Tag Archives: open science

Our experiment in open science begins!

Bartopen

In early 2012 I came across the SciFund Challenge started by two ecologists from the US National Center for Ecological Analysis and Synthesis in California, Dr. Jai Ranganathan and Dr. Jarrett Byrnes. With a passion for communicating science to the public, and spurred on by budget cuts, Jai and Jarrett wanted to see if the crowdfunding model successfully used by artists and musicians could be applied to support science.

Rather than relying on one wealthy benefactor for full funding, crowdfunding seeks small contributions from lots of people to get projects off the ground. Using the popular crowdfunding site RocketHub as a platform, the SciFund Challenge has run three rounds, with scientists raising money for projects as diverse as parasitic plants, flying foxes, Amazonian crabs, domesticating algae, duck erections, Roman slaves, zombie fish and undersea kelp forests.

I took part in Round 2 of the SciFund Challenge in May 2012, to support a fledgling project in the lab that had been something myself and an old colleague of mine, Bill Hanage (now an Associate Professor at Harvard) had talked about doing for years. I have tried to get this project fully funded several times through traditional grants but, despite excellent feedback from overseas reviewers, have had no luck. Fortunately I was given a little seed money from the Maurice Wilkins Centre for Molecular Biodiscovery, one of New Zealand’s Centres of Research Excellence, to get the project started. Through the SciFund Challenge, 79 people from all over the world, half of them strangers to me, donated about US$4500 to help this project along. In this funding environment, every little helps!

So what is the project? It is based on the fact that bacteria are masters at adapting to their environment, rearranging their genetic material or gaining new genes from their surroundings. This has allowed them to colonise pretty much every conceivable environment, from boiling hot geysers to human beings. While many are harmless or pretty beneficial, plenty have evolved to cause us serious harm. In fact, bacterial adaptation is how we get antibiotic resistance and new diseases emerging. So what I want to know is, how do bacteria evolve to cause disease?

We are studying the evolution of a bacterium called Citrobacter rodentium which infects mice using the same ‘modus operandi’ as food poisoning strains of E. coli do in humans. They go in one end… and come out the other! And because mice like to eat poo (more technically known as coprophagia) they easily spread C. rodentium to each other. We have spent this year allowing the bacterium to spread from mouse to mouse to mouse to mouse to… you get the picture, each time freezing bacteria that are shed in the poo. We now have a freezer full of ‘evolved’ bacteria that we are itching to analyse. What changes might have happened? And if they have, will they have made the bacterium more or less infectious?

As this project has already made its web debut, it seemed a perfect candidate for an experiment of another sort – the Bioluminescent Superbugs Lab’s first open science project. We have created an online lab book and Hannah, who is working on the project for her PhD, will be publishing her lab notes in real time, for all to see.  Working with such a limited budget, it doesn’t make sense to do this project as normal – beavering away in the lab for years and then having reviewers turn around saying “you should have done x,y & z”. Instead we are hoping to engage others in the field to help guide our experiments in real time. If we should be doing things differently, we need to know now!

So feel free to drop by and see how we are getting on from time to time. Even better, if it looks like we are barking up the wrong tree, tell us!