RE: Emergence of information out of nothing?

From: Glenn Morton (
Date: Thu May 09 2002 - 00:45:23 EDT

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    Hi Peter, you wrote:

    >-----Original Message-----
    >From: Peter Ruest []
    >Sent: Wednesday, May 08, 2002 9:21 AM

    >Of course, a function can only be executed if the appropriate substrate
    >is available. The operation on this substrate is what defines the
    >particular functionality (or capacity for functioning). But this
    >functionality requires a certain specific structure. A different
    >structure will perform a different function - or none at all. Now this
    >structure is inherently present in this protein molecule, whether or not
    >its substrate is around. The function just is not being executed.

    This fits exactly my point as the substrate is merely another molecule. and
    functionality is only seen in relation to a given molecule. Bring another
    one in and you will have a different functionality or none at all. Function
    is relative not absolute.

    >Therefore, I consider some kind of functional, structural, or semantic
    >information (II) to be contained in the structure of this protein, and
    >this structure is a consequence of its amino acid sequence, which in
    >turn is a consequence of the DNA sequence coding for it, and this
    >information (II) is a certain (usually unknown) fraction of the
    >information capacity (I) of this length of DNA.

    You use the example of Yockey's work with cytochrome c below. He found there
    were 10^93 different cytochrome c's which would perform the work of that
    molecule. What he didn't prove was the possibility of huge numbers of other
    FAMILIES of proteins which will also do that job. Given the work of Joyce
    and others (which you didn't mention in your reply) they have found that if
    you choose a function and search for it with random molecules and random
    mutation, you can find any given function with a probability of 1 in 10^14
    to 1 in 10^18. I cite this:

    Andrew Ellington and Jack W. Szostak "used small organic dyes as the
    target. They screened 10 13 random-sequence RNAs and found molecules
    that bound tightly and specifically to each of the dyes.
            "Recently they repeated this experiment using random-sequence
    DNAs and arrived at an entirely different set of dye-binding
            "That observation reveals an important truth about directed
    evolution (and indeed, about evolution in general): the forms
    selected are not necessarily the best answers to a problem in some
    ideal sense, only the best answers to arise in the evolutionary
    history of a particular macromolecule."~Gerald F. Joyce, "Directed
    Evolution," Scientific America, Dec. 1992, p. 94-95.

    And I cite this:

    "We designed a pool of random sequence RNAs, using the minimal ATP
    apatamer as a core structure. By creating a pool that was
    predisposed to bind ATP specifically and with high affinity we hoped
    to increase the likelihood of generating molecules with ATP-dependent
    kinase activity. The ATP apatamer core was surrounded by three
    regions of random sequence of 40, 30 and 30 nucleotides in length,
    respectively. The ATP-binding domain itself was mutagenized such
    that each base had a 15% chance of being non-wild-type, to allow for
    changes in the apatamer sequence that might be required for optimal
    activity. To increase the likelihood of finding active molecules, we
      attempted to create a pool containing as many different molecules as
    possible. Because it is difficult to obtain an acceptable yield from
    the sysnthesis of a single oligonucleotide of this lenght (174
    nucleotides), we made two smaller DNA templates and linked them
    together to generate the full-lenght DNA pool. Transcription of this
    DNA yielded between 5 x 10^15 and 2 x 10^16 different RNA
    molecules."~Jon R. Lorsch and Jack W. Szostak, "In Vitro Evolution of
    New Ribozymes with Polynucleotide Kinase Activity," Nature, 371,
    Sept. 1994, p. 31

    We can act as if the probability is very low to find a given functionality,
    like YECs act as if the earth is young, but acting like it isn't going to
    change the fact that functionality is found much more readily than
    anti-evolutionary activists want to believe.

    So, given that I am mentioning this work for a second time, will you respond
    to it's import now?

    >This only works because you first give me the book, which contains all
    >the relevant semantic information. With the signal, you just send me
    >ln(3) bits of information, not lots.

    I believe that is exactly what I said in my note. I haven't sent you lots of
    shannon information, but I have sent you lots of colloquial information.

      You want to keep the signal small
    >in order to transmit it fast, therefore it cannot carry all the semantic
    >information you want me to have for executing your plan, so you transmit
    >the large amount of information beforehand and make the signal nothing
    >but a pointer to one of the 3 large texts you transmitted beforehand.

    You miss my point. You had stated that semantic information is related to
    SHannon information. I gave you a case where that wasn't the case. Shannon
    information isn't related to semantic information.

    >> Because of this private agreement for meaning, one can't quantify it. And
    >> unless one can quantify it, he can't quantify your 'biologically relevant
    >> information'.
    >I agree that any semantic information or meaning depends on language
    >conventions agreed upon beforehand. But the only reason you cannot
    >easily quantify it is linguistic ambiguity (synonymous words, phrases,
    >sentences, paragraphs,... errors, imprecision, errors,...).

    I disagree strongly with this assertion. The reason you can't quantify
    semantic information is because you can't quantify the agreement. You know
    that gift doesn't mean the same in German. Poke doesn't mean the same in
    American english as it does in English english. And American english doesn't
    have terms like 'jobworthy', or 'puckle' or 'bobbies' as English english and
    Doric english do. How do you quantify the clear and obvious (to me) semantic
    meaning when you don't know the semantic meaning. And because of this,
    semantic information becomes SUBJECTIVE not OBJECTIVE. It has nothing
    whatsoever do do with ambiguity. Puckle is a clearly defined word with no

    Hearing German means nothing to me because I don't know the language. I
    can't even tell if someone using a gutteral language is really speaking
    German. I can have an idea that they are, but that doesn't mean that they
    are. Thus I can't OBJECTIVELY determine meaning without being in on the
    private agreement about what sounds mean what.

    >> It is the same problem as trying to determine which of the following
    >> sequences has meaning.
    >> ni ru gua wo shou bu de bu dui jiao wo hao hao?
    >[I skip some of your long "message"]
    >> If you can tell which has meaning, then you can determine biological
    >> functionality.
    >Which meaning? Which functionality? What language or code? I.e. I agree
    >that meaning or biological functionality is not derivable from the
    >sequence alone, but must be found by the knowledge of the language or
    >biological observations.

    The very fact that you have to ask what meaning, what language what code
    admits of the fact that meaning isn't objectively determinable. I have
    presented this type of test to everyone who has made the claim you do, that
    semantic information is a scientific concept and not a single one of you has
    had the guts to even guess which sequence. The sequence which had meaning


    Which was a caesar cypher for a Mandarin message in pin yin (lacking the
    tonations) which said:

    ru gua wo shou de bu dui ni jiao wo, hao bu hao?

    If Adrian Teo works hard, I bet he can tell you what it means. But you still
    don't know if I am telling you the truth that it has meaning. Meaning is not
    a scientific concept. It can't be quantified and it isn't objective to an
    outsider. You all keep saying that it is 'information' but you never, ever
    even guess which sequence has it much less tell me HOW MUCH semantic
    information there is in the sequence.

    >> Information is related to entropy and must have a p log(p)
    >format. Can you
    >> derive such a thing for what you define as information II? If you can't,
    >> then it isn't any form of information. It may be something else, but just
    >> not information.
    >It is not (unqualified) Shannon information. It is information about in
    >the same way as a written paragraph contains information. It tells us
    >something. Therefore I call it semantic information.

    But you can't tell me the first thing about this supposed 'semantic
    information' other than that it tells us something. How much 'tells us
    something' was in the chinese expression I gave you? How much 'tells us
    something' is in this sentence? What is the difference in 'tells us
    something' between the German 'gift' and the English 'gift'? Is there any
    difference between 'ma(1)' in chinese and 'ma' in English? Or how much
    difference in the 'tells us something' is there between pa(4) in chinese and
    'pa' in English? Is there a difference in 'tells us something' between 'nai
    nai' in Chinese and 'Grandmother' in English?

    The concept is useless, empty and misleading. It does nothing for us other
    than make us feel like we are really being scientific when in fact we

    >H.P. Yockey, "Information theory and molecular biology" (Cambridge
    >University Press, 1992, ISBN 0-521-35005-0) has defined the information
    >content of iso-1-cytochrome c family of enzymes with respect to their
    >common functionality (excluding the unknown additional information due
    >to species-specific requirements). He took into account genetic code
    >degeneracy and mutational transition probabilities between amino acids
    >equivalent with respect to enzyme function in this protein family. By
    >defining sequence similarity in terms of "mutual entropy" in p log(p)
    >format, he linked semantic information with information potential for
    >the given sequence length.

    I believe this is a total misreading of Yockey. He does not connect semantic
    information with information potential. But I will admit that my copy of his
    book is in storage in Houston while I live here.

    >> As to multiple pathways. I recall back in the early 1960s, the argument
    >> against the chance formation of a peptide was based upon the chance of
    >> finding a single sequence out of all sequence space. So for
    >oxytocin, an 8
    >> amino acid peptide, the chance of making human oxytocin was 1 in
    >8^20 or 1
    >> in 10^18.
    >We better write 1 in 20^8 or 4 in 10^11.

    You are correct, thank you. Maybe one too many toddies that night.

    >> Of course they would use a 100 unit long peptide and have 20^100
    >> or 1 in 10^130. and give an indignant conclusion as to how could anyone
    >> believe such odds. But as we have learned things over the past
    >30 years, we
    >> have brought those numbers down to 1 in 10^40 because we know
    >now that more
    >> than one sequence can perform the same task.
    >1 in 10^40 is still much too small to be of any use.

    >> And experiments by Gerald
    >> Joyce, Jack Szostak and others, show that functionality in a
    >test tube full
    >> of RNA is found at a rate of 1 in 10^14 to 1 in 10^18. That is
    >We have discussed this before, without coming to an agreement. RNA is
    >not protein. And artificial selection in vitro is not natural selection
    >in vivo - or even random mutatuional walks with no selection.

    Can you cite an experiment which shows that the same is not applicable to
    proteins? I mean experimental data not merely someones opinion. Afterall RNA
    is related to DNA and DNA makes proteins.

    >It will be fascinating to watch possible progress towards interesting



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