rationalskepticism.org

CharlieM wrote:http://www.cell.com/trends/genetics/abstract/S0168-9525%2810%2900128-9?switch=standard

Abstract

Convergent phenotypes provide extremely valuable systems for studying the genetics of new adaptations. Accumulating studies on this topic have reported surprising cases of convergent evolution at the molecular level, ranging from gene families being recurrently recruited to identical amino acid replacements in distant lineages. Together, these different examples of genetic convergence suggest that molecular evolution is in some cases strongly constrained by a combination of limited genetic material suitable for new functions and a restricted number of substitutions that can confer specific enzymatic properties. We discuss approaches for gaining further insights into the causes of genetic convergence and their potential contribution to our understanding of how the genetic background determines the evolvability of complex organismal traits.

CharlieM wrote:Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution 14 (1999): 177-178.
...the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting. (p. 177)

The authors are talking about a review paper by Michael Lee (Lee MSY, 1999 Trends Ecol Evol 14:177-178), in which he refers to data obtained on one of the proteins involved in the respiratory chain in mitochondria, cytochrome b. The figure below shows the tree as presented in Lee's review paper:
Cytochrome b phylogenetic tree: from Lee, (1999) Trends Ecol Evol 14:177-178

The phylogenetic inconsistency here is the misplacement of a single branch, that of tarsiers (a primitive group of primates), as if they had separated from other primates before cats and fin-back whales. Actually, the data in the original publication (see figure below, Andrews et al. 1998 "Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?" J Mol Evol. 47:249–257) gives a slightly different picture, namely that the analysis of cytochrome b sequence is statistically incapable of resolving the phylogenetic relationship of most of the species in the tree (the numbers in the figure represent a measure of the statistical confidence in each branch of the tree, and numbers below 30 generally indicate lower confidence; the statistically robust values are underlined). In other words, cytochrome b is simply not a good protein to choose for constructing the evolutionary tree of these species. But why is that?

Cytochrome b phylogenetic tree: from Andrews et al., 1998; adapted to match layout and nomenclature in Lee, 1999 (see prevoius figure)
Both the Andrews and Lee papers suggested, based on other data, that the phylogenetic incongruence in this tree was caused by cytochrome b and other respiratory chain proteins having evolved much faster in some primate lineages compared to other mammals, possibly following unique selective pressures. As mentioned above, both accelerated and adaptive evolution can cause errors in phylogenetic tree reconstruction, masking or enhancing the similarities of related genes, depending on the circumstances. And indeed, in more recent years the accelerated adaptive evolution of respiratory chain proteins in monkeys and apes (but not tarsiers and lemurs) has been extensively confirmed (see for instance Grossman LI, et al. 2004 "Accelerated evolution of the electron transport chain in anthropoid primates." Trends Genet. 20:578-585). Thus, the inconsistency in the cytochrome b tree, rather than highlighting hopeless phylogenetic confusion as alleged in Explore Evolution, is the result of real biological and evolutionary processes. The existence of this extensive literature offers opportunities for an inquiry-based lesson on molecular evolution and evolutionary processes. Instead of offering that lesson, the supposedly inquiry-based Explore Evolution throws up its hands in confusion at any sign of difficulty.

Although molecular phylogenetic tree inconsistencies are hardly a fundamental theoretical concern for evolutionary biology, if persistent they could still cause practical problems in assessing certain evolutionary relationships. However, a number of new approaches have recently emerged that address these difficulties. These methods include the combination of large sets of sequence information from genomic databases, as well as the use of genetic features, such as large-scale structural changes or the mapping of mobile genetic elements, that are less prone to convergence and selection-related artifacts. For a thorough discussion of the potential of these approaches, see Lokas A and Carroll SB, (2006) "Bushes in the Tree of Life" PLoS Biol 4:e352.

CharlieM wrote:http://guava.physics.uiuc.edu/~nigel/courses/598BIO/498BIOonline-essays/hw2/files/HW2-Welander.pdf

CharlieM wrote:After the structure of DNA was fathomed, neo-Darwinists predicted a simple scenario. Linear progression from lengths of DNA to proteins to organisms. Sequencing the human genome would reveal the secrets of our evolution. Not so.

http://www.nature.com/news/2010/100331/full/464664a.html

The more biologists look, the more complexity there seems to be. Erika Check Hayden asks if there's a way to make life simpler.

“When we started out, the idea was that signalling pathways were fairly simple and linear,” says Tony Pawson, a cell biologist at the University of Toronto in Ontario. “Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It’s infinitely more complex.”

CharlieM wrote:Further refutation:

Eldredge, N. and Tattersall, I. - The Myths of Human Evolution

Darwin's prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record.

CharlieM wrote:"Clever cells"

CharlieM wrote:To save the Darwinian explanation of blindsnake evolution it has been postulated that these burrowing animals crossed the Atlantic on rafts of vegetation. Observations are made and unlikely explanations are proposed to align with the theory. This is not the way science should work.