I originally posted these thoughts in the comments thread of the blog Ayn Rand Contra Human Nature, where they didn't get much notice. Since I like this little essay, I'm reproducing it here, slightly augmented with some notes in square brackets, with a few links put in for people who want citations on particular points.
Twenty years ago (or more) I was a big Rand fan. Since then my outlook has changed entirely, but I still find it interesting to look at Rand's ideas and where I think they went wrong.
In an essay that originally appeared in The Ayn Rand Letter, Rand speculated that the so-called anticonceptual mentality might literally be the missing link in human evolution. (This essay was titled either "The Anti-Conceptual Mentality" or "The Missing Link," as I recall. It was reprinted in one of her collections, probably posthumously.)
[The anticonceptual mentality was Rand's characterization of people who think only in terms of concretes, rather than abstractions.]
What is worrisome about this notion is that, if accepted, it would entitle Objectivists to classify anyone who is "anticonceptual" as nonhuman or subhuman. I happen to think that this was Rand's actual opinion. Although she never came right out and said it, it is strongly implied throughout her writings. Just look at all her pejorative references to irrationalists as subhumans, savages, cavemen, etc. It is also implied in her habitual reliance on the term "man qua man," a phrase denoting the rational, conceptual-mentality man, as opposed to the irrationalist, who is presumably not "man qua man," i.e., not really man at all. (Bear in mind that an irrationalist in Rand's terms may be almost anyone who broadly rejects her system.)
[Rand uses the term "man qua man" all the time. See this Wiki article, esp. the section "Values."]
Again, she did not state this view unambiguously, but I believe a close reading of her work will reveal it. Perhaps this explains why many Objectivists find it so easy to condemn their critics in language suggesting that they are not human ("insects, lice, animals, brutes, parasites," etc.). Perhaps it also explains why the Winston Tunnel disaster ends the way it does.
[The Winston Tunnel disaster is a major scene in Rand's novel Atlas Shrugged, in which hundreds of ordinary people perish in a railroad accident. The narrator makes the point that all of them deserved it, because each had sacrificed rationality in some way. The link above takes you to a long excerpt from the scene.]
If this was indeed Rand's view, then her biological argument for metaethics starts to make more sense. Rational man is literally a different species from irrational man, and therefore the requirements of his survival are qualitatively different from those of moochers, looters, second-handers, and other irrationalists.
But of course the downside of this view, besides the fact that it has no evident biological foundation, is that it divides the world into authentic human beings and counterfeit human beings, with the latter being disposable. Rand's stated views on American Indians fit neatly into this model. [See the comments as well in the last link.]
Perhaps Whittaker Chambers caught a whiff of this idea when he famously wrote that on nearly every page Atlas Shrugged he could hear a narrator intone, "To a gas chamber - go!" After all, are subhumans entitled to human rights? Maybe human rights are reserved only for those who are "truly" human ...
I'm not trying to be snarky about this. I honestly believe that Rand's viewpoint ran along these lines, even if, for obvious reasons, she chose to present it only by implication.