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First, there is no common view on methodology. You have lots of different studies getting radically different results for the same energy processes, which means that EROI is a pretty useless tool for policymakers or managers.
There is no common single "view" on methodology, but if you go to the original seminal work on EROI, the point that there are different types of EROI each of which are most suitable for distinctive questions is there at the outset.
The three most common seem to be external EROI, final EROI, and emergy. External EROI is the situation referred to in the piece regarding cane sugar ethanol, where the EROI 8 is an external EROI of 8, and its that high since unlike corn starch ethanol, the bagasse from the crushed sugar cane can be burned to heat the production of fermentation for distillation. For a country facing an oil price shock and with a sunk investment in gasoline powered vehicles, the external EROI of 8 is a good indicator of how effective it is in terms of shifting away from petroleum ~ which is dramatically more effective than corn ethanol (with its heavy upstream reliance on fertilizer, pesticide, herbicide, mechanized agriculture and harvest drying) is every going to be.
Its final EROI which seems likely to be closer to 2 is a better index of how it would stack up against some other biomass source in a longer term view, looking at building toward a sustainable, renewable power source over a period in which one can consider shifting away from vehicles designed to run on gasoline to a different motive power source entirely. Planting the same fields in coppiced wood or some permanent nitrogen fixing grass such as switchgrass, harvesting that feedstock for biocoal, and putting it into a slurry for a hybrid electric / direct carbon fuel cell vehicle would generate far more vehicle miles from the same hectare. And since, given the flexibility of biocoal you have a very wide range of choice of feedstock, likely far more ecologically sustainable as well, since you are free to optimize for ecological sustainability.
I've been accused of being a Marxist, yet while Harpo's my favourite, it's Groucho I'm always quoting. Odd, that.
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