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A Schooner
of Science

Did I hear you right? McGurk and other illusions

The other day I was chatting about muddled senses. Do we really see what’s around us, or do we just assume it’s the same as yesterday and fill in the blanks. How do we understand half-uttered mumblings we don’t properly hear, and when we think we’ve understood, have we actually listened to the other person or just heard what we want to hear?

It lead us to talk about some illusions that show how intertwined and untrustworthy our senses can be.

Case one: The McGurk Effect

What you see changes how you hear. Take the sound “ba”. When an audio recording of “ba” is dubbed over a silent video of someone saying “fa” – then “fa” is what you hear.

If the video silently mouths “ga” or “da”, while playing a “ba” audio – it turns into the harder sound “da.”

Close your eyes and the effect stops. Open them and it starts right back up again. No matter how much you try to hear “ba”, the visual information overrides the audio. Check it out.

Try it with your eyes open, then watch it again with them shut. Whaaaaa???

This BBC video has more of an explanation and the ba/fa illusion.

Nice, but what are the applications? Firstly, I should move my mouth more clearly when I talk to people instead of my usual pirate mumble-slur.

Second, if speech recognition software uses video as well, it could possibly become more accurate.

University of Adelaide research week begins

Today marks the start of Research Week at the University of Adelaide, so if you’re SA based like me, might be worth heading in for a look.

Monday 5pm there’s a seminar on wind energy that looks good. We’re always spotting turbines when we road-trip to Melbourne.

On my way to Whyalla for a science show earlier this year we stopped in the infamous bodies-in-the-barrels Snow Town. A turbine blade fell off a truck years ago and, damaged, they put it on show in a fenced outdoor spot. They are MASSIVE!!! The bank where the bodies were found, in barrels of acid, so the killers could receive their government payments from what I heard, was all boarded up.

Wednesday evening it’s a toss-up between African Research Safari, where directors of the Joanna Briggs Institute talk about challenges and success stories to evidence-based health research in Africa, and a Meet the Researchers event, with a short introduction from ten world-class researchers and a chance to chat with them over tea and cake. Both sound really good!

Though it’s not super sciencey, I’m keen to go to the History of Emotions workshop on Thursday 12 – 5 (if I can justify taking the afternoon off.) There’s Shakespeare, which I freaking love to be honest, and discussions on how shifting cultures change emotional regimes over time. Sounds difficult to research – is historical evidence different because the emotions are different, or because the writing style and language was different? On the other hand, without the language to describe emotion, can we even experience the emotion… maybe not. And how could we tell? Takes me back to my philosophical Theory of Knowledge days.

Click here for the full event calendar.

Prehistoric kraken lair with fossilised ‘self-portrait’? Probs not.

It would be remiss of me not to write about this wonderful, but rather unlikely story, given its about a subject close to my heart – giant squids.

Within Nevada’s Berlin-Ichthyosaur State Park are nine fossilised remains of ichthyosaurs, marine reptiles that looked a little like dolphins, but much bigger. Nine remains all in one spot! How did they die? Why were they all found in one place? And don’t they resemble, just a little, the suckers of an octopus, a squid or a GIANT KRAKEN!

At least, that’s an idea presented to the annual meeting of the Geological Society of America on Monday. Here’s the press release and the presentation blurb.

According to the blurb, the fossil remains are from a giant cephalopod midden, a collection of bones arranged by a huge prehistoric squid, octopus, or the mythological Kraken. Perhaps this fearsome beast of the sea hunted ichthyosaurs like the epic, iliad-worthy battles of giant squid versus sperm whale. Powerful tentacles curling about the undulating reptilian body, a lover’s embrace turned fatal attraction, tightening, strangling until still and dragging to the depths of the ocean.

The arrangement of the bones resembles suckers because, according to the blurb, they are a particularly grisly self-portrait. An intentional arrangement of the vertebra to resemble the creature’s own suckers. Imagine it – An introspective kraken rising up from the deep and looking deeply at its tentacles with saucer-eyes. Did it want a friend? Was it an homage to the suckers on which its lonely life depended? Was it not a self-portrait, but a picture of a friend, a lover, a child? We simply don’t know.

Granted, these ichthyosaur vertebra do look a lot like suckers, but a self-portrait is a big call.

The media release has received a lot of attention, not all of it good. There’s a rather scathing report from the brilliant fossil-blogger Laelaps and a reply of (sarcastic) support from Deep Sea News.

Unfortunately, cephalopods are soft-bodied and don’t fossiise well, so there’s no evidence of the prehistoric kraken, and certainly none that it created self-portraits. Still, it’s a nice story.

(Just to be clear, I’m not giving this guy a hard time. I think it’s great he has the opportunity to discuss his ideas publicly. It would take some bravery, and I respect that. I wouldn’t agree with a reporting of the presentation as if it were widely accepted fact, though. But even then, I don’t think it’s particularly harmful to readers. That’s my humble opinion, and I love a good giant squid story.)

Crocheting a coral reef

It was my birthday last week, and to celebrate I went to a crochet workshop at the Royal Institution of Australia to whip up an addition to their artistic coral reef.

I was lucky to nab some chunky bright orange yarn and made the piece pictured in about two hours.

It was good times – a glass of wine and nibbles, plenty of wool and spare crochet hooks and a group of thirty or forty people creating a hum of conversation and creativity.

My friends grabbed a spot on the floor (the tables were taken, and I prefer floor-sitting anyway) and started talking. A couple of the group were beginners, and I’m not much better, but they picked it up in about forty minutes.

The hyperbolic shapes, curvacious and wiggly, are made by frequent increases on each row. It’s kind of a funky shape, and it might look good as a scarf or fascinator, even a cuff. What do you think?

The RiAus Adelaide Reef in their downstairs gallery has closed over spring to make room for a new art installation Energy landscapes, a new frontier. It opens again over the holiday period from early December to the end of January.

I saw the exhibition a few months ago and it’s HUGE! A large room is full of pieces, handmade by people in Adelaide. They’ve linked the crochet to environmental problems plaguing the Great Barrier Reef, like coral bleaching.

A section on coral bleaching. Image by RiAus.

I’m keen to go to the next workshop, which is on Thursday 17 November 6-8pm. You can register here. It’s free.

The project is a satellite of the worldwide Hyperbolic Crochet Coral Reef project created by Margaret and Christine Wertheim of the Institute For Figuring in Los Angeles.

Tales of the demon core


Plutonium sphere and tungsten carbide blocks. Image by Los Alamos National Laboratory

On August 21, 1945, the demon core claimed its first victim. Harry K. Daghlian, Jr. was at Los Alamos, a secret laboratory in New Mexico where scientists worked feverishly on the equally secret Manhattan Project. To the outside world, at least those with sufficient security clearance, it was known simply by the mailing address – postbox 1663.

This particular night, Harry was working alone in the lab, stacking heavy blocks of tungsten carbide bricks around a core of plutonium. The bricks were to act as a neutron reflector, which would hopefully cause plutonium to reach the critical threshold at a much lower mass.

Criticality was, well, critical to making a nuclear bomb. It was that particular point when moments of nuclear fission supply the energy for more fission. At that point and beyond, fission runs away with itself and becomes self-sustaining, exuding radiation as it goes.

Just as he was about to place the final brick, intent on the delicate construction like a small child building their first block tower, the neutron counters sounded a warning. He froze. The numbers showed that if he added that one last brick, the plutonium would become supercritical. Slowly, heart pounding in his ears, he moved his hand back. As he did, the brick slipped through his fingers, fell, landed right in the center with a thud like a nail in a coffin.

What was it that made him drop that brick? Was it the beads of sweat that coated his hands as he realised what could happen? Was it that infallible fear-fulfillment that sends learning bicyclists directly to the obstacle they want to avoid? Or was it indeed a demon?

Either way, that final brick flipped the system into a critical reaction and radiation began bursting forth.

Harry panicked and tried to knock the brick off. No luck, it was a good four kilos. With a deep, shaky breath and a sour taste in his mouth, he disassembled the bricks as fast as he could until the reaction stopped.

By that time, Harry had received about 510 rem of neutron radiation, resulting from 1016 fissions. Unfortunately he became the first known fatality resulting from a criticality accident, and died less than a month later from acute radiation poisoning.

The demon core smiled.

Nine months later to the day, physicist Louis Slotin was tickling the dragon’s tail. It was an extremely high risk experiment to find the point when a sphere of plutonium, the same one which claimed Harry’s life, would become critical from the position of neutron reflectors – in this case, two half-shells of beryllium. Plutonium was placed inside one half, like a yolk inside an eggshell.

Recreation of Louis Slotin's experiment with plutonium core and beryllium

As the top half was raised and lowered, machines measured the activity from the core. Louis was showing seven other scientists how it was done.

“Lift it up and the activity is reduced,” said Louis, demonstrating. His thumb was crooked inside the thumbhole of the beryllium, allowing him to hold it rather like a bowling bowl. “Watch as I carefully lower the beryllium.” He slowly moved it down, down, down. The scintillation counters started to beep faster. Louis had done this almost a dozen times before, and had helped assemble the Trinity core, the first detonated atomic bomb. It never failed to amaze him, but he didn’t particularly like his work with bombs, and was training a replacement, Alvin Graves, to take over while he went back to biophysics.

“If you allow the beryllium spheres to close completely, the plutonium will reach critical mass,” he cautioned, brandishing a flathead screwdriver with his other hand but keeping both eyes on the core. “To get it as close as possible to that point, I have found a simple screwdriver does the job quite well.” He put the screwdriver tip between the beryllium as he lowered his hand further, until only a tiny space separated the two halves.

At that point, the unseen demon flexed. The screwdriver slipped.

The watching scientists later described a blue light and a wave of heat, and Louis tasted something sour in his mouth. Immediately, as if on reflex, he jerked his hand back to break the beryllium sphere and end the reaction. His body, crouched over as it had been during the experiment, had shielded the other scientists from most of the radiation.


Detonation of the demon core at Bikini Atoll

At once they all left the building, Louis vomiting as soon as he was outside. He was rushed to hospital, but even numerous blood transfusions couldn’t save him.

Louis had received the equivalent radiation of someone standing one and a half kilometres from an atomic bomb blast and died nine days later in the presence of his parents.

After the accident, all future criticality testing was ‘hands off’ and scientists worked through machines like the Godiva devices.

As for the demon core, it was detonated later that year during Operation Crossroads testing at Bikini Atoll, which remains uninhabited to this day.

Green potatoes are poisonous

Is this not the best potato ever? Image by courhome

So I was cooking dinner tonight and had a hankering for potato wedges. Unfortunately, in a fit of nonsense I had put my potato in the fruit basket to ripen. Ridiculous. So it had turned greenish.

Now I’m a pretty frugal, food-saving kinda person and hate throwing stuff out, but I had a feeling that this was one of those times. One of those “better safe than sorry” times, so I checked the interwebz and then threw it out.

If you’re ever in a similar quandary, here’s why not to eat green potatoes.

Potatoes make glycoalkaloids, chemicals that protects them from insects and fungi. They are especially fond of these chemicals when they are damaged or growing new plants, when they go green and sprout from their eyes.

One of these chemicals is called solanine, a poison made by deadly nightshide (a member of the same family, Solanaceae, along with tomatoes).

Solanine poisoning resembles gastroenteritis, so vomiting, pooping, and generally upsetting symptoms. The CSIRO says that, seeing as the symptoms are the same, some undiagnosed cases of gastro might be due to green potatoes. (So glad I didn’t eat them.)

I usually keep potatoes in the fridge, which is apparently also bad. At the chilly 2-6 degrees celsius of a fridge, the starch turns quickly into high levels of sugar, causing them to brown quickly during frying. So you’re supposed to keep them in a paper bag in a dark cupboard.

So much dinner-time learning! Oh – and the replacement meal, curried roast vegetable couscous, was delicious.

Photographs from the first day of spring

Spring has sprung here in South Australia, bees buzz in the blossoming trees and the air is warm and sweetly scented. So I took my camera for a stroll around my neighbourhood and took some pictures to capture the first day of spring.


Wattle – nothing says Australian spring so much as the smell and sight of these fuzzy yellow coated trees. The picture doesn’t do justice to the sound of all the bees collecting nectar and pollen overhead. Try to imagine the buzzing.

Trees which line a street just around the corner from my house. Gorgeous days like this remind me of a line from Moby Dick, Herman Melville, my favourite book:

The warmly cool, clear, ringing, perfumed, overflowing, redundant days, were as crystal goblets of Persian sherbet, heaped up—flaked up, with rose-water snow.


In among some rocks, I noticed a colony of ants going nuts! It was queen day, as I like to call it. When young princess ants fly away to start a colony of its own. There were a few drones, fertile male ants with wings who were smaller than the princesses. It was their nuptial flight.

princess ant

A worker ant helps a princess prepare for a nuptial flight.

Hen mothers for ducklings, cross-fostering species

hen and ducklings

Image by cod_gabriel

When I was young and living on a small farm in the Adelaide Hills, we used to raise ducklings under chickens. The hens were more inclined to sit and warm the eggs, and once hatched were better at protecting their young from rats. So we took duck eggs, placed them under brooding hens, and everything was cheery.

Those hens loved them little ducks, at least, they looked after them just as well as they did their own chicks. They’d go out foraging together, chattering away in their different tongues at a handful of scattered grain. But there was one place where their differences became obvious. The pond.

At the first sight of water, the ducklings would be in and swimming, having a great time duck-diving underwater and eating duckweed. Meanwhile, mother hen would be going absolutely spare! You could almost hear the concerned clucks saying “now get out of that water at once! Don’t you know you can’t swim? Oh heavens, what have I done to deserve such unruly children?”

What she’d done, somewhat unintentionally, was to be a cross-foster mother. A species which raises children of another species.

Peahen and guineafowl chicks

Image by Chicago Zoological Society

Chicago’s Brookfield Zoo recently raised two clutches of guineafowl chicks with peahen mothers. The parents protected their brood from hawks, and showed them the ropes of living free-range in the zoo – such as how to avoid pedestrians.

From the press release:

“‘Zoogoers may not notice anything unusual between the moms and chicks, but there are definitely differences and several barriers that they needed to overcome, including language and behaviors,’ said Tim Snyder, curator of birds for the Chicago Zoological Society, which manages Brookfield Zoo. ‘The first two weeks were a little precarious because the chicks needed to learn what the peahens’ vocalization meant and adapt to different behaviors that are not instinctual to them.’

“For instance, Guineafowl chicks naturally scatter and hide when frightened or threatened, while peachicks run toward their mother. Additionally, Guineafowl moms and chicks move as a group and help care for each others’ young, which is the opposite of independent peafowl.”

Black Robin on Rangatira Island

Image by Frances Schmechel

Cross-fostering for conservation helped bring Black Robins from the brink of extinction. In 1980, only five survived in the wild on Little Mangere island in New Zealand, including a just one fertile female called Old Blue.

Each Spring, the first clutch of eggs was raised under a Chatham Island tit, giving Old Blue time to breed twice in the season.

Bit by bit the population has crawled back and is now a relatively comfortable 250 individuals. The fostering program has been used as a model for other endangered bird species.

My picks for National Science Week 2011 (dinosaurs, quizes and citizen science)

So it’s that time of the year again – National Science Week (which now spreads across the whole month) is already upon us. See what’s on in your area.

Apparently there are dinosaurs in towns across Australia, at least, virtual ones. I haven’t seen them myself, but I’ve seen similar augmented reality exhibitions and its fun technology. If you see one of these yellow symbols, and you own a smartphone, then you can do some phone magic science and hunt for dinosaurs through your phone’s camera. Sah-weeet! I’m going to hunt me some dinosaurs. I’m watching Stand By Me right now, which feels like Jurassic Park for some reason…

If, like me, you enjoy a good quiz night and have left it too late to jump on someones team at the last minute (and have no expertise in history, sport or music – but an embarrassing enthusiasm for biology and chemistry) then this might appeal. The CSIRO have a DIY quiz with questions and answers for download. You can host your own, and ensure an appropriate balance of alcohol, dips and science.

For the past few years, National Science Week have organised a citizen science project. In 2009 it was a National Star Hunt. In 2010 it was a Big Sleep Survey. This year they want to know if you are any good at multitasking. It’s a fair question. I was once a proud multitasker myself, until I read research that showed it was far less efficient than just picking one job and doing it properly. Want to help? Take the test.

Exploring the blurry line between colony and individual

I found this great post on the Portuguese man-o-war, known as the bluebottle in Australia, over at Deep Sea News the other day. It’s eating a fish!

The post also said:

Remember this species is colonial and made of four different polyps or zooids, working in unison and dividing labor. The bladder is a single polyp called a pneumatophore. The long tentacles are dactylzooids used for fishing. The dactylzooids bring the fish up to another set of zooids, gastrozooids, responsible for digestion. Last, there is set of zooids, gonozooids, in charge of reproduction.

So it looks like a jellyfish, but it ain’t. It’s a colony of four specialists working together, each with their own nervous system but incapable of living by themselves.

Bluebottle on Woolongong Beach, NSW. Image by Fiona Wilkinson

As I was doing a bit of research about bluebottles and how they sting even when dead and dried up, I came across an interesting question. How do they reproduce? If the gonozooids are responsible for getting jiggy with it, don’t they just make more gonozooids? Where do the rest of the polyps come from?

Well, no one really is a hundred percent sure. I guess that’s fair enough, studying a swarm (a navy) of man-o-wars during mating season doesn’t sound too good. But here’s what they think.

A gonozooid from one man-o-war will make sperm which combines with an egg from another man-o-war gonozooid. Hey presto, you’ve got fertilisation and one embryo – which will become the bladder polyp at the top. That embryo divides several times, then reproduces asexually to make more zooids, which bud out of it. The budding polyps will become either tentacle, digestion or reproduction individuals.

That’s where I got confused. Does this mean that each of the zooids actually come from a single polyp? Are they just differentiated forms of the original polyp, specialised for their particular role? How is this different to a human embryo producing heart cells?

One explanation uses phylogenetics – comparing organisms to see how similar and different they are. Each zooid is similar to solitary Cnidaria (the phylum that includes jellyfish, coral and bluebottles), so can be considered an individual in its own right and a bluebottle as a colony.

But if we define an individual as something with similarity to other individuals, then all the cells of a multicellular organism would be individuals. Are individual humans really colonies of individual human cells? Really, the microbes on and in you outnumber your human cells 10 to one, so you’re more like a walking microbial factory anyway.

White poplars, a kind of aspen, form clonal colonies. Image by Jacob Halun

I think we have a very human-centric model for defining individuals, which is not surprising really. But most species on the planet don’t reproduce like we do, the boundaries between individual and colony are much less clear.

Take aspen trees, which can grow by seeds (sexually) or by underground runners which sprout a tree-clone (asexually.) Over time the runners can decay separating the trees. How can we tell if the trees are individuals or clones, and if we can’t, how do we study adaptation and natural selection?

Tasmania has these Huon pines that are the oldest genetically identical stand of trees which has lasted 10,000 years. Each tree lives about 2,000 years, but the original tree renews itself through genetic clones. Tassie also has the oldest genetically identical plants, clones of King’s lomatia estimated to be at least 43,000 years old.

Strawberries do it too, as do fungus. A single specimen of Armillaria solidepes was found in Oregon the size of 1,220 football pitches and estimated at 2,400 years old. It’s one of the largest organisms in the world.

Where does the individual end and a colony begin? Looking at all the bizarre stuff out there, I can’t help but wonder if we’re the weird ones.

Clarke, E. (2010). The Problem of Biological Individuality Biological Theory, 5 (4), 312-325 DOI: 10.1162/BIOT_a_00068

Read it at the homepage of Ellen Clarke

The red queen, sex and nematode worms


Alice and the Red Queen by John Tenniel

In Lewis Carroll’s Through the looking-glass– a whacky book if I ever read one – the laws of physics don’t really apply. Hills can become valleys, straight can become curvy, and forward is really backward.

In one scene, Alice chases after the Red Queen, both running as fast as they can, but when they stop Alice realises they are still right where they started. “Now, here, you see, it takes all the running you can do to keep in the same place” says the Red Queen.

And it might be the same with the evolution of predator and prey, host and parasite. Running doesn’t get you anywhere. So says the Red Queen Hypothesis.

c elegans embryo

C elegans embryo. Image by Monica Gotta

As the host adapts to fight the parasite, the parasite evolves to infect the host. It’s an endless race, and extinction faces the first organism to stop running.

So what’s this got to do with sex? Sex is evolution on turbo. Mixing and matching genes increases genetic diversity, giving a species more opportunities to outlast in the ultimate game of survivor.

Field data supports the Red Queen Hypothesis as describing an adaptive advantage of sex. Models and maths support the idea that coevolving species could select for rare genes and unusual combination randomly created by sex. Direct experimentation of coevolution and nookie is tricky business.

New research, published in Science, grew several populations of nematode worms (C. elegans, roundworms) which are usually asexually, but reproduce sexually 20% of the time.

The populations were differently exposed to bacterial parasites (Serratia marcescens) as shown.

C Elegans Sex Research

C Elegans image by Bob Goldstein, University of Carolina, Chapel Hill, remixed by Science Journal. Creative Commons License

One population was given the parasites and left to their own devices. They and their bacteria could evolve together. These nematode worms increased their rate of sexual reproduction to 80-90% over time, and maintained a high level of sexy-times.

The other nematodes were given frozen stocks of bacteria every generation, so the parasites weren’t evolving as the worms did. At first, sexual reproduction increased in the worms, but then it dropped back down to 20% – the same level as nematodes which hadn’t been exposed to the bacteria at all.Alice meets dodo

Parasites on their own don’t increase sex – coevolution does.

A second experiment supported their conclusion. Nematodes mutated to be unable to reproduce sexually (asexual obligates) became extinct after 20 generations when exposed to the parasites. But mutants that always required sex to reproduce (sexual obligates) never became extinct.

When it comes to coevolution, it’s fall behind and be left behind.

Never stop running.

Morran, L. et al (2011). Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex Science, 333 (6039), 216-218 DOI: 10.1126/science.1206360
Brockhurst, M. (2011). Sex, Death, and the Red Queen Science, 333 (6039), 166-167 DOI: 10.1126/science.1209420

Happy Pi Day!

Hooray, it’s Friday Pi Day! Today, 22 July, is Pi Approximation Day – 22/7 being a sweet close-to value for that wonderful mathematical constant. Celebrate by eating pie, either for dinner or dessert (or both!) and indulging in a pint of your favourite beverage.

The electric, flashy development of tadpoles

Tufts researcher Dany Adams was filming the development of tadpole embryos, when she decided to leave the camera hooked up to a microscope going overnight. She was hoping to get some good time-lapse footage. What she got was bioelectric patterns which flashed across the developing tadpole face, outlining the future positions of eyes, nose and mouth.

“I was completely blown away.” said Dany, Ph.D, according to the Tufts press release. “I think I thought something like, ‘OK, I know what I’ll be studying for the next 20 years.” It had never been seen before, and was published in the August issue of Developmental Dynamics. Watch the video below.

“When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,” said Dany. “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”

Bioelectric signals cause cells to form patterns marked by differences in pH levels and membrane voltage, according to the researchers. The tadpoles were stained with a reporter dye that caused negatively charged areas to shine brightly while other areas look dark.

There were three bioelectric waves they saw in the footage.


It's Xenopus! Image by Luis Beltran

First, a wave of negative ions flashed across the whole embryo at about the same time as cilia formed, tiny hairs which allow the embryo to move.

The second flash was a patterning that matched shape changes that were soon to occur in the face region. Bright areas, negative ions, show places where the surface will fold in.

Thirdly, localised regions of bright, negative areas formed, grew and disappeared without disturbing the existing pattern. At this point, the embryo began to elongate.

If bioelectric signalling is important to embryo development, you would expect development to be altered by screwing around with the signal process – and that’s exactly what happened. The researchers disrupted signalling by inhibiting a protein involved called ductin, which transports hydrogen ions. Some embryos grew two brains, others had unusual nasal or jaw development, and so on.

Interesting, I guess, but a bit sad for the baby tadpoles imho. Plus, I feel like it doesn’t take much to disrupt embryo development. Take away any protein that’s switched on at that sensitive time and development takes a detour…

All the same, bioelectricity may play a crucial role in embryo growth. Laura Vandenberg, another author on the paper, said “developmental biologists are used to thinking of sequences in which a gene produces a protein product that in turn ultimately leads to development of an eye or a mouth. But our work suggests that something else – a bioelectrical signal – is required before that can happen.”

Vandenberg, L., Morrie, R., & Adams, D. (2011). V-ATPase-dependent ectodermal voltage and ph regionalization are required for craniofacial morphogenesis Developmental Dynamics, 240 (8), 1889-1904 DOI: 10.1002/dvdy.22685

On being busy and finding time to write

So you may have noticed my blogging schedule has been a little lax lately. I’ve been pretty busy with other writing and research, and been finding it really hard to give the blog attention and love.

To balance things, I’m dropping my posting frequency down to once a week. I just wanted to let you know that I’m not abandoning the blog, I still love you, it’s not you, it’s me – all that kind of stuff.

I’ll get back to you in a day or two with a proper (gasp!) post about the Red Queen hypothesis and the evolution of sex, with some sweet research on nematode worms with bacterial parasites.

In the meantime, have a rum for me!

Alcoholic art, crystals of liquor

So it’s appropriate that I’m a little bit tipsy while writing this.

Alcohol under a microscope! That’s today’s post. BevShots take photographs of alcohol crystallized on a slide, shot under a polarized light microscope. It can take up to four weeks for the alcohol to dry completely on the slide. It’s art, distilled. And quite magnificent.


Mmm margarita. And do you like pina colada?

Pina colada

What pretty rum. I think the citric acid helps. Anyone for a pint?

English oatmeal stout

Bevshots sell the pics (there’s heaps) as metallic prints, on canvas or as merchandise – like hip flasks, for example. Look, I’m not big on promoting items, but these would make a sweet gift for a 21st birthday. They’re stunning, and only $28. It’s a nice personal touch if you know their favourite drink.

Oh, and vodka shot glasses! So cool…

Vodka shot glasses

There’s even an iPhone app, so you can pick your poison and see the bevshots version. I imagine this will increase your popularity and attractiveness with every drink. Kind of like beer glasses.

Isn’t this just the best mix of science, alcohol and art? They should be paying me for this kinda publicity (feel free to send me a gift, guys!)

Spongiforma squarepantsii, fungus found in Borneo

Absorbent and yellow and porous is he,
Spongiforma squarepantsii.


Found: Spongebob. Image by ep_jhu

Named for the best cartoon character ever, Spongebob Squarepants, this recently discovered species is not a sponge, but a fungus.
Discovered in Borneo Spongiforma squarepantsii has a characteristic smell which is “vaguely fruity or strongly musty,” according to the paper published in Mycologia.

It’s a weird fungus though. Not much of a mushroom. Dennis Desjardin from San Francisco State University said “It’s just like a sponge with these big hollow holes.” (via the press release.)

“When it’s wet and moist and fresh, you can wring water out of it and it will spring back to its original size. Most mushrooms don’t do that.”

Though it looks different, Spongiforma species are related to the edible porcini mushroom. It’s ancestor would have had the traditional cap and stem fashion too, but has been lost over time.

Caps and stems are an evolutionary adaptation designed to keep spores moist and alive. A stem lifts the fungus up so spores can be dispersed better, and an umbrella-like cap keeps spores from drying out.


Spongiforma Squarepantsii, image by Tom Bruns, U.C. Berkeley

Spongiforma fungi are a little different. It stores water in its sponginess, and revives quickly if it dries out by absorbing moisture from humid air.
Finding new fungi is an adventure… I wonder if they’re looking for any volunteers? “We go to underexplored forests around the world, and we spend months at a time collecting all the mushrooms and focusing on various groups,” said Dennis.

“When we do that type of work, on average, anywhere from 25 percent to 30 percent of the species are new to science.”

And I just love Spongebob. He has just the best outlook on life and work ethic. Who else wakes up and says “I’m awake!” “I’m ready, I’m ready!” When I grow up, I want to be Spongebob.

Oh, and can someone make me these cupcakes for my birthday?

Modelling catastrophic dam collapse and natural disasters

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?

Models of Geheyan town before and after dam collapse

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.

Genetically engineered ‘transgender’ goats makes poor reporting

Random goats not used in this experiment. Image by emdot.

“Scientists genetically engineer female ‘Frankenstein’ goats in male bodies to create ‘human’ breast milk” exclaimed the Daily Mail on Tuesday.

The article leaned on a press release titled “AgResearch Transgender Goats To Be Milked” sent out by the Soil & Health Association of New Zealand last Sunday.

What follows on the Daily Mail and in blogs all over the net is extremely shoddy science reporting. Here’s a taste.

“Genetic engineers are deliberately breeding transgender goats to see if their milk is similar to that produced by humans.

“The goats being created are effectively a female trapped in a male’s body, complete with the full male anatomy.

“The company behind them wants to see if their milk contains the same proteins as human breast milk – with a view to one day possibly selling it in stores.”

And I’m not just picking on Daily Mail. Lots of blogs picked up the story.

Here’s my understanding of the situation.

First this “girl goat trapped in a boy goats body” business. Honestly, how can anyone know if a goat feels like a girl or a boy? Transgender is about self-identity. No, these goats are intersex.

Specifically, they have XX chromosomes and sterile male bodies. It’s quite common in goats. At the bottom of the article, they finally quote Dr Jimmy Suttie from AgResearch, who says “It was inadvertent. This is something which normally happens about 10 to 15 per cent of the time in this breed of goat. It just happens to be the cell line that was used.” For the 15 goats in the study, 75% were intersex.

So they aren’t “deliberately breeding transgender goats.” It was inadvertent.

The Daily Mail also says “All the ‘males’ have been sterilised to stop them breeding.” But the goats are sterile anyway because they lack a Y chromosome.

Being intersex isn’t weird or wrong, and I don’t like that the article takes a “oh noes! girlboys!” angle. Whatever! Humans can also be XX and male, or XY and female, sometimes without realising it until they are tested for fertility. Life goes on as normal.

These goats aren’t transgender. They’re just goats. End rant.

So what about the genetic engineering?

A human protein has been inserted into their genome so it will be expressed in milk, a concept called biopharming and an area AgResearch is interested in. Human proteins can be extremely useful in medicine, just take insulin as an example.


Commercial insulin to treat diabetes, was originally taken from cows and pigs after they were slaughtered for food.

Later the insulin gene was cloned into bacteria so they could make human insulin, which had fewer side effects.

More recently, the gene was cloned into safflowers to produce insulin at a reduced cost.

Proteins like insulin are long chains of amino acids, and that is exactly what a gene codes for – the order of the amino acids. But to work in the body, a protein not only needs the right order, it has to be folded to have the correct three dimensional shape to do its job. Often it also needs extra bits and pieces added to it, like a sugar chain. Sometimes it needs to be cut in certain places.

Think of it like an intricate origami with the instructions written on it. Often bacteria can’t read the instructions written on animal proteins. In that case, you need animal cells.

If the protein is made in animal cells, you then need to get it out. If you can get the protein expressed in milk, say goat milk, then you can collect it without harming the animal more than milking for food does. It’s been done before.

So the aim is to produce a human protein of medical interest in milk, so they can extract and study it. Not just sell human breast milk from goats in stores, as the Daily Mail seems to suggest.

Finally and for effect, the article threw in some outraged comments from random bloggers.

The whole thing is misleading, exaggerated and I hope it will be retracted. Plus it’s really mean about the goats, calling them unnatural and Frankensteins. Poor goaties.

There are some real concerns about biopharming, and people who are worried about it should have easy access to factual information. We can discuss the science of biopharming, the risks and benefits, how ethics approval is given, and how the goats are treated. With access to the whole story, people can draw their own conclusions rather than being spoonfed fear.

The last thing we need is a grim fairytale about Frankenstein transgender goat breast milk.

Nubia, irrigation and parasitic worms, a tale told by a Mummy

A few months ago I wrote about Ancient Nubians and their antibiotic beer, delivering a dose of tetracycline in every brew.

Now bioarcheologist George Armelagos has co-authored a study showing that early irrigation channels changed how humans were affected by parasites.

I’ll describe the research at the end, but first – a story! Make yourself a cup of tea and come back to read it.

Nubia, 500AD

Cotton. Image by Martin LaBar

Since he’d taken his first wobbly steps on Nubian soil, Alara had been pulling his then insubstantial weight on the family farm. He’d pull up weeds with grubby fingers under the watchful eye of his older cousins by day. Lunch was often a paltry loaf of flat bread to share between the lot of them, supplemented with whatever local edible plant was in season, eaten hastily and followed by a brief break in which he built dirt pyramids with other children.

Now 30, Alara remembered his childhood as carefree and unplanned. His memories swam together like waves billowed out from boats on the Nile. Only small moments stood out with any clarity. A snarling dog snapping at his leg. The taste of bread warmed by the sun, seasoned with hunger. Buzzing with disbelief at the stories told by his cousins of things adult and forbidden.

A life in the sun had baked him hard and capable, and he still worked on the same farm he had as a toddler. His extended family shared the plot of land, shared the work, shared the harvest, shared the income. Shared the good years and the bad. He was a cotton farmer through and through, born and raised to the plough.

A friendly slap on the should shook Alara out of his reverie. “Wake up, brother, you are asleep on your feet! It’s time for lunch and then I need to walk to the river and check the channels. The water is not flowing as it should. Will you go with me?”

“Lunch already, Arty? I didn’t notice the sun was so high. Of course I’ll come with you.”

The midday meal of onion and lentils served with flat bread for eating with was waiting hot on the table. They ate quickly and had a weak cup of tea before walking to the Nile.

They could hear the river well before they could see it. The sound of saqiya irrigation was like music that infiltrated the whole valley, though they were so used to it they barely heard it. As they approached their saqiya, they called out a greeting to Nala who was driving the cow.

“Nala! We have brought food for you.”

“Thank you uncle,” she called back. “I’ll come down to eat.”

Al-Jazari's Water-raising-device ca 1205AD

The saqiya was the heart of the farm, pumping the water of life from the river to the fields where it was needed. Made of wood, it consisted of cogs and a large open-spoked wheel. The cow, encouraged by young Nala, moved a wooden arm around, turning the wheels and cogs to move a pulley.

That pulley was studded with jars which dipped down into the water and lifted up to the farm’s main channel. Each jar then deposited its precious load which ran to the farm and branched out into smaller channels, delivering water for the cotton.

Alara inspected the cow and saqiya while Nala ate lunch. Despite a slightly thirsty cow, everything seemed to be working fine. The problem must lie in one of the channels.

Walking along the main channel, he stopped now and then to check the water level. Sometimes silt and aquatic plants collected at the bottom, blocking the flow of water. When he and Arty came to the first branch in the channel, they separated to cover more ground. Following his channel through several other branches, Alara found one that was a problem.

The side of the channel must have collapsed recently. Mud clogged the small stream, causing water to dam up behind it and overflow. Alara reached in and started to pull up clumps of the stuff. The water became turbulent and muddy, and he noticed more than a few of the fresh-water snails that liked to live in the slowly flowing channels. As he cleared it, the water began to run clean again and move into the farm. He spent the rest of the afternoon checking other channels, clearing several that were silting badly.

Though he didn’t know it, those snails were responsible for the troubling, itchy spots many adults had on their arms and feet. Well, it wasn’t the snails exactly, it was the tiny worms inside them.

Several species of trematode of the genus Schistosoma could infect humans. These tiny parasitic worms hatched in water and quickly found snails to infect, burrowing into their large feet. They moved through the life stages of miracidia and sporocyst inside that host, emerging as free swimming cercariae which needed a mammal host to continue to the next stages.

In contact with humans, or for some species other animals, they penetrated the skin and lost their tails, moving through the circulation as schistosomulae. In the liver they would mature into adults, pair, and migrate so the eggs they produced would be shed in stool. Those eggs would make their way to water to repeat the cycle.

Two weeks later, Alara woke in the night with a pain in his stomach which sent him running to the toilet area. By morning he was exhausted and feverish. Though the disease didn’t kill him, researchers would later find evidence of the parasitic worms in his mumified remains.

The research

Schistosomiasis, the chronic disease caused by these worms, is thought “the most important water-based disease from a global public-health perspective” in modern populations. It infects an estimated 200 million people per year. It has a low mortality rate, but causes development problems in children and damages internal organs.

Modern irrigation systems, particularly slow moving ones, boost the disease by providing habitats to the snails. But what about ancient populations?

To find out, Armelagos, Hibbs, Secor and Van Gerven studied dessicated remains (aka mummies) from two Nubian populations. Wadi Halfa (N = 46) lived in 500AD when the Nile was lower, and used saqiya irrigation on their crops. Kulubnarti (N = 191) lived 300 years later, during a time when Nile flooding was good and irrigation was less critical. They hypothesised the Wadi Halfa population would have more Schistosoma mansoni, and it would be more prevalent in children and men due to differential water contact.

One out of three ain’t bad. Indeed, Wadi Halfa people had more of the parastic worms: 26% to Kulubnarti’s 9%. However peak prevalence of infection did not occur at a younger age in the Wadi Halfa, and there was no sex difference.

ResearchBlogging.orgHibbs AC, Secor WE, Van Gerven D, & Armelagos G (2011). Irrigation and infection: The immunoepidemiology of schistosomiasis in ancient Nubia. American journal of physical anthropology, 145 (2), 290-8 PMID: 21469072

Note: I tried to be accurate about life in Nubia, 500AD, but please correct me in the comments

(Also, I want to be a bioarcheologist! Should I apply for one of these Graduate Programs at Emory University?

Mind share, musings on social connection via technology

“Catch up for a coffee at 5?” I smsed a friend. I had to be at the RiAus at 6 for the Mind Share talk with Mark Pesce.

“Yep, see you then.” I met her at the usual place, creatures of habit that we are.

At the RiAus I settled into a chair with my laptop and logged into Twitter. Mark began his talk, taking notes from a little black book as he confidently conversed on the nature of online and mobile connection. Live tweeting the event was a surreal experience – transmitting his thoughts on connectivity to a connected online audience.

Five minutes before the end, as Mark fielded final questions, I smsed my partner. “Almost finished, can I get a lift?”

How did I live before mobile phones? Strange to think it wasn’t that long ago.

I remember crouching around a small computer screen playing communal Wolfenstein at age five with my two cousins. A shared mind working together to navigate the maze, shoot, and time escapes. These days massively multiplayer online role-playing games (MMORPG’s) connect thousands to fantasy realms for co-operative play. When did that start?

Think, for a second, how much has changed in your lifetime. Remember the days before Wikipedia, before Facebook, before iPhones?

In about five years we have become a culture of complete connection, and as Mark put it “we stink at it.”

For many of us, the connection is addictive. I’m a nervous wreck when without the net for three days. I get the shakes. Logging on is like a drug, flushing the mind with dopamine and serotonin, telling us everything is okay again.

Log on too often, though, and the shadow side emerges. Sometimes its impossible to switch off nor the heightened mental state required to constantly process new information be maintained.

A binge ends well after midnight with an untouched coffee long cold, a blossoming headache, and a final 140 character flourish to followers.

This is a problem.

Mark urged that we need to think as individuals and ethicists about disconnect time. The soul needs time for reflection, time for itself, he said.

I think the biggest danger with our constantly connected culture is a strong sense of self. With pure ego directing our actions, we look for like-minded people and become locked into a community that thinks only of itself. We become converters, preachers, know-it-alls.

Perhaps to truly communicate we need to relax and stop worrying what others think of us. Stop trying to have the wittiest tweet, a well-liked wall, and just one more follower. We have to stop wanting to be noticed, and start noticing others. Start listening.

Does any of this ring true for you, or am I just giving myself advice?

I’m waxing philosophical. Time to disconnect and reflect.

SKA, supercomputers and information technology

Image by SPDO/Swinburne Astronomy Productions

Since seeing the RiAus event on the Square Kilometre Array (SKA) with Professor Peter Quinn speaking, I’ve been posting bits and pieces from the night.

I wanted to touch on the huge computing requirements needed to support just the insane amount of data collected by this radio telescope.

To recap: the SKA will be 10,000 times more powerful than any existing radio telescope. Either South Africa or Australia will host the spiral of dish antenna extending over 3,000 kilometres across, the decision will be made next year.

Every day the SKA will collect one exabyte of data. That’s a ten with 17 zeros behind it, a binary bucketload of information.

To process it all, we’ll need the world’s largest supercomputer on site at the SKA core, so the data is processed real-time as it’s collected.

According to the SKA website, they need something about 50 times more powerful than the world’s most powerful supercomputer in 2010, the processing power of a billion PCs.

Optical fibres will be critical for the physical network, as they can transmit large amounts of data at high rates. These fibres are as fine as human hair, and made of silica glass.

Okay, so this is fibre optics rather than optical fibre. Same difference, right? Image by Twistiti

Because the SKA antennas extend for such long distances, up to 5,500 kilometres, or from Western Australia to New Zealand, the length of cable they need would be enough to wrap around the globe – twice!

The national broadband network proposed for Australia would hugely benefit the SKA, providing some of the infrastructure needed for data transmission. We need the NBN! It would make everything so awesome!

Once collected and processed, the data will be available to an international community of astronomers – yet another challenge.

Can it be done? Professor Quinn says yes, though it will require new technologies and creative problem solving. This is no small step for mankind, but we’ll be going much further than the moon.

More information on the SKA technology can be found here.

Exploring first light from the cosmic dark ages

One major project the Square Kilometre Array (SKA) will be working on is first light, how light arose in the Universe.

A quick recap on the SKA: It’s a radio telescope 10,000 times more powerful than current models. Made up of dishes linked to a data processing unit, the instrument will stretch at least 3,000 kilometres across Australia or Africa. My last post talks more about the SKA itself, what it is and what it means for science.

But now let’s talk about first light.

Our whole universe was in a hot dense state
Then nearly 14 billion years ago expansion started, wait
Barenaked Ladies – Big Bang Theory

But before the earth began to cool and the autotrophs began to drool a lot had to happen. The creation of stars, galaxies, and all things seen and unseen has taken billions of years.

By observing cosmic microwaves we can study how the universe looked at the age of 300,000 years, smooth and uniform. Through telescopes we’ve looked back to when the universe was a billion years old, as protogalaxies merged into galaxies.

But between those times, we know very little. This period is called the dark ages, before stars were formed and started to shine.

First light is the end of the dark ages, the moments when the first protogalaxies and quasars came into existence.

How can we look back six billion years to first light? Telescopes are time machines.

Look at something near you right now, say a pen. What you’re really seeing is light bouncing off the pen, travelling through the air to your eyes. Light moves very fast, but it’s not immediate. It takes a fraction of a second for the light to reach you.

Look a bit further now. Light from our tide-turning moon takes just over a second to get to Earth. Light from our dawn-breaking ball of exploding gas the sun takes a leisurely eight minutes to shine upon us. The next nearest star, Proxima Centauri, is four lightyears away. Light takes four years to travel the distance separating us. You can look thousands, millions, even billions of years into history. (source: Wikipedia)

credit: NASA

The further away you look, the further into the past you gaze. I always imagine what has changed out there in the thousands of years the light has taken to reach us. Is that star still there? Is it in the throes of death, spreading out into a supernova?

First light, then, though it happened long ago we can still see it happening in celestial newly-forming bodies that are very, VERY far away.

Distant and only faintly glowing protogalaxies defy current telescope technology. Finding first light is heralded as the next frontier in cosmology.

Here’s more about the SKA projects.

SKA – Something Kinda Awesome and a tremendous telescope

The Australian Government just announced it will spend 40 million dollars over the next four years to support Australia’s bid to host the Square Kilometre Array (SKA.) If, like me last week, you’re not really sure what the SKA is and Google seems to think it’s some kind of music – here’s the lowdown based on the RiAus event I went to on Thursday hosted by Professor Peter Quinn.

The SKA is a radio telescope 10,000 times more powerful than any other, a single scientific instrument comprised of individual dish antennas 15 metres wide working together.

Artist impression of SKA

Artist's impression of dishes that will make up the SKA radio telescope. Credit: Swinburne Astronomy Productions/ SKA Program Development Office.

From a central, densely packed core, receiving dishes will spread outward an area of over 3,000 kilometres. Combining their signals creates a telescope with the collecting area equivalent to a single dish one square kilometre in area.

Where will this massive instrument live?

The shortlist has been whittled down to two: South Africa and Australia. If in South Africa, the dishes will reach onto islands in the Indian Ocean. If in Australia, they will extend into New Zealand.

The final decision will be announced next year. Being Australian, naturally I’m hoping we’ll get the honour.

Murchison SKA candidate location

The candidate core site in Murchison Shire, WA. Credit: Ant Schinckel, CSIRO.

Our bid puts the SKA core in the Western Australia desert, Murchison Shire.

From here, the dishes would spiral out in five long arms across Australia and New Zealand.

The proposed core site is a space the size of the Netherlands, it contains 110 permanent residents.

With low population comes low radio interference. CSIRO scientists are working on innovative solutions to keep the site radio-quiet.

For example, trains in the region currently communicate by radio, and there’s dialogue to come up with an alternative that will work for trains without interfering with the SKA.

What will we find out there with our powerful telescope? Well, if ET phones home within our galaxy, with the SKA, we’ll hear it. In the next post, I’ll talk more about finding first light, when the galaxies began to glow.

Here’s more about the SKA: Australian site and International site.

The white whale, sighted, in pursuit

The white whale has been sighted off the starboard bow, and I’m hard on its trail. All hands to decks, no time for telling tales! Something in me must chase that whale, it haunts me… It has stolen from me, swallowed in its vast maw, some essential element of my foundations. The pursuit is all.

I will write more when I can, when slumber eludes me and the vision of the white whale plays most on my imagination, when the wind drops away and, foundering, I have nothing but time.

Meanwhile, you might like this funny video about the environment. It’s satirical, amusing, and just slightly offensive to damn near everyone. Enjoy!

Ferrofluid patterns and dancing art, fun with magnets

Behold ferrofluid, nanoparticles of iron coated in a surfactant and suspended in a solution of oil or water.

The surfactant can be citric acid or soy lecithin, among other things, and is used to stop them sticking together

It’s like magnetic dust.

Put a magnet under some ferrofluid and the particles align themselves in patterns to show the field.

The magnetic attraction is so strong, the ferrofluid will stick to a magnet and then you’ll never get all the iron particles off it. They’re stuck for good.

To prevent that happening, people usually play with ferrofluid inside a sealed container.

And play it is, this stuff is fun.


A friend of mine put a magnet above some ferrofluid with the lid off, and was abruptly COVERED in black gunk which stuck to him despite three showers. He wasn’t too happy, I think it smelled pretty bad. Hardcore.

Like most hardcore stuff, it’s been turned into kickass art. This video pretty well blew my mind.

Sachiko Kodama and Yasushi Miyajima created the piece, two ferrofluid sculptures which move synthetically to music. The two towers are iron cores of electromagnets sitting in a pool of ferrofluid. Etched with a helix pattern, the ferrofluid can move up the tower if the magnetic field is strong enough, stretching out in spikes as it goes.

The strength of the electromagnet is linked to metadata in the music controlling the voltage and AC pattern. To correct for the time delay, the electromagnet controls starts early so the maximum size of spikes coincides with beats of the music.

The result is a choreographed pattern that dances and winds like a living thing.

You can buy ferrofluid from Emovendo.

Hat tip to @DrSkySkull, who bought some ferrofluid as a classroom demo and supplied the picture at the top of the article.


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