This whole ethanol subject is awfully thick to to argue about as non-scientists, but, if you read the Time cover story, I noticed that there was very little reference to specific scientific studies.
The story mentions that most of our politicians-congress are sold on ethanol and acts like they are being fooled. But where are the scientific references? I really believe that the anti-ethanol movement is spurred by people who want us to feel obligated to stay in the middle east and maybe it's driven by a hawkish pro-Israel mentality. But the primary 'expert-author' referenced throughout the article is a guy named Tim Searchinger. Below is a link to his website at Princeton, he's just a lawyer, not a scientist and the whole article is filled with lawyerly smarm, I think. For example, if you read closely, the article is adding in the pollution from clearing land to grow bio-fuel crops, into the pollution from the bio-fuel, even though the clearing is a one-time-only proposition.
And what about the fact that oil has gone up 500% in recent times? How does that affect food prices, to plant, harvest and process and transport? And of course, the article doesn't even consider the fact that oil is a limited commodity. We could run out, what then?
Here's the guys site and the article.