This article offers the results of emergy analysis used to evaluate four different soybean production systems in Brazil that were divided into two main categories: biological models (organic and ecological farms) and industrial models (green-revolution chemical farms and herbicide with no-tillage farms). The biological models show better environmental, economical, and social performance indicators; however, at the national level, discussion of transgenic soybean seed release considers only industrial models without any mention of biological models. Classic emergy analysis shows biological options are the better alternatives but does not explain why decisions taken by farmers and government in Brazil were in opposition to these options. New research is proposed to identify and quantify the external forces that strongly interfere in the definition of public policy for soybean production. New parameters are proposed to enrich emergy methodology: Renewability of each input was considered in emergy calculations and negative externalities were included as additional services.