Update on “Extra DNA” and Other Problems with Crop Genetic Engineering

I received an email recently from a distinguished professor of plant sciences who encouraged me to update my knowledge of the “extra DNA” problem I mentioned in an article published in the January 2018 issue of Comstocks magazine. He sent me a copy of “Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes“–a paper published in the latter half of 2017 and authored by 13 people (Glenn et al.), 10 of whom were employees of Monsanto Company–to help me do that. He indicated that Glenn et al. “describes all of the procedures, checks and tests that are done on commercialized transgenic traits to address the problem” that I had told the author of the Comstocks article has not been solved in 25 years.

Monsanto’s Current Selection Practices, According to Glenn et al.

I have to admit that I am pretty impressed with the procedures, checks and tests carried out on potential genetically engineered (GE) crop products as documented by these (primarily) Monsanto authors. For example, they indicate that molecular analyses are conducted “to ensure: (i) that only one copy of the DNA insert was in the selected events, (ii) the intactness and integrity of the DNA insert, (iii) the absence of any undesired DNA from the transformation process (e.g. the vector backbone), and (iv) that the DNA insertion had not interrupted endogenous genes.” Additional RNA and/or protein analyses “to confirm that the intended gene products were being produced” are also mentioned in the paper.

I think it should be mandatory for all developers to conduct all of these tests, and for any GE “event” (i.e. individual GE plant) being brought to market to have successfully passed them all.

The “Extra DNA” Problem is Still a Problem

But the bottom line is that the “extra DNA” problem is still a problem. Vector backbone sequences (and other unintended DNA, see below) can still get unintentionally inserted into GE crop plants. Therefore, this problem has not been solved; Monsanto still has to check to ensure “the absence of any undesired DNA from the transformation process (e.g. the vector backbone),” and that is the “extra DNA” problem I referred to in the Comstocks article. In fact, according to Glenn et al., Monsanto checks for “extra DNA” not just once, but twice during the course of bringing a new GE plant variety to market. At Calgene, Inc., back in the early 1990’s, we also checked for “extra DNA” in our tomato, cotton and brassica GMOs, and then threw out any of those GE plants that had any. Based on Glenn et al., Monsanto is doing the same thing…25 years later.

Hopefully, all other developers of GE crop plants designed for human consumption: 1) know about this problem, and 2) are doing the same.

But Monsanto’s Selection Practices Were Not Always This Strict

Take selection criterion (ii) from Glenn et al., for example: to ensure “the intactness and integrity of the DNA insert.”  In the past, Monsanto Company has commercialized multiple GE corn varieties in which the intactness and integrity of the DNA insert was not maintained during the genetic engineering process; the DNA that ended up in the GE crop after the genetic engineering process was not the same as the DNA that was intended to be inserted.

And one of the best examples of a Monsanto GE corn variety in which the integrity of the DNA intended for insertion was not maintained in the final GE corn product is NK603. NK603 is the GE corn tested by Séralini and colleagues in a long-term rat-feeding study, a study that raised concerns–and subsequently controversy–regarding possible toxic effects of NK603 (and of glyphosate-containing herbicide) on animals (see, e.g., this article on the subject in Nature). NK603 GE corn was not only commercialized as an individual GE corn product; according to a report out of Purdue University, it also has been bred into at least half a dozen other GE corn products, some of which are associated with DowAgrosciences and Pioneer Hi-Bred as well as Monsanto.

The Lack of Integrity of the DNA Insert and Intended Gene Products in NK603

The integrity of the DNA inserted into NK603 was not maintained during the genetic engineering process used to create NK603. And that lack of integrity at the DNA level resulted in a lack of integrity of the RNA expressed from the inserted gene(s), and to lack of integrity in the form of a mutation in one of the foreign proteins produced in the GE corn varieties carrying the GE locus from NK603.

According to Monsanto, in addition to a single complete copy of the DNA the company intended to insert into the recipient corn plant (which comprises two versions of genes designed to convey resistance to the herbicide glyphosate), NK603 also includes an “inversely linked 217 bp piece of DNA containing a portion of the enhancer region of the rice actin promoter at the 3’ end of the inserted DNA.” This is another type of “extra DNA” that developers of GE crops do not intend to insert into GE crops: an extra copy of a random chunk of the DNA they do mean to insert, placed randomly adjacent to the intact complete copy of the DNA they do mean to insert.

And as a result of sequencing the inserted DNA to verify its “integrity” in NK603, Monsanto identified not only the extra, inverted piece of the rice gene promoter, but also two point mutations in one of the genes conveying glyphosate resistance, “one of which results in a change of the amino acid leucine to proline at position 214 in the protein.” The other point mutation did not change the amino acid sequence of this protein. Nevertheless, the integrity of the introduced foreign protein had not been maintained.

Additionally, and perhaps of most concern in terms of understanding how the lack of integrity of the DNA insert might affect the biology of the recipient corn plant, Monsanto scientists found that expression of the inserted gene(s) in NK603 produces an RNA transcript comprised of not just information stored in the inserted DNA but also information stored in the corn DNA adjacent to the position in the corn genome into which the insert was randomly placed. That is, “mRNA transcription was detected to initiate in either one of the two promoters of the NK603 insert and…continue into the corn genomic DNA.” RNA is an intermediary molecule that conveys the information stored in DNA to the cellular machinery; some RNAs translate the information coded in DNA into a protein that, in this case, provides resistance to glyphosate; other RNAs are now known to play roles in regulating how other genes are expressed. The upshot is that an unintended gene product, a chimeric RNA molecule comprised of intended insert-DNA-associated sequences plus sequences derived from the corn DNA that just happened to be adjacent to the spot in the corn genome where the foreign DNA insert landed, is produced in NK603 GE corn and any other GE corn varieties into which NK603 has been bred using traditional breeding methods.

More Safety Studies of NK603 are Needed

 We do not know whether the lack of integrity of the DNA inserted into NK603 results in any physiological changes in GE corn plants comprised of this GE corn event.

But we do know that if NK603 had been put through the procedures, checks and tests described in Glenn et al., it would have failed them.

In the meantime, we also know that Séralini and colleagues documented problems in rats fed NK603 over their lifetimes in a study that passed peer-review and was published in a reputable international journal (Food and Chemical Toxicology), but was retracted–more than a year after it had been in print–by the journal’s editor-in-chief after he deemed it “inconclusive.” We also now know that Monsanto played a behind-the-scenes role in the public attack on that study that resulted in its retraction.

What we need now is for that study to be replicated “by a truly independent laboratory using appropriate sample sizes” (David Spiegelhalter, a statistician at the University of Cambridge, UK). We need an update on NK603.

I, for one, would like to know–conclusively–the safety status of NK603 GE corn.

I would hope that the United States Food and Drug Administration, and its counterparts in other parts of the world, would want to know as well.


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Monsanto, Henry Miller, and the FDA

I have been reading with interest various articles reporting on the trove of internal documents obtained from Monsanto during the discovery phase of a federal multidistrict litigation against that company that is currently pending in the United States. (The documents, and a list of articles from all over the world that have been written about them, can also be found on the website of the NGO US Right to Know.)

Attorneys with Baum, Hedlund, Aristel & Goldman, the firm representing hundreds of plaintiffs across the US in the case, indicate that these so-called “Monsanto Papers” “tell an alarming story of corporate malfeasance. They reveal that Monsanto has been manipulating the science…ghost-writing scientific literature…bullying scientists that publish anything negative…and colluding with regulators to ensure ‘positive’ assessments.”

I was especially intrigued to learn that Henry Miller, who was described in The New York Times as “an academic and a vocal proponent of genetically modified crops,” is implicated in the ghost-writing scandal, albeit in regard to a non-academic journal. As reported in The Times, Dr. Miller “asked Monsanto to draft an article for him that largely mirrored one that appeared under his name on Forbes’s website in 2015.” Forbes has since taken the article in question down from its website and ended its relationship with Dr. Miller.

What was not mentioned in the article in The Times, and the reason for my intrigue, is the fact that Dr. Miller was the founding director of FDA’s Office of Biotechnology from 1989 to 1994. During that timespan, Calgene Inc., was seeking approval from FDA to commercialize what turned out to be the first genetically engineered (GE) whole food to enter the marketplace, the Flavr Savr™ tomato. Back then I was part of a team of scientists at Calgene conducting safety studies, explaining to FDA scientists how the genetic engineering process we were using worked, and participating in a dialogue with those FDA scientists about what possible risks might be associated with crop genetic engineering technology.

I have always felt that the timing of the release of FDA’s policy for dealing with GE food and feed products (not to mention the policy itself) made no sense. And now I am wondering how long the relationship between Dr. Miller and Monsanto, which appears to have included ghost-writing in support of that company, has been going on.

Initial safety data on the first GE whole food had been submitted to FDA, but not yet evaluated by the agency, when the May 1992 FDA policy was established

We at Calgene had submitted a large package of data that we hoped demonstrated the safety of our GE tomato to FDA in August of 1991. We had submitted a similarly large package of safety data related to use of a gene conferring resistance to the antibiotic kanamycin, a gene Calgene and most other biotech companies insert(ed) into crops during the genetic engineering process, some 10 months earlier.

But before FDA had responded to these data packages, first by asking questions about their scientific contents and then by asking for more data to support our safety claims—which the agency ended up doing on at least five occasions, FDA came out with its policy for how to “regulate” GE food and feed products in May of 1992. That FDA policy was simple. With only a couple of exceptions, it called for developers of GE food/feed products to voluntarily consult with the agency about them.

The timing of the May 1992 policy just didn’t make sense to me. Why hadn’t the agency waited until it had thoroughly evaluated the safety of (at least) the first GE food product, Calgene’s Flavr Savr™ tomato, before it came out with its policy for “regulating” all GE food/feed products? And, because FDA had not completed evaluation of Calgene’s—or any other developer’s—safety-related data prior to publishing its policy for “regulating” GE foods, how could that policy be based on science?

Thorough evaluation of Calgene’s safety data revealed scientific “surprises” that I feel are relevant to FDA regulation of GE foods

As it turned out, FDA scientists, and we Calgene scientists as well, continued to discover and deal with scientific issues related to the genetic engineering process in general, and the Flavr Savr™ tomato in particular, for some 18 months after the May 1992 FDA policy was published.

For example, FDA contacted Calgene multiple times between December 1992 and September 1993 about concerns they had with one scientific experiment in which minor gastric lesions developed in the stomachs of 7/20 female rats fed one particular variety of Flavr Savr™ tomato. In response, Calgene conducted multiple, various additional studies on that GE tomato variety until FDA was satisfied as to its safety.

And some six months after the May 1992 FDA policy was published, FDA scientists also asked Calgene to carry out experiments to demonstrate that only the foreign DNA we intended to insert into our tomatoes was, in fact, inserted into them. I, for one, was flabbergasted to find out that in about 20% of our GE tomatoes (and other GE crop plants transformed using the Agrobacterium method), much more foreign DNA—and DNA that was not well characterized at that—had been inserted than we had intended. To my knowledge, this “extra DNA” problem still has not been solved and so crop genetic engineers just have to look for extra DNA in each GE plant and throw out those that contain any.

What might FDA’s policy for regulating GE foods/feeds have looked like had the agency waited until after it had concluded evaluation of Calgene’s safety data to set its policy?

If FDA had waited until after it had reviewed all of Calgene’s data, and until after the scientific issues that surfaced during that review had been resolved to its satisfaction—i.e. until a point at which it could base its policy on some actual science—its policy for regulating GE crops might have been very different. FDA might have required that developers check their GE crops for DNA that was not intended to be inserted into them, for example, and/or required animal-feeding studies of new GE crops as is required in the European Union.

So why didn’t FDA wait until it had evaluated all of (at least) Calgene’s data, and then establish its policy based on that relevant science?

Could FDA’s failure to wait until after it had completed evaluation of the relevant data it had in hand before publishing its policy for “regulating” GE foods have had anything to do with a relationship between Henry Miller, Director of FDA’s Office of Biotechnology at that time, and Monsanto?

Back when Henry Miller was serving as the first director of FDA’s Office of Biotechnology (1989-1994), we at Calgene had heard rumors that Monsanto was not happy that Calgene, a little start-up company, might set regulatory precedence with FDA by being first to commercialize a GE whole food. And we knew that Monsanto employees were also in dialogue with FDA during the years leading up to publication of the FDA policy in May of 1992.

I have read many of Miller’s writings since then and often wondered how much he might have been influenced by Monsanto as the 1992 policy was being set. Especially since, as Monsanto’s Vice President for global strategy, Scott Partridge, told The Nation recently, “the [regulatory] process requires a tremendous amount of contact and interaction with the government.”

Now that it has come to light that Monsanto has apparently ghost-writen for Miller about RoundUp/glyphosate, I am even more curious about what kind of influence that company might have had over Miller back when the FDA policy was being formed.

Monsanto’s influence on EPA

After all, the “Monsanto Papers” suggest that Jess Rowland, a (now former) deputy director of the EPA’s pesticide division, had the kind of relationship with Monsanto that caused Congressman Ted Lieu to ask the Justice Department to investigate the possibility of collusion between Monsanto and EPA employees reviewing glyphosate, the herbicide-active ingredient in RoundUp. (And, as reported in The Nation, the EPA’s Office of the Inspector General has claimed to be looking into that.)

So I wonder: how might Monsanto have influenced Henry Miller, back in the early 1990s when he was director of FDA’s Office of Biotechnology (1989-1994), on the subject of how genetically engineered foods should be regulated by FDA?

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Transparent Information about the GMO Ingredient(s) in the “Impossible Burger”

Have you heard about this new non-meat burger that—due to an ingredient produced in a genetically engineered (GE) yeast—has a taste and “blood” like what you would expect from the real thing?

Or, since they are already commercially available for human consumption in 56 restaurants across seven American states, perhaps you’ve already eaten one?

Well, whether you are eating them daily or you’ve never heard of them, you may want to get to know them better because, as quoted in The New York Times [explanatory insertions mine], “F.D.A. believes the arguments presented [by the developers of Impossible Burger], individually and collectively, do not establish the safety of [the GE] soy leghemoglobin [it contains] for consumption, nor do they point to a general recognition of safety.” It was also reported in that article that the “agency has expressed concern that [soy leghemoglobin] has never been consumed by humans and may be an allergen.”

Yes, you read that correctly. The United States Food and Drug Administration (F.D.A.), the U.S. agency “responsible for ensuring the safety of most of the U.S. food supply,” has expressed qualms about the safety of a “key” ingredient in this new “plant-based” burger…and yet you could have one for lunch today at a Hopdoddy or Umami Burger near you.

How is that possible? you may be asking yourself. (Or, “Isn’t that impossible?” might be more appropriate in this case.)

Stephanie Strom’s NYT article is a good place to start for information on this Impossible Burger specifically, as well as for the basics on how food additives and ingredients are—or are not—regulated in the United States more generally.

Turns out, Impossible Burger and other high-tech food developers, have been interpreting a 1958 amendment to the 1938 Food, Drug and Cosmetic Act (FDCA) to mean that they can “self-affirm” a food additive or ingredient as “generally recognized as safe” (GRAS) and then go ahead and market such self-affirmed foods without consulting with, or even notifying, the F.D.A.

But advocacy groups like the Center for Food Safety and the Environmental Defense Fund do not interpret the 1958 amendment that way. EDF’s Tom Neltner was quoted in the NYT article as saying that “The [1958] exemption was meant to cover ingredients that had long been used in the food supply…. It wasn’t meant to allow companies to simply bypass the F.D.A.” And it was not, I would explicitly add, meant to exempt a protein that “has never been consumed by humans and may be an allergen.”

The U.S. Government Accountability Office (GAO) also has a problem with this state of affairs. It released a report in February 2010 titled “FDA Should Strengthen Its Oversight of Food Ingredients Determined to Be Generally Recognized as Safe (GRAS).” But, apparently, F.D.A. has yet to do so.

As I mentioned in my last post, F.D.A. and other U.S. government agencies are currently re-evaluating how foods and food ingredients developed using the techniques of modern biotechnology should be regulated. Hopefully, this major “GRAS loophole” will be eliminated as part of overhauling that regulatory process. (But I, for one, am not holding my breath.)

In the meantime–and especially since Rachel Konrad, a spokesperson for Impossible Burger, informed the NYT that “we believe the public wants and deserves transparency and access to any information they need to decide for themselves whether any food they might eat is safe and wholesome”–below you will find additional information about the GE soy leghemoglobin (etc.) in Impossible Burgers:

  • Konrad stated that “A key ingredient of the Impossible Burger—heme—is an ancient molecule found in every living organism.” But the GE protein that releases that heme in Impossible Burgers when they are cooked–soybean leghemoglobin produced in a GE yeast strain–is a protein naturally found in soybean roots that, as mentioned by the F.D.A. (and noted in the NYT article cited above), “has never been consumed by humans.” It therefore only seems sensible that F.D.A. should not allow a protein that has never been consumed by humans to be self-affirmed by its developer as GRAS.
  • In a document acquired from FDA through the Freedom of Information Act (by the ETC Group, a Canadian environmental organization, and shared with the NYT), Impossible Burger argued that soybean leghemoglobin “is substantially similar [my emphasis] to proteins consumed daily by the global population, in the form of meat and other vegetables” and that “Impossible Foods does not believe that consumption of this protein presents any issues of safety to the consumer.” But this is not a scientifically sound argument, and F.D.A. noted in the FOIA-acquired document that discussion of proteins other than soy lehemoglobin “is not relevant” to safety assessment of the Impossible Burger; and that is because for proteins, even “a relatively small difference in sequence or PTMs [post-translational modifications] can result in a large difference in function, which can be important in predicting protein functions, regulation of protein functions, and in the evolution of new functions” (Jeffery 2016). This “substantially similar” argument comprises a whole new level (a new order of magnitude?) of the “substantial equivalence” argument that has been used by the developers of GE foods up until this point in time. It is an argument that has no basis in protein science as related to safety evaluations and, in my opinion, rather than GRAS, Impossible Burger’s leghemoglobin could be considered a food additive and regulated as such at F.D.A.
  • Additionally, Impossible Burger told FDA that the soy leghemoglobin will be extracted from GE yeast “cells and purified away from other cellular proteins, with a resultant purity of approximately 73% leghemoglobin. The non-target proteins which may co-purify are expected to be safe for consumption based on history of safe consumption of the whole yeast in animals.” But among the many non-target proteins that “may” co-purify with the GE leghemoglobin, Impossible Burger lists “Hypothetical proteins” and “Unnamed protein products.” Impossible Burger may expect those hypothetical proteins and unnamed protein products to be safe, but that doesn’t mean that consumers like me have to.


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Informing USDA’s and FDA’s Thinking About Crops/Foods Derived From Plant Varieties Produced Using Genome Editing Techniques Like CRISPR-Cas9

Both the U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) and the U.S. Food and Drug Administration (FDA) have asked the public for comments on how these agencies might deal with crops and foods derived from new plant varieties produced using new genome editing techniques like CRISPR-Cas9. Public comments are due to both agencies by June 19, 2017 and can be submitted to USDA APHIS here and to FDA here.

I submitted the following comments to these agencies in response to the notices published by APHIS and FDA in the Federal Register last January.


June 16, 2017: Comment to APHIS Re: Proposed revisions to the regulations at 7 CFR part 340

My name is Belinda Martineau, I am trained as a plant molecular geneticist and I was a part of the team of scientists at Calgene, Inc. that carried out safety studies of the Flavr SavrTM tomato in Calgene’s successful effort to gain U.S. regulatory approval for commercializing that genetically engineered (GE) crop product. I thank USDA APHIS for providing this opportunity for the public to comment on the agency’s proposed revisions to the regulations applying to GE crops and for being transparent throughout this process.

It is long past time to make the piecemeal and loop-hole-filled “coordinated” framework for regulating GE crops and other organisms more science-based and more coordinated among the U.S. regulatory agencies involved. Rather than “concern in the 1980s that if an organism was modified using genetic material taken from a plant pest, or a plant pest was used as a vector or vector agent to carry genetic material into an organism, the resulting GE organism could also be a plant pest,” APHIS has used its authority over plant pests to regulate GE organisms over the last three decades because it appeared to be its only means for doing so. The best option for regulating GE crops, back then and now, would be to pass specific legislation for regulating GE crops, rather than to continue forcing a round technology into a square and scattered regulatory hole—an option that would have to be taken by the legislative branch of our government. APHIS mentioned several putative options related to regulating GE crops that would require new legislation in the Federal Register (Vol. 82, No. 12); a complete overhaul of GE crop regulations via legislation should also be considered.

In the meantime, APHIS now considers it “both appropriate and necessary to begin to evaluate GE plants for noxious weed risk.” And, based on the definition of a noxious weed provided in the 2000 Plant Protection Act (PPA), i.e. ‘‘Any plant or plant product that can directly or indirectly injure or cause damage to crops (including nursery stock or plant products), livestock, poultry, or other interests of agriculture, irrigation, navigation, the natural resources of the United States, the public health, or the environment,’’ this aspect of APHIS authority could be used to regulate most GE crops. (NB: no mention of “invasiveness” is made in the PPA definition of a noxious weed.) For example, APHIS now knows that deregulating glyphosate-resistant GE plants has indirectly caused substantial damage to various crops and other interests of agriculture in tens of U.S. states through the development of glyphosate-resistant superweeds. And based on the scientifically based concept of selection pressure, there is every reason to believe that deregulation and consequent wide cultivation of any other herbicide-resistant GE crops will similarly result in development of superweeds resistant to those herbicides and thus result, indirectly, in similar damage to crops and other interests of agriculture. Thus, based on the 2000 PPA, any herbicide-resistant GE crops should be regulated by APHIS; i.e. the regulatory status of herbicide-resistant GE plants should definitely not be “not regulated” (as they are currently on APHIS’s example list).

Additionally, glyphosate-resistant plants could indirectly injure livestock and/or public health since glyphosate is an animal carcinogen and a probable human carcinogen. Therefore, glyphosate-resistant plants should be categorized as noxious weed risks and should be regulated.

In a truly “coordinated” framework for regulating GE crops, APHIS should take the damaging indirect effects of herbicide-resistant GE plants into account when evaluating GE crops for noxious weed risk as per the 2000 PPA definition, and not simply categorize damage associated with application of an herbicide as a concern for the EPA instead. And the “asynchronous timing of the deregulation of herbicide-resistant plants and the associated herbicide registration” must simply end; if APHIS and EPA can’t coordinate such timing for GE crops and the herbicides or other chemicals designed to be specifically applied to them, the “coordinated” framework is broken.

Based on the 2000 PPA definition it also appears that most, if not all, GE crops could be classified as noxious weed risks in terms of their ability to indirectly cause damage to “other interests of agriculture,” such as the economic interests of U.S. farmers who grow non-GMO crops. When the crops of these farmers become intermixed with GE crops, via cross-pollination or post-harvest, economic losses in sales within and outside of the U.S. have been, and can be again in the future, substantial. USDA has expressed concern over this intermixing problem in the past. And the as yet unconfirmed possibility that a GE corn crop developed for biofuel may have been intermixed with corn used for masa and tamale production last winter (http://www.huffingtonpost.com/entry/gmo-ethanol-corn-contamination-raises-concerns-about_us_58e52857e4b0ee31ab9533dd ) serves as an example of how this intermixing problem could cause economic losses to “other interests of agriculture”…or worse. Therefore APHIS should utilize the PPA of 2000 to regulate GE plants/crops to protect against damage to important “other interests of agriculture” in the U.S.

I agree with APHIS’s definitions of genetic engineering and GE organism, but not with its exclusion “from its definition of GE organism, certain organisms that are created using techniques that fall within the scope of genetic engineering….” It is inappropriate and not scientifically sound to minimize concern over the off-target effects which occur as a result of the use of the new genome-editing types of genetic engineering techniques, as well as those that can occur when using the older Agrobacterium-based and biolistics techniques. APHIS states that chemical and radiation-based mutagenesis can create “thousands of mutations in a single organism, and most of the plant breeders’ subsequent efforts involve eliminating unwanted mutations by repeated crosses and selection….” But an off-target activity rate of ≥50% has been reported in the scientific literature for the CRISPR/Cas9 genome editing technique, for example (http://www.sciencedirect.com/science/article/pii/S216225311630049X ), and thousands of off-target changes were recently reported in a CRISPR–Cas9-edited mouse (https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4293.html ), indicating that “single base pair substitutions, as well as deletions of differing sizes” are not as “precisely administered” using genetic engineering as implied by APHIS. And the fact that these off-target changes may comprise “small genetic differences” which may be “not phenotypically observable” does not mean that they are not of concern; most mutations are deleterious, and crops can produce toxic compounds that are not phenotypically observable. As long as there are such high rates of off-target effects associated with genetic engineering, all GE organisms should be evaluated by APHIS for plant pest and noxious weed risk, no exceptions.

The language in the proposed preliminary/provisional Regulatory Status Evaluation Requirements posted on the USDA website (https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/biotech-rule-revision/2016-340-rule/reg-status-eval-data-reqs ), appears to be appropriate for evaluations of the regulatory status of all new crops produced using any GE technology—including genome editing and synthetic biology. But based on the history of GE crops, which includes indirect damage to U.S. crops via superweeds and economic losses due to contamination of non-GMO crops with GE crops, and the fact that off-target effects can occur during the genetic engineering process, it is appropriate for APHIS to require all new GE products to undergo its evaluation process, no exceptions; all developers of GE crops should be required to request a regulatory status evaluation for each new GE product that is developed, on a case-by-case basis prior to each product’s commercialization, and to fulfill the (putative) Regulatory Status Evaluation Requirements described on the USDA website.

I agree with the requirement in step 2. of the proposed preliminary/provisional Regulatory Status Evaluation Requirements, requiring that developers provide “The genotype of the modified organism, including a detailed description of the differences in genotype between the organism subject to the inquiry and the recipient organism.” However, the more specific requirements listed under step 2. fail to explicitly mention a requirement to characterize modified organisms for off-target effects; just as USDA APHIS is proposing that developers submit alignments of modified sequences with the unmodified sequences for intentionally inserted or edited sequences, a truly “detailed description of the differences in genotype between the organism subject to the inquiry and the recipient organism” would require alignments of the entire genomes of the two in order to identify possible off-target effects. The most recent National Academy of Sciences report on GE organisms recommended that techniques used in the various “omics” fields of biology should be employed in characterizing GE organisms; APHIS should require the use of whole-genome sequencing (WGS) to identify all off-target mutations in GE organisms (as was used in the genome-edited mouse study mentioned above: https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4293.html ).


June 16, 2017: Comments to FDA Re: Docket No. FDA-2016-N-4389, Genome Editing in New Plant Varieties Used for Foods; Request for Comments

My name is Belinda Martineau, I am trained as a plant molecular geneticist and I was a part of the team of scientists at Calgene, Inc. that carried out safety studies of the Flavr SavrTM tomato in Calgene’s successful effort to gain U.S. regulatory approval for commercializing that genetically engineered (GE) crop product, which included FDA’s approval of the kanamycin-resistance-conferring protein in those tomatoes as a food additive. I thank FDA for providing this opportunity for the public to help inform the agency’s “thinking about foods derived from new plant varieties produced using genome editing techniques.”

Comments on Question 1.

The greater the ability of a developer of a new plant variety to specifically target an intended change to a specific, hopefully “safe” locus in a crop genome; and the fewer off-target, unintended disruptions (such as insertional mutations, additions of minimally characterized vector backbone sequences, and changes in the relative positions of protein-coding genes, microRNA genes and other elements of genome architecture like enhancers and silencers) that are made elsewhere in the crop genome; and the more collective knowledge that is available about the technique and that is known to and utilized by the developer; and the more fail-safe systems the technique has, the safer the resulting new plant variety will be. A comparison of genome editing and other means for developing new plant varieties in terms of these safety-related characteristics is shown in the table (below).

Unfortunately, scientific knowledge of and experience with plant varieties developed with in vitro recombinant DNA technologies and commercialized over the last 23 years have not provided much in the way of helpful information to be applied to safety assessment of new plant varieties produced using genome editing. If FDA had required developers to conduct long-term animal feeding studies of these new plant varieties, for example, we would now have a better idea of how often unintended, off-target effects might have negative implications for food safety. In fact, even when a long-term animal feeding study did suggest that Monsanto’s NK603 GE corn variety might have negative unintended effects (even if the study’s conclusions were deemed “inconclusive” after thorough examination of all the raw data associated with that study by the editor-in-chief of the peer-reviewed journal it was originally published in: https://www.elsevier.com/about/press-releases/research-and-journals/elsevier-announces-article-retraction-from-journal-food-and-chemical-toxicology ), FDA did not require that developer to provide additional data and/or information to support the safety of their product; I think FDA should have done so. And the flaws associated with the older non-targeted genetic engineering techniques remain; I know of a company that did not know until recently that backbone vector sequences can be inadvertently inserted into new plant varieties transformed using the Agrobacterium-based method. If FDA had required developers to check to ensure that they had not inadvertently inserted their genes of interest into an endogenous plant gene or vector backbone sequences into the recipient plant genome, and if FDA had required developers to conduct long-term animal feeding studies, we would now know a lot more about how to deal with off-target effects.

Comments on Question 2 and 3.

The fact that developers can select a specific gene in a crop to “edit” as opposed to the relatively random insertion of genes–often (27-63% of the time) into another gene thereby mutating that gene–that occurs when using the older genetic engineering methods is a major advantage of the new genome editing technologies. (Although these technologies will also be used to insert foreign genes into plant genomes, and selection of a “safe” site for intended insertion will be an issue in those cases.) However, an off-target activity rate of ≥50% has been reported in the scientific literature for the CRISPR/Cas9 genome editing technique, for example (http://www.sciencedirect.com/science/article/pii/S216225311630049X ), and thousands of off-target changes were recently reported in a CRISPR–Cas9-edited mouse (https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4293.html ). A professor of plant biology at UC Davis stated at a public lecture recently that of the many, many peer-reviewed scientific papers he had read in which the CRISPR method had been used in the reported study, every single one of them also reported off-target effects. These high rates of off-target effects, and the mutations they may result in, make genome-edited plant varieties more likely than traditional-bred plants to present food safety risks. Most mutations are deleterious. Until we know more about such off-target effects and how they might be reduced/eliminated, all products/foods created using these new technologies should be regulated in the U.S., no exceptions. The high rates of off-target events, combined with the newness and consequent lack of experience in using these new technologies to produce foods for human consumption, provide support for FDA taking this cautious and prudent stance with regard to genome-edited foods at this time.

Comments on Question 4.

The step FDA should take to ensure that small firms—as well as large firms and all aspiring developers of genome-edited food or feed organisms—engage with FDA about the safety of such GE foods or feeds is to make engagement with the agency mandatory prior to commercialization of such products. FDA should also establish a mandatory safety evaluation process for these products. The most recent National Academy of Sciences report on GE organisms recommended that techniques used in the various “omics” fields of biology should be employed in characterizing GE organisms; therefore, FDA should, for example, require the use of whole-genome sequencing (WGS) to identify all off-target changes/mutations in all GE organisms (as was used in the genome-edited mouse study mentioned above: https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4293.html ). Advances in molecular technology should be used not just to create new GE foods or feeds, but to ensure that they are safe for long-term consumption as well.

Summary of differences and similarities of various means for developing new plant varieties:

  Ability to target intended change to particular locus in genome Can create off-target, unintended changes in recipient genome (e.g. mutations) Can cause changes in relative positions of genes* Human experience with technique (years) Presence of evolved bio-chemical checkpoint pathways to help ensure proper function  
Hybridization Yes (in terms of synteny) Yes Not usually ~12,000 (domestication)

~120 (Mendelian genetics)


Chemical mutagenesis No Yes Not usually ~70 No  
Radiation-induced mutagenesis No Yes Yes ~90 No  
Agrobacterium-based** (insertional mutagenesis) No Yes Yes ~30 No  
Biolistics (insertional mutagenesis) No Yes Yes ~30 No  
Genome editing (in/dels, gene editing) Yes Yes Yes or No, depending on use ~4 No

* Changes in the position of a gene within a genome, e.g. abnormally juxtaposing a gene with heterochromatin (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721279/ ), can silence or otherwise alter normal gene expression patterns.

** Approximately 20% of the time, this method also leads to insertion of vector “backbone” sequences (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC160498/pdf/061032.pdf ) which, depending on the vector used, may be associated with additional safety risks.



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What Did Monsanto’s Robb Fraley Really Learn From Bill Nye?

I read a piece by Robb Fraley, Monsanto’s Executive Vice President and Chief Technology Officer, called “What I’ve Learned From Bill Nye” in the Huffington Post a few weeks ago. In it, Fraley wrote that he had Bill to thank for teaching him important lessons, the first of which is:

“When you’re not sure if you fully understand a topic you feel strongly about – and are able to recognize that you may be basing your opinion on ideology rather than data – it’s important to push yourself out of your comfort zone to research and learn more.”

Fred Gould, the chairman of the committee that put together the most recent National Academy of Sciences report on GMOs, is shown in the photo accompanying that HuffPost.

I therefore submitted a comment to Fraley’s post, on a topic I hypothesized he probably feels strongly about…Fred Gould’s opinion regarding a safety study on one of Monsanto’s genetically engineered (GE) crop/food products.

It’s been 2 1/2 weeks since I submitted my comment and, as I write this, it has still not been posted. Therefore, I am posting it herein below.

Comment submitted May 14, 2017, in response to “What I’ve Leaned from Bill Nye:”

Since you mention “retracted scientific studies regarding GMOs,” and Fred Gould, the chairman of the committee that put together the most recent National Academy of Sciences report on GMOs, is shown in the photo accompanying this post, I think you should know that Fred Gould believes that Eric Séralini’s study of the long-term effects on rats of eating your company’s genetically engineered (GE) NK603 corn and herbicide glyphosate should never have been retracted.

For those who may not know, that study, which was peer-reviewed and originally published in the respected international journal Food and Chemical Toxicology, was in print for more than a year when it—very unusually—underwent a thorough review by the journal’s editor-in-chief; he reviewed not only the submitted manuscript and all the reviewers’ comments, but also the raw scientific data from Séralini’s lab. That editor “unequivocally…found no evidence of fraud or intentional misrepresentation of the data” and deemed Séralini’s results “not incorrect” but “inconclusive.” And yet, despite the fact that inconclusiveness is not a benchmark for retraction of a scientific paper, he retracted the paper.

Fred Gould told me that Séralini’s paper should never have been retracted during an NSF-sponsored workshop on “Scientific Uncertainty and Professional Ethics: Getting from Strong Public Science to Sound Public Policy” held last December in Washington, D.C. Other scientists, environmental lawyers and journalists participating in the workshop agreed.

A lot of people feel strongly about this study. Unintended/off-target changes to crop plants can occur as a result of the genetic engineering process and it’s to look for such changes that GE crops/foods are fed to animals in these kinds of studies. In fact, scientists at your company have conducted very similar (although not as long-term) studies, with GE NK603 corn as well as other GE crop products.

Since Séralini’s results have been deemed inconclusive, we obviously don’t fully understand what may, or may not, be unintendedly going on with GE NK603 corn and glyphosate. So Séralini’s data suggest that you and your company may not “fully understand a topic you feel strongly about.”

Therefore, based on your Important Lesson #1, it is now “important to push yourself out of your comfort zone to research and learn more.” The proper scientific response to this situation is to repeat Séralini’s study, with additional control rats, in an effort to conclusively, one way or the other, establish the safety status of GE NK603 corn.

Choosing instead to declare the issue “debunked for years” not only would be unscientific but also could indicate that you are not “able to recognize that you may be basing your opinion on ideology rather than data.”


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Scientific Uncertainty and Professional Ethics as Related to GMOs

Fred Gould, the chairman of the committee that produced the most recent National Academies report on GMOs, and I were invited to speak at the third and final NSF-funded workshop on the topic of “Scientific Uncertainty and Professional Ethics: Getting from Strong Public Science to Sound Public Policy,” which I mentioned in my last post: Pew Research Center Finds “Americans have Limited Trust in Scientists Connected with Genetically Modified Foods.” The workshop was held the Monday following the release of that Pew Research Center report. Dan Charles, a journalist who published a piece on the Pew report for NPR and authored a book on GMOs titled Lords of the Harvest: Biotech, Big Money and the Future of Food (Perseus Publishing, 2001), moderated our session of the workshop.

Workshop participants, comprised of scientists, journalists and environmental attorneys, were using crop genetic engineering as a case study of how scientific uncertainty is communicated, to the public and otherwise. The entire workshop was “on the record.”

In his presentation Dr. Gould reiterated a point made in his NAS report [emphasis mine]:

“With regard to the issue of uncertainty, it is useful to note that many of the favorable institutional statements about safety of foods from GE crops [such as those mentioned in Box 5-1 of the report] contain caveats, for example: ‘no overt consequences,’ ‘no effects on human health have been shown,’ ‘are not per se more risky,’ and ‘are not likely to present risks for human health.'[see * below] Scientific research can answer many questions, but absolute safety of eating specific foods and the safety of other human activities is uncertain.”

Dr. Gould also mentioned that the media often fail to mention these caveats.

(I would add that many crop genetic engineers and other vocal GMO proponents often fail to mention them as well. See, for example, The Absurdity of Claiming that “All GMOs are Safe.”)

I then briefly explained some sources of the uncertainty associated with crop genetic engineering that necessitate—for the sake of abject truthfulness—mention of such caveats.

I described how introducing DNA into an organism via genetic engineering involves biological processes that are very different from traditional cross-breeding (see my post on this topic here), and that plant scientists know that mutation of recipient plant genes and/or insertion of large chunks of vector DNA not meant to be inserted into genetically engineered (GE) crops (when using the Agrobacterium-based method) can occur at what I consider to be relatively high rates (20% to greater than 60%). (For more details about these uncertainties that we know something about please see Crop Genetic Engineering, Warts and All.)

I also mentioned our current lack of knowledge (i.e. ignorance) about the genomes of plants (and other organisms), how we don’t know the function of most of the DNA that comprises them beyond the small amount (~2-3%) that codes for proteins but that it has become clear that at least some of the oft-called “junk” DNA is actually important for proper gene expression and function. And because scientists have no control over where in a crop plant’s genome their foreign genes will be inserted (when using the genetic engineering techniques used over the last 30 years anyway), insertions could disrupt protein-coding genes (causing mutations) or non-coding regions of DNA with unknown but possibly important functions.

I then explained that the reason animal-feeding studies are carried out with GE crops is to look for possible unintended consequences–AKA pleiotropic effects–that might have occurred as a result of such scientific uncertainties. I went on to say that if such studies suggest possible negative consequences—as was the case with the peer-reviewed 2012 study of NK603 corn conducted by Séralini and colleagues, for example—the proper scientific response is to repeat the study; instead, that 2012 study was retracted for being “inconclusive” more than a year after it had been in print. (For more information on various safety-related issues with GE crops, and the controversy over the Séralini publication, see A Dearth of Life-Long Animal Studies of GE Foods and Science-based Regulation of GE Crops Requires More Long-Term Rat Feeding Studies with NK603 Corn.)

I also mentioned that, in my opinion, plant scientists have not done a good job at being abjectly honest and transparent about the scientific uncertainties associated with genetic engineering; instead many have made general statements about its precise aspects, about all GE food/crops being safe, about genetic engineering being just an extension of traditional breeding…statements that gloss over the scientific uncertainties that I believe it is the responsibility of scientists to provide to society so that society, as a whole, can make good decisions, based on all the available information, about how to use and control a technology.

I additionally mentioned that the physicist Richard Feynman expressed this same philosophy of science and technology.

After some Q&A, Dr. Gould and other workshop participants agreed that the NK603 paper by Séralini and colleagues should never have been retracted.

Dr. Gould also agreed that the technology of crop genetic engineering had been “over sold.” He additionally said, and his report indicates as well, that use of new scientific techniques, including the various “omics” technologies, should help in evaluating the safety of GE crop products.

But in response to the final question asked during our workshop session, “Do you believe that all GE crop products currently on the market are safe?” Dr. Gould answered “yes” even after I reminded him specifically about NK603.

I said that I feel the jury is still out on NK603 GE corn.

Just a couple of weeks later, more evidence (along with some controversy) came to light. “An integrated multi-omics analysis of the NK603 Roundup-tolerant GM maize reveals metabolism disturbances caused by the transformation process” was published in Scientific Reports.

I’d say the jury remains out on NK603 GE corn.


* More caveats, as well as means of dealing with them, are mentioned in this last example when the entire quote from the World Health Organization is referenced (rather than the partial quote cited in the NAS report):

“Different GM organisms include different genes inserted in different ways. This means that individual GM foods and their safety should be assessed on a case-by-case basis and that it is not possible to make general statements on the safety of all GM foods.

GM foods currently available on the international market have passed safety assessments and are not likely to present risks for human health. In addition, no effects on human health have been shown as a result of the consumption of such foods by the general population in the countries where they have been approved. Continuous application of safety assessments based on the Codex Alimentarius principles and, where appropriate, adequate post market monitoring, should form the basis for ensuring the safety of GM foods.”



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Pew Research Center Finds “Americans have Limited Trust in Scientists Connected with Genetically Modified Foods”

I started this blog because I strongly believe that when a technology is heading out of scientific laboratories and into the public marketplace, it is the job of scientists who use it to provide the public and its government with full and accurate information about how that technology works and what its potential pitfalls might be. Only with all of the information available about the technology, including any uncertainties or aspects about it that could be cause for concern, can societies make the best possible decisions about whether or how best to use and regulate that technology.

I am not the only scientist who feels this way.

Great scientists like Richard Feynman encouraged scientists to be abjectly honest in explaining their science to lay people (see quotes on the “About” page of this blog). More recently, participants in a workshop on “Scientific Uncertainty and Professional Ethics,” conducted by the Environmental Law Institute and sponsored by the National Science Foundation (NSF), concluded that scientists should aim to “provide all the information needed to help others judge the value of their work, rather than to steer that judgment in a particular direction.”

My aim has been “to provide all the information needed to help others judge” genetic engineering of crops and other organisms for human and animal food.

But I also started this blog because I felt other scientists were—by neglecting to mention the imprecise aspects of crop genetic engineering technology and/or evidence of problems associated with specific genetically engineered (GE, AKA genetically modified, or GM) products—steering judgment of GE crops/foods in a particular direction. I worried that scientists steering judgment in this way would some day undermine the public’s trust in scientists.

And now, according to a recent report from the Pew Research Center, that day has apparently arrived.

The authors of that report, based on a nationally representative survey of 1,480 adults conducted in May and June of this year and released on December 1st, concluded that “in general people’s views of scientists connected with genetically modified foods…are largely skeptical, or at best, tepid.” They also found that there is “considerable skepticism about scientific understanding, consensus and influences on research about genetically modified foods” with fully 80% of the Americans surveyed indicating that “scientists’ desire to help connected industries influences the research findings,” either most of the time (30%) or some of the time (50%).

I cannot say that I am surprised.

For more than 20 years now, scientists who promote the use of genetic engineering for producing food crops have largely neglected to mention the scientific uncertainties that accompany it, or even the fact that there have been commercialized GE crops that were found to be problematic and then pulled off the market. (See “Crop Genetic Engineering, Warts and All” for more information on these subjects.) Some have also neglected to mention, or have otherwise misled the public about, their ties—financial and otherwise—to the ag biotech industry, as reported in The New York Times.

Rather than providing all the information needed to help others judge this technology, a number of plant scientists have instead participated in efforts to suppress reports on specific GE products that suggest there could be cause for concern—the most egregious instance being the ruckus raised by plant scientists over a peer-reviewed animal-feeding study of NK603 GE corn and the herbicide glyphosate which led to the paper being retracted, more than a year after it was published, because it was deemed “inconclusive” by the journal’s editor-in-chief. And nearly all scientists (see my response to one here) who speak publicly in support of agricultural genetic engineering have made sweeping generalizations about the “safety” of all GE foods/crops.

To me, these actions seem meant to steer judgment in a particular direction.

Rather than the standards of abject honesty that Feynman encouraged scientists to meet, they bring to mind the advice of another Nobel laureate, André Gide, who said: “Believe those who are seeking the truth. Doubt those who find it.”

Based on the Pew Research Center report, the American public has taken Gide’s advice in regard to scientists connected with genetically engineered foods.

Hopefully, those scientists will take the report’s findings seriously, reevaluate and incorporate more abject honesty into their current “outreach” efforts, and start the long, hard process of (re)building trust with the public.

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