Hi TB,
"The genomes contain species-specific and cellular-process-specific folds"
as far as i was aware the distribution of protein folds follows the pylogeny proposed by evolution. For example there are eukaryote specific folds that bacteria do not share, these common folds are used in a large number and variety of proteins consistant with an ancient origin followed by diversification. As you go up the tree there are plant specific folds and these are used in fewer proteins than the eukaryote wide folds consistant with a more recent origin.
It is true that the occurence of new folds is difficult to explain and seems to be a rare event, which is why there are so many folds specific to groups of organisms. Because they split from related groups before the specific folds were formed. Does fold distribution define 'kind' if so then 'kind' may well include many organisms, How about mammal 'kind'. I am also not aware of any species specific folds, i would be interested to find out what they are.
In fact the distribution of folds according to relatedness rather that according to function would seem to indicate common descent rather than common design. Why would a designer restrict certain folds to certain groups of organisms?.
"We can watch a bacterial phosphatase sequence morph according to environment - it is still always a phosphotase."
There are examples of genes that change function completely, antifreeze from trypsinogen in fish for example. Similar events that happened anciently would no longer be recognisable.
Although genes do exhibit minor variation due to environmental pressures there are many genes that are subject to very intense diversifying selection and so have a very high nonsynonymous mutation rate, this leads to genes changing alot not just into different alleles. So although functional category such as 'gamete recognition' may be preserved from an ancestoral protein to the current one it may no longer be possible to recognise the origin of the protein.
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