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. 1997; de Souza 2003). 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. 1995). Furthermore, there is a small, but significant excess of symmetric exons—ones whose flanking introns have the same phase number (Long et al. 1995). 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. 1996, 1997, 1998; Roy et al. 1999; Fedorov et al. 2001). 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 2003). 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 EvolutionAnd 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 Roy1 and Walter Gilbert2 About the authors
Top of pageAbstractThe 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
 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
 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 13:37:16 2006