It may be fine to think of the ear as doing a Fourier transform as a first, 
crude approximation. For a more accurate description however, some nonlinear 
effects would have to be considered. And some of this already happens in the 
ear.
As for hearing being LTI, think about forward and backward masking. Although it 
happens at a rather short time scale, it implies that time invariance is not 
always the case. Harmonic distortion and intermodulation of two sinusoids 
played loudly enough also speaks against linearity.
I haven't tried the experiment, but I recall a composer collegue once 
complaining about repetition in the noise generator of Csound. I think they 
used a random generator with period 2^16 in those days, but it's been improved 
now. 
Risto Holopainen

                                          
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