It's really interesting to see a scientist say that we don't really know how Earth works. I thought the debate was over.
The natural sciences are incredibly complex. You're not dealing with nice simple interactions, and we can't run experiments on the time, spatial, or energy scales needed to directly test hypotheses in the way you would in an experimental science.
Instead, we observe.
We try to understand the present to understand the past and the past to understand the present.
When you're observing an uncontrolled system, it's very tough to isolate one variable from another. Geology is often accused of not being "quantitative enough". What people don't realize is that the quantitative part is usually stupidly easy. It's choosing the right physics to model that's hard. We usually don't fully understand exactly which physical process are at work.
It was not known previously how deep these plumes go. Many thought they were much smaller and shallower.
It's in some sense surprising that even basic facts like this are the current frontier.
"Hah, what do you know, scientist? You already admitted you don't know how the brain works!"
"Oh, you're damn right, what was I thinking? Please carry on."