Theory goes that the earth is a coalescense of materials in our area of the orbit, not once, but twice (including the moon forming collision). Helium being a noble gas would have to settle in using its own form. But that form would be incredibly light and likely rise to the top of our atmosphere, if not get blown off by solar wind, right? So how do we have helium here at all?
In: Earth Science
So you are right about the formation of the earth. What you are missing is that earth has a lot of radio active metals. Some of these decay into Helium atoms. That is how all helium came to be on earth.
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