![]() Instead HW encoded pice of code communicate via MOSI (Master Out, Slave In) and MISO (Master In, Slave Out) pins, with timing done by CLOCK pin. While the reset is hold, Arduino does not work, none of your programs are running. On the other hand ISP programming first set RESET on target Arduino (or other chip) and holds it. Basically you are communicating with some program on Arduino and the program (which you can modify) stores some data to Arduino flash memory. When you send in the right commands, it read data from the serial connection (usually converted from USB (Universal Serial Bus) by ATmega8u2) and stores the received data to selected program memory. ![]() The normal way you program Arduino is serial, where on the Arduino is loader program (bootloader), which communicates with you. ![]() I would like to just add my point of view:
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