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Re: [ontolog-forum] Ontology and methodology

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Ingvar Johansson <ingvar.johansson@xxxxxxxxxxxxxxxxxxxxxx>
Date: Mon, 19 Mar 2007 16:11:07 +0100
Message-id: <45FEA80B.4010600@xxxxxxxxxxxxxxxxxxxxxx>
David Decraene schrieb:
> Note that one might also debate on the nature of 'enzyme', is that a protein, 
>or a role that can inhere in a protein?
I think the only way to solve this and similar problems is to make a 
*tripartite distinction* between (i) 'inhering properties' (e.g., shape 
and mass), (ii) 'inhering capacities', and (iii) 'roles/functions'. The 
ordinary way of talking about enzymes (= proteins that catalyze chemical 
reactions) fuses, if not all three, at least the last two categories. A 
protein can have the capacity to catalyze a certain chemical reaction 
even if this capacity is never used/realized; therefore, the capacity 
*inheres* in the protein, i.e., the protein has the capacity 
independently of context. Nonetheless, the capacitiy is not an ordinary 
property such as its mass, in relation to which a distinction between 
being used/realized and not being used/realized makes no sense. On the 
other hand, to have the role/function of 'being an enzyme' is an 
implicitly *relational* characterization; role/functions relate 
something, here  proteins, to some kind of surrounding, context, or 
functional whole.    (01)

/Ingvar J    (02)

Ingvar Johansson
IFOMIS, Saarland University
     home site: http://ifomis.org/
     personal home site:
     http://hem.passagen.se/ijohansson/index.html      (03)

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