Synthetic biology is an exciting new field that uses engineering principles and mathematical modeling to design and construct biological devices. Synthetic biology projects include the construction of bacterial computers that can solve mathematical problems. Microbial machines, in the form of genetically engineered E. coli cells, have solved a variety of mathematical problems, which have had important applications in biology, medicine and technology. This investigation introduces students to synthetic biology principles as they use genetic recombination in bacterial computers to solve the Burnt Pancake Problem. In the project, the biological equivalent of a burnt pancake is a functional module of DNA. Similar to stacks of pancakes burnt on one side, DNA modules have directionality, require a specific order and can be flipped by genetic recombination. The bacterial computer is investigated using a modular system in which pancake stacks are assembled from flippable DNA segments. Flipping of the DNA segments “pancakes” is performed by a DNA recombination system and the flipping is monitored by antibiotic sensitivity of the bacteria and colony color. The investigation interlaces biology laboratory work with mathematical modeling, thereby allowing students to explore the rich interface between biology and mathematics. Sufficient sterile media, antibiotics, cells, plasmids and other materials are provided so that 16 students working in pairs can perform the analysis.