David Tribe has an interesting post on organic crop yields. In short, he asks: from where does the nitrogen come? For organic crops, it's often manure. But, where does that come from? Often from animals fed conventional grains made possible by synthetic fertilizers. He also raises an interesting point about the need to count cover crops as an input into production of commercial organic crops when considering overall productivity.
It is an important point that has been addressed by others such as Adam Merberg who humorously noted now synthetic nitrogen is "laundered" to make it fit for organic agriculture:
A while back, I discussed some of the issues involved in comparing organic and non-organic crop yields, and included the following figure and explanation: