Is there more genetic difference between men and women than men and male chimpanzees?

Question

I got into trouble with someone yesterday for poo-pooing this idea as it smelled of apples and oranges to me.

The specific statistic was that genetically there is a 5% difference between men and women, while there is only a 2% difference between men and (I assume) male chimpanzees.

Googling briefly brought up this (hardly authoritative) quote.

So, is this even true? And if it is, what gives?

EDIT I chose a bad example, as vartec points out below. I actually heard this in French, here's an example, which (roughly) says:

"Genetically, there is only a 2% difference between men and male chimpanzees, whereas there is a 5% difference between men and women: thus there are twice as many differences between men and women than between men and male chimpanzees"

Answer 1

The only genetic difference between men and women is that men have 1 Y chromosome and 1 X chromosome on their sex determinative chromosome.

The Human Genome

The human (Homo sapiens) genome is stored on 23 chromosome pairs and in the small mitochondrial DNA. Twenty-two of the 23 chromosomes belong to autosomal chromosome pairs, while the remaining pair is sex determinative.

So there are a total of 46 chromosomes on the normal human. Any 45 of them can be shared by men and women and only 1 belongs to men only. Simple math (1/46) says that the difference is < 2.2% if 100% of the Y chromosome is unique to the Y chromosome and the number of genes on each is roughly equal.

However the Chromosomes are not equal.

The human chromosomes that determine sex, the X and Y, are a bizarre pair. The other 22 sets of chromosomes in our cells consist of wellmatched partners, as alike as twin candlesticks. One chromosome in each duo comes from the mother and one from the father, but both are normally the same size and carry the same genes. (Genes are the DNA blueprints for proteins, which do most of the work in the body.) In stark contrast, the Y chromosome is much smaller than the X; in fact, it is positively puny. It harbors no more than several dozen genes, far fewer than the 2,000 to 3,000 on the X. A number of the Y genes have no kin at all on the X. And the Y is riddled with unusually high amounts of "junk" DNA: sequences of code letters, or nucleotides, that contain no instructions for making useful molecules.

The human genome is estimated to contain 20,000-25,000 genes. The Y chromosome has 231. Other than those 231 sequences that do not exist in the female all of the genes are shared. So the math says (231/20000) so < 1.2% difference.

So the numbers in the quote are wrong. But is there more difference between Men and Women than humans and Chimps? For that I found this research which found:

Humans and chimps can have 95% or >98.5% similar DNA depending on which nucleotides are counted and which are excluded.

So even using best case Men vs Women < 1.2% : Man vs Chimp > 1.5%

Clearly this is false.

Answer 2

See "Relatedness" article on "The Tech Museum of Innovation" site, part of "Stanford at The Tech Understanding Genetics" where this question is answered by a Geneticist. Here's the pertinent excerpt from the article:

So is the bottom line that men and male chimps have more in common than men and women? Of course not. If we take a closer look, we see some of the dangers of looking at raw percentages instead of individual changes.

—source

Another way to think about this is the 55 million or so differences between men and women are all concentrated on one chromosome and 78 genes. For chimps, the 42-150 million differences are spread out all over the chromosomes over many, many more genes.

In other words, while the quantity of changes may be the same, the quality is different. Even though we share most of our genes with a chimpanzee, lots of the chimp's genes have changed in ways not seen in people. These changes make a chimp a chimp and a human a human."*