Article] Genome scan shows human-chimp differences

This is a speculative counter argument. Whenever new data comes out there will always be some careless scientist is going to jump the gun.

This is not a situation were genotypes will be meaningless some will be meaningful and some will be meaningful in proportion to their differences. However the whole process of determining the meaning of these differences will take time to resolve. The sequencing of the chimp genome (hopefully we will see genomes as in bonobos, also) and addition of information from gorilla, can be used together to sense out superfluous mutations and functional mutations. I expect that the rate of cognative science will move forth in leaps and bounds now that the ability to compare large numbers of genes are available.

The percentage difference between chimps and humans is irrelevant except with regard to the differences within each species. The specific information that one is looking for in within the gene structure (promotors, coding regions, alternative splicing) such differences might not be easy to detect because a single amino acid change in another gene may alter a cell to the degree that it causes certain genes to undergo different alternative splicing within that cell. OTOH a gene may have a difference that has a profound affect.

One way to establish the functionality of a gene is to see how small or large the variation is in the gene in the population. If a gene is highly variable in chimps and humans then it is possible that it is under heterozygous selection or simply neutral variation. Certain other genes may have undergone recent fixation in hominid lines and variation may be constrained by selection as a result of the biology of humans. Vice versa the same thing may occur in chimps.

I strongly suspect that certain genes will have direct dominant or recessive genetics as they are found in humans (all, except trace loss of function mutants) and not in chimpanzees, and these genes will be implicated in specific changes along the path of human evolution. You are probably going to see a number of these genes highlighted in the next 2 years, and the comparisions may actually dominate the PA/MA literature.

By comparing the human genome with that of chimpanzees, people's closest living relative, scientists have identified a partial list of the genes that make people human.

They include genes for hearing and speech, genes that wire the developing brain, genes for detecting odors and genes that shape bone structure. ... But the process of transforming the joint human-chimp ancestor, who was probably a very chimpanzeelike creature, into a human seems much more complicated in light of the new analysis. In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.

A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear. Dr. Clark suggests that the genes governing speech and hearing are most likely to have evolved in parallel and that evolutionary tweaks in the alpha-tectorin gene may make humans hear somewhat differently from chimps.

Another group of selected genes is involved in brain development. Of particular interest is SEMA3B, which helps guide growing nerve axons to the proper regions in the brain. Differences in the human version might help

Genes involved in recycling amino acids, the building blocks of proteins, have changed in the human line, the Science article reports. Those could reflect changes in diet when humanlike descendants of the mostly fruit-eating ancestor switched to meat. There are also changes in the human genes for odor detection. Some of those genes have become inactive, reflecting a lesser reliance on the sense of smell, while others have developed new sensitivities, suggesting adaptations to a new environment.

Geneticists can often estimate the time a gene started to evolve by looking at how variations in the gene have evolved from a single ancestral form. The human version of the FOXP2 gene has been estimated by that method to be 100,000 years old.

Dr. Clark said similar dates could be derived for the genes that he has found, if their variations in the human population were known. That may shed light on the timing of many milestones in human evolution. But the dates derived by geneticists often have very large ranges, which can make them less useful. ...

This seems to be mostly focusing on brain functions; it'd be interesting to know about, say, skeletal related changes...