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A lot of scientific studies and credible sources indicate that agriculture is one of the major contributors of greenhouse gases. The exact numbers seem to vary a lot, I've seen everything from 8% to 45% of global greenhouse gas emissions.

What makes me unsure how to really interpret these numbers is the fact that the process of growing feed to feed livestock, raising livestock, and then eating that livestock, is a cycle. The very same plants that the livestock is eating has during the course of its growth acted as a sink, i.e. absorbing carbon dioxide from the air. This is totally different from pumping oil out of the ground and burning it, which is (in the relevant short term) only production of greenhouse gases, without the sink.

I would assume that any serious study on greenhouse gases would factor in the entire cycle of absorption through animal feed and release back into the atmosphere, yet none of the studies I have seen say exactly how they arrived at the emissions.

Aside from the fact that oil is used in agriculture, when only considering the actual gases released from animal farming vs plant farming, it doesn't really make basic sense to me that there could be a net production of greenhouse gases - where did the surplus come from?

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The issue is that it is not always a cycle, when you drain wetlands or burn forests to make more farmland that's not a cycle that is permanent change. A change that can continue having effects for centuries. Then of course you have petroleum fuel used to run tractors and the production of fertilizer which are often not cycles either but pure extraction.

One of the reason the number varies so much is because of disagreements about what falls under agriculture, does the fuel used to run a cargo ship moving bananas count? How about mining equipment used to extract minerals used to make fertilizer? Many simply forget to include things like peat bogs or changes in soil bacteria.

For instance draining a peat bog releases tremendous amounts of carbon, as a functioning net carbon sink is changed into a carbon producer. Sometimes this happens as water is diverted to farmland but often it is done just on purpose to get more farmable land. Exact impacts vary from place to place leading to wide ranges of estimations further complicating it.

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    $\begingroup$ I reckon this is worth a new question, but off the top of my head, I think there's a figure that it takes 4kg of grain to produce 1kg of meat, or equivalent calorie content. Then methane is a major greenhouse gas and apparently cows are gassy animals, so still very complicated... $\endgroup$ – Oliver Houston Jun 2 '17 at 7:45
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    $\begingroup$ @OliverHouston Methane is a major greenhouse gas, but isn't stable in an oxidative atmosphere. We can't ignore it, but it doesn't accumulate. Water vapour (produced when methane breaks) is similar - it's by far the biggest contributor to Earth's greenhouse effect, but the atmosphere cannot really hold more of it - it spontaneously condenses out of the atmosphere. $\endgroup$ – Luaan Jun 2 '17 at 8:14
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    $\begingroup$ @BadCash The whole thing is absurdly complex; it can't really be covered in a couple of SE questions. Consider that as carbon dioxide content increases, plants grow faster (lack of carbon is limiting the growth of most plants, not lack of energy; higher temperatures also promote growth, though only up to a point); this may very well cause agriculture to be more efficient (more food per square meter, which means less work for the same amount of food) or less efficient (more weed growth, disease...). Is transportation of meat cheaper or more expensive than fruits, vegetables, grains? $\endgroup$ – Luaan Jun 2 '17 at 8:19
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    $\begingroup$ @OliverHouston Transportation is ridiculously cheap, especially for non-perishable goods - I don't remember the exact numbers (and can't find the reference), but I recall that the break-even point is somewhere in thousands of kilometers over land (ships are pretty much unlimited). There is always something that can be produced and distributed locally cheaper than imports, but that's rarely a consideration - the main decision is political (self-sufficiency, nationalism, ...). But do consider that we mostly feed the animals with crops, so those can't be more efficient than crops, at least. $\endgroup$ – Luaan Jun 2 '17 at 8:39
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    $\begingroup$ @BadCash the type of farming is often more important that what is being farmed, for instance small scale pig farms can often be closed cycle while it is nearly impossible to do with large ones, organic farms can pollute more than industrial due to yield, Many farms are horribly wasteful just becasue of where they are, a farm in kansas can be way more efficient than one in california. Even something as simple as what feed is used matter, in the US we favor corn as feed but not everyone does this, many countries favor barley which is more environmentally friendly $\endgroup$ – John Jun 2 '17 at 14:18

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