If you want more technical information on these two papers, note that the 'supporting information' is available for FREE from the Science website links for each of the papers. The Searchinger et al paper has almost 50 pages of very detailed information. Also note that a very good summary of the same information for the Searchinger et al study is in a report he authored by the German Marshall Fund - http://www.gmfus.org/publications/article.cfm?id=385

I agree that you can't always assume that just because something is published in a prestigious scientific journal that is the gospel truth. The devil is always in the details and the assumptions, and I think there is plenty of room for reasoned debate about the methods and conclusions here.

But please note these kinds of papers do get a lot of critical review before publication. The same authors of a major pro-ethanol ethanol study in Science two years ago (Kammen et al from UC-Berkeley) have looked at this new work carefully and they are publicly stating that it is a valid analysis. The ethanol industry routinely cites that earlier study as proof of the benefits of ethanol. They should stop looking for Big Oil Bogeymen behind every tree, and begin to recognize the biofuels / agriculture / energy / climate are all huge, complex systems that we really don't understand that well yet, and need to if we are going to manage them responsibly.

A Q&A with the lead author of the Nature Conservancy study is at Climate Change and Energy: The True Costs of Biofuels
http://www.nature.org/initiatives/climatechange/features/art23819.html

Papers were also discussed intelligently on NPR's Talk of the Nation
http://www.npr.org/templates/story/story.php?storyId=18800996&ft=1&f=1007