First Apple came up with Thunderbolt, the crazy fast port that it developed with Intel and they followed that up with the Lightning connector for the new iPhone and iPods. If you think of weather, we don't get bolts of thunder, we get bolts of lightning. The ports should probably be called LightningBolt and Thunder.
Then there is the problem of physics. Lightning is of course the arc of electricity that we see as a bright flash of light. Light travels at about 700 million mph. Thunder is the sound that accompanies a flash of lightning and it travels at about 700 mph. Despite the fact that thunder travels at about 1/1,000,000th of the speed of light, that's the name that has been applied to the speedy computer interface while the Lightning is used to label the relatively laggardly USB2 based iOS connector.
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