On January 14th Monsanto received some unwelcome news – the U.S. Justice Department was opening a formal investigation of its business practices surrounding its Roundup Ready soybean, the most popular genetically modified (GMO) crop. For the many farmers and seed cleaners who have lost their livelihoods fighting Monsanto, it was surely bittersweet news after years of ignored pleas and support from the Justice Department.

This formal investigation is no David vs. Goliath moment, or in any way an indictment against Monsanto. This is Big Ag vs. Big Ag. The timing coincides with the Pioneer Hi-bred seeds unit, owned by DuPont, filing its own complaints regarding Monsanto’s business practices around its patented Roundup Ready technology division. DuPont is concerned that the emergence of generic genetically engineered (GE) competition (something it plans on leading) will be gravely impacted if Monsanto is allowed to continue with its current practices. (On January 16, a U.S. District Court ruled in Monsanto’s favor—holding that DuPont violated it contract with Monsanto by developing GMO soybeans created with Monsanto’s technology—but left open DuPont’s antitrust challenge on biotech seeds.)

And what practices are those? Primarily they include forcing seed companies and farmers to switch to its second generation patented Roundup Ready technology as the patent on the first generation is set to expire in 2014.

This case is not about the use of GMO seeds (impact or otherwise) – it is strictly about market share and money. The Justice Department investigation wants confirmation that farmers and seed companies will have access to the first generation Roundup Ready trait, which enables Roundup Ready seeds to survive the application of Roundup Ready herbicide. This would allow farmers to save seeds from harvested crops, something they have not been able to do since the product was introduced in 1996. It would also allow seed companies, like Pioneer Hi-bred, to use the trait in its own GE seed modifications – big money and big market potential.

Monsanto is fighting with everything they’ve got. The bottom line impact could be a loss of a half a billion dollars a year in royalties if they are not able to get farmers and seed companies to switch over to their second generation technology. According to the Center for Food Safety, it is estimated that up to 85 percent of U.S. corn, 91 percent of soybeans, and 88 percent of cotton (cottonseed oil is often used in food products), is genetically engineered, which means an estimated 70 percent or more of all processed foods on supermarket shelves–from soda to soup, crackers to condiments–contain genetically engineered ingredients. I’ll state the obvious – this is one huge market.

So how does the issue of the ge technology fit into this investigation? It doesn’t, at all. There will be no opportunity to put Monsanto, and others on trial. There will be no questioning of whether or not GE seeds might actually do more harm than good. The examination of studies that have shown that the Roundup Ready seeds don’t actually increase crop yields. A deep look at seed drift and contaminated acreage, even in areas where GMO seeds are not allowed by law, like Oaxaca, Mexico. There will also be no discussion of U.S. Foreign Aid policy and a new push for a Green Revolution Part 2 that is heavily reliant on GE seeds. We won’t get to hear about soil degradation, and the ever-increasing use of herbicides to combat the super weeds that are invading farms across America.

That day will come, in fact perhaps even before the above case sees the light of day. On January 15, the U.S. Supreme Court agreed to hear a case about the risks of genetically engineered crops. Named Monsanto v. Geertson Seed Farms, No. 09-475, the case will center on GE alfalfa seeds, and stems from a 2006 lawsuit filed by the Center for Food Safety on behalf of a coalition of non-profits and farmers who wished to retain the choice to plant non-GE alfalfa. Now that is a day in court I don’t want to miss.

Until then, you go U.S. Department of Justice. Every little bit counts.