Actually that isn't fair. It isn't wrong. The percentage of difference just depends heavily on what you define as a difference.
Using novel yardsticks and the flood of sequence data now available for several species, researchers have uncovered a wide range of genomic features that may help explain why we walk upright and have bigger brains--and why chimps remain resistant to AIDS and rarely miscarry. Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of "humanness" versus "chimpness." "There isn't one single way to express the genetic distance between two complicated living organisms," Gagneux adds.
When King and the rest of the researchers in the Chimpanzee Sequencing and Analysis Consortium first detailed the genome of our closest relative in 2005, they simultaneously provided the best validation yet of the 1% figure and the most dramatic evidence of its limitations. The consortium researchers aligned 2.4 billion bases from each species and came up with a 1.23% difference. However, as the chimpanzee consortium noted, the figure reflects only base substitutions, not the many stretches of DNA that have been inserted or deleted in the genomes. The chimp consortium calculated that these "indels," which can disrupt genes and cause serious diseases such as cystic fibrosis, alone accounted for about a 3% additional difference (Science, 2 September 2005, p. 1468).
Entire genes are also routinely and randomly duplicated or lost, further distinguishing humans from chimps. A team led by Matthew Hahn, who does computational genomics at Indiana University, Bloomington, has assessed gene gain and loss in the mouse, rat, dog, chimpanzee, and human genomes. In the December 2006 issue of PLoS ONE, Hahn and co-workers reported that human and chimpanzee gene copy numbers differ by a whopping 6.4%, concluding that "gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes and certainly a greater role than has been widely appreciated."
The issue of the difference between chimps and humans was always a socio-political one more than a scientific one. It is inextricably linked with the merits of evolution, with proponents of evolution pointing at the genetic similarity as evidence for their case. Observing that there are more differences than we thought does not erode the validity of evolutionary argument, but it does remind us that our standards for similarity are pretty arbitrary and that the real issue is identifying what these genes actually do.
The 1% idea also shows up frequently in anti-animal research arguments, but the opponents have a lovely catch-22 going on there. When scientists show similarities, they say "they are so much like us, it's wrong to experiment" and when scientists show differences they say "they are so different, it's pointless to experiment." So no idea if this will be helpful on that front, but thank you for the informative post.
I apologize for the obviousness of the comment, but it's a bit like being a mosquito in the presence of a bug-lamp. The sentence "The issue of the difference between chimps and humans was always a socio-political one more than a scientific one." is what got me. I must concur. If we compare GWB's DNA with a chimpanzee will we be able to detect significant differences in copy number? Sorry, just had to ask.