An analysis of retractions of scientific papers in India

August 12, 2011

From Professor T.A. Abinandanan on his blog Nanopolitan:

Scientific Misconduct in India: An Analysis of Retractions in PubMed

I presented this work at the Workshop on Academic Ethics organized by Rahul Siddharthan, Gautam Menon and N.S. Siddharthan about a month ago.

Quick summary: PubMed database lists ~103,000 papers published by Indian authors during the previous decade (2001-2010); 70 of these papers have been retracted, and 45 of the retractions are due to some form of misconduct. Plagiarism is overwhelmingly the primary mode of misconduct: all but one of the 45 misconduct-related retractions were due to plagiarism.

If that doesn’t sound bad enough, consider this: At 44 per 100,000 papers, India’smisconduct rate is far higher than that of countries such as the UK, the USA, Germany and Japan.

There’s some silver lining, though: Retraction of papers from Indian authors show a steep fall since 2007 — either because Indian researchers know better now, or because plagiarized papers are ever less likely to make it to print in the first place due to increasingly widespread use of plagiarism detecting software by journals.

Here’s the html version; if you prefer a pdf, get it from here.

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Indian exports up 82% as focus shifts to new markets in Africa and S. America

August 12, 2011

Financial turbulence in India’s traditional markets in Europe and the US have threatened to limit  development. Even though domestic consumption has increased significantly in the last decade the Indian economy is still very dependent upon exports. There has been a shift of emphasis in the last few years as India has tried to emulate China and develop new markets in Africa and South America.

Although exports had contracted for 13 straight months beginning November 2008, India rebounded from the crisis quickly, logging an unprecedented 37.6% growth in 2010-11 on the back of incentives and a push into new markets in Latin America and Africa.

July exports surged nearly 82% from a year ago to $29.3 billion while imports grew 51.5% to $40.4 billion, trade data released on Thursday showed. 

Exports of engineering goods, which now account for as much as 30% of the export basket, to Latin America increased four-fold during April to July. The IT industry too intensified exports to the region while the pharmaceutical industry found huge demand for its generics in Brazil and Mexico.

This strategy targeting Latin America and Africa has its limits since in absolute terms the US and EU still account for a third of the country’s exports and a large portion of India’s imports. Any decline in exports to these regions will create a balance of payments problem. In April-July 2011, imports grew 40% to $151 billion, expanding the trade deficit to $42.7 billion. In July alone, the trade deficit was $11 billion.

Fortunately the 2011 monsoon looks like being  close to an “average monsoon” which should keep domestic demand buoyant. But the best long-term demand hedge for India will be in differentiating from Chinese products and increasing exports to China. Imports from China are growing fast and to get trade with China into a more healthy balance will also reduce the balance of payment risks.

From the Hindu Business Line (which is by far the most balanced and reliable financial newspaper in India):

NEW DELHI, AUG 11: 

Exports in July grew by an astonishing 81.8 per cent to $29.3 billion, according to provisional data released by the Commerce Secretary, Dr Rahul Khullar, on Thursday.

The drivers of this growth – the fastest since April 1995, according to Bloomberg – were sectors such as engineering, petroleum products, readymade garments, gems and jewellery. The strategy to diversify to new markets in Asia, Africa and Latin America has helped in maintaining high growth rates.

Dr Khullar, however, told reporters that the growth rates will definitely slowdown from August due to a demand contraction in traditional markets such as the US and Europe. He said the increase in interest cost is hurting small and medium exporters, adding that, “I am trying to get something done on that front”. …..

Since consumers in the US and Europe — owing to lower income and fear of job losses — are likely to switch over to cheaper products, exporters adapting quickly to cater such a demand will survive, Dr Khullar said. He added that the country is “better prepared” to face any slowdown than it was in 2008 during the global financial crisis.

Dr Khullar said that monthly exports are likely to fall to less than $25 billion, which would make it tough to achieve a figure of $300 billion for the entire fiscal. In 2010-11, India’s merchandise exports were valued at a record $246 billion. …… 

Meanwhile, imports in July rose 51.5 per cent to $40.4 billion. Trade deficit (gap between imports and exports) in July widened to $11.1 billion, up from $7.7 billion in June and $8.9 billion in April 2011. It had touched a $15 billion–high in May.

Dr Khullar said the high level of trade deficit continues to be a worry, adding that it could be over $130 billion for this fiscal. Trade deficit during April-July 2011 is already $42.7 billion.

Exports during April-July 2011 jumped 54 per cent to $108.3 billion, while imports during this period increased 40 per cent to $151 billion.

Engineering exports were $8.7 billion in July alone and $31.6 billion during April-July 2011 due to a huge increase in such shipments to Africa and Latin America. Thanks to high oil prices, shipments of petroleum products also rose. They were worth $4.6 billion in July and $18.6 billion in April-July, an increase of 60 per cent.

Mr Khullar said exports of most sectors have shown huge growth due to the ‘lag effect’ as these were the orders that Indian exporters received months before the recent crisis in US and Europe, tsunami in Japan, huge inflation in China and a robust growth in Latin America.

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If you can’t kill the virus, kill the cells that contain the virus

August 11, 2011

An ingenious way of getting around the problem of attacking viruses. An MIT press release desribes a development that could transform how viral infections are treated. A team of researchers at MIT’s Lincoln Laboratory has designed a drug that can identify cells that have been infected by any type of virus, then kill those cells to terminate the infection.

Rider TH, Zook CE, Boettcher TL, Wick ST, Pancoast JS, et al. (2011) Broad-Spectrum Antiviral Therapeutics. PLoS ONE 6(7): e22572. doi:10.1371/journal.pone.0022572

Todd Rider invented the PANACEA and DRACO antiviral therapeutics, and previously invented the CANARY (Cellular Analysis and Notification of Antigen Risks and Yields) sensor for rapid pathogen detection and identification: Image MIT

In a paper published July 27 in the journal PLoS One, the researchers tested their drug against 15 viruses, and found it was effective against all of them — including rhinoviruses that cause the common cold, H1N1 influenza, a stomach virus, a polio virus, dengue fever and several other types of hemorrhagic fever.

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory’s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

Because the technology is so broad-spectrum, it could potentially also be used to combat outbreaks of new viruses, such as the 2003 SARS (severe acute respiratory syndrome) outbreak, Rider says.

Other members of the research team are Lincoln Lab staff members Scott Wick, Christina Zook, Tara Boettcher, Jennifer Pancoast and Benjamin Zusman.

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McGill University reprimands Professor for medical ghostwriting

August 11, 2011

Something stinks when academics are “helped” to write their papers by professional ghostwriters who are paid for by pharmaceutical companies. It is even worse when the papers are written by the pharmaceutical companies  and academics in the field are flattered or otherwise persuaded by their agents to put their names to the papers. McGill University has “reprimanded” a senior professor, Barbara Sherwin, for the practice but are at pains to point out that she has not been “sanctioned”.

What exactly does a reprimand – which is no sanction – accomplish?

The ghostwriting for what was ostensibly a peer-reviewed scientific article was essentially just promotional literature for Wyeth Pharmaceuticals’ and hormone replacement therapy (HRT). Wyeth paid a New Jersey professional-writing firm, DesignWrite, to help Sherwin produce a paper on treatment options for age associated memory loss that was eventually published in the Journal of the American Geriatrics Society. The paper was published in 2000. Sherwin was listed as the sole author of that paper, even though Karen Mittleman, an employee of DesignWrite, was involved in the process. The paper was published just when critics started raising doubts about hormone-replacement therapy.

Wyeth – through DesignWrite – had commissioned at least 40 scientific papers endorsing the therapy. During 2001, Wyeth sold hormones for HRT worth $2.1 billion.

Apparently Dr. Sherwin is no longer a member of the Quebec Order of Psychologists, which means she can no longer practice under the title of psychologist.

The Montreal Gazette has the full story.

Even more worrying is the Macleans story that Karen Mittleman of DesignWrite – on behalf of Wyeth – actually solicited this paper. There is also a hint of a rather cozy relationship between the Journal of the American Geriatrics Society and DesignWrite.

The stink is more of a stench!

Her alleged transgression came to light in a class-action suit involving 8,400 women against the drug company Wyeth (now part of Pfizer). Lawyers representing the women, who claim they were harmed by their hormone replacement therapy (HRT) drugs, discovered that scientific research papers extolling the virtues of the treatment while downplaying potential harm appeared to have been written, not by the academics who signed their name to the papers, but by writers hired by the pharmaceutical company.
According to court documents filed by the plaintiffs, Wyeth paid the Princeton, New Jersey-based medical communications company DesignWrite to produce articles on HRT for publication in academic journals between 1997 and 2003. DesignWrite would write the papers, then approach leading academics to claim authorship for them.

Sherwin’s relationship with the pharmaceutical company started innocently enough. In the early 1990s, she was invited to give a presentation about her work on androgens and psychological functioning in women. There, she met a woman named Karen Mittleman during the lunch break. Mittleman introduced herself as a PhD and a former academic who worked in medical communications. The pair hit it off, and kept in touch. “I liked her, and considered her a casual friend,” Sherwin told Maclean’s over the phone from her office at McGill.
Several years later, in 1998, Mittleman called Sherwin to ask if she wanted to write a paper for the Journal of the American Geriatrics Society at the invitation of the journal’s editor. The subject was pharmacological treatment options for age-associated memory loss. Sherwin, an expert on hormones and how they influence memory and mood in people, had just completed a grant proposal on the subject, and said she’d be happy to write the article. 
“[Mittleman] told me she would provide support by typing the manuscript and formatting it in the style of that particular journal,” explains Sherwin. The work itself would be based on Sherwin’s notes. In return, Mittleman, a senior writer at DesignWrite, promised to send Sherwin typed drafts for editing, and hard copies of references the professor requested. “I was completely under the impression that [Mittleman] was working for the journal, that it was the journal who hired her.” 

What Mittleman never revealed was that her employer, DesignWrite, had a business relationship with Wyeth and other pharmaceutical companies.

Karen Mittleman, as Antidote has noted, has the perfect Dickensian name for her job as the go-between finding researchers willing to sign their names to papers written by drug companies.

The reprimand by McGill seems little more than a very mild slap on the wrist.

Related: McGill sets bad example on integrity

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Chinese trade surplus at a record high as US downgrade threatens their holdings

August 10, 2011
National emblem of the People's Republic of China

Image via Wikipedia

The Chinese economy is not immune to whatever craziness is going on around the world. They hold such a large amount of US treasury bonds that the gridlock and political irresponsibility in Washington is leading to some fundamental policy changes regarding their reserve holdings. The People’s Bank of China owns about $1.1 trillion of US Treasury bonds out of the  $1.5-trillion treasury bonds or so of foreign treasuries that it holds amid China’s total reserves of about $3.2 trillion.

It is not therefore surprising then that China is among those most concerned by Standard & Poor’s recent downgrade of the United States’ AAA credit rating. It was sufficiently concerned to publicly chastise the US for its irresponsibility!

“The U.S. government has to come to terms with the painful fact that the good old days when it could just borrow its way out of messes of its own making are finally gone,” reported the Xinhua news agency.

Meanwhile

BEIJING, Aug. 10 (Xinhua) — China Wednesday reported faster than expected growth in exports, imports and trade surplus in July, but analysts said the picture would become worse in the coming months amid a faltering global economy.

The trade surplus rose sharply to a record high of 31.48 billion U.S. dollars in July from June’s 22.27 billion U.S. dollars and the 28.7 million U.S. dollars in the same period a year ago, the General Administration of Customs (GAC) said on its website.

July exports rose 20.4 percent year-on-year to reach 175.128 billion U.S. dollars, a record monthly high compared with 17.9 percent in June. Imports quickened from June’s 19.3 percent to 22.9 percent to 143.64 billion U.S. dollars.

The robust readings suggests both China’s competitiveness in exports and domestic demand are in relatively good shape, Bank of America-Merrill Lynch economist Lu Ting said in an email to clients.

Exports to the EU and Japan rose to 22.3 percent and 27.2 percent year-on-year in July from 11.4 percent and 20 percent in June.

And exports to the United States expanded 9.5 percent, down slightly from 9.8 percent in June, but down significantly from 13.3 percent in the second quarter and 21.4 percent in the first quarter, which indicated weakness in the U.S. economy has been weighing on its imports from China, according to Lu. ….

On Wednesday morning, yuan hit a record high of 6.4167 against the U.S. dollar.

US politicians in the Administration and those grand-standing in Congress will need to get their act in order if they are to avoid the day when the Chinese are no longer around to buy their debt. As it is, China is now engaged in diversifying its foreign reserves away from US dollars to other currencies and even other asset classes and is under severe internal pressure to accelerate this diversification.

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Marc Hauser’s lobbyists get to work but only end up excusing scientific misconduct

August 9, 2011

Marc Hauser’s friends have started on the process of repairing some of the damage to his reputation brought about by his own misconduct. He has “resigned” from Harvard but – with a little help from his friends – he will no doubt pop-up with a fancy title at some other institution soon.

 The Harvard Crimson reports that a group of academics have written a “letter” criticising the investigation of Hauser’s misconducts by Harvard. The letter was written by Pierre Pica, a scientist at the National Center for Scientific Research, Bert Vaux, director of studies in linguistics at King’s College in the University of Cambridge, and Jeffrey Watumull, a Ph.D. student at the University of Cambridge. Watumull previously worked in Hauser’s lab. Eight other academics including Naom Chomsky have added their signatures.

But they protest too much about one of their own. I felt on reading their letter that while they accuse Harvard of a witch-hunt and express concern about the undermining of scientific inquiry they actually end up trivialising ethical behaviour and excusing scientific misconduct. Their concern does not ring true. The letter talks about a media frenzy against Hauser but ignores the fact that nothing came up in the media until after the 3 year investigation had shown the misconduct and Hauser had taken a year’s gardening leave.

Harvard Crimson: Monday, August 08, 2011

The letter—which was signed by MIT Linguistics Professor Noam Chomsky, one of Hauser’s mentors—criticizes the scope of the inquiry into Hauser’s research, the media frenzy that followed the release of Harvard’s findings, and insinuations that Hauser’s body of work has been thrown into question by the investigation. ….

Eight academics from the United States, the United Kingdom, France, and Brazil signed the letter, including Harvard Professor of Molecular and Cellular Biology Florian Engert. It has been circulated among top academics.

The Crimson obtained a copy of the letter—titled “Could the Process of Investigating Scientific Misconduct Undermine Scientific Inquiry?”—from the authors.

Following allegations that Hauser falsified research data, a three-year investigation into Hauser’s research found him “solely responsible for eight counts of scientific misconduct,” Dean of the Faculty of Arts and Sciences Michael D. Smith wrote in a letter last August. Reports attributed the source of those allegations to his graduate students.

In the fallout from the investigation, Hauser took a year-long leave of absence, was then barred from teaching for another year, and ultimately resigned from his tenured position this summer.

Related: Hausergate posts

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Arctic Ice: “Rapture” of an ice free Arctic now postponed till 2030

August 9, 2011

The ice free Arctic which was to have happened in 2008 according to Mark Serreze of the doomsday crowd has now been postponed till 2030 while scientists find that current concerns over a tipping point in the disappearance of Arctic sea ice may be misplaced.

From WUWT’s Quote of the week:

WUWT

We all cringed, then laughed when Dr. Mark Serreze of NSIDC first said it, then marveled about it as it got a life of its own, being the buzzphrase for every alarmist who wanted to shriek about declining Arctic sea ice.

In 2007 we heard him say:

“The Arctic is screaming,” said Mark Serreze, senior scientist at the government’s snow and ice data center in Boulder, Colorado.

So far, the “screaming” hasn’t kept anyone awake at night, and we have not returned to the low of 2007 in the last three melt seasons.

In 2008 Serreze made the  bold claim:

The ice is in a “death spiral” and may disappear in the summers within a couple of decades, according to Mark Serreze, an Arctic climate expert at the National Snow and Ice Data Center in Boulder, Colorado.

And in 2008 we had the forecast from NSIDC’s Dr. Mark Serreze of an “ice free north pole”.  As we know, that didn’t even come close to being true. Summer 2008 had more arctic ice than summer 2007, and summer 2007 was not “ice free” by any measure.

With those failed predictions behind him,  in an interview in The Age just a few weeks ago, Serreze pulled a Harold Camping, and changed his prediction date. Now he’s saying the new date for an ice free summer is 2030.

”There will be ups and downs, but we are on track to see an ice-free summer by 2030. It is an overall downward spiral.”

And in the meantime research reveals that ice levels in the Arctic were about half the present levels some 5000 years ago and had no problems in recovering.

Scientists say current concerns over a tipping point in the disappearance of Arctic sea ice may be misplaced. 


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Guradian to hold Masterclass in hacking?

August 9, 2011

I just noticed that the Guardian is holding – for a £500 per person fee – a two-day course in September ostensibly on “investigative journalism”.

In this intensive, weekend course, two of the UK’s leading investigative journalists will give students the skills needed to reach the next step. Paul Lewis and Heather Brooke will teach the secrets of their trade in a series of interactive workshops and skill-based sessions.

The course will cover among other things “convincing people to talk” and “advice on data journalism” and “the course will reveal how new technology and recent innovations have revolutionised investigative journalism”.

I note – but without much surprise – that there is no mention of ethics anywhere in the course description.

Presumably David Leigh will be the guest lecturer and will explain the techniques of phone hacking  and the importance of always having noble objectives. He could also explain the finer points of utilising the public interest defence under the Data Protection Act to justify non-compliance with the Act. To cover ethics they could invite Rebekah Brooks who is probably available except that she is apparently still on the payroll of News International.

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Why are street riots in the UK a “bad thing” but a “good thing” in Egypt or Syria?

August 9, 2011

The scenes from Tottenham and other parts of London were distressing and the looting and vandalism is – I think – despicable.

It has been depressing to watch.

But I found similar scenes not so long ago – though perhaps without the same level of mindless vandalism but with much more severe loss of life – in Egypt and Tunisia were actually uplifting and I took these as a “demonstration” of democratic forces at work”. The ruthless putting down of protests in Syria is also distressing and all my sympathies are very clearly with those protesting.

I am still trying to reconcile my own “double standards” in my own mind.

Was the level of hopelessness and despair in Egypt and Tunisia which forced ordinary people onto the streets and caused governments to fall so different from the hopelessness and powerlessness felt by the crowds in Tottenham or Brixton? Is the feeling of being oppressed in Syria any different from that felt by some in the UK?

Opportunists and hooligans and plain criminals were surely present in all of these scenes.

But I am still struggling to clarify the differences in my own reactions to myself.

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Pamela finds anti-matter in the Van Allen belt

August 9, 2011

I had no difficulty as a student and later as an engineer in using  imaginary and complex numbers  involving i, where

i 2 = −1

and I am reasonably confident that I grasp the general concept of imaginary numbers. It took me a while when I was a student to realise that “imaginary” here meant “being capable of being imagined” and not something that ” did not exist and could only be imagined”.

I have much greater difficulty in following the concepts of “anti-matter” and why it is rational and necessary that anti-matter must exist. But I am no high energy physicist. On the other hand, I have no difficulty in “imagining” an alternative universe composed of anti-matter subject to anti-gravity, lit up with anti-light and which presumably began with an anti-Big Bang (an implosion)! But why anti-matter must exist in our universe is something I am content to leave to physicists. But like black holes they make me vaguely uncomfortable and I suppose it’s a good thing that anti-matter does not exist naturally on the earth’s surface. Of course if the physicists could suggest how I could use anti-matter to annihilate about 20kgs of my mass I would sign on immediately!

Anti-matter

The modern theory of antimatter begins in 1928, with a paper by Paul Dirac. Dirac realised that his relativistic version of the Schrödinger wave equation for electrons predicted the possibility of antielectrons. These were discovered by Carl D. Anderson in 1932 and named positrons (a contraction of “positive electrons”). Although Dirac did not himself use the term antimatter, its use follows on naturally enough from antielectrons, antiprotons, etc.A complete periodic table of antimatter was envisaged by Charles Janet in 1929.

Antimatter cannot be stored in a container made of ordinary matter because antimatter reacts with any matter it touches, annihilating itself and an equal amount of the container. Antimatter that is composed of charged particles can be contained by a combination of an electric field and a magnetic field in a device known as a Penning trap.

In any case, when cosmic rays smash into molecules in the Earth’s upper atmosphere, a shower of smaller particles is created. Physicists have assumed that a small number of those resulting particles will be anti-protons. Most of those will be instantly annihilated when they collide with particles of ordinary matter. But those which don’t collide should get trapped in the Earth’s torus-shaped Van Allen radiation belt, and form a layer of antimatter in the Earth’s atmosphere.

Van Allen radiation belts : image stars.astro.illinois.edu

Wired reports on the paper in The Astrophysical Journal Letters –  The discovery of geomagnetically trapped cosmic ray antiprotons bu O. Adriani et al. 2011 ApJ 737 L29 doi: 10.1088/2041-8205/737/2/L29

Data from the cosmic ray satellite PAMELA has added substantial weight to the theory that the Earth is encircled by a thin band of antimatter. The satellite, named Payload for Antimatter Matter Exploration and Light-nuclei Astrophysics, was launched in 2006 to study the nature of cosmic rays — high-energy particles from the Sun and beyond the solar system which barrel into Earth.  ……

It was one of PAMELA’s goals to hunt out those tiny numbers of antimatter particles among the ludicrously more abundant normal matter particles, like protons and the nuclei of helium atoms. To find them, the satellite regularly moved through a particularly dense section of the Van Allen belt called the South Atlantic Anomaly. Over a period of 850 days — from July 2006 to December 2008 — sensors aboard PAMELA detected 28 anti-protons. That might not sound like much, but it’s three times more than would be found from a random sample of the solar wind, and is the most abundant source of anti-protons ever seen near the Earth.

But what does this discovery mean, other than proving that a bunch of theorizing physicists were correct? The discovery opens the doors to harnessing those anti-protons for a variety of medical, sensing and, most importantly, rocket-propelling applications.

In a 2006 NASA-founded study by Draper Laboratory, researchers wrote, “it has been suggested that tens of nanograms to micrograms of anti-protons can be used to catalyze nuclear reactions and propel spacecraft to velocities up to 100 km/sec.”

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