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My attitude coming in here is anti-petroleum and pro-renewable, but I think that industrial farming is a suspect solution to America's nascent energy crisis. I haven't yet delved into what internals or externals factored into this new research, but I can think of many that probably weren't, and the most important of these is fertilizer. Modern phosphorous-rich fertilizer requires enormous amounts of energy to produce and it is an absolute necessity for modern intensive farming, as is the heavy machinery so quickly pooh-poohed in Leonard's review. That machinery is every bit as important as the pump on an oil well. The pump for an oil well uses only a tiny fraction of the energy being pumped, whereas the tractors going back and forth over agricultural fields use a substantial fraction of the energy being grown. (Whether or not they are or could be running on ethanol is irrelevant from an efficiency perspective, but obviously if they can't grow enough ethanol to run on that would indicate a pretty serious problem!)
Ultimately, farming is another form of solar energy collection. Whether or not planting and harvesting crops is the most efficient means of collecting this energy is doubtful, given the fact that we've grown dependent on the rapid burning of our saved inheritence of millions of years of collected solar energy.
My father has written extensively about issues of clean vs. unclean energy sources and the thermodynamic reality that the distinction is a false one. He's had me post some of his articles online here:
http://www.asecular.com/forests/vfw/energy/