“Let the nominations begin!”

On June 20, the White House will host a Champions of Change event to highlight outstanding individuals, organizations, or research projects promoting and using open scientific data and publications to accelerate progress and improve our world. The White House Champions of Change program highlights individuals, businesses, and organizations whose extraordinary stories and accomplishments positively impact our communities.

Access to scientific research can help fuel entrepreneurship, innovation, and scientific breakthroughs. Freely available data generates new ideas, builds new businesses, and generates economic growth that impacts the lives of Americans every day.

That’s why, in February 2013, OSTP Director John P. Holdren issued a memo to the heads of Federal agencies that aims to increase public access to the results of federally-funded research—including scientific data and publications.

Open sharing of research results is a proven strategy for driving positive change. For example, the rapid and open sharing of genomic data from the Human Genome Project revolutionized biomedical research, spurred major growth in the biotechnology industry, and provided $140 in economic returns for every dollar of public investment. And, the Federal Government’s liberation of Global Positioning System (GPS) satellite data led to an explosion of geospatial information systems and the creation of many companies, smartphone apps, and car navigation systems.

We are asking for your help to identify “Open Science” Champions of Change—outstanding individuals, organizations, or research projects promoting and using open scientific data for the benefit of society. For example, a Champion’s work may involve:

• Providing free access to data or publications generated from scientific research; or
• Leading research that uses publically available scientific data.

What are we working on that could qualify for this event? Why, our GENetic Engineering Risk Atlas, of course! Please consider taking a moment to nominate us as an Open Science Champion of Change, and tell them why you think we would make a good fit.

Here is some information which can help you fill out the form:

Nominee Name: Biology Fortified, Inc.

Nominee City: Middleton

Nominee State: Wisconsin

Nominee Email: contact @ biofortified . org

Nominee Occupation: Scientists!

Reason for Nominating: Mention GENERA, and give them a link to our site to help them find the good stuff. Tell them in your own words why you think we deserve it!

Nominations close Thursday May 23 (tomorrow!), so if you want to nominate us, please do it soon! Thanks very much!

Swiss albino mouse by Rick via Flickr.

The Organic Consumers Association (among others) has gleefully announced: New Study Links GMO Food To Leukemia (also saved as a PDF). This article by Sayer Ji was originally published on Green Med Info on 12 May 2013. The paper is Hematotoxicity of Bacillus thuringiensis as Spore-crystal Strains Cry1Aa, Cry1Ab, Cry1Ac or Cry2Aa in Swiss Albino Mice by Mezzomo et al, published first in November 2012 then again in March 2013 (more on that later).

The article states: “Bt toxins are capable of targeting mammalian cells, particularly the erythroid (red blood cell) lineage, resulting in red blood cell changes indicative of significant damage, such as anemia. In addition, the study found that Bt toxins suppressed bone marrow proliferation creating abnormal lymphocyte patterns consistent with some types of leukemia.”

Except, the article doesn’t actually say that at all. I have a few quick observations, then a rebuttal from our own Dr. David Tribe, and I wrap up this latest edition of whack-a-mole with a revelation. There’s a lot more to say about this paper, and hopefully we will learn more as time goes by, but this post is just a fast attempt to help people know that this is not a good paper to be pointing at.

Are organic Bt sprays dangerous?

The strangest thing about the rush by OCA and other anti-GMO folks to call this the latest “GMO” scandal is that the study didn’t test Bt toxins expressed by biotech crops. It didn’t even test the Bt toxins expressed in bacteria then purified. Instead, the paper says they used “spore-crystals Cry1Aa, Cry1Ab, Cry1Ac and Cry2Aa from B. thuringiensis var. kurstaki were obtained in lyophilized form”. Some Bacillus thuringiensis bacteria can go dormant, forming a spore, and form crystals around the outside of the bacteria to protect themselves.

In other words, this study used the whole bacteria – the exact same thing that is used in organic Bt sprays. According to Organic Consumers Association, Bt sprays are used by “at least 57 percent of organic farmers” and “does not have detrimental effects on mammals, birds or non-target insect species and microorganisms. In addition, Bt sprays leave no poisonous residue on crops or trees and are readily degraded into the environment.” Yet somehow the exact same active ingredient, when expressed in a transgenic plant, lasts a long time in the environment and is now toxic to everything, according to OCA et al (despite the pesky science that says it doesn’t).

Anyway, the authors resuspended the whole bacteria in water, then orally administered them to the mice in incredibly high concentrations: 27, 136, and 270 mg of bacteria per kg of body weight.

The most important thing that sticks out to me here is that there could be all sorts of other things about the bacteria besides the presence of the Bt toxin that could be affecting the mice. Since the negative control was water instead of culture medium with Bt bacteria that don’t express the toxin, we have no idea what it is in the solution that might have affected the mice.

Strangely, they never mention this and while they are careful to conclude “results showed that the Bt spore-crystals… can cause some hematological risks to vertebrates” rather than saying it was the Bt crystals themselves, they then conclude there is “increased risk of human and animal exposures to significant levels of these toxins, especially through diet”.

So, I have to wonder – are the authors worried about organic farming? To reiterate, genetically engineered plants have only the Bt toxin, not the whole bacteria, while organic farmers use the whole bacteria as a spray. Realistically the dose of “spore-crystals” from a Bt spray residue is much lower than what these researchers claim harm from, but still. According to the Pesticide Information Profile published by Cornell, Bt sprays show every indication of being safe (and so do Bt toxins themselves).

David Tribe’s Analysis

David Tribe wrote a great but short analysis over at Reddit and I wanted to make sure more people were able to see it:

• They used spore/crystals from modified Bt strains, rather than isolated protein. As per Schnepf, 2012a, such sporulating cultures are about ~20% Bt crystal proteins by dry weight. In other words, 80% of what the mice were fed is God knows what.
• The results seen are not due to use of too high a level of protein (270 mg/kg) , as there are reports of up to 5280 mg/kg of purified proteins fed to mice without any adverse effects (Schnepf, 2012b)

So,

1. The real negative control should have been wild type Bt strains, not water, as water lacks the other stuff floating around the culture medium
2. The amounts fed the mice do not reflect human dietary levels– they were some ~ 10⁶ to 10⁸ time higher than exposure from GM or organic crops ( as per Hammond, 2012)
3. The use of 3 mice/sex/group, as compared to OECD standards that call for 5 mice per sex per group.
4. The historical incidence for these pathologies in the mice used was not reported. Thus, it is not clear if they are looking at treatment effects or natural biological variability for the mice
5. The results did not all show the expected dose-response, with the lower dose resulting in the highest symptoms, as opposed to the other way around (eg, the 136 Cry1Ab had reduced MCH, but not the 270 mg/kg group)
6. The reduction in MCV and RDW in all groups suggests a contaminant is involved rather than different Bt proteins
7. For dose response, they get U shaped or inverse U shaped curves, a la Seralini. These could be a result of small animal numbers, not of hormesis.
8. In the lit review, they say that Thomas and Ellar (1983) previously showed that cry proteins were hemolytic. However, Thomas and Ellar (1983) tested cyt proteins, not cry proteins. Even then, the cyt results were in vitro– there were no results when mice were fed the cyt proteins, presumably because they are digested.
9. They also cite Aris and LeBlanc (Bt in mother and fetal blood) to support their work. (a rubbish paper)
10. Their results are at odds with all the other studies whereby Bt (the bacterium) and cry (the bt protein) have not had adverse results in feeding studies.

Also — the journal is not a high quality journal.

Revelation

I think we’ve established that this paper has some methodological issues. It’s not just us, though. The paper was originally published in Food Chem Toxicol, a generally reliable journal that has been around since 1982, and then withdrawn. Surely there is another story about that – Why was it published in the first place? Why was it withdrawn? Who requested the withdrawal? But the point is that the study as currently published is not in a “high quality journal”, as David puts it.

The Journal of Hematology & Thromboembolic Diseases is brand new, without any impact factor or history of quality to support it. This study appeared in issue 1, volume 1. The National Library of Medicine reviews scientific journals based on their scientific merit, strength of their review process, etc for inclusion in PubMed. OMICS, the parent company for this journal, is pointedly not indexed in PubMed, and has been dubbed “fake journals” by many scientists.

Why does the journal matter? High quality journals have a high quality review process. They seek out reviewers with the relevant expertise to do a proper science-based review of the methods, results, and conclusions. Low quality journals, simply put, do not.

Finally, I will end with a note from Karl Haro von Mogel, who is currently looking a little deeper into this paper’s curious history: “There’s something going on here that matters to everyone who cares about the peer review process that we depend upon to sift reliable studies from specious claims. Paired with rapid amplification through political advocacy, the reputation of science is at risk of being hijacked to obscure the truth.”

Peppers produce a variety of natural pesticides, including capsaicin. Peppers by James Walsh via Flickr.

The Environmental Working Group (EWG) says that it “helps protect your family from pesticides.” The purpose of this post is to “help protect your family from dangerously misleading information from the EWG.”

Each year since 1991, the USDA has been publishing the results from a large-scale pesticide residue monitoring program called the Pesticide Data Program (PDP). Each year, a different set of crops is chosen and samples are purchased from regular stores and tested. Year after year, the results of those studies confirm the safety of the food supply. Year after year the EWG misrepresents the data to say otherwise. To understand what that is like for the people who farm those crops, consider this analogy:

Imagine that you are taking a college course that is critical for your graduation, but your entire grade is based on the performance of thousands of other students you don’t even know and with whom you can not communicate. Some of those students’ test results will be chosen at random and the grade for everyone in the class will depend on how they did. When the grading is done, you find out that the class score was over 99%: A+!  Then, someone who doesn’t really understand the topic of the class, or chooses not to,  re-grades the test and tells your potential future employers that you got a D, and many of them believe the incorrect grade.

This is much like what farmers have been experiencing for years. They grow a crop as best they can, and use pesticides only as necessary and within the strict rules established by the EPA. Much of what they use are pesticides with very low toxicity. In years that their crop is selected for the PDP, random samples of their commodity are purchased in stores, including examples coming from other countries. They are taken to federal and state laboratories and scrutinized for trace residues of hundreds of different chemical pesticides. When the data is finally published (usually two years later), the highly qualified experts of the USDA, EPA and FDA conclude that the system is working and that consumers should confidently purchase and eat the crop without concerns about residues. In fact, studies show that the anti-cancer benefits of eating fruits and vegetables far, far outweigh any minuscule risk that might be associated with pesticide residues.

Each year, the EWG takes advantage of the transparent availability of the USDA-PDP data, but then performs their own “analysis” which experts have rejected as utterly anti-scientific. They generate an incorrect “grade” for each crop and post it in their “Shopper’s Guide” and on their notorious “Dirty Dozen List”. The grower’s virtually perfect grade is forgotten and an un-critical press and blogosphere passes along the distortion that the crop is “dirty”. Many consumers believe the misinformation and heed the EWG’s suggestion that they must buy organic versions of that crop. Worse still, there is some evidence that this disinformation causes consumers to purchase and eat less produce. At a minimum, many consumers feel guilty for not buying organic.

As you can imagine, this is very frustrating for farmers. Some have joined in groups which are trying to get out a much more accurate interpretation of the data which is to say that the PDP confirms the that pesticides are well regulated and that the farming industry is doing a very good job.  They want to reclaim their rightful A+!

What Does The Data Really Say?

Figure 1. Click for larger image.

I decided to do an independent analysis of the latest PDP data (for growing year 2011, released earlier this year). The information is freely available from the USDA, but doing anything with the data requires a lot of work. The zipped file expands to 92MB because it contains 2.2 million rows of information covering each of the hundreds of pesticides or metabolites looked for in each of the thousands of food samples. Of those, 1.75 million are for fruits and vegetables. Fortunately, even using the extremely sensitive analytical techniques available today, less than 1% of these rows are cases where some detectable residue was found. I’d be happy to email you the 15,450 row Excel table left after eliminating all the non-detects.

To understand the significance of each detection, we need to know what the chemical is and what “tolerance” the EPA has established for it on each crop.  The tolerance is a very conservative threshold for how much residue is an acceptable margin away from any health risk.  It is based on the best data and risk assessment tools available to EPA. Not surprisingly, the tolerances for different chemicals are very different based on the details of their toxicological profile. I’ve plotted the distribution of all the detections relative to crop/chemical-specific tolerance in Figure 1.

For all 20 commodities tested from 2011, 99.33% of the residues were below the EPA tolerance. In fact, fully 1/2 of the detections were 100 times lower than the already conservative tolerance.

Figure 2. Click for a larger image.

There are differences between crops and between country of origin, but they are only between good and very good.  Snap peas were the “worst” example, particularly those imported from Central America, but they still had 94% of detections below tolerance.  The few that were above are not particularly scary either (Figure 2). If you’d like more details, you can see my complete analysis on SCRIBD.

Figure 3. Click for a larger image.

Many crops had a “perfect score” of keeping all the residues below the tolerance. Quite appropriately, one of the “cleanest” crops was pear baby food.  When EPA sets the tolerance for baby food it is even more conservative than ever.  In this case all the detections were below tolerance and more than 99% of them were 10 times or more lower than the tolerance (Figure 3).

The people collecting samples for the PDP  track whether the sample was labeled organic. For most crops the number of organic samples is too low to make a meaningful comparison, but for pear baby food, 11.5% were organic. Interestingly, among those 67 samples, there were 101 pesticide residues detected, only 33 of which are for the organically approved insecticide, Spinosad. The rest were for synthetic pesticides including some that are applied after harvest (such as DPA which prevents scald in storage). As with the conventional samples, these residues were at such tiny levels as to be of no concern, but for this and other crops, choosing organic does not guarantee “no pesticide residues”. Instead, the risk assessment process suggests safety for both the organic and conventional options.

How Does The EWG Ranking Compare to One Based on Science?

Figure 4. Click for a larger image.

I conducted an analysis that pays attention to what the chemical is, what levels are found, and what the EPA has concluded from its risk assessment process.  The EWG’s ranking ignores all of those factors.

In Figure 4, I’ve taken the EWG’s ranking (higher numbers are supposedly “cleaner”) and  compared it with a tolerance-based measure which is the percent of the detections that are not even as much as 1/10th of the tolerance (again, high number = cleaner).  Not surprisingly, there is no correlation between these two approaches.

While none of the crop residues are actually problematic, EWG’s methods actually rank produce incorrectly. Cauliflower, which EWG calls part of the “clean 15″ and ranks as number 34 in their list, has more detections over 1/10th of the tolerance than other crops. Apples, which are the worst according to EWG, have 92% of detections below 1/10th of tolerance – better than many other crops. Canned beets, for which not even one detection was noted among 756 samples from 2011, doesn’t appear on EWG’s “Clean 15″ list or in the list at all. Again, the real “grades” are all “A’s,” just to different degrees. It’s like Lake Wobegon – all the crops are above average.

What is the take home message? Eat more fruit and vegetables! And don’t worry about whether it is organic or not. The fact is, we know less about what is on organic produce than on conventional.

Want to learn more? View the full analysis: An Independent Analysis of the 2011 PDP Data on SCRIBD. Want to analyze the data yourself? Download the full dataset from the USDA, or save yourself some trouble and contact me at savage.sd@gmail.com for an Excel table that includes detections only.

I can’t say if it’s intentional or unintentional, but there definitely seem to be many cases where a panel discussing aspects of agriculture consists of representatives from EWG, UCS, CFS, etc and there might, if we are really lucky, be one person who has some understanding of the science.

One example is of this is an episode of the Melissa Harris-Perry show on MSNBC that was about agricultural genetic engineering. Her producers rounded up a celebrity chef, Marion Nestle (known for her dislike of biotech among other things), and Ricardo Salvador of the UCS, which has a stated anti biotech platform. Their pro-science representative  was Ramez Naam, a computer scientist and author. Now, Ramez is great, but why didn’t they choose a crop scientist with expertise in biotechnology, an agricultural economist with expertise in consumer preference and labeling, a farmer that uses biotechnology… ?

What if they wanted to find other experts but just didn’t know who to ask? Let’s make it easier for all of those journalists and panel discussion organizers out there to find us.

Fill out the Biotech Experts Form with your information. Encourage your friends and colleagues to share their information, too. Finally, tell people about Biology Fortified’s newest resource* so everyone can be better informed!

*For now, the responses are displayed in a Google Doc, but as we accumulate a good sized list, we will publish the results to a new page on Biofortified: Biotech Experts.

“I’m paying part of a lab assistant’s salary…  and already as a result of the cuts we’ve had to eliminate that position.” Now Fletcher has less money to spend on supplies and won’t be able to hire new research assistants, post-docs, or support new graduate students for the foreseeable future. When asked how this will affect her lab’s work on stem cells in plant development, Fletcher replied, “by overall slowing the progress of the research, and narrowing the focus.”

Stories like Fletcher’s are becoming common now that the cuts are taking effect in ways that were hard to imagine only weeks ago. The USDA’s Agricultural Research Service (ARS), which funds Fletcher’s lab, protected professors’ salaries and indirect research costs like facilities, but left direct research costs, such as personnel and supplies, to take the hit. This explains how agency-wide spending reductions of a seemingly modest 5 percent, pinched actual research by 40 percent.

Most academic plant scientists are feeling the sequester through dimmer prospects for funding by competitive granting agencies like the National Science Foundation (NSF) and the National Institutes of Health (NIH). The NSF announced it will trim spending by 5 percent by reducing the number of new grants it awards by approximately 1,000, or about 10 percent. To spare staff and existing obligations, the NSF is leaving young researchers and new projects to bear the brunt of the cuts.

Many fear the sudden funding drought will turn a cohort of young scientists away from research. “For those scientists who are near the threshold of getting funded, this isn’t just some belt tightening. It will completely alter their career trajectory,” explains Timothy Nelson, a plant biology professor at Yale University. “The impact of this seemingly small squeeze can be huge.”

According to recent estimates, the NIH is cutting $1.56 billion from its 2013 budget. While it remains to be seen exactly where the axe will fall, preliminary calculations predict it will issue somewhere between 600 to 2,700 fewer grants. The American Association for the Advancement of Science (AAAS) estimates the NIH’s R&D budget under sequestration will return to 2002 levels through 2021.

The outlook for basic plant research is bleak, but applied plant research faces even more difficult times. The ARS, which is the USDA’s internal research arm, and the Agriculture and Food Research Initiative (AFRI), which administers the USDA’s external funding, support most of the applied plant science research in the US. According to the AAAS, the sequester is sending USDA R&D funding back to 1998 levels.

Farmers depend on improved crop varieties developed through UDSA-funded plant breeding work. Since climatic conditions, disease pressure, and quality issues are ever-evolving, cuts to breeding programs put future harvests at risk. “Developing a new variety of wheat typically takes about ten years. The danger of these cuts is that we won’t feel their true effect until many years down the road, at which point it will be too late,” warns Melissa Kessler, Director of Communications for the National Association of Wheat Growers.

Like the proverbial eating the seed corn, today’s slimmer budget comes with a price. Studies show that public spending in agricultural research is a matter of common sense. According to a Council for Agricultural Science and Technology report, average estimated rates of return on investment are near 50%, with an overall benefit-cost ratio of 32 to 1.

When congress will replace sequestration with a more reasonable deficit reduction strategy is still anyone’s guess. The president’s proposed fiscal year 2014 budget, however, offers a glimmer of hope. The plan seeks an additional 3.2 percent in funding for the NSF and a 28.7 percent boost to AFRI. Will the president’s intentions bear any resemblance to what comes to pass? Recent history instructs us to be cautious.

Beautiful (and sustainable?) farms in Benton, PA by Thadd Selden via Flickr.

Everywhere I go, I hear farmers argue over the word ‘sustainable’. So much so, that I really want to puke. It gets brought up at policy meetings, on social media sites, and in blog entries. When I hear farmers discussing what it means, I only hear Charlie Brown’s teacher… wha wha wha wha whaa, wha wha wha wha whaaa.

What brought on this latest episode of word fatigue? Yet another article written that only serves to divide farmers into groups. Organic vs conventional, small vs large. It’s like we’re a huge dysfunctional family who can’t even manage a holiday dinner without arguing over an issue that started out so minor, but has now caused family members to quit speaking to each other.

.

I Googled the phrase ‘sustainable agriculture’, and the usual websites popped up. I looked at Wikipedia – not one of the most reliable sources according to English teachers – and wasn’t too surprised when I found this definition:

“Sustainable agriculture may be defined as consisting of environmentally friendly methods of farming that allow the production of crops or livestock without damage to human or natural systems. More specifically, it might be said to include preventing adverse effects to soil, water, biodiversity, surrounding or downstream resources—as well as to those working or living on the farm or in neighboring areas. Furthermore, the concept of sustainable agriculture extends intergenerationally, relating to passing on a conserved or improved natural resource, biotic, and economic base instead of one which has been depleted or polluted.”

Do you see anything that doesn’t apply to all of agriculture? Shoot, every single farmer out there should be trying to be sustainable. If you look at the regulations that we have under the USDA, EPA, FDA, state, county, or whomever, their rules point to this goal. What farmer isn’t trying to leave their farm better than when they started?

This brings me to my next point. Why are we getting so stuck on terminology, and who is “better” than the “other”.  And, why are we so worried about everyone who does things differently? If we look at differences under the same narrow focus, does that mean that corn farmers cannot get along with peanut farmers? What about fruit and vegetable farmers? They are different…why are they not arguing over methods of raising produce?

I think farmers need to get over the whole “I need to feed the world” thing, and focus on their own farm. If we continue to argue about who is doing the better job at being sustainable, or who is the one producing the most to feed the world, we are going to miss out on the important signs that maybe things are not going well at home.

This brings me back to the family holiday gathering scenario. Agriculture is the parental unit here. Ag gave birth to farmers with different personalities; different wants, needs, practices. While the farmers are their own people, they need to stick together through thick and thin as any strong family unit does. We need to stand together when the Farm Bill is struggling to make it to the floor, when droughts stress families to the max, when animal rights activists and organizations are doing everything they can to divide and conquer.  These are issues that require that we stand together in order to stay together.

Carolyn Olson raises organic corn, soybeans, field peas and small grains with her husband and their three daughters on 1,100 acres near Cottonwood, Minnesota.  They also finish about 7,000 conventional hogs annually.  Their farm will be recognized as a century farm this year. Carolyn is an active member of her community, serving on the Minnesota Department of Agriculture’s Minnesota Organic Advisory Task Force, as co-chair of the Minnesota Farm Bureau Pork Chop booth at FarmFest, and much more. Carolyn blogs at Carolyn Cares and tweets as @Westacre2CJ.

Both full interviews will be up and available soon, along with more footage of the protest, but now I have a special treat for you. I pitted the statements of the two conflicting sides against each other in a dramatic fashion, to find out who knew what they were talking about. Frank N. Foode™ joined in to award points and declare a winner.

Watch Apple Activists vs Scientists!

You can also watch it directly on YouTube. If you enjoyed it, please spread this far and wide!

Vernon Bowman is a farmer in Indiana, who grew genetically engineered Roundup-Ready soybeans on his farm, and signed license agreements not to save and replant those seeds. However, he wanted to grow a second, late-season crop of beans, which were too high-risk to justify paying the licensing fees for the seeds, so he devised a plan to work around the license issue. He bought generic “commodity” beans from a grain elevator, which were destined for consumption, and planted his second crop from these. He even sprayed these fields with Glyphosate herbicide to kill the weeds and all non-Roundup Ready plants, thus specifically selecting for the trait, and he did this for 8 years on his farm before this practice was discovered.

When Monsanto found out about this, they sued Bowman for patent infringement, and won through two levels of the court system. He appealed to the Supreme Court, which elected to take up the case. Both sides presented their arguments on January 19 this year, amid a flurry of media activity and speculation. The case attracted wider attention outside the agricultural community because a ruling on the case could have far-reaching implications for the development of other forms of self-replicating technologies.

Patent Exhaustion is the legal concept that “the initial authorized sale of a patented item terminates all patent rights to that item.” Buying the first batch of soybean seeds for planting would “exhaust” the patent, and allow the buyer the right to use the soybeans produced from that crop for purposes such as processing, feeding to animals, selling to a grain elevator, etc. Bowman argued in January that patent exhaustion also applied to replanting the soybeans to grow another crop, hinging on the use of the term “make.”

Patent Exhaustion does not apply to the act of making copies of an invention, which would still be covered under patent law and require permission of the patent holder. So Bowman’s legal argument was that by growing a crop from seeds the plant is growing copies of the invention, but the farmer is not “making” them. In legal briefs and public comments, Bowman and his legal team argued that the act of farming itself was almost an accidental enterprise. Farmers are instead actively keeping seeds from sprouting as they would naturally do, and by planting them are allowing nature to take its course.

From the brief filed by Bowman,

Supreme Court of the United States, from SupremeCourt.gov

Bowman’s use of commodity seeds for planting has nothing in common with “reconstruction.” No parts were worn out and replaced; the seeds were simply used. In the context of patented seeds, use as contemplated by all parties to the first sale may simply result in the creation of a new item.
(…)
The seeds at issue here will self-replicate or “sprout” unless stored in a controlled manner to prevent this natural occurrence. Humans can (and most often do) assist in the process of self-replication. For instance, Bowman planted Roundup Ready® seeds and treated them with glyphosate. This activity led in part to the creation of new soybeans having the patented Roundup Ready® trait. But it was the planted soybean, not Bowman, that “physically connected” all elements of the claimed invention into an “operable whole.”

In the ruling written by Justice Kagan, this argument was soundly rejected.

Justice Elena Kagan

The exhaustion doctrine does not enable Bowman to make additional patented soybeans without Monsanto’s permission (either express or implied). And that is precisely what Bowman did. He took the soybeans he purchased home; planted them in his fields at the time he thought best; applied glyphosate to kill weeds (as well as any soy plants lacking the Roundup Ready trait); and finally harvested more (many more) beans than he started with. That is how “to ‘make’ a new product,” to use Bowman’s words, when the original product is a seed. (emphasis added)

To drive the point home, they added,

Still, Bowman has another seeds-are-special argument: that soybeans naturally “self-replicate or ‘sprout’ unless stored in a controlled manner,” and thus “it was the planted soybean, not Bowman” himself, that made replicas of Monsanto’s patented invention. “[F]armers, when they plant seeds, they don’t exercise any control. . . over their crop” or “over the creative process”. But we think that blame-the-bean defense tough to credit. Bowman was not a passive observer of his soybeans’ multiplication; or put another way, the seeds he purchased (miraculous though they might be in other respects) did not spontaneously create eight successive soybean crops.

In other words, the Supreme Court affirmed that which would seem to be patently obvious: Farmers actively create or make seeds when they grow crops. It was clearly stated in his court brief just how involved Bowman was in the process of growing these crops, and this fact was not missed by the nine justices, who ruled 9 to 0 against him. The very readable rulingspent considerable effort to outline the reasons why exhausting a patent after only one generation of growing a crop from genetically engiineered seeds would effectively undermine the entire patent concept, and reduce the patent monopoly from twenty years to less than one. Their reasoning was motivated by the directives of Congress on maintaining reliable incentives for the invention of new and useful technologies.

Another argument made by Bowman also did not escape notice of the Court. He argued that planting is the natural consequence of seeds, even when they are sold by a grain elevator with the intention of being processed into food or other products. This line of argumentation led George Kimbrell and Debbie Barker from the Center for Food Safety (CFS), to even say in an LA Times editorial that genetically engineered soybeans are “natural products.”

Monsanto’s claim that it has rights over a self-replicating natural product should raise concern.(Emphasis added)

An unnatural position for them to take.

Monsanto was claiming rights not over any seed, but over a genetically engineered seed, so Kimbrell was describing genetically engineered seeds as natural products. The Center for Food Safety, which filed a brief in support of Bowman, has long argued that genetically engineered crops are not natural, so this apparent change in position brought about by this argument was significant. If the seeds are not natural, then there is no precedent set that the “natural and foreseeable use” of them is for replanting. Therefore, contrary to previous statements, they needed to argue in favor of the naturalness of growing second-generation genetically engineered seeds. The term “natural” was used widely in the brief filed by CFS.

Commentators noticed that planting commodity beans intended for processing was deviating from the foreseeable use of those beans. Moreover, as farmer Brian Scott pointed out, planting generic commodity soybeans is not good agronomic practice. Soybeans come in different maturity types bred for different regions, and will reach harvest at different dates after planting. By planting a mixture of maturity types, which are mixed together at the grain elevator, the crop will be inconsistent in maturity during growth and harvesting.

The High Court also addressed the “natural use” argument.

Bowman himself stands in a peculiarly poor position to assert such a claim. As noted earlier, the commodity soybeans he purchased were intended not for planting, but for consumption. Indeed, Bowman conceded in deposition testimony that he knew of no other farmer who employed beans bought from a grain elevator to grow a new crop. So a non-replicating use of the commodity beans at issue here was not just available, but standard fare.

The case was expected to have far-reaching implications for other self-replicating technologies, however, the court explicitly stayed away from such a broad ruling.

Our holding today is limited—addressing the situation before us, rather than every one involving a self replicating product. We recognize that such inventions are becoming ever more prevalent, complex, and diverse.

Nevertheless, the reasoning presented behind today’s ruling may have long term effects on the development of other self-replicating technologies, suggesting that as these technologies develop into maturity that they, too, may be protected against unlicensed reproduction.

RepRap: A project to develop a self-replicating 3d printer. Such technologies are sure to be affected by cases like Bowman v Monsanto

See Also:

NY Times on the ruling.

American Soybean Association statement, which welcomes the ruling.

Center For Food Safety statement, which is displeased with the ruling.

By Arpita Bhattacharjya

Bananas by Fernando Stankuns via Flickr.

Flowers are traditional, yes, but this Mother’s Day I am thinking about bananas. Specifically, the plan to grow iron fortified bananas in India. This plan, predictably, is being met with resistance in some quarters. But, first, some background: India is the world’s largest producer of  bananas and almost all of it is consumed domestically. India also has a very high incidence of anemia. The India Human Development Report 2011 noted that approximately 55-35% of women in the age group 15-49 were anemic and this number had increased  by 3% from 1998-99.

Anemia in pregnant women increases the possibility of pre-term or low birth rate babies. It also implies less than optimal development in utero which means that the physical and mental development of  a new generation is impaired and the cycle of poor health outcomes continues. We also need to consider  a new variable in all of this: climate change.  It is predicted that climate change will have critical impact on maternal and new born health from adverse environmental consequences. It would make sense, therefore, to give special attention to improving maternal health before the worst of the crisis is here.

Given this scenario it makes sense that the Indian government has approved a project for the transfer of technology from Australia to grow iron and nutrient fortified bananas. Bananas, grown locally and easily available, would be an ideal way to meet the nutrient needs of women suffering from anemia. And  where a busy mom pressed for time may not have time to prepare an iron-rich dish separately, she can always grab a banana on the go.

It has, however, been met, with resistance from groups that claim that the “indigenous biodiversity” which is supposedly sufficient for India’s nutritional needs will be “destroyed” and suspect a plot by dark forces to take over the banana domain in the country which is the biggest producer of the fruit. Well, if the indigenous bounty of nature would have been sufficient, we would not be facing these alarming  health statistics. Clearly, women’s diets still remain nutrient deficient and this needs to be addressed. The indigenous variety does not have the same iron content as the fortified one, of course, and none of these critics seem to have suggested any options for either increasing access to indigenous bananas or meeting the nutrient needs in any other way.

To understand the threat to biodiversity, I started researching banana cultivation and found that this is done by planting stem cuttings, so the possibility of threat to the native species is hard to discern. The other fear that this will result in “monocultures” is not a significant one because the most widely eaten banana on the planet is already the Cavendish, the kind familiar to us from grocery stores. In addition , some local varieties are grown in several countries but one variety of banana seems to be dominant already. The technique to fortify bananas already exists and we can speculate that the time taken to bring the fruit to the market would not be that long, so that some improvement in health outcomes might be expected despite the expected adverse impact of climate change in the coming years.

Along with the adoption of fortified bananas,efforts should also be made to revive indigenous iron rich crops which have been overshadowed in recent years.This is not an either/or situation, we can and should take advantage of all the solutions available to us. Certainly we need to protect biodiversity but we cannot overlook the health of mothers and children which will determine how strong our next generation will be. An interesting example in this regard is that of Uganda: faced with banana wilt which was destroying crops and could have resulted in the abandoning of banana cultivation, scientists have developed a variety with a sweet pepper gene which stays can combat banana wilt. Better a GM banana than none at all in a country which prides itself on its banana tradition.

Just like biotechnology, the celebration of Mother’s Day in India in recent years is sometimes criticized  as a western import, alien to indigenous traditions. So it is fitting that my wish for all the moms on this Mother’s Day is that India does grow fortified bananas and we have healthier moms and babies in the future.

Arpita Bhattacharjya ‏studies and writes about food:  from school lunch to global hunger, biotechnology to cooking dinner at home, she am curious about everything. In an earlier life she was an economist, now a Mom and food policy issues advocate. She tweets as @greenfork. Her blog, Thought + Food is a thoughtful look at the journey of food from the fields and oceans to the fork.

Haven Baker, Vice President of Plant Sciences at J.R. Simplot Company

There’s a new genetically engineered potato in town that doesn’t brown when cut or fried, nor does it make acrylamide. J. R. Simplot Company petitioned the USDA to deregulate their Innate™ potatoes, and the public comment period has just been opened up on that petition. We sent Simplot some questions about their new potatoes and the technology used to make them, and their Vice President of Plant Sciences, Haven Baker, was happy to respond. Here is that interview, and if you have more questions about it feel free to ask more, as we have asked Haven to stick around for the discussion.

1. Can you tell us about the new Innate potato traits? How was it decided that these traits would be important to work on?

Absolutely. Simplot is both a pioneering potato processor and food company. With over 60 years in the potato business, we are aware of a number of significant areas where biotechnology can benefit many of the entities that make up the potato food chain. The trick is always matching what is scientifically feasible with what makes business sense. We think that seed growers, farmers, processors and consumers can all benefit from reduced black spot bruise, low asparagine, and slow degradation of starch to sugars during storage.

We know that potatoes’ susceptibility to black spot from impact and pressure during harvest and storage results in significant product losses. Innate™ potatoes’ reduced black spot from bruising will therefore result in a larger usable yield, making potato farming more profitable. Reduced sugars – under certain conditions – provide consistent golden color, providing ideal taste and texture qualities. Reduced levels of asparagine decrease the potential formation of acrylamide, a chemical compound that occurs when potatoes, wheat, coffee, and other foods are cooked at high temperatures. In California, Innate™ potatoes provide a potential means for potato processors to address the acrylamide issues under Proposition 65.

2. It seems that “Innate” is more than just the traits, but is a technology for introducing many traits into potatoes. Can you tell us how this works? Is it intragenic/cisgenic? Why did you choose the name “Innate”?

We thought “Innate” technology was an appropriate term because of the inherent nature of the potato DNA transferring to the potato plant. Simplot’s Innate™ technologies allow researchers to isolate genetic elements from any plant genome, rearrange them, or link them together in desired permutations, and introduce them back into the genome. Inserting an extra copy of a gene into the potato activates a self-defense mechanism known as RNA interference, which silences the genes related to expression of black spot bruise, asparagine, and reducing sugars in tubers.

The inserted genes come from cultivated potatoes or wild potatoes (a group of related plant species that are sexually-compatible with potatoes). We incorporate no foreign genes, no antibiotic resistance markers, and no vector backbone sequences, into the plant genome. We used a vector called pSIM1278, which incorporates two silencing “cassettes” into the potato. Expression of the first cassette lowers transcript levels for the Asn1 (asparagine synthetase-1) and Ppo5 (polyphenol oxidase-5) genes and, consequently, limits the formation of the acrylamide precursor asparagine, and the formation of impact-induced black spot bruise that occurs when the enzyme polyphenol oxidase oxidizes phenols to produce dark pigments. The presence of black spot bruise results in lower quality and subsequent production losses during processing into fries or chips.

A reduction in the formation of reducing sugars is accomplished by the down-regulated transcript levels for the PhL (phosphorylase-L) and R1 (starch associated) genes resulting from expression of the second cassette. These traits function by slowing the conversion of starch to reducing sugars (glucose and fructose). Benefits include improved quality, especially relating to color control, and thus contributing to the desired golden brown colors required by most french fry or chip customers. Also, the reducing sugars react with amino acids, such as asparagine, to produce Maillard products including acrylamide. So by reducing the levels of these sugars in stored potatoes, we can significantly reduce the levels of toxic acrylamide in the food.

Acrylamide is formed when Asparagine is heated to high temperatures (like when frying) in the presence of some sugars. Less Asparagine and sugars means less Acrylamide.

3. How many and which varieties have been transformed with the new traits, and was each transformation done separately?

We transformed five different varieties including three popular varieties – Ranger Russet, Russet Burbank, and Atlantic – and two proprietary chipping varieties. These varieties each involved transformation for two traits (the genes related to expression of black spot bruise & asparagine, and the genes related to reducing sugars in tubers) for a total of ten events, which were done separately.

4. Can Innate potatoes be baked, fried, or cooked like regular potatoes? Do they look of taste different after cooking compared to regular potatoes?

Yes. In extensive field tests and subsequent tasting research, Innate™ potatoes were found to look, taste and have a similar texture as their conventionally grown commercial counterparts and can be cooked exactly the same. However, due to the non-browning trait, they no longer need to be soaked after cutting to prevent browning (for those who used to do that).

5. How long do the non-browning potatoes last after being cut compared to normal potatoes? Would Innate Potatoes help to decrease food waste?

Innate™ and conventional potatoes 10 hours after being sliced.

Innate™ potatoes will not turn brown after being cut for many days until they dry out and degrade naturally, while normal potatoes often begin to turn brown within ten minutes. Obvious signs of potato degradation due to blight, rot or virus will still be apparent in Innate™ potatoes in advanced stages and these will be identified during normal quality control at the grower or processor level since potatoes are typically stored after harvesting. At early stages of growth, most conventional potato varieties do not express the polyphenol oxidase (PPO) enzyme that creates browning when cut or damaged so Innate™ would be no different.

(Editor’s Note: this is the same gene and mechanism that was changed to make the non-browning Arctic Apples.)

In terms of food waste, the blackening that occurs after potatoes are bruised affects the quality and recovery in processing French fries and chips – in bad years this can be more than 5% of all loads, according to the industry. The affected potatoes must be trimmed or face rejection before processing, resulting in quality challenges or economic loss. In fact, some processors reject loads with reducing sugar content above 2%, which we understand can be up to 20% of potatoes produced. However, Innate™ potatoes exhibit significantly less black spot bruising and lower reducing sugar content, which could save growers and processors tens of millions of dollars.

6. How many potatoes are lost during and after harvest due to bruising and black spot?

The answer to this question is more complicated than it seems. Weather, soil temperature, storage conditions and different potato varieties can all affect black spot bruise. It can vary significantly from year to year. That said, in terms of food waste, processors and growers tell us that low black spot bruise will result in savings of up to 5% in rejected loads, reducing post-harvest waste significantly.

7. What sorts of efforts have been made to achieve these traits with conventional breeding? Are there any barriers to developing these traits through breeding?

Traditional plant breeding has undergone efforts to reduce acrylamide and eliminate plant viruses and pests, however the progress has been slow and commercially ready solutions are many years away. Today’s traditional breeding techniques simply result in random genomic rearrangements and trait segregation, and do not allow for the simultaneous addition of multiple desired traits.

There currently are no varieties available that produce tubers with low acrylamide potential, reduced black spot bruise and reduced sugars, while displaying all other traits important to the food industry. Therefore, instead of attempting to develop new varieties, the J. R. Simplot Company improved the quality of five existing potato varieties by transforming them with Innate™ technology.

Transformed Innate™ potatoes in growth medium

Because our Innate™ technologies effectively accelerate the process of conventional crossing, it allows desired changes in traditional varieties to occur much faster than is currently possible, while maintaining the desired characteristics of the original parent plant. For potatoes, InnateTM technologies are particularly attractive because potatoes are notorious for having a high degree of heterozygosity, suffering from inbreeding depression, and limited predominantly to clonal propagation. These inherent factors significantly hinder and prevent us from commercially introducing quality, sought-after traits into this valuable crop.

(Editor’s note: see this video to see how potatoes are bred.)

8. What is the current regulatory status of the Innate Potatoes in the US and elsewhere?

Simplot initiated its USDA regulatory approval in January 2013, and the public comment is now open and will be open until July 2. We hope that approval will come in the following year. In addition, we have initiated the FDA voluntary safety review process and should receive approval as early as this fall. We are currently pursuing regulatory approval in foreign export markets in Canada, Mexico, South Korea and Japan.

9. Will Innate potatoes only be sold to commercial growers, or will they also be available for home gardeners to grow? Will we see Innate potatoes in the supermarket, or are these destined only for processors?

When approved, Innate™ potatoes will initially be available to commercial growers due to the limited availability of mini-tubers used as seeds. We are investigating the opportunity to introduce these potatoes into the supermarket via the fresh market in the future. In the near term, they most likely will not be available for home gardeners.

10. What types of safety evaluation have been conducted for Innate potatoes? How do we know what effect they will have on the environment or on human health? How much of a concern is cross-pollination?

Potatoes are grown from seed potatoes, which are clones of their parents. No pollination involved!

The USDA safety review process is extensive and involves an environmental assessment with results from widespread field trials. These field trials demonstrate that Innate™ potatoes were found to pose no health or environmental risks, create no harm to other species, and grow just like conventional potatoes without the need for special pesticides or fertilizers. There is virtually no risk of cross-pollination since commercial potatoes are grown from tubers, not seed. In addition, many commercial potatoes are either sterile or not sexually compatible with wild potatoes. Wild potatoes are rare and flowers are not frequented by honeybees due to a lack of nectar.

The FDA’s parallel review of Innate™ potatoes, which is also underway, will ensure that they are safe for consumption. Although the FDA submission is voluntary, we consider the FDA review to be an important endorsement of food safety. Simplot’s extensive testing shows these potatoes have the same nutrients, taste, and appearance as conventional potato varieties, which have been proven safe over many years.

In addition, we do extensive internal reviews on the safety of the junction sequences of our Innate™ lines, along with an assessment of potential open reading frames and allergens. For example, the plasmid pSIM1278 was inserted with all expression cassettes intact. An analysis of the insert and junction regions shows no new proteins or allergens that would change the safety of the Innate™ lines compared with the parent varieties. Addition evidence that normal potato characteristics regarding taste and plant growth were not changed was provided in agronomy and composition studies provided to the USDA and FDA.

11. What work has been done on assessing consumer attitudes to these potatoes? Are the details of the acceptance study available for people to examine, or will it be published?

There have been several consumer studies conducted over the past few years. The International Food Information Council (IFIC) has done some research on consumer attitudes to biotechnology foods in general. According to IFIC, 69% of consumers are either likely or somewhat likely to accept biotechnology vegetables, including potatoes if they are tastier or fresher.

In addition, Simplot has commissioned its own proprietary research available on its brochures and website that shows that consumer approval of Innate™ (93%) is similar to traditional plant breeding (94%).

12. It seems that the reduced asparagine trait (and perhaps even the non-browning trait) could be important to consumers. How will they be able to find out about these differences when it comes to purchasing the eventual products, whether as whole potatoes, chips, fries, etc.?

When approved, Innate™ potatoes containing the lower acrylamide will be available in a limited basis in 2014. For 2015 onward, Simplot will increase the supply of Innate™ seed to meet the expected market demand. As appropriate, Simplot will work with chip, fresh and fry processors to communicate the benefits.

13. What do farmers think about them?

Several farmers have been involved in field trials and many more have attended grower-briefing days to see the results. They have told us that they are very excited at the results, in which Innate™ potatoes have the same taste and growth characteristics as their commercially grown counterparts and contain marketable traits for lower asparagine, lower black spot bruise and lower reducing sugars.

One sizeable grower who has seen our field trials, Duane Grant, recently wrote an editorial about them in Truth About Trade & Technology.

14. What other traits are being developed by Simplot that we might see in the future?

This technology shows great promise for future crop enhancements. Simplot Plant Sciences plans to add benefits to current Innate™ potato lines, different potato varieties and even other crops. Our second generation of biotech potatoes will store better and reduce acrylamide by up to a 90%. We have an active research program and are working on Potato Virus Y, improved late blight resistance, and other consumer health traits like increased vitamins or nutrients. Through the endless possibilities of Innate™ technology, we aspire to create better fruits and vegetables, farming and human health.

–Haven Baker

Feel free to as additional questions, and if you want to comment on the petition for deregulation you can do so here. Thank you Haven for taking the time to answer these questions for our readers, and to Julie Sally for helping to arrange the interview.

Update May 9, 2013: Haven Baker met Frank yesterday! Here is the photo.