Re: [asa] Re: Origins

In order to appreciate evolution, it may be relevant to point out that
Darwin did not talk about mutation but rather variation.

Allen MacNeill has some excellent postings on this topic
http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html

<quote>
Indeed, Darwin himself proposed that natural selection was the best
explanation for the origin of adaptations, and that natural selection
itself was an outcome that necessarily arises from three
prerequisites:

• variation (between individuals in populations),
• inheritance (of traits from parents to offspring), and
• fecundity (reproduction resulting in more offspring than necessary
for replacement).
</quote>

Allen identifies over 47 different sources of variation. Understanding
that it is variation and not mutation on which selection act and
people may understand better how evolution does and does not work. For
instance mutations do not arise just because there is a need, on the
contrary, mutations in all their forms, maintain or extend the
variation in the genome on which evolutionary processes can act.
Now also comes into play the distribution of fitness effects and
recent research has shown that beneficial mutations arise at a much
higher frequency than initially expected and that most beneficial
mutations are of small impact.
This is important since large effect beneficial mutations will 'sweep'
through the population extinguishing much of the variation in the
population. This is called a selective sweep and during the sweep many
other variations can be fixated in the genome, detrimental as well as
beneficial. Small fitness effect mutations allow these mutations to
build up over time at different locations and spread, enabling
multigene effects.

And then there is of course neutrality which allows significant
variation in the genome even though the phenotype appears to be the
same, and yet the population is far more evolvable.

These are fascinating concept of scientific inquiry and understanding
as to how evolution shaped our genomes.

I believe that many people see evolution as single point mutations
spreading through selection in a fixed population while in fact there
are so many more parameters which play a role and affect evolution
that modeling them all can become quite a problem.

I still see gene duplication as a major innovator as well as the
regulatory genes in development, however that's just the tip of an
enormous iceberg

<quote>
Sources of Heritable Variation (both genotypic and phenotypic) Among
Individuals in Populations

Gene Structure (in DNA)
• single point mutations
• deletion and insertion ("frame shift") mutations
• inversion and translocation mutations
Gene Expression in Prokaryotes
• changes in promoter or terminator sequences (increasing or decreasing binding)
• changes in repressor binding (in prokaryotes); increasing or
decreasing binding to operator sites
• changes in repressor binding (in prokaryotes); increasing or
decreasing binding to inducers
• changes in repressor binding (in prokaryotes); increasing or
decreasing binding to corepressors
Gene Expression in Eukaryotes
• changes in activation factor function in eukaryotes (increasing or
decreasing binding to promoters)
• changes in intron length, location, and/or editing by changes in
specificity of SNRPs
• changes in interference/antisense RNA regulation (increasing or
decreasing binding to sense RNAs)
Gene Interactions
• changes in substrates or products of biochemical pathways
• addition or removal of gene products (especially enzymes) from
biochemical pathways
• splitting or combining of biochemical pathways
• addition or alteration of pleiotropic effects, especially in
response to changes in other genes/traits
Eukaryotic Chromosome Structure
• gene duplication within chromosomes
• gene duplication in multiple chromosomes
• inversions involving one or more genes in one chromosome
• translocations involving one or more genes between two or more chromosomes
• deletion/insertion of one or more genes via transposons
• fusion of two or more chromosomes or chromosome fragments
• fission of one chromosome into two or more fragments
• changes in chromosome number via nondisjunction (aneuploidy)
• changes in chromosome number via autopolyploidy (especially in plants)
• changes in chromosome number via allopolyploidy (especially in plants)
Eukaryotic Chromosome Function
• changes in regulation of multiple genes in a chromosome as a result
of the foregoing structural changes
• changes in gene expression as result of DNA methylation
• changes in gene expression as result of changes in DNA-histone binding
Genetic Recombination
• the exchange of non-identical genetic material between two or more
individuals (i.e. sex)
• lateral gene transfer via plasmids and episomes (especially in prokaryotes)
• crossing-over (reciprocal and non-reciprocal) between sister
chromatids in meiosis
• crossing-over (non-reciprocal) between sister chromatids in mitosis
• Mendelian independent assortment during meiosis
• hybridization
Genome Structure and Function
• genome reorganization and/or reintegration
• partial or complete genome duplication
• partial or complete genome fusion
Development (among multicellular eukaryotes, especially animals)
• changes in tempo and timing of gene regulation, especially in eukaryotes
• changes in homeotic gene regulation in eukaryotes
• genetic imprinting, especially via hormone-mediated DNA methylation
Symbiosis
• partial or complete endosymbiosis
• partial or complete incorporation of unrelated organisms as part of
developmental pathways (especially larval forms)
• changes in presence or absence of mutualists, commensals, and/or parasites
Behavior/Neurobiology
• changes in behavioral anatomy, histology, and/or physiology in
response to changes in biotic community
• changes in behavioral anatomy, histology, and/or physiology in
response to changes in abiotic environment
• learning (including effects of use and disuse)
Physiological Ecology
• changes in anatomy, histology, and/or physiology in response to
changes in biotic community
• changes in anatomy, histology, and/or physiology in response to
changes in abiotic environment
</quote>

On 11/5/07, mlucid@aol.com <mlucid@aol.com> wrote:
>
> I submit that we have just scratched the surface of evolution. We used to
> be
> quite confident in the inviolability of randomly mutated DNA as the whole
> of
> the process. Now we see issues like epigenetics adding an independent
> behavioral mechanism to the expression (and thus selection) of our DNA,
> a mechanism which mitigates the so-called "random mutation" as the sole
> cause of natural selection.
>
> This evolution of our rational understanding will not stop any time soon.
> The
> hand of God will continually be revealed in our ongoing creation. As such
> we
> are inadequate, permanently inadequate, to judge the perfection of Creation
> in
> terms of what we might rationally understand at any given time.
>
> We don't know nearly enough about Creation, purpose, or evolution to make
> a wild guess at how intelligent and perfect the Design may be. But we know
> what we know rationally as surely as we know God is immanent in Creation.
> My faith leads me to an instinctive resolution of Creation, purpose and
> evolution
> in a way my reason will never know. They are all one thing in my faith.
> Reason
> has a place in our lives that is highly restricted, but extremely reliable.
> Faith is
> all the rest from the love of God right down to the color of blue.
>
> The day that we realize the proper jurisdictions of reason and faith is the
> day men of all faiths can put aside their rational minutia and realize that
> God is inherent in the human condition and identical in every heart that,
> in sufficient humility, seeks the truth through faith. I personally think
> that Jesus would tell me it would be a good thing if all men agreed
> that God lives identically in all our hearts regardless of the histories
> that lead us to God.
>
> Histories (like TE, OEC, and YEC) are just means to an end. It is the
> End that is the important thing, n'est pas?
>
> -Mike (Friend of ASA)
>
>
>
>
>
>
>
> -----Original Message-----
> From: David Opderbeck <dopderbeck@gmail.com>
> To: D. F. Siemens, Jr. <dfsiemensjr@juno.com>
> Cc: john_walley@yahoo.com; bernie.dehler@intel.com; asa@calvin.edu
> Sent: Mon, 5 Nov 2007 9:31 am
> Subject: Re: [asa] ORIGINS: pseudogenes are overwhelming evidence for
> evolution...?
>
>
> D.S. said: But this means that God is a sloppy designer or intentional
> deceiver unless it can be proved that every one of these elements has a
> purpose. The exclusion of perfect design applies to finite humans, but
> cannot apply to an omniscient deity.
>
> Why? Exactly the same argument applies against any TE position that holds
> that God is sovereign over and the primary cause of evolution.
>
>
> On 11/4/07, D. F. Siemens, Jr. <dfsiemensjr@juno.com> wrote:
> >
> >
> > This presents one of the OEC approaches, that at various times God added
> new genes to various individuals of groups and then let them develop. The
> other view, which I heard from Hugh Ross, is that God created every species
> de novo at the appropriate time in earth history. But this means that God is
> a sloppy designer or intentional deceiver unless it can be proved that every
> one of these elements has a purpose. The exclusion of perfect design applies
> to finite humans, but cannot apply to an omniscient deity. It can apply to a
> limited deity, as in process theology. But even here a deity should know
> better or not to able to tune the world to provide a place for life. This is
> a radically different notion than the use of secondary apart from the big
> bang, or the big bang and origin of life, or the big bang, origin of life
> and the first human
> > Dave (ASA).
> >
> > On Sun, 4 Nov 2007 08:41:22 -0500 "David Opderbeck" <dopderbeck@gmail.com>
> writes:
> >
> > I think a typical OEC response is that God reused the genetic code as He
> progressively created. I don't think this is a terrible response. The
> counter-argument is, why would God re-use "messy" code? But why not? No
> one argues for "perfect" design, and any complex coding exercise involves
> pieces of code that may have had some functionality in earlier iterations
> but that aren't called upon in later ones. And, the full TE position really
> says exactly the same thing, except that it holds that God's causal
> influence was secondary rather than direct.
> >
>
> ________________________________
> Email and AIM finally together. You've gotta check out free AOL Mail!
>

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Received on Mon Nov 5 12:51:01 2007