From: Denyse O'Leary (oleary@sympatico.ca)
Date: Sat Oct 25 2003 - 08:24:21 EDT
I was interested in this item, and showed it to a net buddy, who then
asked me to get the list's thoughts on this:
"Josh Bembenek thought that the article by Rokas et al., "Genome-scale
approaches to resolving incongruence in molecular phylogenies" (NATURE
425[23 October 2003], 798 - 804) would make Jonathan Wells's critique of
molecular phylogenies "much harder to sustain."
"I've read Wells's 2000 book, ICONS OF EVOLUTION, as well as the NATURE
article by Rokas et al., and two things occur to me: First, Rokas et al.
actually confirm something Wells wrote three years ago. Wells wrote
that the molecular data at that time were not converging as expected on
consistent patterns because "different molecules lead to different
phylogenetic trees," and "the problems extend even to smaller branches,
including animal phylogenies." Now Rokas et al. write in the first
paragraph of their article: "Despite tremendous progress in recent
years, phylogenetic reconstruction involves many challenges that create
uncertainty with respect to the true historical associations of the taxa
analysed. One of the most notable difficulties is the widespread
occurrence of incongruence between alternative phylogenies generated
from single-gene data sets. Incongruence occurs at all taxonomic
levels, from phylogenies of closely related species to relationships
between major classes or phyla and higher taxonomic groups."
"As I recall, Wells's main point was that it is misleading to give
biology students the impression that molecular studies have confirmed
Darwin's tree of life, when in fact those studies are plagued by
inconsistencies. Judging from the 2003 article by Rokas et al., Wells
was certainly correct in his assessment of the situation in 2000.
"Second, Rokas et al. think they have found a way to overcome the
incongruence problem -- i.e., by relying on concatenations of 20 or more
genes. They demonstrate that they can do this within the yeast genus
Saccharomyces. Can the same method overcome incongruences at higher
taxonomic levels? Rokas et al. are optimistic; their concluding
sentence is: "The results of our study suggest that use of genome-wide
data sets may provide unprecedented power not only in testing specific
phylogenetic hypotheses but also in precise reconstruction of the
historical associations of all the taxa analysed."
"If the method of using genome-wide data sets does, in fact, resolve the
incongruence problem generally, then it will indeed be harder (if not
impossible) to argue that molecular studies fail to support evolutionary
theory. Until the method is actually applied to higher taxonomic
levels, however, we don't know whether it will work at those levels.
Maybe it will, and maybe it won't. What if it turns out that a minimum
of 20 genes will suffice for a genus-level analysis, but 200 genes are
needed for an order-level analysis, 2000 for a class-level analysis, and
20000 for a phylum-level analysis? Will it even be practical to analyze
such numbers? We don't know. And until we DO know, isn't it better (as
Wells argued three years ago) NOT to give students the impression that
molecular phylogenies have confirmed Darwin's tree of life? This is not
to say that the tree of life has been DIS-confirmed, but only that we
shouldn't claim more for the evidence than it actually shows."
Any comments?
Denyse
-- To see what's new in faith and science issues, go to www.designorchance.com My next book, By Design or By Chance?: The Growing Controversy Over the Origin of Life in the Universe (Castle Quay Books, Oakville) will be published Spring 2004.To order, call Castle Quay, 1-800-265-6397, fax 519-748-9835, or visit www.afcanada.com (CDN $19.95 or US$14.95).
Denyse O'Leary 14 Latimer Avenue Toronto, Ontario, CANADA M5N 2L8 Tel: 416 485-2392/Fax: 416 485-9665 oleary@sympatico.ca www.denyseoleary.com
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