[FRIAM] random v stochastic v indeterminate

[Roger Critchlow]

Gracious, I'm having fits trying to construct complete arguments this
morning.

The original Darwinian mechanics of natural selection was formulated in
complete agnosticism about where the underlying variety came from.  The
variety existed, under the proposed mechanics it would be winnowed into
more or less fit progeny, and somehow after the winnowing there would still
be more variety for future rounds of winnowing.  The Neo-Darwinian
synthesis identified Mendelian genetics as the mechanism of inheritance
without any idea of how it worked, either, and was limited to recombination
of alleles for their mechanics of variety.  That is a formidable source of
variety given enough alleles on enough loci, and it's also a sustainable
source of variety since unfit allelic combinations could still be preserved
in the population in other combinations.  So if genotype AB was fatal, A
and B might still persist in the genotypes AC, BC, AD, BD, and so on.  Then
with the molecular biology of the gene we finally get a physical mechanism
for inheritance and an embarrassment of riches for the origins of variety.
We have, off the top of my head:

   - single base pair replication errors or point mutations;
   - insertions or deletions where the DNA being copied or the copy gets
   looped out;
   - cross overs where two homologous DNA strands swap ends (though we had
   microscopic evidence for crossing over before molecular biology);
   - chromosome duplications and losses;
   - copy error correction mechanismss;
   - mutators which increase copy errors;
   - viral sequences integrating into chromososmes
   - viral sequences disintegrating out of chromosomes
   - mobile elements jumping from location to location in chromosomes
   - extra chromosomal genetic materials
   - incorporation of other organisms as organelles
   - neutral networks of RNAs or proteins where the underlying function is
   preserved across nucleotide or peptide substitutions
   - differential expression under environmental variation

DNA polymerase is a complex of proteins which synthesizes a new strand of
DNA complementary in sequence to an existing strand.  It takes single
stranded DNA and makes it into double stranded DNA according to the base
pairing rules.  It's actually more complex than that, I believe it unwinds
the existing double strand as goes, cutting a strand to release the
torsion.  There are thousands active in a human cell that is duplicating
its DNA in preparation for cell division.  Embryonic cell divisions take
about 8 hours, DNA replication is happening at 2.08e5 nucleotides/second
according to a google search.  My source claims that: "DNA replication is
accomplished with an average of only 1 error per billion (109) nucleotides.
38 <http://www.ehd.org/dev_article_unit1.php#fb38> 190?39
<http://www.ehd.org/dev_article_unit1.php#fb39>"  (Amusing to me, that 190?
refers to a text book of Molecular Cell Biology by an author who was a
scientific advisor to a company where I was a founding employee.)  That
error rate, whatever its exact magnitude and significant digits, that
replication rate, the concentration of DNA polymerase in the embryonic
cells, the rate of cell division, these are all subject to natural
selection, as are the biosynthetic pathways that supply the raw materials
for DNA replication.

Right, construct complete arguments.

The theory of natural selection does not explain the origin of variety,
however it does depend on variety existing and continuing to exist.  If
natural selection led to runaway fixation of genotypes in a population, it
would be game over.  One would expect that the fingerprints of natural
selection should be found everywhere that living organisms might modulate
the origin and maintenance of variety in their populations.

As for the origin of innovations, I'd say that's a value system which has
nothing to do with natural selection, it's a moral aesthetics that has to
do with measuring progress, curating shiny baubles from evolutionary
history for the purposes of arguing with other curators of shiny baubles.
 (Oops, may have tarred more than necessary with that brush.)

I would guess that most arguments against evolution having had time enough
to get anywhere depend on an assumption of one ancestral genome
diversifying by replication with point mutation.  But natural selection
might have begun curating a diversity of RNAs, peptides, and small molecule
metabolites before the origin of life, and the original life may have
incorporated a lot of existing pre-biotic variety.

-- rec --
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