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We can classify reality in two principally different ways:
1, plain classification – of objects into classes (like cladistics and particle physics), and
2. orthogonal classification – of classes into categories (like Linnean systematics).
The problem with the former (plain classification) is that it ends in paradox (as Bertrand Russell demonstrated with “Russell’s paradox”), because it conflates object with class. The problem with the latter (orthogonal classification) is that it is ambiguous with respect to objects, because it distinguishes object from class.
These two principally different ways to classify are actually two different aspects of the fact that doing (in this case classifying) is orthogonal to done (in this case classification), ie, that operation is orthogonal to operand. Let’s call this fact “the difference between process and pattern”. Doing is the action that turns one operand, ie, a starting point, into another operand, ie, the end point, or done. The former (plain classification) is thus the paradoxically contradictory aspect of this fact (ie, the difference between process and pattern), whereas the latter (orthogonal classification) is the ambiguous aspect of it.
The fundamental problem is that object and class can neither be conflated nor be distinguished by classification, because they are both distinguished and conflated by the process of classification itself (ie, object is both distinct from and conflated with class at the same time in the process of classification). All we can do is to choose between the paradoxically contradictory and the ambiguous aspect of this fact (ie, the difference between process and pattern), that is, between plain and orthogonal classification, respectively.
In concentrate, one can say that we can only be contradictory or ambiguous.
This fact also means that we can’t reach a single truth about reality, because we can’t reach a single classification of reality that is both consistent (ie, non-contradictory) and unambiguous at the same time, contrary to what realists like cladists and particle physics claim. Cladists and particle physicists are thus wrong – we actually can’t reach a consistent and unambuguous truth about reality (ie, neither a “true tree of life” nor a “standard model”). Which I’m sorry to say.