> Why should it even be possible to control it in software?

Because there's usually an IC on the motherboard that reads the temperatures 
and controls the fan PWM.  This is mapped to memory so that the BIOS can 
control it.  Obviously this means any software running (an OS, a special 
program, etc) can also take control.

> The correct algorithm is simple: set the fan to the lowest setting that 
> gives acceptable cooling.

That's what it does!  But you have to take into account that there are many 
different fan and CPU combinations that will be used on a motherboard, not 
giving the option to change the settings would be a bit limiting.  (Plus it 
would make it hard for the BIOS to setup the IC, currently it just writes 
the data to a certain memory address).

> Why would you want to be able to control it in software at all?

How else do you propose doing it, that isn't 10x more expensive than the 
current method?

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