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But I do think they can alter the taste of food in a very subtle way. I really think a glass of water that has been Microwaved for a few seconds tastes different to water that has been in the Kettle for a few seconds.

I think it's like Bitt said, you're probably heating the water in different containers, which I'm sure affects its taste.

Myself, I've never thought twice about microwaved water or any liquids. Then again, I never heat water on the stove so I don't really know what that that tastes like. I'm guessing it tastes like water.

I prefer the third method. I have an instant-hot faucet in my kitchen. Steaming hot water whenever I need it!
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Matt