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Fwd: "Junk" DNA from Jonathan Wells (underlining added)

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  • Phil Skell
    ... [Non-text portions of this message have been removed]
    Message 1 of 2 , May 14 2:50 PM
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      >On ID generating scientific hypotheses: ID (unlike Darwinism) suggests that
      >most biological features are designed. The difference can be seen in a
      >number of cases; I'll use so-called "junk" DNA as my example. When it was
      >discovered several decades ago that the majority of DNA in the human genome
      >does not code for protein, Darwinian theory suggested that it was merely
      >evolutionary noise, accumulated through mutation over millions of
      >generations. We now know that this so-called "junk" DNA is absolutely
      >essential: If the "junk" is removed, the remaining DNA is biologically
      >inert. It turns out the the "junk" consists of regulatory regions, without
      >which a multicellular organism would be unable to differentiate its cells
      >into muscle, nerves, skin, etc. If biologists 20 years ago had been
      >operating with an ID view rather than a Darwinian view, they would have been
      >much more motivated to look for the function of this DNA rather than dismiss
      >it as junk, and our understanding of the genome would now be much more
      >advanced.
      >
      >On whether one would set up experiments differently: Most successful
      >research programs in biology already operate as though ID were true. That
      >is, they implicitly assume that something is designed, then try to
      >understand function through "reverse engineering." An ID view would not
      >change this, but would simply encourage more of what already works best.


      [Non-text portions of this message have been removed]
    • unreve89
      ... suggests that ... in a ... When it was ... human genome ... merely ... absolutely ... biologically ... Misleading. In fact, some of the most common forms
      Message 2 of 2 , May 14 3:28 PM
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        --- In CreationEvolutionDesign@y..., Phil Skell <tvk@p...> wrote:
        >
        > >On ID generating scientific hypotheses: ID (unlike Darwinism)
        suggests that
        > >most biological features are designed. The difference can be seen
        in a
        > >number of cases; I'll use so-called "junk" DNA as my example.
        When it was
        > >discovered several decades ago that the majority of DNA in the
        human genome
        > >does not code for protein, Darwinian theory suggested that it was
        merely
        > >evolutionary noise, accumulated through mutation over millions of
        > >generations. We now know that this so-called "junk" DNA is
        absolutely
        > >essential: If the "junk" is removed, the remaining DNA is
        biologically
        > >inert.

        Misleading. In fact, some of the most common forms of "junk" DNA,
        introns, are routinely removed and reintroduced into cells and the
        genes (and the proteins they encode) function normally. Or if they
        are mutated in specific ways, they function as intended.

        Wells is demonstrating here his "Talented Mr Ripley" impersonation.
        This is where Wells leaves out enough essential information such that
        readers get a false impression of the topic. While it is true that
        there are sections of the genome that do not encode proteins (or RNA)
        yet are nevertheless essential is (now) trivial knowledge.

        Some of these areas are used to control gene expression and are
        called promoters and enhancers. Some much larger regions comprised of
        highly repetitive sequences are used to organize the chromatin (e.g.
        centromeric sequences) or carry non-transcribed instructions for DNA
        modifying enzymes (such as telomerase). These non-transcribed
        control, structural and organizing regions make up about 40-45% of
        the genome. Considering that best estimates for the proportion of the
        genome that is actually transcribed is roughly 4-5%, this still
        leaves gigantic regions of the genome for which there is no known
        function. Some of this "junk" DNA consists of pseudogenes (which nest
        in expected patterns with respect to evolutionary phylogenies),
        LINES, SINES and other endogenous retroviral elements (which also
        nest in expected patterns), all strong evidence of common descent.

        For a less ....um.... creative description of what we know
        about "junk" DNA see; Nature 409, 860 - 921 (2001). A bit extracted
        for your reading pleasure.

        "A puzzling observation in the early days of molecular biology was
        that genome size does not correlate well with organismal complexity.
        For example, Homo sapiens has a genome that is 200 times as large as
        that of the yeast S. cerevisiae, but 200 times as small as that of
        Amoeba dubia(refs). This mystery (the C-value paradox) was largely
        resolved with the recognition that genomes can contain a large
        quantity of repetitive sequence, far in excess of that devoted to
        protein-coding genes (refs).

        In the human, coding sequences comprise less than 5% of the genome
        (see below), whereas repeat sequences account for at least 50% and
        probably much more. Broadly, the repeats fall into five classes: (1)
        transposon-derived repeats, often referred to as interspersed
        repeats; (2) inactive (partially) retroposed copies of cellular genes
        (including protein-coding genes and small structural RNAs), usually
        referred to as processed pseudogenes; (3) simple sequence repeats,
        consisting of direct repetitions of relatively short k-mers such as
        (A)n, (CA)n or (CGG)n; (4) segmental duplications, consisting of
        blocks of around 10–300 kb that have been copied from one region of
        the genome into another region; and (5) blocks of tandemly repeated
        sequences, such as at centromeres, telomeres, the short arms of
        acrocentric chromosomes and ribosomal gene clusters. (These regions
        are intentionally under-represented in the draft genome sequence and
        are not discussed here.)

        Repeats are often described as 'junk' and dismissed as uninteresting.
        However, they actually represent an extraordinary trove of
        information about biological processes. The repeats constitute a rich
        palaeontological record, holding crucial clues about evolutionary
        events and forces. As passive markers, they provide assays for
        studying processes of mutation and selection. It is possible to
        recognize cohorts of repeats 'born' at the same time and to follow
        their fates in different regions of the genome or in different
        species. As active agents, repeats have reshaped the genome by
        causing ectopic rearrangements, creating entirely new genes,
        modifying and reshuffling existing genes, and modulating overall GC
        content. They also shed light on chromosome structure and dynamics,
        and provide tools for medical genetic and population genetic studies.

        The human is the first repeat-rich genome to be sequenced, and so we
        investigated what information could be gleaned from this majority
        component of the human genome. Although some of the general
        observations about repeats were suggested by previous studies, the
        draft genome sequence provides the first comprehensive view, allowing
        some questions to be resolved and new mysteries to emerge."


        >It turns out the the "junk" consists of regulatory regions, without
        > >which a multicellular organism would be unable to differentiate
        its cells
        > >into muscle, nerves, skin, etc. If biologists 20 years ago had
        been
        > >operating with an ID view rather than a Darwinian view, they would
        have been
        > >much more motivated to look for the function of this DNA rather
        than dismiss
        > >it as junk, and our understanding of the genome would now be much
        more
        > >advanced.
        > >
        > >On whether one would set up experiments differently: Most
        successful
        > >research programs in biology already operate as though ID were
        true. That
        > >is, they implicitly assume that something is designed, then try to
        > >understand function through "reverse engineering." An ID view
        would not
        > >change this, but would simply encourage more of what already works
        best.
        >
        >
        > [Non-text portions of this message have been removed]
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