The methane comes from the decomposition of animal waste--manure and has to be considered in the same light as CO2 from non fossil fuel, non contributory to greenhouse gases because the gases will be fixed in the next generation of plants and animals in a continuous cycle.

The 25% lower yield is based on an estimate of how much is lost to massive pest infestation. Yields are actually higher when this doesn't occur as the soil continues to be built.