Hierarchies in biology and paleontology

Hierarchies in natural science are ranked and nested structures such that units at each rank include parts that are units at lower ranks. Hierarchies are able to render complexity tractable, by homogenizing units into collectives and by ordering collectives in ranks of increasing inclusiveness. Hierarchies contrast with positional structures, such as phylogenetic trees, for in trees all positions are occupied by the same sort of entity-there are no ranked collectives-and positions are specified by the order of appearance or precedence of the entities. In hierarchies, interactions within ranks are most important; in trees, sequences of events along branches are of primary concern. As a result hierarchies do, and trees do not, display emergent properties. The value of the hierarchical structure can be lost when ranks are misspecified. A common error is the use of only a fraction of entities that actually occur in a rank, as when genes are considered as a rank below cells, disregarding the remaining cell contents and rendering the nature of cellular organization moot. Misspecification is also common when attributes or processes are used in ranks without indications of the physical entities to which they refer, thus losing track of the proper composition and ranking of the collectives.