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Re: blog: semantic dissonance in uniprot

From: Matthias Samwald <samwald@gmx.at>
Date: Tue, 31 Mar 2009 14:09:54 +0200
Message-ID: <875035B2259F4A67979AE011724F715F@ms>
To: "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "Matthias Samwald" <samwald@gmx.at>
Cc: "Oliver Ruebenacker" <curoli@gmail.com>, "Pat Hayes" <phayes@ihmc.us>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>

>> Reaction equations describe stochastic processes, that's why you can
>> have non-integer molecule numbers
>
> I think you can't have non-integer molecule numbers because it makes
> no chemical sense. Half a molecule is a whole molecule of a different
> kind.

You can have reaction equations that look like

N2O5 ---> 2 NO2 + 1/2 O2

Which means that the number of O2 molecules that would be produced if the 
equilibrium would be shifted to the absolute right side is 1/2 of the number 
of molecules of N2O5 that would exist if the equilibrium would be shifted to 
the absolute left. This only makes sense if we interpret reaction equations 
as descriptions of pools of molecules and their stochastic processes, rather 
than single molecules. Representing reaction equations as processes where 
the participants are single molecules is wrong. In that case, one cannot 
blame OWL if one is running into inconsistencies.

Cheers,
Matthias Samwald

DERI Galway, Ireland
http://deri.ie/

Konrad Lorenz Institute for Evolution & Cognition Research, Austria
http://kli.ac.at/ 
Received on Tuesday, 31 March 2009 12:10:33 UTC

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