RE: Polyphyly and the origin of life

From: Glenn Morton (
Date: Tue May 21 2002 - 00:59:02 EDT

  • Next message: Craig Rusbult: "ASA Science Ed website"

    Hi Peter,

    Peter wrote:

    >-----Original Message-----
    >From: Peter Ruest []
    >Sent: Monday, May 20, 2002 7:54 AM

    >> >That's artificial selection of RNA function in vitro, rather than
    >> >spontaneous emergence of minimal protein function without selection in
    >> >vivo (or in the prebiotic world).
    >> The interesting thing I notice is that in your first statement, the
    >> statement which I criticized, you have no requirement for me to
    >show that it
    >> arose out of nothing and no restriction to non-vitro experiments.
    >Do you mean "in vivo", rather than "in vitro"?

    No, I mean in vitro. In vitro means in glass. One could put it in a coke can
    I presume.

    >My first statement which you criticized (1 May 2002 20:30:36 -0700) was:
    >>>The amount of meaningful or semantic information contained in a system
    >>>may be defined as the minimal length of an algorithm capable of
    >>>specifying it (M.V. Volkenstein, "Punctualism, non-adaptionism,
    >>>neutralism and evolution", BioSystems 20 (1987), 289). This would
    >>>exclude all features irrelevant for meaning or functionality. The
    >>>meaningful information contained in today's biosphere may be
    >>>approximated by a (purely theoretical) minimal set of genome parts
    >>>"streamlined" to include the code for whatever is really required for
    >>>the organisms represented in the biosphere, but nothing else. Its amount
    >>>is such that the improbability of its generation by random-variation /
    >>>natural-selection processes, starting with a prebiotic universe, is
    >>>vastly transastronomical.
    >I clearly was talking about the origin of life (or of the biosphere as a
    >whole), with its crucial first living system(s) originating out of a
    >prebiotic environment, in which there is no biological information (thus
    >"nothing"). As each in vitro experiment using artificial selection
    >artificially introduces plenty of functional information, it cannot be
    >used (at least not without an appropriate correction) for estimating the
    >possible amount of information II originating spontaneously. Thus, the
    >requirements were clearly stated.

    No they don't introduce functional information. If you recall, some of the
    quotes I posted said that they had randomized the sequence so that .25 of
    the sequences were totally random. That is degrading functional information
    (assuming such information really exists).

    >This refers to the general problem of information II. But in order to
    >find any estimate of amounts of information II, we have to consider much
    >simpler systems. And the only one I could think of to-date, which might
    >offer a hope of getting at such values, is the origin of a novel
    >enzymatic functionality in its minimal form, just before natural
    >selection sets in. This situation, of course, can only be investigated
    >in a modern biological system including genetic coding, transcription,
    >translation, folding, and probably only in the context of a large family
    >of orthologous proteins, such as the cytochromes c.

    So I am waitg for you to tell me the 'amounts of information II any
    sequence has. To date you can't define how one would estimate such a
    quantity. Indeed, you have said it isn't possible, but now you say it is.
    What is the equation for estimating the 'amount of information II"

    >As I told you before, information II cannot be determined from
    >artificial selection in vitro because we don't know how much information
    >is artificially introduced into the molecules selected. RNA can only
    >model the purely hypothetical RNA world, of which we don't even know
    >whether it is viable at all - even ignoring the problem of its
    >initiation. And RNA selection experiments are done with the help of
    >biological protein-enzymes! Thus, again, there is no possibility of
    >estimating biologically relevant information II. Remember that, as you
    >have emphasized yourself, information II is absolutely undefined apart
    >from the (right, biological!) context of a molecule considered.

    If you can't define 'biologically relevant information II', then you have
    nothing worth speaking of in science. YOu have a belief, and nothing more.
    Science demands definitions which are objective. The only way I can see that
    you can prove objectivity in your definition of information II is for you to
    determine which sequence contains it, something you keep avoiding.

    >Under the designation "multiple families", you are mixing up some
    >fundamentally different concepts (orthologs and paralogs are
    >subgroupings of homologs (which have significantly similar sequences)):
    >(1) orthologs in different species are derived by common ancestry from
    >the same ancestral protein;
    >(2) paralogs in the same or different species are derived from
    >independent evolution from a gene duplication in some ancestral species;
    >(3) xenologs are homologs obtained by lateral gene transfer;
    >(4) different families are sets of orthologs, where the different sets
    >are (usually) paralogs of each other (domain shuffling may introduce
    >additional levels of complexity between paralogous families, and
    >supersets of families more distantly related may form superfamilies).

    No, I am not mixing up these concepts. I am speaking of totally different
    know what I am saying and it isn't what you are trying to make me say.

    I wrote:

    >> No, not at all. There is indeed evidence of multiple origins of life and
    >> then a period of mixing of genomes among the early metazoans.
    >You mean protozoans or prokaryotes, rather than metazoans.

    You are correct, I miswrote there.

    >It's the
    >protozoans (unicellular organisms), and in particular the prokaryotes
    >(without a nucleus: the archaea and bacteria), which exchanged genes,
    >possibly quite liberally. This became much more difficult with metazoans
    >(multicellular organisms).
    >As far as a possible multiple origin of life is concerned, we don't have
    >anything beyond speculation. The evidence pointing to multiple lateral
    >gene transfers is no evidence at all for multiple origins of life.

    It is evidence that one can't automatically assume a single origin of life.
    Such a mixing would clearly mask any multiple origins of life.

    >Mixing of genes of different origin in the same organism (by means of
    >lateral gene transfer) implies that this organism becomes a hybrid to
    >some extent, and if you want to trace all genes, the phylogenetic tree
    >becomes reticulate.

    Yes, and any multiple origins of life would not be easy to detect under
    these assumptions.

    Yet (apart from domain shuffling) this does not
    >imply any reticulation of the individual gene trees (as opposed to the
    >organismal tree): each gene (or more precisely, each functional protein
    >domain) has its own unique descent and originated in a particular
    >species at a particular time.

    I disagree with your use of this data.

    >And if you look back to the definition of "synonymous families" given
    >above, you see that my claim stands, that "huge numbers" of them are
    >very unlikely.

    I don't agree with your assumption. Indeed, experimental evidence wouldn't

    >Now, this is confusing, Glenn. The relationship between DNA, RNA and
    >proteins is (to a first approximation) coding, transcription and
    >translation. If the code for a multifunctional protein is contained in a
    >gene, of course the resulting protein is multifunctional. The different
    >functionalities usually reside in different domains of the protein.
    >Where did I claim there couldn't be multifunctional proteins? I never
    >believed that.

    Well, you erroneously claimed that there were no multifunctional proteins.
    At least that is what you had written. You were wrong. You wrote Sat
    5/18/02 8:55 that:

    > I replied:
    > >Agreed - in principle. Yet, if there are any other families (let alone
    > >huge numbers) which will perform the same function (in the same
    > >organismal environment), I find it strange that no such example has been
    > >found to date, as far as I know.

    And then I went out to find them.

      In any case,
    >multifunctional proteins perform different functions in the same
    >organism, and if we want to find out anything about the de novo
    >emergence of any one of these functions (information II), we have to
    >look at the family of the domain, in whose (simple) function we are
    >interested, and go back in time to the common ancestor of the domain.

    This simply isn't true. Multifunctional proteins, as I posted last night,
    perform different functions IN THE SAME ORGANISM.

    >Multiple-function proteins are irrelevant to the question under
    >investigation, see above.

    No they aren't, you said they didn't exist. They are relevant to measure
    your knowledge of the field, and they are relevant to the measurement of
    probability. Besides, as I noted, no one believes, save you, that proteins
    were what arose first.

    >You keep mixing up multiple families and multifunctional proteins.

    NO, I am showing that multifunctionality demonstrates that the probability
    of finding a given function in probability space is less than even Yockey
    calculated. Multifunctionality is related to multiple familis. If protein X
    does both function A and B and Protein Y does function B and C, then Y is
    multifunctional and is multifamily.


    for lots of creation/evolution information
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    >"..the work which God created to evolve it" (Genesis 2:3)

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