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Re: blog: semantic dissonance in uniprot

From: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>
Date: Tue, 31 Mar 2009 14:30:59 +0200
Message-ID: <49D20D03.3020502@idi.ntnu.no>
To: Matthias Samwald <samwald@gmx.at>
CC: Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Matthias Samwald wrote:
>>> 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

just that the coefficient 1/2 is not an absolute molecule number here. 
it is a relative molecule number;  here, the ratio of the number of
molecules of O2 to the number of molecules of N2O5 participating in
reactions described by the equation.

i'd agree that having non-integer *molecule numbers* sounds nonsense,
but having non-integer *relative molecule numbers* certainly doesn't. 
in any case, the equation

    N2O2 -> 2 NO2 + 1/2 O2

is equivalent to

    2 N2O2 -> 4 NO2 + O2

and you can always (i guess) avoid non-integer coefficients by
multiplying both sides by a constant.

> 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.


Received on Tuesday, 31 March 2009 12:32:26 UTC

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