Biomedical Engineering Reference
In-Depth Information
Phylum, Class, Order, Family, Genus, and Species. It is somewhat confusing that one
of the classes of organisms is “Class,” and another of the classes is named “Order.”
This means that when the terms “Class” or “Order” appear in a sentence, the reader
must somehow distinguish between the general term and the specific term. In this
topic, classes are unranked. The word “class,” lowercase, is used as a general term.
The word “Class,” uppercase, followed by an uppercase animal division (e.g. Class
Animalia), represents a group within the taxonomy. In the biological hierarchy, each
class has exactly one direct ancestor class (also called parent class or superclass),
though an ancestor class can have more than one direct descendent class (also called
child class, or subclass). See Taxonomic order.
Classification A hierarchical collection of classes in which each class inherits the proper-
ties of its parent class (superclass) and each species (class instance) occurs in exactly
one class. A classification has five purposes: (1) To drive down the complexity of the
knowledge domain; (2) As an informatics key that can be used to retrieve data and
organize data pulled from diverse resources; (3) As a hypothesis-generating machine
(i.e. always calling upon scientists to examine the relationships among classes of
organisms); (4) To distill each class into a set of defining, essential properties that
distinguish one class from all other classes; and (5) As a comprehensive collection of
every member of a knowledge domain. Classifications should be distinguished from
“Ontologies.” An ontology is a system that relates groups of objects by rules. In an
ontology, a class of objects may have more than one parent class (superclass) and an
object may be a member of more than one class. A classification can be considered a
special type of ontology wherein each class is limited to a single parent class and each
object has membership in one and only one class. Classifications have simple hierar-
chical architectures; ontologies do not.
Commensal A symbiotic relationship in which one of the organisms benefits and the
other is unaffected, under normal conditions. An opportunistic commensal is an organ-
ism that does not produce disease in its host, unless the host provides a physiologic
opportunity for disease, such as malnutrition, advanced age, immunodeficiency, over-
growth of the organism (e.g. after antiobiotic usage), or some mechanical portal that
introduces the organism to a part of the body that is particularly susceptible to the
pathologic expression of the organism (such as an indwelling catheter, or an intraven-
ous line). See Opportunistic infection.
Convergence When two species independently acquire an identical or similar trait
through adaptation; not through inheritance from a shared ancestor. Examples are: the
wing of a bat and the wing of a bird; the opposable thumb of opossums and of pri-
mates; the beak of a platypus and the beak of a bird.
Cyanobacteria The most influential organisms on earth, cyanobacteria, were the first and
only organism to master the biochemical intricacies of oxygenic photosynthesis (more
than 3 billion years ago). Photosynthesis involves a photochemical reaction, that uses
carbon dioxide and water, and releases oxygen. All photosynthesizing life forms are
either cyanobacteria, or they are eukaryotic cells (e.g. algae, plants) that have acquired
chloroplasts (an organelle created in the distant past by endosymbiosis between a
eukaryote and a cyanobacteria). Before the emergence of oxygen-producing cyanobac-
teria, the earth's atmosphere had very little oxygen.
Endotoxin These are toxins produced by bacteria that are part of the structure of the
organism (i.e. not an excreted molecule as found in exotoxins). Most of the endotoxins
