Do you have a link that disproves Pimentel’s findings? The only ones that I am aware of were funded by the USDA and had a disturbing air of Lysenko about them.
Pimentel and Patzek also include values like the energy of the food eaten by farmers and labors along the process. They included the energy used to make tractors and other equipment.
If you apply this standard, all choices are net losses of energy.
I think Dr. Wang’s 2005 study was one of the most complete. It is tainted with concerns of the production of greenhouse gases but the energy calculation including what was required to produce the electricity consumed seems quite complete.
http://www.anl.gov/Media_Center/News/2005/news050823.html