Add term 'life'

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Barry suggests adding a high-level term 'life' defined as follows:

a life is a process which has as parts all the processes in which a
given organism is participant

Original issue reported on code.google.com by albertgo...@gmail.com on 20 Nov 2009 at 9:04

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I would suggest "life course" as a label to make it more obvious it is a 
process. 

How would that be linked with developmental stages/process?

Original comment by mcour...@gmail.com on 1 Dec 2009 at 8:26

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My initial thought is that developmental stages/processes would be part_of life
course.  It also occurs to me that a stage would be linked to its preceding 
stage
(except for the "first" one) by a preceded_by relationship.

Original comment by hoga...@gmail.com on 3 Dec 2009 at 2:06

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I guess my concern will be trying to define life will not be trivial. What are 
the
required processes part_of life course?

Often it is reproduction, development, growth and adaptation, but there are
controversial cases like viruses: 
http://en.wikipedia.org/wiki/Virus#Life_properties
Based on the originally proposed definition "a life is a process which has as 
parts
all the processes in which a given organism is participant", and assuming OGMS 
will
use the OBI organism definition (union of Viruses, Bacteria, Archaea, 
Eukaryota) OGMS
would state that viruses are alive. 

Original comment by mcour...@gmail.com on 3 Dec 2009 at 6:30

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None of these definitions seems trivial.

The implication in your question is that processes are defined by their required
parts.  Since a part of a process is itself a process, this is not possible 
without
infinite regress.  What are the required parts of development?  What are the 
required
parts of those parts?  And so on...

I never feel like bumping up against places where the science itself is 
controversial
is a bad thing for ontology.  Yes, viruses are a boundary case.  It seems as 
though,
by including viruses in the definition of organism, OBI has already come down 
on one
side of the controversy.

Original comment by hoga...@gmail.com on 3 Dec 2009 at 7:28

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Barry had originally suggested 'independent continuant' rather than 'organism', 
which
would read

"a life is a process which has as parts all the processes in which a given
independent continuant is participant"

I only suggested 'organism' because it would block readings such as "the life 
of the
chair" which, while a clearly metaphoric reading from a biological standpoint, 
could
have a useful role in reasoning, namely by being the process in which the chair 
is
participant that is not a subpart of any larger such process (and thus 
maximal).  

I will check back with Barry, but I think he just wanted a term to serve this 
sort of
logical need (i.e., to have a maximally containing process in which an IC
participates), not to heat up debates on whether viruses are alive or to define 
the
"meaning of life" :-)

Original comment by albertgo...@gmail.com on 3 Dec 2009 at 7:41

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Yes, whether life is the appropriate term for what Barry intends, is debatable. 
 I
agree that the definition is useful, and that finding a term for it a good 
thing.

With respect to stirring up debate on the meaning of life, Barry has done it in 
the
past, so you never know ;-)

http://ontology.buffalo.edu/smith/courses03/Meaning.html 

Original comment by hoga...@gmail.com on 3 Dec 2009 at 7:46

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Isn't it the purpose of a discussion group to have a 'healthy debate'?  :) And, 
so far 
the discussions have been quite useful.

I agree with Bill in that process parts could be an infinite loop, but we don't 
have to 
go that far. All the parts suggested so far - reproduction, development, growth 
and 
adaptation - appear to be good candidates for terms that can be added too. One 
question 
that does arise is that are all of them necessary conditions?

Original comment by sivaram....@gmail.com on 3 Dec 2009 at 8:27

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Agree with the points above. I think that if the intent is to define 
life(_course) as
a process which has_part some other processes, then there may be a need to 
identify a
minimal set of processes that would be necessary conditions.

Regarding defining organisms and including viruses, we added specific editor 
notes to
the organism term in OBI:
- 13-02-2009: OBI doesn't take position as to when an organism starts or ends 
being
an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
- 10/21/09: This is a placeholder term, that should ideally be imported from 
the NCBI
taxonomy, but the high level hierarchy there does not suit our needs (includes
plasmids and 'other organisms')
Those have been the results of very long discussions and trials, at the end of 
which
OBI found this to be the most suitable solution.

I agree with Bill and it is fine to choose one side - ideally being aware of
potential issues and adding them in editor notes makes it easier in the long 
term.

I am a bit scared by touching on the meaning of life (and clicking on the above 
link ;) )

Original comment by mcour...@gmail.com on 3 Dec 2009 at 8:57

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Why complicate the definition of life course from the first suggestion? Is there
anything unclear about "a life course is a process which has as parts all the
processes in which a given organism participates"? 

I don't see the reason to add necessary requirements for specific developmental
processes to occur during all life courses, and think it will be easy to find
exception for any such restrictions. The relations should be the other way 
round: all
developmental processes are part_of some life_course. 

Original comment by bjoern.p...@gmail.com on 3 Dec 2009 at 10:39

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It seems to me that this definition makes the assumption that we are talking 
about an
alive organism. For example, I would not consider a decomposition process to be 
part
of the life_course of an organism.
Keeping that definition in my opinion means we are just shifting the problem to
defining when is an organism alive. 

Though maybe as mentioned by Albert earlier on, I may be mislead by the label 
"life".

Original comment by mcour...@gmail.com on 3 Dec 2009 at 10:57

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Added 'life course' (OGMS:0000092) in OGMS v0.5

Original comment by albertgo...@gmail.com on 31 Mar 2010 at 4:28

• Changed state: Fixed