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Monday Micro II – lockdowns, manslaughter and murder Siouxsie Wiles Sep 22

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The Ebola outbreak in west Africa continues. According to the CDC’s website, as of the 14th September the number of reported cases was up to 5,347 including 2,630 deaths. The virus is now in five countries. Here’s the latest:

Guinea (942 cases/601 deaths)

A team of health care workers, journalists and local officials have been reported to have been killed by villagers while on a drive to raise awareness of the symptoms of Ebola and how to seek help. Clearly suspicion that health care workers are spreading the disease is still widespread.

Sierra Leone (1673 cases/562 deaths)

Sierra Leone has been in lockdown since Friday with a three day curfew in place so that officials could try to get to grips with the numbers of people infected. There are reports of burial teams being attacked.

Liberia (2710 cases/1459 deaths)

There are reports that Liberia has run out of beds for all but the sickest Ebola patients and the healthcare system is collapsing.

Senegal (1 case/0 deaths)

So far there has been just one case of disease in Senegal, a Guinean man who was under surveillance for having had contact with an Ebola patient but who escaped by road to Dakar to stay with relatives. He arrived on the 20th of August and sought medical treatment on the 23rd when he started to have fever, diarrhoea, and vomiting. He was treated for malaria and went back to stay with his relatives. He was hospitalised on the 26th August and finally diagnosed with Ebola. Question is, how many family members and healthcare workers did he infect? The incubation period is almost up so we should know soon.

Nigeria (21 cases/8 deaths)

Ebola spread to Nigeria via American-Liberian Patrick Sawyer, who contracted Ebola from his sister and then travelled by air to Nigeria. He collapsed at the airport and died 5 days later. For a little while it looked like Nigeria might have managed to put a lid on Ebola, but human nature appears to have thwarted that. Nigeria’s Daily Post reports that a diplomat who contracted Ebola from Mr Sawyer, and survived, may be facing manslaughter charges. He evaded quarantine and travelled from Lagos to the city of Port Harcourt where he was secretly treated in his hotel room. The doctor who treated him contracted Ebola and has now died, but not before having contact with a lot of people while symptomatic.

Reading the WHO report, it sounds like he either didn’t know the diplomat he was treating had Ebola, or was in complete denial. Read this and weep:

After onset of symptoms, on 11 August, and until 13 August, the physician continued to treat patients at his private clinic, and operated on at least two. On 13 August, his symptoms worsened; he stayed at home and was hospitalized on 16 August. Prior to hospitalization, the physician had numerous contacts with the community, as relatives and friends visited his home to celebrate the birth of a baby. Once hospitalized, he again had numerous contacts with the community, as members of his church visited to perform a healing ritual said to involve the laying on of hands. During his 6 day period of hospitalization, he was attended by the majority of the hospital’s health care staff. On 21 August, he was taken to an ultrasound clinic, where 2 physicians performed an abdominal scan. He died the next day.The additional 2 confirmed cases are his wife, also a doctor, and a patient at the same hospital where he was treated. Additional staff at the hospital are undergoing tests. Given these multiple high-risk exposure opportunities, the outbreak of Ebola virus disease in Port Harcourt has the potential to grow larger and spread faster than the one in Lagos.

Several hundred people are now under surveillance so it’s a case of ‘watch this space’. Judging by the number of close contacts the doctor had with people while symptomatic, it’ll be amazing if there aren’t many more cases.

Skeptical Thoughts – gendered marketing Siouxsie Wiles Sep 22

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I’ve started a new radio slot called ‘Skeptical Thoughts’ on Sunday evenings on Graeme Hill’s Weekend Variety Show on Radio Live. A couple of weeks ago we talked about what a scam gendered marketing is – when companies repackage the same product and market it specifically for men or women, often charging different amounts. Australian show The Check Out did a great piece on the topic:

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Speaking of gendered marketing, Nanogirl and fellow Sciblogger Dr Michelle Dickinson tweeted this monstrosity (“for working men”) a few days ago:

mans hand sanitisor

WTF?! Perhaps unsurprisingly, Michelle’s tweet thanking Mitre 10 for removing the sexist product from their shelves was met with a cry of “PC gone mad” by some.

sexism

Which is sad, as it misses the point that products like that in places like a DIY store perpetuate the myth that women can’t do DIY and make women feel excluded. Also sad is the fact that tweet was from the CEO of a tech company.

*sigh*

Lighting up Wellington’s waterfront Siouxsie Wiles Aug 31

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For the last week, Wellington has been positively glowing thanks to the lux festival. This year I collaborated with artist Brittany Byrne to bring a touch of bioluminescence to the proceedings – rather appropriate given the genes that encode bacterial bioluminescence are known as the lux operon.

Previously Brittany created Nimbus – a work involving hundreds, if not thousands, of wooden pegs, suspended in the air and which made a very satisfying sound when touched.

Our piece was called Vibrio Nimbus, and from the outside looked like a boring old shipping containing.

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But on the inside, Nimbus’ wooden pegs had been replaced with hundreds of plastic conical tubes and the sonic nature of Brittany’s previous work exchanged for light, provided by trillions of glowing bacteria. When the tubes were gently jostled, they glowed a little brighter for a brief time, thanks to the little extra oxygen being supplied. Here’s a picture I took – Vibrio Nimbus was a bit like bringing one of Waitomo’s glow worm caves to the Wellington waterfront.

vibrio nimbus

A huge thanks has to go to the Bioluminescent Superbugs Lab and Una Ren for preparing all the media needed to keep Vibrio Nimbus glowing – the bacteria needed replacing with a fresh batch every other day. Brittany and her team became quite adept at growing microbes this week! And if you need reminding about the glowing Vibrio and where it is normally found, check out the Astrosquid animation below.

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Bacterial art in Melbourne – Market of the Mind Siouxsie Wiles Aug 25

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Let's make some bacterial art!

Let’s make some bacterial art!

This week I’ve had the pleasure of taking part in Australia’s National Science Week. My week started in Hobart, Tasmania, where I got to hang out with science communication superstars Carin Bondar, Derek Muller (AKA Veritasium) and Destin Sandlin (AKA Smarter Every Day), performing on stage with them at an event made possible by Science Alert.

After Hobart I traveled to Melbourne for a week of school talks followed by a weekend of fun getting people to draw in glowing bacteria, first at Market of the Mind and then at Living Science. The idea is that people draw a picture on a sheet of paper and then trace over their design onto a petri dish using a cotton swab and a solution of Vibrio fischeri, the bacterium that lives in symbiosis with the Hawaiian bobtail squid. When the bacteria have grown, I then take a photo of the glowing petri dishes and put the pictures up on flickr. You can see the pictures from Market of the Mind here.

And if you want to learn a little more about Vibrio fisheri and Euprymna scolopes watch the animation below or better yet get the beautiful book by Gregory Crocetti, Ailsa Wild and Aviva Hannah Reed.

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Yet another science metric – the Kardashian Index Siouxsie Wiles Aug 08

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Twitter exploded last week after Neil Hall, a professor at the University of Liverpool who studies the genomes of the parasites that cause malaria and sleeping sickness, published a (supposedly satirical) paper in the journal Genome Biology. Rather than read his paper, I recommend you read the annotated version. But first, here’s the abstract:

In the era of social media there are now many different ways that a scientist can build their public profile; the publication of high-quality scientific papers being just one. While social media is a valuable tool for outreach and the sharing of ideas, there is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices. To help quantify this, I propose the ‘Kardashian Index’, a measure of discrepancy between a scientist’s social media profile and publication record based on the direct comparison of numbers of citations and Twitter followers.

Ummm, communicating through social media is “gaining too high a value”?? That’s hilarious. In my experience, being active on social media is given no value by the majority of the establishment (ie silverbacks like Prof Hall). And as to citation indices being a “key metric of scientific value”? Of value to other academics maybe. But science is valuable outside of academia too, and citation indices will rarely capture that.

To calculate a scientist’s Kardashian Index (K-index), Prof Hall says we first need to calculate the number of twitter followers a particular scientist should have, using the following equation:

F= 43.3C^0.32 (Eq 1)

Where F is the number of twitter followers and C is the number of citations.

The K-index is then calculated using a second equation

K−index = F(a)/F(c) (Eq 2)

Where F(a) is the actual number of twitter followers the researcher has and F(c) is the number they “should” have given their citations.

As Prof Hall explains:

“…a high K-index is a warning to the community that researcher X may have built their public profile on shaky foundations, while a very low K-index suggests that a scientist is being undervalued. Here, I propose that those people whose K-index is greater than 5 can be considered ‘Science Kardashians’…”

Prof Hall did a “preliminary proof-of-concept study” using a “randomish selection of 40 scientists”. You can see how they scored in Figure 1 of his paper:

s13059-014-0424-0-1

Prof Hall goes on to conclude:

I propose that all scientists calculate their own K-index on an annual basis and include it in their Twitter profile. Not only does this help others decide how much weight they should give to someone’s 140 character wisdom, it can also be an incentive – if your K-index gets above 5, then it’s time to get off Twitter and write those papers.

Dr Michelle Dickinson, our very own Nanogirl worked out her K-Index and scored 35, the same as Prof Brian Cox. Both clearly need to get back to writing their papers.

There are so many things wrong with Prof Hall’s piece it’s hard to know where to begin. As I say, check out the great annotated version of his paper by Red Ink which points out some of them. Dr Kate Clancy has also written a nice post explaining why this bit of fun isn’t actually funny and Dr Keith Bradnam has turned it on its head suggesting the Tesla index as a measure of scientific isolation.

What really makes my blood boil about Prof Hall’s new index is that he named it after Kim Kardashian, who according to Wikipedia, is a reality TV star famous for being the daughter of OJ Simpson’s defense lawyer, a friend of wealthy socialite Paris Hilton and star of a sex tape. She is now a successful business women with several clotheslines and fragrances to her name and an estimated fortune of $45 million.

Ms Kardashian’s most recent venture is a smartphone game in which players have to build a career in Hollywood, accumulating wealth and fans. You have to give it to her. That lady has a sense of humour. Ms Kardashian is famous for being famous and not ashamed in the slightest. But she is hardly alone. In fact, she appears to be just one of a new breed of such celebrities.

That Prof Hall chose to name his index after a vacuous woman is a wonderful example of everyday sexism. Make no mistake, while Prof Hall’s piece is supposedly satirical, it is a snide swipe at those with a passion for communicating science using a derogatory association with a woman to do so. And he got his paper published in a peer reviewed journal where it will no doubt provide ammunition to those who already belittle the work science communicators do, all with a citation to back their bigotry.

The light at the end of the tunnel though was the #AlternativeScienceMetrics hashtag that was spawned on twitter, storified here by @mcdawg. Gems like these:

From @Protohedgehog: The Sean Bean index, measuring the number of times you write a great paper, only to have it killed by peer review

From @IanMulvany: the george Lucas index, how often a later paper totally invalidates earlier work that you did

From @OSIRISREx: The Viral Factor: how many times your research is misinterpreted into a factoid on a pop social media page

From @quicklyround: The Ulysses Factor – papers cited by everybody but that nobody has actually read to the end

From @LouWoodley: The Lindt Factor – the number of bars of chocolate needed to make the “minor revisions” requested

From @Koalha: Sacrificial efficiency: number of accepted papers / burnt out grad student

Jason McDermott discusses the pros and cons of some of them on his blog. Which would get your vote?!

Ebola outbreak – updates and links Siouxsie Wiles Aug 03

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As the Ebola outbreak worsens, the WHO has announced a US$100 million response plan to help bring the outbreak under control by scaling up control measures and helping neighbouring at-risk countries prepare for any cases.

According to the latest WHO update, between 24 and 27 July, a total of 122 new cases of Ebola and 57 deaths were reported from Guinea, Liberia, Nigeria, and Sierra Leone. This brings the number of cases up to 1323 with 729 deaths. Sadly, it would seem that healthcare workers are still becoming infected, with reports that Sierra Leone’s top Ebola doctor has died.

Ian Mackay is charting all the data from the WHO’s Ebola updates while the UK’s Channel 4 have made a clicable map of the outbreak here.

A scary development has been the death of a man in Nigeria – he arrived in Lagos by air via Lomé, Togo, and Accra, Ghana. The man was symptomatic when he arrived in Nigeria which means he would have been infectious at least on his last flight. Officials are now trying to trace all he may have come into contact with on his travels. According to the report, 59 contacts (15 from among the airport staff and 44 from the hospital) have been identified so far.

The fact the man was American, of Liberian decent, and due to return to his family in Minnesota has now put the Ebola outbreak firmly on the radar of the US press. There are also now reports that two infected US aid workers are going to be evacuated from Liberia for treatment in Atlanta.

There is a good article here looking at how easily infectious diseases spread on planes. The answer from simulations seems to be ‘not very’, suggesting only those in the few rows around the infected person are at risk. As Ebola is spread through bodily secretions, this would also mean the potential for transmission by touching surfaces also touched by someone infectious.

And finally, Daniel Bausch and Lara Schwarz speculate on why Guinea and why now in a paper just published in the open access journal PLOS Neglected Tropical Diseases. In an nutshell, it’s likely to be due to the movement of bats and poverty driving people further into remote areas looking for resources to survive. Add to that porous borders and impoverished and neglected healthcare systems and you get an outbreak of this magnitude.

The academic publishing scam – how much research funding are we losing to journal subscriptions? Siouxsie Wiles Aug 01

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Currently doing the rounds on twitter is this on the massive profits made by academic publishers:

profits

If you are in Australia or New Zealand and want to know how much is spent just on purchasing subscriptions to academic journals then there is a very handy tool on the Council of Australian University Librarians website.

In 2013 New Zealand’s universities spent $51,135,180 on journal subscriptions.

That’s just our universities, so doesn’t include our CRI’s or independent research institutes. $51,135,180 to access work funded by the tax payer published in pay-walled journals that rely on unpaid labour by university academics for peer review and editorial duties.

subs

To put that figure in perspective, the only funder of investigator-led blue-skies research in New Zealand, the Marsden Fund, awarded $59,000,000 in funding in 2013 – enough to fund 109 projects for 3 years.

In other words, we spend almost as much on buying access to research as we spend on blue-skies research.

I vote we scrap the subscriptions and use the money to double the Marsden Fund, giving each project an allocation to publish their results open access. Makes sense to me!

Hat/tip to Alex Holcombe (@ceptional) and Fabiana Kubke (@Kubke).

Monday Micro – west African Ebola outbreak now the deadliest in history Siouxsie Wiles Jul 21

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The Ebola outbreak that likely started in December 2013 with the death of a 2 year old child in Guéckédou, Guinea, has become the deadliest in history. The most recent report, almost a week old now, from the World Health Organisation puts the number of cases at 964 with 603 deaths. The outbreak has spread from Guinea to neighbouring Liberia and Sierra Leone; between the 8th and 12th of July alone there were 30 new cases and 13 deaths in Liberia and 49 new cases and 52 deaths in Sierra Leone.

EVD-outbreak (1)

Key to controlling the outbreak is stopping transmission. This means getting infected people into treatment centres, isolating those who have been in contact with anyone infected, and ensuring that everyone has the knowledge and equipment to protect themselves while looking after the infected and burying the dead.

Reporter Alex Crawford recently went to Liberia and showed the precautions people have to go take to ensure they don’t become infected – the donning of a vast amount of PPE – Personal Protective Equipment – which must be almost unbearable to wear in the heat of west Africa. You can watch her report below – although the part where they shove the camera in an infected nurse’s face and ask her how she is feeling is pretty distasteful. She is extremely ill with Ebola and has about a 30-40% chance of surviving, and if she does survive, will be stigmatised for life. How would you feel, Alex?!

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As an aside, it was disgusting to see Republican congressman Phil Gingrey suggest that migrant children arriving at the US’s southwestern border could introduce Ebola into America. Here’s an extract from the letter he wrote to the CDC:

“As you know, the United States is currently experiencing a crisis at our southern border. The
influx of families and unaccompanied children at the border poses many risks, including grave public health threats. …. reports of illegal migrants carrying deadly diseases such as swine flu, dengue fever, Ebola virus, and tuberculosis are particularly concerning. …..Reports have indicated that several border agents have contracted diseases through contact with the unaccompanied minors. As the unaccompanied children continue to be transported to shelters around the country on commercial airlines and other forms of transportation, I have serious concerns that the diseases carried by these children may begin to spread too rapidly to control. In fact, as you undoubtedly know, some of these diseases have no known cure.”

*sigh*

My previous Ebola FAQ can be found here.

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%.

*sigh*

Reference:
Van Dijk, D., Manor, O. & Carey, L. B (2014). Publication metrics and success on the academic job market. Curr. Biol. http://dx.doi.org/10.1016/j.cub.2014.04.039.

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