The article goes on to say that subsidizing manure to energy projects may artificially increase the size of livestock farms, which has all sorts of impacts on energy consumption and the local environment of those farms. Indeed, subsidies continue to skew all analyses of different project's true value.

I couldn't agree more with the last paragraph of the article:

Using manure as power sounds like a good idea, but it's not. The energy that can be generated from manure is not worth the expense. And by lowering industrial animal operations' cost of production, subsidizing manure power pushes family farms further toward the brink of extinction. Our money would be better spent investing in truly sustainable, sensible ways of producing energy and food.

As I mentioned before which was picked up by the local political blog - Gotham Gazette, we need a common understanding of the boundaries/terminology of a proper EROI analysis of alternative fuels to decide where to invest our resources. At least if everyone can agreed on the terms of the debate we might actually have one!