RE: No one believes proteins are the first form of life.

From: Glenn Morton (
Date: Wed May 22 2002 - 00:07:58 EDT

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    Hi Peter,

    This will be my last post along this thread. I will have to stop soon
    anyway as other tasks are calling me.

    >-----Original Message-----
    >From: Peter Ruest []
    >Sent: Tuesday, May 21, 2002 8:55 AM
    >Hi Glenn, for the context:
    >> >[PR:]... But remember that
    >> >the whole long argument started (04 May 2002 16:46:30 +0200) with my
    >> >simple claim that we have to distinguish between:
    >> >(I) Maximum information carrying capacity;
    >> >(II) Functional information relevant for biological systems.
    >Glenn Morton wrote (19 May 2002 09:01:04 -0700):
    >> >> Pay attention to the issue at hand. I am saying that ignoring
    >the data I
    >> >> posted above is exactly LIKE, ANALOGOUS, SIMILAR to the way
    >the YECs act.
    >> >> And indeed, you skipped right by it without any comment.
    >I thought I'd better just ignore such an unfair and ridiculous reproach.
    >Come on, Glenn, don't just throw anyone criticising evolutionary just-so
    >stories into the YEC bin! I have never been in the YEC corner. Even if
    >you say "exactly LIKE, ANALOGOUS, SIMILAR", you are being unreasonably
    >offensive. I'm not conscious of having ignored any data you presented
    >without at least saying why I'm skipping it. But if you want to come
    >back to such a supposed case, tell me what it was.

    I did in that note on May 19th. You were not responding at the time to the
    data of Szostak and Joyce. You have since at least responded.

      What you seem to be
    >doing is ruling
    >> out any experimental evidence which can be collected today.
    >Nonsense! I started this thread and have the right to come back to my
    >original statement of the problem you criticized. I'm gladly ready to
    >consider "any experimental evidence which can be collected today" - _if_
    >it has any relevance for my statement you criticized. I have rather the
    >impression that you have still not understood what I wanted to say.

    Of course it is rigging the roulette wheel when one says that experimental
    evidence of multifunctionality in biopolymers is ruled out. And this is what
    you do when you deny that there is any applicability of the RNA data to
    biopolymers found in living systems.

    >> If it is in
    >> vitro, you say it has nothing to do with the origin of life and the
    >> emergence of useful proteins. If we put it in a metal dish and
    >do the same,
    >> or in a rock dish, does it suddenly become ok? I doubt you
    >would accept any
    >> experiments with zeolites which might show interesting effects merely
    >> because they took place on a university campus. We have no time machine
    >> with which to return to 3.8 Gyr and watch the process. So what you do by
    >> ruling out the discussion of any experimental evidence is firmly
    >plant your
    >> head below the ground so that one can not see observational data.
    >Please stop such unfair talk which has nothing to do with what I wrote!
    >If you resent my skipping such remarks, just try to better understand
    >what I am saying!

    You are the one who wrote on Sat 5/18/02 8:55 AM:

    >This is in vitro RNA chemistry using some biochemical molecules. It may
    >not have much to do with biology.

    I don't know another way to understand that. You seem to rule it out as
    irrelevant to biology. I am sure that some biochemists would be interested
    that RNA chemistry is irrelevant to biology. And what they are doing with
    those chemicals IS relevant to the RNA world thesis. So, you are rigging the
    roulette wheel whether you want to hear it or not.

    >> We weren't discussing the minimum length proteins can be. We
    >were discussing
    >> if other families of proteins could perform a given task than the one we
    >> find doing it today. That was the issue. Not how short a protein can be.
    >> Tell me how short the sequence for 'be' can be and still have
    >you understand
    >> what is meant?
    >Right, "if other families of proteins could perform a given task than
    >the one we find doing it today" is one of the important questions, not
    >the length of the protein. I hope you are talking about "synonymous
    >families", as I defined them in my last post, "Polyphyly and the origin
    >of life".
    >Last time, I paid no attention to your adding "of smaller length". The
    >small length of such "miniature proteins" is not at all the critical
    >point, either with Lombardi or with me. What is important, instead, is
    >the minimal number of specified amino acids (what I called the
    >"invariant" above) - just as with Yockey's work. The protein may be
    >longer, if the identity of the other amino acids adds nothing to the
    >functionality. The question is: at how many positions in a protein do I
    >need a particular amino acid (or for less stringent positions, any one
    >in a given restricted set of amino acids), in order to get the function
    >looked for? This is the "amount of specification" required for the

    Not entirely. If one can then play the Yockey game and substitute
    hydrophylic for hydrophylic amino acid etc, then the specification of
    functionality becomes even less. And then one must also be sure that other
    sequences of similar length don't perform the function. Shortening the
    sequence doesn't tell you anything about other sequences.

    >In contrast to Yockey, I add the theoretical requirement that this
    >sequence is not derivable, by evolution with natural selection, from a
    >different one with _less_ specification, but having nevertheless some of
    >the function.

    What you add as a requirement is meaningless. The work of Gerald Joyce does
    show that molecules with tiny amounts of functionality can be evolved to
    catalytic race horses. See Peter Radetsky, "Speeding Through Evolution,"
    Discover, May, 1994, p. 85

    This is another way of saying that it had to be formed by
    >means of a strictly random-walk mutational path. In this way, I hope to
    >arrive at an estimate of the amount of information II. I would call such
    >a protein a "minimal-functionality protein". This additional
    >requirement, by the way, is not necessarily beyond experimental testing.

    Well, you have to include the things I mentioned above as well as the fact
    that tiny amounts of functionality can arise and Joyce showed it. Go read
    that article. Yes it uses RNA but I contend that it is very relevant to

    >> And to assume that the original proteins performed precisely
    >> the same task as evolved proteins do today is quite a leap.
    >I have never said they did. All I assume for the estimate I am looking
    >for is that it is a "minimal-functionality" protein.

    You must define minimum functionality. Is it minimally functional if a
    protein enzyme is able to catalyze X amount of reactions in 10 hours? in 20
    hours? in 100 hours? One can't define minimal functionality based solely
    upon what minimal length gives the enzyme the ability to catalyze X amount
    of reactants in 2 minutes. Thus, your methodology is flawed.

      Subsequently, it
    >may have evolved further by means of a normal evolutionary pathway with
    >non-negative natural selection at each step. During this evolutionary
    >path, its function may have been modified, as well as increased. But
    >this further path is no longer easily tractable for a determination of
    >information II.

    The only way to define minimal functionality is to somehow define that if a
    molecule catalyzes X amount of reaction in 1000 hours and 1 minute it is
    nonfunctional but if it does it in 1000 hours it is functional. And that is

    >But what happened before the time of that coalescence in the MRCA? The
    >MRCA must have evolved from earlier forms, which probably were simpler
    >and less active, back to the minimal-selectable-functionality (MSF)
    >cyt.c (about which I wrote in the other post, "Polyphyly and the origin
    >of life").
    >And before the time of this MSF cyt.c? The emergence of this MSF cyt.c
    >is the only process not under natural selection (by definition), so it
    >was a random mutational walk through sequence space, whose probability
    >can be estimated if the size of the specification for the MSF stage can
    >be determined.

    >As for the RNA case c, you probably wanted to say that the improbability
    >(rather than probability) is much less. This is correct for artificial
    >selection systems. And it may even be correct for an initial natural RNA
    >world - although we don't know this. But so what? I already explained
    >that the RNA world probably cannot be used to estimate functional
    >information content (II).
    >I dealt in my last post with the irrelevance of the multifunctional

    It seems that everything that goes against your position is 'irrelevant'.

    >Please don't link me with Sydney Fox. Of course, proteinoids are no
    >model for proteins, for many reasons, but primarily because of the
    >problem of sequence information (II), which cannot emerge without
    >reproduction and evolvability, as Joyce says. It's now 40 years ago that
    >I became aware of Fox's proteinoids and immediately started criticizing
    >them as completely useless for helping to explain the origin of life -
    >at a time when everybody was celebrating him. So you are wrong in
    >calling me "way behind the times".

    No I am not wrong. You are linking yourself with Fox by holding that
    proteins are the original informational carying molecules. No one believes
    proteins are the origin of information yet you keep arguing that it is this
    way. It isn't I who am saying what you are saying.

    >Of course, I know the advantages of the RNA world hypothesis, as far as
    >ribozyme functionality and the potential elimination of the
    >protein-or-nucleic-acid- first chicken-and-egg problem are concerned.
    >But we still don't know of any feasible prebiotic emergence of RNA and
    >of replication.

    There are self-replicating RNA's known now. So we do have knowledge of
    their existence. Have we found a pathway from there to life? Not yet, but we
    most likely will if given enough time.
    >Apparently, it's YOU who are the strawman builder! And you can only do
    >it because you either haven't read what I wrote or because you ignored
    >it or because you forgot it. I hope the last is the case. You are
    >constantly upbraiding me for not having read the most recent papers you
    >think were relevant, but you are not even up-to-date on what those you
    >criticize wrote!

    In all the above cases, I point you to your own words. And I will cite your
    rejection of the RNA world as evidence that I am correct. You wrote Sat
    5/18/02 8:55 AM:

    >In my post, I was discussing the evolution of functional proteins in a
    >DNA-RNA-protein world, not evolution in an RNA world.

    >I never claimed proteins were the first to evolve. It's just that I am
    >almost as skeptical about current pet speculations about
    >self-organization as I was about those of 40 years ago.

    So in other words, I am correct that you don't hold the present views. That
    makes you behind the times. Sorry, but that is just the way it is.

      Some serious
    >thinking about the emergence of biological information (II) is sorely
    >needed - both with respect to the origin of life 3.9 billion years ago
    >and with respect to the origin of novel molecular functionalities ever

    As I have pointed out information II is a mirage. You can't recognize it in
    a sequence of letters.

    >I'll repeat again what I wrote x times already: A string of any symbols
    >has a computable Shannon information, and it has a computable maximum
    >information carrying capacity (I). But it is unknown, without any
    >further knowledge, whether it contains any semantic or functional
    >information (II).

    Yes, I know you wrote that and that is exactly my point. You can't even
    define information II. You can't recognize it, it is a mirage, a figment of
    antievolutionary imaginations.

      Unless you know the appropriate language, you can't
    >read it. You may, by statistical analysis, find that, whith a certain
    >probability, it does contain some information.

    What statistical analysis. Be specific. The plain fact is that a sequence
    with lots of information has high Shannon information and a random sequence
    equally has high Shannon information. You show here that you don't really
    understand SHannon information.

      And if the probability is
    >high enough and the text is long enough, you may even be able to learn
    >the appropriate language (including its grammer, syntax,...), e.g.
    >Sumerian. ...


      But 6 words
    >are definitely insufficient to deduce an unknown syntax, which is a
    >requirement for selecting the legal word placement you ask me for. Try
    >the same with Latin! There, you may find many possible word sequences in
    >a sentence to be legal, particularly with poetry.

    Then I would point you to the Beale Papers discussed on page 82-93 of Simon
    Singh's The Code Book. No one knows if it is a language or not. These papers
    are purported to tell where great treasure is, but no one has been able to
    decipher them. No one knows if they are a language or random. How would you
    propose to go about determining that they are or are not a language. There
    are 23 pages. For over 100 years no one has been able to decipher these
    pages. How do you propose to simply tell us that there is a message there?

    I wrote:
    >> And no one believes, like you seem to, that proteins were the first
    >> biopolymers. They weren't, and you are arguing for a
    >50-year-old rejected
    >> idea. At least stay with the program and the current thinking
    >on the topic.
    >> Most researchers beleive that life evolved through the RNA.
    >You are constantly misrepresenting what I wrote. See above. I'll just
    >add some short remarks about the homonyms, which I skipped last time.

    Then why on earth on Sat 5/18/02 8:55 AM did you write:

    >In my post, I was discussing the evolution of functional proteins in a
    >DNA-RNA-protein world, not evolution in an RNA world.

    And in this message above you wrote:
    >I never claimed proteins were the first to evolve. It's just that I am
    >almost as skeptical about current pet speculations about
    >self-organization as I was about those of 40 years ago.

    How can I take you seriously when you say you don't believe that proteins
    were involved in the origin of information, when you turn around and say
    that they were? It is very confusing to discuss these things with you.

    >A homonymous protein would be a given protein sequence which shows
    >completely different functionality in two different contexts. One
    >example comes to mind: an enzyme which is alternatively used as an
    >optically transparent substance in the eye, but I don't remember if it
    >has exactly the same sequence or just a related one. This, however, is
    >something of a special case, because in the eye it doesn't function as
    >an enzyme, but just by means of its physical properties in a
    >concentrated solution. Another example might be prions which are toxic
    >versions of normal proteins folded in a different way. But again, this
    >is special, in this case because it's not physiological.

    >> "The fundamental problem of communication is that of reproducing
    >> at one point either exactly or approximately a message selected
    >> at another point. Frequently the messages have _meaning-, that
    >> is they refer to or are correlated according to some system with
    >> certain physical or conceptual entities. These semantic aspects
    >> of communication are irrelevant to the engineering problem." C.
    >> E. Shannon, " A Mathematical theory of Communication" The Bell
    >> System Technical Journal, 27(1948):3:379-423, p. 379
    >> What part of the term 'irrelevant' do you not understand?
    >> glenn
    >I understand that you completely misapply this quotation from Shannon to
    >our discussion. We may perhaps apply it in a _partially_ meaningful way
    >by saying that there is a communication channel from DNA to protein, and
    >that the semantic aspects of the biological information transmitted are
    >irrelevant to the engineering problem of transcription and translation.
    >That is, the irrelevance applies only apart from the fact that the
    >transcription and translation machineries themselves are also specified
    >by the semantic aspects of the biological information. Thus, unlike
    >information technology, the biological system is self-referential.

    This clearly shows you have no understanding of Shannon. It matters not
    whether the transmission of information is by knotted rope as the Incas did
    it, or by bits, or 8bit bytes, hexadecimal or by letters or by cellular
    machinery. The same pheonomenon is occurring--the replication of sequence A
    at site B. This can take place with a translation (which is what computer
    compression is as well as translation to proteins) except that with
    proteins, information is actually lost in going from DNA to proteins.

    You got the last word.


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