What are the "pin's" uses? How do you program them (as in, what is inside those things?)?
The pin uses are whatever the chip is designed for. If it is a 555 timer then the pins, when hooked up correctly, will flash/turn it on and off at a constant rate. They work using semiconductor materials, and using different materials produces different effects (This isn't the best explanation but I cant explain it any other way).
If you want to program a chip then first you need the software and a programming board that connects to your computer. Then you get a PIC or Programmable Integrated Circuit. Then you plug it in accordingly to the board and plug the board into your computer and program for what you need it to do. You could even program it to do the same thing as a 555 timer if you wanted.
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I meant as in "How" they program. It's basically the same question as how did Microsoft make the Windows hardware? I want to know how they made the system I am using to type this up. How ____ made the program to make Internet explorer, and similar questions. How?