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A shameless plug for the #asc14

Australian Science Communicators are converging today for the ASC conference of 2014. I very much enjoyed the 2010 one in Canberra where I happened to be, and made a special trip to be at the 2011 conference in Melbourne, but unfortunately can’t make it to Brisbane this time around. Instead, I’ll be watching the action on Twitter – #asc14 – and I’m @CaptainSkellett if you want to chat. Some events are being livestreamed and you can join in at the ASC Conference website. The conference is running from 2 – 5 Feb, plenty of time to catch something interesting! As for me, I’m baking coffee scrolls and packing boxes for another move interstate, from Melbourne to Canberra. Hope to catch up with some friends at Questacon, the ANU and CSIRO while I’m there for the next few years. I also feel like I need a new five year plan – perhaps I’ve spent too much time in the corporate world over the past year, and I’ve absorbed the desire for strategic direction through osmosis. Nonetheless, I think the big goal for the future is to focus more on writing and editing. I’ve been freelance writing (and doing a share of editing) for the past four years now, and despite the occasional stress of a creeping deadline, I still really, really enjoy it. I can certainly see myself making a lifelong career from it, which is something that’s been hard to picture in any of my other jobs. So that’s a solid direction to be starting with. There’s a livestreamed ASC event on The Storytelling of Science beginning in an hour, and I’ll pop it on while I pack.

Cuddly robot seals assist in dementia care

Professor Wendy Moyle with residents from Wesley Mission, Brisbane holding the Paro companion robots. Photo from Journal of Dementia Care.

When I was a child, I had a toy from Seaworld that was a baby seal, and man I loved that little guy. I also had a Furby, one of those fluffy toy robots that took the world by storm in 1999, and are having a major comeback now.

Little did I know that, had I smooshed them together in an elaborate Toy Storyesque toy reconstruction, I could have invented Paro, the robotic baby harp seal.

Paro, developed by Dr Takanori Shibata at Japan’s National Institute of Advanced Industrial Science and Technology, is used in dementia care. Its big, blinking eyes gaze at the person interacting with it, responding to sound and light. It can recognise words used by its owner and though it can’t talk back, it can make baby seal noises and nuzzle.

This engagement helps reduce anxiety in people with dementia, according to research led by Wendy Moyle at the Griffith Health Institute in Brisbane, Australia. The research split 18 dementia patients into two groups, one engaging with Paro and the other reading in a group. The results found that people in the PARO group had higher quality of life scores after five weeks compared to the reading group.

Why a fluffy baby seal? As well as being downright adorable it is just about the same size as a baby, so people can hold it on their laps. The researchers also note that some people have had bad experiences with a cats or dogs, and might react with fear. Who could be afraid of a baby seal?

On the downside, each Paro costs about $5,000, and need to be shipped back to Japan for repairs. At such a hefty price tag, it might limit use in care facilities. Then again, if it’s significantly effective at improving quality of life, reducing need for medication or allowing people to live at home longer, maybe it’s money well spent.

That’s the focus of Wendy Moyle’s next project, supported by a one million dollar boost by the National Health and Medical Research Council (NHMRC). The new study will be a large, randomised trial involving 380 people with dementia, and will compare three different care options – Paro, a soft plush toy, and usual care. Large aged care facilities in SE Queensland interested in taking part in the research can click through for more details.

Happy International Talk Like a Pirate Day!

Ahoy mateys! It be the best day of the year once again! Happy talk like a pirate day!

It’s too late to get your ergonomic pirate keyboard, but add plenty of R’s into your day anyway.

Corsair pirate keyboard

The image is from the Language Log, who weren’t sure who to credit it to. They had a little post about the linguistics of Arrr a few years back. O’course, I highly recommend the Official Talk Like a Pirate Day website for all your piratey needs!

I have also fallen in love with the totes and bags at Totes Amazeballs Co especially their pirate and sea lovers collection.

May your timbers shiver and mainsails rise! Arrrr

New approach to gently insert DNA into cells with high-tech lasers

Ethical concerns aside, gene therapy is a really exciting area of science. How cool to explore the functions of DNA and cellular machinery by inserting exactly what you want into a cell of your choice. How many options to treat disease, create better crops or fun novelties like glow in the dark cats.

As an undergrad, when we played with inserting genes into E-coli and yeast we would take a whole bunch of cells and mix them in a tube with the DNA we wanted them to absorb. Then we’d “shock” the cells by heating them up and cooling them, so that – hopefully – a small percentage would be so stunned they would just nom up all the bits of DNA and incorporate them into their own genome. Then would be the tedious bit of plating them out onto agar that contained antibiotics or whatever and checking that they really did take up your bit of DNA that gave them resistance to antibiotics.

Needless to say, it wasn’t easy and many bacteria died in the process – either when I shocked them or, most likely, when I plated them on poison (oh the blood on my hands! Out damn spot.) So I found this press release really exciting.

Scientists from South Korea poked holes in single cells using a high-powered femtosecond laser. Then, with the finesse of a golfer on the green, gently popped in a polystyrene-based microparticle coated in DNA using optical tweezers. The tweezers use laser beams like magnets to attract or repel polar chemicals.

The method of poking holes, or pores, into cells with lasers already existed, as did optical tweezer technology. This research combined the two to ensure that the DNA was specifically inserted into one cell- a big boost in precision.

One of the cool things about this is that it can be done without opening the petri dish, unlike microinjection. With microinjection, which I guess is like those videos where people poke DNA into an egg for cloning, there’s a chance of contamination.

Another benefit is that the microparticle they inserted could be modified to sense things in the cell, rather than just delivering a payload of DNA. So there are a whole bunch of useful functions that they could explore with this technique.

A third benefit – you can play GOLF AT A CELLULAR LEVEL! That is just geekery at its finest. The next question for researchers will be – can you get lab coats to match golf pants?

The paper is open access and available here.

Talking endangered words in Adelaide

On Thursday I’m heading to Adelaide for the Australex 2013 linguistics conference at the University of Adelaide. The topic – Endangered words, and signs of revival.

I volunteer with a project to revive an endangered language called Barngarla, which was spoken by Aboriginal people in the Eyre Peninsula of South Australia. During the missionary days people weren’t allowed to speak their language or teach it to their children, and within a few generations it had all but disappeared.

Old documents written by missionaries recorded a Barngarla dictionary and grammar, and Professor Ghil’ad Zuckermann, who’s also organising the conference, and a team are using them to revive the language. It’s ironic (in a wonderful way) that the missions wiped out the language while also preserving it and ultimately became key to reintroducing it. Barngarla is now being taught to people once more.

The Australex conference is celebrating 175 years of Lutheran Missionaries’ Aboriginal Lexicography (writing dictionaries.)

I find it interesting that linguistics shares so many words with biology. Linguists talk about endangered languages and hybridisation, while biologists have DNA transcription and translation. My explanation is the oft-used by imperfect analogy of DNA as a “recipe book” or “instruction manual” – placing it more firmly in the realms of language.

It’s actually a bit strange that we still think of DNA this way, that we haven’t updated it to, say, a hacked Wiki – sometimes edited by viruses. Hey, that’s not a bad analogy actually. Both are built up over time and the contributions of many, and aren’t exactly perfect but they do the job. Except that there’s not so much junk on Wiki’s as there is in DNA, but in both cases humans are pretty good at sorting the junk from the useful stuff.

I’m looking forward to the conference and meeting more of the people involved in reviving the Barngarla language, and hearing about similar projects in Hong Kong and Tibet. It should be an interesting few days, and I’ll try to keep you posted on what I hear.

3D printers make batteries the size of a grain of sand

A 3D printer made this battery. It's smaller than a grain of sand. Credit: Ke Sun, Teng-Sing Wei, Jennifer Lewis, Shen J. Dillon

A 3D printer made this battery. It’s as small as a grain of sand. Credit: Ke Sun, Teng-Sing Wei, Jennifer Lewis, Shen J. Dillon

A battery the size of a grain of sand has been built using 3D printers, scientists announced yesterday.

It’s the century of smalls, where tiny devices are top dog. Computers shrink into tablets, phones are limited only by screen size, and mini-microphones can fit onto a pair of spectacles or atop a tiny flying robot. Why not? If you’re going to bug someone, you may as well use a robot bug.

As microchips become more and more micro, one thing holding us back is the battery. To get a decent battery life, you still need a rather large and heavy battery. Even my humble Nokia (circa 2002, still works like a charm) is half as heavy if you take out the battery. Think how light my pocket could be with a better battery!

Light pockets are one thing, a light heart is another.

Pace makers depend on lithium iodine-polyvinylpyride batteries, and they must be reliable and long-lasting.

“The battery occupies major portion of the pulse generator in terms of weight, volume, and size. The most important factor for a cardiac pacemaker battery is its reliability. Unlike many consumer products, batteries in implantable devices cannot be replaced. They are hard wired at the time of manufacture before the device is hermetically sealed… In general the power source of the implantable device is the only component which has a known predictable service life, which in turn determines the service life of the implanted device itself.” – Mallela, Ilankumaran & Rao “Trends in Cardiac Pacemaker Batteries” Indian Pacing and Electrophysiology Journal.

Don’t get me wrong, batteries have come a long way over the past twenty years. But there’s always more juice to be squeezed, and when it comes to juicy technology you can’t go past the 3D printer.

To make the sand-sized batteries, a team from Harvard University and the University of Illinois printed layers of concentrated lithium oxide-based inks. The 3D printer squeezed out tightly interlacing anodes (red) and cathodes (purple) using a nozzle finer than a human hair. The ink hardened as it was placed. Then they enclosed the stacks of electrodes in a container and filled it with an electrolyte solution.

The tiny battery was built with interlacing stacks of anode and cathode. Credit: Ke Sun, Bok Yeop Ahn, Jennifer Lewis, Shen J. Dillon

The tiny battery was built with interlacing stacks of anode and cathode. Credit: Ke Sun, Bok Yeop Ahn, Jennifer Lewis, Shen J. Dillon

Tests showed some impressive results for battery performance.

“The electrochemical performance is comparable to commercial batteries in terms of charge and discharge rate, cycle life and energy densities. We’re just able to achieve this on a much smaller scale,” Researcher Shen J. Dillon, University of Illinois, said in the press release.

Tiny and powerful batteries could make all sorts of new devices possible. Medical devices used not just for treating illness, but also for sensing infection or blood sugar levels, perhaps. Iron Man suits, now that would be exciting. And wafer-thin laptops, tablets and phones. Maybe I’ll wait until these new batteries hit the market before I update my Nokia…

The research was published in Advanced Materials yesterday, and here’s a video of the 3D printer in action. Sun, K., Wei, T., Ahn, B., Seo, J., Dillon, S., & Lewis, J. (2013). 3D Printing of Interdigitated Li-Ion Microbattery Architectures Advanced Materials DOI: 10.1002/adma.201301036

Astronaut sings Bowie’s Space Oddity – on the International Space Station

How cool is this? Astronaut Chris Hadfield sings Space Oddity from the International Space Station. He is floating in a most peculiar way, as the guitar spins in front of him.

In another video he talks about having to re-learn guitar in zero gravity, as his brain had to adjust for the lack of weight in his arm. At first, he would overshoot the frets because his arm felt weightless. Plus he would bumping into things while playing.

Chris Hadfield has 17 videos in his YouTube account, showing why you can’t cry in space (well, you can, but it just pools in your eye) and shaking up a can of coke while living on the ocean floor.

Congratulations to The Tesla Science Centre – it’s going to happen!

What a handsome chap! Tesla aged 36, photo by Napoleon Sarony.

What a handsome chap! Tesla aged 36, photo by Napoleon Sarony.

I was so pleased to see on The Oatmeal this morning that the Tesla Science Centre will be going ahead – they’ve purchased the land where Nikola Tesla’s old laboratory stood and still have $800,000 in the bank to start cleaning it up and building the interactive museum.

This is the best crowd-funded campaign I’ve ever seen, mostly thanks to The Oatmeal. If you haven’t seen The Oatmeal’s web comics, well hurry over and find out why Tesla was the greatest geek who ever lived.

To put it briefly: Tesla was genius who wanted to give all his inventions away for free, his story ended really sadly Edison took advantage of him, stole his ideas and refused to pay him, destroyed generators and blocked Tesla’s project to provide free wireless energy. That’s right. Free. Power. Wirelessly. We could have that right now if Edison wasn’t such a jerk.

And to top it all off – history has mostly forgotten him. Just like it has forgotten Alfred Wallace, who worked out the Origin of Species at the same time as Darwin – from the jungles of the Malay Archipelago. On that subject, I highly recommend watching “Bill Bailey’s Jungle Adventure,” which follows his magnificent adventures catching flying frogs and malaria.

Tesla demonstrates wireless power.

Tesla demonstrates wireless power.

Well, he’s forgotten no more. A museum will boldly stand where Tesla was planning his wireless communication and energy transmission tower in Shoreham, New York.

Now that the land has been purchased, there’s a massive clean-up underway. Apparently there are believed to be tunnels underground that might contain some of Tesla’s original experiments, so they’ll need to be secured and explored. There are also rumours of a giant underground resonance chamber…

To celebrate, there’s hopefully going to be an event in New York over the Summer – with more details to be posted on The Oatmeal as they’re confirmed. I would go, if getting to New York was a remote possibility for me, because The Oatmeal owns a Tesla coil and is going to fry up bacon sandwiches with 20,000 volts of pure, unadulterated science awesome.

It will take time and more funds before the Science Centre is open for business, and be sure I’ll blog about it when it is.

Congratulations to the not-for-profit Tesla Science Centre who are now the proud owners of the site. In the words of The Oatmeal:

“Mr Tesla. We’re sorry humanity forgot about you for a little while. We still love you. Here’s a goddamn museum.”

Check out the happy news on The Oatmeal for more information and to donate or volunteer.

Shape-shifting devices, gadgets for the future

I’ve always wanted a computer that would fold up like a newspaper. I could sit on a bench and open it to read, then close it up and cram into a bag. It wouldn’t be backlit like a computer screen, just a soothing paper-like display. There’s something lacking in e-readers today that look terribly phoney. As in, they look like giant phones or tablets. I want one like a book, an extremely lightweight paperback.

That’s been the dream since before iPhone’s were released, and it looks like it’s a step closer now. New prototypes for shape-shifting mobile devices were unveiled today at the Computer-Human Interaction Conference CHI2013 in Paris. They transform on demand, bending up to hide personal information or curving around to make a console for playing games. The press release says they can even curl into a stress ball, which doesn’t sound very healthy for a smart phone, though I can imagine it might come in handy.

Here’s a nifty video of the “Morphees” in action.

There are a few different ways the researcher’s achieved this kind of movement. Some prototypes used wires attached to motors that pulled and pushed them. Others used memory wire, which reverts to its original shape when heated by running a current through the wire.

The research was led by Dr Anne Roudaut and Professor Sriram Subramanian from the University of Bristol. They have also introduced a new metric to help guide the developing industry – “shape resolution.” Like screen resolution, shape resolution allows different devices to be compared easily, measuring the ability to stretch, bend, curve and so on.

On a related note, researcher Roel Vertegaal from Queen’s University is working on thinfilm phones, called the world’s first paper computer. The work was presented at the same conference, CHI, in 2011. Here’s a quick video. Looks incredible.

Pretty keen to head over to the next CHI conference, which is in Toronto on April 26, 2014. Though it might be easier to get to the 2015 one in Asia, as it’s a bit closer to Australia. For more info on the conferences, check out the Special Interest Group on Computer-Human Interaction.

Happy fourth blogaversary

Sorry for the unscheduled downtime last week, all the issues have been sorted now (I think) and we’re back! Just in time for… A Schooner of Science’s fourth birthday! Hooray!

Happy birthday blog! Credit: Captain Skellett. License CC BY 3.0

Happy birthday blog! Credit: Captain Skellett. License CC BY 3.0

If you want to help me celebrate, why not buy me a beer? To date, the Schooner has been running on dreams and tap water, but I received a comment just recently from someone who wanted to donate to the blog. I was floored! Such kindness! So I’ve added a PayPal donation box in the right hand column to help A Schooner of Science stay afloat. Each beer purchased will improve the quality of this blog, by lubricating the brain and bubbling the soul (not to mention offsetting server costs). Cheers!

[gravityform id=”2″ name=”Buy me a beer!” description=”false” ajax=”true”]

Carnivorous snails, so how does that work?

Perrottetia dermapyrrhosa, one of the newly described species from Thailand. Credit: Somsak Panha. License CC BY 3.0

Perrottetia dermapyrrhosa, one of the newly described species from Thailand. Credit: Somsak Panha. License CC BY 3.0

Three new species of brightly coloured carnivorous snail have been found in the limestone hills of Northern Thailand.

Each of the species is only found on one or a handful of hills, some of which have become limestone quarries. Pretty impressive, as a quarry is not a friendly habitat for an animal whose main predator is the boot.

As well as coming in a range of fancy colours, the new species are characterised by nothing less than the shape of their genitals. All from the Perrottetia aquilonaria has a club-shaped penis and penial hooks (sounds painful?), while P. dermapyrrhosa has a long penial sheath, long, scattered penial hooks and vaginal hooks.

It seems like snail penises are a common way to distinguish between species, and there must be quite an art to it. Take this rather lengthy description of P. aquilonaria’s junk.

“Genitalia with a long, slender penis; penial sheath short, about half of penis length; internal wall of introverted penis with black to brown penial hooks; vas deferens passes through a short section of penial sheath before connecting distally to penis; vagina and free oviduct short to long, vaginal hooks may be present; gametolytic duct and sac may not extend as far as albumin gland; seminal vesicle present with about the same length from vesicle to talon.”

If you click through to the complete article, published open-access on peer-reviewed ZooKeys, you can even see some pictures of penial hooks and vaginal corrugated folds. Come on, what else are you going to do with your day?

Perrottetia aquilonaria, another newly described species. Credit: Somsak Panha. CC BY 3.0

Perrottetia aquilonaria, another newly described species. Credit: Somsak Panha. CC BY 3.0

It all sounds rather saucy, and top-notch science research, but I got caught up on this idea of a carnivorous snail. I mean, what IS that? It sounds like something from an old Doctor Who episode, back when the creepy alien du jour was footage of maggots, zoomed in so they looked gigantic. These day’s it’s terrifying ghosts with their mouth all screamy and sideways and it looks like something from The Exorcism of Emily Rose.

They may not be lions and tigers, but carnivorous snails are nonetheless vicious. Some of the species we have in Australia are small and are probably in your garden right now, others are big black ones that live in the Victorian rainforest.

Carnivorous snails hunt other snails, following their slime trail until they catch up with them. Now, most snails have a tongue like a rasp, and they eat lettuce leaves and such by simply licking them away with their tongue-which-works-like-teeth. Carnivorous snails upsize the rasp for big-ass hooks, and when they catch up with their prey they give them a lick and stick their hooks in.

If you’ve ever poked a snail, you know they slip inside their shell and produce gross foam to stop you poking them (no means no). Unfortunately they try the same trick when they get licked by a carnivorous snail, and the attacker has already shoved its hooks in so the snail unwittingly sucks the hunter right into its shell with it. Then the predator just licks away until there’s nothing left.

Actually, that does sound like a creepy Doctor Who episode.

Carnivorous snails also hunt worms, hooking ’em and eating ’em like spaghetti. There’s a great discussion of carnivorous worms on land and sea here on the ABC Radio website.

The research was performed by Chulalongkorn University, Bangkok and the Natural History Museum, London.

ResearchBlogging.orgSiriboon, T., Sutcharit, C., Naggs, F., & Panha, S. (2013). Three new species of the carnivorous snail genus Perrottetia Kobelt, 1905 from Thailand (Pulmonata, Streptaxidae) ZooKeys, 287, 41-57 DOI: 10.3897/zookeys.287.4572

Observations on a sedated cat, and links to Chlorpromazine, an antipsychotic in humans

What a year! I’ve been around the world (Canada, USA, Argentina, Chile, Denmark, Germany, France, Ireland, England, Hong Kong) to be finally reunited with my kitty cat Phobos back in Adelaide, Australia. I know most pirates have a parrot, but I prefer my pets fluffy.

I had just over a month in my home town (during which time I haven’t blogged so much, as I was seeing everybody back home and the house I was staying in didn’t have internet access), and then had to move again. This time to Melbourne, a larger city full of trendy coffee shops, where my partner is studying at University.

It’s a seven hour drive from Adelaide to Melbourne, and the cat would be coming too. Oh dear. Phobos is not one for cars. Like me, she prefers fresh air and sunshine to exhaust and headlights. She’s not good at hiding her displeasure. On the short trips we’ve taken before, she spends the entire time mewling most heartbreakingly, building up into a reverberating crescendo of “RAAAAAaaaaaaAAAAAaaaawaaarrrrr” and then panting for air. It’s quite upsetting.

That, for seven hours? Forget it! So we went to the vet and got some cat sedatives.

The vet gave us some ACP 10mg tablets, the active ingredient is Acepromazine. It is used for pets, including cats, dogs and sometimes horses. In the UK it’s not allowed to be used in horses intended for human consumption, which is hilarious in light of all the ruckus lately about humans eating horses without intending to. Perhaps a little anti-anxiety medication in the “steaks” would not have gone awry?

I shouldn’t jest, I was in the UK when the story broke and I’m pretty sure I accidentally ate horse. I must remember not to eat meat in the UK… you’d think we’d remember that from the mad cow outbreak in the 80’s. Speaking of mad cow, the fourth case in the US was identified in April 2012 in California, perhaps a month before I was there last year. Sure, it was in a dairy cow and bovine spongiform encephalopathy is not passed on by milk, but still…

Anyway, back to the cat! I gave her one tablet and within 15 minutes it had kicked in. Her eyes became unfocused and her third eyelids crept up. I’m glad the vet warned me of that one, it looked creepy – a layer of pinkish white arising from the corner of her nose and covering about a third of her eyes. The third eyelid has a protective function and it’s visible if the eye is injured, as a side effect of sedation, and during deep sleep.

Next she lost some motor control of her back legs and tail, like she had to move her whole hips to get her legs to move forward. Later she would start stepping backwards when she tried to curl into a ball, until she hit a wall and then stopped. She looked like a cowboy kitty.

The real test was when we got her in the car. She had a halfhearted meow or two, tried to look out the window, and then sat on my lap and rested quite peacefully. Acepromazine is an anti-anxiety drug, and she really didn’t seem anxious at all. Every hour or so she’d go for a little walk across our lap and quickly get worn out and go back to sitting with us or sleeping.

So it seemed good to me. She seemed less stressed.



As we were driving, and it’s a long drive, the topic changed to how much easier it was for the cat to be calm, not really for us but mostly for Phobos herself. What about with kids, then? We both knew that some kids are pretty loud and upset on plane flights (not all, but some), and we’ve heard of people who sedate their children with some cough medicine (or even stronger stuff.) It seems pretty unethical to me, on first glance and being childless myself. So why is it different to sedate a cat?

Perhaps it’s partly an age thing… I’m not sure I would sedate a kitten, for example. I have no problem with adult humans sedating themselves on flights, in fact I have a friend who does it due to extreme anxiety and sinus pain. But that’s also a question of consent, and even a grown cat can’t consent to taking drugs.

The next logical step in this conversation was “Do cat sedatives work on humans too?” And now I’m settled in Melbourne with high speed cable internet, I can tell you the answer for Acepromazine is yes, as it was used as an antipsychotic in humans during the 1950’s. However, it is no longer used in humans, and one of the reason’s that it is prescribed by vets is because it is much less likely to be misused recreationally than a morphine-based drug.



Although it’s no longer used as an antipsychotic, the closely related Chlorpromazine is. Chlorpromazine (or Thorazine in the US) has been used since the 1950’s, about the same time that Acepromazine was briefly used. The drug became very popular and was aggressively marketed, but it’s far from perfect. It’s one of the drugs given to patients in Ken Kesey’s book One Flew Over the Cuckoo’s Nest. That book is very critical of society’s reliance on drugs, and the overuse of medication to control mood and make patients compliant.

I agree, I think there is an overprescription of behavioural and mood drugs. All drugs have side-effects, and they should be taken seriously – especially if someone is taking a drug long-term. Also, in my opinion, western society today has a particularly strict view on “normal” and people who don’t fit in with the norm are medicalised.

Chlorpromazine is still used long-term as a treatment for schizophrenia, and I’d rather not give an opinion on that because it’s such a complex issue. However, a long-term usage as prescribed by doctors is surely different to the descriptions in One Flew which was decades ago, very extreme, and let’s not forget, fictional. Both are different again to a short-term one-dose of the closely related Acepromazine to a cat.

It’s hard (often impossible) to know what’s happening in an animal’s head. Hell, it’s hard enough to know what’s happening in your own head sometimes! It’s entirely possible that she hated the experience, that she felt vulnerable and dissociated and confused – but there’s no evidence that this was the case. However, I do know (as far as it is possible to know) that she hates being in a car when she’s not sedated because she cries and cries. So for such a long journey I think the benefits outweighed the risks.

Altogether, I was pleased with Acepromazine. Phobos has completely recovered and is back to her usual inquisitive, scampering self.

Visiting the Royal Institution of Great Britain

This story has been a month in the making, and I should have just posted it back then! I’ve been really busy with visiting Hong Kong and coming back to Adelaide and seeing friends and family again, excuses excuses. Still, here ’tis, better late than never.

One of the things I was most excited to see on my trip to London this month was the Royal Institution of Great Britain. Over 200 years of science history are within those walls, where Michael Faraday toyed with electricity and magnetism in the basement.

Today the basement is a museum, but it still has Faraday’s lab down there – at least a recreation – right opposite a mini modern lab all sterile white and bright. Personally I loved Faraday’s soft yellow lamplight on parchment and sprinkling of dark carbon… the old lived-in laboratory, where the mind is encouraged to jump between ideas and tinker with equipment. Give me a well-stocked garage over a chrome kitchen any day! I hate bright lights *hiss* *hides in the shadows*. I may be part vampire. I hear that’s trendy right now.

The museum wasn’t terribly interactive, but it was brilliantly nerdy – as in “ooh, this is the actual journal Michael Faraday wrote his results in.” That was cool actually, they had one journal full of experiences from taking different drugs (like laughing gas) where the scientist described what it felt like to be under the influence. There was a lot of drawings of Isaac Newton’s name (like a teenager might doodle in love hearts) – apparently he was an inspiration.

It’s a terribly fancy establishment, a nod to the days of top hats and cravats in illustrious May Fair. Right from the moment you walk through those big wooden doors you feel like you’ve stepped into a manor house, with proper marble busts of notable minds beside the staircase. If a cluttered desk of a scientist hides the lofty ideals of science, the Royal Institution sees to it that the art is esteemed and valued.

Painting by Thomas Hosmer Shepherd (1793-1864)

Nonetheless it’s not a stuffy sort of place, especially not in December when they hold the Christmas lectures – which are more like shows for students with explosions and bright colourful demonstrations. As much as it values brilliant minds, it values young ones too. Children are encouraged not just at Christmas time but in the standard lectures too, I’ll get to that shortly.

Apparently the beautiful building and new conference rooms and updated lecture halls have come with a hefty price tag, that has now put the RiGB into several million pounds worth of debt. There’s now an online petition for the Department of Business, Innovation and Skills to purchase the building (for 60 million pounds) to allow the RiGB to stay in their historic building indefinitely.

Off topic, it just occurs to me that a lot of Aboriginal Australians lost their historic land, and 60 million pounds would buy quite a lot of it back. Guess that’s not relevant though.

If you’re keen, you can read and sign the petition to save the Royal Institution of Great Britain.

I feel sure the government won’t let something as historic and important as the RiGB to simply be sold and moved. It would be such a waste. Even if they don’t buy the whole building, I’m sure they would sort something out.

On a snowy Friday night I was lucky enough to attend one of the monthly lectures, which was on biology and quantum physics titled “Quantum life: how physics can revolutionise biology”. It was one of those topics which is incredibly hard to wrap your head around, because the quantum world is so counterintuitive and downright weird that even Niels Bohr said “if you aren’t confused by quantum mechanics, you haven’t really understood it.”

For example, the speaker Prof Jim Al-Khalili said that during photosynthesis an energised electron will appear to take multiple paths through a cell to its destination, find out which is the most efficient, and then rewind time and decide it took the most efficient route all along. Say wha???

The part I most remember was a kid, probably 10 years old, asking at the end of the lecture whether a particle moving faster than the speed of light would constitute a paradox by Einstein’s theory and rip the fabric of space and time. No joke, a 10 year old. Mind. Blown. Everyone applauded, and Al-Khalili agreed it would, but fortunately that neutrino particle travelling faster than light which was announced a couple of years ago actually wasn’t, there was a mistake with the equipment. So the fabric is intact, no paradoxes have yet been found.

Since I’ve been back in Adelaide I’ve visited the sister institute, the RiAus a couple of times for Fringe events. It’s great to see it’s still going strong and thankfully a financially independent group that isn’t suffering the same issues as the RiGB. Though the RiAus is a bit smaller, I prefer the casual atmosphere it has and the fact that speakers are encouraged to mingle with the audience after a show. Just that fact is what makes science more accessible to the public, because it pulls down the boundaries and invites dialogue. I quite wanted to speak to Al-Khalili after the quantum life event, but he was taken into another room behind a curtain, and if he reappeared later I didn’t see it.

Toothbrushes and breath testers for tuberculosis

Far-advanced tuberculosis diagnosed by x-ray. Image from the CDC, accessed on Wikipedia.

Tuberculosis is a major health issue, with around a third of the world’s population infected with the bacteria mycobacterium tuberculosis. Not all these people actually have signs of illness, only 10% will go on to have any symptoms during their life. For the rest it remains latent, the bacteria is present but not causing any problems.

As tuberculosis is only contagious and dangerous when it’s active, that’s usually what people test for. Chest x-rays can check whether TB has affected the lungs, and are required for people travelling from high-TB countries to low-TB countries including Australia and the United Kingdom. The other avenue for diagnoses is the slightly grosser method of analysing the gunk people cough up, to see if there’s bacteria in it. For  mycobacterium tuberculosis, growing a sample in agar takes weeks.

A breath test would be a much safer and faster way to see if bacteria are present in the lungs, and that’s what our first paper is looking at. Researchers from the University of Vermont are finding out whether bacteria can be identified by their “chemical fingerprint,” a cocktail of chemicals that makes its way from the lungs to the breath. Their research is published in the Journal of Breath Research.

Now, it’s some time before police can pull you over for a quick TB test when you’ve been swerving off the road from a coughing fit. “Honestly, it’s just the flu!” But it’s got to be a cheaper option for many countries with low health care budgets.

TB poster, image from Wikipedia.

It is early research. They studied the tiny puffs from mice, rather than humans, and looked at two different bacteria that cause lung infections Pseudomonas aeruginosa and Staphylococcus aureus (Golden staph), neither of which are the TB bacteria. Clearly there is more research to be done, but it’s a promising start.

Read more about it here.

TB can be cured with a course of antibiotics, or more specifically a combination of several antibiotics that have to be taken for six months. Like Golden Staph, the bacteria that causes tuberculosis is becoming increasingly drug resistant. Drug resistant strains need different antibiotics and take 18 months or more to cure.

In Papua New Guinea, extensively drug resistant TB is a problem. A recent outbreak there and movement of patients to better health facilities in Queensland and the Torres Strait Islands has triggered alarm and, frankly, scaremongering media reports and political backlash. You can read about it on the Conversation, because I’ve been out of Aus too long to be in on the goss (but I’m back in a month, yay!)

The next weapon against drug resistant TB may come in the unlikely form of a traditional toothbrush. The South African toothbrush tree contains a compound called diospyrin, which inactivates an enzyme critical for bacteria reproduction (but does not affect the similar enzyme found in human cells.) The enzyme is a DNA gyrase… would you care to know how it works?

When DNA is replicated, the two strands normally joined in a double helix are broken apart, and you can imagine it’s like putting your fingers into a rope and pulling apart the strands. If this imaginary rope is a circle (as DNA in bacteria is) then it can’t just unwind itself at the ends. Instead, things will get messy, and the DNA will coil and twist up on itself. These “positive supercoils” are a bit like like twisting a shoelace until it bunches up, and is bad for the DNA. Gyrases relax the positive supercoils by cutting the DNA and moving one strand to the other side, then joining them up again.

Circular DNA supercoiling. Image by Richard Wheeler.

Circular DNA supercoiling. Image by Richard Wheeler.[/caption]

By stopping gyrase activity, the bacteria can’t replicate its DNA. The research by a team from the UK and South Africa described how this compound from the toothbrush tree interferes with gyrase, and importantly, that it acts in a different way to existing antibiotics. This will hopefully be a chink to exploit in the armour of drug resistant bacteria.

Here’s the paper from the Journal of Biological Chemistry and the press release.

New species of supercute slow loris

Slow loris species can be identified by markings around their eyes and head. Image by Helena Snyder. Wikimedia commons

With huge eyes peering through a bundle of fluff, slow lorises are the epitome of adorable. Just look at that face!

And that’s just what scientists have done – looking at the facial markings of slow lorises to identify one completely new species, and officially recognising two more as unique which had previously been considered possible sub-species.

The distinctive markings that separate the species include the mask-like patterns around the eyes and varying shapes of cap on the head. The newly described species, Nycticebus kayan, is named after a river running through their habitat in Borneo.

It’s their toxic bite that makes slow lorises unusual among primates.

More unusually, the toxin isn’t produced in the mouth but in glands on the arm. Licking or nuzzling the gland, they mix the toxins with their saliva to create an irritant.

Not only do they use it for defending themselves, but they also spread their spit onto their young, protecting them too.

Bit like a grandparent spitting on a napkin to rub the dirt off your face. Except afterwards you have AWESOME TOXIC POWERS! Still gross though.

The new Kayan species, notice the different markings around the eyes and cap to Bengalensis, above.

Unfortunately, lorises are endangered due to habitat destruction and the fact that they’re so damn cute, everyone wants them as pets. Illegal animal trade has taken a toll.

Still, it’s hard to imagine an animal like this going extinct. Insects and spiders, you know, they just haven’t got the same marketing department. Although, having said that, snow leopards are beautiful as well, and it sounds like they’re close to going extinct in the wild, so you never can tell.

Thinking about endangered animals makes me so sad! I saw a David Attenborough documentary a few days ago about his life and how the planet has changed and a couple of species had gone extinct since he saw them. Just made me feel a bit crap for being a human.

Still, even Attenborough did some silly things when he was young (like eating a clutch of sea turtle eggs), and his work has probably saved thousands of animals by now. People change.

So there’s always hope! Because a world without slow lorises in it… well, it’d be no kind of world at all.

More info at Wiley press releases.

On the lost and foundness of blogging

We were 90% sure it was gone. At one point this week, we were 100% sure. Through an old e-mail address, a missed reminder to pay for server space, and a dash of travel confusion, the Schooner was deleted. Unfortunately, just a few days earlier, we’d also deleted our back-up of it.

Let this be a lesson to never delete your back-ups, no matter how chockas your external hard drive may be.

There was an old back up from a year ago back in Australia (somewhere…) but that was no good for us, seeing as we were in Ireland.

And to tell the truth, I wasn’t that heartbroken. Not really. “It’s an opportunity,” I thought, “to make it bigger and better next time, to get back to the roots of the matter, to the important stuff. To feed the dragons of my curiousity, rather than the stressing and search for new newsy news and the technical technics. Like, why are all the kettles of Europe caked with white flakes, like someone has been boiling milk? And how did glaciers form the Brecon Beacons, where I am writing from today?”

Long story short, there was a back-up after all! My brilliant partner uploaded it and with a grin and a proud “you’ll never guess what I found!” gave me back my blog. Hooray! Not a post missing! She’s quite the genius, and it’s because of her I started the blog in the first place.

So filled with enthusiasm, I’ll crack on!

Why is that kettle full of white flakes?

As with ginger beer, Europe has harder water than Australia, at least in my neck of the woods. The white stuff is minerals in the water that have calcified, forming hard white stuff called limescale or calcium carbonate. It’s not too pretty to look at, but it’s pretty harmless to drink. After all, you drink it whenever you drink the tap water, it’s just all invisible making it less gross.

I’ve been cleaning the kettles with some detergent and a brush to get the worst of it out, and tipping out leftover water when the white stuff starts floating about. Apparently boiling a bit of white vinegar in there does the trick too. Ah, the cleaning power of acetic acid. And it’s delish on fish and chips!

Limescale sure looks good under an electron microscope. Looks like it’s called Kesselstein (kettle stone) in German. Image by Stefan Diller, D- Wuerzburg

Powering devices with the battery in your ear

Mammals have natural batteries within their ears. Image by אני, CC license.

Did you know there’s a battery in your inner ear? It was news to me when I found this on Turns out not only is there a natural battery, but a group is working to utilise it to run medical devices.

The natural role of your ear battery is to turn sound vibrations into electrochemical signals, which travel down nerves to the brain. An imbalance of sodium and potassium ions (as with nerve cells) is created using cells that pump ions back and forth across a membrane – this is the battery.

It’s crucial for good hearing, and could be tapped to power devices.

Though it is very low voltage, the team was able to harness a small proportion of the natural battery to power a radio transmitter. In the future, this transmitter would be coupled to a sensor, and send data about how the ear is performing to a nearby computer.

During the experiment they used a guinea pig (literally) as a substitute for a human ear. The guinea pig responded normally to hearing tests, even with the implant. The chip itself was located outside of the guinea pig’s ear, but would fit inside a human’s middle ear cavity. We have got bigger ears than guinea pigs, after all.

They estimate it would take between 40 seconds to four minutes to build up enough juice to run the radio transmitter, but after that it keeps itself going.

To get around the lag time, they could send a burst of radio waves to provide that initial power – a kick-start.

It’s one of many developing technologies to explore new ways to tap into existing energy. Cell phones that can power themselves from the mechanical vibrations of being tapped, touched or carried are also in the pipeline. Rolex has been powering its wristwatches for decades using movement energy it collects when worn.

This research could open new ways to study the inner ear for people with hearing difficulties or problems with balance. It could also provide treatments, such as by improving hearing aids. All with the battery in your ear!

Oh no, it’s been so long since my last update!

Oh dear, I’m seriously struggling to keep up this blog at the moment. Europe is just so distracting! So many pretty things to see and history to learn, when I get home I usually just zonk out and berate myself silently for not having the strength to blog.

I did see another cool clock today, it was a sphere with the daylight hours in gold and the nights in black, and it had a circle marking the seconds, the hours, and the day of the week (at least, I think that’s what it said – it was in Czech.)

I’d appreciate any advice on how to keep this blog cooking while I’m so distracted by things. Should I write short articles about things I see that are sciencey (like the astronomical clocks), or start a google alert and write about ever mention of one specific topic – leprosy, maybe? Dinosaurs? Ancient medical treatments for gout?

Anyway, a lot has happened since I’ve been galavanting in Germany and the Czech Republic, such as the Nobel Prize Ceremony. Woo! Only the biggest science event of the year, tiny thing like that, you might not have heard about it.

I was really pleased to hear the Nobel Prize for Medicine going to the people who showed how to turn adult cells into embryo-like stem cells. What a brilliant way to dodge a tricky ethical issue! Mushing up embryos to treat other humans is some shade of grey, so why not take the cells from a consenting adult! An added bonus, you can take cells from a sick person, transform them into stem cells, then use them back into the same person – no organ rejection.

The physics one was so fitting, because it was for for “ground-breaking experimental methods that enable measuring and manipulation of individual quantum systems”, and quantum optics is such a vast and growing field. I feel like it will be the future of computing, it has that same latent excitement that I imagine early computer scientists would have felt decades ago. If there’s anything I should tag on my google alerts, it should be quantum computing and optics.

The Nobel Prize for Chemistry was awarded for studies in G-protein-coupled receptors, a group of receptors that allow cells to sense their environment, picking up sensitive chemical cues like smells and tastes. According to the press release, half of all medications work by triggering G-protein-coupled receptors.

On a non-science note, the Nobel Prize in Literature was awarded to Mo Yan “who with hallucinatory realism merges folk tales, history and the contemporary.” Sounds really cool! I haven’t read any of his work, but I’m pretty keen. It sounds similar to the magical realism in Like Water for Chocolate.

Well, I have to go pack my bags now! Moving towns again, and have a train to catch in the morning. I’ll try to do better and update more often! Any advice/support really appreciated 🙂

Talk like a pirate day!

Arr, it be talk like a pirate day yet again! Be sure to get yer pirate talk on, mateys, and make the most of this special occasion! Sadly, there ain’t be much happenin’ in Lubeck, where I am on this fine day, but even without an official parrrty I will be celebratin’ all the same!. All yer tips on speaking right, events ‘n even knitting piratey treasures can be found on ye olde official site, Talk like a Pirate Day.

Brilliant brass astronomical clock in Denmark’s finest castle

Sorry for the lack of posting, I’m currently in Denmark and out most days visiting castles and museums. It’s a hard life!

I recently went to a renaissance castle just North of Copenhagen called Frederiksborg Slot. It was a bit of an accident, actually, because I was looking for Hamlet’s castle at Helsingor and got on the wrong train. It turned out well though, because Frederiksborg Slot has been restored and converted into the Museum of National History, and inside was this beautiful astronomical clock.

An astronomical clock in Fredriksborg Slot, Denmark. Scorpio is in blue underneath the bare bottom, and Sagittarius to the right.

On the armillary it says “Dies verck von mir selbst Inventiert hab ich mit Gott wol ausgefuhrt. Andrews Bosch Buxenmacher von Limpurg Anno 1657.” Seems German to me (though could be Danish, seeing as it was Denmark) and my rough translation makes it something like “this work, by myself invented, have I with God created.” Made in 1657.

It shows a Copernican solar system, with clockwork inside the sphere and within a wooden base. Back in those days, it would have been hand cut – just imagine the precision required!

Clockwork inside the astronomical clock.

The sphere on the outside shows a fixed outer frame of the horizon system, with zodiac pictures. Inside is another frame that is moved by clockwork, showing the celestial equator. One rotation within it takes 25,000 years, the time it takes for the precession when the Earth’s North axial pole moves in a complete circle around the ecliptic pole, during the movement (after a few thousand years) Polaris will no longer be the North Star.

In 1825, it was moved to the Copenhagen observatory to replace Tycho Brahes globe, which was destroyed by fire about a hundred years before. Shortly later, it was donated to the Museum of National History inside the castle by J.C. Jacobsen of Carlsberg fame.

The clock in entirety.

Shining brass and bright paint made it magnificent, worthy of the maker’s skill and scientific understanding of the stars. Art and science, gotta love it. There’s something about astronomy that engenders art, I think. It invites imagination.

Gold and blue constellation art on the ceiling.

Brains compensate for a stuffy nose

Image by Miguel Angel Pasalodos, licensed on Creative Commons CC BY-SA 2.5

Nothing like a stuffy nose to ruin your day. You sound like a ponce, food tastes like cardboard and you have to sleep with your mouth open for spiders to crawl in. No joke. It happened to a friend of a friend of mine.

But have you ever noticed how quickly your sense of smell returns? Almost as soon as the sniffles are gone, you’re back to sniffing roses, and new research is finding out how our brain can adjust so fast to changes in sensory input.

What I love about this study is how they did it.

For a whole week, 14 people had their noses completely blocked during the day. At night, they slept sans-nose-blockers in a special low-odour hospital room.

A low odour hospital room? All the ones I’ve been to smell weirdly like custard. I wonder if all 14 shared the same room, or if they were spread out… I mean, even if you do have a spesh no-custard hospital dorm, if 14 people spending the night there it won’t be low odour for long.

Brain activity in response to odours changed after a week of smell deprivation in two regions. Activity increased in the orbital frontal cortex, but decreased in the piriform cortex, both are related to our sense of smell.

“These changes in the brain are instrumental in maintaining the way we smell things even after seven days of no smell,” said lead author Keng Nei Wu, Northwestern University Feinburg School of Medicine, in the press release.

“When your nostrils are blocked up, your brain tries to adjust to the lack of information so the system doesn’t break down. The brain compensates for the lack of information so when you get your sense of smell back, it will be in good working order.”

Once the 14 participants were released to sniff wildly, their brains soon returned to normal, showing pre-experimental levels of excitement when offered something smelly.

This rapid reversal in the realm of smell is quite different to sight, where deprivation usually has longer-lasting effects. Wu suggests this could be because smell deprivation is pretty common, given our penchant for catching colds and having allergies. Perhaps it has evolved to be more agile, or perhaps the endless sniffles we get in primary school gave our brains ample chance to practice.

Either way, it seems the quick adjustments by our brains protect our sense of smell, so it can rebound quicker than you can say “the one who smelt it dealt it.”

Wu ends by saying “more knowledge about how the system reacts to short-term deprivation may provide new insights into how to deal with this problem in a chronic context.”

Chronic loss of smell is nothing to be sniffed at (lol.) It really takes the fun out of life. This column, 20 years of living without a sense of smell, was clearly written from the pits of despair for want of a whiff of fabric softener.

ResearchBlogging.orgKeng Nei Wu, Bruce K Tan, James D Howard, David B Conley & Jay A Gottfried (2012). Olfactory input is critical for sustaining odor quality codes in human orbitofrontal cortex
Nature Neuroscience : 10.1038/nn.3186

Nikola Tesla, the best geek in the world

This is the greatest comic I have ever read.

Of course, it comes from that brilliant, somewhat bent mind of The Oatmeal – who’s take on life is always on the most hilarious angle (such as how to have a pet Tyrannosaurus.)

But on this piece he’s a little more serious. He begins with the bold statement that Nikola Tesla was the greatest geek that ever lived, then backs it up with incredible detail into an uncharmed life. His constant hassling from Edison, who first employed him and then never paid what he promised, then sent goons to wreck his work.

And his PLANS – my goodness! I had no idea that Tesla had planned, and started to build, a tower in New York capable of sending electricity through the air to wirelessly power devices. That technology is only just becoming available now, as shown in this TED talk.

Tesla also promoted green electricity back in 1890, while Edison said fossil fuels would last us 50,000 years.

The amount of technology around today that hearkens to his patents is staggering, including remote controls, neon lights and the modern electric motor.

I don’t think we give him enough credit. I think he gets missed! That said, I guess David Bowie did play him in the movie The Prestige alongside Hugh Jackman… and man, is that an honour! Wowzers! Died alone and in debt… but then played by David Bowie! I think that makes up for it in some small way.

Highly recommend you read the whole comic here, and appreciate the brilliant geek that was Nikola Tesla. Thanks, The Oatmeal, for doing such a service to society as to create this comic. Hats off.

The brewer’s yoke, the domestication of microbes

Something happened when I was spliced, something wrong. Some random event in my chromosomes, I suppose it was. In any event, I wound up lacking. My sister took all the toxin genes, and I was left with nothing.

It’s a scary world out there for a fungus without a toxin. How would I strike fear into the hearts of all animals who dared to eat the plants I was eating? How, without my precious aflatoxin to attack the liver, causing acute sickness or eventual cancer?

Quite simply, I’m surprised I lasted as long as I did before they found me.

Indeed, I’m not sure how they did find me. I had a pretty good disguise, growing colonies of blue along the endless islands of white rice grains, just like my toxic cousins always had. Safe from munching animals by my don’t-eat-me mimicry, the promise of sickness is the discoloured rice.

For some reason, these sake brewers saw past it all. I thought I was a goner when they lifted me up from the wild and plonked me into a house of wood.

Then I saw the food.

A. oryzae in heaven. Image by Forrest O.

It’s hard for mould like me to see, lacking in the eye department, but I knew it was there. An endless carpet of steamed rice. With my filamentous fronds I could touch it. Drill down into it and grow cottony soft, sprout fruiting bodies on the surface and spread on and on.

Call me legion, for we are many. Better yet, call me qū meí jūn in Pinwin, kōji-kin in Japanese, nulook-gyun in Korean or the grandiose Aspergillus oryzae in scientific circles. Back then, some 2000 years ago, I didn’t know who I was, or that I would one day be the National Fungus of Japan.

That’s when the changes happened.

I didn’t notice at first, I don’t know that there was ever a master plan. It felt… natural. Human hands, bristling with microbes and pitted with pores, dropped me into heaven. And when I had eaten the heaven for a time, they picked me up and dropped me once more into fresh heaven.

Incomprehensible! These hands must have spent hours polishing the rice to remove all the husks, then steamed it to perfection, cooled it so I didn’t burn my filaments, then spread it out – just for me! It was like being a king! King Kōji-kin!

I'm a national icon, and pretty cute too. Image by Ryoku Kasinn

As they fed me and I ate, we gradually adapted to please one another. Heaven grew ever more heavenly, until the temperature and humidity was just so.

For my part, I started growing much faster, hell, I had brilliant conditions for it and not a doubt in the world that I could grow as fast as I pleased. Fearlessly fast.

Over generations, they selected only the best for their purposes, which at that stage I knew nothing about. They selected the sons and daughters (hell, we’re all of one gender here) that could best turn rice starch to sugar. They also preferred fungi of least colour, but most smell and flavour. Each generation, the best of me would be plucked and propagated.

Turning starch to sugar is a tricky thing. I suppose the point of starch is to tie up the sugar molecules into a big, complex network so the plant can use them later. For me, kōji-kin I secrete the amylase enzymes, biological machine that chops starch into pieces of sweet. From a couple of recently-licked hands, I’ve learned humans make the same enzyme in their saliva. My amylases, however, not only make glucose, but a few other sugars that produce a wonderful flavour.

But why, pray tell? Have you worked it out yet?

Winemakers use yeast to turn the natural sugars in grapes into alcohol. Beer brewers must malt their barley, partially growing the seed to convert starch to sugar, to ferment it with yeast into alcohol.

And I, the humble fungus, plucked from the wild a millennia ago for a deficit in character. My non-toxic self excels, above all other moulds, in turning rice starch into sugars.

From the beds of heaven, me and my alchemical rice is transferred to the fermenting tank. Mixed with yeast, water and more rice, then left to stew in our own juices for a month.

This mash is pressed and filtered, and the sweet, alcoholic liquid that pours forth is bottled as sake.

Not to ring my own bell filaments, but I make soy sauce and miso too. That’s a whole meal – appetizer, main, and a drink.

Domesticated A oryzae (left) and wild A flavus (right). Image by John Gibbons, Vanderbilt University

These days I hardly recognise myself! So much of me has changed by growing with the sake brewers. Though I still share some 95% of my genome with my wild and toxic cousin A. flavus (and you, human reader, share 99% of yours with a chimpanzee), I am given all I could ever want to eat and praised world-over for my skill in sake making. While A. flavus, the wild thing, is targeted daily for a war against fungi with resistant crops and competitive yeasts.

What must the wolf think of the dog? Or the auroch of the cow? Well, to their accusations I say this: We may change our genes and appearance for protection and care, but, in doing so, we also mould the humans who cooperate with us. Through their attentions and skills, they, too, are domesticated.

This story was inspired by this recent research by Vanderbilt University into the domestication of microbes. “Although people don’t often think about it, we haven’t only domesticated animals and plants, but we have also domesticated dozens of different microbes.” – Assistant Professor of Biological Sciences Antonis Rokas in the press release. You can find more information on brewing sake here, and a beautiful description of koji pampering by interns at a sake house in Japan who blogged their experiences.

ResearchBlogging.orgGibbons, J. et. al. (2012). The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae Current Biology

Good God Particle, is that the Higgs boson?

higgs boson

Simulated model of Higgs boson decaying into four muons (shown in yellow). Image by CERN.

The world of science is abuzz with the news! CERN have discovered a new particle, and it looks like the elusive Higgs boson. That large hadron collider has really come in handy!

It was announced today at CERN as a ‘curtain raiser’ for the International Conference of High Energy Physics – ICHEP2012 – currently on in Melbourne, Australia. And what a curtain raiser it is.

The Higgs boson is a subatomic particle that, theoretically, gives mass to everything. It interacts with the Higgs field which permeates the Universe, kicking up a drag as it moves. That drag, or attraction, gives protons and electrons their mass as they zoom through the Higgs field. In the model, the Higgs boson is absent in photons of light, which is why they have no mass.

It’s been a long, hard road to find it – taking 45 years. Why? Partly because, after the collisions, they decay very fast, and partly because the way in which they decay doesn’t stand out. It seems to vanish into very normal smoke, that is, quarks, antiquarks and muons the same as those made by run-of-the-mill activity from other LHC collisions. It’s like trying to spot stars in daylight, according to this neat article by Matt Strassler.

The physicists are being cautious with their discovery, describing it as a Higgs-like particle. There’s more data analysis and experiments to be done. But if it looks and smells like a Higgs boson…

Peter Higgs

Will Peter Higgs, theoretical physicist, be winning a Nobel Prize for this? Image by CERN and Claudia Marcelloni.

What it looks and smells like, to be precise, is a ‘bump’ in the data with a mass of 125.3 gigaelectronvolts, about as heavy as 125 protons.

Analysing the data, so far, has put it at a confidence level of 5 sigma. That means there’s less than a one-in-three million chance of receiving the same result completely by chance, without a Higgs boson. Put another way, that means they can feel over 99.999 percent sure this is it – a boson that acts like a Higgs.

“The results are preliminary but the 5 sigma signal at around 125 GeV we’re seeing is dramatic. This is indeed a new particle. We know it must be a boson and it’s the heaviest boson ever found,” said CMS experiment spokesperson Joe Incandela in the press release. “The implications are very significant and it is precisely for this reason that we must be extremely diligent in all of our studies and cross-checks.”

“It’s hard not to get excited by these results,” said CERN Research Director Sergio Bertolucci in the same release.

It is exciting! Even though it’s still a preliminary result – guys, it could be the God particle! How cool is that?