I've summarized as much as I can to get the reality into one post.
The 99 percent genetic similarity has been enshrined as a cultural icon. For many naturalists, this resemblance represents one of the most compelling arguments for humanity's evolutionary origin. Presumably, the 99 percent sequence overlap for proteins and DNA proves that humans and chimps arose from a common ancestor some time in the relatively recent past. According to this view, the small genetic differences arose after the human and chimpanzee lineages split as a consequence of mutational changes within each species' genetic material. Evolutionary biologists have used chromosomal similarities and differences among primates to establish evolutionary relationships. According to these types of analyses, chimpanzees are the primate species most closely related to humans, with gorillas and orangutans the next closest relatives.
Studies that reveal a 99 percent genetic similarity between humans and chimpanzees have stacked the deck in a way that guarantees a high degree of likeness. Comparisons made between corresponding regions of the human and chimpanzee genomes, which researchers already suspected to be nearly identical, showed striking similarity. But when made unbiased comparisons of larger regions of these two genomes, differences began to emerge.
One of the first studies to make a genome-to-genome comparison between humans and chimpanzees was reported early in 2002 by the International Consortium for the Sequencing of Chimpanzee Chromosome 22. TO make this whole-genome comparison, the Chimpanzee Genome Project team cut the chimp genome into fragments, sequenced them, then compared them to corresponding sequences found in the Human Genome Database. For those chimp DNA fragments that were able to align with sequences in the Human Genome Database, the project team found that the sequences displayed a 98.77 percent agreement. However, the project team found that about 15,000 of the 65,000 DNA fragments did not align with any sequence in the Human Genome Database. They appear to represent unique genetic regions.
A few months later, a team from the Max Planck Institute achieved a similar result when they compared over 10,000 regions (encompassing nearly 3 million nucleotide base pairs). Only two-thirds of the sequences from the chimp genome aligned with the sequences in the human genome. As expected, in those that did align, a 98.76 percent genetic similarity was measured, and yet one-third found no matches.
The Chimpanzee Genome Project team discovered another difference between genomes during a detailed comparison of the chimpanzee genome DNA fragments with human chromosome. The team found that this human chromosome possesses two regions apparently unique to the human genome.
Even if you disregard all but this naturalist argument the differences that matter are coming to light. It's important to remember that sometimes even single genetic differences can be significant. For example, the fact that our DNA is more than 80% similar to a mouse does not imply that we are related to mice.
That's right: Comparison of the mouse genome (reported in December 2002) with the human genome supports Marks's point. Of the 30,000 genes found in each of the human and mouse genomes, around 99 percent are the same. Only 300 genes are unique either to mice or to humans. Gene-to-gene DNA comparisons for humans and mice reveal roughly an 80 percent sequence similarity. Are humans 80 percent similar to mice? Are mice 80 percent similar to humans? Given that humans and mice essentially possess the same genes, something more than genes and genetic similarity must define organisms. Biologists are starting to look to differences in gene expression as a way to account for anatomical, physiological, and behavioral differences among organisms. As part of this effort, anthropologists are examining and comparing the gene expression patterns in humans and the great apes.
Until recently, evolutionary biologists have looked for only a single type of difference between human and chimpanzee DNA sequences, namely substitutions of one nucleotide for another. When researchers expand the comparison to include differences that involve insertions and deletions (called indels), marked dissimilarities between human and chimpanzee genomes become evident. For example, a study that compared five regions of the chimpanzee genome collectively (encompassing about 780,000 nucleotide base pairs) with corresponding regions of the human genome found a 1.4 percent difference when substitutions were considered. But a 3.4 percent difference appeared when these five regions were examined for indels. Both types of differences combined show a 95 percent genetic similarity, not 99 percent. Another study that used this type of approach found a much more limited genetic similarity when a 1,870,955-base-pair segment of the chimpanzee genome was compared with the corresponding human genome region. When indels in the comparison were compared similarity dropped to 86.7 percent. As research continues, indels appear to account for substantial differences between human and chimpanzee genomes. As for mitochondrial DNA, a 91.1 percent sequence similarity was seen when the entire sequence was compared, not a 99 percent similarity. This factor promises to be significant because mitochondria play a role in energy metabolism. Several neurodegenerative and muscular degenerative diseases actually stem from mutations in mitochondrial DNA.
Although human and chimpanzee genomes display great similarity, that similarity has been magnified to some extent by research methodology. Reiearchers are starting to uncover significant differences. Results of large-scale comparisons must be considered preliminary, as it's not yet clear what the genetic differences mean in terms of anatomical and behavioral characteristics. However, greater clarity will likely come as research progresses. Already the newly recognized genetic differences between humans and chimpanzees complicate the picture for biologists who view the high degree of genetic similarity between humans and chimpanzees as proof of shared ancestry. Advancing research is uncovering what appear to be extensive genetic differences between humans and chimpanzees, it's important to remember that sometimes even single genetic differences can be significant.
Separate studies conducted at the University of California, San Diego (UCSD), the Max Planck Institute, and the University of Chicago supply important examples. This work demonstrates that subtle genetic differences translate into marked disparities in human and chimpanzee brain biochemistries. Researchers think these discrepancies may explain, at least in part, the unique qualities of the human brain. Several other recent studies demonstrate that even subtle genetic differences can manifest themselves dramatically in terms of an organism's anatomy, physiology, and behavior.
The complexity and the intricacy of biological systems, especially those in the brain, underscore the improbability that random mutations could bring about the exacting changes in gene structure necessary to support new biological functions, particularly when structure-altering mutations to single genes more often result in devastating diseases and disabilities.
The same is true for changes in gene expression. As indicated by the data, differences in gene usage play an important role in generating the differences between humans and chimpanzees. The intricacy of gene-to-gene interactions and the biological effects manifested when gene expression is altered make it difficult to envision how coordinated and extensive changes in gene expression could occur to generate the anatomical and physiological characteristics that define humanity. Changes in gene expression are frequently harmful and play a role in the etiology of many diseases. Each new discovery coming from genetic comparisons between humans and chimpanzees seems to weaken the case of evolution.
The large number of shared genes found among the genomes of humans, chimpanzees, mice, rats, and other animals reflects elegant design efficiency. The Creator appears to have selected a gene set that could be used to construct a wide range of organisms. This design principle is commonplace. A child with a set of building blocks may be observed to take advantage of this approach. Depending on the child's wishes, he or she can make numerous structures from the same set of blocks. Computer engineers produce computers with fixed hardware that can be programmed with software for an enormous array of functions. Even human languages rely on this principle. A relatively small set of words can be used to communicate an immeasurable number of ideas and concepts.
In terms of raw DNA there are similarities between chimpanzees and humanity. And this is exactly what we expect to see in scripture. But a high degree of similarity when it comes to raw DNA factors really teaches us nothing about the image of God contained within humanity.
Beyond DNA: Chimpanzees are about as smart as average four or five year old children. But if you are impressed with the chimpanzee, then let me introduce you to a bright seven year old. The qualities and character of small children immediately begin to transcend what the primates are capable of. From radically different brains and brain chemistry that allow abstract reasoning and complex language skills to drawing complex logical inferences humans are far different (and not simply advanced from a same root hominid) than primates. You don’t have to tell a fourth grader that Aristotle discovered laws like the law of noncontradiction, excluded middle, and identity. They have natural capacities to reason. And those natural capacities are what we expect from the Bible; the image of God.