Archive Science

And now for some science… the marvels of skin Siouxsie Wiles Jun 06

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Apologies for the lack of actual science posts recently. Let’s see if we can remedy that!

Last month I had the great privilege of interviewing skin cancer surgeon Dr Sharad Paul* for a session at the Auckland Writers Festival. We talked about his recent book Skin – A Biography, published in 2013 by Fourth Estate. Here’s what I found out:

Having skin is more important than having a brain!

Sharad is as enthusiastic about skin as I am about nasty microbes and makes this assertion based on the fact that there exist creatures that have done away with their brains but not their skin! Sea squirts are a group of bag-like marine filter feeders that are actually closely related to humans – they belong to the same phylum, Chordata, and start life out as a little tadpole like larvae with a primitive backbone called a notochord, which allows them to navigate in response to light. It’s what happens next though that’s quite amazing. The tadpole wiggles and twitches around until it settles headfirst onto a suitable surface. Next it cements itself to that surface and then starts to transform, losing it’s notochord, gills and twitching tail to become the ‘brainless’ bag of ‘skin’ that is an adult sea squirt. As Sharad put it, the sea squirt eats its own brain but has to keep its skin!

Picture of Halocynthia sp. taken by Yuri A. Zuyev, Hydrometeo. Univ., St. Petersburg - NOAA Photo Library.

Picture of Halocynthia sp. taken by Yuri A. Zuyev, Hydrometeo. Univ., St. Petersburg – NOAA Photo Library.

Skin colour is down to one single pigment – melanin

Melanin is the pigment that is responsible for producing all shades of all human skin colours and is found in our melanocytes. What I found fascinating is that regardless of skin colour, we all have the same number of melanocytes! That’s 10,000 for every square centimeter of skin (at least on our arms). The reason we humans come in different shades it that our melanocytes contain different amounts of melanin. In dark skinned people the melanin deposit in each melanocyte is huge, whereas those with white skin have lots of tiny little deposits. Sharad used the analogy of umbrellas to describe the melanin deposit in each melanocyte: people with black skin have the equivalent of a large solid umbrella whereas those with very pale white skin have an umbrella that is full of holes! This explains why those with very pale white skin freckle rather than tan.

Light-skinned early humans turned into dark skinned Africans to protect their folic acid

The last common ancestor humans and chimps shared 6 million years ago was light-skinned with dark hair. Apes in Africa are still like this whereas Africans are dark-skinned and relatively hair free. When our early ancestors started walking upright and lost their layer of hair, they needed to protect the folic acid in their skin from being broken down by the sun. Folic acid is important for normal neural tube function and a lack of folic acid can result in birth defects like spina bifida. This is why it is recommended that women take folic acid supplements during pregnancy. Melanin acts like a filter, preventing the penetrating UV light from damaging folic acid. Interestingly, spina bifida is much less common in Africa and the Tropics.

Humans who migrated out of Africa lightened to prevent rickets

When humans migrated out of Africa and into Europe 100,000 years ago, the shorter days meant that dark-skinned people would have likely have suffered from rickets due to a lack of vitamin D. Vitamin D is required for proper calcium absorption from the gut. Rickets causes skeletal and bone deformities and infertility so its likely that people’s skin lightened to allow better penetration of sunlight so they could produce sufficient vitamin D. This is supported by the fact that people who had a cereal-based diet low in vitamin D were lighter than those living at similar latitudes but who had a fish-based diet high in vitamin D. This also explains why Inuits are quite dark skinned, despite living somewhere with so little sunlight for such large parts of the year. Meanwhile back in Africa, black-skinned people were developing mechanisms which gave them higher levels of vitamin D to compensate. People in Tanzania have around 115 nmol/L of serum 25-hydroxyvitamin D, compared to 30-60 nmol/L for Westerners. Interestingly, Indian people tend to have very low levels of vitamin D, about half that of Westerners. Their darker skin colour emerged again to preserve folic acid as the lighter-skinned people moved out of Europe and into sunnier climates. Sharad says many Indians who move to New Zealand and Australia end up with vitamin D deficiency despite being exposed to plenty of sun.

Know your skin type and how quickly you will burn in the sun

How long you can safely spend out in the sun depends on three things: your skin type, the UV index and your sunscreen. In 1972 Thomas Fitzpatrick developed his scale for grading skin types: from the Celtic red-head who always burns and never tans (type I) to the black African skin that does not burn (type VI). The UV index was developed in the early 90′s by Canadian scientists and takes into account the thickness of the ozone layer, cloud cover and altitude. The scale originally went from 1 to 11 but it soon became apparent that scale wasn’t sufficient – New Zealand routinely sees a UV Index of 12 in summer while Western Australia has recorded a peak of 17! People with type I skin can spend 67 minutes/UV Index unprotected in the sun which would be less than 6 minutes in the NZ summer. For type II (usually blonde and blue-eyed) it is 100 minutes/UV Index, for type III (usually brown/black haired and brown-eyed) it is 200 minutes/UV Index and for type IV (Mediterranean, Spanish or lighter Indian skin) it is 300 minutes/UV Index.

Using factor 50 sunscreen is a bad idea!

Wearing sunscreen allows you to stay out in the sun longer but probably not for as long as you think! A sunscreen with a sun protection factor (spf) of 15 will block 93% of the UV falling on your skin allowing you to stay out in the sun 15 times longer, so about 75 minutes for the person with type I skin in an NZ summer. A sunscreen with an spf of 30 will block 97% of the UV giving you 2 and a half hours in the sun, while an spf of 50 will block 98% of the UV allowing you to stay in the sun for just over 4 hours. Sharad said the US Food and Drug Administration now inhibits sunscreens and cosmetics from claiming an spf of 50 as it gives users a false sense of security and means they end up spending much longer in the sun than they should.

I’ll finish with two of my favourite passages from Sharad’s book. This quote by Aristotle: “Touch is the one sense that the animal cannot do without. The other senses which it possesses are the means, not to its being, but to its well-being”, which I think is a lovely sentiment. And lastly: “skin wears its health for all to see – everything is unashamedly laid bare”. Nothing could be further from the truth as I approach the big four o!

About Dr Sharad Paul
*As a little background, Sharad (@DrSharadPaul) is skin cancer surgeon who runs a busy practice in Auckland where he offers free skin cancer checks. As well as having worked as a surgical consultant and GP, he also has a degree in medical law and ethics. In 2007 he pioneered a new skin graft technique which reduces costs, pain and healing time for patients and has also developed a range of skincare products designed for brown skin. He single-handedly brought Waitemata Health’s waiting times for skin cancer treatment down from a year to a month and won a Health Innovation Award for this in 2003.He also teaches at the University of Auckland and for one week a month at the University of Queensland in Brisbane. In 2012 Sharad was awarded the New Zealand Medical Association’s highest honour, the Chair’s Award which goes to an individual or organisation which has made a substantial contribution to the health of New Zealanders. He has also featured in Time magazine and was a finalist for New Zealander of the Year in 2012 – he lost out to Weta’s Sir Richard Taylor. He has also appeared at Goa’s THiNK festival alongside Robert De Niro and Bianca Jagger. To keep him sane he says, Sharad writes, and has had 3 novels published as well as his non-fiction book on skin. His love of literacy has seen him start his own book shops, first in Newmarket and then in Brisbane, and once a week he teaches creative writing in low decile schools around Auckland.

So you want to be a PI?! Siouxsie Wiles Jun 05

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David van Dijk, Ohad Manor and Lucas Carey have just published a paper in Current Biology (sadly it’s behind a paywall) in which they used papers listed in PubMed by over 25,000 scientists to determine whether becoming a principal investigator (PI) is predictable. They have showed that it is (at least for the cohort who first published between 1996 and 2000). Would you be surprised to find out that success depends on the number of publications and the impact factor of the journals those papers are published in? It does. The researchers have created a website so that anyone can calculate their likelihood of becoming a PI.

Read the Nature editorial here. Science also made their own prediction tool which you can play around with here.

And in keeping with the ‘science is sexist‘ theme, the researchers found that being male is also a positive predictor for becoming a PI. Their results suggest that, on average, having an identical publication record but being a woman lowers the chance of success by 7%.


Van Dijk, D., Manor, O. & Carey, L. B (2014). Publication metrics and success on the academic job market. Curr. Biol.

Why Science is Sexist Siouxsie Wiles Jun 05


Dr Nicola Gaston is a Senior Lecturer in the School of Chemical and Physical Sciences at Victoria University of Wellington and a Principal Investigator of the MacDiarmid Institute. Recently she gave a talk at the University of Auckland entitled ‘Why Science is Sexist’. The storify of the tweets from her talk are available here. The talk was also recorded so I’ll post a link to that when possible.

Much is made of the difference between the numbers of men and women in STEM careers, with calls for more role models to attract girls into STEM subjects at school and university. It’s certainly clear that more could be done for subjects like maths and physics, but what is happening in biology shows there is more to the problem than a lack of role models for girls. We have plenty of girls studying biology at undergraduate and PhD level. Hell, there are also plenty at postdoc level. But then it all starts to fall apart, with a dramatic drop in the number of women becoming group leaders and eventually professors. This ‘leaky pipeline’ as it is called is often blamed on women wanting to have babies and sabotaging their career for their husband.

I’m one of these women. I gave up a lectureship at an excellent university to move to New Zealand with my husband after our daughter was born. I got a Hercus Fellowship from the NZ Health Research Council and started again, trying to finish all the projects I had going in London while building a new lab in Auckland. It has been hard. Really hard. So hard, I wonder would I still do it with the benefit of hindsight. It doesn’t help that the research I do is expensive but grant success rates here are in the single digits. While I would probably now be an Associate Professor had I stayed in London, I still don’t even have a permanent job. But is it all my fault? I sometimes wonder.

Nicola talked about how she started to think more seriously about sexism in science when she was sent a flyer for a ‘Women in Leadership’ session aimed at scientists which included a 2 hour session on how to dress appropriately. It was held by a woman who hosted a show called ‘Does my bum look big in this’. Seriously. Between shit like that, the European Union’s disgraceful Science: its a girl thing video involving make up and high heels, and comments like that made by Employers & Manufacturers’ Association chief executive Alasdair Thompson who actually went on record as saying the gender pay gap can be explained by women taking more sick leave because of having periods, Nicola started to look at the literature more closely.

So what’s going on? Nicola thinks its a combination of four things:
1. Actual sexism
2. Imposter syndrome
3. Unconscious bias
4. Stereotype threat

While it is hard to do much about imposter system – that feeling many people get that they aren’t good enough and will be found out an ejected from the ‘club’ (I get this on a regular basis), dealing with unconscious bias is the one we need to be working on. The studies Nicola talked about paint a depressing picture in which women essentially have to have better CVs to be considered equivalent to men. And that’s when women are being assessed by men and women. We are all biased. Nature ran a feature on the issue of sexism in science if you want to read more about it.

Nicola’s message was clear. We need to be transparent about how decisions are made, and collect data so we can see how we are doing. We also need to distinguish between role models and mentors. They are not the same thing. While it is clear we need good female role models to get women into STEM*, they then need proper mentors to keep them there – and these mentors can be men and women. Finally, Nicola says we need to educate and train people on encountering unconscious bias. Studies show that bias can be removed if, for example, specific criteria are defined before CVs are evaluated.

Nicola ended on a thorny issue – should we be adopting a quota system in science, like is being done in business? On the one hand this will force the issue, but it is likely to stigmatise those women who fill the quota, leaving them open to whispers that they wouldn’t have got there on their own merit. But maybe it’s time to stop ‘leaning in’ and teaching our girls to be ‘resilient’, instead demanding quotas and ignoring the whispers. As Nicola said, our priority shouldn’t just be to make it equally possible for women to succeed in science, but equally easy. We’ve been waiting long enough for the old guard to die out and look where that has got us.

*Speaking of role models, how awesome is it that Lego are going to be releasing a female scientists minifigure set? Of the six designs submitted by by Alatariel Elensar in 2012, Lego have just announced that 3 are going into production, with a release date of this August. They will be the astronomer, paleontologist, and chemist. Woohoo! (Although I still think our idea for dual-faced minifigs would be better…)

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How much should NZ spend on science and what kind of science? YOUR input needed! Siouxsie Wiles Jun 03


Last week saw Science and Innovation Minister Steven Joyce release the National Statement on Scientific Investment, a lengthy document outlining how funding should be spent on science in NZ over the next decade. You can download the draft statement from here. The government have asked for feedback and we have until the 22nd August to give it.

If you are a scientist working in NZ, a student who wants to be a scientist in NZ or a Kiwi working overseas who wants to return to NZ in the next decade, I urge you to read the document and send feedback. This is the science funding system that we will inherit (if we survive..) and we have to engage NOW!

The government has seven objectives for it’s investment in science, which it lists as:
1. Producing excellent science of the highest quality; (this really should go without saying)
2. Ensuring value by focusing on relevant science with the highest potential for impact for the benefit of New Zealand; (Ah, politicians. Relevant science? Impact? By whose definition?!)
3. Committing to continue increasing investment over time; (Good to hear!)
4. Increasing focus on sectors of future need or growth; (Again, who defines this?)
5. Increasing the scale of industry-led research;
6. Continue to implement Vision Mᾱtauranga; (Wouldn’t have expected any less)
7. Strengthening and building international relationships to strengthen the capacity of our science system to benefit New Zealanders. (Most of us are pretty well connected)

In the Statement, science in NZ is divided into 3 categories (with current rough yearly investment) [SEE CHART 1, Page 14]:
1. Investigator-led science defined as science of which the value “can be significant but may not always be clear at the outset”; ($102M + some share of $300M PBRF)
2. Mission-led science defined as science which may require scale, or which business may not be incentivised to invest in; ($548M + remaining share of $300M PBRF)
3. Industry-led science in which the government sees it’s role as to “encourage” ($284M).

Those categories then allocate money using three different funding systems (with current rough yearly investment) [SEE CHART 1, Page 14]:
1. Contestable (Marsden Fund [$52M], Health Research Council [HRC, $77M], MBIE [$189M], Business R&D [$141M] and Primary Growth Partnership [$65M])
2. Collaborative (Centre’s of Research Excellence [CoREs, $50M], National Science Challenges [NSC, $127M])
3. Institutional (eg the Performance Based Research Fund [PBRF, $300M], the Crown Research Institutes [CRIs, $137M] and Callaghan Innovation [$78M])

The Statement goes through each funding scheme in turn, explaining what the government’s rationale is for the future of each scheme. The Table on Page 18 shows how the government proposes to allocate its investment for each scheme over the next decade. The NSC’s are the only scheme that the government proposes to increase spending on, from $46.6M in 2014/2015 to $79.6M in 2023/2024. Everything else either stays static or decreases.

Priority number 2 to “ensure value by focusing on relevant science with the highest potential for impact for the benefits of New Zealand” makes me nervous. It suggests that we are capable of predetermining which research will have the highest impact, whatever ‘impact’ may mean. Many huge changes come about through serendipitous findings, the precise opposite of focusing on ‘relevant’ science! Funding for such ‘blue skies research’ (mainly through the Marsden Fund) makes up less than 4% of our investment in science. With 1167 proposals to the Marsden Fund in 2013, there are clearly no lack of good ideas. But with only 109 of those proposals funded, what ‘next big thing’ could we have already missed out on?

The government also says that it wants to “attract, retain and developed talented researchers” and has allocated $11.6M a year for this, with $533,000 to be spent on sending graduates to the USA to do their Masters or PhD (Fullbrights), $8M for the Rutherford Discovery Fellows, $1M for the Rutherford Foundation and $700,000 for the James Cook Fellowships. This statement from page 69 is interesting:

“There is no consistent data on postdoctoral numbers in New Zealand although it is possible to point to an increase in the number of doctoral graduates in New Zealand.”

Does it sound to you like the government might be assuming that the increase in successful PhDs means we have more postdocs?! Unemployed, maybe!

From a personal point of view, the Statement provides much food for thought for my future career in New Zealand. It appears from Page 41 that much of the Health Research Council’s funding will be moved to focus on the topics of the three health-related National Science Challenges. As someone whose research area is specifically excluded from the NSCs, I’m left wondering how I am going to fund my research here and whether I’m going to be forced to move back overseas. The UK have just added averting the coming antibiotic resistance apocalypse as a priority area for the Biotechnology and Biological Sciences Research Council (BBSRC) and as one of the 6 challenges currently being voted on by the British public to become the focus of the $20M Longitude Prize 2014.

I guess the government’s response would be that I should change what I work on to align with their idea of “relevant” science. Apart from being a massive waste of the investment already poured into my career to date, I work in an area that without drastic action could see a massive change in our way of life in the next decade – the very time frame of the government’s Statement.

Science funding down under – a tale of opposites Siouxsie Wiles May 16


This week has seen budget announcements from both Australia and New Zealand and it is a story of opposites when it comes to science funding. The fabulous Keith Ng (@keith_ng) has produced a great dynamic infographic if you want to see where New Zealand is going to be spending it’s money and how this has changed from the previous budget.

Science in NZ is doing pretty well under the current government, even if the focus is skewed towards innovation and advances now, rather than the slow burn ‘outside the box’ stuff from which real game changers come. There has been a boost of NZ$58.6 million for contestable science funding, although the increase to the Marsden fund was not an increase in real terms.

The big surprise was the announcement of a further NZ$53 million over the next four years to support the Centre’s of Research Excellence (CoREs). Just last week the 6 new CoREs that will be funded for the next six years were announced. This new money isn’t to further support these 6 centres but to help establish another four. One of these will be a dedicated Māori Centre of Research Excellence, which is good news and important for New Zealand.

The three new CoREs will be funded from 2016 and this is where it gets interesting. In the recent contestable round to select the new CoREs, 27 applications were whittled down to a shortlist of 8 which included only three of the current CoREs and led to press releases from a couple of those left out in the cold, expressing their surprise and disappointment, including this one from Gravida, the National Centre for Growth and Development. There were even whispers of the decision being challenged.

Yesterday Steven Joyce announced that the three new CoREs will be selected through a closed tender of the remainder of the unsuccessful 21 applicants. This is curious. Why has the government not chosen to fund the 2 unfunded shortlisted applications, which went through a transparent, contestable process, and were selected for their excellence? Now suddenly everyone is back in the game, and that raises eyebrows. The science community is going to want the government and Tertiary Education Commission to be able to fully justify their choice of the next three CoREs. If the new CoREs plug huge gaps in the NZ science landscape, like the ‘One Health’ infectious diseases proposal or the Allan Wilson Centre, then we can see why this might be justified. However, if Gravida, which fits well with one of the National Science Challenges and has the government’s Chief Science Advisor Distinguished Professor Sir Peter Gluckman listed as one of it’s Principal Investigators, is one of the three funded then questions will be asked.

On the other side of the Tasman science funding has taken a hammering, although this was sweetened with the creation of a new AUS$20 billion Medical Research Future Fund. The Australian Renewable Energy Agency will be abolished saving AUS$1.3 billion, the Commonwealth Scientific and Industrial Research Organisation (CSIRO) will lose more than AUS$111.4 million, the Australian Research Council (ARC) will lose AUS$74.9 million, the Defense Science and Technology Organization will lose AUS$120 million, the Australian Nuclear Science and Technology Organization will lose AUS$27.6 million and the Australian Institute of Marine Sciences is down AUS$7.8 million.

The Medical Research Future Fund is a curious new beast. It will be made up of a $7 payment each time people go to the GP and will operate like a kind of investment trust. Once the fund reaches $20bn, the profits will go to fund medical research. John Pickering muses about what this fund might mean to NZ over on his blog. I find this proposal a very curious way to fund medical research. In essence what the Australians will be doing is ‘taxing’ the sick. While this might seem equitable to some, I think its very backwards thinking. If we think about those who got to the GP most, its the elderly and young kids. I would worry that this would stop those on limited incomes from going to the doctor when they need to, which in the long run could mean a bigger burden on health services as presumably potential health problems wouldn’t be caught as early.

The Australian governments attitude to science is perfectly summed up by this little gem in the budget: there is AUS$5 million for science in primary schools but a staggering AUS$245 million to put chaplains in schools! I’m lost for words.

Government announces new Centres of Research Excellence (CoREs) Siouxsie Wiles May 08


The NZ government today announced the country’s next Centres of Research Excellence (CoREs), who between them will receive just under $35 million per year for 6 years starting in January 2015. They are:

The Maurice Wilkins Centre for Molecular Biodiscovery, hosted by University of Auckland
MacDiarmid Institute for Advanced Materials and Nanotechnology, hosted by Victoria University of Wellington
The Medical Technologies CoRE, hosted by University of Auckland
The Dodd-Walls Centre for Photonic and Quantum Technologies, hosted by University of Otago
Te Pūnaha Matatini – The Centre for Complex Systems and Networks, hosted by University of Auckland
Brain Research New Zealand – Rangahau Roro Aotearoa, co-hosted by University of Otago and University of Auckland

The CoREs are funded through the Tertiary Education Commission and have at their heart the development of future capability by training the new generation of Kiwi scientists. They must also do excellent collaborative research of strategic importance to New Zealand.

The scheme was first established in 2001, with 5 CoREs funded in 2002 and a further 2 funded in 2003. These were refunded in 2006/7. In 2013, the government announced that there would be a further contestable funding round, in which existing CoREs would have to compete with applications to establish new CoREs. The details of the criteria for funding and the process are available here. According to this report, 27 applications were received and there were many raised eyebrows when four of the existing CoREs (Gravida: National Research Centre for Growth and Development, Ngā Pae o te Māramatanga – New Zealand’s Indigenous CoRE, the Bio-Protection Research Centre and the Riddet Institute) failed to make the shortlist of 8. There was even talk of some staging a revolt against the decision.

Of the 6 CoREs that have been successful in this funding round, two are existing CoREs (Maurice Wilkins Centre and MacDiarmid Institute) with the remaining four being new initiatives. In many ways this is great news for NZ science and clearly shows that new ideas and collaborative networks are forming all the time. Looking at the research areas covered by the new CoREs, they represent a very varied portfolio which has got to be a good thing for NZ. I am especially pleased to see the Maurice Wilkins Centre refunded given that infectious diseases have been locked out of the National Science Challenges.

There is also a clear message here that just because a CoRE has been funded and operated successfully in the past, this doesn’t mean that it should be funded ad infinitum. A difficult lesson for those existing CoREs who were unsuccessful. So is this decision the end of those networks? Gravida, which according to it’s website “seeks to reveal how conditions encountered in early life affect the way an individual grows and develops throughout life” seem to be very closely aligned with the ‘A better start/E tipu e rea’ National Science Challenge which will be receiving up to $34.7 million funding over the next 10 years. Likewise, Lincoln University’s Bio-Protection CoRE, whose website says it “focuses on finding innovative, natural and sustainable solutions to protect New Zealand’s plant-based, productive ecosystems from pests, diseases and weeds” seems well aligned to the ‘New Zealand’s Biological Heritage/ Ngā koiora tuku iho’ National Science Challenge, which will receive up to $63.7 million over the next 10 years to protect and manage our biodiversity, improve our biosecurity, and enhance our resilience to harmful organisms.

As for Ngā Pae o te Māramatanga, there must surely be support for ring-fenced funding to support research of relevance to Māori communities and to address disparities in Māori participation and success in tertiary education and research training which this CoRE has done so well.

The surprise in today’s announcement has to current CoRE, the Allan Wilson Centre for Molecular Ecology and Evolution hosted by Massey University, missing out on refunding. Many AWC researchers are international leaders in evolutionary biology, and have developed many excellent tools for data analysis. They have also been very active in communicating their science to the public and hosting many great public speakers on visits to New Zealand. AWC researchers are currently sequencing the genome of the tuatara*. They are hoping this project will aid efforts to conserve the species, so perhaps some of their activities fall under the ‘New Zealand’s Biological Heritage/ Ngā koiora tuku iho’ National Science Challenge too.

*Read David Winter’s excellent post on why we should care about sequencing the tuatara genome.

Conflict of interest statement: I am an Associate Investigator of the Maurice Wilkins Centre and have had a great deal of support from them over the past few years, for both my research, and some of my science communication activities, including my Art in the Dark project with Rebecca Klee and my firefly animation.

Life as we know it could end in ten years if we don’t start taking drastic action Siouxsie Wiles May 01


Life as we know it could end in ten years if we don’t start taking drastic action. This is the message to come out of a new report by the World Health Organisation (WHO), their first look at antibiotic resistance around the world. The report finds that antibiotic resistant superbugs are present in every region of the world and that many countries lack even the basic systems to track and monitor them. It also highlights that microbes responsible for gonorrhoea, urinary tract infections, pneumonia, bloodstream infections, infections in newborns and intensive-care unit patients are now resistant to the most effective antibiotics used to kill them.

“Without urgent, coordinated action by many stakeholders, the world is headed for a post-antibiotic era, in which common infections and minor injuries which have been treatable for decades can once again kill,” says Dr Keiji Fukuda, WHO’s Assistant Director-General for Health Security.

Alongside vaccines, antibiotics are arguably one of the most important discoveries in medical history. In antibiotics, humans are exploiting the weapons produced as part of an arms race that has existed between microbes for millennia. The first antibiotic was used to treat people in 1937 and not long after that we became aware of the other side of the microbial arms race – that microbes can become resistant to these wonder drugs. Resistance to penicillin was known before the antibiotic even came into use.

Latest estimates put the number of potential antibiotic resistance genes that exist at more than 20,000. But it doesn’t end there, microbes have crafty ways in which they can share resistance genes among themselves, and this has exacerbated the problem. It’s not just a case of each species of bacteria having to develop its own resistance mechanism each time they come into contact with an antibiotic. Instead, different species of bacteria can share the genes with each other.

The fact that antibiotics have been is use for over 80 years, and it is only now that the WHO have produced their first global report on the state of antibiotic resistance, shows just how much we underestimated the impact antibiotic resistance would have. The report highlights what microbiologists have been shouting for a while now, that a world without antibiotics is a scary place, and we are likely to be living in that world in as little as ten years.

The report has a clear call for action on a number of fronts. It urges individuals to only take antibiotics when necessary and to complete their course. It urges health workers and pharmacists to do all they can to prevent infection and to prescribe the right antibiotics only when they are really needed. It also urges policymakers to regulate and promote the appropriate use of antibiotics in medicine, veterinary practice and agriculture.

In addition to these measures, it is clear that we also need new antibiotics, more vaccines and novel ways to tackle infectious microbes and the WHO placed fostering research and developing new tools as a way that policymakers and industry can help. Earlier this year, the UK held a parliamentary review of antibiotic resistance and President Obama recently announced he was committing $30 million annually for the next five years to detect and prevent infections in the USA.

So what is New Zealand’s government doing? Apart from trying to tackle the country’s shocking rates of rheumatic fever, not a huge amount. The recent inter-institutional application to set up an infectious diseases Centre of Research Excellence (CoRE) didn’t make the shortlist and infectious diseases were specifically excluded from the three health-related National Science Challenges announced by the government last year. In a country with increasing rates of infectious diseases, if tackling these aren’t a national challenge, then I don’t know what is.

UPDATE: There’s been a fair bit of media interest in this story. If you are interested you can see a clip of me talking about the issue on NZ breakfast TV here. Some people seem to have taken the call for us to develop novel ways to kill microbes as a sign we should be investigating complementary/alternative ‘medicines’. In fact, after I appeared on TV I was sent a tweet sending me to psychosomatic healing website. Let me be clear, we need new antibiotics, vaccines and innovative strategies to stay ahead of this apocalypse, not hand waving, magic water and the like.

When I wrote the post, the WHO report was still under embargo so I couldn’t link to it. You can now read it here. They have also made a handy infographic: infographic-antimicrobial-resistance-20140430

Male researchers scare the sh*t out of laboratory mice! Siouxsie Wiles Apr 30

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According to this press release, researchers at McGill University in Montreal have discovered that the presence of a male researcher (or even his worn t-shirt) stresses laboratory mice and rats, the equivalent to making them swim for 3 minutes or restraining them in a tube for 15 minutes. The research has just been published in the journal Nature Methods (1), but its not available open access so I haven’t been able to read it yet.

A knock on effect of stress is a phenomenon called stress-induced analgesia – in other words, pain relief. Researchers injected the rodents ankles with a chemical which induces an inflammatory reaction, which should cause pain, and then measured the level of pain they were experiencing using the ‘grimace scale’ (2). This measures pain using things like the position of the animal’s ears and whiskers and how open their eyes are.

The researchers found that when the mice could smell a male researcher (or even bedding belonging to male guinea pigs, cats, dogs, and unfamiliar rodents) they had lower scores on the ‘grimace scale’, that is, they were experiencing pain relief. But the presence of female researchers produced no such response. The researchers also noted that the amount of poo the animals produced was also affected, with more produced when the male researchers were present.

I’m keen to read the paper and read the nitty gritty (how many different types of laboratory mice and rats they used, what ages, etc) but the results are very intriguing and could go some way to explain why it is difficult to reproduce some experiments from lab to lab. As the researchers say, at the very least this data suggests that the gender of the people handling the animals should be stated in the materials and methods sections of papers.

1. Sorge RE, et al (2014). Olfactory exposure to males, including men, causes stress and related analgesia in rodents. Nature Methods doi:10.1038/nmeth.2935
2. Langford DJ, et al (2010). Coding of facial expressions of pain in the laboratory mouse. Nature Methods. doi:10.1038/nmeth.1455

Monday Micro II – update on Ebola and MERS Siouxsie Wiles Apr 28

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A quickie to point to a paper in the New England Journal of Medicine which summarises the ongoing outbreak of Ebola in Guinea (1). Sequencing of the virus from several patients points to a new strain of Ebola Zaire, related but distinct from the strains which have caused previous outbreaks in the Democratic Republic of Conga and Gabon.

Figure 2 demonstrates the suspected chain of transmission for some of the cases and makes for sad reading. The index case is thought to be a 2 year old child who got sick on the 2nd December 2013 and died on the 6th of December. Their mother died on the 13th of December, their 3 year old sibling on the 29th and their grandmother on the 1st January 2014. The nurse and village midwife also died as did relatives and friends who attended the grandmother’s funeral.

As of the 22nd April, the World Health Organisation put the number of cases in Guinea at 208, including 136 deaths, while there have been 6 confirmed cases, including 6 deaths, and 2 probable and 26 suspected cases in neighbouring Liberia.

The World Health Organisation is also worried about the number of cases of Middle Eastern Respiratory Syndrome (MERS). Since April 2012 there have been 254 lab‐confirmed cases, with 93 deaths. Cases are mainly in the Middle East but have been reported in Europe, North Africa and Asia. As much as 75% of the recently reported cases appear to be as a result of human to human transmission and there have been a number of healthcare associated outbreaks, which is a worry. The Canadian Press reported a few days ago that the number of known infections has skyrocketed in recent days, with Saudi Arabia alone reporting 48 cases over a two day period last week.

1. Baize et al. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report. NEJM. DOI: 10.1056/NEJMoa1404505

Monday Micro – could microbes help our understanding of the evolution of language? Siouxsie Wiles Apr 28

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It seems far-fetched, but researchers are claiming that microbes could help us understand how language evolved, specifically combinatorial communication, in which two signals are used together to achieve an effect that is different to the sum of the effects of the component parts. Humans use combinatorial communication when we join words together to give a word with a new meaning. For example, when we hear the word ‘swordfish’, what springs to mind isn’t usually swords and random fishes but a swordfish. Despite the ease with which information can be conveyed using combinatorial communication, it has long been thought to be unique to humans and perhaps some other primates. Until now.

Swordfish or fish with sword?! Cartoon by Aaron Foster (@theGagaman)

Swordfish or fish with sword?! Cartoon by Aaron Foster (@theGagaman)

Research just published in the open access journal PLOS One shows that the bacterium Pseudomonas aeruginosa, also uses combinatorial communication, albeit in chemical form (1). P. aeruginosa is an opportunistic pathogen which can cause a number of nasty disease manifestations; chronic lung infections with P. aeruginosa are a leading cause of death for patients with the inherited genetic condition cystic fibrosis.

P. aeruginosa is known to use a form of communication called quorum sensing* in which the bacterium releases chemical signals which, when they reach a critical concentration, turn on particular genes. Thomas Scott-Phillips and colleagues looked at the different genes switched on in response to two of the bacterium’s quorum sensing molecules when applied individually and then in combination and found that the outcome fitted the definition of combinatorial communication – different genes were switched on when the quorum sensing signals were provided in combination, compared to either signal alone. The researchers conclude by saying that their data suggests that advanced cognitive abilities and large brains are not necessarily the reason why some species, such as Homo sapiens, have combinatorial communication systems while others don’t. In other words, our big brains don’t make us as special as we think!

*For a reminder of what quorum sensing is and how the Hawaiian bobtail squid makes us of it, watch the animation I made with graphic artist Luke Harris and his team:

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1. Scott-Phillips TC, Gurney J, Ivens A, Diggle SP, Popat R (2014) Combinatorial Communication in Bacteria: Implications for the Origins of Linguistic Generativity. PLoS ONE 9(4): e95929. doi:10.1371/journal.pone.0095929

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