Re: Stereotypes and reputations

From: Cornelius Hunter <ghunter2099@sbcglobal.net>
Date: Mon Aug 01 2005 - 02:59:11 EDT

Pim:

There are *hundreds* of UCEs -- sequences with 100% identity between the
human, mouse, and rat. Even if these sequences had known function their
sequence identity would be very strange. You'd have to hunt and hunt to find
*known* functional sequences with 100% identity between these species. This
finding of 100% identity in these hundreds of sequences means that their
putative function would have to be absolutely contingent on *every*
residue's identity. And on top of this, there is no known function, making
this finding even stranger.

Now what has been done at Livermore and elsewhere, is the complete knockout
of these UCEs in mice. Mind you they did not merely substitute for a few
nucleotides here and there. They knocked the whole sequences out! The result
was no apparent change. The mice were put through 100+ tests, with virtually
no change. This is a direct falsification of common descent which predicts
that functionally unconstrained sequences are not conserved.

Phylogenetic incongruencies are common. A systematic study was done on the
genomes of 5 different light-harvesting bacteria showed dramatic
inconsistencies. Every conceivable phylogeny found support, and no one
phylogeny was significantly preferred (Science, 298:1616). Mitochondrial
sequences are at odds with nuclear sequences. In one study they clustered
frogs and chickens with fish. I gave you the citations. Alan Feduccia wrote
that the growing gap between molecular analyses and the fossil record "is
astounding" (TREE, 18:172).

You say I cite Doolittle though his "views give little support to your
thesis." Huh?? Doolittle is saying that the evolutionary tree model isn't
working. Are you now saying common descent doesn't require the tree model?
Even though the tree model fails, common descent feels no pain? And for
early life, the tree+vine+rapid transfer hub model does not support
evolution unless you give it the special license to use whatever model it
likes, regardless of whether or not the model actually has been observed.

About retro viruses, one widespread germline provirus is missing in chimps
and gorillas. Since it is widespread, it must have been in a distant common
ancestor according to common descent. But in that case the chimps and
gorillas should have inherited the provirus. But they didn't, so CD needs
some clever story about an unlikely event that we can never verify or
falsify. What's worse, it must have happened twice -- once in the chimp and
once in the gorilla. There are other retro viruses that don't make sense on
CD, and as we continue to sequence whole genomes we'll probably find even
more.

The finding of nonhomologous development means that similar structures, in
similar species, come from different genes or embryonic development
pathways. How could this be on CD? Imagine, over eons of time evolution
produces a frog. The limbs, bones, internal organs, eyes, etc. are all
there, having been produced by the genes working through the embryonic
development process. And of course this finely tuned process, and the highly
complicated genes were produced by evolution (somehow). Now, a speciation
event occurs, and you now have 2 frog species, diverging from the 1. And
we're to believe that now, a the eye of one of the frog assumes a completely
different development pathway, though the completed structure itself is
conserved? This is by no means exceptional. It is the rule rather than the
exception: homologous structures switching to different genes and
development routes. This makes no sense.

Then there are complexities, such as protein synthesis which uses the DNA
code. Protein synthesis in the cell is a phenomenal process involving
hundreds of macromolecules performing feats of copying and translating,
proofreading, checking, etc. And we have no idea how it could have evolved.
For this, and myriad other complexities, evolutionists can only provide
broad speculation that has no basis in reality. This is not like complaining
about the mechanic who has not fixed your car yet because he is busy. These
structures are very well understood and evolutionists have spent countless
hours trying to figure out how they could have evolved. Highly trained
scientists with powerful computers cannot figure out how a dumb process
could have done it. Hmm.

--Cornelius

----- Original Message -----
From: "Pim van Meurs" <pimvanmeurs@yahoo.com>
To: "Cornelius Hunter" <ghunter2099@sbcglobal.net>
Cc: <asa@calvin.edu>; "Glenn Morton" <glenn_morton@yahoo.com>
Sent: Sunday, July 31, 2005 9:15 PM
Subject: Re: Stereotypes and reputations

> 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 03:01:55 2005

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