From: Glenn Morton (glenn.morton@btinternet.com)
Date: Wed Nov 20 2002 - 14:54:18 EST
Wayne wrote:
>Sent: Wednesday, November 20, 2002 4:57 PM
>Subject: RE: Dembski and Caesar cyphers
>But that is not what I am saying. Language is generally something
>that we _want_ to be understood (presumably). On the other hand
>code is something we don't want understood except by certain "trusted"
>readers. So for most language "intelligibility" is an essential
>constraint.
>Admittedly some people are unintelligible regardless of whether they write
>in code or not, but that is not the issue here.
>
>For example, a sentence like
>
>"xg5bob^nx k8?5x b^b5km5l5mblmg8"
>
>looks like nonsense, but if you used a translation table
>x=t; g=o; 5=' '; b = e; o=v; ^=r;
>n=y; ' '=h; k=i; 8=n; ?=g; m=s; and l=a,
>you eventually would get:
>
>"to everything there is a season"
>
>Because of constraints on the spoken language there
>are several repeated patterns that are too frequent.
>Too many 5s, too many x's too many m's for example. For
>a much longer fragment, it becomes increasingly easier
>to see that it is probably a language. I'm sure we
>could also write nonsense that looks like language by
>weighting certain characters to show greater frequency
>than others, but that is a different issue.
That situation doesn't work for a Vigenere cypher. I quote from Singh:
"Cracking a difficult cipher is akin to climbing a sheer cliff face. The
cryptanalyst is seeking any nook or cranny which could provide the slightest
purchase. IN a monoalphabetic cipher (Caesar cipher--grm) the cryptanalyst
will latch on to the frequency of the letters, because the commonest
letters, such as e,t and a, will stand out no matter how they have been
disguised. In polyalphabetic Vigenere cipher the frequencies are much more
balanced, because the keyword is used to switch between cipher alphabets.
Hence, at first sight,t he rock face seems perfectly smooth." Simon Singh,
The Code Book, (London: The Fourth Estate, 1999), p.67
The way a Vigenere cipher is cracked is if the person uses too short a
sequence for the keyword.
>
>Proteins use "standardized" translation machinery (with
>some exceptions of course) essentially without encryption.
>That's why pathogens can make a nuisance of themselves. On
>the other hand, the immune system is there to adaptively recognize
>"foreign words" and "delete them" from the database. So
>recognition is critical to biology and readability also.
>This significantly reduces the number of possibilities,
>although I agree that it is probably still enormous.
>
>> ...there are,
>> according to Yockey's calculation 10^94 different proteins
>> which will perform the same functionality as cytochrome c. see Hubert
>> Yockey, Information Theory and Molecular Biology, (Cambridge: Cambridge
>> University Press, 1992), p. 59.
>
>Not having easy and immediate access to Yockey's work here in Japan
>I cannot comment, but let me take a stab at it anyway. First I assume
>that cytochrome c roughly half coil and half alpha helix. Mutations in
>the coil regions are less damaging than secondary structural regions,
>so I estimate that the average variability in the amino acid sequence is
>about <13> residues (if you go through the some hundreds of cytochrome
>c sequences that are reported for different species). For the three
>alpha helices, I would expect less variability so about <5>
>residues variability
>per position. So that means for a protein of 104 amino acids that obeys
>the pairing behavior of random protein sequences, I would arrive at
>
>(52ln(5)+52ln(13)) --> 10^93.
>
>So I conclude that Yockey probably went through the database and looked
>at the per position variability of the sequence giving a more
>precise estimate
>than my off the seat of the pants shot can.
You didn't do bad. Yockey also paid attention to hydrohilic and hydorphobic
amino acids in his calculation.
After reading what is below, I want to say wait, a minute. I am really just
trying to point out that Dembski's method of detecting design doesn't work.
I am not here trying to explain how molecules come about. Dembski claims he
can detect design. It is true he uses that with biomolecules, but he bases
his argument with letter sequences, which I showed in another post tonight,
can not be ruled out as a Vigenere cipher.
>
>Here's my objection. This is still treating the sequence as thought
>it is stupid letters on a page. The properties of proteins depend on
>their nearest neighbor interactions AT LEAST. That means one should
>look at tri-peptide patterns and this drastically reduces your degrees
>of freedom. In the above calculation, I would estimate it kills
>the exponent
>by half.
>
>
> (1/2) (52)( ln(5)+ln(12)) --> 10^46
>
>And now, on top of that, you have folding dynamics that make this structure
>the MINIMUM free energy. Forget that nonsense about suboptimal yada yada.
>It's mostly hogwash. Out of the set of sequences that can lead you toward
>a global minimum, I would estimate you need to half it again. So finally
>we have about 10^24 for the upper end, and possible 10^10 at the
>lower end.
>
>That is still enormous and far greater than the number of species, but it
>is finite compared to 10^94 or 10^135 (if you allow all degrees of
>freedom).
>
>At any rate, please note that I said:
>
> What function
> a given protein "serves", _might_ be somewhat
> arbitrary, but thermodynamics rules (as always)
> and that will set limits on what structures can be
> "meaningful" in that "some context".
>
>
>I'm not interested in taking sides on the main issue of this post,
>although I am inclined to think that Dembski's approach is not
>likely to make much progress especially since nature _wants_ to
>be intelligible, and he is approaching the matter from an "encryption"
>standpoint which is just the opposite of how the system seems
>to behave. Nevertheless, I think these probabilities require more
>thought because they are not quite as free as I often hear them
>implied to be.
No, Dembski is saying merely that random letters can be excluded from being
designed unless one is provided with a cipher code. But that means 2
things. 1. that random letters are not designed unless someone TELLS Dembski
that they are designed. and 2. it means that Dembski is ignoring the
infinitude of Vigenere cipher codes which can turn any random sequence into
any meaningful sentence of the same length. Because Dembski can't rule out
that some given random sequence is a cipher, he can't claim that something
ISN'T designed. If EVERYTHING has a possibility of being designed, then
Dembski's method is worthless.
>
>by Grace alone we proceed,
glenn
see http://www.glenn.morton.btinternet.co.uk/dmd.htm
for lots of creation/evolution information
anthropology/geology/paleontology/theology\
personal stories of struggle
>Wayne
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