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Yeah, this is something that I think doesn't really resonate with people well. The reactor site is 25 meters above sea level. I'm not exactly sure how high the generators were, but they were well above the level that experts thought was safe at the time. The earthquake was a 1 in 1000 year event and so there was no data on record to help them model the resultant tsunami. In the years following the tsunami, the way people modelled waves radically changed based on the new data.

There are a couple of caveats. First, there were markers saying that an historic tsunami had come in much higher than models would have predicted. However, the are very old. It's just a rock stuck in the ground with some writing on it. Stuff like that is all over Japan (there are lots of markers around where I live -- I don't think anybody pays any attention to them at all. Probably we should, but usually they just mark boring stuff ;-) ). It's like seeing a roman road marker in Europe. Interesting, but not really note worthy. It's only after the tsunami that people saw the markers and said, "Holy cow. There's a marker here showing that a tsunami came up this far". Even then it's a far cry from seeing that to saying that we need to invalidate all our wave building models.

Secondly, I think there is some evidence that in a few years preceding the tsunami that researchers were getting worried that their wave models were not correct. I think it's even the case that nuclear plant companies were aware of this. When I first moved to Japan in 2007, there used to be a section of the Meteorological Agency of Japan that showed, among other things, a map of the farthest in a tsunami would theoretically go for all parts of Japan. It also listed maximum wave size for every single place along the coast. It noted places where sea walls were not high enough and estimated worst case damages and numbers of casualties. Around about 2009 it disappeared. I tried to find out where it went and the response I got was that it needed to be updated and that it would return at some point in the future. Of course, it never came back. At the same time, I've heard that literally a few years before the Tohoku earthquake that there was serious debate about whether or not the wave models were correct. However, I think it's pretty clear that in 1967 when they started construction at Fukushima they had absolutely no idea that they were building in a potentially unsafe area.

It really sucks and I think it's fair to say that as humans we probably have too much hubris when it comes to our science. That fact that you have no reasonable way of knowing that you are making a mistake doesn't mitigate the problems that result from that mistake.