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

[Amelia Ireland]

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