KNOWN AS THE ‘ABORTION PILL’ or RU486, the synthetic steroid mifepristone has had a long and controversial history in Australia. Available via prescription in many countries, the drug can terminate a pregnancy up to the first nine weeks. From the late 1990s, the drug was essentially banned in Australia. Then in 2006, overturning of the Harradine amendment in Parliament – an amendment that classed mifepristone as ‘restricted goods’ – meant the drug could be imported and used.

For six years doctors (including ourselves) used the authorised prescriber legislation of the Therapeutic Goods Administration (TGA) to import the drug for use in their own practices. Some 50,000 women were treated this way, with results consistent with overseas experience, namely that the drug is safe, effective and acceptable to most women.

Last month [March 2013], the Pharmaceutical Benefits Advisory Committee (PBAC) met to consider an application from not-for-profit pharmaceutical company MS Health (which has recently been licensed to market mifepristone nationally) to include mifepristone, and the misoprostol used with it, in the Pharmaceutical Benefits Scheme (PBS). If approved, the price of these drugs for consumers would be controlled and affordable for most Australian women.

There are strong arguments in favour of this move. There is now enormous worldwide experience of the drugs. They are on the World Health Organisation’s list of essential medicines. Having the drugs available on the PBS means they will potentially be accessible to women in rural and remote areas of Australia who have difficulty reaching surgical abortion services.

Until mid-2012, supplies of mifepristone were imported from Istar, a not-for-profit company formed by New Zealand doctors who themselves import the drug from France. We paid $60 for a single tablet of mifepristone, which is the dose required for a medical abortion, and charged patients this same sum. This represented a very small markup for the Kiwis, who put their profits back into education; the cost of the drug in the French public health system is less than 20 euros per tablet.

CURRENTLY, MS HEALTH have set the price of mifepristone in Australia at around $300 per tablet. Undoubtedly there have been significant costs involved in gaining TGA approval to market the drug nationally. MS Health are also required to closely monitor outcomes in the first 20,000 cases and report these to the TGA, as well as run an online training program for all doctors not already authorised prescribers or who have not had specialist training. They are also required to provide a 24-hour telephone helpline. It’s reasonable that the cost of these investments be recouped. But the drug’s high price makes it very difficult for many women to access, particularly those travelling from rural and remote areas. PBS approval is highly desirable to ensure equity of access for Australian women.

Members of the PBAC may also like to consider two certain consequences if the drug is not put on the PBS. One is the use of methotrexate for medical abortion. Methotrexate is a drug used for rheumatoid arthritis and psoriasis, among other things, and available on the PBS in Australia. It’s less effective and has more side effects than mifepristone but, appropriately prescribed by a registered medical practitioner, it is legal and safe, and no online learning program is required. It is also very cheap. If mifepristone remains inaccessible to many Australian women the use of methotrexate is likely to increase.

Secondly, there is undoubtedly some private import into Australia of drugs for medical abortion. Anecdotal reports of this are supported by the circumstances leading to the 2009 prosecution of the young Cairns couple who quite openly imported mifepristone for the woman’s use. Such import and use of drugs for abortion without medical supervision is risky and highly undesirable, but the history of abortion everywhere shows clearly that when women cannot access safe legal abortion they will seek less safe and less legal alternatives.

Typing ‘RU486’ into a search bar will within two clicks lead to an apparently reputable site providing an online medical consultation and a supply of the drugs needed for medical abortion, discreetly mailed.

Over the past six years Australian women have become increasingly aware that their sisters in many countries overseas have choices not always available in Australia when faced with an unplanned pregnancy. As with methotrexate, internet purchase of the drugs is likely to become more common if they are not accessible in Australia.

We eagerly await the decision of the PBAC.

Caroline de Costa is an author and professor of Obstetrics and Gynaecology at James Cook University School of Medicine. Mike Carrette is a gynaecology specialist working in Cairns, Queensland.

The post The cost of choice appeared first on COSMOS magazine.

My first full-time office job was with Cosmos Media; I started as a trepid grad in March 2008. Filled with highly educated, literary writers and designers from diverse backgrounds, the office teetered constantly on the edge of debate.

From the philosophy of knowledge and Plato’s allegory of the cave to whether one should limit their use of toilet paper for sustainability reasons, these good-humoured and passionate debates would explode at some point during the day and at 5:30pm would often continue out the door and down to the pub. If there is such a thing as the office lottery, I thought I’d won it.

The office was like this every day. Except Thursday.

Thursdays would begin like any other day: sporadic conversation would rock and lull about the office, like a sailboat at sea and in want of a breeze. A passing comment or a news story would begin to stir someone, a flicker of passion would cross their face.

But before any debate could begin, before any raised voices could echo though the stylish warehouse office in inner Sydney, someone or other would glare at the offender. “Shh!” they’d hiss. Our voices would drop and we’d all whisper to one another, ominously: “It’s newsletter day.” Back then, COSMOS Update was laboriously put together in a seemingly unending string of HTML, where a single interruption and lost train of thought could lead to a load of additional work.

Since its inception on 31 August 2006, COSMOS Update has been churned out every Thursday by the COSMOS online editor. And it is with sadness that today, its 324th issue, I will send the last one.

There are several reasons for this. Partly, we are seeing a changing digital landscape – where communications are rapidly shifting to social media and other platforms. In an era where even Facebook is increasingly passé, the future of digital media will not be found in email.

But I appreciate that some of you might still want to receive science updates through your email. I can recommend ABC Science Online’s Science Updates, which has a broad spread of science news from around the world as well as audio from ABC Radio National, the monthly CSIRO Snapshot which gives in-depth reports at the work done by Australia’s national science agency and the Australian Geographic Newsletter, which is more narrative-driven, magazine-style articles, and has a strong Australian slant.

Also, two weeks ago, big changes were announced at COSMOS. Two of the magazine’s four founders, CEO Kylie Ahern and Editor Wilson da Silva, sold their portion of the business to the other two founders, Alan Finkel, Melbourne entrepreneur and chancellor of Monash University, and Elizabeth Finkel, contributing editor and award-winning science writer. This will see several changes across the company, including moving operations to Melbourne. As we focus on a seamless transition, we needed to put time into other areas of production.

The COSMOS Update has seen a few twists and turns along the way. From 29 September 2007, the online editor wrote a mini-editorial for the Update, called In Focus. This was one of the most popular parts of the Update, and would eventually evolve into the blogs section of COSMOS Online. We used the Update’s editorial to discuss trends we were witnessing across science and science reporting, important developments in science, and, well, as a way to mouth off about a topic that we wouldn’t ordinarily publish in the magazine or on the website. Headline rules were relaxed and we had fun with them: “Sorry about the whole genocide thing” (Wilson da Silva, May 2011), “Congratulations, you survived Valentine’s Day” (Becky Crew, February 2012) and “The ‘C’ word” (Jacqui Hayes, 23 July 2010).

Most notable, though, was the fourfold increase in the number of subscribers after COSMOS Media ran Hello From Earth in August 2009. In an intense 13-day project, COSMOS collected messages from the public, which were then beamed to the nearest Earth-like planet by NASA. Many of the participants chose to receive the weekly COSMOS Update.

So to those who joined us in the beginning, those who joined us during Hello From Earth and those who joined us somewhere in between, thanks for coming on the journey with us. So long, and I hope to see you out there again, somewhere in the cosmos.

Jacqui Hayes
Digital Editor

The post A farewell to COSMOS Update appeared first on COSMOS magazine.

Confronted with conflicting reports, instant internet conspiracies, and a media clamouring for information, the world’s scientific community sprang into action.

The first task was the easiest: determining whether the two asteroids were somehow connected. 2012 DA14 was coming from the south: indeed, Australia was well placed to observe it in the early hours of Saturday morning.

In Chelyabinsk, all of the videos show the meteor entering Earth’s atmosphere to the left of the rising sun. This meant that its origin – often referred to as the event radiant – was in the northeast.

While the exact location of the radiant is difficult to pin down, there’s one thing of which we can be sure: the two asteroids were coming from different directions!

This is apart from the fact that 2012 DA14 was more than 500,000 kilometres away at the time of the Russian meteor. The chances of the two events being related are therefore next to zero.

The next and more difficult task was to estimate the Russian object’s size.

Here a lot of assumptions need to be made: in particular the angle of the meteor’s trajectory and the impact velocity. Without any meteor fragments, its composition could only be guessed (stony, since that’s what most of them are made of).

The biggest aids in determining the size were large number of videos taken including audio. Despite the uncertainty surrounding the location of those who took the videos, a group at the Sodankylä Geophysical Observatory estimated the size to be between 10 and 20 metres across.

Some hours later, on Friday evening US-time, NASA’s Asteroid and Comet Watch revised this to 17 metres. They estimated that the amount of energy released when the meteor exploded was around 30 times that of the nuclear bomb dropped on Hiroshima.

Thankfully the explosion occurred around 20-to-30km above Earth’s surface! And unlike a nuclear explosion, there will be no significant radiation effects.

Amid all the drama of shock waves, injuries and damaged buildings, 2012 DA14 sailed sedately by early on Saturday morning (Australian time). Amateur astronomers pointed their telescopes along its expected path and, sure enough, there it was.

Australian astronomers at the newly-reopened Siding Spring Observatory also turned the 3.9 metre Anglo-Australian Telescope to watch the asteroid at dusk (AEST) on Friday. Their resulting video (see below) is striking: in two and half minutes, 2012 DA14 travels approximately 1,200km through space.

As I commented on Friday, these two asteroids provide a stark reminder of how vulnerable we are and why we need to monitor the skies very closely for potentially larger objects.

The post Forensic astronomy: the Russian meteor and 2012 DA14 appeared first on COSMOS magazine.

Free and widespread access to scientific knowledge via the Internet will generate greater economic, social and environmental benefits. Credit: iStockphoto

IN THE OLD DAYS, pirates prowled sea-lanes stealing the cargoes of legitimate traders. Today, a new piracy prevails – and it applies to the thing most central to civilisation’s destiny: knowledge.

This issue was highlighted in February 2012 when more than 8,000 scientists protested against the restrictive behaviour of a leading scientific publishing house. Essentially, they objected to the big journals monopolising their published science, profiteering and imposing large fees and restrictions on public access to the science.

More than three quarters of the world’s science is funded by the general public, via taxes levied by national governments, and with the intention of generating public benefit. This makes the public the primary owner of research science. Yet scientific publishing houses and intellectual property (IP) ‘owners’ assert they have exclusive control over this new knowledge – and everyone else must pay them to see or use it.

Try downloading a scientific paper generated with public funding from a major science journal website. If you aren’t a subscriber, you’ll be asked to pay $30 or more to access science you already paid for with your taxes. The scientists who wrote the paper are asked to pay hundreds of dollars for its publication, which they will extract from their public grant money. So, today’s academic publisher stings the public both coming and going.

But there is a more serious issue at stake – and it stems from an important principle described by 18th-century jurist and philosopher Jeremy Bentham, who noted it was almost impossible for the public to access the law unless they first hired a lawyer. He argued that free access to the law was a basic liberty and that we all have a right to know the rules by which we are governed, without a middleman levying a hefty fee. The advent of the Internet has since made most important legal documents freely available worldwide.

Bentham’s reasoning applies equally to the issue of publicly funded science. Knowledge is a basic liberty and a right – not a private good. Historically, both the British Royal Society and Academie Francaise were founded on the principle of freely sharing scientific knowledge among humanity for the general good. This is a foundational ideal of science that is rapidly being prostituted and polluted in the great age of ‘free enterprise’.

Today, a host of middlemen – including publishers, lawyers, and the managements of universities and research institutions – are hard at work encroaching on the public’s right to science and taxing its access to new knowledge. Bluntly, this is a restraint of trade. The Open Science movement represents a nascent attempt by IT and biotech scientists to resist this negative trend.

As most scientific journals have small circulations and charge high fees, they constitute a hindrance to the free flow of publicly funded scientific knowledge in the age of the Internet. Knowledge vitally needed by human society to deal with disease, climate change, poverty, safety, biodiversity loss, contamination, hunger and so on – that could save and improve billions of lives, accelerate global economic growth and enhance sustainability – is being locked up and privately exploited. Much of it is being wasted.

More than any other single element, knowledge defines the prosperity and progress of society. And so it follows that the more obstacles, levies and rip-offs you impose on knowledge, the less effectively it will disseminate, the fewer benefits it will generate and the longer it will take to be applied. This injures the interests of society and reduces the value of the public investment in science.
Superficially, the piracy of science may appear to be simply a fresh case of private greed triumphing over public good, of the same ilk that gave us the global financial crisis. Most academic publishers, IP lawyers and universities will object to this characterisation, claiming that giving them private control of knowledge allows them to see it is commercialised and applied. This is an argument rooted in vested interest and with scant supporting evidence.

It entirely ignores the alternative view: that free and widespread access to scientific knowledge via the Internet will generate greater economic, social and environmental benefits – especially in poorer countries – for all of humankind and the planet we inhabit. This was illustrated by the Green Revolution that freely distributed advanced agricultural know-how worldwide, laying a foundation for the modern economic miracles of China and India.

It is the contemporary model of science publishing and IP management that is sick – not the act of publication itself. For the sake of humanity facing a challenging and dangerous future, it needs to change.

The post The piracy of science appeared first on COSMOS magazine.

Credit: iStockphoto

IN 1995, THE U.S. Office of Research Integrity, which investigates allegations of fraud in federally funded research, found that Weishui Y. Weiser, at one point a researcher at Harvard University, Boston, had faked data. As part of an agreement with the agency, Weiser said she would retract three papers.

She retracted one in 1997. But the other two, both published in the Journal of Immunology, were retracted just last month, 17 years after the agreement. In those 17 years, Weiser’s two papers were cited 78 times by other researchers – which shows just how much fraudulent work can corrupt scientific literature.

Why didn’t anyone act sooner? When I asked the journal’s editor, for a post on Retraction Watch, the blog I co-founded, he wouldn’t say, simply referring me to the retraction notice. I also spoke to one of the scientists who signed one of the notices, who said he really wasn’t sure why the retraction was published now, as opposed to 10 years ago, or even more.

But another author, Eddy Liew of the University of Glasgow, gave what may have been an unintentionally honest answer: “This is due to the value of organisations like yours.”

It’s unclear whether Liew was complimenting us or making a dig. But, whatever he meant, it’s clear that a number of blogs – Retraction Watch is just one – are forcing scientists, journals and institutions to get serious about correcting the scientific record when misconduct is exposed, a goal they have often paid lip service to in the past. Some have only acted after anonymous bloggers pointed out glaring examples of image fraud. And other journals have even cited Retraction Watch in their retraction notices.

Some members of the scientific community are acting on their own, as they always have. There’s Steven Shafer, the editor of a journal on anaesthesia, who rightfully pressured German and Japanese institutions to investigate authors. These institutions should become the current and recently deposed retraction record holders, with 88 and 172 likely apiece.

Those big numbers reflect a clear trend: retractions are on the rise – 2011 was a record year, with about 400. The annual incidence of retractions is 10 times higher now than it was a decade ago, as Nature has reported, based on Thomson Reuters data, far outpacing the 44% increase in published papers.

There are a number of possible reasons for the increase. One is that we’re simply better at picking up misconduct. Plagiarism software can find duplication, for example, and the availability of papers online means more eyeballs. But more concerning is that there may simply be more fraud, as argued convincingly by Ferric Fang, editor of Infection and Immunity.

That there are fraudsters in a human endeavour is not surprising. But science prides itself on being self-correcting and our experience at Retraction Watch tells us many scientists aren’t particularly interested in exposing malfeasance in their midst. These are the scientists who find reasons to ignore whistleblowers, journal editors who publish mealy-mouthed or opaque retraction notices, and institutions that refuse to reveal the findings of their misconduct investigations.

We often hear that scientists are afraid to retract papers or say too much about misconduct because it will decrease trust in science at a time when the enterprise feels under attack by global warming sceptics and others. If politicians think there’s a lot of fraud in science, they’ll fund it even less than they already do. But this superficial logic misses the point. I’ve pointed out elsewhere, the real foundation of mistrust is a ‘nothing to see here’ attitude built upon by well-publicised incidents that insiders tried to cover up.

Waiting 17 years for an official notice of retraction feels more like a cover-up than a good-faith effort to correct the literature. And it’s consistent with too many other examples of stubbornness that seem more concerned with advancing careers than furthering knowledge honestly and efficiently. Scientists rail against this lack of transparency in politics. So, why should they expect us to put up with it in science?

The post Failure is an option appeared first on COSMOS magazine.

Credit: iStockphoto

SYDNEY: New species of humans, colonising the Moon and our obsession with non-Homo sapiens couplings – these are the most read opinion pieces on COSMOS Online in 2012.

COULD THE RED DEER CAVE PEOPLE BE A NEW SPECIES?
~ by Darren Curnoe
The fossilised remains of an ancient human-like species have been found in southwest China. Do these Red Deer Cave people belong to our species, or a previously unknown species? Co-lead researcher Darren Curnoe explains.

CAN WE COLONISE THE MOON?
~ by Leonhard Bernold
An outpost on the Moon would offer incredible opportunities for scientific advancement and cooperation. But do we have the technological know-how to make it happen? Leonhard Bernold looks at the challenges ahead.

CELEBRATING YOUR REASON
~ by Lawrence Krauss
Being Atheist doesn’t have to mean that someone misses out on being part of a group, or celebrating the wonder in the world.

SPLITTING THE SKA: WHY IT’S GOOD TO SHARE
~ by Bryan Gaensler
The decision to share the SKA between South Africa and Australia/NZ is a positive sign of our nations’ priorities, says Bryan Gaensler.

GOLDEN AGE OF GEOLOGY
~ by Iain Stewart
The 21st century could be a golden age for geology – but geologists will first need to work on their communication skills for that to be recognised.

OUT OF THE DARK
~ by Lawrence Krauss
Physics has drastically altered our picture of reality, and continues to throw us some curve balls.

TWO SIDES OF THE SAME COIN
~ by Matthew Bailes
From astrophysics to genetics, all published scientific research is subject to rigorous challenge by other scientists, scrutinised for errors and the evidence tested. So why are some disciplines treated differently, asks Matthew Bailes.

SEX, SCIENCE AND THE MEDIA
~ by Paul Livingston
Sex sells, and it seems nothing escapes the media’s attention. Not even jargon-loaded scientific papers on non-Homo sapiens couplings.

SECURING THE FUTURE OF THE GREAT BARRIER REEF
~ by Terry Hughes
The economic and cultural worth of the Great Barrier Reef far outweighs short-term gains from poorly regulated coastal development and coal mining.

INNOVATIVE, ENTREPRENEURIAL THINKING VITAL FOR AUSTRALIANS
~ by Alan Finkel
Australians are worse at innovation than discovery by a factor of six, and this is something we have to address.

MILITARY RESEARCH: WHY THE CUTS MATTER
~ by Hamza Bendemra
As military-backed research around the world is being cut back, Hamza Bendemra argues that war can be a powerful driver for innovation, but we need to address the lack of transparency that goes with it.

NO, YOU’RE NOT ENTITLED TO YOUR OPINION
~ by Patrick Stokes
The problem with “I’m entitled to my opinion” is that, all too often, it’s used to shelter beliefs that should have been abandoned.

The post Most read opinion pieces of 2012 appeared first on COSMOS magazine.

Credit: iStockphoto

You’ve probably heard the ‘boiling frog’ anecdote, based on 19th-century experiments: if a cold-blooded frog is dropped in boiling water, it will jump out; but if it is placed in cold water that’s slowly heated, it won’t perceive the danger and will, ultimately, be stewed to death.

It’s often used as a metaphor for our inability to react to momentous changes that occur gradually. But we now know, thanks to modern biologists, that it isn’t true: frogs detect the danger and escape before it’s too late.

Another version of this experiment is under way, but on a much larger scale, and on a different species: humans. And the medium isn’t a saucepan of water, but the oceans, the lands and the atmosphere of our entire planet: it’s global warming.

And the question is: are we as clever as frogs?

In July 2005, the Australian Government released a report entitled Climate Change Risk and Vulnerability. It outlined a disturbing future for Australia, with more frequent and more severe droughts and floods; more severe storms and cyclones along the eastern seaboard, with storm surges amplified by rising sea levels; remote northern communities facing depopulation, and even some towns “at risk” of being unliveable.

These changes would occur “over the next 30 to 50 years irrespective of global or local efforts to reduce greenhouse emissions,” it said.

In my foreword to a themed issue on climate change in September 2005, I concluded: “Climate change is no longer a topic of debate, it’s something you prepare for – like your retirement, or paying off a house, or planning a big overseas trip.”

Our special issue was based on the best science available at the time, but the future it forecast seemed strange and unbelievable.

I added a comment from environmentalist Tim Flannery that I felt was justified by the evidence, although I feared it would be seen as exaggerated, that there’s “a real possibility that within a century, some cities in Australia will fail and be abandoned. It’s likely that large numbers of people will perish the world over as the changing climate plays havoc with crops, rainfall and sea levels, or as freakish weather intensifies and natural disasters like cyclones become more common and more ferocious.”

On the day that issue hit newsstands, Hurricane Katrina struck New Orleans. The world watched in horror as bodies floated along flooded streets, people fought each other for food and shelter in cramped stadiums, overwhelmed police abandoned their posts, and buildings were smashed as if made of matchsticks.

Within three days, New Orleans – one of the world’s unique cities and the birthplace of jazz – fell to its knees, and officials called for residents to leave. The toll: 1,833 dead and US$100 billion in damage.

In October 2005, I wrote: “The fall of New Orleans is a warning: it shows us how quickly our proud cities – seemingly powerful and resilient – can buckle in the face of Nature’s onslaught. How quickly our technologies fail and our intricate networks and vast resources can nevertheless be overwhelmed.”

Seven years later, Hurricane Sandy struck several Caribbean countries and later, winding down into an enormous superstorm, numerous U.S. states. It hit New York on October 29.

At dawn the day after, one of the world’s wealthiest and best known cities was crippled: streets flooded, half of Manhattan was without power, and the subway – relied on by more than five million people every day – was under water. All of this in the last week of a hard-fought national U.S. election where climate change was hardly, if at all, mentioned by political parties.

New York Governor Andrew Cuomo, a Democrat, broke the political silence: “Anyone who says there is not a change in weather patterns is denying reality… part of learning from this is the recognition that climate change is a reality, extreme weather is a reality, it is a reality that we are vulnerable.”

He added, “It is not prudent to sit here… and say it’s not going to happen again.”

Did global warming cause Sandy? No: climate change does not create storms; but it was likely a performance enhancer, turning Sandy from appalling to horrific.

Did global warming make Sandy worse? Yes: the storm flung the sea onto the northeast U.S. coast, and because of warming, there’s 15–20cm more ocean there to fling.

If such instant destruction can happen to a rich and iconic city in a powerful nation, what of the hundreds of cities that may be battered – again and again – as freakish weather becomes commonplace and storms more violent?

Scientists have been warning us that this is the kind of world we can expect by 2030 or 2040; but what if it’s already here?

The post You have been warned appeared first on COSMOS magazine.

The rise of antibiotic-resistant 'superbugs' in and around health care facilities can be alarming, but there is a budding field dedicated to tracking superbugs back to their source using genomics. Credit: iStockphoto

In the U.S. alone, 100,000 deaths annually are attributed to infections acquired at health care facilities such as hospitals, medical centres and nursing homes. In Australia, a 2008 study in Australia found that there were 180,000 hospital-acquired infections, and these occupied nearly two million bed-days. These deadly infections are cause for serious concern when they spread through health care facilities, but are downright alarming when they spread beyond the borders and into the local population. The current procedures put in place at hospitals – isolation of patients, protective clothing, vigilant hand-washing, using disinfectant – are not enough, and needs to keep pace with modern technology.

High-throughput genome sequencing technologies were used to determine the DNA sequence (the order of nucleotide bases that make up the genetic code) of the human genome. This technology has also been used to investigate the DNA sequence of multiple microorganisms capable of causing human disease. With improved and faster sequencing technologies, we are on the verge of genomics impacting on clinical epidemiology that is undertaken in hospitals. This new field of microbial research, ‘genomic epidemiology’, may be defined as the application of whole genome sequencing to monitor infection transmission in the clinical setting. While many hurdles remain, recent studies have proven that the technology now is available to significantly impact the way hospital-acquired or nosocomial infections are tracked.

The advantage of this technology, in comparison to pre-existing standard operating procedures used in clinical service laboratories, is that genome analysis can be used to compare microorganisms down to the last nucleotide. In our own work in New South Wales, Australia, with the human pathogen Streptococcus pyogenes, closely related isolates may vary by only 50 or 60 nucleotides across a 2 million nucleotide bacterial genome. Thus, genomic technology can determine whether a patient has been infected with a different bug that is nonetheless closely related (i.e. 50-60 nucleotide differences) versus the identical bug (0 nucleotide differences). These small differences have large consequences. If multiple patients are infected with the identical bug, it suggests a breakdown in clinical practice. This can be addressed to prevent further transmission by sterilisation of surfaces, treatment of patients, treatment of patient contacts, and treatment of potential carriers of the infection. It has not previously been possible to figure out whether patients had been infected with the same bug due to a breakdown in patient management practices, or alternatively closely related bugs, that happen to cause otherwise unrelated infections.

Several groups, including our own, have separately reported the use of genomic epidemiology research in the scientific literature. An outbreak of antibiotic-resistant Klebsiella pneumoniae bacteria was tracked at the U.S. National Institutes of Heath Clinical Center, in Maryland. Eleven patients died during this outbreak, but the application of genomic epidemiology allowed the identification of the source of the infection, and also identified a contaminated ventilator that may also have been a potential source of infection. In a report out of Cambridge, England, an MRSA ‘Golden Staph outbreak was investigated in a neonatal hospital ward. Genomic epidemiology was able to identify an attending hospital staff member who was a carrier of the MRSA bug, precipitating the control of the outbreak by the treatment of the carrier.

In our own recent study, we investigated a possible outbreak of Streptococcus pyogenes in nine patients using genomic epidemiology. Four of the isolates could not be differentiated by standard techniques, but genomics confirmed that three of the isolates were identical across the entire genome. This suggested a single case of patient-to-patient, or staff-to-patient transmission, but ruled out an outbreak scenario.

Genomic epidemiology must overcome several hurdles before it becomes a standard practice in hospital and patient care settings. The first hurdle is cost – the cost of the equipment, the cost of reagents to undertake sequencing, and the cost of employing trained staff to undertake these analyses. Reagent costs are coming down all the time, and will come down further – it now costs a few hundred dollars to sequence a bacterial genome. The second hurdle is time – the bug must currently be cultured, which can take anywhere between one day for fast growing bugs to several weeks for slow growers such as Mycobacterium tuberculosis. Many bugs cannot be cultured on media at all, or only with great difficulty. Sequencing can take less than a day, or a much longer time period, depending on the technology and equipment used. Metagenomic approaches, the sequencing of human samples directly without bacterial culture, may eventually circumvent much of this the time hurdle in the future. The third hurdle is expertise – hospital clinical services are not set up to undertake genomic epidemiology, and there is a major bottleneck in the analysis of genomic data (bioinformatics).

Despite these hurdles, the rapid progress that has been made in improving our capacity to generate and analyse genome sequence information will continue, and the hurdles described above will be overcome. Genomic epidemiology technology will prove a useful tool in the prevention of transmission of microbial infections with hospitals and health care facilities, and will lead to better health outcomes in the near future.

The post Tracking superbugs to their source appeared first on COSMOS magazine.

European red foxes may be on the verge of becoming established irreversibly in Tasmania, and a massive up-scaling of the eradication program is needed to stop the invasion. Credit: iStockphoto

Many Australians were deeply alarmed by the unusual transmissible cancer spreading through populations of the Tasmanian devil. Not only is the iconic devil linked to cinema heroes Errol Flynn and Walt Disney, but it is also a top predator in an ecosystem that includes many species that are either extinct or rare on the mainland. Indeed, the devil was formerly a mainland species, as was the now extinct Tasmanian tiger.

The loss of the devil, a top predator, is likely to have significant flow-on effects through the network of species with which it either competes with or predates upon. The government and research response to the appearance of the facial tumour disease has been swift, focused and impressive with quality science seemingly matched with an educated debate and widespread public support.

As devil populations decline, there has been growing evidence of European red foxes (Vulpes vulpes) on the island – ever since a fox was seen leaving a container ship docked at the port of Burnie, in northwest Tasmania, in 1998. The evidence for foxes now includes more than 2,000 sightings, four road kills, and DNA evidence from predator faecal material and even blood. Evidence points to a series of isolated introductions, but the populations have not yet become fully established.

Foxes represent a major threat to Australia’s last, relatively intact vertebrate communities, yet their presence and the threat they pose is little known outside of the island state, and their eradication a topic of ongoing controversy within the Tasmanian community. Foxes are a top predator in many ecosystems, and the introduction of foxes to the Australian mainland has been linked with the contraction in range of many taxa and the extinction of over 20 species of mammal. Should the fox become established in Tasmania, are some 78 vertebrate species would be at risk, not to mention impacts on agricultural production, so its presence is a matter of grave concern.

The Tasmanian government recognised this threat by establishing the Fox Free Tasmania Taskforce (later to become the Fox Eradication Program) in 2001, and charging it with the responsibility of assessing the extent of the problem and then overseeing the eradication. That program has continued uninterrupted since then, but amid much local public debate and with closure threatened at least once. A quick search for ‘fox’ on blogs and forums, such as the Tasmanian Times, will give you a feel for how such online forums can generate opposition on this topic, much of which revolves around skepticism about even the presence of foxes.

The source of the controversy (and much misunderstanding) concerning the program to eradicate foxes are difficult to isolate, yet the contrast between the early engagement of the academic community around the two problems (devil decline and fox introduction) is stark. I think the difference lies, at least in part, in the nature of the two problems. The first involves clear, definable, biologically interesting questions about a problem that is immediately and clinically obvious. The second, although superficially simple – Where are foxes and how do we kill them? – is much harder to define and study because in this case the animal is rare, highly cryptic and very difficult to detect. While, ecologically, fox eradication represents considerable challenges, it seems at times that dealing with sparse data is more like a challenge for detectives than for scientists. Yet the need for good science is overwhelming. Much revolves around how to distinguish between true and false occurrences of individuals at any given location while research is critical to determining how all free-living foxes can be placed at risk of early death via control operations.

Invasions into new and vulnerable ecosystems by species that are likely to be detrimental must be subject to prompt and rigorous action. Designing a successful invasive species eradication program requires among other things a science base, exposure of all individuals to eradication techniques, no risk of reinvasion, methods that can detect the last survivors, and a monitoring phase to ensure that eradication has been achieved. The last two points are especially difficult to implement effectively for recently introduced species which are usually rare and difficult to detect and exacerbated by the huge scale of the task in Tasmania. Successful eradications also require widespread public support because eradication invariably involves the use of lethal techniques that are often controversial.

This week, the Journal of Applied Ecology published the results of a broad survey for fox presence in Tasmania conducted by myself and colleagues from the University of Canberra, Arthur Rylah Institute, NSW Department of Primary Industries and the Tasmanian Fox Eradication Program. We used molecular approaches that target the DNA found on the surface of predator faeces (scats) to determine whether faeces collected systematically across eastern Tasmania contained traces of fox DNA. Canid scats can persist in nature for weeks or even months, and several species, including foxes, tend to leave them in prominent places. We found that 56 of over 9,500 scats collected before 2011 contained fox DNA. When combined with carcasses and other hard evidence, there is strong support for the presence of foxes in the central north, midlands, and in isolated areas of the northeast and southeast. Although widespread, the distribution appears fragmented into eight clusters and our modelling shows that they have not yet spread to all areas of suitable habitat.

Our data suggest that foxes may be on the verge of becoming established irreversibly in Tasmania. It is conceivable that the moment may even have passed; although now is not the time to stop – quite the reverse. Given the widespread distribution, the current approach of broad-scale baiting in a sweep across the island converging from the northwest and the southeast, is appropriate but it will need to be completed rapidly and thoroughly. The baiting sweeps will also need to be repeated and their effectiveness assessed. A massive up-scaling of effort is likely to be required to achieve this. Furthermore, to be successful, this eradication is going to require widespread community support because it involves the use of 1080, a poison that is controversial in Tasmania for reasons unrelated to fox baiting. That, along with the widespread scepticism about even the presence of foxes, presents a real challenge to the Tasmanian government and community.

Failure to ensure fox eradication in Tasmania will have far reaching consequences. That the arrival of a top mammalian predator is coincident with the decline of another top predator, the devil, is a double whammy for Tasmanian wildlife. The cascading effects of such loss and gain are very hard to predict, but they are likely to herald big changes in the interactions and even persistence of much of Tasmania’s fauna. A worst case scenario is that devils cease to be ecologically relevant and foxes become established as the top mammalian predator in Tasmania. It is scary to think that the extinction dynamics that played out on the Australian mainland 100 years ago could be repeated this century – and soon.

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Paul Davis, physicist, cosmologist and writer at Arizona State University.

TWO-AND-A-HALF millennia ago, a group of Greek philosophers conjectured that beneath the stunning complexity of the physical world lay an elegant simplicity. The entire universe, they said, was comprised of nothing but particles moving in a void. They called the particles ‘atoms’. What we today call atoms are composite bodies with bits inside them. But the notion that on a small enough scale of size there are fundamental, indecomposable building blocks of the physical world remains a focus for research.

In July 2012, physicists announced a major step forward with the discovery of a particle created in the enormous Large Hadron Collider (LHC) at the European Organisation for Nuclear Research (CERN) laboratory in Switzerland. Widely tipped to be the long-sought Higgs boson, the particle seems to be the last piece in the jigsaw of the Standard Model of particle physics, a set of equations that describes much of what is known about the fundamental structure of matter.

But, impressive though this achievement may be, it represents only a partial completion of the project begun in ancient Greece. A glaring omission is the so-called dark matter that makes up the lion’s share of matter in the universe. Astronomers can see the effect of dark matter as it tugs on stars and galaxies, but physicists have no idea what it is. The best guess is that dark matter consists of particles coughed out of the Big Bang that interact with normal matter so feebly that they mostly go right through us unnoticed. Searches for dark matter particles coming from space have so far yielded nothing definite.

MODERN PHYSICS aims not merely to draw up an inventory of particles such as electrons, neutrinos and quarks (the components of protons and neutrons), but also to explain the four forces that act between them: electromagnetism, gravitation and two nuclear forces known as weak and strong. Quantum mechanics permits a description of forces in terms of the exchange of yet more particles – photons in the case of electromagnetism and a variety of less familiar particles for the other forces. The Standard Model involves a partial unification of the forces, by joining electromagnetism and the weak nuclear force in a common scheme. The strong force is successfully described in terms of the exchange of a set of particles known as gluons, but this system is not yet mathematically integrated with the electromagnetic and weak forces. Gravitation, meanwhile, lies outside the scheme altogether.

So, theoretical physicists are yearning for additional unification and simplification. One idea, around since the 1970s, is called supersymmetry. It provides a common mathematical description of particles of matter and the particles that convey the forces. If nature is supersymmetric, there ought to be a whole zoo of additional particles, as each species of known particle should have a supersymmetric partner. The hope is that some of these hypothetical particles might explain the dark matter puzzle. Yet, against expectations, the LHC – by far the best bet for discovering this bizarre particle zoo – has so far shown no sign of any.

Another hope is that the strong force should be fully unified with the electromagnetic and weak forces, but experimental evidence for this is slim. The dream of total unification, in which gravitation is also brought into the scheme, has captivated a generation of theorists, including Einstein, and produced – among other proposals – string theory. This postulates that all particles and forces are manifestations of tiny loops of ‘string’ vibrating in different patterns.

SO HAS THE HIGGS discovery pushed any of these theories further forward? Tantalisingly, it seems the boson lies at the crossroads of supporting the Standard Model, and hinting at exotic new physics that may move us into even stranger realms of theory.

The job of the Higgs boson is to bestow mass on other particles such as electrons and quarks. Left out of the scheme, however, are neutrinos, ghostly particles that have no charge and pass through solid matter almost as if it didn’t exist. Neutrinos make up a very small fraction of dark matter. They have a tiny mass, less than a millionth of that of the electron, the next-lightest known particle. But physicists do not understand how this mass arises.

Even more enigmatic is the so-called dark energy that dominates the universe, making up nearly three quarters of its mass. The best way of describing it is the energy of empty space itself, a weird concept that makes sense only in quantum physics. But theorists are at a loss to explain its observed value, and disagree about whether it will stay constant over time as the universe expands.

All these puzzles point to important physics beyond the Standard Model. Hopes are pinned on more discoveries at the LHC, and perhaps elsewhere, such as dark matter experiments buried far underground. But the completion of the ancient Greeks’ elegant concept will depend more than ever on physicists’ ingenuity. At eight billion euros, the LHC is the costliest particle accelerator ever built. If we want to go beyond the Standard Model of particle physics, we may need to go beyond the standard model of funding too.

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