Formaldehyde fixes we assume by creating cross links between proteins
thereby creating a gel; soluble proteins are bound and that gives strength
to the gel and helps to withstand processing. These cross links are between
basic acid lysine and other groups (amido, peptide, hydroxyl, etc). Formalin
is not a coagulant (precipitant) fixative but it's an additive fixative; it
does not harden and is reversible; however it stabilises the proteins and
prevents subsequent hardening by alcohols.
Ethanol disrupts the hydrophobic bonds which maintain the structure of
proteins (coagulant fixative); hydrogen bonds are more stable in ethanol
than water and so the structure is preserved. Both bound and unbound water
molecules will be replaced during fixation.
I can only conclude that formalin is unable to prevent the damaging effects
of processing if the gel has not been allowed to form adequately or if it
the gel is disrupted by 'washing'. I also assume that too much 'processing'
collapses the gel (removes soluble proteins) and allow ethanol to 'harden'
proteins (look at the bottom of the processing retort or the waste); maybe
this collapse is in part due to the removal of 'bound' water or the
condensation/ removal of proteins. Different tissues or different species
contain differing proteins and therefore the effects of fixation and
processing will differ to. The effects of raised temperatures will be to
exacerbate the condensation/ removal of proteins from the gel or to increase
the deleterious effects of ethanol on 'unfixed' tissues (increase its rate
of action). I don't follow the illogical presumption that fat has anything
to do with it as the effects would not only differ between species but would
differ within species (fat one's would process differently than thin one's,
in any given species). It may well be that the difference is the result of
the different proteins that make up tissue in the differing species and the
vagaries of the stabilising effects of formalin which include its removal by
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