From
http://en.wikipedia.org/wiki/Bioengineering:
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Biological engineering (also biosystems engineering and bioengineering) deals with engineering biological processes in general. It is a broad-based engineering discipline that also may involve product design, sustainability and analysis of biological systems. Generally, bioengineering may deal with either the medical (see biomedical engineering) or the agricultural fields (see agricultural engineering).
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Furthermore:
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Biological engineering is called Bioengineering by some colleges and Biomedical engineering is called Bioengineering by others, and is a rapidly developing field with fluid categorization.
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So don't expect consistent terminology between different programs at different schools.