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Re: [ontolog-forum] Self Interest Ontology - Bacteria Use Case 1

To: "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Rich Cooper" <rich@xxxxxxxxxxxxxxxxxxxxxx>
Date: Sat, 27 Aug 2011 14:46:41 -0700
Message-id: <5C28F2C8F43F435980BE2CF9C1DC8785@Gateway>

Self Interested Ontologists,


Re Doug’s categories of interest and rewards, as applied to the scenario I sketched in John’s bacterial world of Use Case 1, I think the following cumbersome binding expressions work as a very first approximation, at least for discussion purposes.  Someone who knows CycL might be able to formulate these better:


Agents: Strepta, Chlamy, Bacilla, Amoebi;


Actions: (sends-message Strepta),

            (receives-message Chlamy),

            (splits Chlamy

(list Bacilla Amoebi)),

            (flails-cilia Bacilla),

            (pushes-with-gravity Bacilla),

            (moves-further-into-cavity Amoebi),

            (pops Bacilla),

            (is-coated-protectively Amoebi)



            (highest-benes Amoebi),

            (middle-benes Chlamy),

            (middle-benes Bacilla),

            (lowest-benes Strepta)



            (highest-mals Strepta),

            (middle-mals Chlamy),

            (middle-mals Bacilla)


Clearly Amoebi is the most benefacted by the actions of all four bacteria, but since the four share most of their genes anyway, all four receive benes in some amount, if you consider that the interest of all is to propagate their genes.  But Amoebi’s genes aren’t actually propagated by the actions in Use Case 1.  Her benefit and interest is entirely in surviving the noxious toothpaste, perhaps to propagate at some future date, but perhaps not.  That is,



            (propagate-genes Strepta),

            (propagate-genes Chlamy),

            (propagate-genes Bacilla),

            (survive-event Amoebi)


By rewriting these approximations into some more CycL format, perhaps we can specify the Situation-Action-Reward spectrum for all the players in the Use Case 1 so that Doug’s ontology of self interest can be more aligned with that use case. 


Comments, suggestions, critiques, curses?





Rich Cooper


Rich AT EnglishLogicKernel DOT com

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

From: Rich Cooper [mailto:rich@xxxxxxxxxxxxxxxxxxxxxx]
Sent: Friday, August 12, 2011 6:31 PM
To: '[ontolog-forum] '
Subject: Self Interest Ontology - Bacteria Use Case 1


Self Interested Ontologists,


Let’s consider a use case for the bacterial film example.  I will propose one, and if there are comments, please feel free to add your $0.02 or to correct mine as appropriate. 




A bacterial film covers teeth.  One bacterium, Strepta, senses a chemical gradient she associates with problems to come.  So Strepta sends a chemical message M to the film at large. 


Further away in the film, Chlamy identifies the message, which she interprets as “Watch it; there is dangerous antibacterial toothpaste in the vicinity.” 


Chlamy senses the direction of the message, and quickly forms a waist in the plane of the message direction, then splits at right angles in the cross product, splitting into two daughter cells Bacilla and Amoebi, while Chlamy ceases to exist as a unit, having split. 


Bacilla is on top, and her weight plus her flailing cilia push Amoebi one micron down into the cavity.  When the noxious chemical (was it really toothpaste?) touches Bacilla, she pops, spreading proteins, fats and carbohydrates which coat Amoebi in her cavity, effectively protecting Amoebi from the noxious chemical gradient. 


Strepta may share very few genes (self interest objects) with Chlamy, but Chlamy’s offspring have very accurate copies of Bacilla’s genes, so both have mutually high self interest.  By splitting, Chlamy preserves her genes.  Bacilla preserves her genes, which are faithful copies of Chlamy’s, by protecting her twin sister Amoebi with her (Bacilla’s) own life. 


What is in it for Strepta?  She may be millions of generations distal from Amoebi, the ultimate beneficiary of Strepta’s message.  So the gradient of the film should somehow represent the contribution of Strepta’s gene pool to Amoebi, which is what gives Strepta (through their shared ancestral forebears) genetic reasons to send her message to distal parts of the film. 


Should there be a limit to the distality with which Strepta uses her cellular resources to send the message far and wide?  It should be related to the likelihood of Strepta’s genes being preserved as compared to the likelihood that her resources consumed to send the message are wasted, if the chemical turns out not to be toothpaste but simple custard. 


Wouldn’t statistical decision theory hold in this use case 1; wouldn’t the likelihood of resource loss be approximately equal to the likelihood that Amoebi, with genes that are equal to Strepta’s, is saved from annihilation to continue propagating those genes into a future film?  Wouldn’t the sensors and effectors used by Strepta evolve to be quantitatively related to the survival benefits enjoyed by her sacrificed materials?


Comments welcome,




Rich Cooper


Rich AT EnglishLogicKernel DOT com

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


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