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Re: blog: semantic dissonance in uniprot

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Thu, 26 Mar 2009 15:45:09 +0000
To: Pat Hayes <phayes@ihmc.us>
Cc: Oliver Ruebenacker <curoli@gmail.com>, Mark Wilkinson <markw@illuminae.com>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-ID: <87bprothiy.fsf@newcastle.ac.uk>

Pat Hayes <phayes@ihmc.us> writes:
>> Besides which, the issue being discussed here is one of equality. When
>> are two proteins the same protein?
>
> TWO proteins are never the same protein. Two mangelwurzels are never the same
> mangelwurzel, either. What 'same' means, is that there is ONE  thing with two
> names. Being the same as is never a relationship  between two different
> things.


This is obvious; the question is about types of proteins. A statement
like: "every protein molecule in the world is different from every other
protein molecule" is true, but more or less totally useless. 

We are talking about proteins not protein molecules; if I give you a
solution of protein molecules, all the same, and you split it into two
halves, do you now suddenly have two proteins?

Protein is a mass term. You would agree that two glasses of water both
hold the same substance; just so for protein. The question is, then,
when are two samples of protein, samples of the same protein. A
secondary question is, how do we represent this computationally. 

We are going around in circles here; I think that I have said enough. 

Phil
Received on Thursday, 26 March 2009 15:46:06 UTC

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