A Schooner of Science

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

// February 3rd, 2012 // No Comments » // Science at Home, Science Communication

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Notes from the international barcode of life conference #bol4

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Future floating laboratory, prospectus of the HMS Beagle Project

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

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

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

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

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

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

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

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

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

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

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

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

More coral crochet (and brief patterns)

// November 25th, 2011 // 1 Comment » // Science Art

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

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

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

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

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

University of Adelaide research week begins

// October 28th, 2011 // No Comments » // 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.

The Stupid Species – a science comedy

// March 11th, 2011 // No Comments » // Just for Fun, Science Communication

I just got home from seeing Daniel Keogh (from ABC’s the Hungry Beast, aka Professor Funk) performing in the 18+ science comedy show The Stupid Species – Why Everyone (except you) is an Idiot.

It. Was. Awesome.

From the complex and perplexing placebo effect to the Asch Conformity Test, it was a playful romp through the psychology of stupidity. Why is love risky (or whisky) business? How can different colours cure the sick? Why are expensive things deemed better than the cheap, but free things are the absolute best?

I could tell you, but not with as much pizazz as Professor Funk.

Go for the science. Stay for the hair (or the epic pants and jokes.)

I awarded major bonus points for starting the show with Venn Diagrams and Pie Graphs. Plus the video on the placebo effect was simply mind-blowing. Also there’s free wine testing *hell yeah!*

The show toured during last years National Science week, and is now in Adelaide on Saturday and Sunday night at the RiAus. Tickets are still available for Sunday at a tiny $10, or $8 for students (book here) and are worth double that. Take your friends, they’ll appreciate your confidence and good taste in comedy.

“We all like to think we’re special. In fact on average everyone thinks they’re above-average. Although we think we’re pretty smart our tendency towards irrational behaviour is what unites us all as humans – the stupid species,” says Daniel Keogh. Follow him @ProfessorFunk.

Inspiring Australia and the barcode of life, conferences

// February 7th, 2011 // No Comments » // Science Communication

Couple of interesting conferences coming up this year. The first one is Inspiring Australia in Melbourne from March 28-29. ‘Tis a science communication conference, tackling topics like social media, politics, and a whole bunch of exciting sci-comm stuff. Registration opens today, and it will be good.

The second conference is the Consortium for the Barcode of Life which will be hosted in bonny old Adelaide in November this year. Adelaide Uni scored the gig after competition with 19 applicants from around the globe. Previously the event has been hosted in Mexico City, Taipai and London.

DNA code is a bit like a barcode to begin with: Information hidden in a mysterious pattern that only a computer can analyse. The barcode of life refers to specifically to a certain small section of DNA which can be used to compare species. The section changes between species, but stays the same within members of the same species, and is accurate for most mammals and bees.

The consortium is to discuss and co-ordinate how to take DNA samples from all the animals IN THE WORLD, and have them on a giant database. Then when future scientists find a weird animal, they can take a sample, scan it in and *beep*, one lemur for $9.99. It’s a neat idea, and totally exciting that Adelaide is hosting this International event.

A night of chocolate at the RiAus

// February 3rd, 2011 // No Comments » // Science Communication

Love chocolate? Tonight at Adelaide’s RiAus the spotlight is on gluttony and chocolate addictions.

It’s sold out, but you can watch the livestream here from 6:00 Adelaide time and have your own chocolate tastings at home.

Brendan Somerville from Haighs will talk about what makes chocolate so good. Chocolate has been around since the Aztec’s were big, originating some 3000 years ago in South America. Back then it was a bitter tasting drink, and nowhere near the delight we enjoy today.

Last year the cacao tree genome was sequenced, creating a blueprint of the source of chocolate. With it trees could be altered to become resistant to disease and to produce higher quality chocolate.

As well as using science to improve chocolate, we use it to justify eating just one more piece. Like red wine, chocolate in the right doses can be good for you. The medicinal powers ascribed to the “food of the gods” include:

Chocolate can suppress coughing.
Chocolate can lower blood pressure
Chocolate reduces stress

But there’s a downside, namely sugar and fat and a potential for addiction. The best chocolate to eat is small quantities of very dark chocolate, low in the bad stuff but high in the good stuff. Fortunately this is my favourite.

In the world of Food Porn Daily and Not So Humble Pie, any one of us can become a weapon of mass chocolate consumption. Cravings and addictions aren’t just limited to chocolate, I know for a fact they extend to Banana Caramel Cream Pie, particularly the one at Café Paparizzi in Malvern. So far I’ve managed to resist, but it’s only a matter of time.

Or is it? Dr Robyn Vale is also speaking tonight about how to resist temptation and avoid food cravings.

But purely for medicinal purposes, I think you should have a bit of chocolate while you watch the livestream.

So what are you craving right now?

Connecting via common ancestors and Genographics – Interview with Wolfgang Haak

// December 8th, 2010 // No Comments » // Recent Research, Science Communication

At the Genographic Event at the RiAus I also interviewed Dr Wolfgang Haak, who spoke about Y-chromosome markers to determine paternal ancestry. He’s been involved in the Genographic Project for three and a half years.

What are the benefits of understanding ancestry?

It’s pretty much a personal thing, at the end of the day, because I suppose everyone’s interested in his or her own genetic history. This is my personal driving force, finding out more about myself. Where’s my place in this planet, in this world, where do I tie into the global picture? That’s a big motivation for me, and as I find out more as I work with people that it’s the same motor or driving force with them as well.

We share a common ancestry after all, there’s a common interest in our genetic history as well.

What first attracted you to the Genographic Project?

I have always been interested in genetics, but I actually come from an anthropologic background and genetics is certainly a part of that. I also come from an Ancient DNA lab. This was a step further into more modern population genetics. This is about getting both things together. Having a modern day perspective, plus adding a timely depth to that picture that we get from modern day diversity.

Tell us about your own ancestry, have you genotyped yourself?

Yes, I’ve done both. Mitochondrial, I’m haplogroup H, and I can further pin that down to group H1, so that is a Palaeolithic, Mesolithic one that might have come into Europe prior to the last glacial maximum, around modern day Spain or Italy or even a South Eastern refuge. It’s not entirely clear but we’ll find out over the next couple of years.

On the paternal side its even more enigmatic. I’m part of a North African lineage that probably originated around the Horn of Africa, so there’s that connection on the Eastern side of Africa where it connects to Saudi Arabia, and that has a high frequency there into the Nile Valley, and from it spreads into South Eastern Europe. Not entirely sure when it spread across the Mediterranean region, but probably historic times rather than prehistoric times.

Genographics, Neanderthals and Cannibalism, an Interview with Carles Lalueza-Fox

// December 8th, 2010 // 1 Comment » // Recent Research, Science Communication, Sex and Reproduction

After the event last night about the worldwide Genographic Project, I caught up with Prof Dr Carles Lalueza‑Fox, the first speaker on the night, for a quick interview. He’s an expert on Neanderthals, or Neandertals I think we call them now. Named after the Neander Valley where the first specimen was discovered.

What first sparked your interest in studying Neandertals?

When the first Neandertal sequence was retrieved in 1997 I had been working on ancient DNA for a while, but then Neandertals seemed to be something in a different league.

In the first ten years it was only possible to get mitochondrial DNA from Neandertals.

For me, I really liked Neandertals and human evolution as a child. Ancient DNA was something particularly difficult at the time, and the thing that brought me to the subject.

How human do you think Neandertals were?

How human?

Yes, tricky question.

Haha, yes. It’s a very long question, a very difficult question. One must always take into mind our tendencies are always fluctuating. We saw them as a very primitive human lineage in the early 20th Century, but I’d say that now we’re turning to the point where we see them as very similar to us.

Maybe the best thing to think about Neandertals is they are more different from us than any modern human to any other modern human. That’s the way we should think about them.

If we want to think of them as a different species that’s fine for me, but there is a range of difference between us and the Neandertals.

The cuts found along Neandertal bones you suggest are evidence for cannibalism. Could they just be an example of de-fleshing prior to burial?

Well, yeah, it might be right in some circumstances. But this is not only cutting, you know de-fleshing the bones. It’s also fragmenting the bones with small stone tools, very small fragments, and even the skull, and the faces. For me it’s very difficult to think that this kind of post mortem activity is something more because this is a complete destruction of the bones.

It’s very similar to what we see in other sites with fauna, the bones are broken to extract the marrow in the same way.

And it’s a pretty common thing, well, not common these days, but certainly we humans have our own history of cannibalism.

Yes, well there are several sites with the signs in Neandertals. But you almost think that life was very tough and they were structured in very small groups, so the fact that you find another one… I mean you’d say “hey, we are Neandertals all of us,” but I’d say that’s a modern conception.

Whereas for them it might be “hey, you’re not one of my family I may as well eat you.”

Yeah, the idea of humankind, in fact, is very recent. After the second World War, and the UNESCO thing. So even the idea of humankind is more recent than we might think now.

And what do you think of the possibility of Neandertals and humans mating?

I think it’s plausible with the data we have. It was probably something that was a minority, restricted in time and space, it was nothing important in my view. The thing is we can detect it now in non-African modern humans is because this was an expanding population, so even a small event of just a few, say it was, this was amplified later on.