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

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  • unreve89
    ... suggests that ... in a ... When it was ... human genome ... merely ... absolutely ... biologically ... Misleading. In fact, some of the most common forms
    Message 1 of 2 , May 14, 2002
      --- 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
      > >evolutionary noise, accumulated through mutation over millions of
      > >generations. We now know that this so-called "junk" DNA is
      > >essential: If the "junk" is removed, the remaining DNA is
      > >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
      > >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
      > >advanced.
      > >
      > >On whether one would set up experiments differently: Most
      > >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
      > [Non-text portions of this message have been removed]
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