Metaphysics is the science that deals with the most general, fundamental, and ultimate aspects of reality. In studying it we proceed as in other sciences, by asking questions, proposing tentative solutions, and seeing if our solutions meet the relevant canons of evidence. When doing research in systematic zoology, one might suspect that something is wrong when all the "members" of a putative species turn out to be males. Likewise when putting objects of knowledge under metaphysical rubrics, one might decide that something is amiss when people talk about weighing a speciation event. Biology aims to classify life, metaphysics everything.
The distinction between a class and an individual is one of the most fundamental in all metaphysics -on a par with the distinction between true and false. It is at least as fundamental as the distinction between a material object itself and the processes in which it engages. We wouldn't say that a professor is a lecture. Likewise with classes and their instances -it is metaphysically impossible for a class to do anything. That species could not evolve if they were classes is true, even though Rosenberg finds a way of making it appear that way.
My goal has not been simply to deny that species are classes, but to reject the metaphysical premises from which that notion derives. My "radical solution" denies what the dominant modern philosophical tradition affirms. Starting with Frege, and continuing with Russell, Wittgenstein and their successors, a set-theoretical metaphysics has been developed. Set theory, being a purely logical apparatus, treats it as indifferent whether things be individuals or classes. In consequence thereof, all the individuals get turned into classes. In order to be consistent it was necessary to do things like denying that organisms are individuals, and populating the universe with logical atoms. This is one reason why recent philosophy has treated individuals as if they were unimportant. Another reason is that doing so continues a tradition that goes all the way back to the ancients. Even for nominalists the problem has been that of universals. Yet another reason has been the positivistic hope that metaphysics would go away if only we cleaned up our logic.