story has been pretty good overall, far better than stories about migration.

One issue they mentioned was the trend to look for a magic bullet, fixing just one thing to solve the whole population problem. It’s also hard for journalists with limited inches to talk about all the factors in a complex issue like population science.

Stopping population growth won’t work unless you take consumption into account, as well as the other factors. There needs to be a holistic approach. That doesn’t end (or even start) with policy – everyone needs to make a decision to change their consumption.

Australia

How many Australians should there be? There is no magic number where everything will fall into place. There are definite demographic problems regarding aging populations and dispersion (or lack thereof).

The scientists agreed we need a policy that allows for sustainable growth. They said it would devastate Australia if we stopped population growth tomorrow, but it would be also devastating to have uncontrolled growth.

“Every day we waste about 40% of the food (in Australia),” says Saikia. “There is some hope that the 10 billion population can survive very well, depending on distribution and consumption.”

Paul Willis summed up by asking whether Australian’s should “be concerned, not alarmed.” It’s not the end of the world, but we do need major changes and responses to population dynamics, says Hugo. “Be concerned, AND alarmed – about consumption,” says Saikia.

This post was also featured on the RiAus website.

Notes from the international barcode of life conference #bol4

// December 5th, 2011 // 1 Comment » // Science Communication

On Friday I went to day three of the international barcode of life conference, which happened to be in my hometown of Adelaide, actually at the home of my undergrad – The University of Adelaide – how convenient!

DNA barcoding matches a region of DNA to a species, at the moment there’s still plenty of work on building up that barcode database (called BOLD, though GenBank is also used). There are about a million and a half barcodes recorded so far and it’s streaming along.

The database is open access, and people can use it to match a barcode region from an unknown sample to a species.

So far, people have used this to check out the slice of fish in sushi, illegally collected shark fins, and plenty of other stuff.

It’s a powerful technique now in it’s ninth year and with some serious momentum behind it. There were 450-ish delegates at the conference from around the world, and Australia is a fair trek for most of them.

There’s talk that one day DNA sequencing will be so fast and cheap, you could take a sample while walking through the woods and be linked to species information on a handheld device – you would know if it was poisonous, endangered, new to science or what. Still a while away, but sci-fi in its possibilities.

This cool video gives a neat overview. It’s about a project proposal for student/citizen science in barcoding which is unfortunately currently unfunded and basically on ice at the moment. Nonetheless it’s a cute cartoons and great summary.

The region used for barcoding is called CO1 (found in mitochondira) in animals. It’s x base pairs long, and is generally very different between species, but pretty similar within one species. It’s short enough that sequencing is cheap and quick. A different region is used for fungi (called ITS, which was announced as the official fungi barcode at the conference), and plants use two regions, rbcL and matK, (found in chloroplasts).

The session I went to was on education and engagement – how to get people involved in DNA barcoding.

I love open access, power to the people, breaking down barriers stuff, and they’ve got some sweet plans. Already some projects have been successful, like the urban barcode project that gets high school students involved, and one group, who found the ingredients of tea didn’t always match what’s on the label, were even published in a journal (No less than Nature Scientific Reports! Amazing!) One group found a new species of cockroach, which is like my least favourite insect, but still a good effort.

BOLD are in the process of adding education and engagement to their online database so students can add to the database and store their results in a quarantined area. So they have a safe space to experiment with barcoding. Plus then they don’t screw it all up, right? Karen James, who moderated the session, actually pointed out that students may be less likely to make mistakes, as they are only working with a small number of samples and there’s less chance of losing track and accidental mislabeling.

Still in development, the BOLD 3.0 interface will look less intimidating than the current version, making it clearer for n00bs like me, and with links for educators at the bottom. They’re beta version is online here. Neat. I played around with BOLD before, taking a look at the barcode regions out of curiousity, and with my amateur skillz found it a bit tricky to navigate. Can’t wait to see the new one up and running so I can play with it.

If you want to read more about DNA barcoding, I recommend the iBOL website. I’ve got some more bits and pieces, but will post them separately once I’ve had a chance to flesh them out properly.

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.