Re: Is evolution really the central theory for all of biology?

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Tue Sep 20 2005 - 13:07:35 EDT

Cornelius Hunter wrote:

> Terry and Pim:
>
> Pim mentions that "trees inferred from for instance morphological data
> are largely substantiated by the underlying genetic data." Again, one
> hardly needs evolution here. This is common sense. I wouldn't expect
> the arabidopsis blueprint not to correspond to its morphology. Of
> course there is going to be some sort of correlation between genetic
> data and morphology. On the other hand, there are many examples where
> the correlation breaks down, and evolution has difficulty explaining
> these because the observed genetic differences / similarities would
> not have arisen according to gradual change occurring over time with
> common descent. So various epicycles need to be invoked.
>
So we accept the evolutionary evidence of common descent and similarity
? It's after all common sense? Yes, correlations break down and it is up
to science to explain them. Your assertions that evolution has
difficulties explaining them and your assertion of epicycles need to be
invoked seem self contradictory. In other words, either evolutionary
theory explains the data and you consider these explanations to be ad
hoc or evolutionary theory does not yet explain these data. Either way,
I fail to see the problem.

> Pim also mentions that "As I understand it there are very few if any
> examples of convergence at the sequence level." I guess he is not
> familiar with the so-called UCE's (ultra conserved sequences) where
> vast stretches of genetic sequences between distant species are
> identical, yet not functionally constrained. This is something that
> should falsify evolution (indeed, that is precisely what an
> evolutionist told me a few years ago before these findings came out),
> but when these findings came out, of course, the possibility that they
> could harm the theory was not so much as whispered. Terry, this is yet
> another example of folks ignoring evidence that you seem to be sure is
> not happening.

Your unsupported accusations are becoming tiresome. Yes I am familiar
with UCE's and I fail to see how this relates to the topic of
convergence, after all they are conserved sequences which appear to not
be functionally constrained. A minor puzzle again. Please explain why
this should falsify evolution when we do not even fully understand UCE's?

Evolutionary theory explains the data better than any other 'theory' and
certainly ID has failed to present ANY explanation. Why UCE's should
falsify evolution could benefit from a more coherent argument though. My
limited understanding of UCE's, which have as I recall little to do with
convergence, is that they are an interesting puzzle which is slowly
unraveling.
UCE's may be non-coding but the claim that they are not functionally
constrained may be a bit premature. As was the case with evolvability
and evolution of the genetic code, science is finding more and more data
that help them understand evolution.

So what is known about UCE's?

They are: Segments longer than 200 base pairs that are absolutely
conserved, showing 100% identity with no insertions or deletions,
between orthologous regions of the human, mouse, and rat genomes

They are: Generally located in genes involving RNA processing or near
genes involved in the regulation of transcription or development

Now we get to the interesting part, namely under a neutral model of
evolution these UCE's are improbable, although not improbable enough to
hit the Dembski limit

*5% of the human genome is more conserved than would be expected based
on neutral evolution since the split with rodents
*These highly conserved segments contain a large number of non-coding
elements
*They exhibit almost no natural variation within the human population
*The probability of finding one such element in 2.9 billion bases is
less than 10^-22 under a neutral evolution model

There are exonic and non-exonic UCE's. Exonic UCE's are randomly
distributed around the genome, and associated with RNA processing.
non-exonic UCE's cluster around transcription factors and developmental
genes and regulate transcription at the DNA level

Thus researchers have postulated based on the evidence that:

"Genes that flank intergenic ultraconserved elements are enriched for
developmental genes, suggests that many u.c.e.s may be distal enhancers
of early developmental genes "

Thus the conclusions

-Ultraconserved elements are important for organism development and gene
regulation
-Ultraconserved elements evolved quickly and have become “near-frozen”
-This evolution seems to be ongoing
-Conservation seems to have arisen from increased negative selection or
decreased mutation rate

Evolution of UCE's also presents an interesting data point

"“The most exciting thing for me is that the ultra-conserved regions we
have identified do represent evolutionary innovations that must have
happened sometime during vertebrate development, because we see such
large pieces that no longer match in fish, and almost nothing in sea
squirt. They must have evolved rather rapidly while our ancestors were
still in the ocean, with some further evolution when animals first
started to colonize land; after that they must have essentially frozen
evolutionarily."

Experiments which knocked out UCE regions in mice did not find any
observable differences in phenotypes. And so the mystery continues.
http://www.newscientist.com/article.ns?id=dn5063

If the findings are correct that UCE's are important for development and
gene regulation then why should we accept UCE's as evidence against
evolution? So when Cornelius states, that UCE's are not functionally
constrained, I assume he means that they are not involved in coding of
proteins.

The following recent paper:

Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L.
Genome Res. 2005 Jan;15(1):137-45. Evolution and functional
classification of vertebrate gene deserts.

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.

The paper ends with "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."
Received on Tue Sep 20 13:08:52 2005

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