As I've said before, science is a tool, not a philosophy. Science is a way of understanding natural phenomenon.
As with any tool, it must be applied properly.
"Are vaccines effective" is a scientific question. "Should vaccines be mandatory" is not a scientific question (though it has a scientific answer if maximum effectiveness is the goal, it would require a specific percentage of coverage). That's a different kind of question though and must be answered with respect to governance, human rights, etc.
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