Ontology is a philosophical method which attempts to show that there are distinct kinds of thing in the world, and that the divisions between these kinds are natural, not the product of human thought. Once such divisions are established conclusions can then be drawn from their existence or their distinctness from each other. Some ontologies make their divisions between more abstract concepts, leaving the material world as one kind of thing, while others divide even the physical world into natural kinds. Although I find both types of ontology dubious I cannot refute more abstract ontologies here (i.e. I haven’t thought of a good refutation yet), and will restrict myself to directing my arguments against those ontologies that divide the physical world into ontological categories.
Such an ontology might argue that pine trees are a naturally distinct type from other kinds of trees. It could be argued that even if humans were to disappear pine trees would still be distinct from other kinds of trees, and thus the division of trees is natural and not a product of human reason. The fallacy of such arguments is that they rely on the idea that there are distinct objects which can be divided into such types. Under a non-ontological view of the world however there are no distinct objects, such distinctions are the product of human thought. What the world (actually the entire universe) ultimately reduces to under such a view is simply an uneven distribution of atoms and energy. The fact that we classify some atoms in complicated molecules as belonging to a tree and the simpler molecules adjacent to them as belonging to the atmosphere can be seen as a product of our perceptions, i.e. we are naturally disposed to perceive the atmosphere as distinct from solid objects, probably due to evolutionary pressures. Under such a view if there were no observers to make the distinction (thus no animals as well, if you consider them to have rudimentary minds, since they act as though there were a distinction between trees and air) then there really would be no trees, and thus no pine trees either.
However this is not to say that ontological arguments are necessarily flawed. To hold the kind of view regarding ontology that I have proposed here is not to necessarily embrace the post-modernist view that all distinctions are subjective and dependant on the observer. If the categories we impose on the world are distinct from each other, and based on objective facts, then it is indeed possible to argue using such categories. For example we might argue that our category of pine trees is objective in the following way: what makes a tree a pine tree is the particular arrangement of its atoms, which is not present in other trees, specifically the atoms in its DNA. Because this is a fact that is the same for everyone we can all agree that certain trees are pine trees while others are not. If one then wanted to go on and argue that pine trees had certain properties (based ultimately on their DNA) and draw conclusions from those properties, as one would in an ontological argument, it is perfectly valid to do so.
Note: I am not entirely satisfied with this piece and may have cause to revise it later.