Wednesday, February 3, 2016

Unclassifiable objects

Classifications create a class for every object and taxonomies assign each and every object to its correct class. This means that a classification is not permitted to contain unclassified objects; a condition that puts fussy taxonomists in an untenable position. Suppose you have an object, and you simply do not know enough about the object to confidently assign it to a class. Or, suppose you have an object that seems to fit more than one class, and you can't decide which class is the correct class. What do you do? Historically, scientists have resorted to creating a "miscellaneous" class into which otherwise unclassifiable objects are given a temporary home, until more suitable accommodations can be provided. I have spoken with numerous data managers, and everyone seems to be of a mind that "miscellaneous" classes, created as a stopgap measure, serve a useful purpose. Not so. Historically, the promiscuous application of "miscellaneous" classes have proven to be a huge impediment to the advancement of science. In the case of the classification of living organisms, the class of protozoans stands as a case in point. Ernst Haeckel, a leading biological taxonomist in his time, created the Kingdom Protista (i.e., protozoans), in 1866, to accommodate a wide variety of of simple organisms with superficial commonalities. Haeckel himself understood that the protists were a blended class that included unrelated organisms, but he believed that further study would resolve the confusion. In a sense, he was right, but the process took much longer than he had anticipated; occupying generations of taxonomists over the following 150 years. Today, Kingdom Protista no longer exists. Its members have been reassigned to various classes of unicellular eukaryotes. Nonetheless, textbooks of microbiology still describe the protozoans, just as though this name continued to occupy a legitimate place among terrestrial organisms. In the meantime, therapeutic opportunities for eradicating so-called protozoal infections, using class-targeted agents, have no doubt been missed (1). You might think that the creation of a class of living organisms, with no established scientific relation to the real world, was a rare and ancient event in the annals of biology, having little or no chance of being repeated. Not so. A special pseudoclass of fungi, deuteromyctetes (spelled with a lowercase "d", signifying its questionable validity as a true biologic class) has been created to hold fungi of indeterminate speciation. At present, there are several thousand such fungi, sitting in a taxonomic limbo, waiting to be placed into a definitive taxonomic class (2), (1).

[1] Berman JJ. Taxonomic Guide to Infectious Diseases: Understanding the Biologic Classes of Pathogenic Organisms. Academic Press, Waltham, 2012.

[2] Guarro J, Gene J, Stchigel AM. Developments in fungal taxonomy. Clinical Microbiology Reviews 12:454-500, 1999.

- Jules Berman (copyrighted material)

key words: classifications, ontology, classes, taxonomy, jules j berman