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CronoDAS comments on Justifiable Erroneous Scientific Pessimism - Less Wrong Discussion
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"Continental drift" is usually the go-to example. For one, the mechanism originally proposed was complete nonsense...
They didn't have a mechanism at all until subduction and hence plate tectonics was discovered. The expanding earth theory was actually considered not implausible by geologists for quite a while - it didn't have anything like a plausible mechanism, but neither did continental drift. I was surprised to discover how recent this was.