(Fwd) on the ccai issue/ reading frame by kampis
Cliff Joslyn (joslyn@KONG.GSFC.NASA.GOV)
Thu, 9 Nov 1995 11:19:41 -0500
>From: "Hans-Cees Speel" <HANSS@sepa.tudelft.nl>
>To: Cliff Joslyn <joslyn@kong.gsfc.nasa.gov>
>Date: Thu, 9 Nov 1995 10:45:34 MET
>Subject: (Fwd) on the ccai issue/ reading frame by kampis
>Reply-To: hanss@sepa.tudelft.nl
>Priority: normal
>
>clif, could you forward this for me, since I can't seem to reach
>Bruce, and his automatic forwarding doesn't work at this time?
>thanks
>
>Dear pcp-ers.
>I have red the papers by Kampis and Pattee in the ccai-special issue
>on self-reference etc., and would like to start a discussion. To
>start with the paper of Kampis. I think this is relevant to our
>previouss discussion on self-reference, etc.
>
>Since I am not into logic and computation, I will leave the
>turing-bits in his paper to other memebers of this list. I would like
>to focus on his comparison between a turing machine with shifting
>readingframes, and the DNA machinery, to call it that.
>Kampis talks about self-modifying systems, and to do that he makes
>the comparison mentioned. He does this in section xI of his paper on
>http://ssie.binghamton.edu/people/rocha_docs/kampis.html
>
>He begins with an example of a virus that has a double coding in one
>dna-molecule. The molecule is one sequential string, but because
>there are two beginning messages on it [the message that tells the
>rna to begin reading there] it contains two codes.
>The environment of the DNA contains the information which tells the
>rna to begin reading at what place [1 or 2]. Kampis calls this
>environmental tinkering with reference to F Jacob [see my autograph].
>Of course the molecules that hold the 'environmental information' can
>also be controlled, and kampis says that this introduces an 'infinit
>depth' of layers that come into light by newer and newer 'contexts'.
>He calls this 'window of interaction' for the information readout a
>"reading frame".
>Then he says that in a Turing machine the reading frame consists of
>that encoding that connects the read-write head with the machine tape
>where the infromation is stored. In the simplest case this frame is
>one-to-one, a fixed interpretation.
>Tah nhe shifts back to the genetic case. He says the role of the tape
>is played by the genome. The role of the read/write haed by the
>biochemical routes from the genome to the ribosome, where proteines
>are made on the basis of the code [transcription]. The reading frame, he
>says, is
>'the current expressability of the genes in terms of their structural
>products'.
>He goes on to say that the changing transcription method in this
>case, the corresponding contextually defined production rules
>correspond to changing or shifting reading frames. [stuff deleted]
>Then he says that this is an example of causally generated
>self-reference. Later on the same page he continues tosay that there
>is a fundamental difference between a bounded and a unbounded set of
>reading frames, where the first refers to algoritms, and the second
>to self-modifying systems.
>
>I add that I interpreted his paper a bit, so you might want to read
>it yourself.
>
>My problems are as follows:
>1) He says that the DNA-RNA-proteine pathways are equal to the
>read-write head. I agknowledge that DNA can be red, but not written.
>It is firstly random addited [ written] by mutations, etc. and after
>that selection can take out the badly written stuff.
>
>2) The relation between which context in the
>cell is present [i.e. what proteins are there that have a controle
>over dna-reading] and the dna that is red, can alter, but only by
>mutation.
> Kampis does not refer to evolution, only to an existing
>cell-mechanism. We need evolution, especially weeding-out, to explain
>why potential mutated control-mechanisms are still functional
>[because they die if they are not functional, given they {or the body
>they are a part of} have to compete].
>His argument misses the reference to evolution as a
>mechanism to explain the shifting context [reading frames] ,
> that is if he wants to
>claim that this context is an unbounded set. He says that
>self-modifying systems have such an un-bounded set of frames.
>Now it is possible that I understand him wrong, and that he takes the
>stand that the reading frames in an organism are indefinite without a
>shift by mutation. In that
>case he needs not refer to evolution of course. But I don't see how
>this can be.
>
>3) He describes the reading frame as
>a] the encoding between writehead, and tape
>b] the expressibility of the genes in terms of their structural
>products
>c] a window of interaction for the information readout
>and c] changing reading frames are contextually defined production rules
>
>I can't seem to see the common feature here:-(
>
>So far my comments. Ihave the feeling that Kampis confuses
>self-modifying systems with self-referent systems, or that I make
>this distinction, where it doesn't exist. I think a self-referent
>system, like an organism has a lot of internal signalling to steer
>itsself. It cannot modify its encoded DNA structure however, since for
>that we need mutation. With mutation added, you get a self-modifying
>system, like a learning system. But a learning system is not always
>equivalent to
>an autopoeietic system. A species can learn by natural selection, not
>an organism. And since Kampis talks about DNA code, he must be
>talking about evolution.
>
>Well, am I right, or confused?
>
>Hans-Cees
>
>Theories come and go, the frog stays [F. Jacob]
>-------------------------------------------------------
>|Hans-Cees Speel School of Systems Engineering, Policy Analysis and
>management
>|Technical University Delft, Jaffalaan 5 2600 GA Delft PO Box 5015 The
>Netherlands
>|telephone +3115785776 telefax +3115783422 E-mail hanss@sepa.tudelft.nl
>
>HTTP://www.sepa.tudelft.nl/~afd_ba/hanss.html featuring evolution and memetics!
>
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| Cliff Joslyn, NRC Research Associate, Cybernetician at Large
| Mail Code 522.3, NASA Goddard Space Flight Center, Greenbelt, MD 20771 USA
| joslyn@kong.gsfc.nasa.gov http://pespmc1.vub.ac.be/joslyn 301-286-5773
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