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SCIENCE & AGRICULTURE: Can the Scientific Reputation of Pamela Ronald Be Salvaged?



                                  PART 1


------------------------------- GENET-news -------------------------------

TITLE:   CAN THE SCIENTIFIC REPUTATION OF PAMELA RONALD BE SALVAGED?

SOURCE:  Independent Science News

AUTHOR:  Jonathan Latham, PhD

URL:     http://www.independentsciencenews.org/news/can-the-scientific-reputation-of-pamela-ronald-public-face-of-gmos-be-salvaged/

DATE:    12.11.2013

SUMMARY: "Professor Pamela Ronald is probably the scientist most widely known for publicly defending genetically engineered (GE or GMO) crops. Her media persona, familiar to readers of the Boston Globe, the Wall Street Journal, the Economist, NPR, and many other global media outlets, is to take no prisoners."

----- archive: http://www.genet-info.org/information-services.html -----


CAN THE SCIENTIFIC REPUTATION OF PAMELA RONALD BE SALVAGED?

Professor Pamela Ronald is probably the scientist most widely known for publicly defending genetically engineered (GE or GMO) crops. Her media persona, familiar to readers of the Boston Globe, the Wall Street Journal, the Economist, NPR, and many other global media outlets, is to take no prisoners.

After New York Times chief food writer Mark Bittman advocated GMO labelling, she called him ?a scourge on science? who ?couches his nutty views in reasonable-sounding verbiage?. His opinions were ?almost fact- and science-free? continued Ronald. In 2011 she claimed in an interview with the US Ambassador to New Zealand: ?After 14 years of cultivation and a cumulative total of two billion acres planted, GE crops have not caused a single instance of harm to human health or the environment.?

This second career of Pamela Ronald?s, as advocate of GMOs (which also includes being a book author, and contributor to and board member of the blog Biofortified) is founded on her first career: at the University of California in Davis she is Professor in the Department of Plant Pathology, Director of the Laboratory for Crop Genetics Innovation, and Director of Grass Genetics at the Joint BioEnergy Institute, among other positions.

This background is relevant because Pamela Ronald is now also fighting on her home front. Her scientific research has become the central question in a controversy that may destroy both careers. In the last year Ronald?s laboratory at UC Davis has retracted two scientific papers (Lee et al. 2009 and Han et al 2011) and other researchers have raised questions about a third (Danna et al 2011). The two retracted papers form the core of her research programme into how rice plants detect specific bacterial pathogens (1).

When the mighty fall, others try to catch them

The first paper was retracted on January 29th 2013, from the journal PLoS One (Han et al 2011). News of the retraction was (belatedly) published on the 11th of September 2013 by the blog Retraction Watch under the headline: Doing the right thing: Researchers retract quorum sensing paper after public process (2).

The second retraction, from Science, was officially announced a month later, on October 11th 2013 (Lee et al 2009). This time, retraction was accompanied by a lengthy explanation (Anatomy of a Retraction, by Pamela Ronald) in the official blog of Scientific American. In this article, Ronald blamed the work of unnamed former lab members from Korea and Thailand. Retraction Watch reported the retraction, this time the same day, as: Pamela Ronald does the right thing again. Also on the same day, The Scientist magazine quoted Pamela Ronald saying it was ?just a mix-up? and repeating her claim that ?Former lab members who had begun new positions as professors in Korea and Thailand were devastated to learn that [we] could not repeat their work.?

Scientifically, the two retractions mean that the molecule (Ax21) identified by Pamela Ronald?s group (in Lee et al 2009) is not after all what rice plants use to detect the pathogen rice blight (Xanthomonas oryzeae) and neither is it a ?quorum sensing? molecule, as described in Han et al 2011.

The media coverage of the retractions didn?t query Ronald?s mea non culpa. Instead, reports added, as UC Berkeley professor Jonathan Eisen put it, ?Kudos to Pam? for stepping forward.

Did Pamela Ronald jump, or was she pushed?

In fact, scientific doubts had been raised about Ronald-authored publications at least as far back as August 2012. In that month Ronald and co-authors responded in the scientific journal The Plant Cell to a critique from a German group. The German researchers had been unable to repeat Ronald?s discoveries in a third Ax21 paper (Danna et al 2011) and they suggested as a likely reason that her samples were contaminated (Mueller et al 2012).

Furthermore, the German paper also asserted that, for a theoretical reason (3), her group?s claims were inherently unlikely.

In conclusion, the German group wrote:

?While inadvertent contamination is a possible explanation, we cannot finally explain the obvious discrepancies to the results in..?..Danna et al. (2011)?

Pamela Ronald, however, did not concede any of the points raised by the German researchers and did not retract the Danna et al 2011 paper. Instead, she published a rebuttal (Danna et al 2012) (4).

The subsequent retractions, beginning in January 2013 (of Lee et al 2009 and Han et al 2011), however, confirm that in fact very sizable scientific errors were being made in the Ronald laboratory. But more importantly for the ?Kudos to Pam? story, it was not Pamela Ronald who initiated public discussion of the credibility of her research.

Was it ?just a mix-up??

Reporting of the retractions also accepted Pamela Ronald?s assertions that simple errors by two foreign and now-departed laboratory members were to blame. But her more detailed description of events, which appeared in Footnotes with technical details for those in the discipline below her Scientific American blog, contradict that notion.

Ronald?s footnotes admit two mislabellings, along with failures to establish and use replicable experimental conditions, and also minimally two failed complementation tests. Each mistake appears to have been compounded by a systemic failure to use basic experimental controls (5). Thus, leading up to the retractions were an assortment of practical errors, specific departures from standard scientific best practice, and lapses of judgement in failing to adequately question her labs? unusual (and therefore newsworthy) results.

Who is responsible?

The International Committee of Medical Journal Editors (ICMJE ) published the first and most widely cited principles of authorial ethics in science. These recommendations are followed by thousands of medical and other scientific journals. The following is the first paragraph of the section regarding authorship:

?Authorship confers credit and has important academic, social, and financial implications. Authorship also implies responsibility and accountability for published work. The following recommendations are intended to ensure that contributors who have made substantive intellectual contributions to a paper are given credit as authors, but also that contributors credited as authors understand their role in taking responsibility and being accountable for what is published.? (italics added)

The ICMJE guidelines go on to state that authorship should not be conferred on those who do not agree to be accountable for all aspects of the accuracy and integrity of the work.

Some scientific journals, have their own policies that provide more specifics. The journal Arteriosclerosis, Thrombosis, and Vascular Biology states:

?Principal investigators are ultimately responsible for the integrity of their research data and, thus, every effort should be made to examine and question primary data.?

Likewise, Columbia University?s guidelines on responsible authorship and peer review concludes:

?Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content.?

Lastly, Science (publisher of Ronald?s retracted Lee et al 2009 paper) has this policy on authorship:

?The senior author from each group is required to have examined the raw data their group has produced.?

It is perhaps surprising then that a senior scientist should publicly disclaim responsibility for research carried out in their laboratory.

Footnotes

(1) Pamela Ronald appeared to be a leader in understanding the mechanisms by which rice, and other plants, detect and resist important pathogens. She and others have (or in the case of Ronald, thought they had) identified specific molecules characteristic of each pathogen that are detected by dedicated receptors in plants. In this case, rice cultivars resistant to the bacterium Xanthomonas oryzeae detect a small protein molecule called Ax21 that derives from the pathogen. The ability to detect Ax21 enables rapid activation of defences and thus confers resistance to the pathogen. This line of research, as it pertains to Pamela Ronald and Ax21, is now retracted.

(2) Retraction Watch does not explain the delay of over 8 months between the retraction and their report of it. Neither is the ?after public process? part of the headline explained.

(3) The theoretical reason is that molecules that warn of incipient plant pathogen infection (as Ax21 was supposed to do) are typically detected by receptors at very low concentrations?otherwise they wouldn?t serve as useful warning molecules. Yet in the experiments from Pamela Ronald?s laboratory (Lee et al. 2009 and Danna et al. 2011) Ax21 is required to be present at concentrations millions of fold higher than other elicitors to achieve the same effects (Mueller et al 2012).

(4) The rebuttal argued, among other points, that: ?experimental differences may explain the failure of Mueller et al. (2012) to observe FLS2-dependent defense-related responses.? (Danna et al 2012).

(5) The errors noted by Pamela Ronald in her Scientific American blog were: a) ?By careful sleuthing, [lab members] found that two out of 12 of the strains??were mislabeled.? b)?In the more recent experiments we found that although the modified (sulfated) Ax21 peptide did induce resistance in Xa21 plants, it also induced resistance in plants lacking the Xa21 immune receptor, an important control.? c) ?Furthermore, results of the pretreatment test were highly dependent on greenhouse conditions.? d) ?They also made mistakes in their complementation tests of the Ax21 insertion mutant with the wild-type Ax21 gene.? (italics added). e) These errors were not caught prior to publication because experiments in the Ronald lab lacked controls. Apparently: ?When laboratory members first established the pretreatment assay years ago, they included diverse controls to optimize the assays. However, in subsequent experiments, some of the controls were dropped to reduce the size of the experiments.?

References

Danna CH, YA Millet, T Koller et al (2011) The Arabidopsis flagellin receptor FLS2 mediates the perception of Xanthomonas Ax21 secreted peptides. PNAS 108: 9286-9291.

Danna CH, XC Zhang, A Khatri, AF Bent et al (2012) FLS2-mediated responses to Ax21-derived peptides: response to the Mueller et al. commentary Plant Cell 24:3174-3176.

Han SW, M Sriariyanun SW Lee, Sharma, O Bahar, Z Bower, PC. Ronald (2011) Small Protein-Mediated Quorum Sensing in a Gram-Negative Bacterium. PLoS One

Lee SW, SW Han, M Sririyanum, CJ Park, YS Seo et al. (2009) A type I secreted, sulfated peptide triggers XA21-mediated innate immunity Science 326: 850-853.

Mueller K., Chinchilla D., Albert M., Jehle A.K., Kalbacher H., Boller T., Felix G. (2012). The flagellin receptor FLS2 is blind to peptides derived from CLV3 or Ax21 but perceives traces of contaminating flg22. Plant Cell 24: 3193?3197.



                                  PART 2

------------------------------- GENET-news -------------------------------

TITLE:   BUDDHIST ECONOMICS AND A GMO RETHINK

SOURCE:  Scientific American

AUTHOR:  Pamela Ronald

URL:     http://blogs.scientificamerican.com/food-matters/2013/09/06/buddhist-economics-and-a-gmo-rethink/

DATE:    18.09.2013

SUMMARY: "Discussions about plant genetic engineering often reflect two starkly opposing narratives. On the one side are the angry mobs who invade research farms to destroy fragile green rice seedlings deemed ?GMOs?. On the other, are the scientists who call for calm and respect for publicly funded research. Too often, it seems, there is little mutual understanding."

----- archive: http://www.genet-info.org/information-services.html -----


BUDDHIST ECONOMICS AND A GMO RETHINK

Discussions about plant genetic engineering often reflect two starkly opposing narratives. On the one side are the angry mobs who invade research farms to destroy fragile green rice seedlings deemed ?GMOs?. On the other, are the scientists who call for calm and respect for publicly funded research. Too often, it seems, there is little mutual understanding.

But times may be changing.

In a forum yesterday hosted by the Boston Review Magazine, a group of  journalists, activists, plant biologists, and farmers as well as academic experts in food security, international agricultural and environmental policy sat around a virtual table to find common ground. All accepted the broad scientific consensus that the process of GE does not pose inherent risks compared to conventional approaches of genetic alteration and that the GE crops currently on the market are safe to eat and safe for the environment. That agreement allowed the discussion to move forward to a more societally relevant issue- the use of appropriate technology in agriculture.

Few consumers question the utility of reading Scientific American?s Food Matters online or using the most efficient technology to do it. Yet many are hesitant to embrace technology when it comes to food and farming. Some find the use of plant genetic engineering (GE), a modern form of plant breeding particularly distasteful.

Yet GE is just one of many technologies used to alter the genetic makeup of our crops. Today virtually everything we eat is produced from seeds that have been genetically altered in some manner.

Conventional methods include grafting or mixing genes of closely related species through forced pollinations, as well as radiation treatments to induce random mutations in seeds.  Such approaches are imprecise, resulting in new varieties through a combination of trial and error, without knowledge of the function of the genes affected.

GE introduces one to few well-characterized genes resulting in fewer genetic changes. In contrast to most conventional approaches, GE allows for introduction of genes from distantly related species, such as bacteria. Over the last twenty years, scientists and breeders have used both conventional and GE technologies to create crop varieties that thrive in extreme environments or can withstand attacks by pests and disease.

What criteria can scientists, farmers and consumers use to assess which type of these genetic technologies is most appropriate for agriculture?

In his 1973 book Small is Beautiful, economist E. F. Schumacher states that an appropriate technology should be low cost, low maintenance and promote values such as health, beauty, and permanence. Environmentalist Stewart Brand used a similar framework to select new technologies for inclusion in his 1969 Whole Earth Catalog. One of the purposes of the Whole Earth catalog was to facilitate a creative or self-sustainable lifestyle.

We can apply Brand and Schumacher?s Buddhist economic criteria to evaluate modern agricultural technologies.

Take, for example, Golden Rice, a provitamin A?enriched rice developed through genetic engineering that comprises many of the properties advocated by Schumacher and Brand. Consumption of Golden Rice, within the normal diet of rice-dependent poor populations, could provide sufficient vitamin A to reduce substantially the 6,000 deaths caused every day by vitamin A deficiency and save the sight of several hundred thousand people per year. This ?biofortification? approach is important to poor farmers and their families in developing countries who lack nutrients and cannot pay the price of improved seed. It is widely considered an improvement on conventional supplementation programs, such as the World Health Organization?s distribution of Vitamin A pills, which costs 40 times more and often does not reach the rural poor who have little access to roads.

Golden Rice is an excellent example of how a particular genetic technology can appropriately serve a specific societal purpose ? in this case, enhancing the health and well-being of farmers and their families. It is a relatively simple technology that scientists in most countries, including many developing countries, have perfected. The product, a seed, requires no extra maintenance or additional farming skills. The seed can be propagated on the farm each season at no extra cost through self-pollination and improved along the way.

Can we conclude from the example of Golden Rice that all GE seeds fall into the category of appropriate technology? Unfortunately it is not that simple. Each agricultural technology must be evaluated on a case-by-case basis.  It is not informative to group all ?GMOs? together without regard to the purpose of the engineering, the needs of the farmer, or the social, environmental, economic, or nutritional benefits.

This central point is addressed by several participants in the Boston Review forum. Journalist Marc Gunther highlights the conspiratorial narrative about GE technology favored by some corporate supported anti-GMO activists. Greg Jaffee, Director of Biotechnology at the Center for Science in the Public Interest points out that better farm management is crucial  to ensure that future GE crops benefit farmers, consumers and the environment. Margaret Mellon, Senior Scientist at the Union of Concerned Scientists argues that GE is not a transformative technology. Rosamond Naylor, Director of the Center on Food Security and the Environment at Stanford University discusses the ethics of GMOs in light of persistent hunger and malnutrition. Robert Paarlberg, author of Food Politics: What Everyone Needs to Know outlines the effectiveness of anti-GMO campaigns in blocking the use of modern technologies in the developing world. Nina Fedoroff, Professor of Biology at Pennsylvania State University and former President of the American Association for the Advancement of Science describes the pervasive disconnect between what is true and what people believe to be true about GMOs. Tim Burrack, Farmer and Vice Chairman of Truth About Trade and Technology  gives an account of today?s farmers who are growing more food on less land than ever before using biotechnology as an essential ingredient. Jennie Schmidt, Farmer and registered dietician reports that farmers choose GE crops because they are economically and environmentally advantageous.  Jack Heinemann, Lecturer in Genetics at the University of Canterbury reminds us that reliance on seed technology alone will not avert agricultural catastrophes. Their commentaries are posted online (just click on names to view each one) and the entire forum will be available in print form in the September Issue of the magazine. Kudos to Boston Review?s editor Deborah Chasman and Managing Editor Simon Waxman for launching this forum.

One unusual and important aspect of the forum compared to many other discussions on GE crops is that it was science-based, critically reviewed and included the perspectives of farmers ?the 1% of US workers that actually produce the food that the rest of us eat and who are at the forefront of evaluating the effectiveness of specific agricultural technologies.

Despite the massive number of technical reports attesting to the safety and environmental benefits of GE crops over the pasts decade, science-based information about food, farming and genetics has only trickled out to the public through government agencies and science-based blogs such as Biofortified.org, Ucbiotech.org, Academicsreview.org. Recently, however, to the delight of plant biologists, farmers, food security experts and skeptics, this trickle has turned into a torrent of excellent reporting.

Consider for example the investigative reporting by a bevy of talented journalists such as New York Times Pullitzer Prize winning author Amy Harmon, DotEarth?s Andy Revkin, Slate?s Daniel Engber, the New Yorker?s Michel Specter, Grist?s Nathaneal Johnson, Discover magazine?s Keith Kloor, Greenwire?s Paul Voosen, and Genetic Literacy Project?s Jon Entine. All have tackled the science behind GE crops eloquently and accurately. A number of informative and entertaining books on the subject have been published over the last few years as well. See for example, Stewart Brand?s Whole Earth Discipline, Michael Specter?s Denialism, and James McWilliam?s Just Food.

As more information is made available demystifying what farmers and plant breeders actually do, the public dialog about GE crops is becoming more sophisticated. Even chefs are taking time out of the kitchen to reevaluate their stance on modern agricultural technologies. Mark Bittman, widely admired for his culinary skills (check out his practical lunch tips) and beautiful prose, but not for his support for genetic engineering,  recently visited one of my neighbors here in the Central Valley (the source of 50 % of U.S. fruits, nuts and vegetable) to learn about tomato farming. He wrote an unusually thoughtful and respectful piece on the approaches the Rominger farm in Winters is taking to advance ecologically based management practices using modern technologies.

What technology then is truly ?appropriate? for agriculture? There is no simple answer to this question. Instead of focusing on how a seed variety was developed, we need to frame discussions about agriculture in the context of environmental, economic, and social impacts?the three pillars of sustainability. We must ask what most enhances local food security and can provide safe, abundant, and nutritious food to consumers. We must ask if rural communities can thrive and if farmers can make a profit. We must be sure that consumers can afford food. And finally we must minimize environmental degradation. This includes conserving land and water, enhancing farm biodiversity and soil fertility, reducing erosion, and minimizing harmful inputs. The most appropriate technology for addressing a particular agricultural problem depends on the context.

Technology evolves. Just as today we source tools through the internet rather than the Whole Earth Catalog (Steve Jobs called the Whole Earth Catalog ?Google in paperback form?), few breeders now rely on primitive domestication for seed production.

As the physicist and philosopher Jacob Bronowski pointed out fifty years ago, ?We live in a world which is penetrated through and through by science and which is both whole and real. We cannot turn it into a game by taking sides. . . . No one who has read a page by a good critic or a speculative scientist can ever again think that this barren choice of yes or no is all that the mind offers?.