Wednesday, November 27, 2013

Death Match: Transgenesis vs Traditional Breeding

For this week's blog, I wanted to learn and read papers about a common claim made by the pro-GMO scientists: that creating a crop by transgenesis is better than traditional methods for creating plants. I'll explain a bit more, but we'll have to start with the very basics: as this paper outlines, there are three broad categories of plant breeding, and for the sake of simplicity, we'll be focusing on only two of these:
  • Transgenics: when you take a gene from an organism and stick it into another organism that it traditionally could not breed with. These new species are popularly known as GMOs, and are subject to regulations.
  • Traditional breeding: every other method of creating a plant and are not subject to regulations. This includes mutagenesis through chemicals or through radiation, which brings about random mutations creating new traits. Reminds me of X-Men, the first movie, where they zapped the senator and made him a mutant. But that was in the good 'ol X-Men movie days... 
So, the pro-GMO parties state that creating a new strain of a plant through transgenesis can be better than mutagenesis, where you get random mutations, or even cross-breeding, where two genomes with thousands of genes integrate (although I wonder where Napoleon Dynamite would be if he didn't have a hybrid Liger). A few recent news articles have reported that plant breeders are turning more frequently to radiation and mutating chemicals to create new strains because there are fewer regulations, so this topic is all the more relevant.

Before you read on, I feel the need to clarify a few things. I've been working on this blog article for over one week, because the spouse is stuck on one fact: "How can nuking a plant be OK, but a GMO isn't? Do you mean to tell me that if a pomegranate with grape-size seeds appears in Fukushima, that's OK?" Spouse: you'll be reading this again in a few hours when I ask you to review. Don't get stuck on that. Read on. The whole point of this is to find out whether it is OK or not. (Addendum: it's important to note that plants derived through mutagenesis are not excluded from the "Certified-Organic" label. Transgenic crops, however, are excluded).

So this week, it's the battle of the methods thunderdome-style: traditional breeding vs transgenesis. Two methods enter, one method leaves... Or maybe neither one leaves. Or maybe both leave a little
bloody. We'll see. (BTW, I'm pretty proud of my little image here.)

Round 1: Mutagenesis vs Transgenesis

To get started, I reached out to the folks at I had tried finding a review on the topic, but I couldn't find a good comprehensive paper that summarized the different methods. Someone should get on that :) Anyway, they sent me a paper from the Proceedings of the National Academy of Sciences (PNAS), which served as a great starting point, because then I could start cross referencing.

This paper, released in 2008, looked at the expression of thousands of genes to find out if there were any unintentional changes in gene expression in transgenic crops (I can hear the spouse now saying "huh?"). Gene expression refers to how much of a gene is turned on or turned off, and is measured by amounts of RNA. If you remember high school biology, DNA is transcribed into RNA which is then translated into protein, and the protein is generally considered to be the final goal. Now, proteins generally do not work independently and often regulate one another. For example, if protein A and protein B work together in the cell and you change the amount of protein A, you might also affect protein B. That consequence is often easier to identify, particularly if you know that protein A and B work together. But sometimes, you see a change in protein C and then you scratch your head and try to think of how protein C could possibly be affected by protein A. So, in this study, they wanted to determine if there were any unintended changes in gene expression when you add a gene in a transgenic plant (i.e. GMO), and compare it to the unintended changes in gene expression when you create a plant by the more "traditional" mutagenesis route, such as by gamma-irradiation. Yes... Gamma-radiation is real and is not confined to creating the Hulk or other super-heroes (BTW, don't scientists in comic books seem incredibly error-prone?)

The study seemed pretty straightforward and included the appropriate controls (although the plants were grown in the lab). The authors compared transgenic rice strains (i.e. GMOs) and strains of rice generated through mutagenesis, to the closest non-modified strain (i.e control). The authors found that in all the strains, there were unintended changes in the expression of genes that are related to plant stress or defense, and the paper spends a lot of time breaking down these genes into various categories. There are also changes in gene expression in certain genes that might be related to the transgene or mutant gene itself (i.e. changes in protein B in my previous explanation). The authors draw several conclusions:
  • Although there were unintended consequences in gene expression using both methods, transgenic strains had fewer changes.
  • Changing a plant through mutagenesis or transgenesis creates stress in the plant and leads to changes in gene expression, which are carried through several generations.
  • The authors recommend that food safety assessments should be carried out on a case-by-case basis and not just limited to foods obtained through genetic engineering.
Round 1 Results: advantage to transgenics

Round 2: Hybrids vs Transgenics

So, at first I was a bit disappointed. I couldn't find a paper that had done a battle between hybrids created by cross-pollination/cross-breeding and GMOs. But then when I thought about it, a head-to-head battle didn't really make sense. What would you use as a control? What would be the GMO equivalent of a broccoflower? As a consolation, there were plenty of papers that had examined genetically modified strains of corn vs their non-GM control strains.

The most comprehensive paper I found was a 2010 paper that had looked at changes in gene expression, as well as proteins and metabolites, in Round-Up Ready corn and Bt corn, compared to the closest unmodified control. They used seeds from the same location over several years, as well as different locations in the same year, to make sure that they had accounted for geographical and year-of-harvest effects. Their conclusions are:
  • Year-to-year variation can account for more differences in gene expression, protein levels and metabolites than whether the plant is genetically modified.
  • Geographic location can account for more differences in gene expression, protein levels and metabolites than whether the plant is genetically modified.
  • The authors also reiterate that food safety assessments should be carried out on a case-case basis, rather than just lumping all genetically modified foods into one category.
There are many other papers that have done assessments on changes in gene expression in plants, and this freely available 2011 review does a really nice job categorizing the studies based on crop. If you quickly scan through it, you will see that it's a topic that has been studied quite a lot. So why is any of this important? Well, "substantial equivalence" is the starting point for food safety assessment. That means that you have to show that the food item is equivalent to conventional food in several different categories including nutrients, toxins, allergens, etc. So examining changes in gene expression is a different way (and I'd argue that it's a more rigorous way) of determining "substantial equivalence". There are a few conclusions from the review that are worth highlighting:
  • There doesn't seem to be a single, consistent method for assessing changes in gene expression. Each paper looks at different variables and factors, different number of plants, and with plants grown in different conditions. It would be nice to have some consistency.
  • Environmental effects consistently play a bigger role in gene expression than the transgene.
  • None of the large scale studies examining thousands of proteins, genes, and metabolites have raised any food safety concerns.
  • Since transgenics has less of an impact than other breeding methods, the regulatory standards on transgenics should be lowered (the authors highlight that the more likely scenario is that conventionally bred plants will be regulated).
I agree.  I fail to see how mutagenic technologies are any safer than transgenesis. I agree with the fact that food safety should be regulated and determined based on the trait and not based on the method used to generate that trait.

So, unfortunately, there was no clear victor in today's thunderdome because there haven't been enough head-to-head battles. What is clear is that stringent regulations against all forms of transgenics don't make sense considering their history of safety and substantial equivalence.

Sunday, November 17, 2013

The Secret Oath of Scientists

This week's blog is a departure from my usual format. Because I have something to confess. To all my fellow scientists: the jig is up. It's time. I hate to be the first person to say something, but I think that people are on to us and it's better for us to come out with our hands up.

For me, it all started when I was a teen. I wanted to become a scientist because I wanted to increase the rate of cancer in our population. Not only cancer, but I wanted to make something that would cause autism amongst children. You heard me right. At first, this dream was a small flickering of a flame, but during grad school it became a full blown bonfire. The thousands of dollars that I made during my 10 years of education only fanned these flames and pushed me onward towards my goal. Soon I learned that I wasn't the only one with such hidden secrets: while chatting with my professors in 3-star Michelin restaurants, I learned that my fellow grad-students all had similar goals. Some were trying to figure out how to extend the life of the rich and famous in wealthy countries. Others had less lofty goals like figuring out how to cause irritable bowel syndrome in adults. I signed the Oath, which is signed by every scientist throughout the world, where we solemnly swear to maintain the secrecy of our true natures and passions.

We fooled our friends and families into believing that we were working long hours and that our careers were toilsome. But in truth, we made tons of money mostly by reviewing papers. Reviewing papers was a cash-cow. Reviewing a paper that the government or a company didn't want published was a dream come true: not only would you get paid by the journal, but you'd also get paid by the government/company for rejecting the paper!! My professor bought his first Porsche when he rejected a paper that conclusively proved that an herbal supplement cured cancer. My supervising post-doc bought his first apartment in Paris for burning a paper that showed how GMOs cause some weird leaky gut disease. Why on Earth would we want to get that knowledge out!??! Oh, the naïveté of some people is just plain cute.

Once I graduated, I started working for big biotech companies because I thought it would be the best way to accomplish my goals. I have a few friends in big pharma and we all agree that it's been a really interesting experience! We've learned that if we make bad products, no one really cares. In fact, our shareholders just buy more and more stocks and the media never reports on it. Also, all the big pharma and biotech companies don't compete against one another; if one company manages to make a vaccine that causes autism, not only do all the other companies stay quiet about it, but they all share the knowledge with one another. It's all part of the Oath. And an additional dream of mine has finally come true: I have the enormous blessing of never being allowed to quit or to take advantage of the federal whistleblower laws. Even if I disagreed with all the cover-ups that these companies do or disapproved of all these untested drugs that get released, there's nothing I could do about it. It's so great working for companies where every employee shares your vision of world domination and control.

Some day I hope to work for a company that slaughters puppies to fuel our manufacturing systems, where we make drugs to remove arm flab, test it on the homeless in Panama, and have a survival rate of 30%.

So there you have it. It feels real good to get this off my chest. I really want to thank everyone who has recently posted articles about the evils of vaccines and GMOs. It has made me realize that there's now a critical mass of people who are aware of what we scientists do, so we'd better quit while we're ahead.

Sunday, November 10, 2013

IRT - GM food supplement caused deadly epidemic

Before I get started, I have a confession to make: I love pomegranates. Love probably isn't a strong enough word. I ate 2-3 a day while I was pregnant, to the point that the hubby planted two trees for me (one of which had it's first fruit this year). But it's a "work food". Like crab legs. Or pumpkin seeds. You have to put in a good amount of effort before you can eat the stuff. Anyway, since it's pomegranate season, I've been eating them all the time and I woke up thinking "someone should make a pomegranate that's easier to clean". And I'm guessing I'm not the only one who wishes for this: Wikipedia has a good section dedicated to suggestions on cleaning out pomegranates (including my preferred method of cracking them open under water). Well, according to this review, a genetically modified pomegranate tree is possible because one has already been made to express GFP (green fluorescent protein). It's probably what Sheldon used to make his goldfish glow in the dark. The authors recommend making pomegranate crops that are stress tolerant or have other horticulturally-beneficial genes, but none have been made (although that hasn't stopped people from marketing GMO-free pomegranate juice). None of the suggestions in the review included recommendations on making the fruit easier to eat...

Now, getting onto juicier topics (no pun intended!)

If you've been following this blog, you'll know that I started reviewing the "Health Risks" section on the Institute for Responsible Technology's webpage several months ago. This was due to the fact that numerous anti-GMO webpages were using it as a resource, so I thought I should look into it. Today, I finish its review by covering a section entitled "GM food supplement caused deadly epidemic". I'll be honest here: I started out upbeat and open minded when I started reviewing the IRT's site, but I haven't come across a single valid statement. Consequently, every time I sit down to read from this webpage, I feel the same way as when I think about Jar Jar Binks. Or just Episode 1 in general. A sense of dread and gloom. Consequently, it's only this bowl of pomegranate that I'm currently eating that will get me through this last section.

The segment would have been more aptly entitled "Dietary supplement produced using recombinant DNA technology was associated with a deadly epidemic". Here's the first section directly from the IRT: "In the 1980s, a contaminated brand of a food supplement called L-tryptophan killed about 100 Americans and caused sickness and disability in another 5,000-10,000 people. The source of contaminants was almost certainly the genetic engineering process used in its production." It goes on to state that it took years to "find" the disease and that an investigation only took place because the symptoms were so dire. The IRT argues that there is no monitoring of GMO-related illnesses - particularly long-term effects - and it may take decades, if ever, to identify the source of a problem. I've already reviewed the topic of long term effects of GMOs, so I'll focus on the first part of their argument.

Unfortunately, there are only two citations. The first is to an article on the IRT's webpage and the second is to a book written by one of the founders of the IRT. So neither one are peer reviewed sources. However, Wikipedia has a pretty good entry about this event, with several citations. The disorder is known as eosinophilia-myalgia syndrome (or EMS) and the outbreak took place in 1989, leading to an eventual ban of tryptophan dietary supplements by the FDA. I started by reading a few abstracts for papers that investigated the cause of the EMS outbreak:
  • The abstract for the first paper simply states that they traced the bad lot of L-tryptophan to a single manufacturer from Japan.
  • The second abstract says the same thing (a different population was tested) and hypothesizes that a contaminant was introduced in the manufacturing process.
  • The third abstract says the same thing, adding the point that the incidence of EMS decreased drastically once the product was recalled.
So far, there's nothing about a mysterious genetic engineering contaminant. There's reference to a contaminant, but no mention of when/where/how it could have been introduced.

If I were to magically design the perfect pomegranate, I think it would peel like a tangerine.

The next item I read was a 2001 report by the FDA (I thought it was odd that the IRT article did not mention the FDA's involvement). The FDA report was written up to clarify their position on tryptophan supplements. The report stated that 37 people died as a result of the bad batch of tryptophan. They state that there were numerous impurities in the batch, several of which were associated with EMS, but no one really knows how. They pointed out that not everyone who took the contaminated supplements got EMS, so there may be a genetic predisposition/factor involved as well. Again, nothing about a contaminant from the genetic engineering process.

I'd also magically make that white fluffy stuff disappear so that the seeds would just drop out. I looked it up and the white fluffy membrane doesn't have a specific name. You'd think it would have an uber-geeky scientific name.

Next, I found a New England Journal of Medicine article that looked into the whole tragedy. The article points out the fact that the manufacturer in Japan had switched to a new bacterial strain for the synthesis of tryptophan in 1988. In 1989, they made another change in their manufacturing process: instead of starting with 20kg of one of the starting materials, they cut it down to 10kg. During that same time period, some of the batches of tryptophan that they were making skipped one of their filtration steps. The authors find statistical significance between the amount of starting material used with EMS. They also find correlation between the bacterial strain used and EMS. However, they highlight numerous times that they cannot disassociate the bacterial strain used from the amount of starting material used, so they cannot tell the impact of the bacterial strain alone. Then they state: "For this reason, it is possible that strain differences were unrelated to the production of the etiologic [disease causing] agent." They also mention that the manufacturer's tests had shown no difference in the biological and physiological properties of the old and new bacterial strains. So the New England Journal of Medicine does not point to a weird by-product of the genetic engineering process. Also, article sheds a lot of light on the timeline: the first cases of EMS were identified in October 1989 and by early November 1989 the link between tryptophan and EMS had been found. It didn't take months or even years for this to be identified.

I only have two pomegranates left in the fruit basket... I'd better add 'pomegranates' to the shopping list. I wish I could write 'peel-able pomegranates'. I'd pay extra for those suckers.

So here's why I think that this is, by far, the most ridiculous "health impact" on the IRT's webpage and the molecular geneticist in me cringes at the thought that this is even considered a GMO, as defined in the GMO debate. In 1922, the first human patient received an injection of insulin isolated from a calf pancreas, and patients had to rely on insulin isolated from animals until the 1980's. To make human insulin, the DNA sequence of insulin is inserted either into bacteria or yeast, which then start making the protein. It is isolated, purified, and sold to millions of patients worldwide who rely on this lifesaving technology. Patients are not exposed to the bacteria or the yeast. These organisms are just used in the manufacturing process of insulin to make it scalable and, often, easier.

Statistically, insulin is a drug that me or someone I love and care for will probably end up taking in our lifetimes. And insulin isn't the only drug produced this way. Countless other drugs and dietary supplements,  including tryptophan, are produced using recombinant DNA technology (this article highlights that malarial drugs are being made this way). So why is the IRT focusing on this story about tryptophan and EMS? I really can't explain it.

In my perspective, the EMS outbreak highlights another issue altogether: the need to have more stringent regulations in the world of dietary supplements. The quick sequence of changes introduced in the manufacturing process of tryptophan and their immediate rollout to the market would have never even been contemplated if it were regulated as strictly as pharmaceuticals. Or if they wanted to make the changes, they would have had to perform rigorous testing to demonstrate that there's no change in the function of the product. Cutting back on starting material by 50%?? Changing the strain of bacteria used once the product is in the market? Utter craziness!! Please do not misconstrue this and think that I'm implying that the pharma/clinical world is perfect. Far from it. I worked on my first project in regulated markets this year and learned first-hand of the craziness that exists. But at least the regulations and trials that they have to go through put a few checks and balances in place.

Whew! With that rant I finish the review of the IRT's health risks. My conclusion: they focus on fear-mongering. Most statements were misleading or misrepresented the studies, and several statements were outright lies.

Till my next post, I'll continue enjoying pomegranate season and keep my fingers crossed that someone out there is working on a peel-able version of the fruit.

PS: After reviewing this, the spouse thought that the pomegranate seeds should be the size of grapes. Pure genius!

Sunday, November 3, 2013

GMO DNA and your health

I'm behind on my blog: I've been on vacation. My new job also has a longer commute time, so I've been falling asleep in front of the TV every night, instead of diligently reading papers. Someone
should really start working on that teleporter.

A reoccurring statement that I've read time and time again on anti-GMO webpages is about the dangers of eating GMO DNA. I've always just glossed over these claims, because they seemed a bit too science-fiction-y. But before I proceed, a voice in my head (which sounds like my husband's) is reminding me to give a bit of an intro on why I've glossed over these claims. Here are my top two reasons:
  • Nearly every cell-type in the body of every living creature has DNA. Whether that cell is from the organic beef of a cow or a pesticide-infested fruit, they all have DNA. And your digestive system does not know the difference between the two. So if GMO DNA is going to "sneak into your body", so will the DNA of that delicious bacon you ate this morning. As well as the DNA from those pork-chops. And ham. (Those are all from the same animal you say? That's preposterous!)
  • Even if DNA from your food got into your body, then what? The DNA would have to hijack your body's cellular processes in order for anything to happen, similar to how a virus operates. 

So that's why I've ignored these statements, which really seemed like fear mongering when I read them. However, I've read a few articles that claim that the DNA doesn't necessarily have to transfer into you. It might just transfer into the healthy-bacteria that lives in your gut. Due to this possibility, I decided to look into matters. In fact, taking a look at the Institute for Responsible Technology's section on "Health Risks", there's a whole section on "Functioning GM genes remain inside you".

The most commonly cited paper tied to these statements is from a  2004 Nature publication entitled "Assessing the survival of transgenic plant DNA in the human gastrointestinal tract". Apparently, the publication of this paper was quite the coup for the anti-GMO field. The paper looks at the survival of GMO DNA in the intestinal tract, because in order for the DNA of a GMO to transfer into bacteria from the gut, then it has to survive the digestive process. The authors looked at DNA from GMO soy and native soy, in ileostomists (basically, individuals who do not have a lower intestine) and individuals with intact digestive systems. Here's the summary:
  • GM soy and regular soy were fed to participants. DNA from soy and GM soy was detected in the "digesta" of the ileostomists, but it was not detected in regular individuals. The authors conclude that the DNA can survive in the upper intestine, but not lower intestine.
  • GM soy and regular soy DNA were degraded at similar rates.
  • The authors identified fragments of GM soy DNA in bacteria from the intestinal flora in ileostomists at very low concentrations (probably existed before the study started). The authors were unable to isolate the bacteria. Additionally, they were unable to reproduce this experiment in individuals with intact digestive systems.
I'd like to take the liberty of copying the conclusion from this paper (my clarifications are in brackets): "In conclusion, we have shown that a small proportion of the transgenes [GM DNA] in GM soya, like the native soya DNA, survives passage through the human upper gastrointestinal tract but is completely degraded in the large intestine. Although we found some evidence of preexisting gene transfer between the GM soya and the human small intestinal microflora, the bacteria containing the transgene represented a very small proportion of the microbial population, and there was no indication that the complete transgene [full gene from the GMO] had been transferred to the prokaryotes [bacteria]. Thus, it is highly unlikely that the gene transfer events seen in this study would alter gastrointestinal function or pose a risk to human health. Nevertheless, the observed survival of transgenic DNA from a GM plant during passage through the small intestine should be considered in future safety assessments of GM foods."

Note the sentence that I highlighted. Contrast this with the health risk from the Institute for Responsible Technology's webpage that refers to this paper: "The only published human feeding experiment revealed that the genetic material inserted into GM soy transfers into bacteria living inside our intestines and continues to function. This means that long after we stop eating GM foods, we may still have their GM proteins produced continuously inside us." For the first time in this blog's history, I will use the phrase: 'that is a blatant lie'. First of all, the genetic material wasn't found in bacteria of individuals with intact digestive systems (i.e. the overwhelming majority of people on the planet). Second, the whole gene was never found in bacteria, which makes it impossible for an intact protein to be produced, much less for that protein to "function".  #EpicFail #IRT

The next three statements on the IRT's webpage are:
  • "If the antibiotic gene inserted into most GM crops were to transfer, it could create super diseases, resistant to antibiotics.
  • If the gene that creates Bt-toxin in GM corn were to transfer, it might turn our intestinal bacteria into living pesticide factories.
  • Animal studies show that DNA in food can travel into organs throughout the body, even into the fetus."
Let's start with the first two statements. Note that there's no evidence for them, they're "if" statements. Let me make a few "if" statements:
Do I have any evidence? Well, I provided a few links and citations there, didn't I? And they're all to legitimate sources. Note that that is more evidence than the IRT provided for their two hypothetical scenarios.

There's one final statement: "Animal studies show that DNA in food can travel into organs throughout the body, even into the fetus." This is tied to a slew of articles and a quick scan through the titles and abstracts indicates that it's accurate. However, as I pointed out earlier, "then what"? DNA in food can travel into organs throughout the body, even into the fetus, whether that DNA is GMO or not. So DNA from our food has been circulating through our systems ever since we started eating.

If your argument is "Mother Nature never intended for us to eat foreign DNA", then what about when you eat a broccoflower? Or a pluot? In fact, if you eat any fruit or vegetable that is exotic, then Mother Nature never intended for you to ingest the DNA from that plant. For example, if you're Northern European and you eat a banana, or a mango, or a dragon fruit, isn't that DNA foreign to your system?

There's one final argument in my head that puts a nail in the coffin of this whole deal: humans aren't the only species that have bacteria in their gut. Mammals have been eating plants for millions of years. If any sort of absorption of genetic material were to happen between gut bacteria and plants, wouldn't it have happened by now? We've been part of this "human feeding experiment" ever since mammals starting eating plants, and even birds and fish before that (birds also have bacteria in their guts, as do little Nemos). If you consider that the most abundant protein on the planet is thought to be RuBisCO (a plant protein), then throughout the course of evolution, the bacteria in the gut of some animal would have taken up RuBisCO DNA. But that has not been identified (however, my husband wisely points out that this may have been the origin of the Ents in LOTR).

There are dozens of papers that have looked at the absorption of DNA in our food. All of them have the same conclusions: DNA from our food behaves the same, whether its GMO or not. Our digestive system breaks down the vast majority of the DNA (although this paper did find that complete genes may make their way through, but I reiterate: then what?). That DNA can be detected in feces and our organs.

Well, that's all I've got. If you have any questions, please comment below.