There are a lot of poorly supported claims circulating regarding ethanol.
This analysis is an excellent look at the some of the science behind these claims.
The pro-ethanol contingent is quick to point to certain studies published by the USDA to support the claim that the energy balance of grain-ethanol is positive. Many anti-ethanol advocates will point to studies by Professors Pimentel and Patzek (1) to support claims that the energy balance is negative. Say what you will about the Pimentel and Patzek studies, but they have one thing going for them that that USDA studies do not: They have been published in peer-reviewed journals. Why does this matter? Peer reviewed papers have been examined by reviewers familiar with the subject matter (but who are not colleagues of the authors) who are looking for deficiencies or gross errors. Peer review is no guarantee that errors won’t slip through, but it is a check on papers that establishes that they have met certain scholarly guidelines. Peer review can be a pretty rough ordeal, but does a pretty good job of weeding out poor arguments.
Now, having said that, I will acknowledge that some of the criticisms of the data that Pimentel used may be legitimate. So, the purpose here is not to defend Pimentel’s work, but instead to take a rigorous look at the USDA studies. http://i-r-squared.blogspot.com/2006/03/how-reliable-are-those-usda-ethanol.html