Biological Engineering (BE) is a relatively new and evolving discipline that is fundamental in nature and uses principles of life science at its core. Considerable literature has been devoted to the emergence of BE as a profession during the past 30 years. Compared to traditional systems, biological systems present special challenges, which require new tools and approaches that are just now being developed. Traditional engineering approaches result in limited success because biological systems are characterized by non-linearities in system properties and dynamics, temporal and spatial variation, and emergent properties. We discuss these properties and the resulting need for novel approaches to problem solving in biological engineering. We assert that to truly serve society, the biology of the system, as well as cultural, social, and ethical issues, must be central to the design process in biological engineering. These issues are addressed through case study and literature review.