The evidence is not quite clear enough that organic food is better for the atmosphere. The debate on whether organic agriculture reduces greenhouse gas emissions is a lively and sometimes acrimonious affair. The calculations are complex, the results depend on myriad factors that are difficult to quantify, and much research remains to be done. Those who give unequivocal answers to the question 'is organic better?' may not be recognising the extraordinary uncertainty that still surrounds many aspects of agriculture. Rather than produce a simple answer, this note offers a statement of the competing cases.

This topic has been widely researched but has produced very varying answers. There is certainly no consensus. In general, organic farming seems to be slightly better for the atmosphere than conventional cultivation, but for every ten studies that say this, five say something different. Almost all the conclusions are the subject of passionate debate.

The argument against organic agriculture: conventional farming is better for the planet

Conventional farming produces far more food per acre than organic farming. Though comparison is surprisingly difficult, organic yields probably vary from about 50% to about 70% of the conventional equivalent. I say 'probably' because some people give figures that are well outside this range. It depends on the crop, the type of soil, and the climate. The importance of lower productivity for climate change is that for every unit of input, the output is lower. Think about organic milk, for example. The cows need to be fed, at least in winter, and the food requires a lot of energy to produce. If an organic cow gives half as much milk as a conventional milker, the energy cost is double. This argument is even clearer when includes the methane output of cows. Methane is a powerful warming gas, and cows produce huge volumes of it. Organic cows produce less milk than conventionally farmed cattle so the methane output per litre tends to be much higher.
Most organic agriculture is more labour-intensive than conventional farming. Usually, but not always, the tractor needs to criss-cross the field more often. And if yields are lower anyway, the cost of the energy used is far greater per unit of output. Or take organic tomatoes grown in a heated greenhouse: the labour needed is the same, but the yield is less.
Organic agriculture can involve more disruption of the soil. It needs more ploughing, for example. This may increase the losses of soil carbon, though this conclusion is fervently disputed by organic proponents.
A system that relies on natural manures may require more methane-producing animals on the farm. Methane is a dangerous greenhouse gas. More manure may also result in higher emissions of nitrous oxide, an even worse climate-changing gas. Replacing inorganic fertilisers with farmyard manure certainly does not have an unambiguously beneficial effect on GHGs.
Organic food tends to be imported. The food miles are greater.
There may be more wastage in organic systems. Organic fruit and vegetables are more likely to suffer pest damage, perhaps reducing storage life. Data on this is particularly sparse.
Ruminant animals in organic systems mature more slowly, so they emit methane for a longer period before becoming productive. (This is particularly important with cows.)
Conventional farming may work better with the new(ish) 'no-till' or 'min-till' cultivation systems. These techniques entail the maximum avoidance of ploughing, which is thought to cause the loss of soil carbon to the atmosphere.

The opposing view: organic farming is the way forward

Organic farming avoids nitrogenous fertilisers. These fertilisers take much energy to produce. Their use also adds, perhaps very substantially, to nitrous oxide. Nitrous oxide is far worse than methane or carbon dioxide. Agriculture is the single most important source of this gas.
Organic cultivation probably helps build carbon in the soil. Soils that receive inorganic fertiliser tend to have lower carbon levels than fields in long-term organic cultivation.
The methane output from the manure from free-range animals in organic systems is far less than from the slurry tanks in intensive beef farming, for example.
Though much organic food is imported, the percentage is tending to fall as consumers react to the poor publicity about food miles and adjust their purchasing behaviour.
Organic farmers tend to work harder to sell their food locally rather than to the supermarkets or to processors. This reduces the energy in transportation and in manufacturing.
Cows do take longer to mature in organic systems, but they don't wear out so fast from exhaustion, so fewer calves are needed at any time to maintain the stock of productive animals.
It is possible that people may waste more organic food, but the consumer will be conscious of the price and the general need to cook and eat the food soon after purchase. The purchase of organic food tends to bring with it an enhanced sensitivity to the need to use foods as soon as possible and not waste expensive ingredients.
The calculations of emissions from conventional agriculture very rarely include the impact of GHGs from liming soils to redress the increased acidity coming from the use of inorganic fertilisers. The lime will degrade to give off CO2.

Typical research conclusions Most research suggests that organic agriculture has marginally lower emissions than conventional methods. But the results are debatable and depend on the crop, the soils, and the skill of the farmer. It is often remarked that comparisons are difficult because organic farmers may well be better at their job. Good farmers become organic farmers. This may artificially advantage organic methods.

Unfortunately, we probably need even more research to get clearer conclusions. Until then, the protagonists on either side will continue to debate the issue with passionate intensity. Of course, organic food is almost certainly better for biodiversity, for the maintenance of soil quality, and for animal health. It may, only may, be better at providing micro-nutrients, but there is very little to support the view that organic food is inevitably healthier. But there is intriguing early evidence that vegetables stressed by the need to protect themselves against pests that would be destroyed by pesticides in conventional farming contain higher levels of complex compounds useful for human health.

'Is organic better?' may not be the right question to ask Organic tomatoes grown in March in heated Dutch glasshouses will be far worse for the environment than imported conventional Israeli fruits. Someone trying to minimise the GHG impact of the food he or she eats would probably do best to follow some simple rules:

Animal products are generally worse for GHGs than plant-based foods, so vegan diets are far better than carnivorous. This result is generally agreed.
Raw food is better than cooked. Cooking can represent a large fraction of the total energy in the life cycle.
Food processing, particularly keeping foodstuffs chilled in factories and in supermarket refrigerators, is usually worse than equivalent minimally processed ambient foodstuffs.
Local food is not necessarily better than food from afar. 'Food miles' do not necessarily imply high greenhouse gas emissions. Sugar made from Brazilian sugar cane, which has very low fertiliser input, may have a much lower carbon impact than East Anglian sugar beet, which has taken large doses of nitrogen fertiliser and then required substantial amounts of energy to process. But, all other things being equal, local food grown and sold in its natural season and not retailed through energy intensive supermarkets is better than products grown on the other side of the globe.
So, in a conclusion that will not please high-living gourmands, the best foods from a climate change viewpoint are unprocessed, unpackaged vegan wholefoods sold locally and produced in season.