The mistake that is made is the assumption that science is capable of explaining these things at all. Who says it can? Or that it should? We are talking about the sound of music; human expression. In all the talk about wether differences in cables (and whatever else) can be heard or not, very little time is spent talking about music; what it is, and what a miracle it is that one can reproduce something that is capable of touching our emotions. Can a "scientific" explanation really be expected to fully explain that which is the result of the soul of a performer; and how it may touch any given listener's sensibilities? I don't mean to get overly metaphysical about this, but to make this leap is to not really understand just how deep and fragile music is. That it can travel, via electrons, through a maze of electronic componentry and come out the other end sounding anything like the original is truly miraculous. That it should be altered to some degree by any and all the parts of that maze should not be a surprise at all.
Science has, for decades, been trying to analyze what it is that makes Stradivarius violins sound the way they do. They have analyzed every single aspect of their makeup; down to analysis of the varnish and glue used, in the hope of being able to replicate their sonic magic. They can't do it.
