Re: Stereotypes and reputations

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Mon Aug 01 2005 - 00:15:29 EDT

Cornelius Hunter wrote:

> Answering posts from Pim, George, Dick, Randy, Glenn and Michael.
>
>
>
> Pim:
>
>
>
> You say that abrupt appearance of fossil species are not evidence
> against evolution;

Indeed, the abrupt appearance is not evidence against evolution. While
there was undoubtably interesting diversification during the Cambrian,
more and more research shows how the evidence supports a gradual,
Darwinian explanation.

> you quote Valentine, an evolutionist, as saying that evolution is
> confirmed (that's not surprising);

Your comment about Valentine suggests that you are not surprised that
experts find that there are no real problems for Darwinian theory. But
Valentine in his earlier days saw various problems, and Valentine is
regularly quoted by creationists to argue that there is a problem. Of
course over time, many of these problems were resolved when new data
became available

> you say that phylogenetic incongruities are due to incomplete data
> (which is false by the way);

You have so far not given much support for this claim but my claims is
not that incongruent data is due to incomplete data uniquely but rather
that such incongruities are often found to be the result of our ignorance.

> you cite Penny and say that similarities between the species are
> highly unlikely to have occurred by random chance (so what?); you
> question whether UCEs might have function (mice with UCE's knocked out
> did just fine). So what you have are several erroneous points about
> the evidence. You might want to go read the Penny (1982) paper to see
> how meaningless it really is.
>

So far it seems that most of your evidence against common descent has
gone up into smoke. Woese, Doolittle, the tree with vines all are well
supporting Darwinian theory. More importantly there seems to be no
alternative presented by Hunter.
If Hunter wishes to focus on the few puzzles and argue that they show
how evolution has been falsified then I argue that he does not
appreciate the nuances of falsification. Time after time, such minor
puzzles would have forced us to reject evolutionary theory when in fact
additional data and increased understanding of mechanisms helped resolve
much of the issues.
If you have a coherent argument about why UCE's are a problem for common
descent or evolutionary theory and if you have a better explanation for
their existence then I am all ears. So far your arguments, once closely
scrutinized have failed to sustain themselves against an onslaught of
scientific data and knowledge, much of which is quite recent.
To confuse the Cambrian with 'abrupt appearance' seems to suggest an
unfamiliarity with both the fossil and genetic data.
What may seem to be evidentiary problems to you, seem to be mostly some
interesting puzzles, many of which are slowly unravelling and showing
exquisite support for evolutionary theory.
I suggest you focus on a single aspect or argument, UCE and HERV would
make for good candidates since our understanding is still quite limited
and explain why you believe they are evidence against evolution. How
does our ignorance or lack of understanding indict an evolutionary theory?
You may want to present the arguments with sufficient references for us
to be able to evaluate them.
What references to UCE and knock out experiments with mice do you propose?
Are you refering to Edward Rubin's work and Nobrega? What UCE's were
involved?

I assume you are familiar with
*Evolution and functional classification of vertebrate gene deserts.*

*Ovcharenko I*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Ovcharenko+I%22%5BAuthor%5D>,
*Loots GG*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Loots+GG%22%5BAuthor%5D>,
*Nobrega MA*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Nobrega+MA%22%5BAuthor%5D>,
*Hardison RC*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Hardison+RC%22%5BAuthor%5D>,
*Miller W*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Miller+W%22%5BAuthor%5D>,
*Stubbs L*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&term=%22Stubbs+L%22%5BAuthor%5D>.

Energy, Environment, Biology, and Institutional Computing, Lawrence
Livermore National Laboratory, Livermore, California 94550, USA.
ovcharenko1@llnl.gov

Large tracts of the human genome, known as gene deserts, are devoid of
protein-coding genes. Dichotomy in their level of conservation with
chicken separates these regions into two distinct categories, stable and
variable. The separation is not caused by differences in rates of
neutral evolution but instead appears to be related to different
biological functions of stable and variable gene deserts in the human
genome. Gene Ontology categories of the adjacent genes are strongly
biased toward transcriptional regulation and development for the stable
gene deserts, and toward distinctively different functions for the
variable gene deserts. Stable gene deserts resist chromosomal
rearrangements and appear to harbor multiple distant regulatory elements
physically linked to their neighboring genes, with the linearity of
conservation invariant throughout vertebrate evolution.

[quote]
Some of these gene deserts have been shown to contain^ regulatory
sequences that act at large distances to control^ the expression of
neighboring genes (Nobrega et al. 2003
<http://www.genome.org/cgi/content/full/15/1/137#REF20>; Kimura-Yoshida^
et al. 2004 <http://www.genome.org/cgi/content/full/15/1/137#REF14>;
Uchikawa et al. 2004
<http://www.genome.org/cgi/content/full/15/1/137#REF30>). By contrast,
other large^ gene-sparse regions are potentially nonessential to genome
function,^ since they can be deleted without significant phenotypic
effect^ (Russell et al. 1982
<http://www.genome.org/cgi/content/full/15/1/137#REF26>; Rinchik et al.
1990 <http://www.genome.org/cgi/content/full/15/1/137#REF24>; Nobrega
2004 <http://www.genome.org/cgi/content/full/15/1/137#REF19>). It^ is
possible that these differences reflect the existence of^ distinct
categories of gene deserts, such that some deserts^ harbor sequence
elements with critically important and conserved^ biological roles
whereas others do not.
[/quote]

Leading to the conclusion

[quote]Although much remains to be explained about the function^ of gene
deserts in general, these findings provide some potential^ new insights
to distant regulatory activity. Our evolutionary^ analysis emphasizes
the importance of stable gene deserts and^ suggests that they are likely
to play a critical biological^ role in vertebrates.[/quote]

But of course they are evolutionists... Of course so far I have yet to
hear any ID explanations for these data.
How does ID explain the congruency between trees as documented by
Theobalt? Why do you quote Doolittle and Woese when their views give
little support to your thesis?
Received on Mon Aug 1 00:17:25 2005

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