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The plum trees growing in an orchard in Kearneysville, West Virginia, look like any conventional variety. Arranged in neat rows, verdant oblong leaves crowding their unkempt branches, they produce respectable yields of sweet purple-black fruit each year. Yet they’re quite different in one respect: These trees aren’t likely to succumb to the devastating plum pox virus (PPV). That’s because they’ve been genetically engineered to resist the disease, which has infected 100 million trees in Europe and surfaced in Pennsylvania, Michigan, and New York during the past 12 years.

“We couldn’t find a gene for plum pox resistance in any plums, so we turned to genetic engineering,” says Ralph Scorza, a horticulturist and lead scientist at the USDA’s Appalachian Fruit Research Station, walking through the one-acre HoneySweet plum orchard. “We’ve had test-field plantings in Europe since 1996 and the U.S. since 1995, and we’ve never had a single tree infected.”

Like all genetically engineered, or GE, crops—also called transgenic or genetically modified—HoneySweet plums contain foreign DNA that alters them in a desirable way. Beginning in the early 1990s Scorza and his colleagues isolated a gene from the virus, inserted it into a bacterium, and then introduced that into a single plant cell. Adding hormones spurred that cell to grow into a PPV-resistant tree.

Eight years after being submitted for approval, the transgenic plant will clear final regulatory hurdles this year. Not that Scorza expects farmers to start planting it anytime soon. Instead he envisions breeders using it to develop PPV-resistant varieties adapted to their region in case there’s an outbreak. Pennsylvania spent ten years and tens of millions of dollars eradicating plum pox by cutting down infected trees, and New York is still battling the virus on a small scale. The real fear, explains Scorza, is that it will hit California, which produces all U.S. prunes and half of the world’s supply. Furthermore, all stone fruits, including peaches and apricots, are susceptible. “It’s preemptive,” says Scorza. “Right now growers don’t need HoneySweet because plum pox is under control. But if it blows up here, farmers can start planting resistant varieties.”

Safeguarding orchards might also protect wild plums. “We don’t know what would happen if it got into those trees,” Scorza adds. “Would they die? And what would that loss of fruit mean for birds or other animals? We don’t want to get movement from agriculture into the wild.”

To date the USDA, one of three regulatory agencies, has approved more than 70 applications for transgenic plants created for commercial use, although HoneySweet is only the second approved GE fruit tree, after a virus-resistant papaya. As with its predecessors, HoneySweet has raised environmental red flags. The transgenic pollen could be harmful to wild pollinators or possibly pollinate non-GE trees. “My activist friends might not like to hear me say this, but it’s not something I’d lose sleep over,” says Doug Gurian-Sherman, senior scientist with the Union of Concerned Scientists, a nonprofit alliance of more than 250,000 citizens and researchers. “Yes, there are risks. But I’m more concerned about other GE crops in the pipeline.”

When it comes to genetic engineering, a knee-jerk reaction is more common than Gurian-Sherman’s nuanced take. On one extreme are groups like Greenpeace, which considers transgenic crops “genetic pollution.” On the other is U.S. Agriculture Secretary Tom Vilsack, who calls agricultural biotechnology, including genetic engineering, a “powerful tool that can be used to boost agricultural productivity.” Vilsack’s support of genetic engineering was clear in January, when he opted against a controversial proposal that would have restricted GE alfalfa planting and protected organic alfalfa farmers from potential contamination. Instead, he said the USDA would authorize unrestricted commercial cultivation of the plant, although he assured the public that his department would work to ensure that non-bioengineered seeds remain available to farmers.

What’s certain is that plants and animals awaiting approval hold both promise and peril. The promise is intriguing. Monsanto’s drought-tolerant corn, for instance, might withstand the drier conditions climate change is expected to cause. Then there’s the South Dakota biotech company whose cattle are resistant to mad cow disease; an “Enviropig” that produces low-phosphorous manure (which could reduce water pollution from industrial hog farms); and another pig that produces omega-3, so consumers could get their dose of heart-healthy fatty acids from bacon instead of fish oil or flaxseed.

Yet no one knows exactly what will happen when transgenic products are released into the environment. After decades of dependence on Roundup, an herbicide applied to transgenic crops ranging from sugar beets to cotton, it has come to light that one of the world’s most popular pesticides is lethal to amphibians. Then there’s the controversy surrounding the soil bacterium Bacillus thuringiensis (Bt). Organic farmers use it as a natural pesticide against bugs like the European corn borer. Biotech companies have engineered Bt crops that produce the protein themselves, negating the need to spray. After laboratory studies in 1999 indicated that Bt corn pollen is toxic to monarch butterfly caterpillars, extensive field investigations determined that the threat was negligible. “One variety of corn, Bt-176, had high enough toxin levels to cause impacts on larvae, but fortuitously that one wasn’t commercially successful,” says Gurian-Sherman. A 2007 lab study found that pollen from Bt corn was harmful to caddisflies, leading researchers to posit that it “may have negative effects on the biota of streams in agricultural areas.” Today organic farmers fear that Bt crops will spur pests to become resistant; in 2008 researchers reported some of the first such populations: bollworms in Bt cotton fields in Arkansas and Mississippi. According to the Organic Trade Association, “Without Bt, organic farmers will be left with far fewer effective strategies, while conventional farmers, who also have relied on Bt sprays, will have to turn to pesticides that are more toxic.”

The debate over genetic engineering’s ecological dangers has been raging since farmers planted the first transgenic crops 15 years ago. Their use has since skyrocketed; today they account for a whopping 92 percent of U.S. soybean crops and more than 80 percent of corn and cotton. That means that as much as three-quarters of the processed foods in U.S. grocery stores—soda and hot dogs, bread and frozen pizza—contain ingredients from GE plants, the Grocery Manufacturers of America estimates. At the same time, polls show that most Americans prefer not to eat GE foods and support labeling of GE products, which the government doesn’t require—a bone of contention with consumer groups, activists, and some politicians. The government, for its part, hasn’t seen any significant environmental risks to date in approved plants, says Jack Okamuro, one of eight U.S. Department of Agriculture national program leaders of crop production and protection.

Still, there have been mishaps. In 2002 experimental corn plants engineered by ProdiGene to make a pig vaccine sprouted in a soybean field. The USDA fined the company $250,000 and forced it to purchase and destroy tainted crops at the cost of approximately $3.5 million. The agency also tightened its rules on field-testing GE pharmaceutical crops. GE sugar beet planting is restricted until the USDA completes its environmental impact statement in May 2012. Several environmental groups sued the agency, alleging it issued permits without adequate environmental study. (Depending on how they’re used, all genetically modified organisms must get the green light from up to three agencies: USDA-APHIS, which oversees GE crop planting; the FDA, if the GMOs are food sources; and the EPA, which regulates all GE plants that have resistance to something, like a disease, an insect, or a weed.)

Now GE products that have raised concerns among activists and scientists may be nearing approval, including salmon that grow twice as fast and soybeans that can withstand multiple herbicides. Plenty is at stake—products with traits like these can take more than a decade and $100 million to bring to market.

“There’s a lot of debate about the cost and the technology and the need for new products,” says Gurian-Sherman. “We need to start with the bigger picture and ask, ‘Will this harm people or animals or the environment?’ ”

While HoneySweet plums haven’t received much attention, “Frankenfish” have caused a huge stir, in part because they’re poised to be the first transgenic animal sold as food. This past September hundreds of people gathered outside the White House to protest biotech company Aquabounty’s fast-growing Atlantic salmon, and more than 160,000 sent comments to the FDA urging the agency not to approve the fish, trademarked as AquAdvantage salmon.

The fish are grown entirely outside U.S. borders. At Aqua-bounty’s Prince Edward Island facility, millions of fertilized pink eggs sit in vertical incubators reminiscent of the pneumatic tubes at drive-through banks. Spliced into each egg is a promoter from the eel-shaped ocean pout that turns on a growth hormone gene from a Chinook salmon. Presto: an Atlantic salmon that grows year-round instead of only in the warmer months. The eggs are shipped to a farm in Panama’s highlands where thousands of fish in green tanks grow to market size in 18 months instead of three years. 

The company has been seeking FDA approval since 1996. It got closer in September when the agency’s Veterinary Medicine Advisory Committee ruled that the transgenic fish are as safe to eat as any other Atlantic salmon. Still, the panel recommended that the government more rigorously assess the health and environmental effects before making a final decision. The FDA hasn’t set a timeline, but if approved, it will take about two years before any fillets appear in supermarkets. Under the current application, Aquabounty would produce the eggs in Canada and then sell them to a land-locked fish farm in Panama owned by another company. If Aquabounty wanted to sell eggs to other farms producing fish for U.S. consumers, each would require its own FDA review.

Aquabounty considers its land-based approach more eco-friendly than the ocean nets used on most salmon farms. “Having fast-growing fish is a benefit to the environment,” says research director John Buchanan, pointing out that transgenic salmon eat about 10 percent less than their traditionally farmed counterparts over the course of their lifetimes. An inland system also allows easier control of the waste and antibiotics coastal farms release directly into marine ecosystems, and reduces the likelihood of escapees. The saltwater would kill any Prince Edward Island hatchlings that somehow made it to the ocean, Buchanan says, and in Panama the water is too warm for runaways to survive. As an extra precaution, they’re all engineered to be female and infertile. “As with any biological process, there’s some uncertainty, but we think 99.8 percent or better are sterile,” he says. “We’ve done a lot of studies looking at fish health and haven’t found anything unusual. We didn’t find any differences in fatty acids, minerals, amino acids. It’s just a salmon that grows fast.”

Critics contend that if Aquabounty successfully expands the salmon market, the growth will amplify the industry’s negative aspects: Pollution from waste. Disease. Increased pressure on wild fish stocks used as feed.

Still, dominating the debate is the fear that the fish might escape and outcompete their wild counterparts. “Atlantic salmon populations have been in decline for a very long time, and there’s always a concern domestic salmon will hurt wild populations,” says Carl Safina, head of the Blue Ocean Institute. Every year an estimated two million salmon escape from North Atlantic farms alone. A multiyear study found that the hybrid offspring of farmed and wild salmon are shorter lived than their wild counterparts. Because they’re raised in ocean nets, diseases and parasites are passed to wild stocks. The results can be profound. Overall, research shows that wild populations drop by half when associated with farmed salmon.

Safina argues it’s impossible to guarantee that no salmon will escape, especially if more farms are built, but he doubts they could hack it outside. “Would they be able to breed? Are they capable of surviving in the wild? I’d tend to think the answer is no.”

Bill Freese, science policy analyst at the Center for Food Safety, questions more than the animals’ fitness. “I was struck by how poor the science was overall. I’m shocked that they didn’t look at disease resistance,” he says of Aquabounty’s 84-page report. “They used six to 12 salmon per study, which is just ridiculous. The testing Aquabounty did doesn’t represent the population of salmon that consumers would eat.” Furthermore, the panel consisted almost entirely of veterinarians. “To have only one scientist that has some fisheries expertise is really troubling,” Gurian-Sherman says. He views the entire process as problematic, starting with the fact that the FDA is evaluating the fish under the new animal drug provision, which is designed to assess medications used to treat animals. “Our laws were not designed for this technology. Back in the Reagan and first Bush administration, instead of taking the time to do it right, the government just stuck genetically engineered organisms in wherever they thought they fit with existing laws.”

Just as GE livestock is wending its way through the regulatory process, new transgenic crops are getting closer to the field—something farmer Ken Hartman regards with a mixture of optimism and impatience. His family has farmed in Waterloo, Illinois, since the 1850s. Today they grow corn, soybeans, and wheat on their midsize farm. Hartman isn’t loyal to one seed company. “I see what works, and many of my crops are genetically modified,” he shouts over the whir of a fan circulating air through towering soybean-filled silos. Biotech has provided him with some extra security. Bt corn kills the destructive corn borer, and he uses fewer chemicals than his father did, thanks to soybeans designed to tolerate the herbicide glyphosate (the generic form of Roundup, produced by many companies). “We used to use five or six different chemicals, but with Roundup you just need the one,” Hartman says. “You can spray it on the plants without killing them, and you don’t have to till as much.”

Farmers spray glyphosate directly onto crops and surrounding weeds. The weeds die; the crop survives. This approach has had both advantages and drawbacks. On the plus side, the increased reliance on Roundup has decreased overall herbicide use. In corn it dropped from 2.61 pounds per acre in 1995 to 2.06 in 2005. Spread over tens of millions of acres, that’s a huge difference. It also has allowed farmers to cut back or even eliminate tilling, which curbs soil erosion and fossil fuel use.

Those benefits are the reason the vast majority of U.S. soybean, corn, and cotton crops are glyphosate tolerant. Unfortunately, this practice doesn’t work as well as it once did. Glyphosate-resistant weeds, like horseweed, are popping up in Hartman’s fields. And his aren’t alone. The first ones were found in 2000 in a Delaware soybean field; by 2009, 5.4 million acres were affected. As of June 2010 the 19 immune weed species had infested 11.4 million acres.

As with any herbicide, the more it’s used, the more likely resistance will emerge. “This isn’t particular to genetic engineering,” says Matt Liebman, Iowa State University agronomy professor. “It’s happened throughout the history of pesticides. Resistance develops to one and it becomes less effective, so you create the next one, and so on.” The problem, says Gurian-Sherman, is that “no one has developed any new effective herbicides since Roundup.”

Monsanto’s solution is to engineer a trait for resistance to an older herbicide called dicamba. By stacking dicamba resistance on top of glyphosate resistance, one crop can tolerate both herbicides. “Roundup has been revolutionary in helping farmers control weeds and is still effective on more than 300 weed species,” says Roy Fuchs, Monsanto’s global oilseed technology lead. “If we can give farmers a more dynamic weed-control system, it will ensure the longevity of Roundup.” Only five weeds are resistant to dicamba, he adds. Other companies are developing dual-herbicide products, such as a soybean from Dow Agrosciences that’s resistant to glyphosate and the herbicide 2,4-D.

Critics say the problem isn’t the soybeans themselves but rather the chemicals applied to them. Though glyphosate is only slightly toxic to birds and practically nontoxic to fish and honeybees, the EPA concludes, it is deadly to amphibians. Most pesticides don’t have to be tested on amphibians, and few people looked into the effect, until University of Pittsburgh biologist Rick Relyea.

In 2005 Relyea found that in tanks designed to mimic ponds, recommended Roundup doses caused an 86 percent drop in total tadpole mass. Even at one-third the concentration, it killed up to 71 percent of tadpoles. The culprit is a surfactant added to make Roundup penetrate leaves, not the herbicide’s active ingredient, says Relyea. Because so little is known about how pesticides affect amphibians—and the resulting domino effect through the food chain—it’s difficult to predict what might happen as farmers adopt dicamba or 2,4-D on top of glyphosate, says Relyea. “But there’s often concern when you put more pesticides in the environment.”

Penn State weed ecologist Dave Mortensen estimates that if 2,4-D and dicamba-resistant soybeans are widely adopted, herbicide use on that crop will increase by 70 percent in a few years. That’s what Monsanto is counting on. “Dicamba is older, farmers know how to use it, and it’s off-patent, so it won’t be expensive,” says Fuchs. He notes that there are concerns about volatilization—the herbicide readily converts to a gas and drifts onto nearby plants. To reduce that risk, Monsanto, with chemical company BASF, is developing a less volatile formulation. Of course, it would be patented and would thus cost more. Mortensen has found that dicamba moves 60 to 180 feet from where it’s sprayed. He’s also looked at one of the new formulations, which “are less likely to move as gas, but they’re still moving outside the field.”

“Dicamba is a lot nastier than glyphosate, because of volatilization and its toxicity,” says the Center for Food Safety’s Freese. It’s slightly toxic to bobwhite quail and mallards, and may cause developmental or reproductive problems in mammals that feed on plants exposed to it. Any nearby broadleaf plants, including tomatoes, peppers, and cabbage, are susceptible. Steve Smith, director of agriculture for Red Gold, America’s largest private canned-tomato processor, told Congress last September that “the widespread use of dicamba herbicide possesses the single most serious threat to the future of the specialty crop industry in the Midwest.”

While frustrated by the weeds, Hartman says dicamba isn’t an option for him at this point. “Dicamba will kill the weeds, but it could also kill my neighbor’s grapes. He’s a friend,” he says, adding with a smile, “and I drink his wine.”

It could also hurt habitat just now being recognized for its ecological importance. “We’re realizing that the weedy field edge, the non-crop elements like hedgerows and forest, are really important to habitat provision,” says Mortensen. “It’s important for pollinators like wild bees and other insects.” Colony collapse disorder, which has devastated some commercial honeybee colonies, is spurring research into wild bees as important backup pollinators. Most plants on the fringes are broadleafed, and thus vulnerable to dicamba. “Herbicide drift will clearly restructure plant communities on the field edges and in these fragmented pieces,” says Mortensen. “We certainly expect that the insect populations built on these edges will be affected. And anything eating those insects or nesting in those plants would potentially be at risk, too.”

Instead of GE and chemicals, Liebman advocates the “many little hammers” approach—employing varied management methods that together control weeds. This might mean rotating diverse crops, planting cover crops that suppress weeds and bolster soil health, limiting tilling to prevent erosion, and applying sparing amounts of pesticides. “It’s not a panacea,” he says. “If you use a range of tactics, each of them is relatively weak, but cumulatively they’re strong. It works, but it requires more management.”

Whether Big Ag would adopt the approach is another matter. “We have a whole bunch of pesticides that work,” Liebman says. “They’re convenient, and farmers will start using those in sequence.” As with glyphosate, resistance will crop up, he says. Some weeds already tolerate multiple herbicides, which might lead companies to stack resistance to several herbicides. Asks Liebman, “The question is, do you want to be on that pesticide treadmill forever?”

Monsanto has no intention of getting off the treadmill, but it is diversifying, as a visit to its facility outside St. Louis makes clear. In a sticky-warm sixth-floor greenhouse, dozens of potted, four-foot-high corn plants sit in neat rows. A sign on one wilted stalk reads: “Do not water.” These plants are being developed for drought tolerance. Their more advanced predecessors are being field-tested on the western Great Plains. Mark Lawson, head of yield and stress traits research, says that as climate change causes arid regions to become even drier, it could become an important crop here and in sub-Saharan Africa, where the company, with funding from the Gates Foundation and the Howard G. Buffett Foundation, is developing drought-tolerant corn hybrids.

Monsanto expects to introduce the product to U.S. markets after trials in 2012. It’s something farmer Hartman has been waiting for. “I’d love to try it on the drier pieces of land. It seems like every year they say it’s one year away.” The delay shows how tricky this particular aim is. “Drought is the most complex trait you can work on,” says Lawson. The crop has to grow well under arid conditions but also produce adequate yields in rainy years. And testing for unintended side effects—like increased disease susceptibility—takes years.

Gurian-Sherman, meanwhile, favors looking to conventional breeding for drought-tolerant corn. In fact, such products are expected to hit the market around the same time as Monsanto’s. It’s too early to say which will win out, but there’s a lot of money at stake: Analysts say the drought-tolerant-corn market may top $2.7 billion.

Such crops are just one example of the new directions corporations, governments, and academics are pushing genetic engineering. Not all the products will make it to market, but some certainly will. At the same time, the public backlash against GE isn’t dying down, as demonstrations against GE salmon show. With so much in motion, Mortensen would like to see broader, science-based discussions that weigh the risks and benefits. “In the end, I probably won’t be on board supporting a lot of genetically engineered crops with stacked resistance,” he says. “But I would really love to see us take a step back and see if this is the best way to go.”