Science Drinks #1: Proportion data; Zika; Stipends

Welcome to Science Drinks! This is a fortnightly meeting of folk in Biological and Environmental Sciences (BES) at the University of Stirling, which has taken place, at various times, in seminar rooms with cake, or in the pub with drinks. BES has plenty of lab meetings, seminars, and paper discussions in the department, so Science Drinks was started by Luc Bussière as a way of getting people together to chat about science in a more informal way. People come along and show their weird new data (often using air-graphs), enthuse about a cool new paper that no-one has read, grumble about/solve issues in academia, or discuss science news stories. I’m writing this up partly because Luc is away, partly as a reminder to myself about what gets talked about and partly in order to practice writing. Who knows though, maybe you (or even I!) may find something useful here one day…

Stuart Auld, Lilly Herridge, Frances Fraser-Reid and myself met in the Meadowpark pub. I had a shandy made with an unspecified ungulate-themed bitter from North Yorkshire. Um, anyway…

We began with Stu talking about some new data he’s grappling with in R. Stu’s running a cool long-term experiment looking at the epidemiology of Pasteuria infectious of the water flea Daphnia, more of which on Stu’s website. He’s got a bunch of mesocosms (large tubs buried in the ground!) in which he’s running the infections and he’s analysing data on how the proportion of infected Daphnia changes over time. As this is ecology though, the data aren’t behaving! He’s been analysing his data using ‘glmer’ in R, with the proportion infected and uninfected as the binomial response variable, which seems sensible, but has problems with overdispersion. Various solutions were discussed, including arcsine transformation, which has fallen out of favour recently, and that the data may be zero-inflated. Stu’s going to try a zero-inflated model in MCMCglmm and get back to us!

Daphnia_magna_infected_with_Pasteuria_ramosa
On the left is a happy Daphnia magna, with a brood pouch full of eggs. On the right is a sad and lonely Daphnia with an empty brood pouch- the consequence of infection with the dastardly Pasteuria ramosa! Pic from Wikimedia Commons.

Next, we discussed one of the big science stories of the week- the link between Zika virus and microcephaly in babies born in Brazil and other parts of South America. The virus has existed in humans for decades, apparently without significant effects, but infection in pregnant women has been linked to cases of neurological defects in their babies. The virus is spread by the mosquito Aedes aegypti, meaning that a very rapid spread of infection is possible and with no vaccine, the WHO has predicted several million cases of Zika infection in South America in the next year. We particularly discussed a recent report of a trial conducted by a British biotech company, which released sterilized male mosquitoes into an area of Brazil near Sao Paulo. Releasing sterile males reduces the reproductive rate of the mosquito population and since only female mosquitoes bite, could help prevent spread of the disease. They reported an 82% reduction in disease carrying mosquitoes. There was plenty of discussion about the impact of the sterile male technique more generally, the burden that caring for affected children may have upon countries in the Americas, and some cynicism about results from biotech companies…

Aedes_aegypti_during_blood_meal
A female Aedes aegypti mosquito having a lovely dinner for one. Probably not infected with Zika. Pic from Wikimedia Commons.

Thirdly, we discussed the funding of PhDs in the UK. A standard studentship provides a three-year stipend, yet the vast majority of people (mostly evolutionary biologists/ecologists) we know took longer than three years to finish their PhD. This means that many PhD students, as well as dealing with writing up their thesis and looking for a post-doc, are often haemorrhaging away their savings or working part-time. Some, like me, are lucky enough to get extra funding, while others, like Stu, write up having already begun a post-doc. There was a lot of debate about solutions to this, but in essence we all agreed that no-one in their right mind could think that this was a good system. Milder comments suggested that rigorous project management by supervisor and student could help people, while at the other end of the spectrum was the feeling that PhD students are taken for a massive ride and are essentially obliged to work for free. Certainly we all agreed that funding PhDs for four years and setting an absolute deadline at the end of this would be a good thing.

Finally, we talked about the best software for teaching statistics to undergraduates. Frances was shocked to hear that I’d never learned to use R until the start of my PhD (which is a shame, because I now do little else!). Having talked to many people about this, using a menu-driven program such as MiniTab or SPSS is better for teaching statistics because students don’t have to worry about coding, but R is more useful, flexible and free! So there’s a bit of a trade-off. I didn’t really see why R couldn’t be used to teach basic stats…but anyway, stomachs were rumbling, so we left it there.

We didn’t have time for the exciting paper about sex hormones and immune function which I’d brought along, but perhaps we’ll get to that next time…

 

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s