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Several colleagues of mine have been analysing for amino acids in fossil
material for many years now.  They are also doing some DNA sequencing of
more recent fossils.  There is quite a lot of organic material held
within the crystalline structure of the skeleton of animals
(intracrystalline organics).  Most of the studies have centres on
brachiopods, both articulate and inarticulate, but more recently due to
media pressure they have also analysed vertebrate material (including
dinosaur).  I had my dinosaur eggs analysed by two laboratories and
found the egg shell to contain virtually no amino acids (we didn't use
EDTA as this can cause contamination of samples).  There was, however,
some organic material left which we have not yet analysed but think it
may be amides.

As for the fossilization of bones etc., Most fossils I deal with retain
a substantial amount of their original material although, in the case of
vertebrates and some invertebrates, the replacement by phosphates
appears to have taken place at the molecular level.  The microstructure
of the skeleton down to micron level is retained.  Much of the
replacement may occur quite rapidly.  In the case of crustaceans,
probably a matter of days.  With vertebrates the skeleton is more solid
and the mineralization is not necessarily as fast (in fact in some cases
it may take thousands of years).  

Neil Clark
Glasgow University