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Besides which, there are millions of genes. Even if humans have a 1% deviance in genetic material (which seems pretty high for a species), you're looking at tens of thousands of genes with the ability for variable expression.
That's a lot of basis for differences in a species. Hell, chimpanzees and bonobos are only 1% different than the average human genome and they're drastically different from humans.
It's true that we're not reproductively isolated, but neither are dogs, yet we classify them by breeds.
The simple fact of the matter is that race is more often than not equivalent to the genetic origin that gives rise to human "breeds". There are people in central europe that were of a race/breed/genetic origin that were resistant or immune to the plague. They largely kept to themselves, so their genes diverged in a way that made them not susceptible to the same disease.
Now, socially you run into some issues with the terms.
I find that a lot of Americans tend to use race and nationality interchangably, which seems to irritate people who use them for "place of origin" and "current location". For example, asking an American what nationality they are over here will result in them usually giving their race ("I'm German"). But asking about nationality in a place with less immigration usually seems like a weird thing to do (go to Finland and ask what nationality they are, it'll seem odd, since it's assumed that most people originate from Finland).
Additionally, while I have the issue brought up, how do people feel about places with high immigration (especially America), discussing their nationality without mentioning the country they live in (saying German instead of German-American). This can be confusing when discussing matters on the Internet, and cultural differences in how language is used can rear up issues too.
To me, I think the issue comes up because in places like America, everyone is an immigrant, so saying you're American is really irrelevant on the local level (you're not going to say to a neighbor "hello, I am, X! my family is German-American."), it's a level of redundancy, so it's just not done compared to places where nationality is more likely to be ambiguous with immigration and tourism and such.
I've had this discussion on another board, but unfortunately it got heated before anyone could really give a good perspective on the matter.
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