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A Schooner
of Science

Heaven in a grain of sand

Missing Australia! Image by freeaussiestock.com

I’m in San Pedro de Atacama, Chile, just next door to the Atacama desert, the highest desert in the world. So what better than a post about sand?

To see a world in a grain of sand,
And a heaven in a wild flower,
Hold infinity in the palm of your hand,
And eternity in an hour.
– William Blake, Auguries of Innocence

I actually came off my bike in the Valley of the Moon when I hit a patch of sand on the road, so my feelings about the stuff are somewhat ambivalent. However, HOWEVER, science has come to my aid yet again and opened my eyes.

Because under a microscope, sand is actually quite stunning!

Unfortunately I don’t think I can post the pics myself due to the copyright, but these links are worth clicking through.

Geology.com share a gallery of sand microscopy by Gary Greenberg, in promotion for his book. My favourite is the polished pieces of olivine, found on the green Lumahai Beach of Hawaii.

Gary has also photographed samples of moon sand, collected by Buzz Aldrin and Niel Armstrong. The otherworldly images are in his Moon Sand Gallery.

Without atmosphere or water, sand on the moon goes through a very different process to form. Rather than small sea shells and rocks polished by the oceans, the moon sports fine dust created by meteorite microimpacts. Some impacts are so hot they become molten microdroplets. When these collide with existing sand grains, they create wiggly shaped specks called agglutinates.

Transit of Venus – it’s happening tomorrow!

Transit of Venus. Credit: culture-and-current-affairs.com

Unless I’ve got the time difference wrong, the Transit of Venus is happening tomorrow! That’s where Venus crosses between us and the Sun, the rarest of all eclipses. The next one happens in 2117, over a century away, so don’t miss this one.

Australians can see it on 6 June 2012 in the morning until about 2 pm. Like a Solar eclipse, you can’t look directly at the Sun to watch it happen, you need special glasses or to look at the shadow. Alternatively, watch the livestream on the RiAus website.

Everything you need to know is at this page on the ABC website.

Australians get a sweet view of the transit this time around, and I’m totally bummed to be in South America right now – it’s the worst place to see it! I’ll be living vicariously through your Aussie eyes…

The transit of Venus has a special importance to Australia, as Captain Cook first came to the area on scientific mission to record the transit from Tahiti. His second, secret mission was to search for the Great Southern Continent.

Cook’s data and pictures allowed astronomers to measure the distance between the Earth and the Sun, getting a sense for the first time of how immense our Solar System is. Back in the 18th Century, it was all a bit of a mystery – one worthy of an Apollo-level international solution.

People were sent around the world to get a different view of the transit, noting down when the transit started and when it ended. Then the data was compared, and used mathematically to see how far Venus was from the Sun.

This is similar to pointing at a far away object with your finger, then recording how the image looks when only your left eye is open, and then how it looks when only your right eye is open. Go on, try it! Then try doing the same thing, but with your finger much closer to your face. Did you do it? Spoiler alert: Your finger seems to move much more when your finger is close-up.

Substitute your face for Earth, your finger for Venus, and the distant object you’re point at for the Sun – and you have a pretty good idea for what they were going for. ‘Cept they used more maths!

Man, I really wish I could see the transit tomorrow! I’ll watch the livestream instead, it will be weird to watch the Sun over Australia while it’s midnight in South America…

SKA decision announced, split between Aus and South Africa

Members of the SKA Organisation have just announced the locations – there’s two of them – for the square kilometre array, which will revolutionise astronomy with the world’s most sensitive radio telescope peering into the dawn of the Universe.

South Africa was chosen to host most of the SKA, including all the dishes and mid-frequency aperture arrays. Western Australia and New Zealand will host the low-frequency aperture arrays. Construction is scheduled to start in 2016, and Phase I will cost around 1,500 million euros.

Astronomer Dave Reneke was excited about the news when he spoke on ABC radio yesterday – and as he says this is still a big opportunity for Australia, with more jobs for scientists, engineers and loads of other people involved in setting it up.

I’m excited too! Will the SKA find extraterrestrials by listening to their radio waves? Even if it doesn’t, it’s one of those big scientific endeavours that captures my imagination. A big international quest to explore the unknown. And there will be experts on the site just a shortish plane trip from home!

I heard the news via facebook from a friend who posted this awesome comic.

Big Science

Comic by Firstdog, click thru for link

Paper-based device tests blood type, Harry Potter style

Blood test device

Easy reading. Blood test device from Monash University

An easy to read blood test spells out your results, and the diagnostic device was developed with Harry Potter in mind, say researchers from Monash University.

It’s even easier to read than the books!

Monash describe it as “the first equipment-free, bioactive paper-based diagnostic device capable of reporting multiple conditions in written text.”

How does it work? Printed onto the surface is water-repelling chemicals, with gaps for the letters A, B and O, and the +/- sign. Into each of these letters, the device is embedded with antibodies that stick to antigens on blood cells. Antibody A sticks to antigen A, if the blood sample is A. Antibody B sticks to antigen B for B-type. AB blood contains both antigens, and will stick to both spots.

Blood is added onto the device, given time to stick to the antibodies in each letter, then rinsed off. Clumps of blood stuck to the surface antibodies remains, leaving the result displayed out in letters of blood. Pretty cool.

O-type has neither B nor A antigens on the cells, and so won’t stick at all. Only the preprinted O will be visible (see it’s in a slightly different colour to the A in the picture?) The cross inside the O must be embedded with both A and B antibodies, picking up either blood-type and crossing out the default option.

Rhesus factor, the +/-, works much the same way. The default is a preprinted horizontal -, with embedded Rh-antibodies on the vertical line to make a +.

They say the device was inspired by Tom Riddles diary in the Chamber of Secrets, where answers could be received in writing. I love the idea of this easy to use, easy to read blood test, but designing it from a Horcrux? Hm…

The paper was published in Angewandte Chemie, and a Monash press release with picture is here.

Happy birthday blog

Who’d have thought it? A Schooner of Science turned three just the other day. They grow up so fast…

Here in Seattle the tulips are blooming, spring is springing, and they are celebrating the 50th anniversary since the World Fair was held around the space needle. Time flies…

Tomorrow I’m going down the west coast of the US, so please point out any poignant science spots on the way. I hear there’s some cool fault lines near Las Vegas, big trees near San Francisco, and vampires in Forks.

I need some encouragement to keep the blog updated while I’m gallivanting about – if you want to read more about something, please poke me by posting a comment. It’ll help me get to the fourth birthday.

Thanks for stopping by and reading, hats off to ye.

Catch the wind with a sailing GPS, arrr!

Betsie (adapted, credit USFWS)

‘Twas getting dark and mighty cloudy as I consulted, yet again, the map. An X, in red like clotted blood, marked dead Betsie’s buried treasure. That magnificent cow had plowed these oceans, churning the sea foam to cream, for years beyond her species, yet in the end we all come to naught… She mooed her last moo beneath the moon, and hid this map in her very own cowbell, whence I found it floating in the ocean some two weeks prior.

Apologies, again, for the inconsistencies of my posts. Events such as the Cowbell of 2012 tend to distract.

In any case, I made hasty haste to the udder-shaped island. I soon ran into troubles. I had marked on a dotted line the most direct direction to the treasure, straight as an arrow she flies, and the wind would not have it.

Oh ho ho no, the wind would blow sideways, wouldn’t it.

Then, dear friends, last week I read about a GPS for sailing! Rather than pointing as the crow flies (or in this case, cow), it shows the ideal zigzag to tack, catching the optimum amount of oomph from an errant wind.

By adding in the size of my substantial boat, and the speed of the prevailing wind, it does all the brain work for me to get me to the X quickest. Quite clever. At $399, it’s a steal!

So I followed it, on and on, night and day without pause.

And there she lays, like a speck of cheese, the island.

Before long I was there, on her, traipsing across the lands dotted here and there with milk vetch, all over with long and luscious green grass. Across the hill, through the shrubs, into a lowland meadow, and ah. The cross. Thoughtfully decorated in large cow pats, courtesy of Betsie herself I’d wager, which I carefully avoid with my boots.

Then, with my shovel, I dig.

Down and down, further than you would think possible for a bovine with hooves and not hands, but Betsie and her crew were of a brilliant breed, as all who did battle with those cattle will attest. Down and down, until the stars wink and glitter at me. Down and down and DRING! There it is!

Brass and mahogany, the chest gleams under my lamplight. With shaking fingers I open the latch.

Peeouw! What a whiff!

‘Twas nothing but goat’s cheese.

Well I sealed it, hoisted it up and got back on me boat. Perhaps I can sell it in port, and make me funds back on this awesome GPS (as seen on Gizmodo.)

It’s eggbot!

Happy Easter everyone! And if you don’t celebrate, than happy spring themed holidays that happen in August in the Southern Hemisphere.

Check out this robot ($195) that decorates eggs, golf balls, baubles and other strangely shaped objects. You can make designs from Inkspace on Mac, Windows or Linux. How geeky and Eastery is that?

Their website is egg-bot.com, and this picture of eggboot in action is from their homepage.

Their flickr page has some amazing designs. Very cool.

Chasing the aurora

Own picture, free to use or share

A brisk wind flowed through the trees as I retreat for the car. Ignition on, -17°C outside, warm air flows through the vents. Another cold clear night – perfect for viewing the elusive aurora borealis. We’d been sitting out for almost two hours, but it was 1:20 am and we were throwing in the snap frozen towel for the night. Nada.

The next day we went on a wildlife tour, and the British travellers in front of us were showing off their pictures on a camera. “When did you see the Northern Lights,” I asked. “They look amazing!”

“Last night,” one of them replies, “about 1:30am”.

Bummer.

That night we stayed inside and watched TV until 1 am, then took a mug of hot chocolate and plenty of warm clothes to go aurora hunting. It’s 4:30 am before we give up, with cold noses and toeses, having missed them again. The next morning (well, afternoon by the time we wake up) we find out the lights had started early, about 10 pm.

Bummer bummer.

Three more days we stay in Whitehorse, Yukon Territory, Canada, hoping for a glimpse of the lights. Once we saw a pale white streak across the sky, which showed up green on the camera under long exposure.

Disappointing, really, as we head back South – away from the elusive Northern lights.

First stop is Liard hot springs, and I recommend it a LOT. Wow, is it steamy! Anyway, we went for a dip, and as we were walking back to the accommodation, we saw them!

Green swirls, curtains and purple streaks!

The colours come from electrons around atoms jumping back and forth between orbits. Electrons absorb light to move up an orbit, then emit light of a particular wavelength to fall back down. Some excited states are more stable than others, and certain transitions happen more readily.

Own picture, free to use or share

Green light is emitted by oxygen atoms at lower altitudes, while a red glow can be seen from another oxygen transition at high altitudes. Purple is from transitions in nitrogen molecules that emit blue and red. A mix of the colours can appear white. A great chemistry-heavy explanation of the colours can be found here.

Did you know the northern magnetic pole is moving towards Siberia at a rate of around 40 kilometres per year? Aurora hunters in the US in 2060 might be more unlucky than we were!

Here’s a screenshot of the aurora predictor on the night we snapped these pictures, to give you some idea of what the conditions were like that allowed the aurora to occur.

Want more aurora? Check out this video which describes how they occur, and shows footage from above filmed on the International Space Station.

Fever dreams – the true tale of Richard Spruce

Richard Spruce had seen some strange villages since arriving in South America in 1849, but this one took the cake. It was a ghost town. Every door was shut tight against the hot, humid jungle, while inside people slumbered away the sunlight.

Being the adventurous sort, he couldn’t comprehend such laziness, not, that is, until he mopped his clammy brow. His hand returned smeared with squashed mosquitoes and his own bright red blood.

He reflected, not for the first time, that life in the jungle wasn’t all it was cracked up to be, all things considered. Charles Darwin had joyfully described the Brazilian rainforest as “a great wild, untidy, luxuriant hothouse.” The tales of Alfred Wallace, a fellow young botanist, absolutely dripped with adventure.

Money truly did grow on trees here – there was a fortune to be made by transporting unusual plant species to England, where new novelties for Victorian gardens fetched a pretty penny.

Plus, the trailblazers in taxonomy whispered, it was delightfully warm, warm being a most thrilling word to Brits.

Had they mentioned the innumerable insects? If so, he still hadn’t expected the particular, primal discomforts of living in a cloud of whining and dining mosquitoes. Likewise, he hadn’t realised that breathing the air’s rich humidity would be as drinking tepid whisky through a straw. Nor how hot the nights were, wrapped tight as a flower bud in his stockings and blanket with a handkerchief over the face to ward away bloodsucking bats.

Nonetheless, Richard Spruce was not one to fret. He was of unfazeable stock, and though inch of his bare skin was soon in welts (not to mention his unmentionables), he followed the river and its plethora of plants to plunder. The cloud of mosquitoes followed too.

It’s not surprising what happened next.

The fever came on suddenly; a shivering, sweating, aching fever that rendered him helpless, striking him down mid-step on the border of Venezuela and Colombia.

His guides carried him shaking to a village. He knew the symptoms, hell he’d seen it before, but he denied his own diagnosis. Though he had the cure in his pocket, quinine from the bark from the Cinchona tree, he was loath to take its bitter rescue. He didn’t want it to be malaria.

Like a pot of swamp water on the boil, was his brain, his temperature climbing like lianas, curling like fern fronds, perching like epiphytic orchids. Images sprung forth from his fertile mind. The first two days he flashed on those damn mosquitoes, a haze of infected blood cells bursting. It didn’t make sense! The mosquitoes had left him three days ago. Certainly it wasn’t malaria, certainly, for it had been weeks since he was around the bad air of stale water, giving the Italian term mal’aria. Still he kept seeing mosquitoes.

As the fever broke into freezing chills, Richard’s guides began to mutter. When those chills turned once more to fever, they sensed his impending demise and sold his scientific equipment for rum. The patient was in no condition to care.

Spruce was stuck on mosquitoes, thriving in stagnant water and stale air, their droning drilled through his brain. He shrunk to the size of a grain of pollen and was sucked up like whisky through a mosquito’s straw. Inside the mosquito gut (it sure was hot and sticky) blood cells burst to release hideous parasites. These sex cells, for he identified them thus as surely as an anther and stigma, combined inside the mosquito. In the gut wall they formed cysts full of eggs. Or were they seeds? Or ferns?

Whatever they were, they grew for over a week, and exploded (much like his mind) yielding youngsters that frolicked freely.

Richard wasn’t frolicking. By the twinges in his aching joints, he knew the pangs of an elderly mosquito carrying young parasites, which had moved to his salivary gland to yield virulent juices. Next time he ate, dipping his mosquito’s double straw through the skin, spitting and sucking simultaneously, he would administer his chemical cocktail – anaesthetics to dull the pain, anti-blood clotting agents and, of course, the parasites.

Through the whisky straw Richard swirled, straight to the liver. His own liver, human and wracked with heat. From the liver, parasites paraded to the blood cells. Inside they ate oxygen-carrying haemoglobin and ran round after round of asexual reproduction, like spores or strawberry runners, each strawberry red and juicy, dripping. Each round took three days to replicate, feast and rupture the blood cells, like clockwork, and his body followed the same ticking cycle, burning fever following freezing chills following fever. Tick. Tick. Tick.

Richard shivered.

From outside he heard the nurse employed for his care, drunkenly yell “die, you English dog, that we may have a merry valorio with your dollars.” Well may she want a valorio, or watch night, but Richard was no a corpse.

After fifteen days of dreaming fever, he relented. Malaria it was. He took the bark of Cinchona trees, which kept him alive (just) by reducing his extreme body heat and causing the haemoglobin-chomping parasites to choke on their own waste. Such sweet relief from such bitter bark.

Thirty-eight days after his collapse, Richard was alive, but exhausted. His full recovery took many months more though, naturally, he kept collecting plants once he found new equipment.

Trudging onwards, Richard felt naught but respect and gratitude for the fine tree, Cinchona (though he preferred moss as a general rule).

Ten years later, having bushwhacked his way through saucer-sized tarantulas and marching fire ants, Richard found himself in the Andes. Gone were the South American rainforests, here roamed high altitude winds and freezing snows. After so long in the heat, the extreme chilliness didn’t suit him at all. But, onwards and upwards, as they say, and he was here to hunt Cinchona trees.

The trees were in high demand by the British and Dutch, both needing supplies for their malaria-wracked colonies. They had no steady supply, as the species had never been cultivated. There were sincere concerns that people would harvest it into extinction.

Richard spent a cold, windswept year collecting seeds and growing young plants. Almost 700 seedlings, well wrapped in moss, were tended all the way to England by a gardener assigned to their care. From the survivors, more than two hundred thousand precious plants were sent on to grow in Indian plantations.

Richard’s success with the species that saved his life did nothing less than change the world, making the heart of Africa habitable and saving millions of lives – but in the end he paid for it with his own health. Another disease cost him the use of his limbs, and he spent the rest of his days on a small pension in Britain.

Today, malaria kills around two million people each year and infects 200 million more. It has quite possibly killed more people throughout history than all our wars and plagues combined. Quinine, along with other chemicals, is still used for cures and prevention, and is gathered from the decedents of Richard Spruce’s trees.

Drinking notes: Enjoy this true tale with warm whisky or gin and tonic. Small quantities of Quinine are added to some brands of tonic water for flavour. Fluorescent, the chemical glows under black light. Many thanks to highly informative Flower Hunters by Mary and John Gribbin for the biography of Richard Spruce.

Feminist and Aboriginal science with Lillian Dyck #AAASmtg

Hon. Lillian Dyck, first female and Aboriginal senator in Canada, took the stage at the AAAS conference to discuss western science, feminist science and Aboriginal science.

Subjectivity is inherent in the western scientific method, she said. We use inductive reasoning, interpret data, and models that are not ideal (eg. animals). A hypothesis may be generated by hunches, mistakes, or serendipity, as well as logical questioning. This, she said, is something we don’t usually acknowledge.

In fact, people try to hide it. In writing up a paper, the sequence of experiments and even the thinking process can be adapted to fit the prescribed, logical process of SCIENCE. We leave out illogical sources of ideas, even if they were important. We remove ourselves by using the third person, and our experience by using the passive voice.

Thus we perpetuate the notion of purely rational, logical science.

However, facts do not exist in a vacuum. Scientists are subject to cultural bias. Though numbers don’t lie, we do interpret what they mean.

Her example of bias in scientific thinking was the Thrifty gene hypothesis describing genetic causes of diabetes in First Nations people. For a long time it was believed a faulty genetic ability that stored extra calories in case of famine was responsible for the disease. Actually, there wasn’t any proof of it at all. You can read the story at “How the diabetes-linked ‘thrifty gene’ triumphed with prejudice over proof” from Globe & Mail, Feb 2011.

How can we correct the bias in science? She says, by knowing and acknowledging it, even taking advantage of human bias.

Feminist science does this, she says.

Feminist science
– is openly biased (doesn’t pretend to be unbiased)
– exposes male bias and the patriarchal nature of western science
– is non-hierarchical
– is by, with and for a community, collaborative
– this pdf article Can there be a feminist science? may be a useful reference.

She says feminist science has changed science as a whole, moving it to a point where collaborative, team research is now the norm.

What about different ways of thinking in different cultures? Not only do different cultures have particular traditional knowledge of areas like astronomy and medicine, they also have particular processes to gain knowledge.

Her heritage is Chinese and Cree, and she mentioned ways of knowing that emphasised listening skills, elders, and a holistic world view (rather than analysing pieces at a time.)

People have claimed only people with Indigenous minds can solve the problems of quantum physics, she said, then pointed out that person was Aboriginal. I recommend reading Dialogues between Western and Indigenous science if you’d like to know more.

Opening ceremony of the AAAS 2012 conference

AAAS opening 2012

Scale: Earth globe = size of my hotel room

The Vancouver Conference Center sure is an imposing place. High ceilings and wall-length windows gazing to cloudy mountains and cold waters. Up above, strung in wooden beams, are three golden eggs.

It’s a fitting spot for the first annual meeting of the American Association for the Advancement of Science (AAAS, pronounced not aaaass, but triple ay ess) to occur outside of the US. A huge number of people are in attendance, filling the seats and lining the corridors.

Jet lag still nibbles at the ragged edges of my mind, not quite satiated by coffee though I’ve certainly drunk my limit. I’ve been here since Saturday, and been busy with work and museums and squirrels – SQUIRRELS! – and identifying coins and notes (the five and ten are, in size and colour, opposite to in Australia.)

The program is as multidisciplinary as it is multinational. From culture to computing, from food to forest fires.

After a welcome from Chief Jacob – who sang a song with his niece, accompanied by drums, and it was totally awesome – the AAAS president Nina Fedoroff spoke for around 40 minutes on her life.

Vancouver conference of AAAS 2012

Giant golden eggs outside the ballroom

She had her first child when she was 17, then went back to school and her partner left her. Single, working mother she made her way through uni, and had another child and a husband a few years later. Then she started working in labs – and back then it was HARD for women in science. Hell, I think it still is.

Guess my age is showing, but I find it strange to think that obvious, even blatant discrimination was happening just a few decades ago. Perhaps it wasn’t so bad in Aus? (Anyone?) Despite that, she did a hell of a good job studying plant genetics, became an expert in the field and was awarded a prize for science in the White House.

It’s nice to hear stories like that – real stories, you know? Bumpy, unexpected journeys that grip success by not only skill, but determination. I’m sure many other stories like hers are out there, and people could really benefit from hearing them.

After that, there was food and drinks in the foyer, but I dashed out to the reporters gala (a GALA, oh my), and missed the lighting of the Olympic torch.

Well, that was day one, and I’ll leave it there for now.

In Vancouver

Picture taken from the plane at dawn

Ahoy me hearties! Thought I’d post a quick one to say I’m on the other side of the world. Arrived today in Vancouver, ready for the AAAS annual meeting to start in a few days.

So I’m feeling pretty exhausted! I’ll recover some energy before making a big push to post plenty of contact during the conference, including the IgNobel award ceremony and a visit to nuclear science lab TRIUMF.

Here’s some of the seminars I want to attend:

Saturday 18 Feb: Globalising Indigenous architecture: The Power of tradition, providing for the future.
Sunday 19 Feb: The next agricultural revolution: Emerging production methods for meat alternatives.
Monday 20 Feb: Radioactive isotopes in medicine.

If anyone else, specially my peeps in Aus, are coming to the AAAS meeting, send me a comment with your tips.

Must snooze! over and out.

Call out to Aussies! Watch transit of Venus on the tall ship Endeavour

HMB Endeavour in full sail

True blue replica of Captain Cook’s tall ship HMB Endeavour is circumnavigating Australia and dropping into me home town Adelaide for a spell. Australians can sail the tall ship replica Endeavour in June 2012 to watch the rare transit of Venus from Lord Howe Island, Cook’s real reason for mapping the east coast of Australia and claiming it for England. Read on, Macduff…

You know how they say when one door closes, a window opens? For me it’s the opposite. I closed all the windows to open the door, and an opportunity has flown SMACK into the glass. I can’t go on the HMB Endeavour, ‘cos I’m leaving Australia soon! Bummed out doesn’t begin to describe it.

For you peeps still in Aus, here’s the lowdown.

Cook’s Endeavour is currently sailing with a full, hammock-napping, rigging-climbing, star-gazing crew about Australia.

Over halfway through its yearlong trek, it’s docking in Adelaide from 16-23 February 2012 to open to those of the public keen to run their hands across the varnished wood and polished brass and marvel at the many ropes. Swoon. Details here.

If you, like me, want a closer inspection of the vessel and to get in those hammocks yourself, here’s your chance.

From end of May to mid June, the Endeavour is sailing from Sydney to Lord Howe Island to observe the transit of Venus on June 6. It’s a prime viewing location, and one of the first spots in Australia to see the rarest of eclipses.

Cook travelled to Tahiti in 1769 to view the transit, part of a global movement to find out the size of the solar system (specifically, how far Earth is from the Sun, an astronomical unit) by watching the transit in different locations around the world. Worked pretty well, too!

All Australia is in a good spot to see the transit, when Venus moves between Earth and the Sun and looks like a small black dot on our bright sun disk.

Don’t actually look at the Sun, will you, ‘cos you’ll damage your eyes. Use eclipse glasses or shadows. Though I do find eye patches rather fetching…

Transit of Venus, credit NASA/LMSAL

Transits of Venus happen in pairs eight years apart, but each pair is separated by over a hundred years. This is the last one in the pair, so if you miss this transit – that’s it until 2117 when we’ll probably be dead or robots.

This is another opportunity that has faceplanted into my closed window. I’m going to be in South America during the transit, one of the few places where you get to see zip, zilch, zero. Bummer…

So I’ll be living vicariously through you, dear Australian readers, so make the most of it! See it at home, or hit up the Endeavour and make a trip from it. The voyage in June is $4000, so quite pricey but a trip of a lifetime! Crew will be selected by ballot, and you need to enter here before 10 February 2012 – which is really soon. Do it now. Are you doing it? Go, right now, click here, live my dream. Take a pirate hat!

I travelled on the Young Endeavour back in me younger days, another replica tall ship used as a training sail vessel, it’s one of those memories that just sticks with you. Like seeing Stonehenge or being in a circus. Ballots for that are open too, but only available to people 16-23 years old. If that’s you, check it out and apply now!

Looks like I’m missing out on the sailing action in Australia this year, but I’ve got some pretty sweet plans myself. I’m heading out that door and leaving in just over a week for Vancouver, Canada, where I’m hitting the AAAS annual meeting. I’ll tell you all about it!

Trojan atom

Rice University graduate student Shuzhen Ye used an ultraviolet laser to create a Rydberg atom in order to study the orbital mechanics of electrons.

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?

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?

Giant anteater

Giant anteater, image by Malene Thyssen

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

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

pudding with holly

Chocolate orange icecream pudding with side of holly. Image by webmink

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.

Holly, image by 4nitsirk, flickr

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

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

Sunglasses made by lasers

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!

Bubble images printed into 3D eyewear. Makes me think science sunglasses!

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

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

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

Image by .jun, flickr

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.

What's in your tea? Image by massdistraction, flickr

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

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.

Space shuttle before docking with space station. Image by NASA

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.

More coral crochet (and brief patterns)

I’ve got some good blog posts up my sleeve, but they’ll have to wait until after NaNoWriMo, because I’m quite sick of typing at the moment!

Instead, here are some more of my contributions to the Adelaide crochet coral reef over at the RiAus.

Fire crochet coral

Fire crochet coral close up

FIre crochet coral birds eye view

The above were made from a huge ball of wool, with probably eight different kinds of yarn rolled up in it. It was fun when the threads changed colour, especially working with the yellow one on the outside, which was quite thick and crinkly. Pattern for the outside: Chain 20, then dc each stitch, but on every third stitch add another dc into it, so it increases. For example: dc stitch, dc stitch, 2 x dc stitch, repeat. Just kept doing that! Then I stitched up the edge to make it a circle, and dc’d in the center with red wool to make the pokey out part.

rope coral

rope coral close up

This one was tricky to work with, especially with my mid-sized hook. It was, basically, just two pieces of rope. Pattern: Chain 10, dc each stitch twice (so you’re increasing every stitch.) At the bottom I used some fine yarn and the same mid-sized hook and just dc’d along the edge really loosely.

My previous post is here with the big orange curly coral. It’s been fun! Happy to talk patterns with anyone who’d like to try it at home. Essentially, it’s just a lot of regular increases to give it the curly, hyperbolic edge. I think it would look good as a hemming on sleeves or pants or skirts.

The physics of pink – why it isn’t in the rainbow

“Did you know there’s no pink in the rainbow?” my brother asked in the car.

“Yeah, it always used to bug me in playschool. ‘Pink and yellow and purple and green?’ Why couldn’t they just put them in order of wavelength!’ I said. “Or teach the Richard of York gave battle in vain acronym so kids don’t just yell ‘It’s a RAINBOW!’ when they see a bunch of random colours.”

“Do you know why there’s no pink?”

“No…”

“It’s because it doesn’t have a wavelength at all. It’s a non-colour, we should call it minus-green.”

“What are you talking about?” I said, and he put me onto this youtube vid, “there is no pink light,” one-minute physics from New Scientist.

Nifty, but I was still confused after watching it, so I did some digging.

The colours in the rainbow can be called monochromatic colours, or spectral colours. They have a single, dominant wavelength that trigger receptors in our eyes that send a message to the brain. We have red, blue and green receptors called cones… though it’s not quite that neat and tidy.

Light colours mix together differently then paint does. In light, all the colours together make white (and on the flip side, sunlight contains all colours), while no colours, and no light, makes black. Red and green make yellow, green and blue make cyan, and blue and red… wait for it… make magenta, or pink.

We see pink when our eyes register a mixture of red and blue light. However, there’s no wavelength corresponding to pink, because the spectrum of light (or electromagnetic radiation) is more like a long line stretching from really low energy radio waves which carry our favourite TV shows, to microwave, infrared, red …your favourite rainbow acronym… violet… ultraviolet, x-rays etc. There’s no red-pink-violet, only red-orange-yellow-green-cyan-blue-violet.

(I actually found this part of the video confusing. It sounded like we could perceive non-visible electromagnetic radiation as pink, and we can’t. We don’t see pink x-rays or pink radiowaves, and most of us are still blind to UV light. Though if you want to see the world through bee-eyes, you should check out flowers under ultraviolet light. These white flowers show a bullseye pattern, invisible to us, that directs pollinators to the centre.)

Back to the rainbow. Those spectral colours, the ones with wavelengths, are found on a Planckian locus below by following the outside curve. The pink colours are in the middle of the bottom, and are non-monochromatic colours, ones without a wavelength of their own, made by seeing two different colours at once. Hey presto, red and blue (and no green) make pink.

There’s another colour left out of the rainbow club. Where does brown come from? A dark colour, we perceive it when we see low levels of light, with a dominance towards red. It’s a dark, dirty red.

Twittarrr

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