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

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Wed Sep 21 2005 - 13:25:47 EDT

Cornelius Hunter wrote:

> Terry:
> In addition to the fossil evidence, you mentioned the nested hierarchy
> evidence from comparative anatomy. Let's have a look at this one,
> according to the criteria:
> ====================
> A. The evidence should not include problems for the theory (obviously).
> B. The evidence should be the fulfillment of a somewhat narrow
> prediction of the theory. That is, if the evidence as well as several
> other outcomes are all accommodated by the theory, then the evidence
> is not compelling.
> C. The evidence severely damages all alternative theories (need to be
> careful not to misrepresent or ignore the alternative theories, of
> course).
> ====================
> The nested hierarchy data suggest or reveal:
> 1. The designs of the species seem to be clustered, and the clusters
> seem to cluster in larger groups, and so on, in what is called a
> nested hierarchical pattern.
> 2. There are a great many exceptions that violate the pattern, at all
> levels, such that, for example, a paper out of Doolittle's lab has
> called for a "relaxation of tree thinking."

Perhaps Cornelius is unfamiliar with horizontal gene transfer. Yes,
Doolittle has suggested that one abandons the tree and yet the data on
HGT has shown that it is a minor component relative to the vertical gene
transfer. In other words a minor problem for early life that science is
slowly unraveling. In addition to HGT, there are various other reasons
why reconstucting a tree can be complicated. Luckily science is
developing additional methods to detect problems and deal with them.

> 3. There is massive convergence, meaning similar designs show up in
> distant clusters.
> It seems obvious that 3 fails on A, but I realize you may disagree.
> Setting that aside then, obviously 2 fails on A and 1-3 all fail on B.
> Also, none succeed on C. So as with the fossil evidence, I don't see
> how this can be compelling evidence for evolution.

Massive convergence ... Wow... I am sure that you can quantify this...
Or are you saying that to the layman, one could easily confuse
convergence with homology? Yes, comparative anatomy can be tricky to the
untrained but it is hardly that tricky once one realizes the potential
pitfalls. And not surprisingly, the findings from comparative anatomy
have been found validated by genetic data.
Such is science... Fast moving, exciting and not limited to a single
statement in a paper from a Doolittle lab...

See Carl Zimmer's tangling the tree
http://www.corante.com/loom/archives/2005/07/08/tangling_the_tree.php

    The net of life: Reconstructing the microbial phylogenetic network
    Victor Kunin1, Leon Goldovsky, Nikos Darzentas and Christos A. Ouzounis2

    *Abstract*It has previously been suggested that the phylogeny of
    microbial species might be better described as a network containing
    vertical and horizontal gene transfer (HGT) events. Yet, all
    phylogenetic reconstructions so far have presented microbial trees
    rather than networks. Here, we present a first attempt to
    reconstruct such an evolutionary network, which we term the “net of
    life.” We use available tree reconstruction methods to infer
    vertical inheritance, and use an ancestral state inference algorithm
    to map HGT events on the tree. We also describe a weighting scheme
    used to estimate the number of genes exchanged between pairs of
    organisms. *We demonstrate that vertical inheritance constitutes the
    bulk of gene transfer on the tree of life.* We term the bulk of
    horizontal gene flow between tree nodes as “vines,” and demonstrate
    that multiple but mostly tiny vines interconnect the tree. Our
    results strongly suggest that the HGT network is a scale-free graph,
    a finding with important implications for genome evolution. We
    propose that genes might propagate extremely rapidly across
    microbial species through the HGT network, using certain organisms
    as hubs.

PNAS | August 19, 2003 | vol. 100 | no. 17 | 9658-9662
Horizontal gene transfer: A critical view
C. G. Kurland, B. Canback and Otto G. Berg

Abstract

It has been suggested that horizontal gene transfer (HGT) is the
"essence of phylogeny." In contrast, much data suggest that this is an
exaggeration resulting in part from a reliance on inadequate methods to
identify HGT events. In addition, the assumption that HGT is a
ubiquitous influence throughout evolution is questionable. Instead,
rampant global HGT is likely to have been relevant only to primitive
genomes. In modern organisms we suggest that both the range and
frequencies of HGT are constrained most often by selective barriers. As
a consequence those HGT events that do occur most often have little
influence on genome phylogeny. Although HGT does occur with important
evolutionary consequences, classical Darwinian lineages seem to be the
dominant mode of evolution for modern organisms.

J. Gough
*Convergent evolution of domain architectures (is rare)*
Bioinformatics, April 15, 2005; 21(8): 1464 - 1471

*Motivation:* In this paper, we shall examine the evolution of^ domain
architectures across 62 genomes of known phylogeny including^ all
kingdoms of life. We look in particular at the possibility^ of
convergent evolution, with a view to determining the extent^ to which
the architectures observed in the genomes are due to^ functional
necessity or evolutionary descent. We used domains^ of known structure,
because from this and other information^ we know their evolutionary
relationships. We use a range of^ methods including phylogenetic
grouping, sequence similarity/alignment,^ mutation rates and comparative
genomics to approach this difficult^ problem from several angles.^

*Results:* Although we do not claim an exhaustive analysis, we^ conclude
that between 0.4 and 4% of sequences are involved in^ convergent
evolution of domain architectures, and expect the^ actual number to be
close to the lower bound. We also made two^ incidental observations,
albeit on a small sample: the events^ leading to convergent evolution
appear to be random with no^ functional or structural preferences, and
changes in the number^ of tandem repeat domains occur more readily than
changes which^ alter the domain composition.^

*Conclusion:* The principal conclusion is that the observed domain^
architectures of the sequences in the genomes are driven by^
evolutionary descent rather than functional necessity.
Received on Wed Sep 21 13:28:50 2005

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