If humans have evolved from a non-human ape ancestor, then the types of mutations that can occur in human genomes-nucleotide substitutions, insertions, deletions, chromosomal inversions, etc.-must be the same types of differences which distinguish the human genome from that of a non-human ape, such as the chimpanzee. If humans and chimps descended from a common ancestor, then human-chimp differences should simply be an extension of the variations observed within each species.


If the creationist model is correct, then not only are humans as unrelated to chimpanzees as they are to every other form of life on earth, there is no reason to suspect that the mutational processes which originated as a punishment for humankind would be the same processes needed to derive human-specific modifications to an ape genome. In the creation model, there is a fundamental difference between the variations (genetic and anatomical) within the groups descended from a common ancestors and those which represent completely separate creations.


If intelligent design is correct, then the types of changes which separate humans and chimps should fall into two categories: those naturally induced changes which produce minor differences and those super-naturally induced which result in the adaptation of complex systems (such as increased brain size or immune reactions). Which of these models is supported by the comparison of human and chimp genomes?


Humans are not chimps and chimps are not humans. Nevertheless, our DNA is close to identical. Both human and chimp genomes are about the same size (2.9 billion base pairs). The overwhelming majority of the nucleotide positions are identical between humans and chimps. At functionally important DNA sites, humans and chimp sequences are 99.4% identical while at less important sites, the homology is 98.4% homologous. Of the DNA sequences which can be aligned between the human and chimp genomes, only 1% of the DNA bases differ. Because of the insertions and deletions, the total difference in the genomes is about 4% (Wildman, 2003; Culotta, 2005). Human-chimp divergence at noncoding regions is thought to be 1.23% (Hellman, 2005). The differences which separate humans from chimps are simply an extension of the same types of mutations which distinguishes one human from another.

About 29% of human proteins are identical in their amino acid sequence to those of chimps. The average protein has two amino acid differences between humans and chimps, one change in each lineage. The average gene possesses 2 synonymous changes and 3 nonsynonymous changes when the two genomes are compared. Although 5% of the genes have undergone a insertion/deletion, the median case is the addition/deletion of one codon. About 585 genes seem to have undergone positive selection when comparing humans and chimps. The X chromosome is the most similar between humans and chimps while the Y chromosome is the most different (The Chimpanzee Sequencing and Analysis Consortium, 2005).

There are about 35 million single nucleotide changes which distinguish the chimpanzee genome from the human genome. In addition, there are about 5 million insertion/deletion events which are specific to one of the lineages and are responsible for 1.5% of the differences in euchromatin sequences (about 90 million bases). There have also been several chromosomal rearrangements including 9 pericentric inversions and the fusion of two ancestral chromosomes to produce human chromosome 2 (The Chimpanzee Sequencing and Analysis Consortium, 2005; Ellegren,). The difference between human and chimp species is 1.4% due to nucleotide substitutions and 3.4% due to insertions and deletions (Britten, 2002).

When considering the most variable regions of the human genome, such as the MHC region, the nucleotide diversity between two humans exceeds the overall nucleotide diversity between the human and chimp lineages. Some of these haplotypes may predate human lineage (Raymond, 2005). These regions where humans differ most from each other are also the regions where the human genome differs most from that of chimps. When taking into account the insertions and deletions in the MHC class III regions, human-chimpanzee sequence similarity drops to 86.7% (Anzai, 2003). For example, in the chimpanzee lineage, a 95 kb deletion between the human MICA and MICB genes resulted in a single hybrid gene in chimps. This region is involved in response to viral infections and autoimmune diseases (Anzai, 2003).

Not only are chimps the animals most closely related to humans, humans are the animals most closely related to chimps. Many researchers have observed that when comparing specific genetic sequences, human and chimp sequences are more similar to each other than either is to any other organism analyzed in the study (Atchley, 1995; Caccone, 1989; Deeb, 1994; Edwards, 1997; Felsenstein, 1987; Fukuhara, 2002; Galili, 1991; Gonzalez, 1990; Goodman, 1984; Goodman, 1994; Salem, 2003; Johnson, 1999; Koop, 1986; Larson, 1996; Maeda, 1988; Messier, 1997; Miyamoto, 1987; Page, 2001; Pilstrom, 2002; Ruvulo, 1994; Sibley, 1990; Vernersson, 2004; Williams, 1989; Ye, 2005; Zhang, 1998a; Zimonjic, 1997).

Not only do human and chimps have the same genes, they also have similar alleles, indicating that the origin of some of the human alleles predate the split between chimp and human ancestors (OMIM). Some alleles of the HLA-A and HLA-B genes are shared between humans and chimps and thus arose before the split between their lineages. The HLA-Cw*0702 seems to have arisen before the separation of the higher ape lineages, producing alleles in humans, chimps, and gorillas (Matsui, 1999). Chimpanzee sequences of Apopliprotein E not only correspond to human alleles, in the majority of cases the most common human allele corresponds to the chimp sequence, suggesting that it was ancestral (Fullerton, 2000).

This genetic difference between human and chimps is quite small compared to the analysis of homologous DNA sequences in other organisms. In the creation model, chimps are completely unrelated to humans-as unrelated as monkeys, plants, fish, and bacteria. There is absolutely no reason to predict this degree of similarity in organisms which are completely unrelated. In fact, the creationist model must accommodate the fact that there is a greater degree of similarity in the DNA of humans and chimps (which creationists claim are unrelated) than between the DNA sequences of organisms that many creationists feel have shared a common ancestor within the past several thousand years.

There are 35 million nucleotide and five million insertions/deletions which distinguish the human and chimp genomes. Is this amount of change too great to evolve? Given the spontaneous mutation rate of many mutations per gamete, a man who generates 300 million sperm a day has generated far more genetic changes that day than which separate the human and chimp genomes. The number of known variable nucleotide positions within human populations after less than a decade of the sequencing of the human genome is already more than ¼ the total differences that separate humans from chimps. The rate at which harmful mutations are generated is comparable in humans, chimps, and gorillas (Hacia, 2001).

Specific sequences of DNA can evolve differences at rates much higher than that observed in the human and chimp lineages since their split. Overall, this genetic difference is exactly what would be predicted when two mammalian species have been separated for 5-7 million years. If the estimated rate at which new changes are fixed to a mammalian genome is about 2 x 10-9 per base pair per year [which is the conclusion of several studies], then mammals with a genome size of 3 billion nucleotides would be expected to diverge from each other at a rate of about 6 changes per year (Kumar, 2002). Six million years of mutation fixation (which is the conclusion of the fossil evidence) would produce more than enough genetic differences to account for the divergence between human and chimps (especially since the human-chimp difference is the result of two lineages diverging independently).