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I'm looking for methodologies to compare the costs a food production requires with the gains it delivers (not in economic terms).

I'm aware of energy returned on investment. Are there other methods used in literature (also including qualitative approaches)?

To be a bit more precise (or rather unprecise?): Costs may include the input of fuel, feed, energy in general or - for me most interesting - the environmental burden to our environment (for example the carbon footprint) while gains should refer to the nutritional output of the product (energy, protein content, other (rare) nutrients).

The purpose is to link (or discuss) the burden of food production chains to their benefits but to find a unit that is quantitative comparable (except the pure energy content) doesn't seem so trivial - so I'm very happy with suggestions how to approach that - in the best case with a link to studies that employed the method.

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This is called "Life cycle analysis" –  David Jun 6 '13 at 5:22
    
@David Thank you. I'm fully aware of that :) I'm rather looking for factors that have a comparable unit when they enter and leave a food production system. Sure, there is for example the output of CO2 linked to the consumption of fossil fuels but I wonder if there are some that are more obviously linked, also speaking in terms of being easier to understand. –  Stockfisch Jun 6 '13 at 9:14
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Calories and dollars are the most obvious and straightforward, but including additional variables complicates the accounting. . A great paper that used energy has been updated in a more recent publication. Emergy is an interesting alternative.

Current work includes the Natural Captial project that "aims to integrate the values of nature into all major decisions affecting the environment and human well-being". Of course, this approach exchanges a simple currency for a more comprehensive one.

Climate regulating value is also a relatively straightforward and relevant currency that can be used to compare the value of food production systems.

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