Hi Joel!
I suspect that creationists and I.D.ists are beginning
to "get" the fact that genomes can mutate even to the
extent of creating a Whole Genome duplicating itself,
or whole chromosomes can duplicate, or portions of
them, or single genes can duplicate. All such
mutations have been observed. And we also can estimate
the general rates of mutations, showing that there was
time for enough mutations to accumulate naturally from
when human beings first branched off from a common
ancestor they shared with their closest living primate
cousins. So evolution has believability in terms of
mutations creating more genetic material to work with,
as well as enough time based on known mutation rates.
The creationists and I.D.ists will continue to argue
that that's still not enough and that mutations had to
be slowly guided over that time, and other mutations
halted or preserved from decay I suppose, since the
Designer would have to keep filling things in and
sustaining those things from decaying in the genome,
for if the Designer is going to do one, "He's" got to
also keep his work in tact, i.e., preserved from any
mutations that might take it back a step (because we
know for a fact that mutations continue happening all
the time). And of course this same Designer also has
to consciously decide to allow neutral mutations to
either happen or not happen (based on future plans
based on genetic drift). So a lot of decisions have to
continue being made by such a Designer all the time.
Of course I.D. could retreat even further into mystery
by advocating that God doesn't actually change the DNA
directly, but simply guides whatever natural mutagens
are already inside each reproductive cell (or that
penetrate the cell, like cosmic rays), in other words,
not popping new genes into existence, but simply
guiding mutagenic agents around, pulling them by the
nose, i.e., undetectably and miraculously. But by
then, would anyone really care that much about I.D.?
The thought of a great and extremely busy "mutagenic
guider" doesn't seem as inspiring as the
"instantaneous creator of new genes."
Most theists would probably switch to theistic
evolution by then, with a Designer who winds up the
cosmos like a watch in the beginning, and then lets
nature take her course, just as nature does inside
stars where all the elements are continuing to be
forged out of simple hydrogen atoms.
Oh, and you MUST see the new issue of Scientific
American with its article on pseudogenes!
Scientific American, August 2006 issue
"The Real Life of Pseudogenes"
Disabled genes, molecular relics scattered across the
human genomic landscape, have a story of their own to
tell. And it is still unfolding
By Mark Gerstein and Deyou Zheng
Our genetic closet holds skeletons. The bones of
long-dead genes--known as pseudogenes--litter our
chromosomes. But like other fossils, they illuminate
the evolutionary history of today's more familiar
forms, and emerging evidence indicates that a few of
these DNA dinosaurs may not be quite so dead after
all. Signs of activity among pseudogenes are another
reminder that although the project to sequence the
human genome (the complete set of genetic information
in the nuclei of our cells) was officially finished,
scientists are still just beginning to unravel its
complexities.
It is already clear that a whole genome is less like a
static library of information than an active computer
operating system for a living thing. Pseudogenes may
analogously be vestiges of old code associated with
defunct routines, but they also constitute a
fascinating record contained within the overall
program of how it has grown and diversified over time.
As products of the processes by which genomes remodel
and update themselves, pseudogenes are providing new
insights into those dynamics, as well as hints about
their own, possibly ongoing, role in our genome.
...continued at Scientific American Digital
--- Joel Cannon <jcannon@jcannon.washjeff.edu> wrote:
> Feel free to share. The articles are better than my
> post. I am trying
> to get away on vacation so I did not have time to do
> anything but skim
> your email.
>
> Nice to hear that someone read my post. I felt like
> I was shouting
> down a long pipe with nobody on the other end.
>
> On Sun, Jul 23, 2006 at 05:08:53AM -0700, Edward
> Babinski wrote:
>> Joel,
>> I read your posts at the ASA site about whole
> genome
>> duplication. Bravo! I'd like to share them with
>> Stephen Jones at his blog site. He is a
> "progressive
>> creationist" (a creationistic I.D.ist) named
> Stephen
>> Jones who used to run a yahoo group called
>> CreationEvolutionDesign, and now he has a blog. He
> is
>> pretty outspoken, but seems to be able to read and
>> comprehend and at least listen to pro-evolutionary
>> arguments and evidence. The subject of whole
> genome
>> duplication came up and I sent him the following
>> information. You may be interested in his reply to
> me
>> as well:
>>
>>
>
http://creationevolutiondesign.blogspot.com/2006/05/massive-
>
>> duplication-of-genes-may-solve.html
>>
>> STEPHEN JONES: Harvard botanist and Neo-Darwinism
>> co-founder G. Ledyard Stebbins pointed out that
>> "polyploidy has contributed little to progressive
>> evolution"
>>
>> ED: Stebbins wrote that way back in 1971. Since
> then
>> geneticists have learned much more about
> duplications
>> of individual chromosomes, and also about
> duplications
>> of ENTIRE GENOMES. And no, the animals in such
> cases
>> do not die from such a massive mutation. In fact
> two
>> similar species of zebrafish live today, one with
>> nearly twice the genetic material of the other,
> though
>> many of the duplicated genes are pseuodgenes in
> the
>> species whose ancestors underwent the duplication.
>>
>> For instance, CONTRA STEBBINS,
>> in 1998 a "Computational Genetics Discussion
> Group:
>> Genome Duplication" wrote on the web:
>>
>> "Whole genome duplication appears to be an
> important
>> evolutionary mechanism (Ohno, 1970).
>>
>> "Despite the rarity of whole-genome duplications,
> we
>> have observational evidence for several of them:
>>
>> "Saccharomyces cerevisiae (yeast) duplicated about
>> 10^8 years ago.
>>
>> "Vertebrates underwent 2 duplications some 2*10^8
>> years ago.
>>
>> "More recent genome duplications have occurred in
> some
>> vertebrate lines such as frogs, the salmoniform
> fish
>> and zebrafish.
>>
>> "Particularly prevalent in plants (i.e. several
>> occurences in the cereal lineage)."
>>
>> ~~~~~~~~~~
>>
>> "In 1999 Holland [a professor] lists understanding
>> �the importance of gene duplication in the
> evolution
>> of development� as one of the two most important
>> questions in evolutionary developmental biology at
> the
>> end of the 20th century.
>>
>> "This statement reflects the particular interest
> in
>> duplications in developmental genes, but also the
>> general interest in evolution by gene
> duplications."
>>
>> ~~~~~~~~~~~~~~~~
>>
>> Since then, "unmistakable" evidence for "whole
> genome
>> duplication" in the vertebrate line of
> evolutionary
>> changes has been found:
>>
>> Two rounds of whole genome duplication in the
>> ancestral vertebrate.
>>
>> PLoS Biol. 2005 Oct;3(10):e314. Epub 2005 Sep 6.
>> Related Articles, Links
>>
>> ABSTRACT
>> <...> UNMISTAKABLE EVIDENCE OF TWO DISTINCT GENOME
>> DUPLICATION EVENTS EARLY IN VERTEBRATE EVOLUTION
>> indicated by clear patterns of four-way paralogous
>> regions covering a large part of the human genome.
> Our
>> results highlight the potential for these
> large-scale
>> genomic events to have driven the evolutionary
> success
>> of the vertebrate lineage.
>>
>> Definition of *PARALOGOUS GENES*: "Two genes or
>> clusters of genes at different chromosomal
> locations
>> in the same organism that have structural
> similarities
>> indicating that they derived from a common
> ancestral
>> gene and have since diverged from the parent copy
> by
>> mutation and selection or drift."
>>
>> ~~~~~~~~~~~~
>>
>> Genome duplication in the teleost fish Tetraodon
>> nigroviridis reveals the early vertebrate
>> proto-karyotype.
>>
>> Nature. 2004 Oct 21;431(7011):916-7.
>>
>> ABSTRACT
>> <...> ANALYSIS OF THE TETRADON AND HUMAN GENOMES
> SHOWS
>> THAT WHOLE-GENOME DUPLICATION OCCURRED IN THE
> TELEOST
>> FISH LINEAGE, SUBSEQUENT TO ITS DIVERGENCE FROM
>> MAMMALS. The analysis also makes it possible to
> infer
>> the basic structure of the ancestral bony
> vertebrate
>> genome" <...>
>>
>> ~~~~~~~~
>>
>> Excerpts from: GENE DUPLICATIONS AND VERTEBRATE
>> PHYLOGENY by James Cotton (circa 2001)
>>
>> "Theoretical studies have shown that gene
> duplications
>> may be relatively likely to lead to new gene
>> functions, and to increase the fitness of genomes
> in
>> which they occur. Walsh (1995) presents a
> population
>> genetic model suggesting that, for large
> populations,
>> �new gene function, rather than pseudogene
> formation,
>> is the expected fate of most duplicated genes�,
> which
>> would make gene duplication an impressively
> powerful
>> mechanism for the evolution of novel biochemistry
> and
>> novel developmental processes. Specifically, new
>> functions are likely to evolve where rS >> 1,
> where S
>> = 4Nes and Ne is the effective population size, S
> is
>> the selection coefficient and r is the ratio of
>> advantageous to other mutations. This model is
> likely
>> to underestimate the rate of evolution of new gene
>> functions, principally because it assumes that all
>> nonadvantageous mutations are neutral, where in
>> reality many will be more or less deleterious.
> Ohta
>> (1989) admits that �gene duplication could well
> have
>> been the primary mechanism for the evolution of
>> complexity in higher organisms�, and presents
> models
>> for the origin of �gene families with diverse
>
=== message truncated ===
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Received on Fri Aug 4 16:29:15 2006
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