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The reason for the difference between Linnean and cladistic classification is simply that:
classification in itself is fundamentally consistently inconsistent (contradictory, ie, ultimately ending in paradox), as Bertrand Russel demonstrated in 1901 with Russell’s paradox.
This fact means that simple classification as cladistic classification is consistently inconsistent (ie, ultimately ending in paradox), whereas orthogonal classification as Linnean systematics is consistently consistent (ie, always consistent).
It means that there can’t be any single “true tree of life” for the simple reason that classes are fundamentally consistently inconsistent.
Another contribution to understanding of conceptualization http://menvall.wordpress.com/