Friday, 27 April 2012

Scientists essentials

Research laboratories function differently than other places of work. There are no set office hours, although you are obviously expected to turn up at some point! But that means that some (crazy) person like me turns up rather early at work to benefit from the first warm rays of the sun. Some people might argue than 7am isn't that early but I shall remind the readers that our research group is in a University and undergraduate students are not renowned for getting up bright and early...

However even the most hardened early riser need something to focus the mind and we are lucky to have some good coffee spots right in the centre of the campus and some pretty enjoyable views to ease ourselves into a productive working day.

Early (or late for some) morning coffee!

Monday, 23 April 2012

So what do you do for a living?

When people ask me what I do for a living and I say "marine microbiologist", the usual assumption is that I play with whales all day long. I'd quite like that myself, however, I work on the things at the other end of the size scale, photosynthetic microbes, that can only be observed under the microscope. Inevitably that sounds less exciting to many people but in reality it is probably one of the most exciting research fields to be in this decade!... So, I have to find ways of explaining how great and important my work is. I could go in the details that cyanobacteria produce more than 50% of the oxygen in our atmosphere, that is to say that every second breath we take is sponsored by my little friends, but I found a way more important reason than that.

A few years back Nestle banned the blue Smarties (another popular and older version of m&m’s) due to health concerns from the artificial colorant needed for its confection. Even though Australia might have gone against other countries and kept the production going (True blue Aussie Smarties won't die off), I was in the UK at the time and this was dramatic!! There were even campaigns launched and facebook pages setup to “save the blue Smarties!”

And then cyanobacteria came to the rescue! The blue Smarties was back, this time coloured with a natural pigment (phycocyanin) extracted from these little bugs. Although a lot of the media referred to Spirulina as seaweed, I won't take much offence to the fact they are not, and keep spreading the word that: cyanobacteria saved the blue Smarties!!! 

A few of my colourful marine cyanobacteria and a (soon to be empty) pack of choccies containing "safe" blue Smarties.

Tuesday, 17 April 2012

Sci-fi science (Part 2): the MinION

After my last post on Sci-fi science, I remembered another cinematic dream of mine.
Being heavily involved in genomics, that is to say doing a lot of sequencing of the genetic material of microbes and teasing out meaningful information out of a large mass of data, I have always been quite wishful of the movie "Gattaca". When Uma Thurman gives a single hair to the sequencing booth and less than a minute later she is informed of the suitability of her love interest. Not that I would like to know how good a match I make with the bugs I grow, but that would save us a lot of time waiting for data to come back and sitting in front of the computer. This year a UK company might have brought sci-fi that little bit closer to reality with their USB sequencer.
The UK company Oxford Nanopore Technologies are planning to release their tweaked USB memory stick that can sequence more than 150 million bases in their 6h life-time (about 20 of those would do a human genome!) and can be purchased for less than US$900! The days of manual sequencing of a couple of 100 bases on large gels are definitely over...

The "old style" room full of machine vs. the  new USB sequencer!

Friday, 13 April 2012

Crowdfunding Science

Crowdfunding is a method of raising money for a project by obtaining small amounts of money from many people to reach a desired monetary goal. Crowdfunding was a central topic of conversation when I had friends over for dinner last Saturday to eat seafood paella (mmmmm, paella). This was due to the fact that one of my favourite webcomics, Order of the Stick, had just raised over US$1.2 million through Kickstarter. And Wasteland 2, a post apocalyptic role playing computer game had just raised over US$2.3 million to turn it into an actual game (Thanks in part to my friend Fraser who contributed to the second of these projects).
Just a day or two later, thanks to the blog of scifi author David Brin, I came across Petridish (great name incidentally), a site for crowdfunding science. Science has long been dependent on rich benefactors, whether individuals or governments, for funding. This goes all the way back to the Middle Ages where one needed a rich patron, preferably the king. Crowdfunding provides an intriguing alternative funding mechanism for scientific research projects. Though clearly scientific researchers can’t yet compete with webcomics or computer games for glamour, since the projects on Petridish are mostly trying to raise $10,000 rather than millions of dollars.
If crowdfunding does become a significant mechanism of scientific funding, this would raise concerns in my mind that we would be prioritizing funding based on gimmicks or pretty pictures rather than on any actual scientific excellence. Of course, whether the current grants system in Western countries really rewards scientific excellence is a topic for future blogging.

Not the paella I cooked, as I drank too much wine and forgot to take a photo of my paella

Sci-fi science on screen

Quite a few years back, while flicking through TV channels, I ended up watching my first (and last) 10 minutes of CSI. My slightly nerdy attention got caught when I saw them in full forensic mode, looking at a sample under a microscope. What was amazing about this microscope was that the characters were able to use it to decipher the entire amino acid sequence of the protein, in real time, contained in their sample. If I had continued watching I would have seen the inevitable arrest of the evil criminal on the basis of his/her protein sequence.

After seeing this amazing bit of kit on CSI I have tried to convince several bosses over the years to buy me one of these molecular microscopes, but they've always laughed at me, though I have not asked Ian yet... 
Working on a particularly puzzling protein sequence...

Tuesday, 10 April 2012

There's more to microbiology than white coats and petri dishes

There is more to being a research scientist than being locked up in a lab in a white lab coat and scaring undergrads with the occasional sinister laugh. I work on photosynthetic microorganisms that are important for the environment and are present in large numbers in seawater. Once or twice a month the lab door is left unlocked and I get to go and sample the tiny phytoplankton that do all of the heavy lifting in the global carbon cycle.

When the weather is not too bad we prepare a small vessel with a few other people and steam out as far as 5 miles off the coast taking water samples from different depths using the fancy bucket in the picture (more about that in another blog). Sometimes the weather is great and we need to make sure we do not get too sunburnt with litres of sunscreen, unfortunately other times the seas are a bit choppy and the whole episode becomes an outing of very green researchers. The Port hacking reference stations are the longest continually sampled time series on the Australian Coast. Our aim is to use the 'microbial perspective' to understand what factors drive the seasonal cycles of primary production along our coast. 

Wednesday, 4 April 2012

The Travelling Postdoc Life

Amy’s farewell party made us all think about our life as researchers (some of us get philosophical after a few beers).

Most science research labs have a strong international flavour with students and staff from all imaginable nationalities passing through. It is fairly rare that we stay at the same place from the start of our career to retirement and most of us have spent at least part of their studies or a post doc appointment in another country.  Mobility is part of the job description and getting to know the working ways of various countries is also personally very enriching.

For my part I have lived and worked in 8 different countries around the world (9 including Tasmania). I was wondering how many places have other people lived and worked in science or other types of jobs?

One annoying side effect of the travelling life is the need to change the plugs of each and every electrical appliance after every relocation :-(