Re: Review of The Extended Phenotype

From: Michael Ragland (ragland37_at_webtv.net)
Date: 09/07/04 

Date: Tue, 7 Sep 2004 15:31:48 +0000 (UTC)

RM:
One way to restrict the definition of gene as nucleotide sequence is to
establish arbitrary upper and lower bounds on sequence length. Lower
bound to prevent calling something a gene if it is re-created at random
more times than it occurs by heridity. Upper bound to assure that a gene
passes through several generations before it's split apart by meiosis.
Perhaps the definition of "optimom" etc. is for the same purpose, except
with a more functional restriction instead of just arbitrary numeric
limits.

MR:
What would be an example of a lower bound sequence preventing the
labeling of nucleotide sequence if a gene is re-created at random more
times than it occurs by heredity? Are there examples of such random
mutations. If these mutations are successful they may ultimately occur
by heredity and if they aren't then they die out. But what about random
mutations which may occur over long periods of time and aren't a fixture
of a particular nucleotide sequence yet apparently are neutral? What
would be an upper bound chromosome to assure a gene passes through
several generations before it's split apart by meiosis. Are you saying
sexual recombination has to occur through several generations before we
know if a "gene" is functional in a nucleotide sequence?

You write, "Defining a gene as any nucleotide sequence is faulty because
it fails to exclude two obvious cases:
- A sequence so very very short that it is re-created billions of times
by random mutation and in fact occurs at random thousands of different
places within any given genome.
- A sequence so very very long, for example an entire chromosome, that a
single act of meiosis is surely going to break it up so that it can't
survive as a unit even a single generation."

What would you call such a short sequence if not a short nucleotide
sequence. What examples of such short sequences be re-recreated billions
of times by random mutation? Why has evolution seen fit to create
thousands of random mutations within any given genome and what roles do
they play?
You mention a sequence very long that a single act of meiosis is going
to beak it up so that it can't survive as a unit even a single
generation. Are you referring to certain terminal diseases?

You state, "One way to restrict the definition of gene as nucleotide
sequence is to establish arbitrary upper and lower bounds on sequence
length. Lower bound to prevent calling something a gene if it is
re-created at random more times than it occurs by heredity. Upper bound
to assure that a gene passes through several generations before it's
split apart by meiosis." I understand your use of the term "arbitrary"
but in the context of science I don't like it. I think there should be
much more scientific research and certainty before making such arbitrary
calls. Who is to say a lower bound sequence isn't a nucleotide sequence
even if some speculate it is created at random more times than occurs by
heredity. Or that a upper bound sequence isn't a long nucleotide
sequence to assure that a gene passes through several generations before
it's split apart by meiosis? I think we are along ways away from
scientifically validating these. But I could be wrong. I'm not a
scientist.

You write, "Note that natural selection is context-dependent on several
levels of context: (1) A part of the coding for a very large protein
might be large enough all by itself to qualify as selectable in its own
right, and two different such parts of such a very large gene might be
somewhat independently evolving, while at the same time they must remain
compatible with each other so that the very large protein continues to
function properly

Ragland:
I question whether the part of the coding for a very large protein might
be large enough all by itself to qualify as selectable in its own right?
Selectable in what sense? As one of several possible genetic markers for
a disease? Or as a Unit of Selection (whatever one defines that as). You
mention each locus along the coding to be independently evolving and
"Codings for all organisms within a single species must co-exist in the
sense that meiosis might someday mix-and-match then randomly and any
that are seriously incompatible with each other would cause mixes to not
survive well."
It seems to me the entire genome should be seen as "selectable" and that
we need to have a more holistic understanding of it through scientific
investigation before certain applications of it are made to society.

RM:
All codings are useful relative to the particular ecological niche that
species occupies. A biochemical pathway unrelated to that niche would
not have any survival value. (5) All codings are useful relative to
other species which exist nearby. A defense against a preditor would
have no value if that preditor isn't ever anywhere nearby. In general,
"different replicators survive best in different contexts" at all such
levels of context."

MR:
I disagree all coding are necessarily useful relative to the particular
ecological niche that species occupies. In some species I would say this
is the case but not in our own. I agree with you a biochemical pathway
unrelated to that niche would not have any "longterm survival value". I
think Homo Sapiens exactly fit that boat. We've immensely advanced in
terms of science and technology but biologically we are much the way we
were 10,000 years ago. With that advanced science and technology we now
have the potential ability to wipe ourselves out whereas in the past it
was knives, swords, axes. spears, catapults, etc. In the modern
industrialized world there really are few predators except man preying
on man. I don't feel comfortable with genetic engineering of people
(enhanced, improved human beings) and how it will be used and who will
make the choices. My greatest fear presently is genetic
screening/testing and the accuracy of many genetic predispositions and
DNA databases and how that information will be used. Of course, the
concerns are genetic discrimination, lack of privacy and creation of a
categorized genetic underclass.

"It's uncertain whether intelligence has any long term survival value.
Bacteria do quite well without it."
 Stephen Hawking

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