This item is from the Yet Another Enhanced IDE/Fast-ATA/ATA-2 FAQ, by John Wehman and Peter den Haan with numerous contributions by others. (v1.92).
To understand the basic concepts of advanced ATA drives, one first needs to understand the basics of drive technology. Basically, when the operating system needs data to be either read or written to secondary storage (the hard disk), the BIOS gets the command, and passes that command to the drive. For operating systems other than DOS, the BIOS is usually replaced by the operating system's own I/O subsystem; the principle remains the same.
How the command is passed, interpreted, and responded to, forms the basis for Advanced ATA. In a nutshell, there are seven registers that the BIOS writes to/reads from to create a command. An eighth register is used to read and write data. The signals that create these reads and writes are controlled by the BIOS, but their timing is determined by the interface hardware, and ATA specifications dictate how fast these signals can be asserted or deasserted. There are currently 4 modes of Programmed Input/Output (PIO) and 4 modes of Direct Memory Access (DMA). The numbers all of you have been reading about are only a small portion of these specifications, but they are the ones that marketing can tout best. These "transfer rates" are a result of the specification that controls how fast the I/O Read and Write cycle time of the data register can operate at.