The first artificial bacterial genome

Just about every science blogger in the world has written about J. Craig's working artificial bacterial genome. Most of them are much cleverer people than me, so I don't have much to say that wouldn't be repeated what has already been said, but I'd just like to point you to some posts that are good, or thought provoking, or hilarious.

Good:
Did scientists play god? 

Thought-provoking:
We can't control everything - evolution takes over immediately

Hilarious:
J. Craig versus Francis Collins

Just to add to that last one, I distinctly remember some lecturers in my undergrad talking about J. Craig Venter and emphatically adding that he's apparently a total asshole. Well, so what? I've met plenty of asshole scientists*; being a meanie isn't unique to JCV and it shouldn't take anything away from his achievements. And boy are they spectacular achievements.

*I would just like to make it clear that I am NOT referring to any of you lovely scientists who I have ever worked with. You guys rock.

The Silence of The Lab

The lab I'm working in at the moment is noisy... we're a bunch of people who talk. A lot.

So on the 27th and 28th of May, we're having two whole days of silence in the lab. No talking at all (believe me - this is a big deal. The rest of the department don't think we can do it haha). Why? To raise money for UNICEF's UnderCover Malaria Campaign.

Malaria is a major cause of death in developing nations killing one to three million people per year, the majority children. Malaria transmission can be reduced through the distribution of simple mosquito nets. Please help purchase and distribute mosquito nets to those who need them by supporting The Silence of the Lab.

Pledge your donation by going to http://www.fundraiseonline.co.nz/thesilenceofthelab/

Time to finally share my experiences at the Global Atheist Convention

...and boy was it not at all what I expected.

I guess I should outline my reasons for attending the convention before I begin, because it turns out that the reasons I enjoyed it so much weren't really the reasons I went.

Basically, I saw a post by PZ saying that he was speaking at this atheist convention in Melbourne, and Richard Dawkins was the headline speaker. Both Dawkins and PZ are people whose writing I enjoy and admire, and Melbourne's awfully close, so I knew that I just had to go. Plus, Dawkins' books are required reading for any geneticist (arguably any biologist), so I really wanted to hear him speak.

The rest of the line-up at the convention was made up of a lot of people I hadn't heard of (or had vaguely heard of but I wasn't familiar with). And, to be honest, I was expecting most of them to be dull. That was totally unfair, but I was basing my assumption on the fact that most speakers at most events are a bit boring, and only occasionally are they punctuated by good, engaging speakers.

Boy, was I ever wrong!

I'll start with the Friday evening drinks... I rocked on up to the Melbourne Convention and Exhibition Centre having walked for half an hour in my heels because I'd gotten off at the wrong tram stop and fluffed around trying to figure out where the heck I was. I was battling blisters for the rest of the evening, but I suppose that'll teach me for wearing silly shoes... Wait, what am I saying? I love those shoes. Anyway.

After nervously downing a glass of wine while trying to spot approachable strangers to make friends with, I spotted PZ through the crowd, surrounded by a bunch of fanboys. Given that he looked totally surrounded by doods, I decided not to make contact at that particular moment. Looking at the crowd was interesting, I think I had expected more old people. And more unattractive people. I started chatting to two (intimidatingly beautiful) medical students from Brisbane, who were both there with the aim of persuading Richard Dawkins to leave his wife Lalla and shack up with them instead. Heh.

Soon enough we were herded into the auditorium to kick off events. The MCs of the convention introduced themselves, Stuart Bechman and Kylie Sturgess. Stuart is the president of Atheist Alliance International, and is from LA. Kylie is an Australian skeptic and blogger. They were great MCs, with excellent senses of humour and very different backgrounds.

The first speaker was Sue-Ann Post, an Australian comedian. She was great - her background as a lesbian ex-Mormon definitely gives her a shitload of material for routines.

(Image from Wikipedia)

Second speaker: Mark Tier. Totally forgettable (I'm sorry! I truly have forgotten his talk - not trying to be rude!). OK, I just looked him up on the convention website again, and now I remember, he was talking about the high level of religiosity in the Philippines (he's an Australian who now lives in in the Philippines). I also remember wondering what the fuck his point was. I still have no idea.

Third speaker: Catherine Deveny, another Australian comedian. Her topic was "God is Bullshit. That's the Good News". She told her story of 'conversion' (I don't like that word, but oh well) from catholicism to atheism, and like Sue-Ann, she was very funny.

Well that was it for the first night, and while the comedy had been great, I was still wondering whether attending the convention had actually been a colossal waste of money.

Saturday abolished all those worries pretty quickly, but that will have to wait for another post...

Extraordinary Embryo of the Week

What a beauty! This is a mouse embryo, and you can tell that it has been stained for the expression of a gene. But this is not just any gene! This mouse has actually been genetically modified to contain some DNA from the extinct Tasmanian Tiger, Thylacinus cynocephalus.

Now, the point of this genetic modification wasn't to create a half-mouse-half-Tassie-tiger (that would just be absurd. Not to mention impossible...), but rather just to study the function of a particular gene. Because it would be damn near impossible to bring the Tasmanian tiger back from extinction, this approach is the best way to study its genetics.


The Tasmanian tiger

What the scientists did was very carefully extract DNA from four 100-year-old Tasmanian tiger specimens that had been preserved in alcohol, and amplify the DNA of interest (not an easy task if you're working with old DNA!). The DNA they amplified was from a region that controls the expression of a gene called Col2A1. You can think of this DNA as the 'switch' that turns Col2A1 on or off.

They attached the switch to an additional piece of DNA, a 'reporter' gene. Then, they inserted the whole DNA construct into a mouse genome. The reporter gene produces the blue pigment you can see. This method tells us where and when in the embryo the 'switch' is turning on. If the switch is turned on, the reporter gene is active and produces a blue pigment.

Basically, this was a really neat method for studying the function of a gene from an extinct animal! The blue pigment allows us to see where the gene is switched on, and then we can compare that to the mouse version of Col2A1. Turns out, Col2A1 seems to perform the same function whether it's from the Tasmanian tiger or the mouse (its function is in cartilage formation, which is why it is expressed in the forming bones).

This may not be a particularly thrilling conclusion, but the applications of the technique are pretty awesome. For example, maybe one day we could examine what dinosaurs looked like, if we could extract the relevant genes from dinosaurs and insert them into another animal!

And actually, geneticists use this technique for non-extinct animals as well. It's a really good way to figure out if a similar gene performs the same function in different animals. These kinds of studies tell us about the evolutionary history of individual genes, which is bloody interesting, if you ask me.

Reference: Pask, A.J., Behringer, R.R., Renfree, M.B., 2008. Resurrection of DNA Function In Vivo From an Extinct Genome. PLoS ONE, 3(5), e2240.

Science cookies

Inspired by these beautiful cookies, my friends and I made a bunch of geeky science-themed cookies today!

Here is one of our (far inferior) electrophoresis gel cookies...



And then we got a little carried away with other geeky things too...



Including the animals we work on: Xenopus laevis, Oncorhynchus tshawytscha, and Ovis aries




Sequencing electropherograms: We designed sequences that spelt out our names in one-letter amino acid codes!




And little models of cells that include features such as a nucleus, rough ER and smooth ER, mitochondria, and Golgi.





I don't think I'll need to eat for a month after all these...

We are made of star stuff

I'm currently reading the very cool book Death From The Skies!, by Phil Plait, which outlines a bunch of end-of-the-world scenarios and then talks about the science behind them. Phil's an astronomer, and a fantastic writer - I've been a fan of his ever since I was about 15 years old, when I discovered his hilarious Bad Astronomy website (his review of the movie Armageddon still makes me chuckle).

Death From The Skies! is one of those books where you just end up thinking "wow, science is so darn cool!". Being a bit of a geek for pretty much my entire life, I thought I knew a reasonable amount about astronomy and astrophysics, for someone who's a non-specialist. But every chapter of Death From The Skies is full of things that I haven't encountered before - and many of these tidbits are extremely cool.

One particular chapter on supernovae is full of "wow-facts". In this chapter, Phil talks about the processes of fusion in the core of massive stars. Our own sun fuses hydrogen nuclei to produce helium, but more massive stars can produce other elements by fusion, once their hydrogen supply has run out. Massive stars produce, in this order, carbon, neon, oxygen and silicon; and the most massive stars in our universe have such tremendous pressure and heat at their core that they can produce iron. These stars, however, do not have long to live once they are producing iron, and will soon explode in a furious cascade of events that we call a supernova.

The early universe contained only three elements: hydrogen, helium, and a little bit of lithium. Nothing else. Then supermassive stars started to form, and began creating heavier elements from the lighter ones, right up to iron, then exploded. The explosions of these stars triggered the formation of new stars... and the cycle continued.

I'll leave you with (what I think is) the most striking paragraph of this chapter:

When you cut your finger and a thin rivulet of blood seeps up into the slice, the red color you see is due to hemoglobin, and the key factor in that molecule is iron. That iron was forged in the heart of a supernova.

As Carl Sagan told us: We're made of star stuff.

http://www.youtube.com/watch?v=XGK84Poeynk&feature=player_embedded

Axolotl development

In our department we have a breeding pair of axolotls in the teaching labs. They've had some babies recently, and the baby axolotls have just hatched from their eggs. They're awfully cute, they look quite similar to Xenopus tadpoles except they've got those fantastic external gills.

I looked up a table of axolotl development and found a site with an excellent series of photographs, depicting the development right through to larval stage. The Late Neurula stage is SO COOL. Go look at it. Now.