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]
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