Re: Stereotypes and reputations

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Mon Aug 01 2005 - 12:45:45 EDT

Cornelius Hunter wrote:

> 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.
>
Indeed, an interesting puzzle. How does Hunter explain these data?
Science is working hard to understand what is happening here. And I am
still interested how our ignorance of these UCE's should be evidence for
or against common descent?

> 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.
>
Yes and as I have shown, recent work has looked at these
Evolution and functional classification of vertebrate gene deserts.
Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L

[quote]

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]

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]

> 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).

As I said, some minor puzzles compared to the overwhelming congruencies
found

>
> 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.

He is saying that the evolutionary tree model needs to be extended to
take into account the (minor) contributions of HGT

> 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.

Your quote mining of Doolittle leads you to not appreciate his argument.
Horizontal and vertical gene transfer are quite in line with
evolutionary theory and the fact that trees and vines can be
reconstructed shows that most of the transfer is vertical. Horizontal
gene transfer, as well as convergence makes recoverying the actual tree
more complicated but that hardly means that common decent is wrong.

>
> 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.

So you object to science trying to explain the data with what you
consider to be 'clever story about an unlikely event' I am sure that you
thus equally reject the clever story of an unlikely event of divine
intervention or miracles?

> 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?

THere are no problems for common descent. If you disagree, please explain.

> 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?

Natural selection works on function not necessarilyon the genetic pathways.

> 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.

Without much supporting evidence, your claims are hard to evaluate but
even the few data you provide fail to show much of a problem for
evolutionary theory. As I said, a minor puzzle to be resolved.

>
>
> 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.

Yes, we surely should let our ignorance reject the vaste evidence of CD
just because we do not understand the details. This is exactly what
makes ID such a scientifically vacuous concept.

> 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.

Hmm what... And why are you claiming that evolutionary processes are
'dumb'. In fact, they are able to do things which are still beyond the
reach of powerful computers and trained scientists. More and more
details arise as to how these structures may have evolved. Of course, ID
proponents continue to 'argue' that there is insufficient detail, while
at the same time providing NO detail at all about their own ideas.
I have evaluated various aspects of your claims why CD should be
rejected and found them to be wanting in various aspects. They either
are not supported by the scientists you quoted, they are slowly being
resolved, or our understanding of them is so limited that a jump to
rejecting CD seems quite extreme, given the history of science resolving
these puzzles in favor of the extremely well supported fact of Common
Descent.

A quick remark on Doolittle who according to you, without much
references, claims that

[quote]
You also have understated Doolittle, who is one of the early
evolutionists to admit to what the data say: the tree model doesn't work
very well. [/quote]

Let's see what DOolittle 'admits' and conclude that Doolittle's argument
to 'abandon the tree' are not because common descent is a failure or
because evolutionary theory has failed, on the contrary, it's because of
the relevance of HGT.

Science. 1999 Jun 25;284(5423):2124-9.
*Phylogenetic classification and the universal tree.*

*Doolittle WF*
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&term=%22Doolittle+WF%22%5BAuthor%5D>.

Canadian Institute for Advanced Research, Department of Biochemistry and
Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7,
Canada. ford@is.dal.ca

[quote]
 From comparative analyses of the nucleotide sequences of genes encoding
ribosomal RNAs and several proteins, molecular phylogeneticists have
constructed a "universal tree of life," taking it as the basis for a
"natural" hierarchical classification of all living things. Although
confidence in some of the tree's early branches has recently been
shaken, new approaches could still resolve many methodological
uncertainties. More challenging is evidence that most archaeal and
bacterial genomes (and the inferred ancestral eukaryotic nuclear genome)
contain genes from multiple sources. If "chimerism" or "lateral gene
transfer" cannot be dismissed as trivial in extent or limited to special
categories of genes, then no hierarchical universal classification can
be taken as natural. Molecular phylogeneticists will have failed to find
the "true tree," not because their methods are inadequate or because
they have chosen the wrong genes, but because the history of life cannot
properly be represented as a tree. However, taxonomies based on
molecular sequences will remain indispensable, and understanding of the
evolutionary process will ultimately be enriched, not impoverished.[/quote]

And is HGT/LGT just an 'idea' or actually supported by fact?

[quote]
LGT among and between bacteria and archaea is not new: Gogarten has been
thoroughly documenting individual (especially prokaryotic) instances for
several years, suggesting in 1993 (28) that, for many genes, the tree of
life becomes a net." [/quote]
Received on Mon, 01 Aug 2005 09:45:45 -0700

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