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I see one problem:

- Entire generation of programmers may not have any knowledge about how computer works

That's not a problem, it's an opportunity for those that do, and there will always be those that do.

No?

If that were to happen, it would be a problem with the programmers more than anyone else.

with JavaScript, there is no need to know how computer works, so why would anyone learn(deeply) about that?

You act as though Javascript will take over the programming world -- I can confidently say that it won't

mind you it will ... ( and i'm not pro javascript ).