RE: Information: Brad's reply (was Information: a very
Brad Jones (bjones@tartarus.uwa.edu.au)
Tue, 30 Jun 1998 13:57:35 +0800> >>
> >> I don't know what to say except to repeat what Yockey says in
> >> his book. In section 5.1.3 he states that the DNA-mRNA-protein
> >> system is discrete, memoryless and unconstrained. These terms
> >> are defined as follows:
> >
>
> Greg:==
> >Is Yockey talking just about the decoding context, where codons
> >are mapped to amino acids? Surely he doesn't mean that there
> >are no intersymbol dependencies in DNA when seen as a big part
> >of the schematic for a system which has to be alive.
> >
>
> Sorry about my delay. Perhaps this turns out for the best as
> I think I understand a little better where your coming from
> after reading your recent posts.
>
> Before going on, I better insert my standard disclaimer. When
> I wrote "I don't know what to say except to repeat ..." I
> really meant this quite literally. I have an amateurs interest
> in information theory and its application to molecular biology.
> I can relay what Yockey and others have said but I'm really not
> proficient enough to defend it.
>
> Having said that it seems to me that Yockey is only concerned
> with the decoding context as you suggest above.
>
> Now let me bring up a point that confuses me a great deal.
> Awhile back I spent some time looking at the controversy
> surrounding "meaning" in information theory. I think its
> important to point out that it is not only creationists
> who are uncomfortable with this aspect of information theory.
> Also, mistakes have been made at the highest levels, so to
> speak. For example, according to Yockey anyway, Manfred
> Eigen errs in this regard by trying to introduce _ad hoc_
> the idea of meaningful information in the development of
> his hypercycles. And again, according to Yockey, his
> hypercycles self-organize only as a result of this
> "meaningful" information in a similar but much more
> complicated way that Dawkins typing monkey always seems
> to find the target phrase :). Yockey is fond of saying things
> like "meaningful to who?" in order to make clear the teleological
> nature of "meaningful" information.
>
> Moving on, I gather from your posts that you would side with
> Yockey on the point that information theory cannot address
> meaning. But here's where I get confused. The analog to
> "meaning" in a biological application is functionality or
> specificity. So, while Yockey spends a great deal of time
> emphasizing the point that information theory cannot address
> the meaning of a message, he also spends a great deal of time
> later on in his book getting an estimate for the amount of
> information needed to specify a molecule of iso 1 cytochrome c (icc).
> Here he uses available information on functionally equivalent
> sites (sites where more than one amino acid can be present and
> retain functionality) in order to significantly reduce the
> information content of icc. So, is Yockey contradicting himself?
> I really don't think so, however, I think I'll leave this as an
> open question for the time being soas to avoid dragging on too
> long.
>
> OK, now there were some things about your recent posts that
> were bugging me for reasons similar to the above. In
> particular your post "More on information, meaning, and
> biological application". For example, you talk about all
> these things that *we* know and how this reduces *our*
> uncertainty and thus the information. But this makes
> sense (to me anyway) only if *we* are the receivers. But
> isn't it more appropriate to consider ourselves disinterested
> observers? The proteins are the receivers, how do all these
> things reduce their uncertainty? This doesn't at first sight
> seem objectionable wrt what Yockey did. The proteins do
> "know" about functionally equaivalent amino acids since
> "know" is just a convenient way of talking about the chemistry
> involved in the functional equivalence. I think. But I tend
> to get more confused the more I think about this.
>
> Brian Harper
> Associate Professor
> Applied Mechanics
> The Ohio State University
>
> "It appears to me that this author is asking
> much less than what you are refusing to answer"
> -- Galileo (as Simplicio in _The Dialogue_)
Brian,
I'd like to add something about how information theory deals with meaning.
1. Meaning is conveyed through information.
2. There is a minimum information that must be associated with meaning.
This is the true information content of a message.
3. Info theory is all about efficient transmission and storage of the
meaning.
4. Information theory REQUIRES that there is meaning. ie anything random is
noise not information.
5. Randomness can carry information (and hence meaning) but it IS NOT
information in itself.
6. Information Theory does not state what the meaning is, but it MUST be
there.
7. Better understanding of the meaning allows more efficient use of
information to convey the meaning.
8. Information Theory treats all randomness as NOISE, nothing else.
9. When a source is "random" it means that the person listening does not
know what comes next. It does not mean it is actually random information. ie
to the source it is not random at all.
10. When a source is being modeled that actually does contain a degree of
true randomness then it is modeled as a source and channel combined.
11. Any information storage medium is modeled as a channel, never a source.
I hope this sheds some light on the relationship between information and
meaning as used by information theory.
--------------------------------------------
Brad Jones
3rd Year BE(IT)
Electrical & Electronic Engineering
University of Western Australia