rationalskepticism.org

Rumraket:
Hey CharlieM, since you appear fond of quoting known liar and ID spokesperson Casey Luskin, could you please go and fetch some of that "evidence against evolution" he speaks of?

I have heard the term used a couple of times but I have yet to actually see something that met the criteria it purpoted to constitute. I feel compelled to state up front that the very idea of having "evidence against" an observed fact strikes me as rather oxymoronic.

Ramray Bhat:
...we have the first really coherent framework to explain the origination and evolution of body plans and organ forms within a short evolutionary period, known as the Cambrian explosion.

...This framework also solves the Molecular Homology-Analogy paradox - why same/similar sets of genes are employed to build functionally or structurally similar organ forms in widely divergent organisms.

All of these are inconsistent with and cannot be explained by the classical neo-Darwinian model. We accommodate the role of natural selection in our framework mainly to lock the already-emerged but immensely plastic forms into place, and to render them robust

Massimo Piattelli-Palmarini:
when Sherman stresses that the sea urchin has, inexpressed, the genes for the eyes and for antibodies (genes that are well known and fully active in later species), how can we not agree with him that canonical neo-Darwinism cannot begin to explain such facts?

http://www.sciencedaily.com/releases/2010/03/100330210938.htm

Floating across oceans seems an unlikely mechanism for a burrowing animal to spread to new continents, but there is a second instance of ocean crossing by blindsnakes among the groups left on West Gondwana: West Gondwana broke up about 100 million years ago, making Africa and South America separate continents, but the genetic split between African and South American blindsnakes occurred only at about 63 million years ago. This finding shows that blindsnakes probably were confined to Africa when West Gondwana broke up and only later traveled to South America -- and still later to the West Indies -- by floating across the Atlantic from east to west.

This journey has rarely been documented. Only six or seven other vertebrates are thought to have crossed the Atlantic in a westward direction. However, the crossing would have taken no more than six months and might not have been too difficult for blindsnakes, which have a relatively low need for food and may have been floating on vegetation rafts along with their insect prey.

"Some scientists have argued that oceanic dispersal is an unlikely way for burrowing organisms to become distributed around the world," observes Hedges. "Our data now reinforce the message that such 'unlikely' events nonetheless happened in evolutionary history."

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.”

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.

http://www.sciencedaily.com/releases/2009/10/091008142957.htm

In a paper featured this week on the cover of the journal Science, they describe a new technology called Hi-C and apply it to answer the thorny question of how each of our cells stows some three billion base pairs of DNA while maintaining access to functionally crucial segments. The paper comes from a team led by scientists at Harvard University, the Broad Institute of Harvard and MIT, University of Massachusetts Medical School, and the Massachusetts Institute of Technology.

"We've long known that on a small scale, DNA is a double helix," says co-first author Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard's School of Engineering and Applied Sciences and in the laboratory of Eric Lander at the Broad Institute. "But if the double helix didn't fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question."

The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment. Chromosomes snake in and out of the two compartments repeatedly as their DNA alternates between active, gene-rich and inactive, gene-poor stretches.

"Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them," says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

Second, at a finer scale, the genome adopts an unusual organization known in mathematics as a "fractal." The specific architecture the scientists found, called a "fractal globule," enables the cell to pack DNA incredibly tightly -- the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

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

A recent study by Mark Collard and Bernard Wood finds several discrepancies between morphological and molecular phylogenies for extant higher primates

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.

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)