Biomedical Engineering Reference
In-Depth Information
finished classification. In practical terms, taxonomists are continually
constructing classes from their own scientific biases concerning the essential
features of organisms. Classical taxonomists tend to be happy with class
assignments that reinforce their original bias. Computational taxonomists
insist that their approach overcomes the self-referential paradox by clustering
similar organisms into classes based on an unbiased (though arbitrary) set
of objectively measured features.
The wise taxonomist understands that new classifications are built upon
old classifications, and that the value of any classification stems from our per-
sistence in testing and revising tentative class assignments; not in our ability
to re-compute a classification from a blank slate.
Here are a few suggestions on the best applications of molecular taxonomic
techniques:
1.
To provide some confirmation for a candidate class construction. You
would expect key sequences among members of a class to be similar.
2.
As an indicator of classification errors. Sequence dissimilarities would
indicate that the taxonomist must seriously consider re-assigning classes
and species.
3.
To provide informative biological markers not found by morphologic
examination, permitting more accurate assignment of species.
4.
To act as a phylogenetic chronometer to determine when subclasses may
have first appeared.
5.
To help explain the biological significance of class markers [taxa] that
have no apparent scientific explanation (see discussion of Class Unikonta
and Class Bikonta in Chapter 15).
The schema for the classification of bacteria that are infectious in humans,
appears at the beginning of this chapter. It corresponds closely to the general
classification of bacteria proposed by Woese and Fox [21]. Each bacterial
subclass will be covered in separate chapters, but there are two divisions
of the bacteria that must be discussed here, because they cross taxonomic
barriers. These are Gram stainability and G
C content.
A cell wall is a chemical structure that lies outside the membrane that
encloses the cytoplasm (i.e., the insides)ofbacteria.Some cell walls con-
tain peptidoglycan, and it is this molecule that reacts with the Gram stain
to produce a blue color. Some bacteria lack a cell wall, and some bacteria
have cell walls that do not contain peptidoglycan. These cells do not react
with the Gram stain. Other bacteria contain peptidoglycan in their cell
walls, but they have a second, outer membrane that covers the cell wall.
Gram stain cannot easily penetrate the outer cell membranes, thus decreas-
ing the Gram stain reaction in these cells. Because there are many different
ways by which an organism's Gram reaction is determined, you might
guess that Gram staining is a taxonomically perverse property: you would
be correct.
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