What a month it’s been for contentious science! The latest scrum is over a new study from the University of Washington agricultural scientist Charles Benbrook, who looked at the rate of pesticide use in the age of genetically engineered seeds, or GMOs. Benbrook’s results undercut one of the main arguments in favor of the seeds — the idea that they have significantly brought down pesticide use. In fact, according to Benbrook’s analysis, since their introduction in the 1990s, pesticide use for commodity crops like corn and soy has increased by approximately 7 percent.

What’s interesting is that the biotech industry’s claim about GMOs reducing pesticide use was true when the first GMO seeds came on the market. Those seeds, known as Bt corn and Bt soy cotton, expressed their own pesticide. And when they were the only GMO game in town, Benbrook confirms that pesticide use did drop.

But then came Monsanto and its herbicide-resistant RoundUp Ready product line — seeds engineered to withstand the pesticide RoundUp (whose active ingredient is glyphosate). These seeds had the opposite effect, encouraging farmers to use a single pesticide, ultimately to excess. Benbrook decided to figure out exactly how much.

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But the U.S. Department of Agriculture had ended its pesticide use tracking program years earlier, so Benbrook was forced to estimate the total use. He had to come up with a model using incomplete data from the USDA combined with other sources, like planting data and pesticide-use models. He arrived at this estimation: Since GMO crops were introduced 1996, U.S. farmers have used 404 million more pounds of pesticide than they would have with just conventional crops.

This conclusion is (surprise, surprise) not without its detractors. Graham Brookes of PG Economics, a U.K. consulting group specializing in biotechnology that has conducted its own industry-funded studies on the subject, told the Huffington Post that Benbrook’s figure was “biased and inaccurate.” And Keith Kloor, who recently compared GMO “skeptics” to climate deniers, has accused Benbrook of being biased because he’s affiliated with the Organic Center, among other things.

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Kloor did not, however, mention that Benbrook is also, according to his bio, former “Executive Director of the Subcommittee of the House Committee on Agriculture with jurisdiction over pesticide regulation, research, trade and foreign agricultural issues” and former executive director of the Board on Agriculture of the prestigious National Academy of Sciences. Sounds like a total radical, doesn’t he! I guess even “realists” such as Kloor are not immune to selective editing.

But the main reason that Benbrook’s work is open to these criticisms has nothing to do with him. It’s the fact that, in 2008, the Bush USDA all but stopped tracking pesticide use. It was supposedly for budgetary reasons — but it is fishy that the last year of USDA data (2006) more or less coincides with widespread adoption of Monsanto’s RoundUp Ready crops — the same ones that encourage farmers to pour huge amounts of glyphosate on American lands.

Which brings me to another main critique of the study: Some scientists claim that while there’s lots more RoundUp used these days, RoundUp is much safer than the alternatives. But how much safer is it really?

We have lots of evidence — some of it from USDA scientists — that RoundUp isn’t the innocuous product it’s cracked up to be. And Benbrook cited evidence of an increase in the amount of RoundUp residue present on retail produce, a phenomenon that was once quite rare. He suggests this is due to farmers using higher doses of RoundUp in fields in an early response to the rise of pesticide-resistant weeds, or as we like to call them, “superweeds.”

The RoundUp residue is a mere harbinger of things to come, however. As I’ve written about before, many farmers are now turning to older, more toxic pesticides to control those weeds. Take 2,4-D, a common replacement; it’s been linked to cancer, neurotoxicity, kidney and liver problems, reproductive effects, and shows endocrine disrupting potential.

Benbrook sums up the implications like this:

A majority of American soybean, maize, and cotton farmers are either on, or perilously close to a costly herbicide and insecticide treadmill. Farmers lack options and may soon be advised, out of necessity, to purchase [GMO seeds] resistant to multiple active ingredients and to treat Bt corn with once-displaced corn insecticides. The seed-pesticide industry is enjoying record sales and profits, and the spread of resistant weeds and insects opens up new profit opportunities in the context of the seed industry’s current business model.

It’s a situation only a biotech company could love. It’s also worth noting that Benbrook calls not for a ban on GMOs, as his detractors intimate, but instead declares that “profound weed management system changes will be necessary in the three major GE crops to first stabilize, and then hopefully reduce herbicide use, the costs of weed management, and herbicide-related impacts on human health and the environment.”

It’s a sad day when a statement like that is seen as controversial. But it’s not surprising either, considering the way the science and media communities have been arguing about genetic engineering lately.

Take the recent, contentious “lifetime feeding study” [PDF] of rats and genetically modified corn that found health risks and high tumor rates, which I wrote about here. While there were issues with the study, especially surrounding the terms over which reporters could get access to the work in advance, the response from both media and other scientists was resoundingly aggressive (not to mention effective. Google the study and the first page of results contains only critical articles). The conventional wisdom quickly became that the safety of GMOs is “settled science.”

But how often is it made clear that this conclusion is based on the safety data provided by … the industry that developed and sells genetically modified seeds?

Even The New York Times hasn’t entirely ignored the lack of independent research on GMOs. A 2009 article documented a protest to the EPA by scientists who have been unable to get access to biotech companies’ seeds in order to do full analyses of their safety:

Biotechnology companies are keeping university scientists from fully researching the effectiveness and environmental impact of the industry’s genetically modified crops, according to an unusual complaint issued by a group of those scientists.

“No truly independent research can be legally conducted on many critical questions,” the scientists wrote in a statement submitted to the Environmental Protection Agency.

… [W]hile university scientists can freely buy pesticides or conventional seeds for their research, they cannot do that with genetically engineered seeds. Instead, they must seek permission from the seed companies. And sometimes that permission is denied or the company insists on reviewing any findings before they can be published, they say.

You cannot claim to understand or defend the science behind GMO safety without grappling with this reality. And Gilles-Eric Seralini, the scientist behind the rat study, is by no means the first scientist who has raised questions about GMO safety only to come under fire from industry (and in turn media).

A group of scientists recently penned a letter, which was cosigned by dozens of researchers, claiming a pattern of harassment of skeptical scientists by biotech companies and governments. The list includes:

Ignacio Chapela, a then untenured Assistant Professor at Berkeley, whose paper on GM contamination of maize in Mexico sparked an intensive internet-based campaign to discredit him. This campaign was reportedly masterminded by the Bivings Group, a public relations firm specializing in viral marketing — and frequently hired by Monsanto

And Arpad Pusztai, whose career as a biochemist “came to an effective end when he attempted to report his contradictory findings on GM potatoes.” The letter goes on to describe his experience this way:

Everything from a gag order, forced retirement, seizure of data, and harassment by the British Royal Society were used to forestall his continued research. Even threats of physical violence have been used, most recently against Andres Carrasco, Professor of Molecular Embryology at the University of Buenos Aires, whose research identified health risks from glyphosate, the active ingredient in Roundup.

It’s not easy for scientists to write letters like this — most prefer to produce research, not protests. It’s when they feel that their work is being suppressed or blocked that they get angry.

Of course, it’s easy to look at all this controversy as proof that all anti-GMO research is bunk — which is certainly a common opinion among traditional scientists. But we do live in a world where deep-pocketed industries can up and decide to “create their own reality,” as the Bushies liked to say. Fossil fuels, tobacco, and more recently, BPA and flame retardants have all benefited from a vigorous (and secretive) “product defense” industry to protect their interests (and bottom lines). Are we to believe GMOs are any different? The essence of product defense is — with apologies to Thomas Dolby — to blind with science. It hasn’t come to that point just yet; but it’s certainly getting hard to see through the fog.