Developing Geneticist

This blog is defunct...

noreply@blogger.com (Developing Geneticist) — Wed, 13 Jul 2011 10:38:00 +0000

...but I'm sure you knew that already.

Time to move on - I'm starting over, in a new location: here.

In which I apologize for being one of those bloggers who never posts

noreply@blogger.com (Developing Geneticist) — Fri, 01 Oct 2010 11:34:00 +0000

... but sometimes life gets in the way!

I applied for a big fancy scholarship today and had to write a statement of proposed research. I'll try to keep the whinging to a minimum, but just to get it out of my system:

Look, I know I'm supposed to tell you exactly what my research project is going to be on, because you want me to be a superstar with lots of ideas and be someone who can plan a project myself. Just so you know, that's not really what I get to do in real life. I have to fit in with what my supervisor is already studying. In fact, I had an interview with said supervisor about projects, and she is in no hurry to discuss the details of projects. We will probably discuss it closer to the time. BECAUSE IT'S A YEAR AWAY.

Phew. Anyway, so I wrote this proposal based on what I thiiink I'll be doing, and it turned out pretty cool. I read it and was like "sweet, that sounds like an interesting project". So hopefully someone else will think the same thing too, when they read it.

My flatmate just found out she got a Fulbright scholarship, which is flipping amazing and I'm so pleased for her, but it also brought back my drive to try my hardest to get a scholarship too. It's always a good motivator when someone you know gets a cool scholarship, because I guess it reminds you that the winners aren't faceless people you'll never meet, they're interesting people who are passionate about what they do.

Oh and in other success stories, my boss scored an $800,000 grant. Just whatever.

Lab coats - again

noreply@blogger.com (Developing Geneticist) — Wed, 01 Sep 2010 07:21:00 +0000

Jorge Cham has done it again:

Hey Jorge, that's nothing like a real lab! So I present to you a real life lab coat rack:

Oh... um... ok, you were right.

Dear Printed Reading Material

noreply@blogger.com (Developing Geneticist) — Thu, 05 Aug 2010 23:41:00 +0000

Dear Printed Reading Material

A story in MS Word documents

noreply@blogger.com (Developing Geneticist) — Wed, 21 Jul 2010 13:31:00 +0000

Dear University of Otago Article Linker,

noreply@blogger.com (Developing Geneticist) — Sat, 17 Jul 2010 04:31:00 +0000

Please stop pissing me off and start working.

Lots of love,
DG

I wish this was how I read papers:

noreply@blogger.com (Developing Geneticist) — Fri, 02 Jul 2010 08:34:00 +0000

http://physioprof.wordpress.com/2010/07/01/how-pis-read-the-primary-literature/

one day...

This is really aimed at myself:

noreply@blogger.com (Developing Geneticist) — Wed, 09 Jun 2010 07:14:00 +0000

Quit yer bitchin and just work harder.

This dude is wise

noreply@blogger.com (Developing Geneticist) — Mon, 07 Jun 2010 01:46:00 +0000

"Science and Mother Nature are in a marriage where Science is always surprised to come home and find Mother Nature blowing the neighbor."
Read more delightful quotes at @shitmydadsays

The first artificial bacterial genome

noreply@blogger.com (Developing Geneticist) — Sat, 22 May 2010 09:00:00 +0000

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.

An open letter to some males...

noreply@blogger.com (Developing Geneticist) — Sat, 15 May 2010 10:23:00 +0000

quit asking me to smile.

Sometimes I have a serious face because I'm doing serious business.

There's lots more I could say on the topic, but it has the potential to turn into a rant, which is no fun. Just google "men who ask women to smile" if you're still wondering why this bothers me.

It's mildly annoying if you're someone I know and respect, but it's downright creepy if you're some random d-bag on the street I've never seen before in my life. Get away from me, strange creepy man, before I hurl chunks on you.

Update: I just did that google search and found the excellent Zuska's article on this very topic. It makes me chuckle. Read it.

The Silence of The Lab

noreply@blogger.com (Developing Geneticist) — Wed, 12 May 2010 02:04:00 +0000

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/

What? But my current paper has all of these sentences in it!

noreply@blogger.com (Developing Geneticist) — Wed, 05 May 2010 05:36:00 +0000

Does that mean I have to re-write? Dang.

From http://www.phdcomics.com/

In which I buy lots of moneys-worth of books

noreply@blogger.com (Developing Geneticist) — Mon, 03 May 2010 06:05:00 +0000

I am still painfully aware that I haven't finished my series of posts on the Atheist Convention, but am somewhat relieved by the thought that everyone is way past giving a shit anyway, so I'm OK. I will finish it soon. Promise.

So I've been very broke for a very long time, and finally got paid on Friday. I was away the whole weekend (at a Genetics Retreat, I might even post about it sometime soon...) so have only just got around to spending some flippin cash. Yay.

On BOOKS. These books:

This is pretty much the reason I do science

noreply@blogger.com (Developing Geneticist) — Tue, 27 Apr 2010 06:12:00 +0000

Because it is BEAUTIFUL!!!!!!

Tip o' the hat to Bioephemera

Faith healers have the power....

noreply@blogger.com (Developing Geneticist) — Tue, 27 Apr 2010 06:00:00 +0000

...to switch off your brain.

http://www.smh.com.au/world/science/they-have-the-power-to-switch-off-your-brain-20100424-tkia.html

Global Atheist Convention: Part 4 - Convention Dinner!

noreply@blogger.com (Developing Geneticist) — Thu, 22 Apr 2010 01:11:00 +0000

It's taking me so long to actually get these posts written that they're hideously out of date, old news... etc. But I shall persevere anyway because I still think it was cool.

So the convention dinner had about 600 attendees. I was seated at a Pharyngulite table, and the other guests on my table were great. There was a couple with their 12 year old son, a couple from Queensland who run a charter boat on the Great Barrier Reef, a couple of singletons like myself, and some lovely elderly women from America. They had come to Australia just for the convention!

Food was faaaaaab. Example:

Lamb with anchovy and green stuff, fried bread with goat's cheese and caramelised pear, and salmon with salmon caviar.

Lamb with mushrooms and potatoes.

The entertainment started off with Julian Morrow and Craig Reucassel from the Australian TV show The Chaser's War on Everything. I looove The Chaser so was quite excited to see them, and even got to have a quick photo and chat with them after the dinner...

Yay.

Other entertainment included a skeezy illusionist (I later saw him inviting pretty girls back to his hotel room after dinner... because he wanted to "just hang out with like-minded people"... HAHAHAHA), and a cool cool guy who makes funny youtube videos.

After dinner I went and talked to PZ Myers! I was possibly a little bit weird and frightening, especially considering the number of wines I'd had, but he was gracious enough to have a photo taken with me:

There was a LOT of mingling after the dinner, and at some point I think we were even kicked out of the convention centre (I mean, because it was really late and they wanted to clear up... not because we were causing trouble...). On the way out, I met AC Grayling, who was lovely, had a great chat, and he even said that he would give me his email address the next day during book signings. And you know what? He actually did!

Global Atheist Convention: Part 3

noreply@blogger.com (Developing Geneticist) — Sat, 10 Apr 2010 08:35:00 +0000

The Saturday afternoon session kicked off with the Women's Panel, "Why saying goodbye to God is Good News for Girls and Women". The speakers were Lyn Allison, Leslie Cannold, Tanya Levin and Jane Caro. Each woman spoke for 10-15 minutes and all had really interesting things to say. The problem I had with this 'panel' was that it wasn't actually a panel discussion at all - each speaker gave their talk and there was no exchange of ideas afterwards. I get the feeling that the Women's Panel was actually a bit of an afterthought, its purpose being to include more female speakers to offset all the blokes who'd been given proper full length talks. Anyway.

The speakers were all good and I think that a couple of them should have been given full-length slots, because they certainly had plenty to talk about. Leslie Cannold was particularly memorable in that she was the only speaker at the convention who identified herself as agnostic (and spent a good portion of her talk explaining why). Ultimately, though, I would have really liked to see an actual panel discussion rather than all the speakers just giving independent talks. I hope the organisers do include a proper panel discussion next time the convention is held.

As an aside, I keep going back and reading the ABC Religion blog of the convention, and blimey, they obviously weren't listening. Margaret Coffey, in her summing up of the convention, criticized the lack of "diversity or range - no such stance as agnostic for example". Uh... well... actually there was an agnostic, as I just noted above. She talked a lot about her stance. Did you sleep during her talk? Wake up. Also, what did you expect??? It was the Global ATHEIST Convention - yeah, the speakers were atheists. It wasn't the Global Religion-versus-Atheism Convention, that's just what you wanted it to be, because of course you wanted to see religious folk like yourself represented. Well, tough luck. I don't go to Christian Conventions and bitch about the fact that there's no Atheist presenters. Fuck.

Back on topic. The next speaker was Tamas Pataki, whose talk was apparently quite unpopular (I was unaware of this, but I heard later that the attendees were quite vicious about him on Twitter) (P.S. Twitter? Seriously??? You're around real people all weekend but you'd rather discuss things on Twitter? Weirdos). There were two main things that people disagreed with in Tamas's talk. Firstly, he talked about the philosophical problem of being able to state that there actually is no god, which is a very good point. Of course, we don't know that there is no supernatural creator. For me, my atheism is a conclusion that I have come to after careful consideration of the evidence. Based on current evidence, I conclude that there is no god. However, when I say that, I am also specifying a type of god - the type of god who interferes in our day-to-day lives, the type of god who answers prayers, the type of god who speaks through human prophets, etc. There is just NO evidence for that type of god. On the other hand, there may well be some supernatural being who magicked the universe into existence, who wrote the laws of that universe, and who just watches, but doesn't interfere. There is no way of knowing whether this kind of being exists. I think that was Tamas's point, and I agree. Personally, I would argue that this type of being is unlikely to give a shit about us worshipping it, so I'm not going to sit around and ponder the existence of some hypothetical deity. I'd rather study things that we can actually observe (yeah, I'm clearly NOT a philosopher).

The other major thing that Tamas spoke about was that we don't know what a world without religion would look like, and it could conceivably be worse than a world with religion. It's true that early humans invented religion to try to understand the world, and for many, many people religion is the only thing that gives them hope. I think it's unlikely that a world without religion would be worse than this world, though. I really believe that religion makes more people feel shit than it makes people feel good. It usually oppresses women, usually makes people feel guilty for being human, usually makes people fearful and prejudiced. Imagine the people you know who are happy, and religious. Do you really think that they would be less happy without their religion?

The two final speakers of the day were AC Grayling and PZ Myers. (Hehe, the guys with initials for their first names). AC Grayling is a philosopher at Birkbeck, University of London, and his talk was on Atheism, Secularism and Humanism: Three Zones of Argument. I would urge you to listen to his talk here if you are interested, because he was a fantastic speaker. He's written loads of books and after hearing him speak I'm very keen to read them all. I bought one of his books that weekend, Thinking of Answers, which talks about the philosophy of everyday life. I also had a great chat with him later that night (which I will talk about in my next post), and he's a lovely guy.

And finally, the infamous PZ. Unsurprisingly, his topic was The Inescapable Conflict Between Science and Religion. He was great - the thing I like about PZ is that he totally seems like Your Favourite University Lecturer. He's very likeable. His style of speaking is quite conversational, and I think it ended the day with a nice relaxing atmosphere. His material was very familiar if you read his blog, so nothing particularly novel, but it was cool to hear him speak in person.

Next post: The Convention Dinner!

Damn you, ezproxy

noreply@blogger.com (Developing Geneticist) — Tue, 06 Apr 2010 02:30:00 +0000

So after procrastinating all Easter weekend, I finally sit down to update my lit review for my journal-article-in-progress.

Except that my uni has blocked my ezproxy access to the academic journal databases because my last contract ended a month ago and I haven't started my new one yet. Crap.

So I've been doing all the dull jobs like looking at journals' 'guides for authors' and drafting an article outline. Yay. I love this stuff. My favourite.

P.S. When did Dunedin suddenly become Antarctica? I think I'm getting frostbite.

The Scoop on Semen

noreply@blogger.com (Developing Geneticist) — Sun, 04 Apr 2010 22:37:00 +0000

ahahahahahahahahahahaha. The best part is the graphic for "5% of women are allergic to semen".

Via: Online Schools

(Tip of the hat to PZ)

Global Atheist Convention: Part 2

noreply@blogger.com (Developing Geneticist) — Sun, 04 Apr 2010 06:44:00 +0000

Getting up on Saturday morning to be at the convention centre at 8.30am was a serious struggle, as I'd foolishly gone out for drinks the night before (as an aside, the bars in Melbourne are pretty darn cool, and the talent is far, far, far superior to Dunedin) (to any Dunedin-residing male readers: your fine selves excepted, of course). However, I made it with plenty of time to spare and managed to get myself a good seat for the whole day.

The highlight of the first set of talks was Phillip Adams, who talked about the dangers of becoming "Atheist Fundamentalists". It's at this point where I wish I had taken notes from the speakers on the Saturday, because I really enjoyed Phillip's talk, but writing about it in detail is a struggle for me, with my dreadful memory. However, I can tell you that Phillip was an engaging and interesting speaker and I really enjoyed his talk.

Phillip Adams (picture from University of Queensland)

Russell Blackford and Max Wallace's talks shared a common theme in promoting freedom from religion, particularly emphasising the unfairness of governmental policies favouring believers over non-believers. Max Wallace is currently looking for support to make a film about How Taxpayers Subsidise Religion around the world. Even though I was aware of tax breaks for religious organisations, etc, I still hadn't realised the huge extent to which religion gets enormous financial support from supposedly secular societies. Max's presentation was particularly eye-opening in this regard.

After morning tea, there were two talks that really hit home about the real human cost of religious fanaticism, specifically within the Islamic faith. John Perkins spoke about Islam and Terrorism, but the real star of the show was Taslima Nasrin, who received the only standing ovation all weekend for her very moving speech about her experience as an ex-Muslim.

Taslima Nasrin was brought up as a Muslim in Bangladesh, and is now an atheist, humanist and feminist. She has a medical degree and is a writer. Her writing, particularly on Islamic oppression of women, has earned her death threats, public assaults, fatwas issued against her, a price on her head, and ultimately expulsion from her home country. She is an exceptionally brave and intelligent woman. To not be able to live in her home country clearly causes her great sorrow, and her life is continually at risk, but she continues to fight for human rights, and for women's rights. I'm almost in tears again, remembering her talk. It is so easy for us in western countries to forget that so many people around the world still do not have freedom of speech, or freedom of religion. So many women are silenced, oppressed, and abused as the norm.

Taslima Nasrin speaking at the Global Atheist Convention. (Image from Wikipedia)

Just a fortnight before Taslima's talk at the convention, 15,000 people in the State of Karnataka in India took to the streets and rioted, and two people died. Why? All because a local newspaper published an (incorrectly altered) article of Taslima's on the burqa.

The conclusion of Taslima's speech was very moving, and I shall reproduce it here:

I am in other words a stranger in my own country Bangladesh, and a stranger in neighbouring India and a stranger in the West, where I am now living. Where can I go? Nowhere.... But I have a home, a home that consists of a family of people, men as well as women, who bravely oppose the forces of darkness and ignorance. These represent my true home. The hearts of people are my home and my nation, my only safe haven, my shelter and my refuge.

... My home is love, the love I receive from women all over the world, that is my home, the love I receive from atheists, free thinkers, secularists, and humanist[s] is my home, the love I receive from you, that is my home. I do not regret what I have done so far, I do not regret anything that I have written, come what may. I will continue my struggle against all the extremists, fundamentalists, intolerant forces without any compromise to my death. I am all the more committed to my cause.

Listen to Taslima Nasrin's talk in its entirety here. (Thanks to the ABC Blog of the Atheist Convention)

Stay tuned for Part 3....

Time to finally share my experiences at the Global Atheist Convention

noreply@blogger.com (Developing Geneticist) — Sat, 03 Apr 2010 09:57:00 +0000

...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...

Richard and Paul

noreply@blogger.com (Developing Geneticist) — Tue, 09 Mar 2010 21:13:00 +0000

Tonight's the night I start my long and tiresome journey to see Richard Dawkins and PZ Myers at the Global Atheist Convention in Melbourne! You know you're jealous. Only problem is that someone's borrowed my copy of the Greatest Show On Earth, so now I'm going to have to buy another one for ol' Richard to sign.

Oh the dilemma! What should I wear to the Convention dinner, where I will be sitting with the Pharyngulites? Tentacles?

I know Nathan wants me to score a pash with Richard Dawkins but I think the best I can hope for is a photo.

P.S. I intend to visit Lord of The Fries when I'm in Melbourne. You know you're jealous about that, too. Ha.

This blog post is intended to distract you from the fact that I haven't updated my blog in ages

noreply@blogger.com (Developing Geneticist) — Tue, 26 Jan 2010 07:06:00 +0000

I think this (including the accompanying comments) is what all blog posts should be like.

Extraordinary Embryo of the Week

noreply@blogger.com (Developing Geneticist) — Wed, 20 Jan 2010 00:38:00 +0000

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.