Thursday, September 13, 2012

About that paper on organic food...

A good biology paper will make you think about life; a few of them make you think about your own life.  A research paper came out this week that made a bit of a splash, and prompted a lot of people—a lot of non-scientists, who may not be used to thinking scientifically—about what they are doing and why.  The paper was a meta-review: essentially, an attempt to compare lots of different studies, with different methodologies, different foci, and different motivations, and reach a coherent conclusion.  The question that the authors were trying to answer is in the title of their paper: “Are Organic Foods Safer or Healthier Than Conventional Alternatives?”

The answer is very, very close to “no,” followed by some asterisks.  Some of the asterisks are whether the government approved levels of pesticides are actually safe, and that while the levels of bacterial contamination were comparable, the contaminants in conventional foods were more likely to be antibiotic resistant.  But on the whole, no difference. 

Looking at NPR and the NY Times blogs and their commenters, a few have their faith shaken by facts, but most have their faith reinforced by being liberated from facts.  They turn to attacks on the paper and its authors.  There’s also a fair amount of triumphal crowing from folks who (like my dad, a biochemist) refuse to buy organic on principle. 

So, as a person who tends to buy organic and pay attention to science, what do I think?  I think I’m going to have a heart attack and die of not surprise.  Whether produce is good and good for you or not—as long as it falls within guidelines for pesticides and other contaminants—is a matter of whether the farmer was competent and the food has gotten from farm to you in a timely and careful fashion.  So, why do I tend organic?

I’ll set aside human reasons, although conventional ag inevitably causes worker exposure to nasty chemicals, which is a good reason to favor organic.  I’ll set aside whether there is any safe level of pesticides in food, because there isn’t yet any scientific agreement on the subject.  I’ll also set aside (for now) the effects of using huge amounts of antibiotics that can leak into the environment.  Instead, I’ll (predictably) focus on microbes, since they make the world go ‘round and are more important than people in the long run. 

I love long-term studies (I mean, what is our planet but a long term environmental study?).  The Swiss government started just such a study in 1978, comparing three variations on farming for typical Swiss crops:  conventional agriculture with pesticides, herbicides, and chemical fertilizer supplemented with animal manure, organic farming with no herbicides or pesticides and only animal or plant manures, and “biodynamic” farming.   They did not address which produce is better for you, or which tastes better; they’re Swiss, so the conventional stuff was within pretty tight government regulations, and they’re scientists, so all the crops were equally fussed-over.  What they did compare was the performance of the farms as if they were factories, and the health of the farms over the course of decades.  (Just to simplify things, I’m lumping together the results of biodynamic and organic practices, since they were essentially the same.)

I’ll start with the result my dad would point out:  yields in the organic fields just weren’t as high as in the conventional fields.  Potatoes, beets, barley, wheat, it didn’t matter, yields from the organic fields rarely equaled those from the conventional fields, and were generally about 80% of the conventional yields.  This is not a trivial point in a world that’s trying to feed 7 billion people with limited amounts of cropland and ever-more-difficult access to water. 

However, there are other factors that are limiting, and energy is right up there.  Comparison of the energy inputs to get those crop outputs is illuminating.  The researchers figured out how much energy was needed for farming activities such as tilling, and added the substantial energy for making mineral fertilizers, nitrogen, pesticides, and herbicides.  Over a six-year period, they discovered that organic farming took slightly more than half as much energy per hectare, so even though yields per acre were slightly reduced, organic farming was still vastly more efficient.  (I’ll also note that about when this study was published, my dad abandoned his SUV for a Prius.)

Soil is the factory that produces food.  Clearly, organically farmed soil is a different kind of factory from conventionally farmed soil—more efficient with energy, though less efficient with space.  It’s the architecture and the workers in the factory, and how they interact and affect each other, that make the difference. 

In this study, there is a visible difference between organic and conventional soils. 
In this picture of winter wheat seedlings, the biodynamically farmed soil shows more weeds, but the soil looks friable and there are plenty of worm casts.  These differences are quantifiable; water drainage is improved, as well as the ability of the soil to cohere. 

The workers in the factory of soil are microbes and small invertebrates.   It’s not too surprising that organically and biodynamically farmed soil has a lot more life in it—the Swiss study found twice as many earthworms, spiders, and beetles, and much more root-associated fungi.  The sheer mass of microbes was higher, as was both their genetic diversity and (as has been found in similar studies) their enzymatic and metabolic diversity.  We are constantly told that a more diverse workplace is better, and at least in the work done in the soil, this seems to be the case.  To really understand this, though, we need to see what these workers do.

We might think of plants as rugged individualists, gamely taking sunlight and water and CO2 and pulling themselves up by their own bootstraps.  In reality, they depend upon soil microbes, both bacteria and fungi, for making many (or most) of their nutrients available and delivering them to their roots.  These microbes break down the components of wood so that the elements therein can be absorbed by plants; they convert chemically inert atmospheric nitrogen into a form that the plant can absorb; symbiotic fungi called mycorrhizae, which grow both in soil and extend their threads into the cells of plant roots, capture these liberated nutrients and inject them directly into the plants.  All the players in this system, plants, fungi, and bacteria, have evolved to work with each other, and all fail to thrive in the absence of the others.  A plant is a visible expression of the health of the soil community.

The Swiss study, as well as studies on Italian rice, Dutch onions, California strawberries, and other combinations of crop and soil, have found that the diversity of the soils microbes and mycorrhizae are higher in organic soils.  (Indeed, as soils go, the champions are wild, uncultivated soils, with many different types of plants growing in them—but that’s not agriculture.)   These soils show increased ability to break down manure, an increased ability to mobilize nutrients such as nitrogen and phosphorus, and increased interaction between mycorrhizae and plant roots.     

When the Swiss researchers examined conventionally farmed soil, they found limited microbial diversity, and reduced metabolic diversity (that is, the number of different types of biological reactions occurring).  However, they found increased metabolic activity (that is, the amount of microbial nutrient consumption aimed at just making energy to live, as measured by the amount of CO2 the microbes exhaled).   In the simplified environment of conventional soil, the microbes had to work harder to do less.  This is not a fluke; a similar observation was made in comparing organic and conventional strawberry fields in California.

This illuminates the gross productivity and efficiency differences seen between the conventional and organic systems in the Swiss study.  The conventional soils had greater yield, but (because they are less efficient factories) they required much higher inputs of material and energy.  Organically farmed soils are healthier.  Arguing for conventional farming because arable land is a scarce resource ignores the fact that, unless there is a large input of energy and skill, conventional farming can result in the degradation and loss of that same scarce resource

Of course, factories have more than one product; even the most efficient factory will produce some waste.  Even here, organic farming has some benefits, and these benefits also are a result of the more diverse and efficient microbial community in organically-farmed soils. 

The job of any factory is to convert raw materials into a mix of useful products and waste, hopefully with an emphasis on the former.  Farmers, whether organic or conventional, add raw materials to their soil factory, and they are particularly mindful of the nitrogen they add.  Organic farmers add various forms of manure for their nitrogen content—chicken or cow wastes, or composted legumes.  Conventional farmers will supplement or replace these nitrogen sources with calcium nitrate or anhydrous ammonia (as an aside—production of this fertilizer consumes upwards of 1% of the global human energy budget).  This is the raw material that enters the factory; some of the nitrogen gets incorporated into the plants, but a lot of it will disappear as waste.  And here is where there is a significant difference between conventional and organic soils, again due to their microbial composition. 

Nitrogen compounds are neat.  Most of the earth’s nitrogen is in the form of nitrogen gas (N2) in our atmosphere; this is inert, so chemically unreactive that it is used to protect precious documents and Guiness beer.  A few microbes have learned how to “fix” this atmospheric nitrogen, to make ammonia (NH3), which is like rocket fuel for plant growth.  Lots of soil microbes love to eat ammonia too, but rather than using it for growth, they oxidize it for energy; in the process called nitrification, they take ammonia and make it into nitrate (NO3-).  Nitrate is a mixed blessing; plants can use it, though not nearly as well as ammonia.  Mostly it leaches out of the soil and pollutes waterways, leading to algal blooms and their resultant die-offs and dead zones.  Microbes can also take nitrate in the soil and use it for respiration the same way we use oxygen, in a process called denitrification.  Some denitrifiers convert the nitrate into nitrous oxide (N2O), which disappears from the soil as a gas; it’s not a good thing, given that it can degrade ozone and is also, gram for gram, about 300 times more effective as a “greenhouse gas” than carbon dioxide.  Other denitrifiers use the nitrate more effectively, and convert it back to nitrogen gas. 

Either way, as a result of this nitrogen cycle, a farmer can add nitrogen to the soil and watch some of it disappear as waste; it’s just a matter of whether the added nitrogen disappears by leaching (and polluting the water) as nitrate, by going into the atmosphere as pollution in the form of nitrous oxide, or by going into the atmosphere as benign nitrogen.   Since the nitrogen cycle is largely driven by microbes, and since organic and conventional farming techniques result in different soil microbiota, it seems like a reasonable hypothesis the way nitrogen leaves the soil would differ in organic and conventional situations. 

No matter what form of agriculture, human activity dominates the addition of nitrogen to the soil.  Conventional farmers add over 80 million metric tons of ammonia to the soil every year, and organic farmers add manure.  This, combined with using legumes in crop rotation, determines the start of the nitrogen cycle.  However, according to a study comparing organic and conventional apple orchards in Washington state, the fate of the nitrogen differs significantly.

In the organically fertilized orchard, nitrogen was added in the form of manure; the soil microbiota broke down the manure, so nitrogen entered the soil more slowly, making it easier to be assimilated.  Of the nitrogen that was not used by the trees and left the soil, only 10% leached out as nitrate.  Because of the denitrifying microbes in the soil, 10% was denitrified to N2O, and 80% was denitrified to harmless nitrogen gas. 

In the conventional orchard, nitrogen was added in the form of calcium nitrate, a common agricultural fertilizer.  The same amount of nitrogen was added, and the trees grew as well, with the same amount of nitrogen in their leaves and a comparable amount of nitrogen leaving the orchard as waste.  Here, only 20% of the nitrogen left by microbial denitrification, half as N2O and half as nitrogen gas.  The remaining 80% of the added nitrogen left by leaching out of the soil as harmful nitrate.  There is a striking correlation between the richer microbiota of the organic orchard and the increased ability of the soil to process nitrogen into environmentally benign forms—with, as the authors of this study note, no effect on the yield of fruit. 

Which brings us back to the whole question of whether or not to go organic, and thanks to the news-making review, we can ignore questions of nutrition.  Those who argue against organics point to increased cost, and less efficient use of land.  I think that some of the costs of conventional agriculture are distributed or hidden—increased energy inputs per acre, and the costs of dealing with increased pollution.  Land use may be less efficient in the short term, but unless there is active and conscientious management of conventional soils (another hidden cost), organic soils are healthier and more sustainable. 

The goal is aspirational; right now, organic stuff is more expensive, and that’s a hardship for some.  Many farmers (not to mention some pretty enormous agribusinesses) are pretty set against organic growing.  There’s also situations that are really difficult to address with anything but conventional means.  I am an example; I am using Crossbow to clean up blackberries and poison oak and vinca that have accumulated after several years of neglect.  But, the goal here is a transition to organic, and it is doable and right.

So, imagine I offered you a couple of MP3 players for sale; they are functionally identical, and both will fill your ears and satisfy your musical desires.  However, one costs 20% more than the other.  What’s the difference?  One is made in a coal-powered factory that produces a large amount of toxic wastes and causes damage to its local environment, while the more expensive one is from a renewably-powered factory that actually collects and recycles waste, cleaning its environment.  Which would you choose?

Galván, Guillermo A.,  István Parádi, Karin Burger, Jacqueline Baar,  Thomas W. Kuyper, Olga E. Scholten, and Chris Kik (2009).  Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands.  Mycorrhiza 19(5): 317-328.  Onions, with their weak roots, are quite dependent upon mycorrhizae; since the farms were in polders, the soils were very new to agriculture, but even so, mycorrhizae were present. 

Kramer, Sasha B., John P. Reganold, Jerry D. Glover, Brendan J. M. Bohannan, Harold A. Mooney (2006).  Reduced nitrate leaching and enhanced denitrifier activity in organically fertilized soils.  Proceedings Natl. Acad. Sci. USA 103: 4522-4527.  A neat paper about denitrification, free access. 

Lumini, E., M. Vallino, M. M. Alguacil, M. Romani, and V. Bianciotto (2011).  Different farming and water regimes in Italian rice fields affect arbuscular mycorrhizal fungal soil communities.  Ecological Applications 21 (5): 1696-1707.

Maeder, Paul, Andreas Fliessbach, David Dubois, Lucie Gunst, Padruot Fried, Urs Niggli (2002).  Soil Fertility and Biodiversity in Organic Farming.  Science 296: 1694-1697. This paper documents the Swiss long-term experiment; since this was published, many more details have come out. 

Orr, Caroline H., Angela James, Carlo Leifert, Julia Cooper, and Stephen P. Cummings (2011).  Diversity and Activity of Free-Living Nitrogen-Fixing Bacteria and Total Bacteria in Organic and Conventionally Managed Soils.  Appl. Env. Micro. 77(3): 911-919. 

Reeve JR, Schadt CW, Carpenter-Boggs L, Kang S, Zhou J, Reganold JP (2010).  Effects of soil type and farm management on soil ecological functional genes and microbial activities. International Soc. Microbial Ecol. Journal 4(9): 1099-1107.  Good paper, underlines the microbial difference between organic and conventional soils.  Also, for brother M:  Watsonville strawberries. 

Smith-Spangler, Crystal, and, Margaret L. Brandeau, Grace E. Hunter, J. Clay Bavinger, Maren Pearson, Paul J. Eschbach; Vandana Sundaram, Hau Liu, Patricia Schirmer, Christopher Stave, Ingram Olkin, and Dena M. Bravata (2012).  Are Organic Foods Safer or Healthier Than Conventional Alternatives?: A Systematic Review.  Annals of Internal Medicine 157(5): 348-366.


  1. Thank you for that post. Mind if I link to it?

    1. You're welcome, and go ahead, link away. Hey, could you send me an email so I have your address? Regards to all there.

  2. Did you get my contact info? I emailed it.