RE: Details on universal code claims, from Re: NCSE Contacts Ever y Living Scientist (fwd)....Discovery Institute's reply

From: Hofmann, Jim (
Date: Thu Oct 18 2001 - 12:23:38 EDT

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    The following essay is a few years old but still looks useful:

    Jim Hofmann
    Philosophy Department and Liberal Studies Program
    California State University Fullerton

     -----Original Message-----
    From: bivalve []
    Sent: Thursday, October 18, 2001 9:31 AM
    Subject: Details on universal code claims, from Re: NCSE Contacts
    Every Living Scientist (fwd)....Discovery Institute's reply

    >><< surrounds the quotes from the one DI reply, DC:
    precedes my replies.

    >>In his press release, Miller writes:

    "Look closely at the figure from this paper, and you'll see
    something remarkable. The variations from the standard
    code occur in regular patterns that can be traced directly
    back to the standard code, which sits at the center of the

    This is false. The variant codes do not "occur in regular
    patterns," but appear independently in unrelated lineages.

    DC: The problem here is what is regular. The change from
    the universal code to the variants is regular in the sense
    that the changes proceed in an orderly evolutionary pattern.
    The occurrence of these changes is erratic, as is to be
    expected for the occurrence of mutations, and this is what
    the DI insists is not orderly. However, there is a pattern in
    that the changes generally occur in those situations where
    changes would be selected for (GC mutational bias and
    genome reduction).

    >>In short, Miller completely misrepresents the Knight et al.
    composite phylogeny. There is no "regular pattern" to the
    variant codes that maps congruently onto phylogenetic
    trees from other data. Thus, far from providing what Miller
    calls "unexpected confirmation of the evolution of the code
    from a single common ancestor," the pattern of variant
    codes represents a puzzle for a single tree of life.<<

    DC: Miller was not talking about the phylogeny, and
    claiming that the variant codes represent a puzzle for a
    single tree of life does misrepresent it.

    >>In his press release, Miller writes:
    "As evolutionary biologists were quick to realize, slight
    differences in the genetic code are similar to differences
    between the dialects of a single spoken language. The
    differences in spelling and word meanings between the
    American, Canadian, and British dialects of English reflect
    a common origin. Exactly the same is true for the universal
    language of DNA."

    This is--at best--a wildly inaccurate analogy. From context
    and other clues, English speakers can discern that the
    words "center" and "centre," or "color" and "colour," refer to
    the same object. Meaning is preserved by context, and the
    reader moves along without a hitch.

    But a gene sequence from a ciliated protozoan such as
    Tetrahymena (for instance), with the codons UAA and UAG
    in its open reading frame (ORF), cannot be interpreted
    correctly by the translation machinery of other eukaryotes
    having the so-called "universal" code. <<

    DC: Unless there is no difference in inferential ability
    between readers of English and ribosomes, there is a flaw
    in the DI interpretation.

    >>Indeed, for two decades (see below), it was exactly this
    deeply-embedded feature of the genetic code that led to
    strong predictions about its necessary universality across
    all organisms. It was widely thought that any change to the
    genetic code of an organism would affect all the proteins
    produced by that organism, leading to deleterious
    consequences (e.g., truncated or misfolded proteins) or
    lethality. Once the code evolved in the progenitor of all life, it
    "froze," and all subsequent organisms would carry that
    code. <<

    DC: Yes, but those decades were not the last two. The
    codon-capture hypothesis, proposed in 1985, provides an
    evolutionary mechanism for departure from the universal

    >>In his press release, Miller writes:
    "...the entire biotechnology industry is built upon the
    universality of the genetic code. Genetically-modified
    organisms are routinely created in the lab by swapping
    genes between bacteria, plants, animals, and viruses. If
    the coded instructions in those genes were truly as
    different as the critics of evolution would have you believe,
    none of these manipulations would work."

    But some manipulations--namely, those involving
    organisms with variant codes--do not work, unless the
    researchers themselves intervene to ensure function. <<

    DC: The deviations typically involve rare codons, so that the
    manipulation might work. Only if a variant codon happens
    to be placed in a crucial position and the new code is an
    inadequate substitute (the latter situation highly likely if it is
    a change to a stop codon but less so if it is another amino
    acid) will the change be significant.

    >>Consider, for instance, the release factor from the ciliate
    Tetrahymena thermophila. Release factors (in eukaryotes,
    these proteins are abbreviated as "eRF" to distinguish
    them from prokaryotic release factors) catalyze the
    separation of completed polypeptide chains (nascent
    proteins) from the ribosomal machinery. Unlike other
    eukaryotic release factors, however, that recognize all three
    stop codons (UAA, UGA, and UAG), the Tetrahymena
    thermophila release factor recognizes only the UGA codon
    as "stop."

    In 1999, Andrew Karamyshev and colleagues at the
    University of Tokyo isolated the release factor (Tt-eRF1)
    from Tetrahymena thermophila. But in order to express and
    purify the protein, Karamyshev et al. had to manipulate it
    genetically first. Why? The Tetrahymena thermophila gene
    for Tt-eRF1 contains 10 codons in its open reading frame
    that would be interpreted as "stop" by other
    organisms--whereas Tetrahymena thermophila reads
    these codons as glutamine:

    "To express and purify the recombinant Tt-eRF1 protein
    under heterologous expression conditions [i.e., in a cell
    other than Tetrahymena--Karamyshev et al. used yeast
    cells], 10 UAA/UAG triplets within the coding sequence
    were changed to the glutamine codon CAA or CAG by
    site-directed mutagenesis." [4]

    Furthermore, Tt-eRF1 would not function when employed in
    combination with ribosomes (translation machinery) from
    other species:

    "In spite of the overall conservative protein structure of
    Tt-eRF1 compared with mammalian and yeast eRF1s, the
    soluble recombinant Tt-eRF1 did not show any polypeptide
    release activity in vitro using rat or Artemia ribosomes." [5]
    Thus, when using an organism with a variant code
    (Tetrahymena thermophila), researchers found that

    They needed to modify (i.e., intelligently manipulate) the
    gene sequences so that they could be expressed by other
    organisms, and

    They discovered that a key component of the genetic code
    (namely, the release factor that terminates translation)
    would not function properly with the translation machinery
    of other organisms. <<

    DC: This souds a bit inaccurate. UGA is still recognized by
    Tetrahymena, so release could work with the right
    sequence. However, it is also possible that in the billion or
    so years since the split between ciliates and the
    fungi-animal lineage, a few mutations have rendered parts
    of the ribosomes incompatible.

    >>Experiments to change the identity of transfer RNA
    (tRNA)--another possible mechanism by which genetic
    codes might reassign codon "meanings"--have shown that
    the intermediate steps must be bridged by intelligent
    (directed) manipulation. <<

    DC: This is false, as shown by the example I cited in my
    post on the universal code. Hemichordate mitochondria
    have an intermediate stage between the universal code
    and the modified code in echinoderm mitochondria. This
    fits exactly with the evolutionary scenario proposed by the
    codon capture hypothesis, which provides an undirected
    change in tRNA identity. The archive of my post is at

    >>Please report any errors to

    DC: I am not sure if these are they types of errors this is
    asking about, but am sending them anyway.

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