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Did the military have any role in the confirmation of plate tectonics by identifying the sea floor magnetic striping patterns?

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Yes.  The military played a role in providing further evidence toward modern day plate tectonic theory.  

Specifically, it was the United States Navy that provided the evidence.  During World War II, the commander of the attack transport U.S. Cape Johnson in the Pacific Ocean was Harry Hess.  Before the war, he was a geology teacher at Princeton, and during the war Harry Hess used naval sounding gear to continually map sea floor and assuage his scientific curiosity.  What he discovered was that the sea floor was not a huge, wide open, flat plan.  Rather it consisted of large mountain ranges and deep trenches.  

During post war time, Hess continued to analyze the increasing amount of information about the sea floor.  One more thing that Hess discovered was that the age of the sea floor was newer closer to the ridges and older farther away from the ridges.  Additionally, he also discovered that the sea floor didn't contain crust as old as continental crust.  Hess correctly concluded what that information means.  It means that Earth's crust is continually recycled as the sea floor spreads at the ridges and is subducted at the trenches.  This "sea floor spreading" also pushes the continents along with it and results in what Alfred Wegener called "continental drift."  

As for the magnetic striping, Vine and Matthews were the two scientists that looked closely at this feature of the ocean floors.  Their data, together with Hess's navy data, gave sea-floor spreading the proof it needed to be widely accepted and eventually become modern day plate tectonic theory. 

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