Subsidies stink, but corn and soy... McDonald's and Wendy's...

I think biofuels are ideal... unless the fertilizer used to produce them was made by consuming fossil fuels. Many of them are. My [admittedly limited] understanding is that most nitrogen based fertilizers require natural gas, and phosphate based fertilizers are made with rocks, sulfuric acid, and (grid-provided) heat. I haven't seen many processes that are 100% efficient, so where do we get the requisite doo doo to replace the manufactured fertilizers? Are we borrowing our way out of debt without clean nuke?