I got 99 Problems but a GMO Ain't One

In the past, I’ve written a short list of problems that are attributed to GMOs, but are actually problems with modern agriculture. Well, I’m going to expand the list to “9 Reasons Why GMOs are Opposed that Aren’t Really About GMOs”, or as the spouse aptly entitled this post "I got 99 Problems, but a GMO Ain't One". But it's really only 9 problems. As I've written before, transgenesis, or the method used to make most GMOs, is a tool and it makes no sense to oppose a method with broad applications. It's like opposing electronics as a category because you don't like the fact that your Roomba chews up your computer cable (which is happening this very instant...) or that iPhones cost too much.  In fact, an article was just written in the NY Times about GMOs, and in the comments section, you'll see the reasons below being listed time and time again.

So, here we go.

9) "GMOs are patented". Yes, many of them are patented, but so are many non-GMO crops. Pluots didn't just drop out of the sky: someone had to work for years to develop those tasty treats, so there are patented varieties. Not all GMOs are patented: there are open-source GMOs, and there are also GMOs where organizations have worked with private enterprises to give away seeds on humanitarian grounds, such as Golden Rice. So using the "GMOs are patented" excuse makes no more sense than saying that you don't like electronics because Windows is under a copyright. 

8) "GMOs cause superweeds". GMOs that carry traits for herbicide tolerance can lead to weeds that develop tolerance to the herbicide, known as "superweeds", and I've reviewed this topic here. Superweeds are far from being an issue unique to GMOs, and even pulling weeds by hand can lead to weeds that look like the crop itself (known as mimicry). The issue of superweeds is a serious one, and this database tracks herbicide resistant weeds as they develop across different nations. Reducing it to a "GMO-specific" problem and severely narrowing the scope of the issue, deters the efforts of finding genuine solutions to the problem. So using the "GMOs cause superweeds" excuse makes no more sense than saying that you don't like computers because they can lead to electric shocks, when the issue is much broader in scope.

7) "GMOs are drenched in pesticides". Yes, pesticides (be they herbicides, insecticides, or fungicides) are used on GMOs, as well as any other form of modern agriculture unless it specifically states "pesticide-free". That includes the U-Pick farm I went to last week for cherry picking and the organic peach farm next to it. That includes the fields of corn that we drove by to get there. It took me a while to come to the realization that no form of agriculture is perfect. If we insist on going pesticide-free, crops will be lost which will increase costs to consumers and we will have to dedicate more land to get the same output. Pesticides are expensive. Farmers don't just decide to spray their fields with pesticide because they feel like it, nor do they "drench" their fields in it. There are laws and regulations on how much can be applied, and why on earth would anyone use any more than necessary when its use can cut from your profits? Here's an excellent post written from a farmer's perspective on the topic of pesticides and why they're used. PLEASE read it. Some GMOs are designed to resist pests so that pesticide doesn't have to be applied, such as the Rainbow Papaya which is designed to resist the ring-spot virus and saved Hawaii's papaya industry.

6) "GMOs are monocultures". When I was preggers, the spouse and I went on a road trip around California. I was miserable. I was one of those people who had morning sickness well into the 3rd trimester. Anyway, I was on medication to control it because I was losing weight, but the medication made me horribly drowsy. So the road trip ended up being more of a sleeping trip. Somewhere between Sequoia National Park and Fresno we drove through orange farms. And we drove. And drove. And drove. I don't know how long it was but it felt like every time I woke up, we were still driving by orange trees. And GMO oranges don't exist on the market. So yes, there are vast fields of GMO corn in places across the US, but there are also vast fields of non-GMO spinach and giant orchards of fruit. When I lived in Venezuela, we lived across from a valley that was a giant sugarcane farm. It was enormous and it belonged to the local sugar refinery. Every year, they'd harvest sugarcane about 3 times. It never changed, there was no crop rotation, and it just went on for miles. There's no GMO sugarcane. Monocultures can lead to crop resistant pests, and farmers are encouraged to rotate their crops from one year to the next so that this risk can be minimized. So, again, reducing the issue of monocultures to a GMO-specific one is highly disingenuous.

5) "GMOs are being made by Big Ag to line their pockets". Unless your problem is with making money in general, then this doesn't make much sense. Of course ag-businesses want to make money. Why would any corporate enterprise embark on a project where they think they'd lose money? Again, the "Big Ag" argument doesn't apply to all GMOs. Arctic Apples were developed by a small company up in BC, Canada that only had 7 employees. AquaBounty, which developed the transgenic salmon (not yet commercialized) only had 12 employees on staff in 2012. And of course, many transgenic crops are being developed by public sector scientists, some of which address undernurishment such as biofortified bananas to address vitamin A deficiency. This reason for opposing GMOs is like saying that you oppose electronics because Apple makes too much money from the iPhone.

4) "GMOs place restrictions on seed saving". This is tied to #10 on this list. Farmers who plant GMOs sign a contract where they state that they will not reuse seeds. In the same way that you're not supposed to copy and give away that Maroon 5 song that you just downloaded from iTunes because it's a copyright violation, farmers are supposed to respect the intellectual property rights of the companies with whom they have signed a contract. Many farmers have written about the plethora of choices they have when it comes to seeds (here's one of my favorite articles). Basically, if farmers do not like the restricted seed use, they don't have to buy the seeds. It's as simple as that. The fact that they do and that they buy the seeds on a fairly regular basis suggests that there's something about GMO seeds that they prefer. Not only that, but there are non-GE crops where farmers have to sign agreements as well (this includes non-GE sunflowers, which Chipotle switched to when they adopted more integritiness). So this has little to do with GMOs: it has to do with patents. If you can think of a better way that companies can recover the dollars they spend on making a product after the first year, by all means, make the suggestion. Farmers who do not use GMOs generally buy their seeds from one year to the next, too, because the seeds they plant are often hybrids. Recalling Mendel's pea experiments, this would mean that if farmers reused the seeds, only a portion of the following year's crop would have the traits they want.

3) "GMOs use the carcinogenic Glyphosate". Glyphosate use is not restricted to GMOs. That by itself is enough to earn it a place on my list. In fact, we just used it this week to get rid of a particularly thorny wild blackberry that we couldn't control and was right in Baby Boy's biking path along the driveway. Regarding the label "carcinogenic", I think that Dr Andrew Kniss wrote one of the most balanced pieces I've read on this topic, and I'd like you all to head over there to take a look. An important point to keep in mind is the time at which herbicides such as glyphosate are applied. Think about it: glyphosate is being applied so that corn/soy can grow heartily without getting choked out by weeds. Does it make sense to apply glyphosate when corn is several feet tall? Here's Pioneer's recommendations for glyphosate application, and they recommend using glyphosate when the plants are just a few weeks old. Between that time and harvest, it might rain, the sun will have beaten down on the crops, and the crops will have been watered. So saying that the corn we eat is "drenched" in glyphosate doesn't make sense to me. Regarding the amount of glyphosate used, I love this graphic by Sarah Schultz where she explains that approximately one soda can-sized amount of glyphosate is applied across an entire acre of crop in one season. More importantly, there are MANY GMOs that are not glyphosate resistant: the Arctic Apple or Innate Potato, for example, could be grown using organic practices (without the organic label), and again, all those GMOs that are being made for humanitarian purposes that have absolutely nothing to do with pesticides.

2-1) "Monsanto". I give Monsanto 2 spots on this list, because there are different aspects to the "I hate GMOs because of Monsanto" reason.

2) "GMOs promote a monopoly." Every time I see this, I think that someone over at Dow Agro is cackling. I work in a field in biotech right now where a single company has between 70-80% of the market. Google web searches are used almost 70% of the time. Android has 80% of the market in operating systems for smartphones. But strangely enough, I've never seen a "March against Google". I tried to find out how much of the seed market Monsanto owns, and the numbers are all over the place, because it's such an easy number to rig to portray your point. For example, Monsanto says that it has 5% of the world market in seeds. The Organic Consumers Association says that Monsanto has 80% of the US GM market on corn. However, GMOanswers.com explains the latter by stating that they license the trait to other independent companies, so they're not sold by Monsanto. Commercial licensing agreements are set up between companies ALL the time, so the stat from OCA is blurring the real numbers. This would be equivalent to saying that the Lenovo laptop I'm typing on was sold by Microsoft because it has a Windows OS on it. No: the laptop and the sales go to Lenovo, which then pays Microsoft a licensing fee. So I honestly don't know how much of the seed market Monsanto owns. Keep in mind that organic and non-GM farmers have to buy seeds from somewhere, and Monsanto does sell organic seeds. Unless you know what seeds your local farmers used when you buy your veggies, you have no guarantee that you're boycotting Monsanto if you boycott GMOs.

The problem with monopolies is a tough one and I don't know what the solution might be. Since it takes such a long time to get a GE product through the regulatory process, it's difficult for a small company to last very long. During that time employees need to be paid, logistics need to be taken care of, and the product pipeline needs to continue its development while no revenue is being generated. By no means is this a problem unique to the agricultural biotech sector. Small tech companies are gobbled up by larger behemoths every day. So the issue of monopolies is far from being a problem about GMOs.

1) "Monsanto made (place your favorite scary chemical here)". This is a topic that I'm struggling with myself. I know that Monsanto has a very checkered past, particularly when it comes to Agent Orange. Very briefly, Agent Orange is an herbicide that was used by the US during the Vietnam War to deprive the guerrillas on the ground of food and cover. Agent Orange production during the Vietnam War contained a contaminant which caused severe health problems in the local inhabitants. The US government placed orders from many companies for Agent Orange, and Monsanto was one of them. I don't know how it came to be that Monsanto is exclusively blamed for Agent Orange. As I see it, there are multiple people to blame, primarily the US government. I'm assuming that all the companies involved could have turned down the US government contract, and I'd like to believe that in an ethical world, they would have. But to blame Monsanto for this issue makes no more sense than to blame Boeing for military airstrikes, and I have yet to see a "March against Boeing". The Monsanto that exists today has gotten rid of its chemical division, however there's no denying that the company is built upon the revenue generated by the company that existed back when it made chemicals. There are many companies that exist today that were built decades or centuries ago under very shady circumstances (see the Hugo Boss brand as an example, where they provided uniforms during Hitler's Germany; here's a short list of companies that benefited from slavery. When the spouse read this section, his degree in Political Science kicked in and he started rattling off companies that benefited from times of war, including IBM). I believe that these companies should acknowledge their past and make amends. GMOanswers addresses the topic of Agent Orange and Monsanto, but they have a very PC statement basically pointing the finger elsewhere. Ultimately, this issue has very little to do with GMOs, but is a discussion that we need to have in our society.



In conclusion: there are many legitimate concerns about modern food production. There are many legitimate concerns about the corporate nature of our society and the undue strength they exert over the American political system. These are the things we should be opposing. But whether you realize it or not, when you yell "No GMO!" and list one of the reasons above, the crops that are designed for you and I as consumers, the crops that are designed for humanitarian efforts, all suffer as a consequence. I know it doesn't make for a catchy slogan, but why not try voice your concerns by stating "No to the patenting of all seeds, regardless of technology used for their development!!" or "Increase funding so that our public institutions have the resources to commercialize and license crops!!". I'd recommend focusing your efforts on the REAL reason why you oppose GMOs, and not on the technology as a whole.

An Intro to Next-Generation Sequencing (NGS) - Part 1

A few months back, I wrote a post about the alleged dangers of eating DNA from a GMO. In summary, our bodies don't know the difference between DNA derived from a transgenic crop or a traditionally bred crop. We've been eating cellular material for quite some time now and we haven't become green from eating veggies. (I wonder if the Creation Museum has a display of a caveman chomping down on some delicious dinosaur ribs.)

However, I still see many arguments about how we've now found DNA from our food circulating in our blood or how we've found RNA from rice inside us. Many of these studies have been enabled through a technology known as Next-Generation Sequencing (NGS). In the spirit of full disclosure, this is my field of work: I've worked in companies that develop NGS technologies for 6 years: the last 4 have been in internal product development, and this last year has been in the R&D lab itself. In this series of posts I'm going to explain the controversies about a few papers that have used NGS technologies and are used as examples of how eating DNA from a GMO is dangerous.

This post gives an overview of the technology and the considerations in experimental design. Next week (or sometime after), I'll post reviews of the papers.

Let’s begin with a brief history of DNA sequencing: prior to NGS, you generally had to know what you were going to sequence. You couldn't just randomly take a DNA sample and tell a lab: “tell me what's in here”. You had to know what you were looking for in order to do your experimental design. Even in forensics, which has yet to adopt NGS, they look at very specific and well characterized regions of the genome. There were ways around this to allow for discovery, but the processes were long and very expensive, which was why the sequencing of the human genome took 13 years (1990-2003) and cost 2.7 billion dollars. The most popular technologies behind next-generation sequencing follow the same general principle: you take your DNA, you chop it up, you amplify it so that the machines have enough to work with and detect, then you put it on a machine that “reads” each DNA base and tells you what’s there. There are several different chemistries for sequencing, each patented by a different company, and each of which has its pros and cons. With the advent of NGS, scientists found that they could virtually sequence anything. There have been a lot of exploratory experiments going on in the past decade based on this technology. Not only that, but you aren’t necessarily restricted to the analysis of DNA. You can indirectly sequence RNA, DNA modifications and structures, as well as DNA bound to proteins.

Here are some examples of the amazing things that have been done with NGS (and why):

• Identify micro-organisms in samples of ocean water from around the world (because there are so many species that we have yet to discover and understand - BTW, when I was a grad student, I really wanted to work on the yacht that was doing this project) 
• Sequence the genome of a panda (because the panda genome is cute and cuddly!) 
• Study the microbial content of our gut by sequencing DNA from feces and mucosa (because we need to determine what the microbial content of a healthy gut “looks like”, in order to determine why/how it goes awry). 
• Identify mutations in infants in the NICU (because doctors need quick diagnoses of genetic illnesses for infants in the NICU due to their critical conditions). 
• Identify modifications to DNA in prostate cancer samples (because these may tell us how genes are turned on/off in cancer samples vs normal samples) 

Pretty awesome, eh? The possibilities are seemingly endless. I actually want a sequencer in my garage, but I’ve been deterred by the thought that my employers would notice if one went missing… (and a shout-out to the spouse for cleaning out the garage for Mother’s Day!! Don’t worry. I won’t turn it into a lab. For now).

Hopefully, you can imagine the applications and experiments that could be performed in agricultural biotechnology, as well as studies pertaining to transgenic organisms. As I've mentioned before, companies use NGS to determine if there were any unintended consequences of the transgenic event. Studies could also be performed to determine the impact of glyphosate on the gut microbiome or on bacteria in the soil, or to determine what happens to the DNA of the food we eat. In another possible application, the mysterious pathogenic organism that Dr Don Huber claims to be enriched in GMOs could also be sequenced, if he were to release the organism (outlined eloquently by Dr Kevin Folta in this change.org petition).

There are a few more concepts that require explanation. One of the key questions in an NGS experiment is “how much sequencing do I have to do”? Here’s an analogy: imagine you’re baking oatmeal cookies with chocolate chips and raisins. You make a big batch of cookie dough. Your kid walks by and throws in a very small handful of dried cranberries. Then you bake cookies. For the sake of this analogy, we have to imagine that the number of cookies you could bake was infinite (i.e. you had an endless amount of cookie dough).

How many cookies do you have to bake and eat in order to determine the ratio of chocolate chips to raisins? If you bake 10 of them, you probably get a good enough idea, right? What if you want to know if there are any raisins at all. You might be able to get away with baking a single cookie. But what if you want to know how many cranberries your kid threw in. Do you bake 20? 30? 100? The number of cookies that you bake depends on the question that you’re asking.

The same is true in the world of NGS. If you’re looking for a mutation that you inherited from your mom and is present in all your cells, you can do a “standard” amount of sequencing for the technology you’re using. But what if you suspect that you might be HIV positive, and the event that led to this suspicion occurred very recently? How much DNA do you have to sequence in order to detect the presence of the virus? The answer will be very different. It's basically a question of abundance. Looking for something that is present in every cell will require much less sequencing than looking for something that is much more rare.

Oatmeal chocolate chip cookies.
Beware! You may become a chocolate chip
oatmeal cookie by absorbing its DNA!
From Wikimedia commons.
But I wish it was from cookies in my pantry.
Alas...

The next concept is that of input material vs contaminant. In our cookie analogy, imagine that you make 2 batches of cookies: a 1 cup batch and a 1 gallon batch. Since the toddler in this analogy is of the “up-to-no-good-variety”, he manages to throw the same amount of cranberries in both batches without you noticing. For the small batch, odds are that you’ll have a cranberry in every cookie you bake. You might even conclude that the cookies weren’t chocolate-raisin, but were chocolate-raisin-cranberry. However, for the second and larger batch, you could probably eat a full dozen without coming across a single cranberry. If you do come across a cranberry, you’d probably say “Huh… What’s that doing in there?”

In the world of NGS, the same is true. If you start with a lot of DNA, you can exclude contaminants more easily/readily than if you start with a small amount, and the inclusion of appropriate controls is a key element. Contamination does happen, however, its impact on your experiment depends on the amount of sequencing you perform and the question you're trying to get answered. For example, the world's first next-gen sequencing diagnostic assay actually allows for 10% contamination before the experiment is deemed a failure. However, the assay's accuracy is still incredible because it does a lot of sequencing and is asking a simple question (i.e, it's only looking for chocolate chips and raisins, not cranberries).

So you see that there are many considerations on how to use the technology depending on the experiment, and every experiment needs to use different controls even though the technology used may be the same. However, such considerations can be often overlooked.

Make sense? Alrighty! I hope to see you here next week when we start reviewing the papers.

BTW, my husband wanted me to change cranberries to walnuts. But I pointed out that walnuts belong in a cookie and would never be mistaken for a contaminant, whereas cranberries don't belong in there. He has seen the error in his views and now agrees.