Introns stump evolutionists ? Re: Darwin's Place on Campus is Secure - But Not Supreme

<quote>This story is not about Enron and Exxon, but about introns and
exons. The proportions of the scandals they are causing in evolutionary
theory, however, may be comparable</quote>

Let's first point out the ID does not present any scientific explanation
for introns, thus the question now becomes, how does evolutionary theory
deal with introns? Are introns and exons really causing a 'scandal' in
evolutionary theory?

For one to understand this, it is insufficient to look at some popular
descriptions of these issues and while a study of the in-depth issues
may be complicated, one has to embark on such endeavors before one can
make the claim that introns stump evolutionists.

<quote> Although the introns-early/introns-late debate still continues,^
a synthesis that combines both theories is becoming prominent^ (Gilbert
et al. 1997Go <http://www.genome.org/cgi/content/full/14/7/1207#REF31>;
de Souza 2003Go
<http://www.genome.org/cgi/content/full/14/7/1207#REF16>). This
"synthetic theory"^ of intron evolution emerged from evidence showing
that a subset^ of present-day introns might have ancient origins, and
that^ these ancient introns have a biased distribution in eukaryotic^
genes. For example, in genes conserved between prokaryotes and^
eukaryotes, there is a large excess of phase 0 introns (which^ break
between two codons) over what one would expect by chance^ (Long et al.
1995Go <http://www.genome.org/cgi/content/full/14/7/1207#REF54>).
Furthermore, there is a small, but significant^ excess of symmetric
exons—ones whose flanking introns^ have the same phase number (Long et
al. 1995Go <http://www.genome.org/cgi/content/full/14/7/1207#REF54>).
Both of these^ traits are predicted by the hypothesis that symmetric
exons^ of phase 0 were originally required to allow exon shuffling.^
Most importantly, these ancient introns seem to be located more^
frequently at the boundaries of units of protein tertiary structure^
than within units of tertiary structure (de Souza et al. 1996Go
<http://www.genome.org/cgi/content/full/14/7/1207#REF17>,^ 1997Go
<http://www.genome.org/cgi/content/full/14/7/1207#REF18>, 1998Go
<http://www.genome.org/cgi/content/full/14/7/1207#REF19>; Roy et al.
1999Go <http://www.genome.org/cgi/content/full/14/7/1207#REF67>; Fedorov
et al. 2001Go <http://www.genome.org/cgi/content/full/14/7/1207#REF23>).
Because these^ characteristics apply only to genes whose origin predates
the^ divergence of prokaryotes and eukaryotes, the synthetic theory^
proposes that a subset of present-day phase 0 introns are ancient,^ and
that these introns are associated with protein modules that^ were
assembled into the first genes by exon shuffling (de Souza^ 2003Go
<http://www.genome.org/cgi/content/full/14/7/1207#REF16>). Most other
introns, especially those in phase 1 or phase^ 2, arose later during
eukaryotic evolution.</quote>

Genome Research 14:1207-1220, 2004

    A Phylogeny of /Caenorhabditis/ Reveals Frequent Loss of Introns
    During Nematode Evolution

And then the exciting paper

* Resolution of a deep animal divergence by the pattern of intron
conservation *
* Scott William Roy^ * , and Walter Gilbert *
Department of Molecular and Cellular Biology, Harvard University,
Cambridge, MA 02138
Contributed by Walter Gilbert, January 18, 2005
The relationship between three biologically important groups,^
arthropods, nematodes, and deuterostomes, remains unresolved.^ It is
unknown whether arthropods are more closely related to^ nematodes
(consistent with the "ecdysozoa" hypothesis) or to^ deuterostomes
(consistent with "coelomata"). We present a method^ in which we use the
pattern of spliceosomal intron conservation^ to develop a series of
inequalities that characterize each possible^ relationship. We find that
only the ecdysozoa grouping satisfies^ these predictions, with /P/ <
10^–6 . Simulations show^ that our method, unlike some previous methods,
is largely insensitive^ to rate variation between branches.

  Researchers Shed Light On Intron Evolution

By comparing four fungal genomes, researchers from MIT and the Broad
Institute have described some of the dynamics of the evolution of
introns, the non-coding portions of genes that comprise a large
proportion of many genomes.
Introns are found in eukaryotic species, which includes all members of
the fungi, plant, and animal kingdoms. Although introns were first
discovered almost 30 years ago, scientists are still asking basic
questions about their role.
The researchers studied fungal genomes that together span 400 million
years of evolution from a common ancestor.
Their findings, published in the December 2004 issue of the Public
Library of Science, describe how an increase in introns plays a
significant role in eukaryotic evolution.
"Our results provide clues about two fundamental unanswered questions
about genome evolution--how introns are gained and how introns are
lost," said Chris Burge, Whitehead Career Development Associate
Professor in MIT's Department of Biology.
Introns are one of the basic characteristics of eukaryotic genomes, said
James Galagan, a computational biologist at the Broad. "We want to
understand what they are doing because they comprise a significant part
of our genomic ecosystem," he said.
To paint a more complete picture of intron evolution, the researchers
are currently looking at other fungal genomes. With additional data and
analysis, they hope to one day apply their whole-genome method to better
understand intron evolution in the genomes of higher eukaryotes,
including animals and plants.
Also on the study team are Bruce Birren, co-director of the Sequencing
and Analysis Program and director of the Microbial Sequencing Center at
the Broad; and co-first authors Cydney Nielsen, a graduate student in
biology, and Brad Friedman, a graduate student in biology and mathematics.
This research was supported by grants from the National Institutes of
Health, National Science Foundation, United States Department of
Agriculture, and the Burroughs Wellcome Fund.
A version of this article appeared in the December 8, 2004 issue of MIT
Tech Talk (Volume 49, Number 12).

and

Nature Reviews Genetics 7, 211-221 (March 2006) | doi:10.1038/nrg1807

    The evolution of spliceosomal introns: patterns, puzzles and progress

Scott William Roy^1
<http://www.nature.com/nrg/journal/v7/n3/abs/nrg1807.html#a1> and Walter
Gilbert^2 <http://www.nature.com/nrg/journal/v7/n3/abs/nrg1807.html#a2>
About the authors
<http://www.nature.com/nrg/journal/v7/n3/authors/nrg1807.html>
Top of page <http://www.nature.com/nrg/journal/v7/n3/abs/nrg1807.html#top>

      Abstract

The origins and importance of spliceosomal introns comprise one of the
longest-abiding mysteries of molecular evolution. Considerable debate
remains over several aspects of the evolution of spliceosomal introns,
including the timing of intron origin and proliferation, the mechanisms
by which introns are lost and gained, and the forces that have shaped
intron evolution. Recent important progress has been made in each of
these areas. Patterns of intron-position correspondence between widely
diverged eukaryotic species have provided insights into the origins of
the vast differences in intron number between eukaryotic species, and
studies of specific cases of intron loss and gain have led to progress
in understanding the underlying molecular mechanisms and the forces that
control intron evolution.

and a link http://gogarten.uconn.edu/mcb221/class21.html

Enjoy

*/Janice Matchett <janmatch@earthlink.net>/* wrote:

    Two items of possible interest:

    * Darwin's Place on Campus is Secure - But Not Supreme
    <http://www.freerepublic.com/focus/f-news/1593928/posts>**Science
    Magazine* ^* *| 2/10/2006 | Constance Holden
    Posted on *03/10/2006 11:57:58 AM EST* by furball4paws
    http://www.freerepublic.com/focus/f-news/1593928/posts [refresh
    browser continually for latest comments and links]

    A link within the above thread: *National Center for Science
    Education Defending the Teaching of Evolution in the Public Schools*
    *On The Front Lines: *
    http://www.ncseweb.org/resources/news/2006/US/848_on_the_front_lines_3_9_2006.asp

    *

    * Introns Stump Evolutionary Theorists
    <http://www.freerepublic.com/focus/f-news/1593782/posts>**Creation-Evolution
    Headlines ^ *| March 9, 2006 | Staff
    Posted on *03/10/2006 9:12:05 AM EST* by DaveLoneRanger
    http://www.freerepublic.com/focus/f-news/1593782/posts [refresh
    browser continually]

    *My post in this thread is here:*
    http://www.freerepublic.com/focus/f-news/1593782/posts?page=18#18

    ~ Janice
Received on Fri Mar 10 13:37:20 2006