Polyphyly and the origin of life

From: Glenn Morton (glenn.morton@btinternet.com)
Date: Sat May 18 2002 - 23:51:50 EDT

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    Hi Peter,

    I will have to shorten some of this in my reply or no one will read it all.
    I will split it into several replies and threads. The first is on polyphyly
    and the origin of life.

    >-----Original Message-----
    >From: Peter Ruest [mailto:pruest@pop.mysunrise.ch]
    >Sent: Saturday, May 18, 2002 8:55 AM

    >At your request, I append - after the current discussion - some
    >statements extracted from my following posts, from our last discussion
    >about "Random origin of biological information":
    >Date: Fri, 22 Sep 2000 13:51:34 +0200 (ASA-digest V1 #1804)
    >Date: Sun, 24 Sep 2000 09:19:09 +0200 (ASA-digest V1 #1806)
    >Date: Wed, 27 Sep 2000 21:03:58 +0200 (ASA-digest V1 #1812)
    >Date: Mon, 02 Oct 2000 20:18:36 +0200 (ASA-digest V1 #1818)
    >It's quite voluminous, though, and if Terry snips it out, check the
    >I am sorry this is a long post, as in your answers you often branch out
    >into many side trails, making the whole discussion somewhat confusing.
    >Yet I dare not snip out things, lest you again misunderstand me. So I'll
    >just comment wherever I can't agree with what you say. 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.
    >Your reaction was that Shannon information is the only valid
    >information, and that (II) has nothing to do with information.

    I noted that II above had nothing to do with Shannon information and that
    there is data showing that there are huge numbers of different families of
    molecules which will perform the same function.

    >> 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.
    >> You replied (13 May 2002 21:03:42 -0700):
    >> I believe I cited an example to you earlier. The work of Szostack and
    >> Ellington points in that direction. This work is cited below.
    >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. And I
    agree that life has not been generated in the test tube yet. But I did show
    that there were lots of other sequences which would perform at least some of
    the functions which means that the probability against life originating on
    its own is not as bad as anti-evolutionists claim.

    And as to your belief that there are no examples of multiple familes found
    to date, you are wrong. Indeed this evidence also indicates that there were
    possibly multiple origins of life. And there are multiple families found in

            "Similarly, the archaeal proteins responsible for several
    crucial cellular processes have a distinct structure from the
    proteins that perform the same tasks in bacteria. Gene
    transcription and translation are two of those processes. To make
    a protein, a cell first copies, or transcribes, the corresponding
    gene into a strand of messenger RNA. Then ribosomes translate the
    messenger RNA codes into a specific string of amino acids.
    Biochemists found that archaeal RNA polymerase, the enzyme that
    carries out gene transcription, more resembles its eukaryotic
    than its bacterial counterparts in complexity and in the nature
    of its interactions with DNA. The protein components of the
    ribosomes that translate archaeal messenger RNAs are also more
    like the ones in eukaryotes than those in bacteria." W. Ford
    Doolittle, "Uprooting the Tree of Life, Scientific American,
    February 2000, p. 90-95, p. 92-93

    >Yes, what I wrote underlines that there was one origin of life, not
    >multiple ones, and having one family is expected. But the point I made
    >is that this fact strongly argues against your assumption that huge
    >numbers of synonymous families are possible. If that were the case, you
    >would expect multiple families, even if there were only one origin of

    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.

            "Even more perplexing, the newly unveiled genomes often
    contain a mix of DNAs, some seeming to come from the archaea and
    others from bacteria. "Features of both bacteria and archaea are
    turning up in eukaryotes, and to a surprising degree, says
    Russell Doolittle, a molecular evolutionist at the University of
    California, San Diego."
            "Many evolutionary biologists are coming to believe that
    these mosaics arose because genes hopped from branch to branch as
    early organisms either stole genes from their food or swapped DNA
    with their neighbors, even distantly related ones. The genetic
    oddballs may simply mean that the branches of the tree of life
    intertwine, but that the basic shape is sound. But if the gene
    swapping was extensive enough, the true branching pattern may be
    quite difficult to discern. Worse, the trees "base may turn out
    to be indecipherable; a network of branches that merge and split
    and merge again before sprouting the modern kingdoms. It may be,
    Woese concedes, that "you cant make sense of these phylogenies
    because of all the [gene] swapping back and forth."

    Confounding genes

            The just-completed sequence of the bacterium Aquifex
    aeolicus, which lives at or near-boiling temperatures embodies
    the problems that molecular evolutionists are now confronting.

    . . .

            The gene for a protein called FtsY, which helps control cell
    division, placed Aquifex close to the common soil microbe
    Bacillus subtilus, even though the two supposedly come from
    different branches of the bacterial tree. Even worse, a gene
    encoding an enzyme needed for the synthesis of the amino acid
    tryptophan linked Aquifex with the archaea. That wasn't the only
    anomaly the Diversa team found regarding the archaea, however.
    Their analysis of the gene encoding the enzyme CTP synthetase,
    which helps make the building blocks of DNA, spread the archaea
    out among all the other organisms evaluated, suggesting that they
    may not be as coherent and distinct a group as the rRNA tree
    implies. ~ Elizabeth Pennis, Genome Data Shake Tree of Life,
    Science 280:(May 1, 1998), p. 672-674, p. 672

    "Further, although archaea do not have nuclei, under certain
    experimental conditions their chromosomes resemble those of
    eukaryotes: the DNA appears to be associated with eukaryote-type
    proteins called histones, and the chromosomes can adopt a
    eukaryotic 'beads-on-a-string" structure. These chromosomes are
    replicated by a suite of proteins, most of which are found in
    some form in eukaryotes but not in bacteria." W. Ford Doolittle,
    "Uprooting the Tree of Life, Scientific American, February 2000,
    p. 90-95, p. 93

    "Nuclear genes in eukaryotes often derive from bacteria, not
    solely from archaea. A good number of those bacterial genes serve
    nonrespiratory and nonphotosynthetic processes that are arguably
    as critical to cell survival as are transcription and
            "The classic tree also indicates that bacterial genes
    migrated only to a eukaryote, not to any archaea. Yet we are
    seeing signs that many archaea possess a substantial store of
    bacterial genes. One example among many is Archaeoglobus
    fulgidus. This organism meets all the criteria for an archaean
    (it has all the proper lipids in its cell membrane and the right
    transcriptional and translational machinery), but it uses a
    bacterial form of the enzyme HMGCoA reductase for synthesizing
    membrane lipids. It also has numerous bacterial genes that help
    it to gain energy and nutrients in one of its favorite habitats:
    undersea oil wells.
            "The most reasonable explanation for these various
    contrarian results is that the pattern of evolution is not as
    linear and treelike as Darwin imagined it. Although genes are
    passed vertically from generation to generation, this vertical
    inheritance is not the only important process that has affected
    the evolution of cells. Rampant operation of a different process
    lateral, or horizontal, gene transfer has also affected the
    course of that evolution profoundly. Such transfer involves the
    delivery of single genes, or whole suites of them, not from a
    parent cell to its offspring but across species barriers." W.
    Ford Doolittle, "Uprooting the Tree of Life, Scientific American,
    February 2000, p. 90-95, p. 93-94

    "More challenging is evidence that most archaeal and bacterial
    genomes (and the inferred ancestral eukaryotic nuclear genome)
    contain genes from multiple sources. If chimerism or 'lateral
    gene transfer' cannot be dismissed at trivial in extent or
    limited to special categories of genes, then no hierarchical
    universal classification can be taken as natural. Molecular
    phylogeneticists will have failed to find the 'true tree,' not
    because their methods are inadequate or because they have
    chosen the wrong genes, but because the history of life cannot
    properly be represented as a tree." W. Ford Doolittle,
    "Phylogenetic Classification and the Universal Tree," Science,
    284(1999):2124-2128, p. 2124

    >> >Glenn, you know very well that I am neither a YEC nor an
    >> >anti-evolutionary activist (cf.
    >> >http://www.asa3.org/ASA/PSCF/1999/PSCF12-99Held.html). All I insist on
    >> >is that an adequate mechanism for producing evolutionary novelty is as
    >> >yet elusive.
    >> This has nothing to do with YEC, it has to do with multiple families of
    >> biopolymers being able to perform the same function. And the probability
    >> argument which you are using IS an anti-evolutionary argument. Very few
    >> pro-evolutionists are worried about it because they know the data I just
    >> posted but which you failed to give comment.
    >Just like in Sept. 2000, when we discussed this last time, you keep
    >talking about RNA artificial selection in vitro, rather than protein
    >natural selection in vivo or prebiotic random walk emergence of minimal
    >function, which is very different, and I explained why. I know that very
    >few pro-evolutionists are worried about this, but this is no factual
    >argument, but an appeal to authority - which I would not expect from

    First off, you need to learn what an argument from authority is. I didn't
    make one in the above. To note that pro-evoloutionists aren't worried about
    the probability argument is not an argument from authority but an
    observation. And argument from authority is like: I am correct because I
    teach law in a University. Or he is right because he is an expert.

    And like the last time, you fail to take note of the relationship between
    RNA, DNA and proteins. Do you seriously think proteins can't perform
    mutliple functions? They are being found all the time. Maybe the fact that
    you don't seem to know about them indicates you aren't keeping up with the
    field here.

    "We now know that many proteins can have multiple functions depending on
    their environment, other proteins it may interact with and the amount and
    type of modification it is subjected to."

    Wang CS, Hartsuck JA. 1993. Bile salt-activated lipase. A multiple function
    lipolytic enzyme. Biochim Biophys Acta 1166(1):1-19.

    Caponigro, Giordano, and Roy Parker, 1995, Multiple Function of the
    Poly(A)-binding Protein in mRNA Decapping and Deadenylation in Yeast, Genes
    & Development, vol. 9, p. 2421-2432.

    And since genes transcribe to proteins, to find multiple functions of a gene
    is to find mutliple functions of the protein.

    Awasaki, T. and Kimura, K.-i. (2001). Multiple function of poxn gene in
    larval PNS development and in adult appendage formation of Drosophila. Dev.
    Genes Evol. 211, 20-29.

    I see no difference between RNA and Protein in their exhibition of muliple
    functionality. Here is another example of proteinaceous multiple

    "However, some functions (e.g. proteolysis) have evolved
    multiple times and can not be accounted for by any single set of residues.""
    E. W. Stawiski et al, "Progress in Predicting Protein Function from
    structure: Unique Features of O-Glycosidases,"

    Here is another:

    "An individual human is intrinsically capable of performing multitasks,
    sometimes, one at a time
    and other times, multiple at once. A talented artist can often play several
    instruments or create
    several arts like painting, playing instruments, dancing and singing. A
    composer and conductor
    can not only play several instruments, but can also compose and conduct, for
    such vastly very
    different activities. This multitask phenomenon is not likely only limited
    to human beings.
    It has become increasingly clear that a large number of biological molecules
    can also
    perform multitasks. For example, RNA molecules have been demonstrated that
    they can not
    only carry genetic information, but they can also catalyze a number of
    biochemical reactions[8]. Could this be true for proteins? The answer is
    likely to be yes. Proteins are sophisticated
    molecules with such a diverse of functions, from enzymes that catalyze
    difficult reactions in a
    seemingly improbable environment at a rate of several orders of magnitude we
    can only envy
    [16], to construct tough structural scaffold on which all cells and living
    systems rely to survive.
    Recent observations on variety of multitask ability of proteins provide us
    with an interesting
    glimpse on what will become increasingly important roles of proteins [26,
    46, 56]." http://web.mit.edu/lms/www/docs/0111multitask.pdf

    The authors site:
    [26] C. Jeffreys, Moonlighting proteins, Trends Biochemical Sciences. 24
    (1999), 8-11.
    [46] A.H. Schonthal, Role of serine/threonine protein phosphatase 2A in
    cancer, Cancer Lett
    170 (2001), 1-13.
    [56] K. Wakasugi and P. Schimmel, Two distinct cytokines released from a
    human aminoacyl-tRNA
    synthetase, Science 284 (1999), 147-151.

    What I have shown here is that proteins have multiple functions, multiple
    functionality implies other families could do a similar task. That implies
    that the probability for producing life is not nearly so impossible as
    anti-evolutionists would have us believe. And multiple families are seen in
    the various kingdoms which implies a possibly ancient polyphyletic origin of

    I am just a geophysicist and know what is happening in this field. Why is it
    that anti-evolutionists don't seem to be able to keep up with the latest
    discoveries? This is what bothers me most about Chistian apologetics. It is
    always always, way behind times.


    see http://www.glenn.morton.btinternet.co.uk/dmd.htm
    for lots of creation/evolution information
    personal stories of struggle created to evolve it" (Genesis 2:3)

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