Author’s note: This would seem to be the week for vegetables I hated as a kid. Yesterday was onion, today tomato, if there’s a story about brinjal/eggplant in the next few days we’ll have hit all the big ones.

Ripening tomatoes. Photo: Photos_by_Lina, fickr (click to see photo in its original context)

I was recently pointed to an early publication paper that went up on the Proceedings of the National Academy of Sciences website on Monday, where a research group at India’s National Institute of Plant Genome Research describes two genes from tomato that, when knocked down by RNAi*, result in tomatoes that can remain ripe but not spoiled for up to three times as long as tomatoes where these two genes function normally.

Their approach targets specific genes involved in breaking down certain proteins found in the cell walls of tomatoes (in fact in the cell walls of all plants). Breaking down the cell wall is a key part of ripening in fruits (which the tomato is, botanically if not culinarily). Which makes sense if you’ll think about it for a moment. One of the traits we associate with ripening is getting softer, from bananas to peaches if it’s still crunchy when you bite into it, it wasn’t ripe. What makes plants stiff and crunchy? The strength of their cell walls. Since, unlike vegetables, fruits WANT to be eaten**, as they ripen they begin to break down their cell walls to make themselves more appealing to passing animals. Unfortunately, ripening and spoiling are, in a lot of ways, the same process. If fruits aren’t eaten when they become ripe, they continue to get softer, transitioning from delicious looking -> unappetizing -> inedible -> a puddle of mush on your kitchen counter.

Preventing ripening entirely is relatively easy, and there are plenty of known mutants in tomatoes and other species that never ripen (these naturally mutant tomatoes stay green and hard no matter how long you wait). But getting part of the way to ripeness but stopping before crossing the line into spoiled is a much less tractable problem.

A spoiled tomato. A rotting tomato is visible in the bottom left, but that's the result of the growth of microorganisms which is a more complex process. Cropped version of a photo from goldberg on flickr. Click to see the original photo on flickr.

To the non-cell wall biologist like me, one of the most attention grabbing parts of this paper was figure 3A, which simply shows photos of tomatoes that have been sitting at room temperature for 10, 20, and 45 days***. At ten days all the tomatoes look fine. By twenty days, the control (normal) tomatoes are shriveled. After 45 days sitting on the scientific equivalent of a kitchen counter the control tomatoes are basically brown balls of goo, while tomatoes with either of the two genes identified in this paper knocked down show no change in appearance over the same period of time. So what are these awesome genes?

Both genes studied in this paper are glycosyl hydrolases, a kind of enzyme that breaks the chemical bond holding a sugar to either another sugar or some other molecule, like a protein. Specifically the two genes, which are normally expressed in ripening tomatoes, each break specific kinds of sugar off of a specific kinds of protein found in the cell walls of plants. Plant cell walls are mostly made of hydrocarbon polymers like cellulose and lignin, but plants also use some structural proteins (usually less than 5% of the cell wall) and it is the sugars attached to these proteins that the glycosyl hydrolases studied here act upon.

This is where it gets scientifically cool. The prolonged ripe-but-not-spoiled state of the transgenic tomatoes they produced wasn’t simply a result of preventing the structural damage caused by the break down of the bonds between cell wall structural proteins and the sugars they’re connected to. Instead, when they looked at gene expression in plants where either of these two genes had been knocked out, they found that genes involved in breaking down cellulose, lignin and pectin (the main components of the cell wall) were also less expressed. The authors speculate that the kinds of sugars/carbohydrates these two genes break free from cell wall structural proteins actually serve as a signal to the plant to increase the production of all the other proteins needed to break down cell walls and in their transgenic plants, that signal never comes, letting the tomatoes stop ripening before the process leads to spoiling.

Tomatoes at a farmers market in NYC. photo: SeenyaRita, flickr (click to see photo in its original context)

The authors themselves point out the huge potential upside to reducing spoilage in the developing world. As much as 50% of produce is lost to spoilage between harvest and diner plate in the developing world. Reducing spoilage is one of those rare almost-a-free-lunch opportunities to increase the food supply without bring more land under the plow, or increasing the inputs (in the forms of fertilizer, pesticide, and all to often back-breaking manual labor).

At this point you may be thinking, haven’t we heard this story before? There are lots of differences between these tomatoes and the Flavr Savr tomato produced by Calgene in the 90s. Scientifically they come at the problem from very different angles, but rather than get into that let me point out two crucial practical differences:

1. The authors present data that the tomatoes with knocked down expression of either of these two genes are twice as firm as normal tomatoes of comparable ripeness. An important trait for transporting ripe tomatoes over any significant distance as illustrated in this segment of First Fruit talking about the Flavr Savr tomatoes of the 1990s:

The shipping test out of Mexico, however, proved to be yet another disaster. It was designed to test, not only whether the Flavr Savr gene would enable vine-ripened fruit to survive 2000 miles in a truck … The test results were clear before the vehicle came to a complete stop. Tomato puree seeped from the truck’s back end.

2. If these research leads to a commercializable fruit, it will likely be grown first in India, where, as described above, spoilage of produce is a major issue. In the United States, the Flavr Savr tomato had to go up against an existing system built on tomatoes that, without any genetic engineering, never ripen on their own, described in this way by MAT_kinase of TheScientistGardener:

Fresh market tomatoes, in nor cal, are all picked green and gassed with ethylene to force ripening (imperfectly). In the midatlantic, virtually all tomatoes have a natural gene mutation that prevents them from ever ripening completely in the first place. Either way, you end up with an inexpensive, pretty, red tomato that’s often hard and white on the inside. Heirloom varieties taste great, but are very susceptible to pests, have to be hand picked and turn to goo shortly after ripening.

When Pamela Ronald of Tomorrow’s Table talks about the development of transgenic crops, she points out that by 2015, it is projected that more than half of transgenic crop varieties will be produced by the national research labs of developing countries like India, China, and Brazil for they own farmers. If this paper is a sample of the sort of research such labs produce, 2015 should be a truly fascinating year for agriculture.

I shouldn’t have to say this, but there are currently no genetically engineered tomatoes on the market. For a short time in the 1990s Calgene sold the Flavr Savr tomato in California grocery stores, but they weren’t able make a profit doing so, so they stopped. The poor taste of most tomatoes for sale in the grocery store today is purely the result of conventional breeding (my post on the subject and Mat_kinase’s)

Meli, V., Ghosh, S., Prabha, T., Chakraborty, N., Chakraborty, S., & Datta, A. (2010). Enhancement of fruit shelf life by suppressing N-glycan processing enzymes Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0909329107

-The gene knocked down in the Flavr Savr tomato was Polygalacturonase.

-The two glycosyl hydrolase genes studied in this paper are alpha-mannosidase and beta-D-N-acetylhexosaminidase.

*Using RNAi means inserting a backwards version of part of a gene into a plant under a strong promoter (so the plant makes lots of RNA copies of the backwards bit.) Those backwards copies will bind to the RNA transcript of the actual gene, creating double stranded RNA. One of the main times a plant cell normally sees double stranded RNA is when it is being attacked by viruses (the genome is made of double stranded DNA and the RNA messages transcribed from the genome are single stranded), so making a double stranded copy of the a particular gene causes the plant to treat that gene itself like an invading virus and keep the protein that gene encodes for from being produced. (<– this is the simplified version of the story, this work actually uses synthetic microRNAs which are a much more refined version of the technique.)

**When a plant produces a sweet and tasty fruit in the wild, its goal is to attract some animal that will eat the fruit and carry the plants seeds to someplace new where the seeds can grow into new plants. Domestication has changed the rules of that bargain somewhat, as we artificially selected for bigger and tastier fruits, but fruiting plants still trade animals (us humans) food in exchange for having the seeds of their species distributed across whole fields by farmers, and have their growth protected and nurtured by human hands and human ingenuity.

***There’s also numerical data which is probably better science (the images only track two fruits of each type which I’m sure isn’t statistically significant), but the best scientific papers will include hooks like that image of unrooting tomatoes to draw the reader in long enough to read the exciting data itself.

Consider three cases:

1. The submergence tolerant rice that’s now being distributed to farmers in Bangladesh could NOT have been made without the collection and study of the wild weedy rice in the first place. And while the gene responsible for the trait was first identified using a transgenic approach, the final rice was produced using only marker assisted breeding. Sub1 rice needed natural biodiversity, and it didn’t need genetic engineering.
2. A single protein P34 (a cysteine protease) is responsible for the allergic reaction of a majority of the people who can’t eat soy. Both genetic engineering and natural biodiversity offer ways to develop plant breeds without a functional copy of a specific gene. In this case researchers (lead by Herman Elliot and Ted Hymowitz) opted to screen over 10,000 lines of soybeans collected from around the world by USDA naturalists, and found two which carried a null allele for the gene.** [Herman Elliot's paper]
3. Golden rice (which may, someday, get past the expensive regulatory hurdles placed before it) was created (and refined) using genetic engineering. It was created after plant breeders like Peter Jennings [one of the creators of IR8 rice***] had spent decades unsuccessfully searching the world for some variety of rice with yellow grains, indicating the production of pro-vitamin A. Golden rice would be impossible without genetic engineering.

It may be that genetic engineering has been used as an excuse by politicians who are reluctant to part with the money needed to fund seed banks, but I don’t know of ANY scientists who think genetic engineering renders seed banks obsolete.

*The first evidence of agriculture is roughly 10,000 years ago. Assume an average human generation was 25 years for most of that time. The oldest family lines of farmers stretch back through four hundred fathers and sons, mothers and daughters.

**A null allele is a verson of the gene that doesn’t function, either because the gene is never made into protein, or because a mutation has changed the protein so much it is completely unable to function. The two most common mutations that create null alleles are premature stop codons: the protein stops getting made partway through, and frameshift mutations: insertions or deletions that aren’t divisible by three. Since genes are written in a language of three letter long words without any separation between words, it the same effect as shifting around the spaces in a sentence (here I’ve deleted the “h” in “which” but kept the spaces as they would be without the deletion):

Whici sa g oodw ayt ow riteg ibberish.

***IR8 was one of the new rice breeds that sparked the green revolution, among other things helping the Philippines becomes rice self-sufficient.

In 1966, a young Indian IRRI agronomist, S. K. De Datta, tested the IR8 variety under different fertilizer conditions. He was amazed with the results – the IR8 rice produced around 5 tons per hectare with no fertilizer and rose to almost 10 tons with 120 kg of nitrogen per hectare. That was 10 times the traditional rice yield.

Source

Cotton and cotton seeds photo credit: Gonzalez's tongue, Flickr (click to see photo in it's original context)

Over 102 million bales of cotton (more than 24 million tons of cotton) were grown around the world last year. I wouldn’t surprise me to hear cotton called the single most important (and widely cultivated) food crop on the face of the planet. But does it have to be a non-food crop?

Clearly no one (nor any livestock) wants to eat the cotton fibers themselves, but they aren’t the only product of the plant. After to cotton plant flowers, the cotton fibers grow around the developing seeds. The combined mixture is harvested each year, after which the seeds are removed from the cotton fibers before the cotton is baled and sold.*

The seeds of the cotton plant are full of protein and oils and since cotton is already grown as a source of fiber (and the seeds are even harvested and sorted out of the cotton fibers already) adding them to the food supply** doesn’t require any further land to be cultivated or increased input costs. Obviously there is a catch…

Cotton produces a chemical called Gossypol which is very effective at controlling insects, but also has a lot of nasty effects on humans and other animals. The AP article I’m going to link to in a little while mentions that chickens die within a week when feed straight cotton seeds. Simply eating oil pressed from the cotton seeds but not properly purified can make men sterile (over prolonged periods of time). Right now some cotton seed is feed to cows, which can break down small amounts of gossypol and much of the rest is pressed for oil that goes through a complex set of treatments to remove gossypol, making it safe for human consumption.

Now scientists and farmers have known about the negative effects of gossypol for a long time, and I’m not the first or even the millionth to suggest how wonderful it would be if humans (or even pigs and chickens) could eat some of the tons of protein produced by cotton plants every year. As far back as the 1950s scientists had discovered naturally occurring mutations of cotton that did not produce gossypol***, but since the chemical plays an important role in protecting against insect pests, the mutant cotton plants were attacked a lot more by insects.

Enter modern genetic engineering in the person of Keerti S. Rathore a professor at Texas A&M. Dr. Rathore addressed the problem of maintaining the cotton plant’s natural defenses while making cotton seeds edible by using genetic engineering**** to create a plant that continued to express gossypol everywhere EXCEPT in the seeds.

The result is plants that are still protected against insect pests, but produce seeds edible to humans and more animals, a major consideration considering over half of all cotton is produced by India and China, two countries that are likely to face difficulty feeding their growing populations in coming decades. Cotton carrying his newly developed trait would also be of great benefit to cotton farmers in the US (the #3 cotton producer in the world) as it would turn cottonseeds that are currently sold as cattle feed and for oil production, into an increased source of value.

Of course while a plant that makes NO gossypol would be completely unregulated (and rightly so), Professor Rathore’s cotton which does the EXACT same thing, only in a much smaller part of the plant will spend at least the next decade jumping through regulatory hoops before it can be sold in the US and that assuming a major agricultural company thinks increase the profits of American cotton farmers and increasing the supply of protein available to poor cotton farmers around the world would be profitable enough to justify the $100 million dollar price tag satisfying all those regulations requires.

If you’re opposed to genetic engineering, I want to hear from you. Does this make sense to you? To me it seems ridiculous that it’s effectively free to commercialize naturally occurring mutations with drastic effects on plants (and has been throughout recorded history), but small, controlled changes like those produced Professor Rathore and his lab are so heavily regulated many beneficial traits will never see the light of day. But I don’t have a problem with the technology is the first place, so have no idea what your perspective would be.

Further Reading:

• Recent AP story on Professor Rathore’s cotton
• Time Magazine’s more in depth piece from back in September
• The most recent (2006) scientific article I could find***** on Prof. Rathore’s work on edible cotton seeds. Published in PNAS (but it should be free to the public, let me know if it isn’t)
• My previous post on cotton and it’s current genetically engineered traits.
• Edit: In the comments Karl points out his own much more detailed coverage of the science behind this trait over at Biofortified.

*Historically, separating the seeds (usually considered waste) from the cotton fibers required lots of human labor, but was eventually mechanized by a device called the Cotton Gin around the end of the 18th century, which had all sorts of economic, social, and political effects on the United States in the pre-Civil war area, which was producing huge amounts of cotton.

**In fact they already show up in our food supply to a limited extent as cottonseed oil.

***Note that this was decades before genetic engineering became possible, these mutants were entirely “natural” and were not then, nor are they now, subject to ANY government regulation

****Specifically he used a technique where a copy of an gene already found in a plant is inserted backwards into the genome. The reversed copy binds to the copy produced by the plant already, which triggers a natural plant response (Called RNAi sort for RNA-interference) which results in the silencing of both copies. This response is used by plants to regulate their own genes, protect against excessive expression of transposons (jumping genes) and defend again viruses. This was the same technique used in the development of the Flavr Savr tomato, a scientific success if economic failure.

*****The professor has the misfortune to share a last name as well as first and middle initial with someone publishing in medical journals. There are a LOT of medical papers out there, which is why top level journals like Science and Nature will often have lower impact factors (effectively the average number of times a paper published in that journal is cited by other papers) than specialized immunology and cancer journals. So many medical papers are written every year that an interesting medical paper will be cited a LOT more than an interesting paper in another scientific field.

China is also in a unique position when it comes to commercializing any form of genetically engineered rice, as the world’s largest producer of rice, but only a small next exporter*** China stands to benefit from any improvements to rice, and is largely immune to pressure from food importing countries such as the members of the European Union. China has also invested (and continues to invest) billions of dollars in developing their own, publicly-funded, domestic crop research and breeding which has kept their per acre crop yields trending upwards, and now means they’re prepared to make the leap to genetically engineered food crops (they’ve had bt cotton for some time) with home-grown technology, killing any narrative about this being western tech foisted off on the developing world.

Whatever bad things you can say about the current government in China (and there definitely are bad things to say), it’s at least clear they’re pulling out all the stops to make sure their people stay fed, but today and in decades to come. Clearly it’s in their own self interest to do so.

When the people are hungry, governments have a way of falling often with bad consequences to those formerly in power (see: The French Revolution). Plenty of societies throughout history have seen problems on the scale of those China will face (feeding a population of 1.3 billion that continues to grow) coming have closed their eyes rather than do everything they can do develop solutions before it was too late.

We’ll have to wait and see if this story is confirmed before much more can be said.

*Even if the routers story pans out, and that’s not assured in a story based solely on anonymous sources, the bt rice is still a couple of years away from large scale planting.

**Since this strain was developed by the government, which I assume isn’t developing genetically engineer traits for a profit, the cost of farmers of buying the new seeds may be quite low. China is also one of the countries that is already producing and using a hybrid rice seed and as a result China farmers are already using purchased seeds.

***China’s rice exports are expected to keep shrinking as demand for rice grows along with the growth of their population.

New York Grapes. Concords I believe, though it's been several years so I may be remembering wrong.

Scientific Name: Vitis vinifera

Supposed Genetically Engineered Trait: Large size/seedlessness

The Real Story:

Seedless grapes are descended from several different mutations that all result in the developing embryos of grape seeds to abort prematurely*. You can still find the tiny dead remnants of seeds in seedless grapes. Of course being seedless raises a new question: How do plant breeders work with seedless grapes? (And breeders definitely do work with seedless grapes. For example they’ve developed more cold tolerant seedless grapes that are well adapted to the vineyards springing up along the finger lakes in New York.)

The answer (I had to look this up myself) is that grape breeders can dissect out the seeds of immature grapes (before they abort) and use tissue culture techniques to grow them in a lab. The technique is called embryo rescue and it’s used effectively in lots of situations where plant breeders otherwise can’t get viable offspring. Once a breeder develops a tasty and hardy new breed of seedless grape, multiplying it for distribution is easy, since almost all grape vines grown today are already produced using grafting.

Normally grape seeds produce a plant hormone called gibberellin that, among many other cool roles in plant development, promotes fruit growth. Since seedless grapes, by definition, don’t have seeds, farmers often spray them with gibberellin to increase their size (otherwise seedless grapes are smaller than their seeded relatives). The enlarged seedless grapes created by gibberellin spraying are probably the cause behind uninformed comments like:

Why do “regular sized” grapes look so teeny to me? Oh that’s right, b/c the ones we have at home now are the genetically engineered ones.

Other facts about grapes:

Grapes growing outside of Prairie Moon Winery (near Ames, Iowa). Photo: rwmsn, flickr (click to view photostream)

I’ve actually fairly familiar with the grape genome, it’s one of the better assembled plant genomes and is great for doing comparisons to other eudicot species since it hasn’t gone through any further duplications since the ancient hexaploidy of eudicot plants. For example one genomic region in grape matches up to four separate regions in Arabidopsis, a species that has gone through two more recent rounds of whole genome duplication.

But enough about genomics. Grapes were originally domesticated in the Mediterranean. People have been making wine from them for thousands of years. The Odyssey talks about Odysseus and his men making wine from grapes at several points.** Wine making is still the primary use of grapes grown everywhere from famous wine regions (like California and France) to good but obscure ones (like the finger lakes of New York) to the truly unexpected wineries (like Iowa).

[This part grabbed from my previous post on grafting] Grapes are a great example of using root stocks to provide disease resistance and climate tolerance while maintaining old flavors, (and no grapes are not a tree but a woody vine). Many of the grapes grown around the world today are old breeds of European grapes that produce the various favors of wine western our culture is accustomed to, grafted on to rootstock from a separate species native to North America which provides resistance against phylloxera, an insect that devastated vineyards around the world. (Yes, disease resistance in the rootstock can sometimes provide protection for the entire plant, and no, I have no idea how it works, but I’m sure others do.)

*As with any complicated system there are a lot more ways to break grape embryo development than for it to work successfully.

**Way back in high school I used that fact to twist an otherwise mind numbingly boring english assignment into a paper on early agriculture and the biology fermentation. As I recall my english teacher was not pleased with me, but it was worth it.

• The 318 million pounds in context
• Chemicals are different
• –Different Toxicity
• –Different Persistance in the Environment
• Herbicide resistant weeds
• One trait vs a technology

318 Million Pounds in Context

Example tweet:

Pesticide use has skyrocketed by 318 million lbs (in last 13 years) with use of #GMO seeds!

Let’s put that number in perspective. The total number of pounds of pesticide active ingredients used in agriculture has remained relatively flat over the past two decades. The most recent number I could find was 480 million pounds of active ingredient per year. Compared to 480 million, an increase of 318 million looks huge but it is not a fair comparison.

I swear there's an xkcd for everything

Since the increase attributed to genetically engineered crops is 318 lbs over 13 years, the honest comparison is 24 million pounds per year to 480 million pounds total every year; approx. 5% of total weight pesticide active ingredients for a given year. While 24 million pounds of ANYTHING is still a lot, I don’t think 5% can honestly be described a skyrocketing.*

Different Chemicals are Different: Toxicity

I always like to make the point that pounds of active ingredient is a deceptive measure in the first place, since toxicity between different herbicides can vary massively, and insecticides will generally be more toxic to humans than herbicides (we’re more closely related to insects than to plants, which means we share more of the same biochemical pathways and enzymes). But the report had some data that really drives it home for me. Back in 1996 when herbicide tolerant crops were new (and therefore couldn’t have yet contributed to the development of glyphosate resistant weeds), the average application was .63-.69 pounds per acre per year for various crops (table 4.1 on page 36). On the other hand, outside of glyphosate, the market has apparently (according to the report) has be moved towards the use of so-called low dose, or even very low dose herbicides. When pyraflufen ethyl, a very low dose broad leaf herbicide** was applied to fields it was applied at an average of only .003 pounds per acre (210 times less than roundup/glyphosate). Anyone think that’s because farmers needed only 1/200th the weed control power? It’s because pound for pound pyraflufen ethyl is much more lethal to weeds.***

Different Chemicals are Different: Environmental Persistence

Farmers in the US used 76 million pounds of atrazine and 135 million pounds of glyphosate (Round-up). Yet in watersheds feed by agricultural run off, atrazine is present at much MUCH higher levels. (source #1, source #2). That’s because glyphosate breaks down faster in the environmental, as well as more tightly binding to the soil in the area it’s first applied to. The half life**** of glyphosate in soil is less than seven weeks. All things being equal pesticides that don’t leave the area they were first sprayed in and degrade too fast to build up in the environment are safer than ones that are more mobile and can persist for years (for comparison the half life of DDT can be as long as 22 years, giving it lots of time to accumulate in the environment).

Herbicide Resistant Weeds:

The report spends a lot of time talking about the emergence of glyphosate resistant weeds. I’ve already addressed the development of herbicide resistance in weedy species and why they don’t by any stretch of the imagination deserve the name “superweeds” here. So I only have a couple of things to say:

• Resistance happens. It happens with antibiotics and other drugs, and while we do everything we can to slow it down, we don’t refuse to use antibiotics because we know by using them we ensure that someday diseases will no longer be susceptible to them.
• The development of resistance could be slowed down a lot if we had more herbicide/herbicide tolerance systems on the market. Right now there are only two Roundup Ready and Liberty Link, and for a lot of crops Roundup Ready was the only system available for most of the time period covered by this. Using a single herbicide over and over again speeds up the evolution of resistant weeds. When herbicides switch from year to year any resistance to to this year’s herbicide will be useless against next year’s so it isn’t selected for from generation to generation. It throws a wrench in natural selection and dramatically slows down evolution.
• Proponents of organic agriculture (like The Organic Center) who complain about the development of herbicide resistant weeds are trying to have their cake and eat it too. If they’ve already sworn off the use of synthetic herbicides, they can’t turn around and complain about weeds resistant to herbicides that they don’t want used in the first place.

That said, herbicide resistant weeds (like antibiotic resistant infections) are a real problem. The solution in both case is continued research into new alternatives, along with the adoption of better practices (rotating between different herbicides) to extend the lifespans of those new alternatives.

Trait vs Technology:

The numbers released by The Organic Center reflect both an increase in herbicide use (subject to all the caveats described above) from herbicide tolerant crops and also a decrease in insecticide use from bt crops. Total insecticide active ingredient usage is much smaller than total herbicide usage so the herbicide increase swamped out the insecticide decrease. But that doesn’t change the fact that one of two biggest traits on the market that genetic engineering has given us, had a positive effect even by the criteria used by The Organic Center. Even if you don’t buy anything else I’ve said, it doesn’t condemn a whole technology for a single use it can be put to. No more than it makes sense to condemn the entire internet for identity theft (or the lawsuits of the RIAA).

*A situation where I would apply the word “skyrocket”: Tuition at UC Berkeley is going to increase 30+% between now and next fall, and at which point it will have increased more than 280% over the past eight years (2002-2010).

**The two biggest group of plants are monocots and eudicots. Broadleaf herbicides kill eudicots, which tend to have wider, rounder leaves than the monocots people are most familiar will grasses (including grains like wheat, rice, corn, sorghum, barley, and oats). Broadleaf herbicides are sprayed on grain crops to kill non-grass weeds.

***For an example in humans, let’s use dioxin and sodium cyanide. The LD50 (the dose that kills half of the animals that receive it) for sodium cyanide is 6.4 milligrams/per kilogram which can be used to calculate that consuming even half a gram has a good chance of killing a 175 pound person. For dioxin, the LD50 is .02 milligrams per kilogram so even 1.6 milligrams (more than 300 times less) stands a good chance of killing that same person. A 10 milligram combined dose of sodium cyanide and dioxin might be completely lethal, or relatively harmless depending on how much of it was each of the chemicals. That’s why reporting total weight of pesticide active ingredients isn’t very informative by itself.

****The time it takes half of a chemical to chemical. After the half life has passed only half the chemical is left, twice the half length a quarter of it is left, after three times the half life an eighth and so on.

Anyway, two new developments seem to have prompted this article. First, Monsanto and Syngenta have been sending signs that they’re both interested in restarting their programs to develop new wheat traits using genetic engineering. Views about among wheat farmers have begun to shift, partly as they see the acreage devoted to wheat shrinking as more and more land is converted to corn production, but also because of the second development.

Wheat growers in the US, Canada, and Australia have banded together to push for a simultaneous adoption of future genetically engineered wheat traits. That’s significant, because those three countries are some of the biggest wheat exporting nations in the world.* US farmers were worried that if genetically engineered wheat was introduced in America, rich wheat importing countries (basically Japan and the EU) would stop buying US wheat and wheat prices would fall in the US. But if more countries switch at the same time, it’s less likely any of them will get cut off.

It’s the same logic as a union. If a big company decides to fire me without cause, there isn’t much I can do about it, there are plenty of other people they can hire to replace me (or pay a little more to many of their current employees to work overtime and cover my job). But they can’t replace all their employees at once, so a union has more bargaining power than individual employees. Wheat farmers in Australia, Canada, and the United States are banding together to increase their freedom to adopt new technologies with less fear of retaliation from countries that are less food self-sufficient. Although I’ll admit it does violate the violate the cliche about the customer always being right. But then again we already knew it wasn’t.

h/t to Amy for pointing out the great article in Nature Biotechnology, and Mr_Subjunctive to the final link.

*India and China are actually the two biggest producers of wheat, but their production is consumed domestically, which means that #1 they’ve got even more interest in increasing yield since for them its a question of feeding their people, not making more or less money on the world market #2 they don’t have to worry about they acceptance of their crops in other countries. The article I linked to above suggests China is much closer to the commercial production of a range of genetically engineered traits in wheat than anything in the research pipelines of western biotech companies, which after all are only just restarting after turned completely off for years.

Greenpeace on Friday called on the International Rice Research Institute to abandon its genetic engineering program as the environmental activist group offers marker assisted breeding as a safe alternative to bioengineering.

Source.

Dear Greenpeace,

I would like to call upon you to abandon your campaign against genetic engineering and offer up an alternative priority your organization could focus on to the greater benefit of the world we all share: Fighting man-made global warming.

-James

Now you could argue greenpeace already is opposed to global warming. And you’d be right. They are. I guess my offering it to them looks pretty stupid doesn’t it?

The same could be said of greenpeace offering marker assisted selection to the plant breeding community that pioneered the technique and is taking full advantage of it, and has been for years in both the private and public sectors. Case in point:

Sub1 rice is much less damaged by flooding, a risk in many rice producing areas, such as Bangladesh. The trait was first prototyped using genetic engineering, and after it had demonstrated its effectiveness, the long hard work of bringing the gene into cultivated rice lines (using marker assisted breeding) began. Now the trait has been freely released to farmers  If you haven’t seen the video of the difference the sub1 trait makes in a flooded rice field, check it out.

Marker assisted breeding is very important for crop improvement. As things stand today, I’d say its contribution to feeding the world is substantially greater than genetic engineering. Make no mistake, genetic engineering has done some cool things, but marker assisted breeding is increasing yields, resistance to draught, pests, and disease every single year!

Marker assisted breeding and genetic engineering are two different tools in the toolbox of plant scientists and plant breeders. There are problems that call for a hammer, and others that call for a screwdriver. You wouldn’t tell someone to stop using a screwdriver to screw in screws and offer to let them a hammer instead. If you do, don’t expect to be taken that seriously. And if the hammer you offer to let them use is one you just took out of their own toolbox…

Photo Reeding, Flickr (Click for photo stream)

Scientific Name: Carica papaya

Genetically Engineered Trait: Resistance to the papaya ringspot virus

Details of Genetic Engineering:

In the 1990s papaya ringspot virus was in the process of wiping out the Hawaiian papaya industry, then the second largest fruit industry in Hawaii. Conventional approaches such as selective breeding for resistant papayas or attempting to grow trees in isolation had failed. The virus is transmitted by small sap-sucking insects such as aphids. Infected papaya trees can be recognized by the discolored rings on their fruit (that the virus gets its name from) yellow leaves, and most importantly from a papaya farmer’s perpsective a 60-100%* loss of fruit production.

Resistant papayas were created by a collaboration between the USDA and the University of Hawaii (with help from Cornell University where the early versions of ballistic transformation** were being developed at the time) by giving papayas a gene from the papaya ringspot virus itself. It worked. Resistant papayas are so successful that they’re used to protect organic papayas from the virus. (second half of the article)

Another point to keep in mind in this case is since the transgene introduced into GE papayas to protect them from viral infection came from the papaya ringspot virus and many organic papayas are still infected with the virus, the average organic Hawaiian papaya has HIGHER concentrations of the papaya ringspot virus protein than the unnatural genetically engineered ones***

Papaya Tree Picture mattkoltermann, flickr (click for photostream)

About Papayas:

The papaya was originally domesticated in central America, and is now grow around the world. Papaya’s actually have a high concentrations of an enzyme that breaks down proteins called papain. A sufficiently concentrated extract might be able to dissolve flesh (though I don’t know that anyone has tried it) and that ability is showcased in the use of unripe papaya juice to tenderize meat.

Special Bonus Section:

While transgenic papayas have been a huge hit in Hawaii, their adoption in the rest of the world has been quite slow. Because the papayas are the product of non-profit and government agencies, there’s no one with a profit motive in their adoption, and leaving local agricultural advocates and researchers outnumbered and outspent by anti-GMO NGOs that draw most of their financial support from Europe. A great case study of the problems they face was presented a year and a half ago in Plant Physiology: “Forbidden Fruit: Transgenic Papaya in Thailand” It’s well worth a read as both a fascinating story in it’s own right, and an example of the tactics that can be used against genetic engineering when scientists aren’t engaged enough to act as a check on misinformation. To close my profile on papaya, let me quote the conclusion of that article:

It is time to meet the press. Although scientists are not generally trained in media communication, who is better qualified to discuss the risks and benefits of GE crops? If scientists do not undertake this task, where will the public get its information?

If the next generation of biotechnology crops is to make an impact on those who arguably have the most to gain and have yet to reap the benefits of the first generation—those of the developing world—then it is time for plant biotechnologists to move beyond the bench, kick around in some barren soils, man a water buffalo for a day, meet the people whose lives will be impacted, and display the same amount of passion for having their technology used in the field as they have for developing it in the laboratory. It is time to get organized, get political, get heard, and get out of the lab. Otherwise, the fruits of this fascinating research may remain forbidden.

*Losses of production per country or per region are often much greater. If papayas are less productive, fewer people will choose to grow them, so increasing yield per plant actually has a multiplicative effect as more people get back into the growing papayas.

**The original gene gun was basically a modified .22 caliber rifle. The principle of a gene gun is basically if you throw DNA hard enough at a layer of cells some of it will end up in the nucleus and get incorporated into chromosomes by natural repair mechanisms. And the crazy thing is that it actually works!

***This is an old statistic, that I believe dates from before genetically engineered papayas were incorporated as a layer of protection around organic papaya production. (The idea is aphids traveling towards the organic papayas will first reach the virus resistant papayas, bite them where the virus is ineffective.)

Anyone who reads about the public policy debates swirreling around genetically engineered crops will be familar with the two letter abbreviation ‘bt’ as in bt corn, bt cotton, bt ginseng (the last is fictional). What always surprises me is that some people STOP reading before they come across an explanation of what bt stands for. Just typing bt into google won’t bring up a relevant result until the 30th hit (two letters just isn’t very unique). I have talked with people who are convinced bt stands for everything from biologically treated to BioToxin. It doesn’t.

Golden Eyed Lacewing Adult. It's not much use, but the larva vicious predators of certain plant pests. (Photo public domain courtesy of USDA. You guys are awesome!)

The name actually comes from a species of bacteria called Bacillus thuringiensis. Different substrains of the species carry different members of a family of genes that code for Cry proteins (and separately can also carry genes that code for Cyt proteins*), which can kill insects. Finding chemical or biological means to kill insects isn’t that hard. What makes the Cry proteins noteworthy is how selective they are in their killing. A given Cry protein is dangerous to only a small subset of insect species. And that’s important, because, for every** western corn rootworm, european corn borer, or earworm there are also benign or even beneficial insects in and around fields like lacewings, trichogramma wasps, or those rootworm eating nematodes I talked about a couple of days ago, which aren’t insects, but also harmed by insecticides. (Agro-ecology is beyond my field of expertise, had to call up my tipster from the previous post to get this list) When a crop is genetically engineered to produce one of the dozens of Cry proteins discovered in Bacillus thuringiensis, it replaces or reduces the spraying of insecticides to control insect pests, with positive effects on insect biodiversity.

The reason Cry proteins are so dangerous to such a specific group of species has to do with their mode of action (the way they kill insects). After an insect eats either the protein itself (for example from the roots or leaves of a plant genetically engineered to express one of the Cry proteins) or Bacillus thuring. bacteria (which can make the proteins in an insect’s stomach), Cry proteins spread through the digestive system until they bind to specific proteins sticking out of cells in the walls of the insect’s gut. Once bound, the Cry proteins form holes called pores in the surface of those cells. Opening holes in cells is a good way to kill them, and Cry does just that. The insect dies from the inside out as its digestive system is destroyed or starves to death with a belly full of food once its digestive system is too damaged to extract energy and nutrients from its food. In the wild, Bacillus can now reproduce and thrive inside the rotting body of the insect. On a farm, insect pests that nibble on crops die too quickly to do significant damage, let alone breed and lay countless eggs that would have each developed into a new hungry insect.

Corn Borer

There are three different things that protect living things other than the target insects (primarily beneficial insects, and the people who eat food from bt crops) from the dangers of Cry proteins:

1. Most importantly, the different Cry proteins’ ability to bind to proteins on the stomach wall of insects. Each Cry protein can only attack the surface of cells once it has bound to its specific protein target. Many insects won’t even produce a protein that specific Cry can recognize, and the protein passes harmlessly through their digestive systems.
2. Cry is only dangerous when eaten, unlike most insectidial sprays which can kill from contact. Even if an insect closely enough related to the target pest to be vulnerable to the same Cry protein is in a field of bt crops, as long as they don’t actually EAT the crops (which if they’re not a pest, they don’t do anyway) they’re completely safe***. People worried about eating bt crops themselves should see point #3.
3. Proteins are like tools, in that their functionality depends on their shape.**** A screwdriver that’s been melted back into a muddle of metal isn’t much use as a screwdriver (or anything else) anymore. Similarly a protein that loses its shape (called denaturing) loses all function. In their natural environments, proteins are very good about holding onto their shape, but when the environment changes, their shape can fall apart. Lots of things can make a protein lose its shape, including heat and pH. One of the reasons we cook our food is that denaturing proteins also makes them easier to digest. More importantly in this particular case is the issue of pH. We humans have acidic stomachs which helps to break down our food. Insects have basic stomachs for the same reason. Both acids and bases are good at breaking things down (think sulfuric acid and drain cleaner respectively), but the two are chemical opposites of each other. Cry proteins have evolved to function in the high pH environments of insect guts, and denature in our own low pH stomachs, and without shape, Cry proteins might as well be any other random string of amino acids.

The specificity and lack of human toxicity were one of the reasons transgenic plants expressing different Cry proteins was first considered a good use for genetic engineering. Because such a wide range of Cry proteins had already been cloned, more companies were able to develop resistance traits in parallel, so the market for BT crops today is split, at a minimum, between Monsanto, Pioneer Hi-bred, Dow AgroSciences, Bayer CropScience, and government developed versions from China.*****

The two crops where Cry proteins are having the most significant effects are corn and cotton.

Eggplant may be the next bt crop to be approved, but it’s still working its way through regulatory approval in India.

If you want to learn more, I highly recommend this site, maintained by a lab at UCSD.

*Cyt proteins are another unrelated group of insecticidal proteins found in some of the same bacteria.

**This is a figure of speech, I’m not actually saying beneficial and insects and pests are always present in equal levels.

***This is a slight over simplification. For discussion of the exception (a study back in 1999 found that caterpillars feeding on leaves coated with excessive amount of pollen from one specific kind of bt corn could sometimes recieve a lethal doese). Here is a more thorough discussion. More importantly here’s a paper that spent two years trying to find effects on butterfly populations without success.

****Proteins are long strings of amino acids, that fold into specific shapes based on the order of amino acids and how attracted or repelled each amino acid is to every other one. It’s very complicated and even our best computer models struggle to predict the shape of a protein based on its sequence (there are too many interactions to easily simulate).

*****Karl has a good post up on Biofortified pointing out that people too often see genetic engineering as solely the province of a single company, when in fact there are a number of competing seed companies in the field as well as genetically engineered crops that are produced by publicly funded and non-profit organizations.