Archive for Science Communication

Notes from the international barcode of life conference #bol4

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

Image by .jun, flickr

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Future floating laboratory, prospectus of the HMS Beagle Project

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

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

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

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

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

Space shuttle before docking with space station. Image by NASA

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

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

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

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

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

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

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

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

// November 14th, 2011 // 2 Comments » // Science Communication

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

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

“Do you know why there’s no pink?”


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

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

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

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

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

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

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

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

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

University of Adelaide research week begins

// October 28th, 2011 // Comments Off on University of Adelaide research week begins // Science Communication

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.

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

// August 16th, 2011 // 2 Comments » // Science Communication

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.

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