Virtually everything I've seen written about chimpanzees mentions the fact that their genomes are 98% identical to ours.  I guess I was mildly impressed by that number, but never gave it much thought.  But after studying plant genetics in graduate school I began to wonder what exactly was meant by 98% identical.  I studied a small weedy plant called Arabidopsis and my research involved looking at genetic differences between two accessions, or strains of this plant.  There was on average one difference in 100 base pairs between the two accessions.  Each difference is called a SNP ("snip").  So that means these two accessions are only 99% identical in their DNA.  They look virtually identical and have just a few phenotypic differences that you need to be a plant biologist to even notice.  It seemed totally incredible to me that humans and chimps are 98% identical if there is so much genetic variation in something as similar as two Arabidopsis strains.  So I wondered if I was comparing apples with apples, or if the human-chimp comparison was a gene-to-gene comparison, ignoring the variation within a gene.

It turns out that yes, I was comparing apples to apples.  The human and chimp genomes each have about 3 billion base pairs.  There are 40 million differences between the human genome and chimp genome at the base pair level (35 million SNPs and 5 million insertion/deletions).  40 million divided by 3 billion is 1.3%.  There are some additional differences, like a smallish number of chromosomal rearrangements, bringing the total difference to just under 2%.  I am totally floored by this.  Totally.  Especially after reading about the amount of variation between different human beings.  A couple of years ago James Watson's entire genome was sequenced (he’s the co-discoverer of DNA).  He has 3.3 million SNPs relative to the "reference" human genome (a compilation of several people's DNA).  82% of Watson's SNPs were already known, and 18% are apparently uniquely his.  This means that Watson is 99.9% identical to the average human.  This also means that there is only about 10 times more genetic variation between a human and a chimp than between a human and another human.  I find this amazing.

Humans and chimps either have a common evolutionary ancestor, or God created us to look a hell of a lot like we do.

Incidentally, there is one other individual who has had his whole genome sequenced.  His name is Craig Venter and he led the private effort to sequence the human genome (Watson led the publicly funded effort).  Venter chose his own DNA as his reference sample.  Watson's DNA was sequenced several years after the completion of the human genome by a private company called 454 Life Sciences.  I first learned about 454 from my thesis advisor, who used their services to sequence some of the cassava genome in her lab (the data never got pulled together and will probably never be published).  The public effort to sequence the human genome cost about 3 billion dollars, but 454 used new technology and did Watson's genome for less than 1 million.  They're saying they think they can do it for $100,000 now and have the goal of getting it to $10,000.  From what I've read it seems that there's a huge lag in what science can actually do with that information, though.  So I don’t see much point in doing it other than for vanity’s sake.