[Ontology-editors] [Transport] calcium ion transport question - necessarily directed?

[Peter D'Eustachio]

Sure. Under any given set of circumstances the movement due to the activity 
of a facilitated transporter has a direction, but that direction is due to 
the environment (on which side of the barrier is the concentration of the 
molecule being transported higher at the outset), not to any intrinsic 
property of the transporter. That, I think, is one of the defining 
properties that distinguishes facilitated transport activities from active 
transport activities - in the latter case, movement is only normally 
possible in one direction and that direction is an intrinsic property of the 
transporter.

Peter

----- Original Message ----- 
From: "Amelia Ireland" <aji at ebi.ac.uk>
To: "Peter D'Eustachio" <eustachi at cshl.edu>; "Chris Mungall" 
<cjm at berkeleybop.org>; "Ontology Editors" 
<ontology-editors at genome.stanford.edu>; "transport" 
<transport at genome.stanford.edu>
Sent: Friday, February 06, 2009 1:36 PM
Subject: Re: [Ontology-editors] [Transport] calcium ion transport question - 
necessarily directed?


> On 5 Feb 2009, at 12:24 PM, Chris Mungall wrote:
>
>>> thought transport sensu GO meant *directed* movement.
>>>
>
>>> If I were to sneak into a zoo at night and unlock all the cages,  would 
>>> I be directing all the monkeys and lions into the  surrounding city? I 
>>> guess it depends on my intentions.
>>>
>>> I think it's similar here. There is a hidden notion of agency in  the 
>>> GO definition of transport. Of course, cells have no  intentions, but 
>>> gene products have evolved to carry out some role,  so there is a form 
>>> of agency here. Even so it may be easier if  describe processes rather 
>>> than ascribing goals.
>
> I also thought that transport meant directed movement, and IIRC in  days 
> of yore, the transport standard def was along the lines of "The  directed 
> movement of xxx into, out of, within or between...". Is it  even possible 
> to have movement without something (e.g. concentration  gradients, 
> physical forces, the will of God...) "directing" it, though?
>
> From a semantic POV, 'transport' implies some sort of conveyor or 
> carrier, so one might consider that carrier as "directing" the  movement, 
> i.e. anything described as 'transport' is directed.
>
> I agree with Chris that if you start taking a more teleological view  of 
> these processes, things get tricky, especially if you're trying to  find 
> or assign a "director" to your transport process. I think it  would be 
> easier if terms simply described the physical movement from A  to B, with 
> appropriate children if there is a specific form of  mediation involved, 
> without trying to discriminate between "directed"  or "undirected" 
> movement.
>
> --
> Amelia Ireland
> GO Editorial Office
> http://www.berkeleybop.org || http://www.ebi.ac.uk
> BBOP Plant Project: http://bbopgarden.blogspot.com
>
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