Thursday, 14 August 2014

My Kardashian Index is 0

Earlier this year, I blogged about metrics for measuring scientific output such as a H-index, AltMetric, etc. I just came across an entertaining little paper in Genome Biology by Neil Hall about a new metric- The Kardashian Index. Neil was wondering whether there are scientists who are like Kim Kardashian- famous for being famous. Or more specifically, whether there were scientists who are famous for their twitter feeds or blogs, but have not produced much in terms of published research papers of significance. So, he came up with the Kardashian Index- your number of twtitter followers divided by your number of citations from your published scientific papers.

I'm proud to say my Kardashian Index is 0 - since I have no Twitter followers, and 32,000+ citations. Ok, ok, since I am a conscientious objector to twitter, Facebook, etc, and have never tweeted in my life, it's probably not a relevant metric to me.

Fig. 1 from the Kardashian Index paper- identifying scientists who are highly active on social media but don't actually produce much scientific output. 

Monday, 11 August 2014

Minions in Action!

Some of you may recall we received MinION sequencing devices from Oxford Nanopore as beta testers. It's taken a while, but Mike Gillings now has them up and running. Whether they can actually generate useful data is still something we're working out, but in the meantime here are some action photos.

The MinION is the USB device plugged into the laptop

Each dot on the screen represents a protein nanopore through which a DNA molecule is moving and being sequenced. The different colour of the dots indicates how the sequencing is going.

Who doesn't love bar graphs- this one shows the lengths of DNA molecules being sequenced. Some of our read lengths are up to 70,000 bps in size

Best Wishes Daniel

The Paulsen lab went on an outing Friday night to the University bar to farewell Daniel Farrugia. Daniel has just submitted his PhD thesis on genomic analyses of the opportunistic pathogen Acinetobacter baumannii, where he was investigating what is different between strains from hospital-acquired infections, community-acquired infections, and environmental isolates. Daniel has published papers in PLoS One and The Journal of Antimicrobial Chemotherapy; another paper about to be submitted to Nucleic Acids Research this week, and a couple more papers in earlier stages of preparation.

Daniel is moving to Malta with his family, and after a break to recover from his PhD is going to be looking for a postdoctoral position in the EU. We wish Daniel the best of luck for the future!

Paulsen group at the pub; Daniel is in the front of the photo holding a beer

I'm hiding up the back away from the camera

Thursday, 7 August 2014

There's more: Microbiology Faculty position available

In addition to the Synthetic Biology/Bioinformatic Faculty positions we just advertised, we also have a new faculty position available in Microbiology at Macquarie University. This would be a level B appointment (roughly equivalent to a new Assistant Professor in the USA). Again, applications close on Sunday 31 August 2014, 11:55pm.

Tuesday, 5 August 2014

New faculty positions in Synthetic Biology/Bioinformatics

Building off our launch of the Yeast 2.0 Synthetic Biology project at Macquarie University, we have just advertised three new junior faculty positions (level B/C- roughly equivalent to Assistant Professor in the USA). Two of these positions are in Synthetic Biology and the third position is in Bioinformatics. We also have three postdoctoral positions to be filled on the Yeast 2.0 project. The plan with these appointments is to build a critical mass of researchers in Synthetic Biology at Macquarie, and position ourselves as leaders in this field in Australia. 

The Macquarie University web site tell me that applications for these positions closes on 11:55pm Sunday 31 August 2014, Australian Eastern Standard Time. If you are interested in one of these positions, I encourage you to apply or to contact me if you have any further questions.

While searching the internet for a suitable image, I came across this synthetic biology comic from Drew Endy and Chuck Wadey- full version here

Friday, 18 July 2014

What the hell is the Anthropocene anyway?

When I was a kid, I used to drag my parents out gem/mineral/fossil hunting all the time. Possibly in revenge for all these field trips, much later my Dad threw out my mineral collection that had been stored in his garage for a decade or two while I was working overseas (Not that I'm bitter about that or anything).

Anyway, as a 12 year old I was an expert on geological eras, periods and epochs. Apparently, my childhood knowledge is now out of date (and probably mostly lost in forgotten recesses of my mind). Mike Gillings has made me aware that there is a growing scientific opinion that we are now living in a new geological epoch- the Anthropocene. As a 12 year old I would have said we were living in the Holocene Epoch, but humanity is now have such an impact on the earth, that it is likely that we would show a strong signal in the geological record from things like changes to atmospheric CO2, biodiversity loss which would show in the fossil record, changes in trace element distribution due to pollution, etc. Hence we are likely now in a new epoch- the Anthropocene (Age of Man).

When the beginning of the Anthropocene should date from is a controversial topic, but there are probably three distinct phases to the Anthropocene: the ‘paleoanthropocene’, corresponding to the widespread adoption of agriculture some 8 to 10 thousand years ago, when clearing of forests and the consequent release of greenhouse gases potentially started affecting earth systems. The second phase began in the Industrial Revolution, coinciding with significantly increased carbon emissions and the environmental degradation associated with industry. The final phase occurred post World War II, and is called “The Great Acceleration”, because it is associated with very rapid growth in human population, resource consumption, energy use and pollution.

Mike Gillings and I have just published an opinion piece (anyone who knows us knows that we're both pretty opinionated) in the journal "Anthropocene". As can be seen in Mike's beautiful figure below, we argue that the different phases of the Anthropocene has resulted in demonstrable impacts on the microbial population of the globe, including-
1. changes to the human microbiome (the community of microorganisms that live in and on the human body);
2. the evolution of bacterial metal ion and drug resistance genes (from exposure to industrial pollution and widespread clinical and agricultural use of antibiotics)
3. the dispersal of disease-causing bacterial pathogens around the globe, e.g., spread of Old World pathogens to the New World during the Age of Exploration
4. Microbiogeochemical changes on a global scale, microorganisms play a key role in the global nitrogen, carbon, phosphrous, sulfur, etc cycling, and human activities from agriculture to industry have undoubtedly affected composition of microbial communities and rates of microbial activity

Some human affects on the microbiological world

Wednesday, 16 July 2014

We're FORC-ed!

So now we have no end of FORC jokes here, as we have launched our new ARC Industrial Tranformation Training Centre: The Food Omics Research Centre (FORC). The aim of our Centre, led by Professor Paul Haynes is to develop a molecular technology platform enabling the next revolution in the food industry. One of my PhD students, Hasinaka, is working within this Centre to investigate whether a sugar cane fibre-based dietary supplement can improve your digestive health through the changing the microbial composition of your gut. Something, I'll probably talk further about at a later opportunity.

Using omics technologies to improve the process of taking food production from "field to fork"