Jonathan Latham, PhD and Allison Wilson, PhD

You may not have heard of it, but a potential landmark document in the fields of development and agriculture (called by some the Intergovernmental Panel on Climate Change (IPCC) of agriculture) is currently in the late stages of reaching fruition.

Drafted by around 400 scientific and social science experts from around the world, it is called the International Assessment of Agricultural Science and Technology for Development (IAASTD). The IAASTD (www.agassessment.org/) is unusual in being a collaborative document evaluating solutions for agriculture, poverty and development that is actively inclusive. Thus, it is not only multi-disciplinary but also inclusive in terms of geography, institution and gender. As such, the IAASTD is potentially extraordinarily valuable as a uniquely representative and holistic document of the best current thinking in agriculture and development. In this it is a significant departure from most international agriculture reports that are typically dominated by one perspective, one government or one interest group (and which typically fails to help poverty for that reason).

In addition to the above, there is a further reason to value the IAASTD. It asserts repeatedly what it terms the multi-functionality of agriculture, by which it means that agriculture is not just a provider of food or fodder, but a provider also of social security, of ecosystem services, of landscape value, as well as other ‘outputs’.

Perhaps inevitably, given this broad and deep perspective, the current IAASTD draft adopts a more sophisticated analysis than is usual in international reports which have a habit of proposing solutions to poverty that resemble Escher’s impossible objects. Each report may be internally consistent but clashes with other goals. Thus agricultural objectives, for example, typically are incompatible with social objectives and environmental objectives for development. IAASTD, therefore, should be seen as a novel attempt to use an inclusive and multidisciplinary approach to circumvent these problems.

Therefore, instead of understanding agricultural development problems as principally functions of low yields and lack of productivity, the IAASTD considers wider issues such as food quality, sustainability, water use, land tenure, and energy use as crucially important components of any solution. Furthermore, it attempts to recognise the rights and needs of small farmers, women farmers and the hungry while also giving appropriate emphasis to the significance of power and its unequal distribution in the creation and maintenance of poverty. In line with this analysis the draft promotes special policy emphasis on small/poor farmers, the involvement of women in farming and non-chemical farming in order to promote food security.

If they are ever implemented, the lessons drawn by IAASTD (at least those in the current draft) would represent a remarkable break with current practices which typically emphasise farm consolidation and chemical-intensive agriculture (though these goals are often not described explicitly).

It is often lamented that our societies have an abundance of knowledge and a shortage of wisdom, but the current IAASTD draft comes as close to providing wise guidance for agriculture and development as we have yet seen. Its chief message is appropriately revolutionary: we have so far fed the world principally by depleting natural capital, and we must now look beyond business as usual if we really want to address poverty.

The GMO Angle

The IAASTD draft document is surprising for still another reason. Although supported by the World Bank, it does not offer much support for transgenic crops as the best hope, or even as a particularly useful tool, to alleviate the agricultural ills that beset developing countries, the hungry and the poor.

Most likely, inclusiveness and scarce support for GMOs by the IAASTD are in fact connected. It is probably no coincidence that a document arrived at transparently, using a tolerably democratic process (i.e. it was not written behind closed doors), and using a multidisciplinary approach, should conclude that GM crops have ‘lingering safety concerns’ and may even be harmful to rural development.

These conclusions in general, and the lack of support for GMOs in particular, are immensely unwelcome in some quarters. The publicity machines of Monsanto, Syngenta and others have not spent twenty years carefully positioning transgenics as the solution to every agricultural problem in order for them to be ignored by the largest and most diverse collection of agriculture and development policy experts ever assembled.

Last October, Monsanto and Syngenta resigned altogether from the IAASTD project. Though they gave no public reasons for their resignation, the industry body CropLife International told Nature magazine that an inability to make progress in arguing for GMOs was the fundamental reason (1).

A Tragedy for the Poor?

In a recent editorial, Nature magazine argued the interesting point that withdrawal of these companies was a tragic event. The companies, said Nature, were ‘deserting the poor’ (1). Leaving aside that Monsanto and Syngenta were a very small part of the IAASTD process, this statement is hard to support from a scientific point of view. Are Monsanto scientists more knowledgeable about poverty, development and the needs of developing country agriculture than university or government scientists? Probably not. Do Syngenta scientists have fore-knowledge of impending agricultural developments not available to the rest of us? They may have, but if so these are company secrets which have not so far been made available for discussion or disputation. Does Nature believe that academics and government scientists are unable to make the arguments for biotechnology? But if the scientific need for the companies’ presence was hardly overwhelming, it follows that neither is their loss a particularly significant one.

The inclusion of these company scientists was primarily a recognition, not of their expertise but of something else – most likely the power and influence of their employers, plus the company presence on the IAASTD steering committee and the companies’ financial support of the IAASTD. All of these are essentially political reasons for inclusion. Once included, it would be naive, however, not to have expected that their primary goal would be anything other than to ensure that the assessment erected no obstacles to the introduction of transgenics, and so it proved. It was predictable perhaps, but Monsanto and Syngenta were about as useful to the assessment as Exxon would have been at the IPCC.

The Real Motive for Withdrawal?

As the science media correctly asserted, the IAASTD is important (which begs the rather important question of why they have up to now ignored it). But if their accounts are to be believed, Syngenta and Monsanto’s withdrawal from the IAASTD can be fully explained by the frustration and difficulties of a handful of mid-level employees (2, 3). But is this really a plausible explanation? That multinational companies base strategic decisions on the ‘frustration’ or convenience of their employees? Far more likely surely, especially given that some negative publicity for the companies would (and did) accompany withdrawal, is that this explanation is not the real one. More plausible by far is the possibility that Monsanto and Syngenta’s withdrawal was carefully calculated.

History tells us that the most common reason participants abandon important but frustrating multi-party negotiations is when they believe they can better achieve their aims by abandoning, and therefore delegitimising, whatever agreement is eventually reached. And for maximum effect delegitimisation has to occur in public. If this was, in fact, their strategy, then Monsanto and Syngenta would have been very pleased indeed by what happened next.

Following their withdrawal, Nature Biotechnology devoted its full editorial page to questioning the credibility of the (post-corporate) assessment, reporting that IAASTD’s criticisms of GMOs were “unsubstantiated” and reflective of a “bias against top-down solutions” and further that the report was “skewed” and not “representative” (2). Nature’s editorial called the report “undoubtedly over-cautious and unbalanced” and agreed that the company defections were “a blow to the credibility” of the IAASTD (1). The largest article of all was a feature in Science (3). As with Nature Biotechnology, the core of the Science article focused on the “question of balance” and assertions that the outcome was negative because of “bias”. Science even reported the no doubt impartial molecular biologist Jonathan Gressel as saying “The whole thing was incredibly stacked”. Though giving more-or-less respectful attention and space to defenders of inclusiveness, Science gave no space at all, in four pages, to anyone prepared to argue the possibility that the IAASTD assessment of GMOs was fair and realistic. Perhaps what would have made Monsanto and Syngenta most pleased was the allegation by a person “who asked not to be named” that the “best scientists” were not on the IAASTD (3).

In placing the blame for the corporate boycott exclusively with the IAASTD, perhaps it never occurred to any of the journal editors that in so doing they were supporting a tiny handful of corporate biotechnologists against the aggregated views of 400 independent scientists?

Monsanto and Syngenta have so far won the media battle, but the real test of their strategy is still to come: will they attempt, and if they do, will they succeed, in derailing adoption (or modifying the text) of the final report? If they were to succeed that really would be a tragedy for the poor, because the IAASTD, at least in its draft form, is a potentially world-changing document. It offers a lot and it asks a lot: a chance to make a real improvement to livelihoods and sustainability in return for rethinking agriculture as usual. It is a shame that the science media would rather support (big) business as usual.

Download the draft executive summary of the IAASTD (called the Synthesis report)

Jonathan Latham, PhD and Allison Wilson, PhD

Commercially, insect-resistant transgenic (GMO) plants are made by inserting a gene coding for one of a family of toxins produced by the soil bacterium Bacillus thuringiensis. These Bt toxins are regarded by most regulators to be safer for the environment than externally applied synthetic pesticides and this is because, as plant-expressed proteins, they are considered specifically targeted to organisms that consume the crop (Glaser and Matten, 2003). As a result of this understanding Bt toxins expressed by transgenics are managed as a ‘public good’ by the US Environmental Protection Agency (US-EPA 1998).

However, Bt toxins are often expressed at high levels within plant tissues (typically for insertion event MON810 this means around 10ug/g fresh weight of Cry1Ab) and they persist in the soil, either within plant cells or as native protein (Baumgarte and Tebbe 2005; Griffiths et al., 2006). Therefore, contained within a field of Bt maize there can be many kilograms of a Bt protein at any one time. As a consequence, there is potential for significant exposure of non-target organisms, both in and around fields growing transgenic Bt crops.

Environmental risk assessments of transgenic crops have until now focused exclusively on consequences for non-aquatic organisms (NRC 2000). A recent study however, showed that debris and pollen of plants transgenic for Bt-toxins can enter nearby agricultural streams in large quantities (Rosi-Marshall et al., 2007). This same paper also reported that two caddisfly species, which are ecologically important stream organisms, are sensitive to Cry1Ab-containing leaves and pollen (Rosi-Marshall et al., 2007). As Bt researcher Angelika Hilbeck (ETH-Zurich) told the BSR News Service: “We have entirely overlooked aquatic ecosystem effects of transgenic toxins”.

Now, a further aspect of freshwater toxicology has been addressed by a study published in the journal Archives of Environmental Contamination and Toxicology. This study reports that Daphnia magna, a freshwater crustacean arthropod commonly used in toxicological investigations, can also be negatively affected by Bt transgenic plant debris containing the Bt toxin Cry1Ab (Bøhn et al. 2008). In this study, D. magna populations were fed either kernels of ground transgenic maize (containing event MON810) or non-modified isogenic maize kernels. The plant material for these experiments was grown in adjacent fields.

The Results

Bøhn et al. found that mortality, growth and fertility of D. magna were all negatively affected by the MON810-containing line compared to the control maize. Interestingly, however, the animals fed transgenic maize showed early maturation, indicating a likely toxic response to a component of the transgenic maize, rather than a response to malnutrition.

The authors suggest that their results reinforce the possibility that Cry1Ab transgenics may have significant implications for aquatic ecosystems. However, the mechanism by which the transgenic maize affects D. magna is not resolved by this data. One possibility is that the assumption that Cry1Ab is lepidopteran-specific may be inaccurate or, alternatively, Cry1Ab may be modified within the cellular environment of plants. In either case, transgenic Cry1Ab, and perhaps other cultivars containing different Bt toxins, may be toxic to non-target organisms to an unexpected degree. Cry proteins may thus be having effects on soil arthropods (for which there are no published studies on Bt toxin effects). Angelika Hilbeck however is cautious: “It is difficult to make cross-comparisons from water to land ecosystems, since they are such different environments”.

Since MON810 was the only Cry1Ab event studied by Bøhn et al., there remains an alternative mechanistic possibility, however, which is that the effects on D. magna are a result of some unanticipated consequence of transgene insertion or expression. Such unanticipated effects are not merely theoretical: Rosi-Marshall et al. normalised their results for C:N ratios because Cry1Ab containing Bt maize varieties have more lignin than non-Bt varieties (Saxena and Stotzky 2001). This normalisation was done to prevent any confounding influences of nutritional quality from affecting their results (Rosi-Marshall et al., 2007).

A recent paper detailing the first proteomic analysis of a MON810-containing cultivar may be relevant to this discussion. The authors found at least 43 significant protein expression differences between the MON810 line and a near-isogenic control (Zolla et al., 2008). Given this perhaps surprising degree of difference between a transgenic cultivar and a non-transgenic isoline, it becomes plausible to imagine that one of these differences might be responsible for the effects observed on D. magna.

A substantial equivalence connection?

Irrespective of whether Cry1Ab (or some other MON810 constituent) turns out to be the specific cause of increased D. magna mortality, Bøhn et al.’s result (and also the caddisfly result) constitute a challenge also to the regulatory doctrine of substantial equivalence. According to this principle, MON810 has been declared ‘substantially equivalent’ and it should be safe for all organisms (other than known targets of Cry1Ab), whether they are D. magna or H. sapiens. Instead, MON810 is apparently substantially equivalent but not safe.

These new results may stimulate discussion of the concept of substantial equivalence and its relationship to GMO safety. One possible interpretation of this data is that it disproves absolutely the existence of any fundamental relationship between substantial equivalence and safety. Instead, it supports the longstanding view that substantial equivalence never was a true scientific concept. Rather, it is a regulatory ‘principle’ associated with no biological relationship nor any theoretical validity (Millstone et al., 1999).

Other interpretations are also possible however: that substantial equivalence is still useful, even if the relationship with safety is not absolute. In this view recent results weaken the relationship but do not disprove it, rather like examples of differences between human and rat toxicology weaken, but do not wholly invalidate, the predictive power of that relationship. Either interpretation however accepts that it may no longer be appropriate to say that a transgenic crop is substantially equivalent and therefore safe.

Thomas Bøhn, however, takes a very different tack: his answer to this conundrum is that MON810 was originally determined incorrectly by US (and also EU) regulators as substantially equivalent. This answer, however, illustrates another apparent problem of substantial equivalence: that there is no agreed, universal or a priori set of criteria of what, in terms of crop composition, constitutes a finding of a substantial difference (Millstone et al., 1999).

Other things being equal, substantial equivalence, it seems, will either have to be reconsidered, or it will acquire the probably unique distinction of violating twice, Karl Popper’s falsifiability criteria of a scientific theory.

Put another way, is substantial equivalence so elastic, either in its specific determination for a particular crop, or in its application as a general measure of safety, that it is not in practice falsifiable?

Jonathan Latham, PhD and Allison Wilson, PhD

Gore Vidal once wrote that “I told you so,” is the most satisfying sentence in the English language. If so, then the imminent launch of Monsanto’s Roundup Ready 2 Yield soybean line is going to provide a lot of satisfaction, though not to supporters of Monsanto. The role of the new glyphosate-resistant line (insertion event MON88978) in the following story is to provide a single, but highly significant, new data point.

The new Roundup Ready 2 Yield line will supercede Monsanto’s original Roundup Ready transgenic soybean (event 40-3-2) and yet it confers the exact same trait and contains the exact same gene as Roundup Ready. So why would Monsanto feel the need, probably at substantial cost, to replace the original Roundup Ready?

A big clue, along with the advertising, is the name. Monsanto claims that Roundup Ready 2 Yield produces a 7-11% superior yield than the original Roundup Ready. This ought to be rather surprising since herbicide resistance is not a yield trait. But the answer is in fact simple: the introduction of Roundup Ready 2 Yield is an admission that the original Roundup Ready had a major yield drag, one of several unanticipated consequences of this insertion event.

What we argued

Many groups and individuals have argued that transgenic plants may be prone to unanticipated consequences, either due to pleiotropy or to effects of transgene insertion (Schubert 2002). Our review papers on the molecular characteristics of transgene insertion sites and the associated genetic consequences of plant transformation techniques provided the first, and still only, review of the mutagenic nature of plant transformation and the consequences for the biosafety of transgenic plants (Wilson et al. 2006; Latham et al. 2006).

Our analysis reached two principal conclusions. The first was that transgene insertions, especially those resulting from particle bombardment, are frequently complex and frequently disruptive, often of multiple coding regions. Secondly, current plant transformation techniques are typically associated with very large numbers of mutations, some of which will inevitably be closely linked to the transgene and therefore hard to separate genetically. Based on these observations we speculated that unanticipated phenotypic consequences were likely to be associated with transgenic plants, and furthermore, that these would sometimes be deleterious or otherwise harmful (see Nature Biotechnology correspondence Bradford et al. 2005; Wilson et al. 2006; Latham et al. 2006).

At the time, a frequent response from regulators, and others, was that, nevertheless, transgene insertion sites and/or linked mutations, were unlikely to result in phenotypic consequences of any significance. This point has been argued in print by Bradford et al. (2005), Altpeter et al. (2005) and Schouten and Jacobsen (2007).

The unanticipated traits of Roundup Ready soybean (event 40-3-2)

Launched in 1996, Roundup Ready soybeans, which express an enol pyruvate shikimate-3-phosphate synthase (EPSPS) gene from the microbe Agrobacterium tumefaciens (and contain no other transgenes), have been an undoubted commercial success. However, they have been controversial, both because of complaints from farmers and because of revelations of unanticipated physiological consequences. These have included stem splitting and probably lignin overproduction (Coghlan, 1999; Gertz and Vencill 1999), small seed size and a yield drag (Elmore et al. 2001; Nelson et al. 2002; Benbrook 1999; Gordon 2007), and last but certainly not least, a significant manganese (Mn) deficiency (Gordon 2007).

Two powerful arguments together suggest that of these unanticipated traits, the manganese deficiency and the yield drag, are caused specifically by the 40-3-2 insertion event, which is contained in all current commercial Roundup Ready soybeans. First, even though the 40-3-2 insertion event has been backcrossed into hundreds of soybean cultivars, Monsanto has consistently failed to separate the unanticipated traits from the transgene, suggesting that they are extremely closely linked to, or inseparable from, the actual site of insertion. This fact alone still allows, however, the possibility that the action of the EPSPS protein might be responsible for the unanticipated traits. The introduction of Roundup Ready 2 Yield, however, suggests that this is not the case. Although Roundup Ready 2 Yield contains different transgene promoter and termination sequences from Roundup Ready, the transgene product, the bacterial EPSPS protein, is identical in sequence (USDA petition 06-178-01p). Nevertheless, according to the same petition, Roundup Ready 2 Yield yields 7-11% over Roundup Ready, which just happens to approximate to the yield penalty that researchers have suggested Roundup Ready confers.

The learning curve

In principle, much could be learned from this story. The first, and perhaps the most significant, is to lay to rest the notion that unintended traits in transgenic plants are invariably unimportant and rare. Not only is 95% of the soybean crop of the United States currently yielding 7-11% less than it should, Roundup Ready soybeans can contain less than 40% of the Mn contained in isogenic lines (Gordon, 2007). Neither of these traits can reasonably be called insignificant.

Secondly, the original petition for Roundup Ready soybeans inadequately analysed the transgenic line prior to commercial approval. As was subsequently shown, the 40-3-2 insertion site of Roundup Ready had a complex and scrambled insertion site and a non-functional transcription termination sequence, which allowed aberrant transcripts to transcribe beyond the transgene and into scrambled DNA (Hernandez et al. 2003; Rang et al. 2005; Wilson et al. 2006). Additionally, the compositional and phenotypic analyses, which were supposed to demonstrate the identity of Roundup Ready to conventional soybeans, omitted important data points. Thus, the petition failed entirely to detect a deficiency in a major nutrient (Mn) as well as the assorted agronomic defects of Roundup Ready soybeans. Attention to any one of these data gaps might have alerted regulators to the problems.

Now available for public inspection is the Monsanto petition for Roundup Ready 2 Yield (USDA petition 06-178-01p). Monsanto, it appears, has learned from some of the mistakes of Roundup Ready. They have replaced the nos terminator, they have also avoided callus culture and instead used meristem culture, which should be much less mutagenic, and also transformed this time with Agrobacterium tumefaciens rather than particle bombardment.

For regulators, however, the learning curve is conspicuous by its absence. Regulators in the USA, the EU and China, as well as elsewhere have already approved Roundup Ready 2 Yield, even though the petition is again flawed. The petition again fails to present a DNA sequence for the insertion site or to analyse DNA flanking the insertion site; it fails to search for aberrant mRNA transcripts; and perhaps most remarkably, its compositional analysis fails to measure even a single mineral nutrient.

Of particular interest to us, the petition also demonstrates that the new Roundup Ready 2 Yield soybean has its own unanticipated plant trait: Roundup Ready 2 Yield plants are consistently 5% shorter than isogenic lines. Evidently, the regulators who have approved Roundup Ready 2 Yield (including the famously ‘stringent’ EU) have agreed with Monsanto’s conclusion that there is “no biological meaning” to this difference (USDA petition 06-178-01p). To us, however, this difference has, in fact, two biological meanings. On a practical level, as any farmer could have pointed out, crop stature is an important agronomic trait: as well as being typically an important weed suppression character; plant stature is important in mechanical harvesting; and also for disease susceptibility, where ground contact and foliage positioning affect in-crop humidity. Secondly, many commercial transgenic crops have unanticipated traits compared to their isogenic lines (e.g. Colyer et al. 2000; Escher et al. 2000; Brodie 2003; Poerschmann et al. 2005; Herrero et al. 2007). Unlike these, however, Roundup Ready 2 Yield used the best available plant transformation methods, yet still has at least one unanticipated trait.

Although Roundup Ready 2 Yield is now approved in many countries, the unsatisfactory nature of the petition means that obvious and important questions regarding its unanticipated traits are still unresolved. Is the reduced stature phenotype an indicator of other defects? Are there other independent unanticipated traits present in Roundup Ready 2 Yield soybeans? These are not unreasonable questions, yet it is difficult not to conclude that regulators are currently uninterested in them.

Perhaps the increasing evidence for unanticipated traits in commercial cultivars will change that and the precision myth of transgenic crops will fade into oblivion. In the meantime, Monsanto has a tricky decision to make, whether to charge farmers more for their ‘yield trait’.

by Jonathan Latham, PhD
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). [CORRECTION: Jan 29th was the date the Ronald group notified PLoS One of probable errors. Retraction formally occurred on Sept 9th. Apologies to Retraction Watch as there was no delay to explain. Footnote 2 is therefore superfluous.]

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 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 own 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.