Posts Tagged ‘Science’

Update: Two more papers retracted by Mount Sinai

September 24, 2010
Mount Sinai School of Medicine logo.png

Image via Wikipedia

There is an epidemic of retractions.

Retraction Watch reports that Gene therapy researcher Savio Woo has retracted two more papers in addition to the 4 retracted earlier.

Mount Sinai School of Medicine researcher Savio Woo, whom Retraction Watch reported last week has already retracted four papers from major journals as two postdocs have been fired from his lab, has retracted two more from Molecular Therapy: The Journal of the American Society of Gene Therapy.

The two papers, both from 2007, were “Metabolic Basis of Sexual Dimorphism in PKU Mice After Genome-targeted PAH Gene Therapy” and “Correction in Female PKU Mice by Repeated Administration of mPAH cDNA Using phiBT1 Integration System.” As Nature noted in its coverage of the other retractions, the papers apparently followed from a now-retracted paper in the Proceedings of the National Academy of Sciences that, as we noted in a previous post, “claimed to have discovered a possible cure for phenylketonuria, or PKU, in mice.”

Li Chen and Zhiyu Li were the pot-docs implicated.

New Scientist permits the sun to join the climate club

September 23, 2010

It does seem as if the AGW establishment are preparing the ground for admitting that the sun is perhaps critical for climate.

The New Scientist runs an editorial today grudgingly admitting that “The sun’s activity has a place in climate science”.

FOR many years, any mention of the sun’s influence on climate has been greeted with suspicion.

People who believe human activity has no effect on the climate staked a claim on the sun’s role, declaring it responsible for the long-term warming trend in global temperatures. Climate scientists were often uneasy about discussing it, fearful that any concession would be misunderstood by the public and seen as an admission that climate sceptics are right.

No one has ever denied that the sun has an effect on climate. But the consensus view has always been that variations in the sun’s activity, such as the 11-year sunspot cycle, have insignificant effects. While this remains true, the latest findings show that the sun might be significant on a more regional scale. It seems changes in solar activity can have consequences ranging from higher rainfall in the tropics to extreme weather events in the north.

Mighty sun

But then they go out of their way in this article (see “The sun joins the climate club”) to denigrate the sun.

THE idea that changes in the sun’s activity can influence the climate is making a comeback, after years of scientific vilification, thanks to major advances in our understanding of the atmosphere.

The findings do not suggest – as climate sceptics frequently do – that we can blame the rise of global temperatures since the early 20th century on the sun. “There are extravagant claims for the effects of the sun on global climate,” says Giles Harrison, an atmospheric physicist at the University of Reading, UK. “They are not supported.”

Where solar effects may play a role is in influencing regional weather patterns over the coming decades. Predictions on these scales of time and space are crucial for nations seeking to prepare for the future.

Over the famous 11-year solar cycle, the sun’s brightness varies by just 0.1 per cent. This was seen as too small a change to impinge on the global climate system, so solar effects have generally been left out of climate models. However, the latest research has changed this view, and the next report by the Intergovernmental Panel on Climate Change (IPCC), due in 2013, will include solar effects in its models.

But the sun does not much care (Beware the Icarus Syndrome) I think for the scientific establishment and will continue to do its own thing.

Habitable planet to be discovered in May 2011?

September 22, 2010

The only thing certain about forecasts is that they are more often wrong than right – and I exclude forecasts made entirely on known science or “laws” of nature where the level of uncertainty is insignificant (e.g. the sun will rise tomorrow). Nevertheless “Future History” which is a study of how forecasts evolve and how accurate they have been is a most powerful tool when making judgements about directions to follow and actions to be taken. In management “Future History” methodology is, I think, one of the most powerful tools for the development of corporate strategies and action plans.

The New Scientist reports that :

“Two researchers have used the pace of past exoplanet finds to predict that the first habitable Earth-like planet could turn up in May 2011”.

In 1965, Intel co-founder Gordon Moore observed that the number of transistors that fit on a chip doubles about once every two years – a trend now known as Moore’s law. Samuel Arbesman of Harvard Medical School in Boston wants to see if scientometrics – the statistical study of science itself – can similarly be used to not only study past progress but also to make predictions.

He and Greg Laughlin of the University of California, Santa Cruz, are testing the idea with exoplanets. Over the past 15 years or so, the pace of planet discoveries has been accelerating, with some 490 planets now known. “It is actually somewhat similar to Moore’s law of exponential growth,” Arbesman says.

To predict when astronomers might find the first planet similar in size to Earth that also orbits far enough from its star to boast liquid water, the team scoured the discovery records of 370 exoplanets.

They focused on two basic properties needed for habitability: a planet’s mass and its surface temperature. They used these two factors to assign each planet a ‘habitability metric’ ranging from 0 to 1, where 0 was uninhabitable and 1 is close to Earth’s twin.

A rough estimate of each planet’s habitability was then plotted against the date of its discovery. Using different subsets of the 370 planets, the researchers made curves from the individual points and extrapolated the curves to find when a planet would be found with a habitability of 1. They then analysed the range of discovery dates to determine which would be most probable.

Habitable planets: http://t2.gstatic.com/images

Their calculations suggest there is a 50 per cent chance that the first habitable exo-Earth will be found by May 2011, a 75 per cent chance it will be found by 2020, and a 95 per cent chance it will be found by 2264.

In fact, exoplanet researchers have made forecasts of the future informally, plotting the mass of planets against the date of discovery to see how the field is progressing. “We’ve done that for many years at conferences,” says Eric Ford of the University of Florida in Gainesville. “The new aspect of this paper is putting an uncertainty on those predictions and unfortunately the uncertainty is quite large.”

One source of uncertainty is how factors like changes in funding and the development of new techniques and technology can alter the pace of discovery. “Like the stock market, past returns are no guarantee of future performance,” Ford says.

“There are always these complex factors of how science is actually done,” Arbesman agrees. But he says the forecasting technique could still prove useful, even if these factors are not accounted for directly. In part, that is because new technologies tend to take a while to ramp up, so they may not lead to sharp jumps in the number of discoveries made.

Previously, Arbesman has quantified how the ease of discovering new mammalian species, chemical elements, and asteroids affects the rate of their discovery. New species and asteroids are more difficult to find the smaller they are, and indeed larger ones are found first. For chemical elements, the opposite is true, since the bigger they are, the rarer and more unstable they tend to be.

After Harvard’s Hausergate, now misconduct at Mount Sinai

September 21, 2010
Mount Sinai School of Medicine logo.png

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Earlier this week, the blog Retraction Watch called attention to four recent paper retractions by noted gene therapy researcher Savio Woo of Mount Sinai School of Medicine in New York City. Today, the school said in a statement that two of Woo’s postdoctoral fellows have been fired for research misconduct and that an internal investigation has cleared Woo of any wrongdoing.

Two of Woo’s post-doctoral fellows at Mount Sinai School of Medicine were dismissed for “research misconduct,” said Ian Michaels, a spokesman for the institution. According to Michaels:

When Dr. Savio L C Woo came to suspect that two post-doctoral fellows in his laboratory may have engaged in research misconduct he notified the Mount Sinai Research Integrity Office. Mount Sinai immediately initiated institutional reviews that resulted in both post-doctoral fellows being dismissed for research misconduct. At no time were there allegations that Dr. Woo had engaged in research misconduct. As part of its review, the investigation committee looked into this possibility and confirmed that no research misconduct could be attributed to Dr. Woo, who voluntarily retracted the papers regarding the research in question. Mount Sinai reported the results of its investigations to the appropriate government agencies and continues to cooperate with them as part of its commitment to adhere to the highest standards for research integrity.

File:HippocraticOath.jpg

Wikipedia: A twelfth-century Byzantine manuscript of the Hippocratic Oath.

According to ScienceInsider, the names of postdocs Li Chen and Zhiyu Li were recently removed from Mount Sinai’s directory. Chen and Li were listed as first authors on the retracted papers. Three  major journals — Proceedings of the National Academy of SciencesHuman Gene Therapy, and the Journal of the National Cancer Institute — recently retracted papers authored by Woo and others.

In a retraction notice issued this month, Woo wrote that:

It was discovered that some of the micrographs in two papers we published [figure 4 in J Natl Cancer Inst 2008;100:1389-1400 (1), and figure 3 in Hum Gene Ther 2009;20:751-758 (2)] are apparently duplicated. This has been reported to the institutional research integrity committee by the authors and while the outcome of an investigation is pending, the undersigned co-authors respectfully request a retraction of both papers and sincerely apologize to our colleagues.

The four papers in question focus on two different areas of gene therapy research. One pair, published in 2008 in the Journal of the National Cancer Institute and in 2009 in Human Gene Therapy, investigate genetically engineered bacteria as a weapon against cancer. The other two papers describe a method for using bacterial enzymes to introduce therapeutic genes. A 2005 paper in the Proceedings of the National Academy of Sciences reports experiments in which mice with the metabolic disorder phenylketonuria appeared to be cured using this method. As a demonstration of the promise of gene therapy, that work garnered some media coverage, includingthis article in Science. A 2008 paper in Human Gene Therapy described the use of the technique in human cells.

Source: http://blog.the-scientist.com/2010/09/20/new-in-a-nutshell/

Harvard reviews Hauser’s work – but is the purpose investigation or vindication?

September 17, 2010
Harvard is reviewing all “relevant” work by Marc Hauser . But there is a large element of “damage control” and “vindication” of Hauser’s co-workers which is mixed in with the investigation. It is to be hoped that they will be able to resist the temptation to stand on the position that if further misconduct by others cannot be rigorously proven then these others can be acquitted. Now that Hauser’s misconduct has been established the onus of proof shifts – and must do so. The default position must be that all his work is now tainted unless shown beyond reasonable doubt to be otherwise.

The focus must be on investigation and not on a pre-planned vindication or on “rescuing” the money spent if the work is suspect.

http://www.thecrimson.com/

With a federal investigation now underway, much of Hauser’s research has been called into question—and with it, the annals of literature that have grown out of it. In response, the Psychology Department at Harvard has set in motion a project to review Hauser’s work and to determine the areas of his groundbreaking research that can be salvaged.

Cotton-top tamarind

In the last 10 years alone, Hauser has published 143 articles and four books, work that has helped form the foundation for an entirely new field of science. “It creates a lot of uncertainty for people in those fields,” said a Harvard psychology professor who asked to remain anonymous, stating that the situation is still evolving. “They may begin to worry about whether they can trust other findings from that lab.”

The department established a committee to begin a process that could include combing through decades of research. “We are starting a process in collaboration with the animal cognition community about how to deal with this,” Carey said. “Clearing the record is the way you deal with the integrity of the science.” Carey said that the department has also assumed the responsibility of vindicating any department members—students and colleagues alike—who may have worked with Hauser in the past.

According to his curriculum vitae, Hauser has advised 24 Ph.D. students and overseen 15 post doctoral students. The CV lists 221 published papers authored or co-authored by him. And in an academic web of peer research, hundreds of published articles cite and work off of Hauser’s research. And in an academic web of peer research, hundreds of published articles cite and work off of Hauser’s research.

Hauser has made a name for himself by executing novel research techniques in the field of animal cognition. His work with primates and cotton-top tamarinds—the subject of Hauser’s only article to have been retracted—has involved a unique set of research skills and costly access to the animals.

“You don’t want to throw out about two decades of groundbreaking work, but you also don’t want to build a science on shaky ground,” said the psychology professor. “How do we rescue millions of dollars of research?” the individual added.

Microscopic secrets

September 12, 2010

The Guardian reports that Spike Walker was awarded the Royal Photographic Society‘s combined Royal Colleges medal for his ‘outstanding contribution to photography and its application in the service of medicine’. A retired schoolteacher, Spike produces photomicrographs in his garage, which he has converted into a laboratory

Dopamine is a key neurotransmitter released in our brains when we do something rewarding. The dopaminergic system is behind most good feelings we have, and it is also the chemical that is targeted by highly addictive drugs such as cocaine.

http://thebeautifulbrain.com/wp-content/uploads/2010/09/Dophamine.jpg

The Beautiful Brain: To create this beautiful micrograph of dopamine crystals, Spike Walker, who won Thursday evening’s Royal Photographic Society‘s Combined Royal Colleges Medal, shone polarized light at the minute chemical structures. The crystals reflect light at different wavelengths depending on their orientations within the overall chemical structure. According to Walker, using this technique highlights more detail in the crystal structure than regular observation through a microscope.

Crystals of stearic acid, a saturated long-chain fatty acid found in animal fat and cocoa butter.

http://static.guim.co.uk/sys-images/Guardian/Pix/pictures/2010/9/8/1283953758659/Crystals-of-stearic-acid-010.jpg

Bike blog: Crystals of stearic acid

Michael Mann and Marc Hauser

September 4, 2010

I am not sure if the cases of Marc Hauser(Harvard)  of Hausergate and Michael E Mann (Penn State and the University of Virginia) of Climategate are strictly comparable since the two gates follow different routes in the faking of science.

Climategate was more of a group activity by a small clique with a great deal of group-think, whereas Hausergate was much more solitary.  The peer-review process was perverted to an end by the Climategate gang but this is not apparent with Hauser. Mann’s “hockeystick” was more a “fudging” of some data, “cherry-picking” and massaging statistical method to support a pre-determined result while Hauser seems to have just plain faked the data he wanted to support his personal theories. The pursuit of tenure and publications and fame (and some associated fortune) are probably common to both cases.

Climategate however affected policy and had a clear political agenda. Many involved around Climategate and the IPCC have murky ties to the multi-billion carbon scam. In Hausergate the political agenda, if any, is rather soft.

But what is noteworthy is the increase in the number of such comparisons being made and that such comparisons seem appropriate:

  1. If Michael Mann Had Worked At Harvard Instead Of Uva, Would He Now Be Working At Burger King Or Mcdonald’s?
  2. David Sheffield ’11: Scientific misconduct
  3. Monkey business?
  4. “HAUSERGATE” IS GOOD FOR SCIENCE
  5. Two Different Approaches to Academic Monkey Business

Amazing: Hauser “solely responsible” but still maintains control of his lab!!

September 3, 2010

Amazing!

The Harvard Crimson reports that:

Harvard Psychology Professor Marc D. Hauser will remain in charge of his laboratory in William James Hall under “supervision established by the Dean of the [Faculty of Arts and Sciences],” a University official said yesterday.

FAS spokesman Jeff Neal declined to elaborate on the nature of the supervision, stating only that FAS Dean Michael D. Smith had imposed the additional oversight.

Neal added that graduate and post-doctoral students were given the option of switching advisers or continuing their research under Hauser “in order to avoid potential disruption to their careers.

Meanwhile, University of Washington Psychology Professor Michael D. Beecher said “people should be patient and let this thing play out and not rush to judgment on Marc.”

“I’m not sure to what extent the problem is Marc was fast and sloppy—and I don’t think he will be anymore,” he said.

“Fast and sloppy” is the current euphemism it seems at the University of Washington for faking results. Fatuous words about “not rushing to judgement”. 15 years ought to be enough. Hauser has been playing this game at least since 1995.

The wagons indeed are circling but while Hauser’s ethics are in tatters those of Harvard with their reluctance to take a stand do not impress much either.

http://www.nonprofituniversityblog.org/wp-content/uploads/double-standards.png


Hauser will not teach Harvard Extension School class

August 31, 2010

From the Boston Globe, by Carolyn Y. Johnson August 31, 2010:

Harvard psychology professor Marc Hauser will not be teaching a Harvard Extension School class on Cognitive Evolution that was scheduled to start today, or a spring class called “The Moral Sense: From Genes to Law.”

Hauser, who was found by an internal Harvard investigation to have engaged in scientific misconduct, is on a one-year leave from research and teaching duties in the university’s main Arts and Sciences school, but the Globe reported earlier this month that he still planned to teach in the extension school.

But the extension school sent an e-mail to students who were enrolled in the class explaining that the course has been cancelled “at the request of the instructor, Professor Marc Hauser.”

If Hauser pulled out does it mean that Harvard found no problem with his continuing the classes?

Peer-review evolves

August 31, 2010

A welcome development.

The traditional method, in which independent experts evaluate a submission, often under a veil of anonymity, can take months, even years. Clubby exclusiveness, sloppy editing and fraud have all marred peer review on occasion. Anonymity can help prevent personal bias, but it can also make reviewers less accountable; exclusiveness can help ensure quality control but can also narrow the range of feedback and participants.

Just as “consensus” science is meaningless so is expecting good science to be subject to a “democratic process”. But when reviewers show bias (in acceptance or in rejection) or misuse and hide behind the cloak of anonymity and are not required to be accountable then Hausergate and Climategate become inevitable.

From Wikipedia: http://en.wikipedia.org/wiki/Peer_review

Richard Horton, editor of the British medical journal The Lancet, has said that

The mistake, of course, is to have thought that peer review was any more than a crude means of discovering the acceptability — not the validity — of a new finding. Editors and scientists alike insist on the pivotal importance of peer review. We portray peer review to the public as a quasi-sacred process that helps to make science our most objective truth teller. But we know that the system of peer review is biased, unjust, unaccountable, incomplete, easily fixed, often insulting, usually ignorant, occasionally foolish, and frequently wrong.

The New York Times reports (http://www.nytimes.com/2010/08/24/arts/24peer.html?_r=1):

Now some humanities scholars have begun to challenge the monopoly that peer review has on admission to career-making journals and, as a consequence, to the charmed circle of tenured academe. They argue that in an era of digital media there is a better way to assess the quality of work. Instead of relying on a few experts selected by leading publications, they advocate using the Internet to expose scholarly thinking to the swift collective judgment of a much broader interested audience.

“What we’re experiencing now is the most important transformation in our reading and writing tools since the invention of movable type,” said Katherine Rowe, a Renaissance specialist and media historian at Bryn Mawr College. “The way scholarly exchange is moving is radical, and we need to think about what it means for our fields.”

That transformation was behind the recent decision by the prestigious 60-year-old Shakespeare Quarterly to embark on an uncharacteristic experiment in the forthcoming fall issue — one that will make it, Ms. Rowe says, the first traditional humanities journal to open its reviewing to the World Wide Web. Mixing traditional and new methods, the journal posted online four essays not yet accepted for publication, and a core group of experts — what Ms. Rowe called “our crowd sourcing” — were invited to post their signed comments on the Web site MediaCommons, a scholarly digital network. Others could add their thoughts as well, after registering with their own names. In the end 41 people made more than 350 comments, many of which elicited responses from the authors. The revised essays were then reviewed by the quarterly’s editors, who made the final decision to include them in the printed journal, due out Sept. 17.

“Knowledge is not democratic,” said Michèle Lamont, a Harvard sociologist who analyzes peer review in her 2009 book, “How Professors Think: Inside the Curious World of Academic Judgment.” Evaluating originality and intellectual significance, she said, can be done only by those who are expert in a field.

At the same time she noted that the Web is already having an incalculable effect on academia, especially among younger professors. In her own discipline, for instance, the debates happening on the site Sociologica.mulino.it “are defined as being frontier knowledge even though they are not peer reviewed.”

The most daunting obstacle to opening up the process is that peer-review publishing is the path to a job and tenure, and no would-be professor wants to be the academic canary in the coal mine.