One of Yura's professors reminds him that bacteria may be beautiful under the microscope, but they do ugly things to people. When does this happen? 

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This happens early in the narrative.  As Yuri studies chemistry en route to becoming a doctor, he is examining the role of bacteria in a laboratory and while viewing under the microscope, the line is spoken.  The line seems to have a great deal of relevancy in the novel as it does express the chasm between beauty and heinousness. The implication in the idea is the duality of concepts and how what can appear to be beautiful can actually do "ugly things" to people.  Certainly, this could be said of how many Russians viewed the Revolution.  Predicated upon the principles of fairness, equality, and justice for all, the Revolution was commenced with these elements of "beauty" in mind and for many, including Zhivago, it came to meant much more.

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