I think I’m having some fun with transitions. Hey, at least I didn’t do any star fades! (You aren’t safe from them, though)

Potentially promiscuous pollen from corn tassels by circulating via Flickr.

Many people, including me, are concerned about potential harm to crop biodiversity from gene flow. Most people’s concern focuses on transgenics. There is a certain probability, albeit small, that transgenes will end up in the progeny of non-transgenic plants, weedy relatives of the crop, or wild relatives that grow nearby due to pollen flow. Transgenes can also be moved from place to place by accidental or purposeful movement of seeds.

How much transgene flow is actually happening is a subject of some controversy, but what about gene flow between non-transgenic plants?

There is potential for problems whenever plants that aren’t supposed to cross stray from their intended mates. Some things to think about include how gene flow happens at the field and genetic levels and what characteristics of the genes themselves can affect permanence of contaminating genes once they get into a variety they shouldn’t be in.

Gene flow with transgenes can help us to think about gene flow of “regular” genes

In the 2004 paper Gene Flow from Cultivated Rice (Oryza sativa) to its Weedy and Wild Relatives, Li Juan Chen showed that a marker gene “flowed” in their test field from transgenic cultivated rice  to weedy rice at rates between 0.011 and 0.046 % and to wild rice at rates between 1.21 and 2.19 %. The marker gene Chen used is called bar, which is easy to screen for because it makes plants resistant to the antibiotic and herbicide biaphalos. Just spray the progeny and you’ll know if they’ve got the gene. Chen confirmed presence of the bar gene with PCR. These rates seem pretty low, but rice is mostly a self-pollinator, and the pollen is very short lived. If out-cross rates in rice reach 2.19 % we could expect to see rates even higher in other species. This tells us that transgenes can be passed to weeds, but also, more broadly, tells us that any gene can be passed from cultivated rice to weed rice.

Gene flow could be a problem in the opposite direction as well. In the 2009 paper Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids, Vinod Shivrain showed that progeny of a cross between weedy red rice and cultivated rice were more successful if their mother was the cultivated plant. These hybrid grains can fall back to the field on accident or be collected and planted the following year with the regular seed. Either way, the rice farmer now has rice plants that don’t have all of the desired characteristics of the cultivated rice. The plants will have at least some genes from the weedy rice that could help it out compete the desired rice plants but produce less grain. This paper shows that gene flow from weeds to crops can happen, and that it can be a problem.

Maize, unlike rice, is a promiscuous out-crosser. The pollen is heavy and still fairly short lived, so mostly pollinates plants that are nearby, but wind-carried pollen and stray seed can carry transgenes away from their intended fields. The story of transgenes in landraces of maize is summed up beautifully in the 2007 paper Gene flow from transgenic maize to landraces in Mexico: An analysis (pdf). Kristin Mercer tells us that research on the subject has had mixed results. Transgenes likely do exist in landraces in Mexico, but the extent of the “contamination” is not as wide as some researchers have proposed. Some of Kristen’s other research focuses on how crop alleles move in wild sunflower populations. The sum of her research is that we can expect gene flow back and forth between any compatible plants: wild, weedy, cultivated, transgenic, landrace.

Gene flow’s effect on biodiversity

Image of corn plant by University of Nebraska Lincoln, adapted by Anastasia Bodnar. All other images in this post by Anastasia Bodnar.

Understanding the impact of gene flow on biodiversity (or more appropriately, crop diversity) requires some understanding of what happens at the genetic level. I like to sit down and draw pictures to help me think about genetics. I hope it helps some Biofortified readers as well!

The image to the right shows two hypothetical varieties of corn. On the left is a modern inbred variety. All the plants are identical. There is no or low genetic variability within the inbred, because there is only one version of each gene present in the variety. On the right is a landrace or heirloom variety. All the plants are different from each other to some degree. There is high genetic variability within the landrace because there can be many versions of each gene present in the variety.

Below  is a (very) simplified view of what happens at the chromosomal level when an inbred is crossed with a landrace (in a hypothetical crop with one chromosome). Note: a hybrid or even an open pollinated variety could be substituted for inbred here, it was just easier to use an inbred. Similarly, a wild variety could contaminate a landrace. One landrace can contaminate another. One inbred could contaminate another. Weedy relatives can contaminate crops. Crops can contaminate wild varieties… you get the idea.

In the inbred (red), the two sister chromatids for each chromosome are identical to each other. There is only one version of each gene in the inbred, also known as two copies of the same allele. In the landrace (blue), the two sister chromatids are different from each other. For each gene in the landrace, there can be two different alleles. The different shades of blue indicate different alleles for some genes on the sister chromatids.

Imagine a situation where a field with the inbred is right next to a field with the landrace. Pollen will flow between the fields (to some degree – depending on weather conditions, pollen size, and tons of other factors). If the inbred and the landrace are crossed (whether pollen from the inbred fertilizes the landrace or vice versa), each of the offspring will have about half of the genetic information from the inbred and half from the landrace. Since the two chromatids are the same for the inbred, none of the information from the inbred is lost in any individual. Since the two chromatids in the landrace individual are different, each of the offspring only receive half of the genetic information from the landrace.

When those offspring make gametes, recombination often occurs which results in chromatids that contain some alleles from each grandparent. Crossing over, shown here, is one type of recombination. If those gametes then combine with the inbred, their progeny will only have about 1/4 of its genes from the landrace grandparent.

Genetic diversity can be lost in certain situations. For example, if a farmer growing a landrace finds plants in the field that have positive traits, the farmer will choose to plant those seeds for the next year. If those beneficial traits are due to genes from the inbred, the farmer could effectively select for plants with one or more genes with the inbred and against plants that don’t contain any genes from the inbred. If pollen from the inbred is reintroduced year after year, the farmer could plant seeds from those plants that contain more and more alleles from the inbred variety, and alleles from the landrace could be lost over time.

On the other hand, if the farmer chooses seeds from plants that look more like the landrace, then alleles from the inbred could be lost fairly quickly. If pollen or seeds from the inbred are introduced infrequently, the landrace would maintain a low level of alleles from the inbred, with those alleles eventually disapearing.

Of course there are many situations in between, and those depend greatly on what effect each gene or allele has on the plants they have contaminated.

Once it’s in there, how long will it stay?

Transgene or not, wild or cultivated, all of the genetic material goes into a big mixing pot to be stirred by random mating and natural selection in the case of wild plants or by breeding and artificial selection in the case of cultivated plants. One of Kristen’s points in Gene flow from transgenic maize to landraces in Mexico: An analysis (pdf) is that the permanence of transgenes in a non-transgenic population depends a lot on what the transgene is exactly, and the same idea applies to non-transgenic alleles.

To break it down: Any given transgene or any allele of a gene can have one of three effects on the plant: positive, neutral, and negative. The effect depends on what plant the allele is contaminating and what trait is conferred by the allele. Finally, how long a contaminating allele stays in a population depends on all of these factors.

Positive

Some alleles would be beneficial in almost any situation. Herbivore resistance, including genetically engineered Bt toxin and increased expression of non-transgenic chemical defenses, would help both cultivated and non-cultivated plants escape damage from susceptible herbivores. These types of transgenes and alleles would be likely to persist in any population they contaminated. These would definitely be bad traits to have in weeds. They could be desirable in a landrace from a farmer’s point of view.

Neutral

A gene that increases the size and number of fruits produced by a plant is desirable from an agricultural perspective, but could have a negative effect a wild plant, because the plant would have less resources to devote to other needs like herbivore defense and drought tolerance. These types of alleles will not persist in a wild population, but could persist in a landrace if it is seen as desirable to farmers.

Negative

Alleles or genes that are specific for certain farming systems won’t persist in wild populations, weeds, or landraces unless they are exposed to those farming conditions. These include genetically engineered genes like glyphosate tolerance and the non-transgenic allele for Clearfield tolerance. If these alleles or genes contaminate a population but that population is never sprayed with the chemical, there is no selection pressure to keep the trait.

Of course these are just three examples of different traits and there are thousands if not millions of traits out there that might have different effects, but you get the idea.

Every day, pollen blows and seed is moved. Every day, genes and alleles are transferred from one plant population to another, no matter if they are transgenes or not. Those naughty plants just won’t keep to themselves! If we are truly concerned about gene flow, we really should be considering gene flow from all sources, not just transgenic crops.

Chen LJ, Lee DS, Song ZP, Suh HS, & Lu BR (2004). Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Annals of botany, 93 (1), 67-73 PMID: 14602665

Shivrain VK, Burgos NR, Gealy DR, Sales MA, & Smith KL (2009). Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids. Pest management science, 65 (10), 1124-9 PMID: 19530257

Mercer, K., & Wainright, J. (2008). Gene flow from transgenic maize to landraces in Mexico: An analysis Agriculture, Ecosystems & Environment, 123 (1-3), 109-115 DOI: 10.1016/j.agee.2007.05.007

Here’s to hoping that I win a prize again! Here are the other submissions, check them out!

Imagine you could wave a magic wand and boost the yield of the world’s crops, cut their cost, use fewer-fossil fuels to grow them and reduce the pollution that results from farming. Imagine, too, that you could both eliminate some hunger and return some land to rain forest. This is the scale of the prize that many in the biotechnology industry now suddenly believe is within their grasp in 2010 and the years that follow. They are in effect hoping to boost the miles-per-gallon of agriculture, except that the fuel in question is nitrogen.

In a play on those who call GE crops an “unmitigated environmental disaster,” he instead calls them an unmitigated environmental miracle. While I wouldn’t go so far as to call them a miracle, it is quite astonishing what has been achieved in the literature in so short a time, and what traits we are likely to see commercialized in the next decade.

The Union of Concerned Scientists, however, just released another report, this time questioning the usefulness of genetic engineering to make crops more nitrogen-efficient. Previously, they claimed that GE crops have failed to significantly increase yields, a couple months after an announcement of a GE trait developed by Mendel Biotechnology that does that remarkably well in soybeans. This time, while people have been talking about nitrogen use efficiency, the report gives the impression that such traits are a long way off. (I’m beginning to notice a pattern here.)

The report is titled No Sure Fix.

Besides the fact that this is not a peer-reviewed report (which does matter), I have already noticed one glaring problem – while the report focuses on pleiotropy (effect on other genes and traits) for genetically engineered traits, it ignores the same topic with regard to non-GE nitrogen-use-efficient genes. Here is the only place where the comparison is made on this topic (page 30):

Since little visible effort has been made thus
far to explore this variation, either within crop
species or their sexually compatible wild relatives,
the potential exists for improving NUE by making
use of this variation through breeding. As with
GE, however, it is possible that NUE traits within
the crop gene pool could have unintended negative
side effects. But we do not believe this risk is
as high for genes that are part of the normal crop
genome as it is for exotic genes introduced to the
crop genome through GE, or engineered genes
expressed in ways outside the typical range of
crop metabolism. (emphasis added)

The bold sentence is a completely unreferenced, unsupported statement in the paper. Notice how they make this statement about non-GE genes for NUE traits, after just saying that little visible effort has been made exploring this variation. This is an error in scholarship and logic.

If you want to change a trait through introducing a new gene from a wild relative, you are technically introducing an exotic gene, just like with GE. Or if you are instead introducing a new allele with different expression from another variety, you are changing the expression of the genes in the crop. The Bottom Line: If you are trying to change the [nitrogen] metabolism of a crop you want to change the genes and gene expression in your crop. If you are not changing expression outside the ‘typical range of crop metabolism,’ you are not making an improvement.

Still, there are some other good things to look for in the report, such as info about enhancing nitrogen use efficiency with precision farming and other practices. I’m interested to see what people think about it?

Sure, it’s cool, and I wouldn’t mind having a taste, but my first thought after reading Barley + Space = Space Beer! on Wired was: were there any mutations in the barley or hops that were caused by the exposure to gamma rays, etc while in space? Should the lucky few who get to try it be worried about unintended changes in the barley and hops from gamma rays and other mutagens in space?

Multiple groups in China have been purposefully using the mutagenizing effects of space as a tool to develop new traits in crops including alfalfa and rice. Unfortunately, these researchers have been publishing in Chinese journals and other journals that I don’t have access to. A 2009 paper in Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis called Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.) has some key ideas in the abstract that can help us consider the potential risks of “space barley” and other “space crops”.

Spaceflight represents a complex environmental condition in which several interacting factors such as cosmic radiation, microgravity and space magnetic fields are involved, which may provoke stress responses and jeopardize genome integrity. … We report here that extensive alteration in both DNA methylation and gene expression occurred in rice plants subjected to a spaceflight … [which] are heritable to progenies at variable frequencies.

The rice that had spent time in space had epigenetic changes that were passed on to the next generation. The changes didn’t have any obvious phenotypes, so it’s possible that similar changes exist in the decedents of space barley that haven’t been detected. Are these changes dangerous? Probably not, but it is possible. All mutagens (and even just breeding) can cause unintended changes, but testing is not required for plants resulting from either. Space induced mutations will likely escape regulatory scrutiny as well.

The 2004 book Safety of Genetically Engineered Foods: Approaches to Assessing Unintended Health Effects lists some classic examples of breeding resulting in unintended effects in Chapter 3: Unintended Effects from Breeding, including increases of naturally occurring toxins that are harmful to humans. These unintended consequences are often due to selecting for one trait that inadvertently selects for a different trait that may or may not be related to the first trait. Interestingly, these authors of this book were not able to find any examples of unintended consequences due to mutagenesis. This is likely a result of the same process that removes any unintended changes from plants with genetically engineered traits – lots of breeding. Seems a bit paradoxical, but this sort of breeding isn’t done with the goal of developing new traits. Instead, the goal of post mutageneis or post genetic engineering breeding is to stabilize the trait of interest in a line that already has other desired traits. Other research, notably the 2008 Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion, showed that both mutagenesis and genetic engineering can cause unintended changes in gene expression. However, obvious phenotypes may be rare.

In the case of space barley, four generations may have been long enough to revert any mutations that had occurred, especially if most changes are epigenetic as suggested by Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.). The space hops didn’t have any additional generations, so there is a greater likelihood that any mutations that occurred were still present in the hops that were used to produce the space beer. Does this make space beer more dangerous than non-space beer? Maybe, maybe not. It might be a good idea to at least consider potential changes induced by space, just as we should be considering potential unintended effects from breeding, mutagenesis, and genetic engineering. We might employ a flow chart, such as this one from Chapter 7: Framework, Findings, and Recommendations in Safety of Genetically Engineered Foods: Approaches to Assessing Unintended Health Effects. It’s time to stop treating crops resulting from non biotech modifications as inherently safe, and start comparing the newly modified varieties to their parental varieties. Then, we’ll be sure that space beer, space rice, and a host of up-and-coming products are safe for us to eat and drink.

Eating locally is great, but since apples only ripen once per year, and they spoil relatively fast, that means we only have fresh apples for a short time each year. That’s too bad, since apples are a wonderful crunchy snack loved by kids and adults that provide health benefits from their fiber and antioxidants.

Shipping the apples from another place (like New Zealand) extends the time that apples are available, but shipping in refrigerated containers is expensive and results in greenhouse gas emissions, and we all know that those apples from far away just don’t taste as good as local ones.

Scab Resistant Selection RS103-130. Image from "Organic Production of a New Australian-bred Scab Resistant Apple in Queensland, Australia" by Middleton, et. al

There might be a way to have local apples available for a much longer time, as well as to have apples shipped in that use less energy and less pesticides!

After more than 20 years of work, researchers in Australia have developed apples that are resistant to black spot aka apple scab, a fungus that destroys fruit and leaves. The scab resistant line, called RS103-130, also stays fresh and crunchy much longer than typical apple lines. They achieved this through some initial crosses with a crabapple species followed by years of selective breeding. The crabapple provided RS103-130 with the Vf gene complex, which has been previously used to produce transgenic scab-resistant apples, which I’ll describe in more detail shortly. You can find the Australian patent for RS103-130 at FreePatentsOnline.

In 2005 and 2006, comparison experiments showed RS103-130 to have many benefits over Galaxy, a typical non-resistant cultivar (see chart below). According to Middleton, et. al, RS103-130 has off white flesh and medium texture, is crisp, sweet, low-acid, and juicy, with a mild flavor.

Chart from "Organic Production of a New Australian-bred Scab Resistant Apple in Queensland, Australia" by Middleton, et. al.

Because of all of these benefits and the reduced pesticides needed, organic apple growers in Australia are very interested in RS103-130. I wasn’t able to find any information on whether RS103-130 has been commercialized yet, or on how long it might be before I can try them. Apparently something happened with RS103-130 lately, because stories appeared in The Independent and in the New York Daily News last week. Neither of the stories say what prompted the coverage, nor does Treehugger, which picked up on the 1st two. If you know what’s new with these apples, please comment!

My first question upon reading these articles was: why has it taken twenty years?! Selective breeding can be painstaking, especially when you’re talking trees. There is a faster way…

The HcrVf2 gene from a wild apple confers scab resistance to a transgenic cultivated variety showed that the Vf gene can be inserted with biotechnology into apple varieties (in this case, the gene was inserted by Agrobacterium tumefaciens into the Gala apple cultivar). In the introduction of this paper from 2003, Belfanti et. al point out that:

the transfer of these genes by classical breeding to cultivated apples is difficult because of the long juvenile phase, self-incompatibility, and the impossibility of exactly reproducing the heterozygous state of cultivated varieties. Starting from the wild species Malus floribunda 821 carrying the Vf gene, breeders have developed several scab-resistant apple cvs. (2), but not one has met with commercial success. Indeed, when compared with such commercially popular cvs. as Golden Delicious and Gala, the main horticultural and fruit-quality traits of these scab-resistant cvs. are notably different and undoubtedly less acceptable.

Using biotechnology, the researchers were able to confer scab resistance in one generation. In this paper, the authors don’t mention any increase in lifespan for the fresh apples – I’ll look on Web of Science for more info tomorrow. I do appreciate that the authors are hopeful for the future of apple biotech.

The cloning of an apple scab resistance gene represents the basis for further investigation of the resistance mechanism. It also represents a step toward a gene therapy (restoring resistance where lost) of the scab-susceptible cvs. that currently dominate the apple industry. This strategy will allow the transfer of resistance from a wild apple species to any commercial apple genotype while maintaining the horticultural and fruit-quality traits growers and consumers prize most. It may also be possible to achieve greater resistance durability by the simultaneous transfer of several resistance genes from wild apple species. Going one step further, it may be possible to use apple promoters and novel techniques that, by eliminating selective marker genes (38, 39), generate transgenic varieties without any foreign genes and, hence, may make genetically modified plants more acceptable to growers and consumers alike.

I’m particularly interested that Balfanti et. al mentioned cisgenics, although they didn’t use the term. There is potential to insert genes like Vf into many varieties of apples, meaning that cultivars developed for specific microclimates may be quickly made resistant to scab (and potentially given a longer shelf life) without any loss of their other traits. This is a good example of how biotechnology and breeding can have the same results – get a gene into a cultivar – although one takes much longer than the other.

Most Europeans don’t consider themselves to be anti-science or particularly technophobic. In fact, Europe’s full embrace of the scientific consensus on another environmental issue, global warming, has enabled the continent to take the clear lead on climate change, with the most ambitious emissions targets, the first carbon trading market, and the greenest urban infrastructure plans on the planet.

Europe’s scientific disconnect is more broadly true of eco-minded citizens worldwide: They laud the likes of James Hansen and Rajendra Pachauri but shrink in horror at the scientist who offers up a Bt corn plant (even though numerous studies indicate that Bt crops—by dramatically curbing pesticide use—conserve biodiversity on farms and reduce chemical-related sickness among farmers).

So why the disconnect? Why do many environmentalists trust science when it comes to climate change but not when it comes to genetic engineering? Is the fear really about the technology itself or is it a mistrust of big agribusiness?

Contributing their views (in order) are Pam Ronald, Raj Patel, Nina Fedoroff, and Noel Kingsbury. Read the article, I’ll offer a few opinions about it after the jump.

In my humble opinion, the opposition is chiefly due to anti-corporate sentiments, some of which are not entirely unfounded. The conflict of interest of making a product and simultaneously ensuring its safety does not go unnoticed – that is why we have government regulators at the EPA, FDA, and USDA. Other nations around the world have set up their own governmental oversight and have come to the same conclusions as in the U.S., and the article does not mention that the European Union has approved several GE crops, while individual nations are sketchy about them. Germany seems to be having a particularly harsh case of food fears, and have gone after public research into the technology as well.

My first complaint about a contribution to the article was when Raj Patel said,

This points to my concerns about the state of scientific debate. The direction of research priorities in agriculture is predominantly shaped not by the relative merit of different technologies, but rather the research priorities of the private sector. The largest publicly funded examination of genetically engineered agriculture—the UK government’s field trials—found GM crops inferior to conventional agriculture in most respects. But conventional and GM agriculture are not the only two comparison points.

First, it is frustrating when people do not give any specific details about when studies were conducted, by whom, and where they were published. It makes it difficult to look up the precise details to verify whether they are accurately reporting the results. Several anti-GE groups have put up position statements about these field trials, which seem to have been completed in 2002-03 and declared the GE crops to be a failure. The Naked Scientists podcast, however, tells more about the story:

After a three years of farm-scale trials looking at the environmental impact of GM crops the results are finally out this week. These were the biggest trials carried out anywhere in the world, showing just how concerned the government are that they get enough information to make a decision about whether Britain should adopt the new technology. The trials were looking at three different crops, sugar beet, maize and oilseed rape- all of which had been genetically modified to be resistant to particular herbicides (chemicals that kill weeds). The idea behind the crops is that farmers will be able to treat fields less frequently with weedkillers, as the treatments will be more effective and only target the weeds without damaging the crops. This would save time and money, as well as reducing the amount of chemicals farmers are using in total.

But the fields trials suggest that at least two out of the three GM crops, beet and oilseed rape, had a harmful impact on the environment in and around the fields where they were grown. This included a decrease in the number of bees and butterflies, as well as a reduction in the number of wild plant seeds available to feed animals like birds. But they did find more soil insects present in the fields sown with the GM beet and oilseed rape, which may be because herbicides were used less often. There was good news for fans of GM technology as well- GM maize was found to be better for wild plants, animals and insects than normal maize. It’s important to point out that these effects on the local wildlife are nothing to do with the actual genetic modification of the plants, but more to do with the levels and types of weedkillers used by the farmers, as well as how often they treated their fields. (emphasis added)

Reductions in insect life that depend upon weeds growing in your fields are going to be fewer when you are controlling the weeds. Interestingly, in the case of herbicide-tolerant beets, it was later discovered that if you strip-sprayed your field of GE beets, it actually provided MORE plants for insect life, without damaging the crop. This is one of the things that happens when you rely on older results. (Here is a link to another option for providing food for wildlife.)

It is good to note that biased reporting of results is going on here. In this field trial (assuming I have found the correct one), they also reported that soil insects were increased in the same fields. They also concluded that the GE Bt maize was better for the environment than the conventional counterpart, mostly because it reduced pesticide sprays.

Next, I would like to comment on Nina Fedoroff’s contribution. She co-wrote Mendel in the Kitchen, which is an excellent book that I highly recommend. In this article, she was straight to the point, accessible, and talked about the way people’s attention spans (including the media) cause facts to be ignored and trumpted stories to be preferred instead. But it may be that Fedoroff is committing a similar sort of error.

With a computer and bit of effort, almost anyone can extract the facts from the gloom and catastrophism. Fact: Modern genetic modification of crops is responsible for most of the crop yield increases of recent years. This means, of course, that the farmers who’ve adopted GM crops have benefited the most.

There have been yield gains in Bt cotton, Bt corn, and with soybean farmers elsewhere in the world that have been able to fit a second soy crop into the same year due to GE technology, however I take issue with her potential mis-statement that genetic modification is responsible for most of the yield increases in recent years. Breeding still provides a large part of yield improvements, which is ongoing, especially for those breeders utilizing marker-assisted or “precision” breeding. The reason why I characterize it as a potential mis-statement is that I know that Fedoroff calls breeding genetic modification. (It is) If she meant that genetic engineering contributed most of the yield gains I would probably disagree, but if she meant all forms of genetic modification then I think she could have been more clear in her statement.

Next, I would like to address a couple of Tom Philpott’s claims. He points out that the kind of consensus that has formed around climate science amongst climate scientists is stronger than the consensus that has formed around GE crops, and I agree with that for the most part. There is a good consensus amongst plant scientists on the subject and some environmentalists, but not all other branches of science fully agree.

The real question becomes: How can serious publications like Seed claim that skepticism toward GMOs reflects a “scientific flip-flop”? To be sure, the illusion of a broad consensus holds sway in the United States, and the IAASTD has clearly failed to correct it. The US media greeted its release with near-complete silence—in stark contrast to its reception in the European media.

The possibility that the IAASTD’s statements about genetic engineering might be symptomatic of this dissonance doesn’t seem to occur to him. There’s a lot of politics involved, for example, the US government was very resistant to climate change agreements under Bush’s presidency, which has quickly turned around now that Obama is in office. The U.S.’s position on GE crops seems not to have changed (and indeed, has been repeatedly emphasized). Could that not be more parsimoniously explained by political opposition to GE crops from people (and even scientists) outside the U.S.? I would like to note that the EU is moving toward growing GE crops steadily year by year.

Next, Philpott brings up a report written by Don Lotter, attempting to explain the pursuit of GE crops in terms of mere economics and politics without the strength of scientific evidence. I have already begun reading the report, and without going into too much detail at this time, its conclusions and analysis are problematic. For example, some major claims are made that do not correspond to the references cited. I will provide more details in another post, but I think referring to a paper with more scholarly rigor would bemore appropriate.

Philpott brings up the multi-generational Austrian feeding ‘study.’

When there have been long-term trials by independent researchers, the results have hardly been comforting.

For example, writes Lotter:

In a 2008 report (Velimirov et al., 2008) of research commissioned by the Austrian government, a long-term animal feeding experiment showed significant reproductive problems in transgenic corn-fed rats when all groups were subject to multiple birth cycles, a regimen that has not hitherto been examined in feeding studies comparing transgenic and non-transgenic foods.

Thus in the first-ever multi-generational study of the effects of GMO food, evidence of serious reproductive trouble comes to light: reduced birth weight and fertility.

As detailed here, this study was raising its mice under poor conditions. How do we know? They fed GE maize and non-GE maize to two groups, the experimental group and the control, and allowed them to breed for several generations. For a properly conducted feeding study, they should have had a very low mortality rate in the control group – about 1%. But as the study authors reported, they lost an average of 8% of their control mice. This means that the mice were living in poor conditions, and is seriously calls into question any conclusions that could be drawn from it. And if you take a look at the average pup losses per generation, you’ll notice something odd:

The curious incidence of silence about mistreated animals

Notice the high numbers of mouse pup losses in the control (ISO), and low losses in the transgenic? The GE-fed mice survived better, yet this is not mentioned anywhere. And the European media is silent on this… the argument goes both ways.

It is also exceedingly important to note that this study was not peer-reviewed – and I daresay it would not have survived even the most lax of scientific journal reviews. David Tribe has posted more about the study and its problems. We need to base our opinions on the best available evidence from reliable studies published in peer-reviewed scientific journals. As Nina Fedoroff said, anyone with a computer can find out this information. Why hasn’t Tom?

Curiously, after claiming that this study was independent, Tom Philpott then ‘flip-flops’ and supports the notion that no truly independent study exists.

A group of 23 US scientists signed a letter to the EPA declaring that, “No truly independent research [on GMOs] can be legally conducted on many critical questions.”

Which one is it?

I would like to note that intellectual property issues when it comes to public research are in issue that needs to be addressed.

Noel Kingsbury, whose book Hybrid, the history and science of plant breeding comes out later this year, closes the deal:

The fact is that the scientific case against GM is pretty threadbare. It is far more precise and predictable than some of the most important breeding technologies of the last 50 years. If you get hot under the collar about GM, why not the far more frightening “radiation breeding”? Mention that to most anti-GM activists and they look puzzled. Radiation breeding involves zapping seeds or cuttings with radiation, or treating plant material with gene-altering chemicals. Many countries in the 1960s invested in “radiation fields” where trees were grown behind big earthen dykes so that they would be permanently irradiated. The goal: obtaining mutations that might be useful, as one in several tens of thousands was. The first radiation-bred rice was sold as “Nuclear Rice” in Hungary in the mid-1950s. Imagine marketing that today! Radiation breeding is unpredictable, uncertain in its results, and causes widespread genome damage. But no one has ever suggested that it has ever done any harm! Much Italian pasta has been grown with an irradiated durum wheat. Nearly all Asian pears are the offspring of irradiated grafts. And—get this— much European organic beer is brewed from radiation-bred barley! No one complains or protests. Wake up! Be realistic! Why get so excited by GM?

GM crops must be looked at and judged variety by variety. The first generation Roundup^™ varieties are giving way to second generation crops with some highly valuable characteristics, like resistance to pests (thousands of deaths by pesticide poisoning have already been avoided by Chinese and Indian caterpillar-proof cotton) and drought-tolerance. Once we start to see soy with omega-3s or nutrient-enhanced tomatoes, attitudes will surely start to change.

World population is increasing, arable land availability is decreasing, and water resources are shrinking. We need every technology possible to increase yields, reduce toxic pesticide use, improve nutritional value, and feed the world. The European and Indian opposition to GM is rooted in a hopelessly romantic view of farming. Farming is not a romantic business—it is about feeding the human race, and we must listen to the overwhelming consensus of plant science—that GM is safe and desirable.

The important distinction being made here is that there is a consensus within plant science, but not necessarily one between disciplines. The key difference between how these two kinds of genetic changes are being treated politically and socially have more to do with the political and social climates in different hemispheres and less to do with the science that has been conducted around the world. In some cases, science is being ignored in the interest of societal issues, and in other cases, bad science is being wielded as a weapon to draw attention away from the good science that exists.

According to this press release, the ACLU charges “that the patenting of two human genes linked to breast and ovarian cancer will inhibit medical research. The organization also claims that the patents are invalid and unconstitutional.”

It continues:

“This is going to turn into one of the watershed events in the evolution of the bioindustry,” says John Sterling, Editor in Chief of GEN. “The pros and cons of patenting genes have been an ongoing, and often acrimonious series of debates, since the in re Chakrabarty decision in 1980. But this particular case seems to have taken on a life of its own with over fifteen plaintiffs. For while the lawsuit specifically centers on the patentability of two cancer-related genes, the ACLU says it plans to challenge the entire concept of patenting genes. What we have here is one group, the ACLU and its allies, contending that gene patents stifle life science research and potentially harm the health of thousands of patients. On the other side are biotech companies who maintain that without gene patents research incentives are seriously diminished and innovation is smothered.”

Kenneth I. Berns, M.D., Ph.D., Editor in Chief of the peer reviewed journal, Genetic Testing and Molecular Biomarkers (http://www.liebertpub.com/gtmb), which is the official journal of the Genetic Alliance, says the “patenting of human genes is a bad idea and that healthcare in the U.S. would be enhanced if the ACLU suit prevails.” Dr. Berns is also Director of the University of Florida Genetics Institute in Gainesville.

William Warren, partner at the Sutherland law firm, thinks the ACLU, in this case, is barking up the wrong tree. “The ACLU unexpectedly based its invalidity challenge on claims to unpatentable subject matter,” he says. “The ACLU might have instead considered challenging the Myriad patents for obviousness.” Warren and Sutherland colleague, Lei Fang, Ph.D., M.D., have authored a legal article, which will be published in the June 1 issue of GEN entitled “Patentability of Genetic Sequences Limited.” It is now available online. (http://www.genengnews.com/news/bnitem.aspx?name=54504126&source=genwire)

Genetic Engineering & Biotechnology News also has an article about the lawsuit.

I’m interested to see what the legal arguments will entail, so I’ll try to follow this as it develops.

Here’s a bit of background into the issue at hand. When you make a genetic discovery, such as figuring out the gene (or allele) that causes X, whether it be a predisposition to breast cancer, added sweetness in sweet corn, etc. Under U.S. Patent law you are allowed to patent that genetic sequence, which gives you certain rights as I understand it.

For a period of time, you are allowed a monopoly on profiting from the specific information of that discovery. In the case of Myriad Genetics, they get to charge people if they want to conduct research on the patented versions of the gene, do a diagnostic test based on that sequence, etc. The idea behind this is that it gives people a financial incentive to not only make these discoveries but also to publish them. Without such a financial incentive, it might be much longer before either public institutions discover it and publish, or companies will keep this information secret in order to protect their investment. Without patents, Myriad may still be charging for a ‘breast cancer predisposition’ screen test – without telling anybody what the gene is.

On the other hand, as a monopoly, it restricts the ability for people to find out such information about themselves, and restrict the ability of public researchers (and other companies) to conduct research on these genes. They would have to arrange a licensing agreement with the patent holder in order to do so. In the case of a crop gene, it might be annoying from the perspective of a breeder that wanted to use a molecular marker to ‘precision breed’ this gene into their crops. But when it comes to public researchers studying diseases like breast cancer, patent restrictions can go from beyond annoying to potentially dangerous.

Now to address a common myth about patents in the life sciences. Some people believe that the patents on BCRA1 and BCRA2, and other patents of this type, mean that the patent holders ‘own’ the genes, and even the organisms that contain them. This is not true. As I understand it (and I’m not a patent law expert!) they own the use of the information about that gene, for example, the specific sequence of the mutant breast-cancer gene. They do not own any part of men or women who possess this gene!

In plants, if one were to patent a gene that gives a desirable trait, then you would own the ability for a breeder to use the sequence of that gene to screen their different plant lines for that gene directly. This is known as a molecular marker, which is a tool for more accurate breeding. If, however, there was a way to screen for the gene that was based upon phenotype, such as a wrinkly seed in a test cross, the patent would have no effect on that.

In fact, there would be absolutely no restriction on such a patented gene being bred into whatever cultivars anyone so chooses. The gene existed before its discovery, and so the patent cannot touch that. You cannot take some native landrace, find a few genes in it, and claim that you own the plant – as is often implied about such patents.

This is distinct from the kind of patent that comes into play with transgenic crops, where a gene is assembled from various components and inserted into the genome of a plant. In this case because the gene itself is owned, people or organizations that generated this new gene own your ability to use the gene and breed it into other crops.

Because these two kinds of patents are different, I don’t think the ACLU lawsuit will affect GE crops, however, if they are successful, it may affect other patents related to plant genetics. Patents are a human construct, not a biological one, and when you apply human concepts to biological realities there may always be conflicts. It will be interesting to see how this plays out.

By William Harvey:

As I always say, “All we know is still infinitely less than all that remains unknown.” As a statement of fact, it is plainly obvious, but what is less obvious is that it also makes a splendid guiding principle for life.

I try as best I can to base my life in the best that science has to offer, but I know (more than most it seems) that often times, science does not have all the information we need to make decisions. In many areas of science, from global warming to evolutionary biology, there are gaps in our knowledge that make deciding on a course of action difficult. So I think we need to return to some of the fundamentals.

Some scientists say that we don’t know enough about global warming, that the gaps in our knowledge of climate science are too big to make policy decisions based upon it. We could just listen to the majority of climate scientists, but ‘consensus’ is not a reliable guide for truth – it merely reflects the current state of knowledge, which in science, is always changing. But what is not changing is that large corporations continue to profit off of climate science denialism, and the risk of inaction outweighs the risk of action.

In evolution, creationists often point to ‘gaps’ in evolution, such as between one fossil and another, and are fond at pointing out when a new fossil turns up that the number of gaps have increased. I think they have a very valid point, and it got me thinking about food safety in the same terms. We are currently grappling with huge gaps in our food safety net, with salmonella-contaminated peanuts and more, and people are calling for more regulations and more checks to fill in those gaps.

In the case of genetic engineering, I have come across studies that claim that GMOs are safe based upon a protein analysis here, or a microarray there. What these researchers are admitting by even doing this research is that there are huge safety risks involved in genetic modification, and they are hard at work filling those gaps in the GMO safety net after-the-fact.

Or post-mortem, I should say. A scientist and author, Jeffrey Smith, has chronicled a laundry list of food safety hazards created by genetic engineering, from dead sheep to increases in allergies. Merely from growing GMO soy in England in 1999, the harvest at the end of the season was enough to increase soy allergies by a whopping 50% earlier the same year. Genetic engineers are frantically trying to figure out what went wrong, while nations around the world (except for the totalitarian regimes of China, Brazil, Cuba, Australia, and the US) continue to reject GMOs.

How did these food risks slip through the thin safety net? Followup studies on the proteins introduced have found nothing, nor have studies that look at the changes in gene expression caused by introducing a foreign gene. Apparently, the changes caused by genetic engineering are less than those caused by traditional breeding.

But every time they close one gap, they open up two more. Sure, the gene expression is below the natural variation, but this just means that that is not the reason why GMOs are unsafe. That gap is filled, but it opens up even more gaps – researchers now have to investigate every single gene that was affected! If those genes are not sufficient to explain what we think is going on, then they have to sink deeper into the mire of endless scientific experimentation.

You may call it ‘moving the goalposts,’ but as long as science continues to not find the danger that we are looking for in GMOs, the danger must still lurk somewhere in the gaps in our knowledge. Only by knowing the totality of everything there is to know about each GMO, from genomics, to transcriptomics, proteomics, and epi-genomics, phenomics, and nutrigenomics will we ever have enough information to state that a GMO is safe to eat.

This may make the pro-biotech folks balk – how can they ever pay for all of this – but that is the genius of the precautionary principle. By weighing down GMO approval with more exacting regulatory hurdles, it will not be worth it to try to use genetic engineering at all – and the use of this corporate technology will dry up. As long as we can stay one step ahead of the science with regulatory policies, we can prevent this scourge from continuing to spread all over the planet.

William Harvey is the Director of Global GMO Policy at Greenpeace International. He makes his own Biodynamic Wine from the safety of Marin County, which is GE Free.

Transposons are really neat. Also known as Mobile Genetic Elements, Transposable Elements, or just “jumping genes,” they are sequences of DNA that are capable of popping out of a chromosome and inserting themselves into another. The most well known kind of transposon contains a gene that encodes for an enzyme called Transposase, which physically chops the transposon out of the DNA strand it is in, and puts it in another. The result is a gene that does not remain in a fixed location, and ‘jumps’ around the genome from Chromosome to chromosome, turning other genes on and off if it inserts in them or near them. Transposons were first described in Maize, by the famous Cornell biologist Barbara McClintock, and are thought of as some of the source of genetic variations that fuel evolution. Sometimes they can incorporate bits of other genes and move them around, causing all sorts of genetic modifications.

The morning talks were full of transpositional goodness. We had one talk about using transposons to help in genetic studies where you try to connect genotypes to phenotypes, and one on studying the relationships between different transposons. One very interesting one described a pair of transposons near each other, that could actually pull an entire gene out (between them) to move them somewhere else. Titled Paired Transposons: Natural genetic engineers – it really makes you wonder what the difference is between genes moved around by the plants themselves or by people intending to move them around?

One transposon talk was truly the highlight of the day for me. It described a newer, quite interesting kind of transposon called a Helitron. It sounds cool, and it is. Helitrons are transposons that have sequence that complements part of itself near one of its ends. What this does is forms a couple “hairpin loops,” which look like little twisty knots that stick out of the DNA strand. Here is a picture of a Helitron (with an ear of corn behind it).

Helitron superimposed over an ear of maize

Helitrons are a little different from other transposons in how they operate. Rather than being snipped out of a chromosome by transposase and re-incorporated elsewhere, they actually “roll” into another strand, making a copy of themselves (Leaving a copy behind as well.) It’s called “Rolling Circle” replication, and here’s a picture of how it works.

Pretty neat, huh? Helitrons have been found with all sorts of pieces of genes inside them. Genes are made up of coding Exons and non-coding Introns that are spliced out of the mRNA before it is used to make a protein. Helitrons have been found carrying one or more Exons that they captured from other genes. We don’t know at this point whether they can contain entire large genes, but they demonstrate a clear mechanism by which parts of genes get shuffled around the genome, providing more mutational fuel for natural selection.

In Maize, Helitrons make up 1.4% of the genome. It’s already half transposon as it is, but just imagine that every 70th bite of sweet corn you’re eating a mouthful of helitron DNA. Mmm, delicious.

David Tribe has also talked about Helitrons before at the GMO Pundit.

It is clear that genomes engineer themselves. Not in a purposeful fashion, mind you, but the random moving and shuffling of genes that has constantly occurred in the evolution of our crops plants makes tweaking or adding one or two genes sound like nothing at all. The analogy between mobile genetic elements and human genetic engineers is not only getting stronger, but was also reflected in the titles of some of these talks.

After lunch, we had the first poster session, displaying grad student posters on topics everywhere from more transposons, to carotenoids (Vitamin A precursors) in maize, database resources, chromosomal variations, outreach efforts, and even a few on switchgrass. Unfortunately for you, the reader, we couldn’t take pictures of the cool posters, because it represents unpublished ongoing research being conducted by grad students, undergrads, and their research groups. But we have heard that poster presenters have the option of submitting their posters to be published online, and when that happens we’ll point out some of the good ones.

This year, I did not have a poster to present, as I already showed off my corn videos last year, and I didn’t have enough evidence in my research to submit an abstract by the deadline in January. (Oh, I will have a lot of sweet sugar enhanced evidence for next year’s conference!) So I had a lot of time to read other posters and get the zeitgeist of maize genetics research. A few techniques here, some strategies there, and I’ve got a few more ideas for my own research goals.

Anastasia, however, did have a poster at the conference, on her research with Maize Zein proteins. Here she is showing off her research… who is that posing with her in the picture? I’m sure she’ll be telling us all more about her project in the near future.

After the poster sessions, it was time to jump back into the lecture hall to learn about some new genetic resources on the web for scientists. One really cool one, called TARGeT, allows anyone to take the sequence of a gene, search for similar gene sequences to find related genes, and then also assemble an evolutionary tree from those sequences. I have been wondering (for years) where I could do this without buying a proprietary program, and rest assured I’ll be trying this out soon. It appears that TARGeT, (originally named TERT in the conference abstract book) was intended as a teaching tool for high schools and college classes, but has since morphed into a research platform as well. If you make it easy to assemble genes in a tree based on sequence similarity, you’ll find scientists flocking to it.

There were also some improvements to MaizeGDB, MaizeSequence.org, and some other resources that maize geneticists use to do their research.

After dinner, we listened to a talk by Pam Johnson, Chair of the Research and Business Development Action Team of the National Corn Growers Association. I will talk about her presentation in a separate post.

Finally, we come to the last event of the day, a panel discussion about Community Gene Annotation. Here’s the problem: We have the sequence of the corn genome in-hand, and there may be upwards of 50,000 genes in it. We have evidence of these genes through sequence analysis, expressed genes discovered through research, and more. But our computer gene-processing algorithms aren’t very good at annotating them, and well-assembled genes in the database will be very helpful for future research.

So the panel discussion set out to get input from the Maize Genetics community. They wanted to Wikify it, allowing researchers to log in, edit, and have their annotations proof-read by others. Bit by bit, with hundreds of people contributing a little, we could complete this task in a few years.

Well, that’s what the panel set out to do, but in my opinion, it was an unsuccessful exercise. The conversation happened between two panelists on the right side, and a member of the audience. More time was spent discussing minor details about how it would work in a technical sense, and those on the left hand side hardly had a chance to contribute. Maybe the one or two scientists in the audience who dominated the discussion should have been on the panel, and the panel should have had a little more direction.

When it came to how to encourage scientists to voluntarily contribute to the maize gene annotation semi-wiki, the emphasis was on the stick rather than the carrot. I felt like going to the microphone to suggest “fabulous prizes” or “fame and glory in the community” for top annotation editors, if I didn’t feel so bored and annoyed. It also went on too long.

Later, I talked to my roommate from Oregon about it and my experience with wikis such as the Davis Wiki. And in a tight-knit-enough community, the social incentive to be a [top] contributor was a pretty powerful motivator that built over 10,000 pages. The Maize Genetics community is pretty tight-knit, and that seems like a good starting point for a massively collaborative project like this. Perhaps with prizes, recognition at the meeting, or dangling other carrots (rather than thwacking potential annotators with sticks), it could get done. Wikis are a ground-up kind of community, and I don’t think top-down requirements will be as helpful. Truth be told, I think I had a better chat with my roommate about the issue than the panel did. There, I said it.

I’m looking forward to being able to contribute to the annotation process, as in my own research I have assembled a few candidate genes for my own gene, only to find out that they were excluded by my latest mapping data. That information is lost and would have to be re-done by someone else, so I plan to enter it in this system when it is ready. This kind of system will be good, because there’s nothing that a few hundred knowledgeable and experienced geneticists can’t do with the maize genome.

At 9:30, we broke for some casual socializing, poster viewing, with a few free drinks sprinkled in. Anastasia and I both had some good conversations with researchers, including one very fortuitous meeting, where we got a lot of good info about resources to look up. We also had a chance to promote the Biofortified blog and make plans for the next day at the Maize Genetics Conference. Stay tuned for more!