If the goal of science is to understand the structure and behavior of the physical and natural world, and the goal of engineering is to design, build, and manage systems that serve society’s needs, then the study of civil infrastructure systems acts as a link between the two. Understanding the reliance of engineered systems on constrained natural resources, as well as their impact on human well-being and the environment, is key to building and maintaining infrastructure that is sustainable in the broader sense. This talk will explore the important role of life-cycle assessment and optimization in assessing such questions as: a.) How will future transportation energy production impact water resource availability in the US? b.) How do greenhouse gas emissions vary between different large-scale cellulosic ethanol production strategies? c.) What can researchers do to develop more robust, realistic alternative energy scenarios? The results include insights into the biofuels research being conducted in the Energy Biosciences Institute, and reveal some unexpected drivers of the environmental impacts of alternative energy.