A Schooner of Science

Feminist and Aboriginal science with Lillian Dyck #AAASmtg

// February 28th, 2012 // No Comments » // Science Communication

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

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

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

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

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

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

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

Feminist science does this, she says.

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

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

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

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

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

Opening ceremony of the AAAS 2012 conference

// February 19th, 2012 // No Comments » // Science Communication

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

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

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

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

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

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

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

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

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

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

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!

Christmas chemistry, the science of holly

// December 21st, 2011 // 4 Comments » // Poisons

Green and red, classic Christmas colours, adorn the spiky holly shrub. A sprig may garnish puddings, but garnish nibblers like me must hold back on holly for it is poisonous in large doses – though some leaves can make a tasty beverage!

Holly includes about 400 species in the genus Ilex. The cultivated species is Ilex aquifolium, and about 20 or 30 of those bright berries can kill an adult. Poisonings are more likely in pets or children, and about five berries will make a kid feel sick.

It’s the usual suspects in symptoms – sleepiness, sore tummy, vomiting, diarrhoea. Larger doses cause paralysis, kidney damage and death.

Chemically, they contain a cocktail of active ingredients. Among them are the triterpenes, precursors to steroids which are cytotoxic (kill cells), steroids and a nitrile called menisdaurin.

Traditional medicines use holly for fever, gout and chronic bronchitis.

A couple of species native to North America, I. vomitoria aka yaupon and I. cassine, make caffeine and were used to make “black drink”, a stimulating brew also used as a vomit-causing emetic.

South American species I. paraguariensis contains as much as 1.6% caffeine (five times more than the above species) and some of the cocoa chemical theobromine in their leaves, and tasty tannins.

Also called yerba mate, I. paraguariensis is brewed to make mate tea, which is delicious. It’s pronounced MAH-tay, but be careful not to put the emphasis on the second syllable. Wikipedia says that makaes mah-TAY, which means “I killed” in Spanish.

So it’s fine to have a sprig of holly in the house for Christmas, just don’t make a holly pie out of it!

Vampire squid on Occupy Wall Street, biology of Vampyroteuthis infernalis

// December 14th, 2011 // No Comments » // The Realm of Bizzare

Occupy Wall Street protesters took up arms – eight of them – in their march on Monday. Carrying craftastic models of vampire squid high above their heads, in homage to Matt Taibbi’s description of the bank as “a great vampire squid wrapped around the face of humanity, relentlessly jamming its blood funnel into anything that smells like money” in Rolling Stones, 2008.

Harsh words, right? I mean, vampire squids are totally awesome!

The vampire squid inhabits the cold, high-pressure environment of the deep sea. Light is absorbed by the water, making it perpetually twilight. A vampire in twilight, that’s not horrifying, that’s dreamy, amiright? Don’t hit your head if you swoon.

We don’t know much about these little dudes because they dwell in that most mysterious of spots, the deep sea. Vampyroteuthis infernalis means vampire squid from hell, but it’s not even technically a squid. Or an octopus. It’s got an order all of it’s own.

They have a consistency similar to a jellyfish, quite gelatinous. Like many jellyfish, it swims by shooting out a jet of water behind it to propel it forward, but it has a couple of fins for manouvering. It has eight arms and two extra arms which hide in its ‘pockets’ and can extend the length of its body when needed.

This National Geographic vid is pure pirate gold for high quality images of the creature.

They hold the title for the largest eyes relative to their body. An individual about six inches long has an eye an inch across, about the same as a full-grown dog. All the better to see you with, my dear. They also have a receptacle behind their eye for spermatangia, the tough sac of sperm ejaculated from the specialised arms of a lover. Just imagine date night

The most brilliant behaviour is their bioluminescence. These guys glow!

When startled, squid may shoot out ink to confuse predators. That’s not much good when you live in twilight, so instead the vampire squid shoots out glowing balls that dazzle and confuse. Over a thousand discrete bright particles within a matrix of mucous. Picture that, you’re out looking for a snack late at night, feeling pretty hungry, you think you smell something good and suddenly there’s some wacko waving glowsticks and snot in your face!

Another defensive ploy is to go into pineapple pose. Turning their bell-shaped tentacles over them, they completely change their shape (going kind of inside out). They light up some spots on their head which animals may take for eyes, which glow and then shrink as if the animal has swum away. Even if you didn’t buy that the animal was gone, looking at the videos, you wouldn’t want to eat that.

Stephen Fry gave respect to these sweet deep sea entities in this clip from QI. Hat tip to Dr M at Deep Sea News.

Oh… and about that quote Occupy Wall Street are marching for. The vampire squid’s diet seems to consist of molluscs, fish and crustaceans. As far as we know, it’s not a blood sucker, and Tree of Life. describes the funnel as absent. That must make it hard to stick said metaphorical blood funnel into anything, whether it smells like money or not.

Recommended links

In the QI link, they say the bioluminescence explosion is like John Barrowman! You might know Barrowman as the immortal Captain Jack Harkness from Dr Who and Torchwood, but blow me down, that captain can dance!

Still got time for more videos? Here’s David Attenborough talking about the deep ocean.

The majority of this info was from Tree of Life.

Science behind the headlines – beyond seven billion people

// December 9th, 2011 // 1 Comment » // Science Communication

We reached a big milestone last month as the world’s population exceeded seven billion people for the first time. Looking behind the headlines was Paul Willis at the RiAus and a panellist of scientists and journalists on Tuesday (event details here.)

In the 20th century we added five billion people to the Earth. Before that, we had only added two billion in total. Part of the reason is a decreased death rate, due to better medical facilities, coupled with an increase of food made possible by the Haber process that produces nitrogen fertiliser from nitrogen in the air. The chemistry makes it possible to, on some level, make food from air.

But population increase is not exponential. The UN expects the population to level off at 10 billion in the next fifty years, after a dramatic decrease in fertility, which no one anticipated.

“It is unconscionable to have a policy to increase mortality!” says Graeme Hugo, Director of the Australian Population and Migration Research Centre at the University of Adelaide. “The only way forward is to decrease fertility, that’s the only thing on the table.”

The world has done very well to reduce fertility, halving it since the 1970’s.

However, in some areas of Africa and isolated pockets in Asia it is not dropping as fast as expected. Two years ago East Timor each woman was having around eight children. The continued high fertility may be because we’ve taken our foot off the pedal when it comes to efforts like increasing contraceptives, women’s education and emancipation.

Beyond numbers

But it’s not all about the numbers, and that was the key point the scientists spoke about on Tuesday. Population is a complex issue, and has to be considered in connection to age and spatial distribution and consumption of goods.

The cost of looking after an aging semi-majority (the baby boomers) is a worry for some political movements. Balanced age groups are important to ensure the number of dependents and the number of workers is stable.

Migration may not change the global numbers, but it’s important for people are spread out in the right way. That means considering how many people a local environment can sustain in terms of food and water.

Consumption is also critical. One baby born in the United States consumes the equivalent of 30 babies born in Africa according to Udoy Saikia, School of the Environment, Flinders University (here’s a relevant link.) “People in developed countries should limit their consumption,” says Hugo. “In many developing countries, consumption needs to go up because they’re not consuming enough to be healthy.”

One way for more developed countries to limit consumption is to go vego. A more vegetarian diet is able to support more people for the same number of resources. Bring on the lentils!

This Tedx talk on the topic, I can’t recommend it enough.

Magic bullets

Scientists agreed that coverage of the seven billion people story has been pretty good overall, far better than stories about migration.

One issue they mentioned was the trend to look for a magic bullet, fixing just one thing to solve the whole population problem. It’s also hard for journalists with limited inches to talk about all the factors in a complex issue like population science.

Stopping population growth won’t work unless you take consumption into account, as well as the other factors. There needs to be a holistic approach. That doesn’t end (or even start) with policy – everyone needs to make a decision to change their consumption.

Australia

How many Australians should there be? There is no magic number where everything will fall into place. There are definite demographic problems regarding aging populations and dispersion (or lack thereof).

The scientists agreed we need a policy that allows for sustainable growth. They said it would devastate Australia if we stopped population growth tomorrow, but it would be also devastating to have uncontrolled growth.

“Every day we waste about 40% of the food (in Australia),” says Saikia. “There is some hope that the 10 billion population can survive very well, depending on distribution and consumption.”

Paul Willis summed up by asking whether Australian’s should “be concerned, not alarmed.” It’s not the end of the world, but we do need major changes and responses to population dynamics, says Hugo. “Be concerned, AND alarmed – about consumption,” says Saikia.

This post was also featured on the RiAus website.

Notes from the international barcode of life conference #bol4

// 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.

Did I hear you right? McGurk and other illusions

// November 4th, 2011 // 2 Comments » // Science at Home

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

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

Case one: The McGurk Effect

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

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

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

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

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

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

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