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Archive 2012

The big scientific discoveries of 2012 Peter Griffin Dec 27

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As we close out a year of scientific discoveries, many of which attracted discussion here on Sciblogs, its worth looking at some of the big science-related stories that captured public attention in 2012.

My colleagues at the Australian Science Media Centre has done most of the work for me – issuing just before Christmas a top 10 of scientific discoveries of 2012. I’ve included it below – minus a couple I’ve swapped out with discoveries I think are more significant.

The science media has also been busy assembling its top 10 lists.

Here’s Wired magazine’s, Wikipedia has an extensive list, New Scientist chips in too.

And here’s the list put together by the AusSMC, with some changes included by me (numbers 4, 7, 9 and 10).

1. Physicists found signs of the Higgs boson

Higgs had it!

– CERN (the European Organisation for Nuclear Research) announced in July that the long-sought-after Higgs boson is real following a series of experiments conducted in the Large Hadron Collider. The Higgs boson, first postulated by Peter Higgs in the 1960s and often referred to as the ‘God particle’, explains why mass exists, and is the final particle required to confirm the Standard Model of physics. “Australian researchers have played a significant role in this research,” said Dr Martin White, a Research Associate with the ARC Centre of Excellence for Particle Physics at the Terascale and the University of Melbourne.

2. Curiosity landed on the red planet – NASA’s $US2.5bn rover Curiosity landed on Mars in August. After a 36-week voyage, the rover has started studying potentially habitable Martian environments. The Canberra Deep Space Communication Complex (CDSCC), which CSIRO manages on NASA’s behalf, was the main tracking station for landing activities. See NASA media release.

3. Our genome was unravelled – Far from being junk, the vast majority of our DNA acts in at least one biochemical event in at least one cell type, according to the Encyclopedia of DNA Elements (ENCODE) Project. Analysing the entire genome to map regions of function and modification has expanded our understanding of how our blueprint is modified, and has identified new leads for understanding the genetic basis of many common diseases. ENCODE was published in over thirty research papers in four journals, including Nature.

4. SpaceX successful mission to ISS – Not a discovery, but proof that the private sector can play an integral role in the future of space travel and exploration. The mission wasn’t flawless with an engine outage causing engineers some heart in mouth moments. But ultimately, the Dragon capsule docked successfully with the ISS paving the way for a deeper partnership between SpaceX and NASA.

5. A quantum leap: Aussie ‘spin doctors’ led the field in quantum computing – Australian engineers brought the futuristic world of quantum computers a step closer in September. UNSW-led researchers created the first working quantum bit (qubit), the basis of quantum computing, by controlling the electron ‘spin’ – or magnetic orientation – of a single atom in a silicon chip. The research was published in the prestigious journal Nature. Several other discoveries by this research team helped move the reality of quantum computers closer this year. They created the narrowest silicon conducting wire and the smallest transistor.

6. Our microbial companions were mappedA consortium of scientists mapped for the first time the genomes of the microbial community that lives on or within the human body. Healthy humans host ten times as many microbial cells as human cells, including bacteria and viruses, and our minute companions play a critical role in human health and disease, say The Human Microbiome Project scientists. This research was published in Nature and PLoS ONE.

7. Scientists drill through to Lake Vostock – A Russian team of scientists drilled down 2.2 miles through Antarctic ice to reach the largest underground body of fresh water in Antarctica. The water there has been sealed away for as many as 20 millions years. Scientists testing samples of the water have found no signs of life, but further searches are underway.

8. The first embryonic stem cell study in humans was completedIn the first report of embryonic stem cells being used in humans for any purpose, US researchers reported that transplants for eye disease (macular degeneration) in two patients appeared safe and gave them some improvement in vision after four months. This was published in the The Lancet.

9. Scientists create synthetic DNA that can evolve – Scientists created a new moleculedubbed XNA that is similar to DNA and RNA but slightly tweaked. The synthetic molecules carried genetic information but were also able to evolve. Scientists suggest the new molecules could be more useful than DNA and RNA in various applications of bioscience and could form the building blocks of new forms of life.

10. Jame’s Cameron’s record-breaking dive – Movie director and explorer James Cameron took his one-man submarine to a record 11 kilometres below the Pacific Ocean, reaching the floor of the Mariana Trench – the deepest point on the Earth’s surface. It was the first solo descent of its kind and during the short period Cameron was on the sea floor, several previously unknown life forms were observed.

The hidden costs of peer review Peter Griffin Dec 14

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Sir Peter Gluckman, the Prime Minister’s Chief Science Advisor has released an interesting discussion paper today looking at peer review and its role in influencing what sort of research gets funded in New Zealand.

Those who have been through the Marsden or Health Research Council wringer will find it particularly interesting.

Many scientists have told me how much they resent the vast amount of time they are forced to invest in preparing funding applications which they have a limited chance of securing given the low success rates on some of our big contestable funds.

Sir Peter’s report tries to put a figure on the costs associated with the application process, using the Marsden Fund, which disperses around $55 million in funding annually, as an example.

…the direct administrative costs for operating the grant process are under 3% of the fund size, but this accounting ignores the vast majority of costs to applicants, referees, and panellists.

These can only be estimated, but they are substantial. The best estimate puts the total cost at 20-35% of the fund size, some NZ$10- 20 million. The majority of the cost falls onto applicants. Estimates suggest that the time spent writing proposals represents over 80% of the total fund cost, with three-quarters of that spent on first stage proposals. International reviewers and panellists make up 10% of the total cost and this is a sig- nificant burden upon the small number of people who are called upon in these roles.

Where are the costs incurred?

According to Sir Peter:

For essentially all funding schemes, the major cost is in proposal writing. For unsuccessful applicants, this may not be time that is entirely wasted – there are clear benefits from researching and clarifying ideas, building networks, and the possibility to use those applications for accessing alternative fund- ing – but nevertheless in a small science system it has a major inhibitory effect on research outputs. This is aggravated in New Zealand by the relatively short-term nature of most funding systems, the tendency to underfund requiring multiple sources of support, and the long cycle of assessment: this means that many research active staff are in a con- stant cycle of either writing grants or assisting oth- ers to write grants.

The volume of grants that senior referees are ex- pected to examine means that they increasingly avoid participating in the process9. This is a feature increasingly noted in small countries. It is unsur- prising that the system is fragile given the variable requirements of review, the sheer amount of re- viewing required, the reality that it has often been expected to be conducted over the holiday season, and the facts that institutionally it is unrecognized and, in New Zealand, unpaid. These issues are not trivial and there are increasing signs of senior scien- tists boycotting requests to participate.

Obviously, many of these costs are unavoidable if we are to have a robust peer-review process. But could we minimise the costs borne by applicants? Yes – by having less applicants.

The major system-wide cost of the funding system is the time spent by applicants in putting forward proposals. Reducing this would allow more re- searcher time to be spent in research. Equally, re- ducing the number of applications to review and the time spent per review would reduce the bur- den on the senior staff who act as reviewers.

Not that Sir Peter is necessarily recommending we tighten up the application process – that could result in significant lost opportunities.

Other areas tackled in the paper:

- Does New Zealand focus too much in the peer-review process on ideas rather than the individuals and teams presenting them?

- To what extent should national priorities feed into proposal assessment criteria?

- Is quality or relevance more important is assessing research proposals?

- How does the science system, particularly in a small country, overcome the issue of panellist bias among those chosen to assess research proposals?

- What is the best way to assess interdisciplinary research?

Well worth a read – download the paper here.

 

 

 

 

 

 

Kiwi-directed Bond films are the most violent Peter Griffin Dec 11

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If you haven’t seen the latest 007 installment Skyfall, do so – it is great. It is also pretty violent as the climax plays out like a version of the three-way graveyard gunfight in The Good the Bad and the Ugly.

Director Lee Tamahori – nasty Bond creator

But how violent are the Bond films, which after all, are rated “as suitable for children or adolescents with parental guidance”?

Well a team of researchers, including the University of Otago’s Associate Professor Bob Hancox, set out to answer that exact question and they made a couple of remarkable discoveries.

Firstly, Bond movies have got gradually more violent over the 46 year history of the series (Skyfall wasn’t included). The researchers write:

In this review of 22 films spanning almost half a century, portrayals of violence increased such that rates of violence in 2008 were double those observed in 1962. This was due to an increase in severe rather than trivial violent imagery. The findings support our hypothesis that movies, in general, have become more violent.

Also – two of the three most violent of the Bond movies – 1995′s Golden Eye and 2002′s Die Another Day  - were both directed by New Zealanders – Martin Campbell and Lee Tamahori respectively. 1997′s Tomorrow Never Dies was the most violent overall – directed by Canadian Roger Spottiswoode. Pierce Brosnan played James Bond in all of those movies boosting the 007 violence stakes considerably (see chart).

Daniel Craig’s first effort as Bond, the fantastic Casino Royale was fairly tame in comparison to the preceding decade of carnage, partly overseen by our bloodthirsty kiwi directors.

So, what does this all mean? Violence doesn’t add greatly to the mix of what makes a great Bond movie – Pierce Brosnan’s Bond movies aren’t as memorable as classics like Moonraker, Goldfinger and even 1973′s Live and Let Die – the lest violent of the series.

But what the researchers have shown – via one of the most consistently popular movie series ever, is that the films have become more violent over time, something that concerns Prof. Hancox and colleagues:

“There is extensive research evidence suggesting that young people’s viewing of media violence can contribute to desensitisation to violence and aggressive behaviour.”

So how did the researchers, who have published their results today in Archives of Pediatric & Adolescent Medicine, determine levels of violence? Here’s their methodology…

Violent imagery was defined as any scene in which there was an intentional attempt by any individual to harm another. This definition includes failed attempts at violence (eg, gunshots that miss) but excludes accidental acts that lead to harm.

Using a scheme modified from the 1997 National Television Violence Study,  each time the perpetrator, action, or target (PAT) changed, a new instance of vio- lence was counted. The total violence in each film equaled the number of PATs. Violent acts were further divided into whether the violence was trivial (eg, an open-handed slap) or severe (punching or kicking, attacks with weapons). Mass scenes of violence, in which it was unclear how many people were engaged in a fight and how many were actually harmed, were noted and an arbitrary 10 PATs per mass scene were added to the total violence score for each film. To ensure reliability, ran- domly selected films were independently coded by a second coder. There were no differences in the mean number of violence instances each coder recorded across these 6 films.

NZ’s own Doomsday prepper – and his flaky science Peter Griffin Dec 10

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Have you seen that show on National Geographic channel? The one where people devote vast amounts of time, energy and money to preparing for the end of the world?

National Geographic’s doom obsession

Some of them build bunkers to hide out in when peak oil causes massive social unrest around the world. Others are preparing for the aftermath of a sudden reversal in the Earth’s polarity. One lady was delivering masks and disinfectant kits to neighbours as she feared a global pandemic was imminent. Its quite quaint, but others are going underground to avoid, you guessed it, nuclear winter.

These Doomsday preppers are interesting in the way they matter of factly toss around wacky theories and predictions, as though they were established scientific fact. Take this advice Survive Pole Shift has issued to help you survive the big flip:

…research your location from the standpoint of the climate that will exist after the pole shift. This is quickly ascertained by looking at the New Geology map. This is a free map which can be cut out and taped together and will give a general idea of the latitude to expect. If your chosen location is where one of the new poles will be, this is a clue that you need to rethink or plan a migration route. This is likewise the case if your chosen location will be on land that will sink below the waves entirely, such as India or western Australia.

Doom metal

New Zealand has its own Doomsday preppers and one of them, Opshop frontman and New Zealand’s Got Talent judge Jason Kerrison is the poster boy for the movement. Kerrison, who has constructed an emergency bunker in Northland, also fears a major pole shift. He told the Herald on Sunday:

“It’s just getting close to home more often. I guess we live such ephemeral lives that we expect this potential global cataclysm we’re discussing to happen overnight or out of the blue. But there are signs everywhere that this accelerated pole shift is being triggered and ramping up.”

Jason Kerrison

Kerrison’s face graces the front of this week’s New Zealand Listener, where he dispenses some more scientific analysis:

“If the shit were to hit the fan as much as some people talk about, you could get a whole crustal displacement of the eight to 20 miles’ worth of crust on this 8000-mile-wide planet, slipping like a peel on an orange.”

The end of the world is front of mind, or decent fodder for journalists anyway, as we approach December 21, the date the current cycle on the Mayan calendar ends. On that date, argue various bunches of Armageddonists, the world will end dramatically. Planet Nibiru might smash into planet Earth, or life may be vaporized as part of the galatic alignment. Kerrison chips in:

“Whether anything happens specifically on that date, I don’t know, but its been happening for years – its just ramping up in its intensity.”

As December 21 looms we can expect more of this sort of talk – which is bizarre, because it isn’t as though the Mayans actually prophesied the end of the world.

Marcello Canuto, the director of Tulane University Middle America Research Institute, says only two recovered Mayan texts reference the end of a 144,000 day b’ak’tun cycle but little more. This for the Huffington Post:

 ”What this text shows us is that in times of crisis, the ancient Maya used their calendar to promote continuity and stability rather than predict apocalypse,”

The Mayans didn’t link the end of the calendar cycle with the end of the world, argue experts, but that is how Christians interpreted it. Via Livescience:

“A lot of the end-of-the-world mythologies are the result of Christian eschatology introduced by Franciscan missionaries,” John Hoopes, a scholar of Maya history at the University of Kansas, told Livescience, referring to missionaries just entering the New World and coming into contact with native people.

Real disaster scenarios

While there’s nothing credible to suggest December 21st won’t be just like any other day, scientists have given considerable thought to what could devastate planet Earth. After all, such events have happened before. Wired has summed up the potential scenarios, ranging from the eruption of a super volcano to a large comet striking the planet.

As this Guardian piece shows, scientists continue to think through disaster scenarios, with the aim of  avoiding world-ending scenarios. The problem, writes the Guardian’s Ian Sample, is that humans only really get around to serious disaster planning after disaster has struck.

Nuclear reactors were made safer after the Chernobyl disaster in 1986. The UN drew up plans for a tsunami warning system in the Indian Ocean a year after 230,000 people died from a devastating wave in 2004. Plans to bolster flood defences around New Orleans are still being thrashed out, five years after hurricane Katrina killed nearly 2,000 and left thousands more homeless. In each case, the risks were known, but they were only acted on after the event.

 Kerrison for his part will be strumming his guitar up north, a short dash from his bunker on December 21,

“I call myself an apocaloptimist, in that shit happens but I’m ready for it if it does,”

he told the Listener, adding probably with people like me in mind:

“I don’t feel downtrodden from the taunts of the short-sighted.”

 

Endace spat reveals classic sell-out tensions Peter Griffin Dec 07

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So another one of our high-flying Kiwi tech firms is about to be gobbled up by off-shore investors.

News broke this morning that Endace, the successful security and networking company founded by businessman Selwyn Pellet and listed on the London Stock Exchange’s Alternative Investment Market, has been approached by “California networking solutions firm Emulex with a cash takeover offer worth US$130 million ($156.76 million)”.

I’m happy for Selwyn Pellett, who stepped down from the company in 2010 and the Endace team. They started over a decade ago working on cutting edge technology at Waikato University and became global leaders with major banks and blue chip companies among their clients.

But it is also disappointing to see yet another innovative company that was nurtured with millions of dollars worth of government grants, leave New Zealand ownership and control completely. Selwyn Pellet acknowledges that today in the Herald:

“People who shouldn’t be happy if they understand the implications are the New Zealand taxpayers. They should be saying, ‘That was one of the highest-tech companies in New Zealand, it could have with appropriate encouragement spawned another four or five companies’ … the company itself has so much IP [intellectual property].”

His comments sparked a testy exchange with Science and Innovation Minister Steven Joyce – via Twitter. It went something like this:

The flurry of tweets is revealing. It shows the guilt discomfort Selwyn Pellett feels about the company he founded, which received over $10 million in government grants, going lock, stock and barrel to a US company. While Endace’s shares are openly traded on the AIM, it still has a significant New Zealand shareholder base and most of its staff are based in New Zealand. But what we have discovered when our tech companies sell is that, despite best intentions, the R&D operation is unlikely to remain in New Zealand long term.

The Herald piece and tweets show that Pellett is sensitive to the issue and has been reflecting on the big picture funding of New Zealand tech companies. After all the Endace story is a familiar one. This TIN100 survey published in September reveals that in the last 20 years, 42 TIN100 companies have been acquired by overseas buyers. Many of them were recipients of millions in TechNZ and other government grants.

So we as taxpayers put millions into companies that become successful and grow, get on the radar of big overseas players and are bought out. We’ve seen this time and again with the likes of Humanware, Navman, The Hyperfactory, Sonar6, Next Window, 4RF and Fisher & Paykel Appliances.

The question is whether this is a problem. Is it worth it for the country to fund this type of thing given the predictable outcome?

It really comes down to the value the companies deliver to New Zealand before they are sold. Some of them generate significant revenues, so will be paying tax. They employ hundreds of skilled New Zealanders. There is much-needed experience gained in developing start-ups to the stage that they become acquisition targets. There is also a fair amount of technology transfer between these companies – so their development has spin-offs for the tech industry at large.

How do you quantify the impact of the government grants? It’s difficult – but this 2009 Infometrics study looked at the impact of TechNZ funding. It concluded:

The total value of TechNZ investment received by surveyed firms (excluding for research that is yet to generate a return) is $39.5m. Therefore, based on the estimated value-added a very crude benefit-cost  ratio is about four. We calculate that the discounted value of the  increment to sales would be $509m and the discounted benefit cost ratio  would be 12.9 based on plausible assumptions, outlined under Return on
investment.

A more robust calculation of the net effect on GDP requires an econometric comparison of companies that received TechNZ funding with those that did not, allowing for possible self selection bias. Strictly speaking one would also have to allow for the deadweight loss associated with the imposition of taxation required to generate TechNZ funds.

Other than higher sales and export earnings, other benefits received from TechNZ funding were brand positioning, skill retention and recruitment,
addition of R&D capacity, and credibility in the market.

The Study suggests that government funding has significant financial spin-offs – and many other benefits. No one is arguing that this type of support should be withdrawn. But is there a way of retaining the value of the direct government investment if the company is sold?

Convertible notes

Here’s where Pellett suggests the idea of replacing grants with convertible notes. I haven’t heard his plan in detail, but I imagine it is a sort of loan that converts into equity if the company is sold – in full or partially –  within an agreed time frame.

So lets say the government issues a tech start-up $2 million to help it with its R&D efforts. This is issued as cash to the start-up which can spend it on the agreed activities. But if the company is bought, the convertible notes the Government holds convert to an equity stake in the company, so the Goverment gets its $2 million back when the company is sold – or when the foreign shareholding in the company reaches a certain stage – say 60%.

Convertible notes are used a lot in the private funding of start-ups with mixed results. In effect though, this vehicle could protect the Government’s direct investment in these types of companies or encourage them to stay New Zealand owned and controlled for longer. For the latter to happen they need better access to capital – but that’s another story.

For the entrepreneurs running the start-ups convertible notes would be less attractive than straight grants because there are added strings attached and they effectively require an interest-free loan to be repaid if they sell out. But its an idea worth considering and increasingly, people like Pellett, Rod Drury and other serial entrepreneurs do seem to care about the bigger picture – value for money for the taxpayer.

Tornadoes don’t indicate extreme weather is increasing Peter Griffin Dec 06

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I popped out for a meeting this afternoon and came back to the office to discover a tornado had torn through the street I grew up in, Waimarie Rd, in Whenuapai, just a stone’s throw from the airforce base perimeter.

My parents were out shopping at the time thankfully, but still can’t get back into Whenuapai where roads are closed until trees and fallen power lines can be removed. The power pole at the entrance to their section is down and their car port has taken a hammering. But they got off lightly compared to the three who died in West Auckland this afternoon, in an extreme weather event that echoes that of last year’s fatal tornado that touched down on Auckland’s North Shore.

My old stomping ground, Waimarie Road in Whenuapai, this afternoon credit: NZ Herald

An obvious question that has sprung up on social networks this afternoon, perhaps with the Sandy disaster still fresh in people’s minds, is whether tornadoes are increasingly frequent in New Zealand and a manifestation of the changing climate.

The answer, according to climate expert, Victoria University’s Associate Professor Jim Renwick, is “no”.

He told the SMC this afternoon:

The occurrence of damaging tornado events is associated with localised severe thunderstorm activity. Analysis of weather records does not show a pattern, nor are there trends obvious in tornado occurrences. These events strike at random from time to time, but they are very localised and sporadic and are not obviously tied to trends in the large-scale climate. At this stage, we have no indication that tornado occurrences will become more or less frequent in future.

Aucklanders will relate to the comments about the tornadoes being “very localised”, but other parts of the country are from time to time ravaged by tornadoes. Just up the coast from me at Waikanae, a tornado tore through houses last year, almost killing members of one family.

University of Canterbury lecturer in meteorology, Dr Marwan Katurji, said the Taranaki region is the record holder for tornadoes, with the Auckland region coming in second.

“The North Island, especially the west coast, is more vulnerable to westerly and northerly winds that are associated with weather fronts. Warm moist air from the warmer Tasman Sea carries within it embedded thunderstorms. When the air hits land it interacts with the topography to create convergence zones and the wind speeds are higher in these areas and the storms get more severe in this case.”

And some comfort for Cantabrians – who have become expert at dealing with disaster:

“In Canterbury we are blessed with the Southern Alps that do shield off the severe westerly storms. But occasionally we do get the odd small waterspout off the Banks Peninsula coast.’’

While environmentalists were gratified to see climate change put squarely on the agenda days before the US election when Sandy caused mayhem along the east coast of the US, scientists there have also warned about overstating the link between extreme weather events and climate change. Writes environmental scientist Amy Luers:

The link between today’s extreme weather and greenhouse gas policy is weak. Policy decisions made today are not going to eliminate or even significantly alter the patterns of these extreme weather events in the next few decades. This is due to the long lifetime of the heat-trapping gases in the atmosphere coupled with the time it takes to change our societal infrastructure.

However, some scientists, such as climate expert and kiwi expat Dr Kevin Trenberth, suggest global warming is exacerbating the effects of extreme weather events. He said this of Sandy:

“Global climate change has contributed to the higher sea surface and ocean temperatures, and a warmer and moister atmosphere, and its effects are in the range of 5 to 10%. Natural variability and weather has provided the perhaps optimal conditions of a hurricane running into extra-tropical conditions to make for a huge intense storm, enhanced by global warming influences”.

Back in New Zealand last year, Dr Trenberth, who is based in Colorado, participated in a Science Media Centre briefing on extreme weather, which you can listen to here.

The TPP – what does it mean for science? Peter Griffin Dec 05

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Right now, hundreds of diplomats and trade experts from around the Asia Pacific region are ensconced at Sky City convention centre in Auckland for top-secret negotations as part of the Trans-Pacific Partnership Agreement.

Credit: GlobalTradeWatch CC Flickr

The level of secrecy alone is of great concern and to some, anti-democratic, let alone what is actually being concocted in the latest draft agreement. Prime Minister John Key has backed the secret nature of the negotiations – commercially sensitive and all that.

But enough information has leaked from previous drafts to raise concerns about what is being hammered out on our behalf.

And enough of a picture of what the TPP contains has also been created to suggest it could have implications for science, research, innovation and the creation and use of intellectual property in New Zealand.

Medicines

The big science-related area of concern flagged so far is around potential changes to how drug buying agency Pharmac operates and therefore the type of access New Zealanders have to important drugs and medicines – and at what price.

The Prime Minister and pharma lobby group Medicines New Zealand have both said that there’s no intention to try and dismantle Pharmac – which is hailed around the world for keeping drug costs low in New Zealand. But the pharmaceutical industry isn’t happy at the amount of power Pharmac, which turns 20 next year, wields when it comes to deciding what drugs will be made available in New Zealand.

Pharmac is the subject of numerous US Government cables that were released by Wikileaks. The cables, such as the following one sent from the Wellington Embassy in 2006, analyse the US drug companies’ desire to use the lever of a free trade agreement to allow them to more freely sell a wider range of potentially higher priced drugs here.

SUBJECT: DRUG INDUSTRY SEES POSSIBLE SALVE TO ITS PAIN IN NEW ZEALAND
06WELLINGTON40 2006-01-13 05:15

“..most drug companies continue to believe that only the lure of a free-trade agreement between New Zealand and the United States would prompt the New Zealand government to make the changes the industry contends are needed to assure its long-term viability  in the country.”
Another cable from 2006 (all those with references to Pharmac are helpfully summarised here) points out the commercial reality John Key faces and explains his public commitment to maintaining Pharmac – we can’t afford higher priced drugs.

SUBJECT: GNZ AIMS TO COOL EXPECTATIONS FOR U.S. FTA
06WELLINGTON230 2006-03-24 04:51

“The New Zealand government would be hard-pressed to meet likely U.S. demands that it open the drug-purchasing system to greater competition and choice. That would be costly, and health care expenses already are the largest component of the New Zealand budget (ref A). “
 So if Pharmac remains intact, what type of changes may be in store for it to placate the drug companies – and the US TPP negotiators?
Medicines New Zealand, which represents the likes of Pfizer, GlaxoSmithKline, Roche and Merck Sharpe & Dohme in New Zealand, have summarised the following changes it would like to see made:
- Better transparency around funding applications and the Pharmacology and Therapeutics Advisory Committee (PTAC) as well as for the scientific evidence on which decisions are made.

- Establish a timeline for processing applications and make decisions (“don’t sit on PTAC recommendations for many years”).

- Clear definition of decision criteria and how they are applied.

- Direct stakeholder representation to the clinical committees.

- All health technology investment decisions made on similar grounds.

- Intellectual property regime brought up to international best practice.

Essentially, the drug companies want to gain a better understanding of how the Government decides to fund drugs, the processes they have to go through and they want more input into the process. They want the same rules to apply to all drugs considered for funding. It sounds reasonable enough, but what the implications of the above would actually be once they’ve gone through the TPP mincer is anyone’s guess.
It may not mean higher-priced drugs, but it could influence the mix of drugs funded by Pharmac and potentially give drug companies ammunition to take legal cases under the investor trade provisions being negotiated (see below).

Possible scenario: A US drug company is able to convince a clinical committee that its drug’s efficacy warrants Pharmac choosing its drug over a rival’s – say a cheaper generic.

Bottom line: Pharmac is certainly a target in these negotiations and its track record of delivering quality low-priced drugs to New Zealanders is at risk. But we can’t afford higher priced drugs, which is driving the Government’s commitment to retain Pharmac.

Genetic modification

Several large and influential US companies develop and sell genetically modified organisms. They’d like to do more business in New Zealand – recently the likes of Du Pont and Monsanto were in New Zealand outlining some fairly credible arguments for why New Zealand needs to get serious about the technology to remain a competitive player in agriculture.

These companies also want to sell products containing GMOs to New Zealand consumers. At the moment, New Zealand has labelling regulations so that products must have a GM label “if they contain DNA or protein from a GM source or they have altered characteristics compared to their non-GM counterpart (such as a changed fatty acid profile).”

But GM is a turn-off in New Zealand – the public is opposed to it and therefore is less likely to buy food which has been genetically modified. That’s why Bio, the major US industry association for the biotech sector, made a submission in 2009 that foods containing small traces of GM-material shouldn’t have to be labelled so. Labels should only be required:

“…if the product has been significantly changed nutritionally or if there have been changes in other health-related characteristics of the food”.

If this makes it into the TPP, some products containing GMOs could end up on shelves in New Zealand without being labelled as such.

The other push from Bio is for GMOs that have been deemed safe and are used in one TPP-member country to be allowed to be used in New Zealand:

“A recognition from the TPP countries that no new approval process is necessary for stacked traits that have already been approved individually by national authorities”.

That could have implications for the extent of the Environmental Protection Agency’s powers. It oversees GMO applications under the HSNO Act.

Possible scenario: Feed imported to New Zealand for livestock may contain GM material but doesn’t have to be labelled as such or go through specific regulatory approval.

Bottom line: Many scientists will welcome any freeing up of regulations around use of new organisms as a sign of progress on technology New Zealand has stubbornly refused to embrace. But the Government will be nervous given the public opposition to the use of GM technology and materials in New Zealand and the GE Free crowd will hit the roof.

Patents on medical prcedures

The treatment of intellectual property under the TPP is highly contentious due to the fact that the intellectual property chapter of the TPP document was leaked in 2011 and revealed some potential fish hooks. There are well documented concerns around the TPP in relation to copyright, software patents and the digital economy which are well documented. I wrote a Listener column about them (sorry behind the new pay wall).

The intellectual property provisions have serious implications for science too. The draft text and submissions from the US appear to seek to tighten up protection of intellectual property, including the use of patents.

While most countries have some sort of patent laws to allow inventors to protect their ideas, the US and others include “carve outs” for “therapeutic and surgical methods for the treatment of humans”. There’s more on the issue here, including a video interview with a legal expert.

The exclusions mean that while you might be able to patent a medical procedure, you won’t be able to enforce it. This is mainly to prevent situations where potentially life-saving treatments cannot be administered because someone has a patent on how the procedure is carried out and the medical practitioner hasn’t secured a license to perform it.

The TPP draft wording covers the above scenario, but little else:

Each Party may only exclude from patentability inventions, the prevention within its territory of the commercial exploitation of which is necessary to protect ordre public or morality, including to protect human, animal, or plant life or health or to avoid serious prejudice to the environment, provided that such exclusion is not made merely because the exploitation is prohibited by law.

The Australia-US Free Trade Agreement has a similar clause, but excludes much more – see bold below:

Each Party may only exclude from patentability: (a) inventions, the prevention within their territory of the commercial exploitation of which is necessary to protect ordre public or morality, including to protect human, animal, or plant life or health or to avoid serious prejudice to the environment, provided that such exclusion is not made merely because the exploitation is prohibited by law; and (b) diagnostic, therapeutic, and surgical methods for the treatment of humans and animals. [emphasis added]

Currently, in most countries, surgeons who perform patented surgical methods are not liable for patent infringement on these activities.

As the New Zealand Intellectual Property Office states:

…claims including methods of treatment of humans by therapy or surgery, and claims including methods of diagnosis that are performed directly on the human body, will not be accepted.

The leaked TPP draft suggests the trade agreement could tighten up that provision to make patents for surgical procedures enforceable. That would put the trade agreement in opposition to the law in several member countries, including the US.

Possible scenario: A doctor carrying out a commonly used but patented cancer diagnostic procedure suddenly finds that he is infringing the patent holder’s intellectual property rights and has to secure a licence to continue carrying out the diagnostic procedure.

Bottom line: Allowing patents on medical, diagnostic and surgical procedures to be enforced could have serious ramifications for how medical practitioners operate and therefore have implications for medical treatment in New Zealand.

Other areas of the TPP could impact the operations of scientific institutions, particularly the much talked about “investor state” provisions that could allow companies to sue governments directly over alleged breaches.

Secrecy breeds paranoia

It is important to point out that all of the above is based solely on snatches of leaked TPP texts. But that is all the public has had to go on throughout this entire TPP negotiating process. The leaked text and the various submissions to the US Government on free trade deals have shown what US industry is pushing for and therefore what the US negotiators are hoping to have included in the final TPP agreement.
It may be that many of these concerns will turn out to be unfounded, that the wording waters down the risks posed. But we have no way of knowing one way or other, which is why science and the New Zealand public in general should care about the impact this free trade agreement will have on our ability to innovate and decide what scientific innovations we wish to employ and adopt in our country.

Scibloggers clean out science communication awards cupboard Peter Griffin Nov 29

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I spent an enjoyable morning at the Prime Minister’s Science Prizes where the glow of last night’s premiere of The Hobbit was obviously still buoying attendees – particularly the Prime Minister, who at one stage suggested there were “cauldrons of opportunity” in science.

Professor Shaun Hendy

The PM’s Science Prizes spell the end of the science awards season, following the New Zealand Association of Scientists awards and last week’s Royal Society of New Zealand Research Honours awards. They also represent the most lucrative of the prizes, with one million bucks going to the recipients collectively.

Full details about the award-winning scientists, science teacher and remarkable student winner Helen Ng are here.

But it was particularly pleasing to see Sciblogger Professor Shaun Hendy pick up the PM’s Science Media Communication Prize. Professor Hendy divides his time between Industrial Research and Victoria University and until recently was Deputy Director of the MacDiarmid Institute. This is Shaun’s second win – he picked up the Callaghan Medal for science communication at the RSNZ awards last week.

Aside from his blogging at A Measure of Science, Shaun has been prolific in the media. He is a regular contributor on Radio New Zealand and is often quoted in science-related news articles, TV and radio pieces. I learnt this morning that the book he is publishing next year will be called Get off the Grass, (great title!) and will carry on some of the ideas first explored in Sir Paul Callaghan’s well-received and through-provoking book Wool to Weta.

Both awards are well deserved and hard-earned. Like Sir Paul, Shaun is able to relate science to the big picture issues facing the country. He understands the needs of journalists. And he isn’t reticent about standing up for what he believes in. Amid the controversy this week over Dr Mike Joy’s comments in the New York Times about the state of our environment, Shaun, in his capacity as President of the Association of Scientists issued a statement defending Joy and attacking a heavy-handed Herald editorial about Joy.

Standing up for science

“The clear statement is that the potential damage to New Zealand’s reputation, and economic benefit of ‘big-spending American tourists’ outweighs the need for truth in  public debate,” the NZAS release stated. “This is an issue that the Association takes very seriously, and emphatically refutes criticism of Dr Joy on this basis.”

I had a chat with Industrial Research Ltd. CEO Shaun Coffey at the PM’s prizes this morning, a man who has been instrumental in giving Shaun the time and freedom to engage with the media. Coffey is running a very successful experiment in science communication himself, having amassed nearly 130,000 followers on Twitter. His updates and links to interesting articles on R&D, science, economics and agriculture are addictive reading for me.

Dr Siouxsie Wiles

Picking up the NZAS Science Communicator’s Award was another Sciblogger, Dr Siouxsie Wiles who blogs at Infectious Thoughts. Currently you can see Siouxsie fronting a national TV ad campaign for the National Science Challenges. She is also active on the media front and has been successfully testing out crowd funding of scientific research through the Rockethub platform.

What is great to see is that we have a growing number of scientists who are skilled communicators, willing to engage with the media, conscious of the news agenda and the interplay between science and the issues of the day and proactive about getting the science out to the public. Others such as Dr Mark Quigley, last year’s PM’s Science Media Communicator’s Prize winner, and Professor Chris Battershill have quickly had to hone their media skills when demand for their expertise put them in the media spotlight. In the case of Quigley, it was the Canterbury earthquakes, for Battershill it was the Rena oil spill.

The better scientists are at communicating their science, at relating its value to society the better the public’s understanding of the importance of science will be. And those who recognise that science communication is an ongoing endeavour, an investment, rather than an obligation tied to the need to promote research findings or secure funding, will ultimately better serve the people who are indirectly paying for their science.

Mike Joy isn’t a lone voice – just a loud one Peter Griffin Nov 27

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Of all the questions raised by the controversy surrounding scientist Mike Joy’s quotes in the New York Times – and the heated response to them, this is the most important: can Dr Joy back up with evidence his claims about the parlous state of New Zealand’s environment?

He can and he has.

Dr Mike Joy

From the peer-reviewed journal PLoS to the Ministry for the Environment’s own reporting on the state of water quality in New Zealand, the literature suggests we have reason to be concerned about the health of our waterways.

How this impinges on the way we market our country to the rest of the world is arguable, but this scientist at least has a credible argument – backed up by evidence, to suggest it undermines our prominent claims to be 100% Pure.

It is not as if Mike Joy is a renegade among scientists, a lone voice in the freshwater science community. He shares the same concerns as many other freshwater scientists I have spoken to. He is just more forceful at putting his views across, more proactive at seeking media exposure. You could say that he is a very effective science communicator.

The only reason Mike Joy has attracted the ire of the Prime Minister and others, is that his comments about New Zealand’s environmental record have travelled so widely – carried on BBC Hardtalk last year and via the New York Times last week.

But you don’t have to look far to see that many of Dr Joy’s concerns are mirrored by his colleagues.

Views mirrored

Take this round-up of scientific commentary we at the Science Media Centre gathered last year in response to the Government’s release of a package of policy initiatives for regulating water quality and usage in New Zealand.

Here’s an excerpt from Dr Joy’s commentary:

“This national policy statement continues that trend of policy containing lots of nice words and lofty ideals but no teeth or standards, so this is a huge opportunity lost and we can expect more of the same the further degrading of the ‘clean green’ myth.”

Here’s what Angus McIntosh, Professor and Mackenzie Foundation Chair in Freshwater Ecology, University of Canterbury, had to say:

 “The need to halt declines in freshwater biodiversity values is critical. The current situation is really quite grim. In a recent survey of small waterways on the Canterbury Plains we have found over 80% are either moderately or severely polluted. For Canterbury urban waterways (pre earthquake), the situation is even worse”.

And Professor David Hamilton, Bay of Plenty Chair in Lakes Management & Restoration at Waikato University and President of the New Society Freshwater Sciences Society, weighed in with this:

“Over the past decade or so New Zealanders have witnessed accelerated degradation of many water bodies in response to diffuse nutrients derived mostly from agricultural sources.

He goes on to say… (full comments here)

“In the interests of ‘100% pure NZ’ we cannot continue along this pathway.”

We have gathered similar commentary from climate scientists highly critical of New Zealand’s emissions mitigation policies and the watering down of the Emissions Trading Scheme. None of them have been slammed for giving their honest, evidence-based views. I presume the only reason why they haven’t is because they haven’t been quoted by a major international news outlet.

Science is supposed to inform public debate – and policy making. That’s called an evidence-based approach. If we write off the work of scientists because the results of their research is inconvenient or because they take advantage of their right to academic freedom to highlight their findings, we are just paying lip-service to science. That’s a dangerous place to be when we face many complex issues that will only effectively be tackled by using good science.

International comparisons

Some will argue that Dr Joy is cherry-picking data and peer-reviewed journal papers to reinforce his arguments. But that is a facile argument – a smoke screen. True international benchmarks of environmental performance show we, not surprisingly, are clean and green compared to many other countries, but our performance is slipping and when you drill down into the details, indicators around freshwater resources, Dr Joy’s area of interest, are indeed concerning.

The Yale Environmental Performance Index 2012 looks at a wide range of countries and ranks them on a range of performance indicators – from air quality to land use to the quantity and quality of fresh water.

In the rankings, New Zealand comes in in 14th place out of 132 countries – between Iceland and Albania. Not a bad result. But Yale also issues an EPI Trend ranking – looking at how we’ve progressed over the past decade. Using this indicator we are ranked 50th, between Armenia and Slovenia.

If you look at the specific commentary on New Zealand, you can see the reasons why our performance is slipping. Where we are losing ground relative to other countries, as the graphic below shows, is in the areas of agriculture, forestry and water resources.

Source: Yale EPI 2012

These types of international comparisons are not perfect, but collectively there is enough evidence to suggest that while New Zealand is relatively clean and green, we are struggling in key areas that could in the longterm see us falling behind other countries overall in environmental performance.

This is what Dr Joy and his colleagues are pointing out and it is their responsibility to do so.

Science journalism that MATTERs Peter Griffin Nov 19

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Over the weekend I paid 99 cents for a quality piece of long form science journalism that I downloaded and read on my iPad.

Members sign up for 99c a month

Who published it? The New Yorker? Atlantic Monthly? National Geographic? No, the article is the first of what will hopefully be a long series published online by Matter, which bills itself as “the new home for the best in-depth and investigative writing about science and technology”.

The piece Do No Harm? – 8,000 words long, was about Body Identity Integrity Disorder. People with the condition struggle with the urge to have a limb amputated and either attempt to do the job themselves – or seek out doctors willing to do it for them. It isn’t the first time the subject has been covered in-depth. But the piece is a fascinating and emotive read and would happily sit in the publications I mention above.

But author Anil Ananthaswamy, an established science writer who would likely have had editors interested if he’d pitched the story idea to major magazine titles, decided to publish the story through Matter. In doing so, he is taking a punt on a new outlet for science journalism that competes with the establishment but exists precisely because of the dwindling space for this type of journalism in the mainstream media.

There are several reasons why Matter has a fair chance of succeeding – the same reasons why its founders raised US$140,000 on Kickstarter when they only set out to raise US$50,000. The pedigree of the editorial talent is very good as Carl Zimmer points out in this backgrounder. The platform is flexible, attractive and easy to use, particularly for Kindle owners.

But most importantly, the founders seem to understand what drives people who consume and pay for long form science journalism. Such people appreciate depth and quality and are willing to nurture an outlet that will deliver it over the long term.

Matter invites you to join as a member, signing up to pay a mere US99 cents per month. In return you get invited to online Q&As with the authors as well as Matter events and get to pitch story ideas you’d like to see investigated. How this will work out is yet to be seen – it employs an open source system for filtering ideas from members which Matter is calling “Editorial Board”. I love this level of engagement and as the membership grows I’m looking forward to being involved in the ideas-generating process.

Matter also has the advantage of being supported by a range of high-level names from the world of science journalism and also the tech sector. Part of the buzz created by these people explains part of Matter’s success on Kickstarter.

It is early days for this online magazine. And what it is setting out to do is anathema to the race-to-the-bottom, twitch-stream media populating news websites. But, hell, we need this type of thing, which taps into the crowdfunding model in a way that could make it sustainable.

As Zimmer points out:

If Johnson and Giles can continue to publish stories of this caliber, they will make an important contribution to the world of science writing. But that doesn’t necessarily mean they’ll ascend to Politico-like heights of commercial success and pose a threat to traditional outlets. Politico does some good reporting, but every day it also serves up the political journalism equivalent of McDonald’s french fries–addictive little bits of information about who said what today in the DC hothouse.

I’m looking forward to Matter’s next release and wish the founders and contributors well in what I consider to be one of the most exciting ventures in science journalism to get underway in recent times.

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