Re: Fwd: "Junk" DNA from Jonathan Wells (underlining added)
- --- In CreationEvolutionDesign@y..., Phil Skell <tvk@p...> wrote:
> >On ID generating scientific hypotheses: ID (unlike Darwinism)
> >most biological features are designed. The difference can be seenin 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 thehuman genome
> >does not code for protein, Darwinian theory suggested that it wasmerely
> >evolutionary noise, accumulated through mutation over millions ofabsolutely
> >generations. We now know that this so-called "junk" DNA is
> >essential: If the "junk" is removed, the remaining DNA isbiologically
> >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 10300 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, withoutits cells
> >which a multicellular organism would be unable to differentiate
> >into muscle, nerves, skin, etc. If biologists 20 years ago hadbeen
> >operating with an ID view rather than a Darwinian view, they wouldhave been
> >much more motivated to look for the function of this DNA ratherthan dismiss
> >it as junk, and our understanding of the genome would now be muchmore
> >On whether one would set up experiments differently: Most
> >research programs in biology already operate as though ID weretrue. That
> >is, they implicitly assume that something is designed, then try towould not
> >understand function through "reverse engineering." An ID view
> >change this, but would simply encourage more of what already worksbest.
> [Non-text portions of this message have been removed]