Posts Tagged ‘simple’

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.

What is a light cone?

// November 28th, 2010 // 1 Comment » // How Things Work

Simultaneous is not simultaneous. Space and time do not exist. These, and other strange and wonderful things, are the hallmarks of Einsteins Theory of Relativity and what we’re talking about today.

A few days ago I got Request a Post which read:
ahoy there, cap’tun! a prawn from beneath your deck speakin’. could you do a post on Light Cones? yeh know, the stuff Stephen Hawking talks about in the second chapter of his ‘Brief History of Time’? i’d love to read a simplified version. i simply can’t wrap the wiki article around my head! danke!

Ahoy there Prawn! Danke for requesting and here be yer post.

Something can’t move through space without moving through time as well. The Theory of Relativity dispenses with time and space, and instead describes a new thing called Spacetime.

Imagine a train moving in a straight line to the Eastward. We can map its movement through Space, Time or best of all, Spacetime! Notice how much more epically cool Spacetime looks. This will be important later.

With our Spacetime graph, we map space horizontally and time vertically.

In the realz world, there are three dimensions of space – length, width and height. Thankfully there is only one dimension of time, and this runs from past to future (unless you’re looking backwards.) To graph something using all four dimensions is hard, so instead we just take two dimensions of space and make a horizontal plane, then map time vertically. This will make sense in a second.

Now imagine a flash of light. Say you were standing on a hill on a moonless night and turned on a torch for a second. The light would spread out in every direction, lighting first the bushes near by, then later the trees in the distance. If we think about it in just 2 dimensions we can draw it like this, kind of like ripples in a pond.

If we map time vertically, and stack these pictures up above each other, we get a cone. So a Spacetime graph looks like this. Notice again that it is epically cool.

So a light cone is a flash of light moving through Spacetime. Usually people draw it as two cones. The bottom one is light collapsing into a single event, and the top one is it exploding out again.

Image by Deibid

You might be thinking – why bother?

Because this is a more accurate way to imagine the world. It shows how the past can influence the present and the future. When light cones overlap, it means two objects or events interact with each other. Every event in the Universe has an associated light cone. It’s a mathematical way to represent the Universe, and the basis for lots of complex physics (such as curved Spacetime, and why simultaneous events are relative to the observer.)

The theory of relativity replaced the absoluteness of space and time with the absoluteness speed of light.

I hope this answers ye question Prawn. Find out more about awesome light cones here.






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