Monday, 26 March 2012

Bon Voyage Amy!

The Paulsen lab went for an outing to the pub Friday night, we went to The Ranch to farewell Amy Cain. Amy is leaving our group take up a postdoctoral position at the Sanger Centre in England, where she will be working in Julian Parkhill’s group. We wish Amy the best of luck there, if anyone is heading over near Cambridge say hi to Amy for us!

Those members of my group who were too slow to avoid the camera- from left to right: Sophie, Martin, Karl, Amy, Kent, Prasanth, Daniel

Wednesday, 21 March 2012

Science in Gaming

I’ve become increasingly interested in the portrayal of science, particularly microbiology, in the media. This is an issue I intend to explore across a series of blog posts. I decided to start with looking at science in gaming. The picture shows Sheldon from the Big Bang Theory with his game “Research Lab”- where the physics is theoretical but the fun is real! Sadly the fun isn’t really real as the game doesn’t actually exist (yet).
Anyway, there are lots of games where one plays as a soldier, cop/detective, criminal, etc. How about games where one can play as a scientist? And specifically as a microbiologist? 
A very few come to mind-

Pandemic is a great board game. In Pandemic you try and save the world from a series of disease outbreaks- battling to contain the pandemics to give yourselves enough time to race for the disease cures. So, just like my job every day :)

In Half Life of course you play as the crowbar-wielding theoretical physicist Gordon Freeman. I haven't come across any games yet with crowbar-wielding microbiologists.

Um, struggling to come up with anything else. Mordin Solus is probably my favourite character in Mass Effect- well along with Garrus.

Now, there’s no shortage of evil Mad Scientist Villains in games, but can anyone think of other games where one can play as a scientist? Or in which scientists are portrayed in a positive manner?

Tuesday, 20 March 2012

Must remember to turn up to my lectures!

My lectures start this week in my 3rd year unit- CBMS336 Molecular Biology and Genomics. Now I just need to remember to turn up for them! Those of you who know me, may be aware I'm getting increasingly vague these days (probably from pouring too many polyacrylamide sequencing gels when I was a young scientist- damn the neurotoxic properties of acrylamide, or maybe being vague is just part of the job description of being a professor), so I do worry about forgetting to turn up to my own lectures. This week will have the excitement of me getting tangled up in slinkies trying to demonstrate DNA transcription.

don't try this at home

Thursday, 15 March 2012

What does the title of this blog mean?

A couple of people have asked me “what does the title of your blog actually mean?” Let me try and answer that.
Over the course of 3.5 billion years or so of evolution bacteria have adapted to survive and flourish in essentially every ecological niche on the planet. One of the main research interests of my group is understanding at a genomic and genetic level how particular bacteria have adapted to their environment. In essence, what are the lifestyle choices of bacteria?
The word “lifestyle” appears to be making repeated appearances in our grant applications. One of our current ARC Discovery projects (DP110102718) is called “Lifestyle choices: genomic analysis of niche adaptations in marine Synechococcus”. The NHMRC grant that Karl and I just wrote is titled “Tolerating a stressful lifestyle: drug resistance in the nosocomial pathogen A. baumannii”
Over time hopefully this blog will look into some of the microbial lifestyles our research group is investigating.

Not my lifestyle choice, but these guys like it. Microbial slimes in limestone caves beneath the Nullabor Plain (photo coutesy of Peter Rogers)

Monday, 12 March 2012

Scary stuff you can find on the internet

You can find all sorts of scary stuff on the internet these days. For instance, Macquarie Uni put up this video on YouTube of me gesticulating like a mad man.

This is a talk I gave at a dinner event at MQ for High Achieving year 11 students from Sydney High Schools. The event was aimed at attracting promising students to study science at MQ. I was very impressed with the enthusiasm and scientific insight from the students at the dinner, I think I got better questions there than I have had at some scientific conferences. The host for the evening was Australian tv science personality Adam Spencer, who was highly entertaining.

At this stage, the video clearly has not yet gone viral yet, judging by the number of YouTube views- the vast majority of which I suspect are from my relatives :).

Sunday, 11 March 2012

Karl puts his life on the line for our grant!

It seems like it has been raining in Sydney straight for the last four months. In Wagga Wagga in rural NSW even the spiders are having to move to high ground to avoid the floods. You may have seen crazy pictures of their spider webs elsewhere on the web:

We haven't really had serious floods in Sydney itself, but Karl (a senior postdoc in my lab) had to wade through the waters below in order to make it to Macquarie University to work on our NHMRC grant.

Karl made it safely to work, but the same cannot be said for his thongs (if you aren't Australian, this means flip-flops, I know the US definition of a thong would make this post very different) which were washed away.
Hopefully the NHMRC appreciates Karl's heroic actions and funds the grant. Anyway, our grants are due at the Research Office on Monday, so I hope soon we can think of something other than grant writing.

Wednesday, 7 March 2012

The Glamorous Life of a Professor

Just a quick post tonight. I'm in the middle of trying to write four NHMRC (National Health and Medical Research Council) grants. So its another late night of staring at my laptop, while Terminator: The Sarah Connor Chronicles plays in the background. But I have the joy of running a 9 am prac class for my 3rd year unit in the morning to look forward to!

Sunday, 4 March 2012

Gaming vs Science

So in my spare time I’m a sad gaming addict. Always have been and I think that’s unlikely to change in the foreseeable future. Over time, my gaming has gone through an evolution from old school pen and paper role playing games like D&D, Runequest, Call of Cthulhu; to board games such as World in Flames and Empires in Arms; to computer strategy games like Civilization, Age of Empires, Starcraft; to massive multiplayer online time sinks like Everquest, World of Warcraft and Lord of the Rings Online. Currently I’m playing on the Xbox Kinect mostly- Skyrim, LA Noire, Fitness Evolved, and waiting for Mass Effect 3 to come out.
At times, for instance when I was a raid leader in Everquest or in the top raiding guild of my server in WoW, I think its undoubtedly true that my gaming hobby absorbed far more hours of my life than science did. In my very rare reflective moments, I wonder if I’d spent less time gaming would I have significantly more scientific output? (Would I have double the number of publications?) On the other hand, has my gaming addiction aided my scientific career in any way? I definitely believe my strategy gaming experience helps me in gaming whatever byzantine systems the university adopts. And I’m sure playing role playing games in my youth helped my confidence as a public speaker. I’m less convinced that my experience as a raid leader in EQ has had any noticeable benefit towards managing my research group, although I guess both experiences are pretty much akin to herding cats.
I know a variety of my colleagues are also gamers (Derek and Uwe, you know who you are!); I’m wondering how other researchers are addicted gamers and whether that’s been a positive or negative influence on your careers?

Old School WoW and EQ

Friday, 2 March 2012

Introducing the team: Sheldon

What does the Paulsen lab and The Big Bang Theory have in common? We're each reliant on a quirky character named Sheldon. In our case Sheldon is our High Performance Computer Cluster- a linux cluster with 18 nodes, each with dual 6 core CPUs, with over a terabyte of RAM in total. Sheldon is crucial to our bioinformatic research, giving us the capability of running millions of BLAST searches or assembling large metagenomic datasets.Sheldon in BBT has his favourite spot on the couch  where "In the winter that seat is close enough to the radiator to remain warm, and yet not so close as to cause perspiration. In the summer, it's directly in the path of a cross-breeze created by opening windows there and there. It faces the television at an angle that is neither direct, thus discouraging conversation, nor so far wide as to create a parallax distortion." Sadly our Sheldon has struggled to find its favourite spot since it has bounced around several locations on campus trying to find a server room it is happy in. Also, why nodes 3 and 15 think it’s a great idea to run their fans flat out under all conditions in an attempt to sound like a jet engine remains a mystery.

Spot the difference?

Thursday, 1 March 2012

Happy Birthday JAMS!

I woke up feeling a little fragile this morning. Yesterday we celebrated the first birthday of JAMS (Joint Academic Microbial Seminars). This is a monthly microbiology seminar series held at the Australiam Museum in Sydney. Its sort of modeled on the San Diego Microbiology group meeting, and provides a venue for the microbiologists scattered around Sydney to meet each other and chat about science. It all came about from a meeting in a pub in Surrey Hills in 2010, where Federico Lauro, myself, Mike Manefield and Andy Holmes decided over a few beers that starting JAMS would be a good idea. Federico has done a heroic job turning JAMS into a reality, and we usually have 30-50 microbiologists turning up every month for JAMS.

To celebrate the first birthday of JAMS, yesterday we had five excellent talks from interstate or international speakers. Thanks to Tim Stinnear, I now know what the bizarre link between Point Lonsdale (Victoria) and Western Africa is (hints- Mycobacterium ulcerans, mosquitos and ringtail possums). Afterwards we had dinner and copious volumes of wine in the dinosaur room of the museum. It was slightly disconcerting to have a video loop showing dinosaurs devouring each other in Triassic era, while we were eating slowly braised beef cheek.

Nevertheless, we had 79 people at the dinner, which would seem to be an encouraging sign for the future health of JAMS.

Dinosaur video- moments before one of these guys had an unfortunate meeting with a larger relative


Welcome to the Paulsen lab blog. We are a microbial genomics research group at Macquarie University.