I'll follow up at length later, but I encourage you to read Andrew Sullivan's response to Ta-Nehisi: http://dish.andrewsullivan.com/2013/05/16/is-race-only-a-social-construct/
Though both authors come solidly from the egalitarian end of the ideological spectrum, Andrew's view is more informed by genetic science.
Locally, most racial groupings do correspond to a biological/genetic reality. For example, "black" Americans share similar genetic heritage from a certain part of Africa, combines with an average of 30% European admixture. Japanese and Chinese "Asians" are much more closely related to each other than they are to peoples from other parts of the world. Their similar features do indicate similar lines of decent.
Applying local notions of "race" to global populations can lead you to error. For example, both the ancestors of Shaquille O'Neal and pygmy tribes are considered "black" by American standards, but there is a vast genetic gulf between them. There is more genetic variation within Africa than there is in the entire rest of the human race due to the founder effects. The most genetic differences in the world between humans are found between Australian aborigines and some Africans, both of whom have dark skin and would probably be considered "black" by Americans.
You'll find that African-local notions of race are far more scientifically accurate. They recognize the difference between khoisan, xhosa, pygmy, and bantu - often to catastrophic effect (in the Congo, Pygmys are hunted like game and eaten). There are a few recent pop science articles on the evolutionary origin of pygmys: http://www.livescience.com/19929-pygmy-height-genetics.html.
It is not hard to construct a human phylogenetic tree based on genetic similarity, here's one I clipped from a paper: http://imgur.com/ZPkTc2C. This article at Discover magazine dives more into the scientific basis: http://blogs.discovermagazine.com/crux/2012/05/02/human-races-may-have-biological-meaning-but-races-mean-nothing-about-humanity/
There is a degree of social arbitrariness to race. For example, in America anyone who is 1/2 black is "black", like Obama. A person who is of a family of Spanish DNA that recently lived in Mexico can claim to be "Hispanic" when applying for college admission or government contracts governed by affirmative action, even though everybody in his life considers him "white". And his genetic lineage is very different from a person from a Mexican family of indigenous background - who have been second-class citizens to Mexicans of European background for centuries.
Social concepts of race aren't logical, but neither are they completely arbitrary.