Obedience is part of military culture, both as a legal obligation and as an instilled reflexive practice deemed essential to survival in combat. Circumstances might require following orders that go against natural instincts.
Military training also encourages initiative and independent thought, and, when appropriate, expressing concerns about decisions or a state of affairs. But it also involves understanding that when a decision has been made you must do everything you can to implement it and influence others to act in the same way.
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