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Re: blog: semantic dissonance in uniprot

From: Peter Ansell <ansell.peter@gmail.com>
Date: Wed, 1 Apr 2009 06:57:37 +1000
Message-ID: <a1be7e0e0903311357m445562b4s54f76a99c2c7eec8@mail.gmail.com>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>
Cc: Matthias Samwald <samwald@gmx.at>, Oliver Ruebenacker <curoli@gmail.com>, Pat Hayes <phayes@ihmc.us>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
2009/3/31 Phillip Lord <phillip.lord@newcastle.ac.uk>:
> "Matthias Samwald" <samwald@gmx.at> writes:
>> To use a (still quite naive) physics example: 'Temperature' is a quality of an
>> object (say, a solution in a petri dish). This quality only inheres in the
>> solution, but not in a single molecule.
>
> I think this is wrong; temperature can be applied to a single molecule.
> If my physics has not disserted me, I think it can also be applied to a
> vacuum; i.e. a bit of space with nothing in it.

Temperature can be applied to a partial vacuum. Space as we know it
does have particles, they are just very very sparsely distributed.
Temperature is just an average, and there is no rule against being
able to derive an average with one sample, they just don't mean much.

>> Rates of change could be described as qualities of qualities (I think
>> the top-level ontology DOLCE allows this, but it would be difficult in
>> BFO, for example).
>
> It can't be done in BFO, as qualities can't have qualities. You'd have
> to describe the rate of change as a quality of the thing; so both
> velocity and acceleration would be qualities of a continuant that is
> moving over time.
>
>
>> 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.

I was always taught that reaction coefficients were really measured in
moles, and not molecules, hence the allowance for any given set of
numbers as long as the overall ratio stayed the same. If you wanted
all integer coefficients then you likely went for the ratio with all
integers and the lowest sum, which might not include a coefficient 1.

Cheers,

Peter
Received on Tuesday, 31 March 2009 20:58:17 UTC

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