First the bad news: The “safest” herbicide in the history of science may be harming us in ways we’re just beginning to understand. And now for the really bad news: Because too much is never enough, the Environmental Protection Agency just raised the allowable limits for how much of that chemical can remain on the food we eat, and the crops we feed to animals — many of which end up on our plates as well. If you haven’t guessed its identity yet, it’s Monsanto’s Roundup, a powerful weed killer.

The EPA and Monsanto are apparently hoping that no one notices the recent rule change — or, if we do notice, that we respond with a collective shrug. But that, my friends, would be a mistake. While Roundup may truly be the “safest” pesticide ever invented, that isn’t quite the same as “safe.” It just may be that Roundup represents a hitherto unrecognized threat to our health — not because of what it does to our bodies, but because of what it does to our “internal ecology,” a.k.a. our “microbiome.”

As Michael Pollan deftly cataloged in his must-read cover story in the most recent New York Times magazine, scientists are just beginning to explore the inner reaches of our bodies to understand how our microbiome affects our health. Nonetheless, there are some growing signs that Roundup might be the last thing you want in there.

Monsanto would, of course, disagree. The common claim is that Roundup’s active ingredient, glyphosate, is less toxic than aspirin. How can one of the most effective broad-spectrum herbicides in the history of humankind be less toxic than aspirin?

I’m glad you asked. For two reasons. First, because glyphosate isn’t well absorbed by our digestive tract: 98 percent of it passes right through us. And second, because its “mode of action” involves a biochemical process that is specific to plants. (For the budding chemists among you, it disrupts the metabolic process known as “the shikimate pathway,” which humans do not have.)

Now, the actual safety and environmental effects of Roundup are the subject of some dispute. It gets into waterways and may affect aquatic plants. New research has implicated it in the catastrophic loss of amphibians. Even the U.S. Department of Agriculture has evidence, which it downplays, that Roundup may damage soil through its impact on beneficial soil microbes and interfere with the growth of plants, including Roundup Ready varieties that have been genetically engineered to resist the herbicide. And there’s the controversial claim by a Purdue University plant pathologist that Roundup has caused an increase in miscarriage and infertility in livestock.

There are studies that show glyphosate is toxic to human placental cells, but you’re unlikely to run into high enough concentrations to show those effects — unless you’re a farmworker. A study of Berlin residents [PDF], meanwhile, found glyphosate levels in human urine that exceeded Germany’s safe drinking water limits [PDF].

While it’s true that glyphosate the chemical has been the subject of much scientific analysis, it’s also true that farmers don’t use pure glyphosate. They use Roundup on their fields — and Roundup is a product with other “inactive” chemical ingredients. And there is increasing evidence that Roundup as a product is far more toxic than glyphosate on its own because the ingredients interact in troubling ways.

All of which is to say that there’s isn’t really a good health argument in favor of increasing Americans’ exposure to the chemical. There are, however, some pretty compelling reasons not to — and that’s where your microbiome comes into the picture. Even if we aren’t absorbing all the Roundup that’s on the food we eat, we are certainly exposing the residents of our digestive tract to it. And here’s the funny thing. While we don’t have the metabolic process that Roundup disrupts, many microbes do.

So, in short, we may be dousing our interior landscapes with a potent and effective intestinal flora herbicide. Oopsie.

Researchers are only now beginning to explore this idea. There is new research out of Germany that establishes that glyphosate kills many species of beneficial animal gut bacteria while not affecting more harmful gut bacteria, like E. coli and the bacteria that causes botulism, which is apparently at epidemic levels in cattle. And it’s not a stretch to say that it likely has a similar effect on the versions of those bacteria that have colonized us.

And, as Pollan explains, our gut bacteria play a core role in maintaining our health, although in ways that are not at all understood. The research is in its earliest days, but it’s possible that an unhealthy microbiome could contribute to obesity and other diseases, especially those caused by inflammation.

It’s all very speculative, but you can see where this is leading. While we’re just beginning to understand how our microbiome works and how it may prove essential to preventing all sorts of diseases, our governments are increasing the amounts of this anti-microbial herbicide Big Ag is allowed to leave on our food.

This is all happening at a time when we have almost no data on how much we’re exposed to this chemical in the first place. One reason that glyphosate has continued to fly under the mainstream toxic chemical radar is that it’s actually very difficult to test for. There are only a handful of labs that can do it and it’s an expensive process. In fact, the USDA’s pesticide monitoring program only tests a single crop, soybeans, for glyphosate residue. This is true even though it’s used on a huge variety of crops, both directly on the plants, in the case of Roundup Ready, and indirectly, through spraying on fields before planting non-resistant crops.

So why would the EPA allow more of this stuff in our food? The agency didn’t decide to do this entirely on its own, of course. It did so because Monsanto asked.

Here’s the thing: As farmers adopted Monsanto’s genetically modified seeds in droves — the majority of corn, soy, and cotton grown worldwide includes the company’s Roundup Ready trait — there has been an explosion in the use of the pesticide for which the trait is designed: You guessed it, Roundup.

In the U.S. alone, it’s estimated that over 200 million pounds of the stuff are spread on fields and farms every year. That’s almost triple the amount used in 2001. (These numbers, by the way, are all estimates, since the USDA doesn’t precisely track glyphosate use because MONSANTO!)

There’s clearly more and more Roundup getting on our food. What else is Monsanto to do but get governments to bless this development? Both the E.U. and the U.S. have now complied. Stateside, the EPA has approved a significant increase on various grains, fruits, and vegetables, and upped the allowable limit on animal feed by a factor of 100.

Does that sound like a recipe for disaster to you? It probably should. It should also sound like yet another reason to buy organic food and either organic or pastured dairy and meat.

If it feels like Monsanto and its biotech brethren get to call the shots when it comes to toxic chemicals on our food, well, you’re right. On the other hand, the EPA is still accepting comments on these new glyphosate limits. Maybe if consumers make enough noise, the agency might reconsider.

While most of Washington, D.C., is consumed with the faux scandals du jour, in a few corners of Congress, actual work is getting done. A day 329 days late and a dollar $20 billion short, perhaps, the farm bill, an every-five-years legislative train[wreck], lumbers slowly forward.

Both the House and the Senate agriculture committees have just passed their own versions of the massive piece of legislation that controls U.S. agricultural policy as well as the federal nutrition program formerly known as food stamps (now called SNAP). A full House and Senate vote is the next step. Congress tried and failed to pass a farm bill last year. The question now is whether Congress can do it this time.

Actually, the question really is whether Congress will ever pass a farm bill again. For the first time, those close to the legislative process are starting to have their doubts. And that may be a really bad thing.

Bah, humbug, you say! The farm bill is larded with bipartisan subsidies for the largest-scale farmers who grow commodities like corn, soy, and cotton. It’s also the bill that authorizes the federal crop insurance program, which has grown like gangbusters over the last decade. Last year (thanks to the drought) farmers received over $17 billion in insurance payouts — almost all of which benefited large-scale commodity agriculture. A chicken pox on all their coops!

That not an unreasonable reaction. But also at stake in the farm bill are billions of dollars for conservation programs that help farmers mitigate the environmental effects of their work, and pay them to set aside marginal farmland as wildlife habitat. It also contains millions in federal funds that support organic farmers, help younger and “new” farmers get their start, and prop up local food efforts, organic research, and farmers markets.

Admittedly, both bills are, by the standards of sustainable agriculture, horrible. The Senate’s is the more “benign” of the two. It “only” cuts food stamps by $4 billion and conservation funding by $3.6 billion. It reduces farm subsidies by $16 billion, but increases crop insurance by $5 billion — a huge gift to corporate ag.

The House hews to the Senate blueprint overall, though it’s even friendlier to agribusiness, if that’s possible. But the House wants to cut a whopping $20 billion from food stamps — dropping from the program up to 2 million hungry Americans who are still suffering the effects of the Great Recession.

Ag Committee members will applaud themselves for also ending the controversial and wasteful subsidy program known as “direct payments” whereby farmers who grow certain commodity crops get cash regardless of how much they actually plant. But almost all the savings harvested from this program are plowed back into the expansion of crop insurance — including the introduction of an outrageous new “revenue insurance” program that would pay farmers in the event of small drops in prices. This would come at a time when crop prices and farm revenue are at all-time highs (more on the history of this proposed policy is here).

There are a few bright spots. Senate Ag Committee Chair Debbie Stabenow (D-Mich.) managed to include a provision in the Senate version that would link participation in the crop insurance program with adoption of conservation practices, and includes additional protections for disappearing native grasslands. The House version boosts funding for “new farmer” programs and a few local food initiatives.

But the bill, as envisioned by both houses of Congress, continues to be a virtual giveaway to the largest farmers while leaving crumbs to sustainable agriculture and small and medium-sized farmers. On many counts, it’s even worse than its 2008 predecessor.

So will it pass in the end? The answer is somewhere between “Reply hazy try again” and “Cannot predict now.” Both the House and Senate leadership have promised a vote by the end of June — so that’s something. But getting it through Congress will be a trick.

House Majority Leader John Boehner (R-Ohio) could use the same trick he used to avoid the “fiscal cliff” earlier this year: pass a harsher version of the bill through the Tea Party-controlled House with only Republican votes, and then turn around and pass a final compromise version — with lower cuts to food stamps — using mostly Democratic votes. But there’s reason to believe that the Tea Party wing may not stand for such a maneuver — and that the farm bill could die on the vine for the second time in a year.

It’s those food stamps cuts that threaten to doom the whole enchilada. The Senate passed a farm bill last year that included $4 billion in cuts and likely will again. But splitting the difference with the House version — say, adding another $8 billion in cuts to food stamps — is a non-starter in the Senate. Meanwhile, the Tea Party wing of the House killed the farm bill last year because food stamp cuts weren’t deep enough, so it is unlikely to support less than the $20 billion figure currently in the House version.

The death of such an abysmal farm bill would likely be greeted with cheers and confetti from some corners. After all, according to an analysis of federal data by the Environmental Working Group, 75 percent of crop subsidy payments go to the top 10 percent of farmers. A mere 10 percent of farmers also received just over half of the total crop insurance subsidies in 2011, including over two dozen farms that received $1 million each in insurance subsidies.

But Ferd Hoefner, policy director of the National Sustainable Agriculture Coalition, warns critics to be careful what they wish for. Reformers “would really be in big trouble” if the farm bill dies once and for all, Hoefner told me in an interview. While subsidies might still get tweaked here and there in a post-farm bill era, “the chance for investment in local food or farmers or organic or anything else will just go up in smoke.”

The reason is that the improvements to conservation policy and organic production and local food and farmers markets and so on have all been funded out of money pulled from the tens of billions of dollars spent on commodity crop subsidies. Without that “piggy bank,” as Hoefner called it, there’s no just no money for those programs, especially in the current era of federal budget sequestration.

If the farm bill fails, crop insurance would persist indefinitely without any further congressional involvement. The food stamps program does need minor adjustments every few years, but those can and have been handled outside of the farm bill. Every other component, however, would require new laws to be passed every few years. And as Hoefner observed, the parts of the farm bill most dear to sustainable agriculture advocates would be the parts least likely to survive as stand-alone bills.

Would the failure of the farm bill lead to a real shake-up in how the government makes farm and nutrition policy? Maybe. A crisis is also an opportunity and all that. But it’s also still a crisis. And very soon, farmers and eaters may find themselves in a big one.

Thirty years ago, scientists figured out how to directly modify the genes in our food crops. No more of that inefficient and slow breeding! Farmers would grab plant genes by the horns nucleotides and bend them to their will!

Now, the preeminent science journal Nature has devoted an entire issue to the question (to paraphrase that legendary IBM ad), where are the magic seeds? We were going to get seeds that would grow faster, yield more, save the environment, and be more nutritious. What we got were seeds for a few commodity crops such as corn, soy, and cotton that made their own pesticide or resisted herbicides, but otherwise provided little, if any, benefit to consumers.

Nonetheless, Nature assures us that the magic seeds are on the way. What the journal doesn’t say explicitly, however, is that there’s evidence that for existing GMO seeds, the best days are already over — and the next generation of seeds may be doomed even before they’re in the ground.

Of course, you’ll have to forgive the large biotechnology companies like Monsanto and Syngenta for thinking that they did in fact supply magic seeds. After all, as Nature observes, every year, farmers worldwide plant $15 billion worth of GMO seeds, covering about 420 million acres — an area larger than Texas and California combined — much of it on U.S. land. And those biotech companies earned tens of billions in profits off of them.

It’s an undeniably impressive feat. Just look at these charts of GMO adoption by farmers:

But popularity ≠ sustainability. What about charts that demonstrate GMOs’ vaunted yield increases and environmental benefits? Not to be found. That’s probably because, for all their marketplace success, it’s very difficult to measure exactly how much GMOs have increased crop productivity. One recent USDA study even found that yields for some GMOs were lower than for their conventional counterparts, though they did decrease the overall risk of crop failure.

In fact, if you look at charts of corn yields over time, what you see amid the volatility is a pretty consistent, modest trend that began in the 1930s with the introduction of conventionally bred hybrid seeds.

You can’t look at the chart and guess when GMO seeds were introduced (hint: 1996) by some huge increase in the yield curve. Certainly, it’s not the way you could glance at a graph of, say, the tuberculosis death rate in the 20th century and instantly identify the date antibiotics were introduced.

The commercialization of GMO seeds starting in 1996 didn’t lead to any agricultural great leap forward. It’s a far cry from what biotech advocates declare: that we need GMOs in order to feed a growing world population or face mass starvation.

As for environmental benefits, Nature was unable to cite any independent assessment. One article [sub req'd] quotes a single industry-funded study which determined that between 1996 and 2011, GMOs drove a 6 percent drop in pesticide on cotton crops, while overall the technology offered about a 9 percent improvement to the “environmental impact quotient” — a measure that takes into account impacts on wildlife and so on.

And the price for this very modest “progress”? We’ve handed over the seed industry — and in a meaningful sense, the agricultural system — to a handful of large companies. In 2010, 85 percent of all corn and 92 percent of soy planted in the U.S. contained Monsanto’s patented genetically modified traits. It doesn’t quite seem worth it.

But even that modest formulation of GMOs’ benefit may be overstating the case. As author Sam Fromartz put it in an essay on the Atlantic, GMOs have actually accelerated agriculture’s decline into unsustainability because:

… we’ve used them bring down the cost of industrial meat production and incentivize a transition to a meat-centric diet. The loss of calories that result from feeding grains to animals instead of humans represents the annual calorie needs of more than 3.5 billion people, according to the UN Environmental Program. In short, GMOs arguably are making matters worse by fueling the production of more animal feed and food-competing biofuels.

And, yes, agrees Nature, they’ve also driven the rise of superweeds that are immune to the effects of common herbicides central to GMO agriculture. It’s this now-established fact that threatens GMOs’ meager benefits. While farmers enjoyed a 15-year window of reduced pesticide use thanks to seeds that make their own or resisted the effects of others, superweeds and superbugs are now causing farmers to increase pesticide use.

In an op-ed in Food Safety News, agricultural scientist Charles Benbrook makes this very point, often overlooked by writers who cover the subject. He notes that compared to the early years of GMOs, farmers now must use twice as much herbicide, and seeds that emit multiple pesticides, to get the same amount of growth as GMOs used to achieve.

Benbrook observes that the growing pest and weed problems for GMOs have caused farmers to turn to seeds that are coated with a different pesticide — a neonicotinoid. If that name rings a bell, it’s because these pesticides that have been implicated in the increasing epidemic of bee deaths. He also reveals something that I have not previously heard — that there has recently been what he calls a “historically unprecedented” 10-fold increase in fungicide use on U.S. crop acres, most of which are planted with GMO corn and soy. So much for those GMO environmental benefits.

And that’s aside from the evidence that biotech’s “next big thing” — seeds that emit multiple pesticides — may be doomed to fail. An international team of researchers, including USDA and biotech scientists, found what they termed “cross-resistance” to these pesticides in bugs exposed to the next-generation GMO seeds. Evidence, in other words, that GMO seeds are hitting a bug-covered wall.

But never mind all that! Nature wants to assure us that we need to remain committed to genetically modified food because the long-promised “jetpack era” — the one we’ve supposedly all been waiting for — is almost upon us. It’s a familiar refrain: Don’t mind the paltry benefits so far; the genetically modified best is yet to come! If only the public is willing to eat it, that is.

And it’s the public that Nature identifies as a big part of the problem, as those pesky humans constantly throw up roadblocks to the latest engineered foods. (Witness yet another state referendum on GMO labeling, this time in Washington state.) Consumers, with what the Nature editors declare are their “fears of the unfamiliar,” truly loom as the bad-guy in this debate.

Nature’s exploration of GMOs, which, given the journal’s — heh — “nature,” understandably restricts its focus to the science, ends up misinterpreting pubic distrust in GMOs. You can’t understand the GMO debate without factoring in the political and corporate system in which it takes place. It’s like considering the causes of obesity without addressing the role of food marketing — obesity is not just about people on their own making bad choices.

GMOs didn’t come to dominate our agricultural system simply because they’re awesome, and they’re not struggling for acceptance because the public is fearful and/or misinformed. Corporations made billions on GMOs and all we got was ethanol and an unsustainable diet. Is it so surprising that we’re skeptical that the next time around will be any different?

OK, meat eaters, do you want the good news or the bad news first? Hey, I know! I’ll start with the bad news: In a just-released study, Consumer Reports tested 257 samples of ground turkey from supermarkets, and found that virtually every one was contaminated with either fecal bacteria, staph, or salmonella. Even worse, most of the fecal bacteria were resistant to one or more antibiotics important to human medicine.

Clearly, between this study and the Environmental Working Group’s recent report on the high rates of fecal (and antibiotic-resistant) bacteria, it’s fair to conclude that the meat industry is struggling to keep its product safe.

The bit of good news here is that Consumer Reports tested both meat raised with antibiotics and meat raised without them. While meat raised without antibiotics had about the same rates of overall contamination as the industrial alternative, it had far lower levels of antibiotic-resistant strains — and it’s the antibiotic-resistant bugs that should scare you. Infection with them puts you at far greater risk of serious illness or even death if you’re an infant, elderly, or immune-compromised.

The message to consumers is simple: Buying meat raised without antibiotics will reduce your exposure to the nastiest bacteria. Which is a good thing.

There’s a message here for the meat industry, too: Restricting agricultural use of antibiotics would have a big effect on meat safety. Of course, any Danish pig farmer would tell you the same thing. But here at home neither Big Meat nor the government agencies that police it are ready to face that reality.

The U.S. Department of Agriculture certainly understands that regulations surrounding meat safety need reform. In fact, the agency is moving forward with a proposed new regulation for poultry inspections that the administrator of its food safety division declared last year would “further the agency’s transformation to focus solely on public health and help address the challenge we have to reduce foodborne illness.”

Sadly, it would take generous definitions of most of the nouns and verbs in that sentence for it to be accurate. The new USDA regs would actually reduce the number of government inspectors, shifting responsibility for visual inspections to slaughterhouse company employees, while increasing the speed at which the chickens move along the processing line and increasing the number and frequency of chemical disinfecting washes used on the carcasses. Sigh.

It may come as a surprise to learn that virtually all of the chicken you buy at the supermarket has been chemically disinfected, most frequently with chlorine but also with other, more toxic chemicals. It’s no sure fix, of course, since pathogens can hide in nooks and crannies that the sprays, which focus on surface contamination, can’t reach. It also does nothing to address the root causes of how the bacteria got onto the meat in the first place.

The USDA claims [PDF] that its new system is a more science-based approach that relies less on inspectors’ eyes and more on risk assessments of where the pathogens are and how to kill them. That claim is, of course, the subject of some dispute. Food and Water Watch uncovered documents that suggest that slaughterhouses that tried out the new regs actually had higher rates of salmonella contamination than those using the old system.

Nonetheless, the USDA estimates the new system will prevent up to 5,000 cases of foodborne illness annually — all this, while also saving taxpayers $90 million per year and lowering industry costs by just over $250 million per year. But it sure seems like the benefits are flowing the wrong way — that is, more toward industry than consumers (as in more chickens processed per hour and more profit).

One industry-associated food safety expert I spoke to, Michael Doyle of the University of Georgia’s Center for Food Safety, said the industry has relied on chemical washes without necessarily using them appropriately, and that these new regs will help address that shortcoming. That may be. But appropriate use for carcasses may not equal appropriate use for the slaughterhouse workers who, along with the chickens, will be exposed to them.

The Washington Post ran an exposé last week on the increasing health problems those workers are suffering as a result of increased chemical exposure. The article features former USDA inspectors critical of the new meat safety rules, both because the line speeds are now too fast for inspectors to see problems and because of the reliance on chemicals.

And these former inspectors aren’t alone. Lawyer Bill Marler, who represents victims of serious foodborne illnesses and their families, agrees that it’s a misguided approach. “The whole system is flawed,” he told me in an email. As he sees it, the problem isn’t in the particulars of the rules themselves. The problem is that the USDA sets allowable levels for the presence of dangerous bacteria like salmonella or campylobacter on meat. Marler believes that the level should be zero.

“Impossible,” you say. “Bacteria are everywhere!” Well, almost 20 years ago, the USDA set a zero-tolerance policy for the deadly form of E. coli (O157:H7 for those keeping score at home) that caused the fatal Jack in the Box outbreak in 1993. And while that strain still causes problems, especially in produce, we don’t see it as frequently in meat — with one notable 2009 exception — because companies were forced to eliminate it from their facilities. They didn’t like it, they complained about cost, but they mostly succeeded.

Many consumer advocates, including Consumer Reports and the Center for Science in the Public Interest, believe that until the USDA does the same with the newer, deadlier, antibiotic-resistant strains of salmonella and other deadly bacteria, no amount of chemical washing will solve the problems with our meat. The USDA has plenty of compelling evidence that attacking the problems at the source — that is, reducing the amount of antibiotics used in meat production — could drastically lower the most dangerous forms of bacterial contamination. But the USDA is too hemmed in by industry to make those changes.

And that’s where you, the consumers, come in. Your role goes beyond practicing good food safety at home and using helpful resources, like the Center for Science in the Public Interest’s new “Risky Meat Guide,” to avoid meat with the highest rates of bacterial contamination.

One of the great food-system success stories in recent years involves the dairy industry’s reluctant abandonment of artificial growth hormones in the face of a virtual revolt by (mostly) mothers of small children. If meat eaters demand meat raised without antibiotics — it’s not significantly more expensive to buy, as it doesn’t have to be organic — the industry will be forced to respond. Producers will have to change the ways they raise animals, which will have the added benefit of lessening the need for repeated chemical disinfection at the slaughterhouse.

That’s better for the animals, for workers, and for consumers — even vegetarians, since antibiotic-resistant bacteria aren’t just on meat anymore.

So, meat eaters. What are you waiting for?

Officials in Texas continue to investigate the cause of the explosion last week at West Fertilizer that killed 15 people and injured 200. The explosion, which could be felt up to 50 miles away, obliterated the facility and destroyed houses. It was fueled by a massive stockpile of nitrogen fertilizer — up to 270 tons of ammonium nitrate, a solid fertilizer that comes in the form of a powder or pellets, and over 50,000 gallons of anhydrous ammonia gas.

But while the explosion last week was spectacular and tragic, the lives lost there and the pain the community of West, Texas, is suffering offer a window into a much larger battle concerning the overuse of nitrogen fertilizers on American farmland.

In 1909, when German chemist Fritz Haber demonstrated a process that synthesized ammonia, the main component in what was to be known as synthetic nitrogen fertilizer, it was considered a miracle. He pulled the stuff from the air, no less! He and another German scientist, Carl Bosch, who figured out how to produce ammonia at an industrial scale, won the Nobel Prize in chemistry.

In the century since, synthetic nitrogen fertilizer has displaced the traditional techniques farmers used to increase soil fertility like cover cropping and livestock manure. (Tom Philpott at Mother Jones has an in-depth look at the history of nitrogen fertilizer’s development and use.) Today, U.S. farmers apply over 11 million tons of nitrogen fertilizers to farm fields every year, mostly in the form of ammonium nitrate. The widespread use of the substance is considered part of the so-called Green Revolution, which radically increased the amount food we could grow.

The problem is that a lot of that fertilizer is wasted — more is applied than plants can absorb — and it washes out of the soil into waterways, or evaporates into the atmosphere in the form of nitrous oxide, a potent greenhouse gas. Grist ran a series on the subject in 2010 with the prescient title “Is America fertilizing disaster?”

While the series did not address the risks of explosion associated with storing nitrogen fertilizer, it did describe the main environmental and health risks. They include threats to climate, to human health through nitrate pollution in drinking water, to fish and other wildlife through fertilizer run-off causing low-oxygen “dead zones” throughout the U.S and the world, and to soil health and thus long-term agricultural productivity.

Since we published that series, the data continue to come in regarding the harm excess nitrogen fertilizer can cause. It’s poisoning the water supply of whole communities in California’s Central Valley — enough so that the state is in the early stages of more strictly regulating its agricultural use.

Nitrogen fertilizer’s precise climate impact — which back in 2010 remained unclear — has also come into focus. Nitrous oxide in the atmosphere has risen by 20 percent since the Industrial Revolution, with a good part of that increase coming in the last 50 years. Researchers recently determined that the steep increase in nitrous oxide since the 1960s is almost entirely due to the use of nitrogen fertilizer. Atmospheric carbon dioxide rates have increased around 40 percent in the same period, but nitrous oxide is around 300 times more potent as a greenhouse gas. And it’s also a major ozone-depleting chemical.

This is especially tragic when you look at this Mother Jones chart and realize that nearly half of the nitrogen fertilizer used in the U.S. goes specifically to growing corn:

What this chart should tell you is that if we grow less corn, we’ll use less nitrogen fertilizer. The benefits of that would be significant — and not just to those who live within a stone’s throw of a fertilizer storage or production facility.

I’ve written at length about agribusiness’s reliance on corn, along with the government policies that continue to prop up production. Weaning farmers off corn won’t be easy, since the entire U.S. agricultural system seems designed to support it. It’s not that there aren’t alternatives that can work within our industrialized system. But we need farmers and politicians to accept that too much corn and too much fertilizer is a bad thing. And right now, as they say on MTV, too much is never enough.

At the moment, Mother Nature seems to be doing a fine job of encouraging farmers to plant less corn: In the wake of last year’s crop-killing drought, heavy rains and flooding in the Midwest have delayed planting and threaten the early corn crop. But bad weather and an unstable climate are only going to make the problem worse in the long term. We instead need farmers, government officials, and regulators to step up and admit we have a massive problem with nitrogen fertilizer pollution — and then take the next difficult step and do something about it.

And therein lies another lesson we can draw from the tragedy in Texas. West Fertilizer had evaded regulatory scrutiny for years — as one member of the House Homeland Security Committee put it, the company was operating “willfully off the grid.” This is a problem when you’re dealing with a substance that, when part of an explosive device, is classed as a WMD. The line between a true accident and negligence can be hard to discern, but when a company operates in a legal grey zone for decades and then has a horrible accident, it’s not unreasonable to expect negligence was involved.

Should investigators find evidence of negligence in West, Texas, one hopes the perpetrators will be brought to justice. But it would be a better legacy of the disaster — though admittedly, an unlikely one — that what one analyst called a “massive failure of the regulatory state” could in turn bring greater scrutiny not only to how nitrogen fertilizer is stored, but how it’s actually used.

Take a deep breath, carnivores: 87 percent of supermarket meat — including beef, pork, chicken, and turkey products — tests positive for normal and antibiotic-resistant forms of Enterococcus bacteria. Fifty percent of ground turkey contains resistant E. coli, 10 percent of chicken parts and ground turkey tests positive for resistant salmonella, and 26 percent of chicken parts come contaminated with resistant campylobacter. Resistant or not, the mere presence of these types of microbes means the majority of our meat comes into contact with fecal matter at some point. Not very appetizing, is it?

The government recently admitted something a lot of conscious eaters probably already suspect: A significant majority of supermarket meat is contaminated with antibiotic-resistant bacteria. But it did so vewwy, vewwy quietly. It came buried in the FDA’s 2011 Retail Meat Report, which reveals the results from periodic testing of common supermarket meat products for bacterial contamination and bacterial resistance to multiple antibiotics. The FDA leaves these numbers opaque, but thanks to calculations by the Environmental Working Group (EWG) using the government’s data, we know just how terrifying these results are.

The threat of these superbugs goes beyond the academic. Three of the bugs listed above cause tens of thousands of illnesses and hundreds of deaths a year. Resistant salmonella-tainted meat recently caused several outbreaks, one of them quite deadly. And E. coli from supermarket chicken has been linked to millions of antibiotic-resistant urinary tract infections in women.

For dedicated Grist readers, this shouldn’t be a total surprise. We’ve been reporting that researchers have been tracking antibiotic-resistant bacteria on meat for several years. But the fact that most forms of superbugs seem to be on the increase is no less disturbing.

The reasons why aren’t a mystery to most scientists. While overuse of antibiotics in human medicine plays a role, the preponderance of evidence suggests that the rampant overuse of antibiotics in livestock drives resistant microbe strains off the farm and into communities.

Medical researchers are all but begging livestock producers to scale back on the heaps of antibiotics fed to food animals every year — sound advice since 80 percent of all antibiotics consumed in the U.S. go to food animals — but the industry contends that such a reduction would be impossible. That’s true in a way: Most livestock would not be able to survive the cramped, stressful, disease-ridden conditions in which they are raised without a constant low-level dosing of antibiotics. As an additional boon, these antibiotics seem not only to prevent disease but also to increase animal size and weight for reasons that are not well understood (although scientists are suggesting it has something to do with screwing up animals’ microbiomes).

Of course, large-scale agriculture has shown the ability to severely restrict antibiotic use in livestock without courting disaster — in Denmark. Back in 1994, that country, one of the largest exporters of pork in the world [PDF], embarked on the so-called “Danish experiment” that prohibited farmers from feeding healthy pigs low doses of antibiotics. Even though farmers were still allowed to treat sick animals with antibiotics, usage since that time has dropped by about 40 percent. Meanwhile, pork production continued to increase.

Agribusiness was so threatened by the Danes’ positive results (which included a general reduction in the prevalence of resistant bacteria on and off farms), that Sen. Chuck Grassley (R) of pork-rich Iowa took to the Senate floor to [erroneously] denounce their methods. The reason for agribusiness aggression? Denmark did have to make changes to the way its farmers raised hogs — something U.S. agribusiness has not been willing to attempt (with perhaps one notable exception).

Meanwhile, the FDA, which gets low marks in this area from government watchdog agencies, remains a willing conspirator in this indiscriminate overuse of antibiotics. It recently ended efforts to regulate their use, preferring to rely on an ineffective, “voluntary” approach. Since companies don’t have to report — and the FDA doesn’t have to track — the exact amounts and types of antibiotics fed to animals, it’s easy enough to deny culpability.

Rep. Louise Slaughter (D-N.Y.), Congress’ sole microbiologist, has repeatedly introduced a bill to restrict agricultural use of antibiotics, but it never gets very far. Rep. Henry Waxman (D-Calif.) has joined her in proposing a reporting requirement for antibiotics in food animals, but that bill hasn’t gotten much further.

For now, it’s up to consumers to protect themselves from superbugs as best they can. As EWG concludes, they must “assume that all meat is contaminated with disease-causing bacteria.” EWG recommends avoiding factory-farmed (i.e. supermarket) meat and instead choosing meat from small producers or labeled as antibiotic-free. There’s no guarantee that local or organic meat will be free from superbugs, but it tilts the odds in your favor. EWG also offers a downloadable guide to avoiding superbugs in meat. Aside from that, practicing food safety in the home becomes more important than ever. Until the FDA or industry gets its act together, we’re on our own.

We all know what Bad Fast Food looks like (I’m looking at you, KFC Double Down!) And we all know that tens of millions of Americans eat the stuff anyway — whether out of choice or necessity. So can there be such a thing as “Good Fast Food”? There had better be — or else the fast food biz is in real trouble.

Here’s food writer Mark Bittman, writing in the latest issue of the New York Times Magazine:

Soda consumption is down; meat consumption is down; sales of organic foods are up; more people are expressing concern about G.M.O.s, additives, pesticides and animal welfare. The lines out the door — first at Chipotle and now at Maoz, Chop’t, Tender Greens and Veggie Grill — don’t lie. According to a report in Advertising Age, McDonald’s no longer ranks in the top 10 favorite restaurants of Millennials, a group that comprises as many as 80 million people.

Fast food companies understand that Bad Fast Food might be approaching its expiration date. Rather than clinging ever tighter to their fattening products like Coca Cola did, they’re remixing them. Some of it is just window dressing: Bittman offers the example of McDonald’s heavily sweetened yogurt parfait, which just replaces fat with sugar. Other outfits toss a few salads at customers, or push healthier items off to the side as if embarrassed by their existence. After all, having healthier options means admitting your main offerings aren’t, well, healthy.

But Taco Bell just announced a new effort to remake its menu along healthier lines. And Chipotle, which has been called the Apple of fast food, is nipping at the big dogs’ heels. The company bills itself as serving “food with integrity,” cares about animal welfare and to some extent the plight of farmworkers, and yet has $3 billion in annual sales with double-digit annual growth. Other fresh competitors are popping up like superweeds.

But it’s not just consumers’ changing tastes that are giving fast food companies indigestion. It’s the outside shocks to the fast food system — which Bittman doesn’t address — that will create the real opportunity for alternatives. The industry has a lot to swallow if it’s going to continue its domination of the food landscape (and make no mistake — it dominates).

First there’s climate change. The ongoing drought is hitting beef producers hard, and this raises the prospect of the end of an era of cheap meat. Maybe not today, maybe not tomorrow, but soon. After all, the current drought may end, but climate scientists project that the Southwest — Texas is the top beef-producing state in the country — will enter permanent drought in a matter of decades. And if meat prices spike, even McDonald’s might decide the time is right for alternative ingredients.

Meanwhile, more trouble for fast food is brewing among its workers. Workers in New York City recently staged a walkout over low wages, organized by the new group Fast Food Forward, which is trying to improve food workers’ lot generally. The prospect of more expensive labor is even more of a threat to fast food companies’ bottom lines than more expensive meat. President Obama’s healthcare reform law will also force change — and not just because menu-labeling at chain restaurants snuck into the law. The law also put in place new healthcare requirements for employers and fast food operators who have traditionally skimped on benefits.

It’s also possible that new upstarts will pull a Chipotle and start stealing a chunk of business from the current fast food titans. Bittman examined promising and popular vegan/vegetarian fast food chains like Veggie Grill, Native Foods Café, and Lyfe as possible models. But as popular as these mini-chains may be, a bit of perspective is helpful. Veggie Grill has 18 locations, about 0.001 percent of McDonald’s nationwide empire. The glass-half-full crowd might say there’s plenty of room for growth. The glass-half-empty crowd might wonder if these healthier alternatives will forever exist in the shadow of giants like McDonald’s and Burger King.

Partly it’s because not one of these upstarts is truly able to compete on price with McDonald’s, certainly not with its [in]famous “Dollar Menu.” That said, it’s a mistake to focus too much on the cheapest end of the fast food menu. In an article a couple of years ago, Bittman himself calculated that “a typical order for a family of four — for example, two Big Macs, a cheeseburger, six chicken McNuggets, two medium and two small fries, and two medium and two small sodas — costs, at the McDonald’s a hundred steps from where I write, about $28.” That’s not cheap!

It’s also a mistake to think that fast food consumers are the most price-conscious. There has been a broad misconception that the main consumers of Bad Fast Food are those at the bottom of the income ladder. But a 2011 study blew that assumption away. As The Atlantic reported at the time, it turns out that “a household earning $60,000 a year eats the most fast food, and one bringing in $80,000 is actually more likely to have it their way than one with $30,000.”

The popularity of the big chains isn’t entirely about price, after all. Remember that billions have been spent perfecting Bad Fast Food so that its combinations of salt, fat, and sugar reach the “bliss point.” And just as important, Bad Fast Food is really, really fast.

In the end, if there’s real potential in this idea of Good Fast Food, I agree with Bittman that it’s not going to be explicitly vegan or vegetarian (for which there is unquestionably a market — just not a McDonald’s-scale one). Rather, for better or for worse, we’ll see familiar menus with alternative ingredients. Bittman makes a nod toward this with his healthy “burger,” “fries,” and “shake” recipes in the article. Veggie Grill already features soy-based “chikin” — although conventionally grown soy as a meat alternative has real problems.

Fast food is no doubt headed for some kind of slow-motion transformation. What, exactly, will end up on those newfangled, Less-Bad (we hope) menus is hard to say. There’s only one thing I’m sure of. It won’t be any of these.

A little over two years ago, Congress passed and President Obama signed a historic reform to America’s food safety laws, the Food Safety and Modernization Act. It was the first major update in over 80 years to the laws that aim to keep our food from killing us.

The new law gave the feds broad new enforcement powers to do things that most Americans probably thought they could do already — issuing mandatory food recalls, for example, and requiring frequent inspections of the riskiest food production facilities, and prosecuting executives of companies that knowingly ship contaminated food. Good news!

And now for the bad news. It looks like several of those new protections were quietly gutted earlier this year by a White House office charged with reviewing new regulations for their impact on corporate America. During a drawn-out review period, the White House Office of Management and Budget (OMB) rewrote rules drafted by the Food and Drug Administration (FDA) that spelled out how the agency would implement new safety protocols for food producers.

When Congress passed the food safety law, it for the first time required food producers to design, implement, and test risk-based food safety plans. The law required testing for contamination in food processing facilities, and then testing the foods themselves. The OMB revisions axed the mandate for verified food safety plans and dropped virtually all the testing requirements, turning them into voluntary protocols. (And we know how well it works out when the food industry regulates itself.)

Without requirements for testing and verification of safety plans, the FDA will remain powerless to stop things like the deadly 2011 listeria outbreak in cantaloupe caused by shockingly unsanitary storage conditions at a Colorado farm. Had that farm been forced by law to produce a safety plan and then to have that plan verified, much less to have its produce tested, the people who died would likely be alive today.

Thanks, OMB.

I asked food safety superlawyer Bill Marler (managing partner of the Seattle law firm Marler Clark and a key player in the lawsuit against Jack in the Box over E. coli poisoning in its hamburgers that killed four children in 1993) for his take on all this. He pointed out that the food industry by and large supported the testing requirements because they leveled the playing field between good corporate citizens that took food safety seriously and bad guys, like the Peanut Corporation of America, that did not. Then along comes OMB “opening up a loophole for people to ignore” the new law, Marler said.

Alarm over these changes isn’t restricted to food safety crusaders. I reached out to Michael Doyle, director of the Center for Food Safety at the University of Georgia, a microbiologist and food safety expert closely associated with industry who has in the past been skeptical of onerous testing requirements — and who was also once in the running to run the U.S. Department of Agriculture’s food safety division. I asked him for his take on the OMB changes and he responded via email with what I can only characterize as dismay:

I do not believe OMB has the expertise to understand the potential adverse public health consequences of its actions, nor does the agency understand the importance of verification testing to a food safety plan and its relevance to enhancing the safety of food.

Or as it’s often said on the internet: “The stupid! It burns!”

Food-safety advocates had expressed relief back in January when OMB finally released these rules. The White House had been accused of delaying the law for months by refusing to publish the new rules. Some speculated it was out of fear that the rules would meet election-year repercussions from the politically powerful food and agriculture industry. This tiptoeing around corporations had become a hallmark of the post-2010 Obama White House.

The revelation about the OMB’s changes to the law comes from an unlikely source — the federal government. As originally reported by industry publication Food and Chemical News [sub req’d] and expanded upon by Food Safety News, some good soul in the Department of Health and Human Services (the parent agency of the FDA) posted documents on a government website that detailed the exact revisions OMB made to the food safety regulations. Ownership of these kinds of cuts are typically a well-guarded secret.

We already knew that Republicans in Congress were unlikely to give FDA the money to fully implement the law — and the sequester is likely to delay the law further. But there is still time to fix OMB’s changes. The comment period on the new food safety rules runs until mid-May.

If you can stomach the bureaucratese, you, too, can leave a comment for the FDA about the changes to the rule here. Believe it or not, the agency reviews every one of them. It may be the best chance you have to ensure that the Food Safety and Modernization Act actually lives up to its name.

The top execs at Monsanto Corp. must be running around HQ these days like director James Cameron post-Titanic, screaming “We’re king of the world!” It’s an understandable reaction. Between a likely Supreme Court win, the recently passed Monsanto Protection Act, and the company’s victory over a government antitrust investigation, the company has been on quite a winning streak.

Odd, then, to remember that less than three years ago, CNBC’s stock market “analyst” Jim Cramer declared that Monsanto’s was “the worst stock of 2010.” This came just before Forbes magazine all but withdrew its 2010 accolade that Monsanto was “company of the year.”

Monsanto had all the hallmarks of a troubled company. Its net income dropped nearly by half in 2010. By October, its stock dropped by almost that much. But those were just the most obvious indicators.

While it’s true that, even at the time, the company dominated the seed industry — 85 percent of all corn planted in the U.S. that year contained Monsanto’s patented genetically modified traits, as did 92 percent of soy — its products were taking a beating both in the fields and in the mainstream press. Word spread of the rise of superweeds that were immune to Monsanto’s pesticides, while farmers complained that Monsanto’s new SmartStax seeds were overpriced and no more effective than the old. At the same time, its flagship Roundup Ready product was about to go “off-patent,” and analysts were expecting a flood of “generic” (and much cheaper) pesticide-resistant seeds on the market.

As if that weren’t enough, Monsanto was locked in a multi-year legal battle with one of its top competitors — DuPont. It was a battle that some analysts thought could topple Monsanto from its perch atop the biotech seed pyramid. Anti-Monsanto activists even looked at DuPont as a potential ally, since it had filed an antitrust lawsuit against its sworn enemy as part of the fight. Then the government got into the act when it initiated its own antitrust investigation that threatened Monsanto’s core business. Oh, how the mighty had fallen!

Fast forward to today. Monsanto Ascendant. Here’s a stock chart that runs from Oct. 8, 2010, to today.

Had you bought Monsanto stock the day you read about Monsanto’s troubles, you would have more than doubled your money — and tripled the return of the S&P 500 in the same period.

Wha hoppen?!

Well, the antitrust investigation disappeared in a puff of bureaucratic smoke — mostly because there’s nothing illegal about massive consolidation and control of an industry if the government can’t find compelling evidence that consumers were harmed. (For those that are interested in going deep into the antitrust superweeds, I explained how this came to be in a recent post.) Ergo, Monsanto isn’t about to be dismantled by the feds.

Meanwhile, the company’s sales recovered impressively. Its 2012 earnings statement shows that its net income doubled since 2010 and now exceeds $2 billion. Sales were driven by record high corn plantings in 2012 — thanks to sky-high demand from both corn ethanol and livestock feed. Never mind that the drought destroyed a good chunk of that year’s crop — no refunds!! (It’s worth noting that Monsanto claimed its seeds outperformed the average yield during the drought year. And with news that farmers will plant even more corn this year — the most since 1936 — Monsanto’s sales will continue to grow.)

As for the other threats to Monsanto’s business, according to this article from Harvest Public Media, it looks like Monsanto has successfully engineered its seeds so that the whole generic biotech seed market will wither and die before it’s fully flowered. This is helped in some part by a Monsanto-related patent case that’s currently before the U.S. Supreme Court. The Justices seem to be favoring the company over the farmer accused of violating the company’s patents by “illegally” saving seeds.

For its part, the U.S. Department of Agriculture seems happy to do Monsanto’s bidding. From giving approval to its GMO alfalfa seed — despite the fact that many organic farming advocates complained that it could put them out of business — to allowing farmers to plant Monsanto’s GMO sugar beets in violation of a court order, the agency seems to agree that what’s good for Monsanto is good for American farmers.

Then there’s the so-called “Monsanto Protection Act,” snuck into the recent federal government’s funding bill, that allows the USDA to override any judge who tells Monsanto it’s not allowed to spread its genetically modified seeds around. It may not have given the company protections that it doesn’t already enjoy from a compliant USDA — and Politico reports that Secretary of Agriculture Tom Vilsack thinks the provision might be unenforceable — but it certainly demonstrates the company’s continued power on Capitol Hill.

Surely if the regulatory and legal processes have failed, a little competition will keep this monster in check, right? What about that titanic struggle between the two biotech giants, Monsanto and DuPont? The one that could knock Monsanto off its perch? Yeah, well, the two companies just kissed and made up. Not only did they drop all the lawsuits, counter-suits, and patent claims, but they also entered into a broad licensing agreement that will allow Monsanto to use DuPont’s genetic modifications in its seeds and vice versa. One of the last stumbling blocks Monsanto faced is now gone.

The upshot is that its genetically modified seeds will gain the ability to withstand repeated exposure to a broader range of herbicides, increasing agricultural chemical use and encouraging farmers to continue planting vast acreages of corn.

Of course, Monsanto’s success is also predicated on a high price of corn — since that justifies the higher cost of the seed and the higher cost of using additional herbicides to combat superweeds. But if this year’s corn harvest comes in as a bumper crop, corn prices are likely to drop, possibly precipitously — there are even early indications that the boom may be ending and prices are returning to earth.

If the recent price drop continues, we’ll soon see if Monsanto’s resurgence is a permanent boom or just an extreme-climate-driven bump. Groups like Food Democracy Now! are hoping for the latter, and are currently pushing back at Monsanto’s powers with demonstrations and petitions. Whatever happens, the company has demonstrated an Energizer Bunny-like resilience. That may make investors happy. But it should make anyone interested in a sustainable agricultural system very, very sad.

Merrigan is best known for her local foods initiative called Know Your Farmer, Know Your Food, which brought all of the agency’s efforts to improve regional and local food systems under one conceptual roof. It was a modest program in terms of budget — its funding was measured in mere millions while agribusiness reaped tens of billions in subsidies — but it was the first effort of its kind at an agency long known for its support of large commodity growers. (And small as it was, it was revolutionary enough to draw the ire of Republicans.)

Merrigan is also credited with preserving strong standards for the Organic label, championing a national farm-to-school program, funding hoop houses to allow farmers to grow later into the season, and acting as a key player in the effort to improve the foods sold in school vending machines. Jerry Hagstrom has a good wrap-up in National Journal.

But it wasn’t just about her favored policies. Merrigan also provided political cover to her boss, Secretary of Agriculture Tom Vilsack. She was a counterweight to the administration’s more industry-friendly moves, especially regarding support for biotech seeds. Decisions like Vilsack’s fast-tracking of approval of so-called Agent Orange corn and USDA’s willingness to ignore a court order and allow farmers to keep growing GMO sugar beets infuriated sustainable-agriculture types. But Merrigan’s presence near the top of USDA’s chain of command convinced them that the agency wasn’t totally in the tank to Big Ag.

Merrigan is the latest of a long line of administration officials to depart as Obama begins his second term, and she’s said that the change has been in the works for some time. But given the abruptness of her departure and the brevity of her resignation announcement, some observers, such as Tom Philpott at Mother Jones, are concerned that she’s being forced out by those who oppose her efforts to reorient the USDA, in however small a way, toward more support for local and regional food. Hagstrom even speculates that Vilsack himself may have engineered her departure because “he was jealous of her public profile.”

Merrigan herself made clear that her departure was not “for personal reasons.” She made a strong statement to USDA staff that she disagrees with those who say that women can’t hold top positions in government, a sensitive topic in the Obama administration.

Regardless of Merrigan’s reasons for leaving, there’s no question that Vilsack supports the policies she championed and a more sustainable agriculture in general. And Merrigan insists that she has institutionalized an interest in local and organic farming within USDA. But hers will be big shoes to fill. Merrigan was not just the government’s highest-ranking sustainable-agriculture advocate, but also perhaps the only such person with the bureaucratic expertise to run the day-to-day operations of the enormous $150 billion-a-year, 100,000-employee agency.

Before joining the USDA, Merrigan was a top aide to Sen. Patrick Leahy (D-Vt.) who was then chair of the Senate Agriculture Committee. There, she helped write the original law that created the USDA Organic program. A few years later, she was brought in by President Bill Clinton to run the USDA’s Agricultural Marketing Service just as it was beginning to implement the organic law — and she’s credited with saving it from regulatory irrelevance.

There are certainly many people at the state level and even within USDA who could serve in her current position, but there is no one else out there who has the breadth of expertise and experience in sustainable ag and in USDA administrative wonkery wrapped up in one hard-nosed, efficient package. The closest such person I can think of currently at USDA is Miles McEvoy, who runs the National Organic Program, but it’s difficult to imagine that he’s seriously in the running to replace Merrigan.

One is left hoping that Merrigan is right — that there’s enough institutional momentum behind her work that it continues in her absence. But institutions like USDA are far more often driven by inertia from the status quo — and at the USDA, the status quo ain’t exactly local and organically grown. Kathleen Merrigan will be sorely missed.