Archive Science

Tales from the Ivory Tower: when ‘Publish or Perish’ becomes ‘Publish & Perish’ Siouxsie Wiles Nov 30


A few days ago the UK media ran a story about the death of Prof Stefan Grimm, a professor of toxicology at Imperial College London. Prof Grimm was found dead in September, and anonymous colleagues are quoted as saying he had felt under increasing pressure by Imperial after a series of unsuccessful grants, and had been placed under performance review.

In academia we live by the mantra ‘Publish or Perish’. Publications are the currency on which jobs are won and lost, and we all know that if we fail to publish we will be unemployable*. The institution I work at has actually set metrics for the numbers of publications required for promotion. Hence the ‘perish’, although I’m not sure the person who coined that phrase meant for it to be taken literally. According to his profiles on Research Gate and Google Scholar, Prof Grimm had published a respectable 53 publications, 11 of them in the last 2 years, and had an h-index of 24. He had also published in a number of high impact journals which is very important to those who believe (mistakenly in my opinion) that the impact factor is a reliable measure of academic quality. My point is that Prof Grimm was publishing.

Research funding is another thing that my institution has set metrics for and I’m sure Imperial is no different. It seems like we are moving into the era of ‘Get Funded or Perish’.Many people outside of academia don’t know that we don’t just get handed a pot of money to carry out our research. Instead we spend a huge amount of time applying for funding. Purses are tight and competition is tough (and many reviewers and panels are unconsciously biased but that’s another story….). All around the world success rates have plummeted and many excellent applications go unfunded.

This year I have written 12 applications to support three different research projects in my lab. I have had the outcomes for 6 of them and they have all been rejected. I was lucky though. Last year I applied for nine grants, one of which was an Explorer grant from the Health Research Council of New Zealand. It’s an interesting new funding stream that awards relatively small amounts of money** at random to three or four of the applications that are deemed to meet the criteria for funding. My application was one of the lucky ones to be randomly selected for funding. The grant started in October and so one of the three projects I have been trying to fund can now progress. But the other two are stuck in limbo. Is there pressure on me to get those projects funded? I’ll let you know after I have my annual performance review early next year.

*Both this and the ‘Publish or Perish’ mentality leads to some interesting gaming of the system by some academics, slicing pieces of work into as many papers as can be squeezed out of it (we refer to this is as the ‘minimum publishable unit’…).

**Just $150,000 over 2 years (‘proper’ grants with full overheads are more like $300,000 PER year).

Skeptical Thoughts – acupuncture, Dr Oz & ‘aboriginal’ medicine Siouxsie Wiles Nov 26

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I now have a regular radio slot, called Skeptical Thoughts, with Graeme Hill on his RadioLive Weekend Variety Wireless show. Here are links to a few of my recent editions:

Here, I do my bit for Acupuncture Awareness Week (revealing my own sordid history with acupuncture), talked about Dr Oz’s bad week on Twitter and was disgusted by a story from Canada about a woman’s right to refuse to allow her child’s leukemia to be treated with chemotherapy in preference for ‘aboriginal’ medicine. Did you know high dose vitamin C was ‘aboriginal’? Me neither.

Here I talk about drinking bleach and a rather fantastic way of spotting ghosts.

Feedback welcomed, as are suggestions for future slots.

Monday Micro: Ebola update and NZ preparedness Siouxsie Wiles Nov 24


With Ebola now moving into Mali, I thought it was time for a quick update and some links. According to the CDC and WHO, as of the 16th November 2014 there have been an estimated 15145 cases, including 5420 deaths. Since the end of October there have been 6 cases in neighbouring Mali; all cases have died. American Dr Craig Spencer who had recently returned from working with Doctors Without Borders in Guinea came down with Ebola but survived and has been discharged from hospital.

What is NZ doing to prepare for an Ebola case?

Good question! The Goodfellow Unit at the University of Auckland recently ran an event for GPs and TV3′s Third Degree programme filmed an exercise with St John’s Ambulance transferring a suspected Ebola ‘patient’ to hospital. You can watch their piece here. [Disclaimer: they interviewed me too...].

Need a quick Ebola recap?

Check out the slides from a recent talk I gave in Christchurch. Most of the slides are in the form of infographics, so are pretty easy to understand without me to explain them. Or listen to Prof John Crump from the University of Otago explain to Graeme Hill how Ebola compares to other diseases in Africa on RadioLive here.

Naturopathy vs Science Siouxsie Wiles Nov 03


Today Wellington’s Dominion Post newspaper ran a piece of (in my opinion..) misleading propaganda they passed of as a cartoon which can be summed up as naturopathy vs science.

I assume it is in response to the bad press that homeopathy received last week after Green Party MP Steffan Browning signed a petition calling for the World Health Organisation to start using homeopathy to treat people in west Africa with Ebola. I had the pleasure of explaining what homeopathy is on breakfast TV.

Inspired by the fantastic @WieldARedPen on twitter, I fixed the cartoon. Enjoy!

Dom Post Naturopathy cartoon - Nov14a

Monday Micro – frozen poop pills! Siouxsie Wiles Oct 13


It’s still Monday so time for a very quick post about a paper just out in the Journal of the American Medical Association. I’ve blogged before about faecal transplants – giving a patient a dose of faeces from a healthy donor to resolve infection with the diarrhoea-causing bacteria Clostridium difficile.

One of the problems with faecal transplants is the way they are delivered – either by a tube through the nose and into the colon, or the more direct route of up the bum. Researchers at Massachusetts General Hospital in Boston have tried something a little more palatable. They took faecal material, blended it to make a suspension, removed all the particulate matter, added glycerol as a cryoprotectant and then froze it in small amounts inside of capsules that could withstand transit through the acidic environment of the stomach. If you are interested, apparently 48 grams of faecal matter makes 30 capsules.

Next the researchers gave the frozen poop capsules to 20 people with C. difficile infection. This involved patients fasting for 4 hours and then taking 15 capsules each day for 2 days. Nobody suffered any serious side effects and that 2 day course of frozen poop pills cured the diarrhoea of 14 of the 20 patients. Of the 6 people who didn’t respond, 4 of them got better after another course of the poop pills, giving an overall success rate of 90%. This is quite promising data, although the study was small and there was no placebo control group.

It will certainly make things easier if the poop needed for faecal transplants doesn’t need to be fresh, and people are definitely more likely to prefer popping pills to tubes up their noses!

Youngster et al. Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection. JAMA Preliminary Communication, October 11, 2014.

Monday Micro: glowing dog bones in Taranaki! Siouxsie Wiles Sep 29


glowing meat

From the Taranaki Daily News comes a story that is right up my street. Fiona Wallis gave her dog a bone and found it to be giving off an eerie blue light. What could it be? It’s most likely to be coming from bacteria so the questions people are likely to be asking are: what is it, is it dangerous, and how did it get on the dog bone?

What is it?

First off, its not radioactive! I think the light is most likely to be bioluminescence coming from a colony of glowing bacteria and there are many different species it could be. Almost all glowing bacteria live in water; there is only one well-documented species that lives on land. Of the species that live in water, the vast majority either live in or on fish and other creatures (like my favourite the Hawaiian bobtail squid). This will be the reason why you can sometimes see an eerie glow coming from fish if you’ve left it in the fridge for a few days.

The glowing bones in question had been packaged in salty water as one of its preservatives (also known as brine). This suggests to me that the bacteria is one that naturally lives in the sea, as they like high salt environments. An interesting feature of bioluminescence is that it is a chemical reaction that requires oxygen. This means that it won’t be possible to see light from the bones if they are in a sealed pack. But as soon as the package is opened and the bacteria get a whiff of oxygen…

I’ve made contact with the manager of the company that produced the product and he is getting samples to our lab so that we can isolate the bacteria and identify it, so watch this space.

Is it dangerous?

It’s highly unlikely. There are a couple of glowing bacterial species that produce toxins; the soil bacterium Photorhabdus luminescens produces toxins that kill insects, while some strains of Vibrio cholerae, the bacterium that causes cholera, glow. But it’s far more likely is that it is a harmless sea bacterium.

How did it get on the dog bone?

Once we know what the source of the glow is, we can start to figure out how it got on the dog bone. I know the company involved are working with their suppliers to find out exactly where everything came from. My guess would be that somewhere in the process, something has come into contact with either sea water or a product from the sea. Another case of watch this space.

UPDATE 29/09/14: Glowing bone has arrived!

This evening we received one of the glowing bones as well as an unopened packet from the same batch. The bone is indeed glowing (below is a picture from taken on our imaging machine) but it was the only one. None of the three bones in the unopened packet from the same batch number were glowing. We’ve swabbed both sets of bones and we’ll see whether any bacteria grow over the next few days.

photo 2

The threats of antibiotic resistant superbugs to New Zealand Siouxsie Wiles Sep 26

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In this week’s New Zealand Medical Journal is a paper by Deborah Williamson and Helen Heffernan on antimicrobial resistance in New Zealand (1). This comes hot on the heels of the WHO report which gave a global picture of antibiotic resistance (2), and highlights what the big challenges are for New Zealand.

So what are the antibiotic resistant superbugs that pose a risk to the health of New Zealanders?

According to the authors, there are four main superbugs we need to be watching:
1. Methicillin Resistant Staphylococcus aureus also known as MRSA
2. Extended-spectrum B lactamase (ESBL) producing Enterobacteriaceae, especially E. coli and Klebsiella pneumonia
3. Mycobacterium tuberculosis which causes the lung diseases tuberculosis (TB)
4. Neisseria gonorrhoeae which causes gonorrhoea

What are the key factors driving antibiotic resistance in New Zealand?

The authors highlight three main drivers which they believe are contributing to the problem:
1. The use and overuse of antibiotics in people and animals
2. Transmission of antibiotic resistant microbes in both the community and within healthcare facilities, including rest homes
3. Increasing globalisation – we are importing many of our antibiotic resistant superbugs from abroad

MRSA – a problem of our own making

Over the last few years there has been a huge increase in the number of skin and soft tissue infections caused by S. aureus in New Zealand. Alongside this, there has been a huge increase in prescriptions for a topical antibiotic called fusidic acid. As a consequence, one of the major clones of S. aureus now causing disease in New Zealand is an MRSA clone called AK3 which is resistant to fusidic acid (3).

Importation of resistant superbugs

Some of the superbugs of worry, notably extremely resistant strains of E. coli, K. pneumonia and M. tuberculosis are mainly being imported into New Zealand from countries like India, China and those in south-east Asia. This is going to be an area to watch, especially given the importance of countries like China for trade and tourism in New Zealand.

Gonorrhoea – the tip of the iceburg for sexually transmitted diseases

In New Zealand, sexually transmitted infections (with the exception of HIV) are not notifiable. This means that the data we have on these diseases is based on the voluntary provision of the numbers of diagnosed cases from laboratories and sexual health and family planning clinics. What’s crucial to this is that many people can have no symptoms, hiding the true burden of disease. Gonorrhoea is one of these. While most men will have symptoms when they have the disease, half of women can be asymptomatic. Importantly, untreated infection can lead to infertility in women.

In 2013 there were 3,334 cases of gonorrhoea in New Zealand (4). What is shocking is that 1,145 of these cases were in young people under the age of 19. In fact, there has been a 43% increase in the rate of gonorrhoea in 15–19 year old women between 2009 and 2013. Less than half of sexually active young people report using condoms (5) which goes some way to explaining why our rates are rising. If we end up with a completely untreatable strain of N. gonorrhoeae taking hold in New Zealand this could have a huge impact on our future fertility.

1. Williamson DA & Heffernan H (2014). The changing landscape of antibiotic resistance in New Zealand. New Zealand Medical Journal.
2. World Health Organisation (2014). Antimicrobial resistance: global report on surveillance 2014. ISBN: 978 92 4 156474 8.
3. Williamson DA et al (2014). High Usage of Topical Fusidic Acid and Rapid Clonal Expansion of Fusidic Acid-Resistant Staphylococcus aureus: A Cautionary Tale. Clin Infect Dis. pii: ciu658.
4. Sexually transmitted infections in New Zealand 2013. Institute of Environmental Science and Research Limited.
5. Clark TC et al (2013). Youth’12 Overview: The health and wellbeing of New Zealand secondary school students in 2012. Auckland, New Zealand: The University of Auckland.

Fighting antibiotic resistance: from Obama to TV3! Siouxsie Wiles Sep 25

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Ascomycetes“. Licensed under CC BY-SA 2.5 via Wikimedia Commons.

Last week President Obama signed an Executive Order aimed at combating antibiotic resistant superbugs. The order establishes a task force and a Presidential Advisory Committee which will look at how the US can implement a national strategy to deal with antibiotic resistance. The order covers areas such as surveillance, antibiotic use (now being called antibiotic stewardship) as well as promoting new and next generation antibiotics and diagnostics.

Speaking of which, Massey University’s Dr Heather Hendrickson and myself featured in a recent TV3 3rd Degree episode on antibiotic resistance in New Zealand, showcasing the work that we are doing in our labs. You can watch our clip from the episode here.

In my lab we are starting to collaborate with researchers at Landcare Research to screen the thousands of species of New Zealand and Pacific fungi that have never been mined for new antibiotics. We are currently writing lots of grants to try to get some money to support this work but if you’d like to help get started and are a New Zealand-based user of Facebook then please consider voting for our project for the People’s Choice Award for an AMP scholarship. And tell all your friends!

Monday Micro – artificial sweeteners & a dose of bad science Siouxsie Wiles Sep 22

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Sugarcubes” by PallboOwn work. Licensed under Public domain via Wikimedia Commons.

There has been quite a bit of coverage of a recent Nature paper reporting a link between artificial sweeteners and high blood glucose levels (1) – an important finding if true, as high blood glucose levels are a step towards insulin resistance and type 2 diabetes. The study was carried out mostly in mice and was found to be mediated by the gut microbes. The paper isn’t open access so you’ll need $32 to read it if you don’t have a subscription to Nature.

The authors report that consumption of artificial sweeteners changes the microbes present in the gut of mice (and 4 out of 7 healthy human volunteers), with some microbes becoming more abundant and others less so or disappearing altogether, and that this is correlated with a rise in blood glucose levels. The effect disappears when mice are treated with antibiotics. The effect can also be transferred to animals who haven’t been fed artificial sweeteners by giving those animals a faecal transplant from animals with the altered gut microbiome.

The researchers first tested the effect of giving groups of mice access to drinking water spiked with three different artificial sweeteners currently used by people: saccharin (marketed as ‘Sweet’N Low’ in the USA), sucralose (marketed as ‘Splenda’) and aspartame (marketed as ‘NutraSweet’ and ‘Canderel’). The results of the blood glucose tests in mice are shown in Figure 1b of their paper, reproduced below. Despite not being widely used as an artificial sweetener in processed food and drinks anymore, saccharin was the sweetener the researchers chose to do the rest of their studies with, including feeding it to their 7 healthy volunteers.

So why did the researchers choose saccharin for their studies?

Let’s take a closer look at Figure 1b. It’s a graph that shows the area under curve of the data for the blood glucose tests for the mice. The higher the value, the higher or more prolonged the blood glucose levels. Each individual symbol is the value for an individual animal.


The first three groups of animals are the controls – the first were fed plain water (black circles), the second sucrose (black triangles) and the third glucose (black squares). The sucrose and glucose groups are an attempt to control for the sweet taste of the water containing artificial sweetener. The next three groups (blue) are the animals that have been fed the artificial sweeteners: saccharin (blue circles), sucralose (blue squares) and aspartame (blue triangles). The red and grey groups have been fed different antibiotics to knock down their gut microbes in addition to being either control animals or having had the artificial sweeteners.

What is immediately obvious to me is that there are about 4-5 animals in the saccharin and sucralose groups who have very high area under curve values – they look quite different from the rest of the animals in their groups. I think we can call these outliers. That doesn’t mean the effect isn’t real – just that they might not be quite representative of the rest of their cohort. When looking at the data for the rest of the animals, and for the aspartame group, there is quite a lot of overlap between the control groups and the groups fed the artificial sweeteners. I’d love to have access to this data to reanalyse it because I’m surprised the groups are significantly different from the controls, especially for aspartame. But this does explain why they chose saccharin – it showed the biggest difference when compared to the controls.

So could something else be going on with the saccharin group?

One of the things the researchers did was put the animals in ‘metabolic cages’. This allows the researchers to monitor the food and drink intake of the animals as well as how active they are. In their paper the authors state:

“Metabolic profiling of normal-chow or HFD-fed mice in metabolic cages, including liquids and chow consumption, oxygen consumption, walking distance and energy expenditure, showed similar measures between NAS- and control-drinking mice (Extended Data Fig. 3 and 4.)”

Let’s have a look at Extended Data Fig. 3, shall we?

extended fig

“Similar measures”? It looks to me like the saccharin group (and glucose group) drank more and ate less than the other groups. The saccharin group also looked like they expended more energy. Hmmmm. I think ‘similar measures’ is stretching the truth a little.

I’d love to know what the reviewers said about this paper. There’s far too much cherry-picking in it for my liking.

1. Suez J, et al (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature doi:10.1038/nature13793

Monday Micro – from cat poo to kai moana! Siouxsie Wiles Sep 15


Hector's Dolphins at Porpoise Bay 1999 a cropped

Last week I attended a symposium hosted by Massey University’s Infectious Diseases Research Centre (IDReC). There were many fascinating talks but one that caught my attention was by Dr Wendi Roe, a veterinary pathologist, about her work on Hector’s dolphins.

Hector’s dolphins are an endangered species living off the coast of New Zealand. [A 2010/2011 survey found only 55 adults remaining. - Edit 17/9/14 oops, that's Maui's dolphins. There are about 6000 Hector's dolphins...] Dr Roe has been looking at causes of death in Hector’s dolphins and her results were surprising; 7 of the 28 she examined had evidence of extensive infection with the parasite Toxoplasma gondii (1).

If you need reminding, T. gondii is the parasite that makes mice lose their fear of cats, and has been associated with the development of schizophrenia, depression and suicide in people (2).

So how on earth are dolphins getting toxoplasmosis?! Dr Roe speculated that the parasite may be getting into the marine environment after being shed in cat poo. She is now wanting to do a study to see if the parasite can be found in filter feeders like mussels and from her pilot data it looks like the answer is yes. This isn’t the first evidence of marine animals being exposed to T. gondii – a survey of sea otters in California found that 42% had antibodies to T. gondii.

1. Roe WD, Howe L, Baker EJ, Burrows L, Hunter SA (2013). An atypical genotype of Toxoplasma gondii as a cause of mortality in Hector’s dolphins (Cephalorhynchus hectori). Vet Parasitol. 192(1-3):67-74. (doi: 10.1016/j.vetpar.2012.11.001)
2. Henriquez SA, Brett R, Alexander J, Pratt J, Roberts CW (2009). Neuropsychiatric Disease and Toxoplasma gondii Infection. Neuroimmunomodulation 16:122–133 (DOI: 10.1159/000180267)

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