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Dr Chris MacLeod said it was an "open wound on the surface of the Earth", where the oceanic crust, usually 6-7km thick (3.7-4.3 miles), was simply not there.
"Usually the plates are pulled apart and to fill the gap the mantle underneath has to rise up. As it comes up it starts to melt. That forms the magma," he said.
"That's the normal process. Here it has gone awry for some reason.
"The crust does not seem to be repairing itself."
Dr MacLeod said the research could lead to a "new way of understanding" the process of plate tectonics.
The scientist will test theories he developed after visiting the area in 2001 - including the possibility the missing crust was caused by a "detachment fracture".
"Effectively it's a huge rupture - one side is being pulled away from the other. It's created a rupture so big it's actually pulled the entire crust away."