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Re: [ontolog-forum] FW: Re: FW: Self Interest Ontology - Bacteria UseCas

To: "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Rich Cooper" <rich@xxxxxxxxxxxxxxxxxxxxxx>
Date: Sun, 14 Aug 2011 12:04:30 -0700
Message-id: <2503B506F3E64790AF807EB5A73EC8F8@Gateway>

Hi Richard,


Comments below,




Rich Cooper


Rich AT EnglishLogicKernel DOT com

9 4 9 \ 5 2 5 - 5 7 1 2

From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx [mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Richard Vines
Sent: Saturday, August 13, 2011 6:29 PM
To: ontolog-forum@xxxxxxxxxxxxxxxx
Subject: [ontolog-forum] FW: Re: FW: Self Interest Ontology - Bacteria UseCase 1


Hi Rich,


> I don't understand the point you are making above.

> Could you explain it in other terms I might be more familiar with

> please?


My overarching point is really about the nature of emergence itself. To untangle the language it might be easiest to look at this diagram on page 162 of this book chapter. This shows what I mean by the focal level between higher and lower order systems.


Here is that diagram:


Some explanation is also provided on pages 161-163. This is set within a context of exploring an "ontology of knowledge". It might not directly be the same form of ontology as this group focuses on, but it is sufficiently related for me to think we are still conversing in line with the objectives of this ontology forum.


The ontology of self interest I proposed must have multiple levels as well.  For example, the individuals Strepta, Chlamy, Bacilla and Amoebi each act in their own self interest.  The film as a whole is at least one level up, and comprises emergence of the individual actions.  Can we say that the film acts in its own self interest?  I think not because the film is not an individual.  We can subscribe to the practice of rampant anthropopathy (which I already used in describing the individual bacteria) and say the film acts in such a way.  But using our language in such metaphorical ways should not lead us to believe in the actuality of the film acting.  Only the individuals truly act. 


Knowledge (in that example) is encoded in the genes of the individual actors, not genes of the film, which is a ménage a trillion (or whatever the French word is for very large).  So knowledge is different, distinct, and possibly partially shared among the individuals, but is not a property of the film at the next level up, IMHO. 


In this book chapter, we suggest emergence is understood as occurring where “the characteristics of the sub-systems (Individuals) and the super-systems (film) do not characterise the emergent patterns”. Your case study seams to be a summary of the different systems and the impact of the interaction between the higher order and lower order systems.


Uh, ok.  It would seem that the film brings together the intervals who, in concert, created the film by multiplying often and with energy provided by their chemical storage, sensors and effectors.  But all the energy was, and remained, in the individuals.  If the noxious chemical really was antibacterial toothpaste, then only a tiny fraction of the individuals in the film remained (maintained genetic knowledge) to create the next film.  Amoebi was one of the lucky ones, but she shared the vast majority of her genes (recorded knowledge) with the likes of Strepta and Chlamy and Bacilla, who acted in an emergent way to protect the stored knowledge. 


> So you prefer the word "related" here, which is ok with me.  It really

> is just a relationship between Strepta's world (as well as a bacterium

> can perceive it) and Strepta's controls over that world.


It is not that I prefer the word "related". I am making the point that what emerges at the boundaries between a higher order and lower order system when a perturbation occurs is non-causal.


This is where I get confused.  The actions taken by Strepta et all were causal (and produced by their individual interpretations of their nuclear genes) and without those actions, the film would not have emerged in the first place, nor would it be preserved after the noxious toothpaste destroyed most of the film. 


There is no relationship between the characteristics of the emergent system and the higher and lower order systems. When I refer to perturbation I am referring to the impact from the higher order system that involves the “application of toothpaste”.


I still don’t get it.  The toothpaste was wielded by the owner of the teeth, who in his own actions, destroyed most of the film for generations.  I could see that position when only the physics of mechanical systems is involved, but there is no knowledge in such a system, only structure.  Strepta et al could evolve to build new knowledge as a result of selection so that some future film might be resistant to the noxious toothpaste.  But hydrogen and oxygen always make water and other well known combinations, but never “learn” new compounds, so don’t evolve new knowledge. 


Strepta's control that you describe is a form of knowledge. Control information is used to maintain the coherence of its own system. This is in line with the radical constructivists position that suggests that Strepra does not know itself to be Strepra, and can only interpret the world from its own frame, and uses control information to manage the boundaries of distinctions between “itself” and "non self".


Yes, I can see reason to believe that way, since Strepta et al are repositories of knowledge that can be advanced through evolution and reproduction to create the new knowledge in genetic recordings. 


> But pure knowledge is so sterile; I can get knowledge of things and

> relationships from a paper, but I have to understand a PERSON to

> really understand that person's self-interest.  I still prefer to

> focus on self-interest as the source of a certain kind of knowledge

> (such as how-to knowledge, not as well covered in the AI world as

> declarative what-is knowledge).


I am not sure if we are on the same page when we are referring to knowledge here. When I refer to knowledge as an emergent property of an evolutionary system, I am suggesting that this idea can potentially extends to lower order systems like bacteria. Strepta's control information is a form of knowledge.


That I agree with. 


Having said that, I am not an evolutionary biologist myself and my interests are more to do higher order expressions of knowledge - not really to do with your case study. We have included as an appendix to the above chapter a preliminary ideas about an ontology of research knowledge support systems (pages 184-188).






Thanks for your thoughts on the subject, and it seems that we agree more than disagree. 





Chapter quoted:

  1. Vines, R., Hall, W.P., McCarthy, G. 2010. Textual representations and knowledge support-systems in research intensive networks. (in) Cope, B., Kalantzis, M., Magee, L. (eds). Towards a Semantic Web: Connecting Knowledge in Academic Research. Oxford: Chandos Press, pp. 145-195.




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