Remove or clarify penicillin example in reference document

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p60 of the ref doc states:

"Each function has a bearer with a specific type of physical make-up. This is 
something which, in the biological case, the bearer is of a type which has 
naturally evolved to carry this function (as in a hypothalamus secreting 
hormones). In the artifact case, it is something which the bearer is of a type 
which is the result of design (as in an Erlenmeyer flask designed to hold 
liquid) or also (as in the case of penicillin) has been deliberately selected 
for"

My reading of this is that penicillin is both the result of design, and has 
been deliberately selected for. Neither is true. The penicillin biosynthesis 
pathway exists in nature, and the genes responsible arose through evolution, 
not design, and were not *deliberately* selected for. Of course, since its 
discovery, there have been many instances of the molecule produced via both 
total synthesis and industrial fermentation processes. Whilst these processes 
involve some aspect of human design, it is incorrect to say that a penicillin 
molecule (whether naturally produced or manufactured) is "of a type which is 
the result of design".

I think this is an interesting example and deserves further treatment (along 
with function of molecules in general). But the current cursory treatment in 
the reference document serves to confuse rather than elucidate.

I recommend removing OR linking to an external reference with a better 
treatment.

(or simply removing evolved function from BFO - evolved function should be 
separated into a domain ontology with input from experts. But that's for 
another discussion...)

Original issue reported on code.google.com by cmung...@gmail.com on 10 Dec 2012 at 1:33