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Defining and measuring sustainability of bioenergy systems are difficult because the systems are complex, the science is in early stages of development, and there is a need to generalize what are inherently context-specific enterprises. These challenges, and the fact that decisions are being made now, create a need for improved communications among scientists as well as between scientists and decision makers. In order for scientists to provide information that is useful to decision makers, they need to come to an agreement on how to measure and report potential risks and benefits of diverse energy alternatives in a way that allows decision makers to compare options. Scientists also need to develop approaches that contribute information about problems and opportunities relevant to policy and decision making. The need for clear communication is especially important at this time when there is a plethora of scientific papers and reports and it is difficult for the public or decision makers to assess the merits of each analysis. We propose three communication guidelines for scientists whose work can contribute to decision making: (1) relationships between the question and the analytical approach should be clearly defined and make common sense; (2) the information should be presented in a manner that non-scientists can understand; and (3) the implications of methods, assumptions, and limitations should be clear. The scientists' job is to analyze information to build a better understanding of environmental, cultural, and socioeconomic aspects of the sustainability of energy alternatives. The scientific process requires transparency, debate, review, and collaboration across disciplines and time. This paper serves as an introduction to the papers in the special issue on "Sustainability of Bioenergy Systems: Cradle to Grave" because scientific communication is essential to developing more sustainable energy systems. Together these four papers provide a framework under which the effects of bioenergy can be assessed and compared to other energy alternatives to foster sustainability.