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[Gofriends] Mistake in GO structure?

Wacek Kusnierczyk waku at
Mon Jan 17 08:31:52 PST 2011

On 1/17/11 9:40 AM, David Hill wrote:
> " The process of gaseous exchange between an organism and its 
> environment. In plants, microorganisms, and many small animals, air or 
> water makes direct contact with the organism's cells or tissue fluids, 
> and the processes of diffusion supply the organism with dioxygen (O2) 
> and remove carbon dioxide (CO2). In larger animals the efficiency of 
> gaseous exchange is improved by specialized respiratory organs, such 
> as lungs and gills, which are ventilated by breathing mechanisms.
>> "
>> This 'definition' says, among others, two things:
>> (a) gaseous exchange is gaseous exchange;
> No, it says it is a gaseous exchange between an organism and its 
> environment. There are other types of gaseous exchange, like the one 
> that happens in the cylinder of my car.

okay: it says that X gaseous exchange is gaseous exchange in Y.  This 
does not clarify what is meant by 'gaseous exchange'.  You seem to mean 
the sum of the processes of gas diffusion between the air and blood in 
the lungs AND the processes of inhaling and exhaling the air to and from 
the lungs.  I mean just the former.

You seem to confuse (in the sense of blending together within the GO, 
and not in the sense of being unable to see the difference) the exchange 
of the gasses *oxygen* and *carbon dioxide* between the blood and the 
air (which is what I think is precisely the meaning of 'gas exchange' in 
human physiology) with the exchange of the *mixture of gasses* called 
'air' between the lungs and the environment.

>> (b) in larger animals (that is?) gaseous exchange is improved by 
>> respiratory organs, which a re ventilated by breathing mechanisms.
>> From (a), it seems that the author wasn't able to give a clear 
>> explanation of what precisely is meant by 'gaseous exchange'.  From 
>> (b), it seems that ventilation by breathing improves gas exchange, 
>> from which it is very hard to me to draw the conclusion that 
>> breathing *is* respiratory gas exchange.
> The second part of the definition explains why in larger organisms, 
> simple diffusion does not suffice.

I'm sorry, but there is no single part of the definition that would 
explain that.  The only thing said is that efficiency of gaseous 
exchange is improved by respiratory organs.  The term 'insufficient' 
does not appear anywhere, lest be it explained what the source of 
insufficiency is.  And insufficiency is certainly not a necessary 
prerequisite for improvement; sufficient can be made better.  You're 
reading between the lines; which is fine with me and you, but may be not 
with the causal GO user (a computer scientist doing work on ontology 
matching, say), and certainly not for an automated system that would 
have to parse (omigosh) such definitions.

Because simple diffusion between the organism and the environment does 
not suffice in larger animals (you should be more specific here, it's 
unacceptably vague for any serious purpose), gas exchange is aided by 
both ventilation and circulation.  The respiratory system takes care of 
the former, and gas exchange (in the sense I'm buying into) is done in 
collaboration between the respiratory and the circulatory system.  It's 
their communication channel.  Anyway, if you agree that breathing and 
ventilation *improve* gas exchange, you should not be willing to say 
that breathing *is* gas exchange, or you'd have self-improving process 
(a nice thing to have, by the way).

And then on top of it there is respiration.


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